Aamer Mehmood, M, Shahid, A, Malik, S, Wang, N, Rizwan Javed, M, Nabeel Haider, M, Verma, P, Umer Farooq Ashraf, M, Habib, N, Syafiuddin, A & Boopathy, R 2021, 'Advances in developing metabolically engineered microbial platforms to produce fourth-generation biofuels and high-value biochemicals', Bioresource Technology, vol. 337, pp. 125510-125510.
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Producing bio-based chemicals is imperative to establish an eco-friendly circular bioeconomy. However, the compromised titer of these biochemicals hampers their commercial implementation. Advances in genetic engineering tools have enabled researchers to develop robust strains producing desired titers of the next-generation biofuels and biochemicals. The native and non-native pathways have been extensively engineered in various host strains via pathway reconstruction and metabolic flux redirection of lipid metabolism and central carbon metabolism to produce myriad biomolecules including alcohols, isoprenoids, hydrocarbons, fatty-acids, and their derivatives. This review has briefly covered the research efforts made during the previous decade to produce advanced biofuels and biochemicals through engineered microbial platforms along with the engineering approaches employed. The efficiency of the various techniques along with their shortcomings is also covered to provide a comprehensive overview of the progress and future directions to achieve higher titer of fourth-generation biofuels and biochemicals while keeping environmental sustainability intact.
Abayarathna, T & Webb, JK 2021, 'Do Incubation Temperatures Affect the Preferred Body Temperatures of Hatchling Velvet Geckos?', Frontiers in Ecology and Evolution, vol. 9, p. 727602.
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In many lizards, a mother’s choice of nest site can influence the thermal and hydric regimes experienced by developing embryos, which in turn can influence key traits putatively linked to fitness, such as body size, learning ability, and locomotor performance. Future increases in nest temperatures predicted under climate warming could potentially influence hatchling traits in many reptiles. In this study, we investigated whether future nest temperatures affected the thermal preferences of hatchling velvet geckos, Amalosia lesueurii. We incubated eggs under two fluctuating temperature treatments; the warm treatment mimicked temperatures of currently used communal nests (mean = 24.3°C, range 18.4–31.1°C), while the hot treatment (mean = 28.9°C, range 20.7–38.1°C) mimicked potential temperatures likely to occur during hot summers. We placed hatchlings inside a thermal gradient and measured their preferred body temperatures (Tbs) after they had access to food, and after they had fasted for 5 days. We found that hatchling feeding status significantly affected their preferred Tbs. Hatchlings maintained higher Tbs after feeding (mean = 30.6°C, interquartile range = 29.6–32.0°C) than when they had fasted for 5 d (mean = 25.8°C, interquartile range = 24.7–26.9°C). Surprisingly, we found that incubation temperatures did not influence the thermal preferences of hatchling velvet geckos. Hence, predicting how future changes in nest temperatures will affect reptiles will require a better understanding of how incubation and post-hatchling environments shape hatchling phenotypes.
Abba, A, Accorsi, C, Agnes, P, Alessi, E, Amaudruz, P, Annovi, A, Desages, FA, Back, S, Badia, C, Bagger, J, Basile, V, Batignani, G, Bayo, A, Bell, B, Beschi, M, Biagini, D, Bianchi, G, Bicelli, S, Bishop, D, Boccali, T, Bombarda, A, Bonfanti, S, Bonivento, WM, Bouchard, M, Breviario, M, Brice, S, Brown, R, Calvo-Mozota, JM, Camozzi, L, Camozzi, M, Capra, A, Caravati, M, Carlini, M, Ceccanti, A, Celano, B, Cela Ruiz, JM, Charette, C, Cogliati, G, Constable, M, Crippa, C, Croci, G, Cudmore, S, Dahl, CE, Dal Molin, A, Daley, M, Di Guardo, C, D'Avenio, G, Davignon, O, Del Tutto, M, De Ruiter, J, Devoto, A, Diaz Gomez Maqueo, P, Di Francesco, F, Dossi, M, Druszkiewicz, E, Duma, C, Elliott, E, Farina, D, Fernandes, C, Ferroni, F, Finocchiaro, G, Fiorillo, G, Ford, R, Foti, G, Fournier, RD, Franco, D, Fricbergs, C, Gabriele, F, Galbiati, C, Garcia Abia, P, Gargantini, A, Giacomelli, L, Giacomini, F, Giacomini, F, Giarratana, LS, Gillespie, S, Giorgi, D, Girma, T, Gobui, R, Goeldi, D, Golf, F, Gorel, P, Gorini, G, Gramellini, E, Grosso, G, Guescini, F, Guetre, E, Hackman, G, Hadden, T, Hawkins, W, Hayashi, K, Heavey, A, Hersak, G, Hessey, N, Hockin, G, Hudson, K, Ianni, A, Ienzi, C, Ippolito, V, James, CC, Jillings, C, Kendziora, C, Khan, S, Kim, E, King, M, King, S, Kittmer, A, Kochanek, I, Kowalkowski, J, Krücken, R, Kushoro, M, Kuula, S, Laclaustra, M, Leblond, G, Lee, L, Lennarz, A, Leyton, M, Li, X, Liimatainen, P, Lim, C, Lindner, T, Lomonaco, T, Lu, P, Lubna, R, Lukhanin, GA, Luzón, G, MacDonald, M, Magni, G, Maharaj, R, Manni, S, Mapelli, C, Margetak, P, Martin, L, Martin, S, Martínez, M, Massacret, N, McClurg, P, McDonald, AB, Meazzi, E, Migalla, R, Mohayai, T, Tosatti, LM, Monzani, G, Moretti, C, Morrison, B, Mountaniol, M, Muraro, A, Napoli, P, Nati, F, Natzke, CR, Noble, AJ, Norrick, A, Olchanski, K, Ortiz de Solorzano, A, Padula, F, Pallavicini, M, Palumbo, I, Panontin, E, Papini, N, Parmeggiano, L, Parmeggiano, S, Patel, K, Patel, A, Paterno, M, Pellegrino, C, Pelliccione, P, Pesudo, V, Pocar, A, Pope, A, Pordes, S, Prelz, F, Putignano, O, Raaf, JL, Ratti, C, Razeti, M, Razeto, A, Reed, D, Refsgaard, J, Reilly, T, Renshaw, A, Retriere, F, Riccobene, E, Rigamonti, D, Rizzi, A, Rode, J, Romualdez, J, Russel, L, Sablone, D, Sala, S, Salomoni, D, Salvo, P, Sandoval, A, Sansoucy, E, Santorelli, R, Savarese, C, Scapparone, E, Schaubel, T & et al. 2021, 'The novel Mechanical Ventilator Milano for the COVID-19 pandemic', Physics of Fluids, vol. 33, no. 3.
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This paper presents the Mechanical Ventilator Milano (MVM), a novel intensive therapy mechanical ventilator designed for rapid, large-scale, low-cost production for the COVID-19 pandemic. Free of moving mechanical parts and requiring only a source of compressed oxygen and medical air to operate, the MVM is designed to support the long-term invasive ventilation often required for COVID-19 patients and operates in pressure-regulated ventilation modes, which minimize the risk of furthering lung trauma. The MVM was extensively tested against ISO standards in the laboratory using a breathing simulator, with good agreement between input and measured breathing parameters and performing correctly in response to fault conditions and stability tests. The MVM has obtained Emergency Use Authorization by U.S. Food and Drug Administration (FDA) for use in healthcare settings during the COVID-19 pandemic and Health Canada Medical Device Authorization for Importation or Sale, under Interim Order for Use in Relation to COVID-19. Following these certifications, mass production is ongoing and distribution is under way in several countries. The MVM was designed, tested, prepared for certification, and mass produced in the space of a few months by a unique collaboration of respiratory healthcare professionals and experimental physicists, working with industrial partners, and is an excellent ventilator candidate for this pandemic anywhere in the world.
Abiero, AR & Bradfield, LA 2021, 'The contextual regulation of goal-directed actions', Current Opinion in Behavioral Sciences, vol. 41, pp. 57-62.
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Goal-directed actions typically transfer readily between contexts, but this is not always the case. Goal-directed actions do not transfer across contexts just after they are initially learned, or when multiple, competing response-outcome contingencies exist, or when the context is highly emotionally salient. Goal-directed actions are, thus, context-dependent under each of these conditions. Here we review the studies that have led to these findings, and discuss the potentially unique psychological mechanisms that could underlie the context-dependency of goal-directed actions in each instance.
Aboulkheyr Es, H, Bigdeli, B, Zhand, S, Aref, AR, Thiery, JP & Warkiani, ME 2021, 'Mesenchymal stem cells induce PD‐L1 expression through the secretion of CCL5 in breast cancer cells', Journal of Cellular Physiology, vol. 236, no. 5, pp. 3918-3928.
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AbstractVarious factors in the tumor microenvironment (TME) regulate the expression of PD‐L1 in cancer cells. In TME, mesenchymal stem cells (MSCs) play a crucial role in tumor progression, metastasis, and drug resistance. Emerging evidence suggests that MSCs can modulate the immune‐suppression capacity of TME through the stimulation of PD‐L1 expression in various cancers; nonetheless, their role in the induction of PD‐L1 in breast cancer remained elusive. Here, we assessed the potential of MSCs in the stimulation of PD‐L1 expression in a low PD‐L1 breast cancer cell line and explored its associated cytokine. We assessed the expression of MSCs‐related genes and their correlation with PD‐L1 across 1826 breast cancer patients from the METABRIC cohort. After culturing an ER+/differentiated/low PD‐L1 breast cancer cells with MSCs conditioned‐medium (MSC‐CM) in a microfluidic device, a variety of in‐vitro assays was carried out to determine the role of MSC‐CM in breast cancer cells' phenotype plasticity, invasion, and its effects on induction of PD‐L1 expression. In‐silico analysis showed a positive association between MSCs‐related genes and PD‐L1 expression in various types of breast cancer. Through functional assays, we revealed that MSC‐CM not only prompts a phenotype switch but also stimulates PD‐L1 expression at the protein level through secretion of various cytokines, especially CCL5. Treatment of MSCs with cytokine inhibitor pirfenidone showed a significant reduction in the secretion of CCL5 and consequently, expression of PD‐L1 in breast cancer cells. We concluded that MSCs‐derived CCL5 may act as a PD‐L1 stimulator in breast cancer.
Abraham, J, Ng, R, Morelato, M, Tahtouh, M & Roux, C 2021, 'Automatically classifying crime scene images using machine learning methodologies', Forensic Science International: Digital Investigation, vol. 39, pp. 301273-301273.
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Abuel, L, Bartsch, F, Berry, A, Buffet, J-C, Cuccaro, S, van-Esch, P, Guerard, B, Holt, SA, Marchal, J, Mutti, P, Ollivier, K, Pentenero, J, Platz, M, Robert, A, Roulier, D & Spedding, J 2021, 'First measurements with the new 3He-filled Monoblock Aluminium Multitube neutron detector developed at the ILL for ANSTO PLATYPUS reflectometer', Journal of Neutron Research, vol. 23, no. 1, pp. 53-67.
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A detector upgrade was carried out on the PLATYPUS instrument dedicated to neutron reflectometry at the Australian Nuclear Science and Technology Organisation (ANSTO). The new detector, developed in the framework of a research collaboration between the ILL and ANSTO, is based on the Monoblock Aluminium Multi-tube (MAM) detector design already in use on several reflectometers and SANS instruments at the ILL. This article provides a technical description of the mechanical design and read-out electronics of the PLATYPUS detector and its commissioning on the PLATYPUS instrument. The main detector performance parameters have been measured and are presented here as well as the characterisation methods and the results of several reflectometry measurements. These measurements show an improvement in experimental data quality resulting from high positional resolution, high detection efficiency and reduced neutron scattering background in the 2.5–19 Å neutron wavelength range used in PLATYPUS instrument.
Acharya, SK, Galli, E, Mallinson, JB, Bose, SK, Wagner, F, Heywood, ZE, Bones, PJ, Arnold, MD & Brown, SA 2021, 'Stochastic Spiking Behavior in Neuromorphic Networks Enables True Random Number Generation', ACS Applied Materials & Interfaces, vol. 13, no. 44, pp. 52861-52870.
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There is currently a great deal of interest in the use of nanoscale devices to emulate the behaviors of neurons and synapses and to facilitate brain-inspired computation. Here, it is shown that percolating networks of nanoparticles exhibit stochastic spiking behavior that is strikingly similar to that observed in biological neurons. The spiking rate can be controlled by the input stimulus, similar to 'rate coding' in biology, and the distributions of times between events are log-normal, providing insights into the atomic-scale spiking mechanism. The stochasticity of the spiking behavior is then used for true random number generation, and the high quality of the generated random bit-streams is demonstrated, opening up promising routes toward integration of neuromorphic computing with secure information processing.
Adesina, AY, Drmosh, QA, Kumar, AM & Mohamedkhair, AK 2021, 'Post-annealing effect on the electrochemical behavior of nanostructured magnetron sputtered W3O films in chloride- and acid-containing environments', Surface and Coatings Technology, vol. 420, pp. 127334-127334.
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Adil, M, Mahmud, MAP, Kouzani, AZ & Khoo, S 2021, 'Energy trading among electric vehicles based on Stackelberg approaches: A review', Sustainable Cities and Society, vol. 75, pp. 103199-103199.
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Ahmadalidokht, I, Mohajerani, E & Mohammadimasoudi, M 2021, 'Fabrication and characterization of large aperture adaptive modal liquid crystal lens with a PEDOT:PSS/PVA/DMSO blend used as the modal and rubbing layer', Optical Materials Express, vol. 11, no. 4, pp. 1259-1259.
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An adaptive modal liquid crystal lens (AMLCL) with a 5 mm aperture and thickness of 20 µm was fabricated and studied. PEDOT:PSS/PVA/DMSO polymer blend film was used as both the modal and rubbing layers simultaneously. Using the modal layer as the rubbing layer facilitates and simplifies cell preparation. An optimal concentration of polymer blend, the 0.1-µm-thick modal layer had a 5 MΩ/□ sheet resistance. AMLCL electrodes were broken down into four parts and the cell placed in the optical setup to study the wavefront shape. It was shown that by applying the trigger voltage to different parts of the electrode and removing parts of the circuit, the cell could function as a spherical, cylindrical, or prismatic lens. Further, the electric power consumption was studied at different voltages and frequencies, showing that the spherical lens requires 0.5 mW to reach its maximum optical power at 1 kHz. Shack-Hartmann wavefront sensor was used to study the AMLCL’s aberrations. Tip aberration in this cell is attributed to the pretilt of the Liquid Crystal (LC) molecules at the surfaces that deflect the transmitting light from its straight path. It was shown that higher-order aberrations are negligible compared to the spherical aberration, which is reduced by raising the frequency to 1 kHz.
Ahmadalidokht, I, Mohajerani, E, Safa, HT & Mohammadimasoudi, M 2021, 'Modeling of a photo-assisted refocusable adaptive modal liquid crystal lens with a photoconductive layer', Optical Engineering, vol. 60, no. 11.
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Ahmadi, VE, Butun, I, Altay, R, Bazaz, SR, Alijani, H, Celik, S, Warkiani, ME & Koşar, A 2021, 'The effects of baffle configuration and number on inertial mixing in a curved serpentine micromixer: Experimental and numerical study', Chemical Engineering Research and Design, vol. 168, pp. 490-498.
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Recently, the application of micromixers in microfluidic systems including chemical and biological assays has been widely accomplished. Passive micromixers, benefitting from the low-cost and a less-complex fabrication process, rely solely on their geometry. In particular, Dean vortices generated in curved microchannels enhance the mixing performance through chaotic advection. To improve the mixing performance at relatively low Reynolds numbers (i.e. 1 ≤ Re ≤ 50), this study introduces baffles into the side walls of curved serpentine micromixers with curvature angles of 280°, which constantly agitate, stretch and fold the fluids streams. Six different baffle configurations were designed and the effects of geometry and the number of baffles were investigated both experimentally and numerically. According to the experimental results, while the maximum outlet mixing index of the micromixer with no baffles was 0.61, that of the micromixer with quasi-rectangular baffles was 0.98 at a low Reynolds number of 20, indicating the major contribution of the generated chaotic advection by baffles. Furthermore, numerical results, which were in good agreement with experimental results, shed more light onto the mechanisms involved in micromixing in terms of the flow behavior and mixing index.
Ahmed, W, Sheikh, JA, Ahmad, S, Farjana, SH & Mahmud, MAP 2021, 'Impact of PV system orientation angle accuracy on greenhouse gases mitigation', Case Studies in Thermal Engineering, vol. 23, pp. 100815-100815.
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Ahmed, W, Sheikh, JA, Nouman, M, Ullah, MF & Mahmud, MAP 2021, 'Techno-economic analysis for the role of single end energy user in mitigating GHG emission', Energy, Sustainability and Society, vol. 11, no. 1.
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Abstract Background Households, as end energy users, consume grid electricity to meet their energy demands. However, grids across the globe for energy production are majorly based on fossil fuel technology and make the highest contributions to global warming and climate change due to greenhouse gases (GHG) emissions. This generic study aims to investigate the minute role of a single-end energy consumer in GHG mitigation by switching to a rooftop PV system to meet his energy demands and trading surplus energy to the grid through its techno-economic analysis. Method For the study impact, NASA Meteorological Data are used to select an ideal single energy user equipped with a 10-kW PV system based on annual average daily solar radiation and ambient temperature through MATLAB/Simulink, for 11 populous cities in Pakistan. Helioscope software is used to select tilt and azimuthal angles to maximize the solar radiation intercept. Afterward, RETScreen software is used for cost, financial and GHG analysis. Result and conclusion A single end energy user equipped with a 10-kW PV system switched to a green energy source from a fossil fuel-based grid has the potential to avoid the burning of 3570.6 L of gasoline by producing 16,832 kWh of green energy per annum, while financially recovering the 10-kW PV system’s 7337$ grid-tied investment in 5 years (equity) and in 9 years (equity) in a 9077$ stand-alone system over its 25-year life. This approach provides relief to end energy users from high priced grid electricity through environmental friendliness by mitigating 8.3 tons of CO2 equivalent emissions per annum from energy production, while providing reli...
Ahrens, CW, Challis, A, Byrne, M, Leigh, A, Nicotra, AB, Tissue, D & Rymer, P 2021, 'Repeated extreme heatwaves result in higher leaf thermal tolerances and greater safety margins', New Phytologist, vol. 232, no. 3, pp. 1212-1225.
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SummaryThe frequency and severity of heatwave events are increasing, exposing species to conditions beyond their physiological limits. Species respond to heatwaves in different ways, however it remains unclear if plants have the adaptive capacity to successfully respond to hotter and more frequent heatwaves.We exposed eight tree populations from two climate regions grown under cool and warm temperatures to repeated heatwave events of moderate (40°C) and extreme (46°C) severity to assess adaptive capacity to heatwaves.Leaf damage and maximum quantum efficiency of photosystem II (Fv/Fm) were significantly impacted by heatwave severity and growth temperatures, respectively; populations from a warm‐origin avoided damage under moderate heatwaves compared to those from a cool‐origin, indicating a degree of local adaptation. We found that plasticity to heatwave severity and repeated heatwaves contributed to enhanced thermal tolerance and lower leaf temperatures, leading to greater thermal safety margins (thermal tolerance minus leaf temperature) in a second heatwave.Notably, while we show that adaptation and physiological plasticity are important factors affecting plant adaptive capacity to thermal stress, plasticity of thermal tolerances and thermal safety margins provides the opportunity for trees to persist among fluctuating heatwave exposures.
Ajani, PA, Petrou, K, Larsson, ME, Nielsen, DA, Burke, J & Murray, SA 2021, 'Phenotypic trait variability as an indication of adaptive capacity in a cosmopolitan marine diatom', Environmental Microbiology, vol. 23, no. 1, pp. 207-223.
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SummaryDetermining the adaptive capacity of marine phytoplankton is important in predicting changes in phytoplankton responses to ocean warming. Phytoplankton may consist of high levels of standing phenotypic and genetic variability, the basis of rapid evolution; however, few studies have quantified trait variability within and amongst closely related diatom species. Using 35 clonal cultures of the ubiquitous marine diatom Leptocylindrus isolated from six locations, spanning 2000 km of the south‐eastern Australian coastline, we found evidence of significant intraspecific morphological and metabolic trait variability, which for 8 of 9 traits (growth rate, biovolume, C:N, silica deposition, silica incorporation rate, chl‐a, and photosynthetic efficiency under dark adapted, growth irradiance, and high‐light adaptation) were greater within a species than between species. Moreover, only two traits revealed a latitudinal trend with strains isolated from lower latitudes showing significantly higher silicification rates and protein:lipid content compared to their higher latitude counterparts. These data mirror recent studies on diatom intraspecific genetic diversity, which has found comparable levels of genetic diversity at a single site to those thousands of kilometres apart, and provide evidence of a functional role of diatom diversity that will allow for rapid adaptation via ecological selection on standing variation in response to changing conditions.
Ajani, PA, Verma, A, Kim, JH, Woodcock, S, Nishimura, T, Farrell, H, Zammit, A, Brett, S & Murray, SA 2021, 'Using qPCR and high-resolution sensor data to model a multi-species Pseudo-nitzschia (Bacillariophyceae) bloom in southeastern Australia', Harmful Algae, vol. 108, pp. 102095-102095.
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Harmful algal blooms, including those caused by the toxic diatom Pseudo-nitzschia, can have significant impacts on human health, ecosystem functioning and ultimately food security. In the current study we characterized a bloom of species of Pseudo-nitzschia that occurred in a south-eastern Australian oyster-growing estuary in 2019. Using light microscopy, combined with molecular (ITS/5.8S and LSU D1-D3 rDNA regions) and toxicological evidence, we observed the bloom to consist of multiple species of Pseudo-nitzschia including P. cf. cuspidata, P. hasleana, P. fraudulenta and P. multiseries, with P. cf. cuspidata being the only species that produced domoic acid (3.1 pg DA per cell). As several species of Pseudo-nitzschia co-occurred, only one of which produced DA, we developed a rapid, sensitive and efficient quantitative real-time polymerase chain reaction (qPCR) assay to detect only species belonging to the P. pseudodelicatissima complex Clade I, to which P. cf. cuspidata belongs, and this indicated that P. cuspidata or closely related strains may have dominated the Pseudo-nitzschia community at this time. Finally, using high resolution water temperature and salinity sensor data, we modeled the relationship between light microscopy determined abundance of P. delicatissima group and environmental variables (temperature, salinity, rainfall) at two sites within the estuary. A total of eight General Linear Models (GLMs) explaining between 9 and 54% of the deviance suggested that the temperature (increasing) and/or salinity (decreasing) data were generally more predictive of high cell concentrations than the rainfall data at both sites, and that overall, cell concentrations were more predictive at the more oceanic site than the more upstream site, using this method. We conclude that the combination of rapid molecular methods such as qPCR and real-time sensor data modeling, can provide a more rapid and effective early warning of harmful algal blooms of specie...
Ajmal, AB, Alam, M, Khaliq, AA, Khan, S, Qadir, Z & Mahmud, MAP 2021, 'Last Line of Defense: Reliability Through Inducing Cyber Threat Hunting With Deception in SCADA Networks', IEEE Access, vol. 9, pp. 126789-126800.
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There exists a gap between existing security mechanisms and their ability to detect advancing threats. Antivirus and EDR (End Point Detection and Response) aim to detect and prevent threats; such security mechanisms are reactive. This approach did not prove to be effective in protecting against stealthy attacks. SCADA (Supervisory Control and Data Acquisition) security is crucial for any country. However, SCADA is always an easy target for adversaries due to a lack of security for heterogeneous devices. An attack on SCADA is mainly considered a national-level threat. Recent research on SCADA security has not considered 'unknown threats,' which has left a gap in security. The proactive approach, such as threat hunting, is the need of the hour. In this research, we investigated that threat hunting in conjunction with cyber deception and kill chain has countervailing effects on detecting SCADA threats and mitigating them. We have used the concept of 'decoy farm' in the SCADA network, where all attacks are engaged. Moreover, we present a novel threat detection and prevention approach for SCADA, focusing on unknown threats. To test the effectiveness of approach, we emulated several SCADA, Linux and Windows based attacks on a simulated SCADA network. We have concluded that our approach detects and prevents the attacker before using the current reactive approach and security mechanism for SCADA with enhanced protection for heterogeneous devices. The results and experiments show that the proposed threat hunting approach has significantly improved the threat detection ability.
Akkaya Hocagil, T, Cook, RJ, Jacobson, SW, Jacobson, JL & Ryan, LM 2021, 'Propensity Score Analysis for a Semi-Continuous Exposure Variable: A Study of Gestational Alcohol Exposure and Childhood Cognition', Journal of the Royal Statistical Society Series A: Statistics in Society, vol. 184, no. 4, pp. 1390-1413.
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AbstractPropensity score methodology has become increasingly popular in recent years as a tool for estimating causal effects in observational studies. Much of the related research has been directed at settings with binary or discrete exposure variables with more recent work involving continuous exposure variables. In environmental epidemiology, a substantial proportion of individuals is often completely unexposed while others may experience heavy exposure leading to an exposure distribution with a point mass at zero and a heavy right tail. We suggest a new approach to handle this type of exposure data by constructing a propensity score based on a two-part model and show how this model can be used to more reliably adjust for covariates of a semi-continuous exposure variable. We also consider the case when a misspecified propensity score is used in a regression adjustment and derive an explicit form of the bias. We show that the potential bias gets smaller as the estimated propensity score gets closer to the true expectation of the exposure variable given a set of observed covariates. While this result pertains to a more general setting, we use it to evaluate the potential bias in settings in which the true exposure has a semi-continuous structure. We also evaluate and compare the performance of our proposed method through simulation studies relative to a simpler linear regression-based propensity score for a continuous exposure variable as well as through direct covariate adjustment. Overall, we find that using a propensity score constructed via a two-part model significantly improves the regression estimate when the exposure variable is semi-continuous in nature. Specifically when the proportion of non-exposed subjects is high and the effects of covariates on exposure and outcome are strong, the proposed two-part propensity score method outperforms the more standard competing methods. We illustrate our method using data ...
Akter, A, Itabashi, E, Kakizaki, T, Okazaki, K, Dennis, ES & Fujimoto, R 2021, 'Genome Triplication Leads to Transcriptional Divergence of FLOWERING LOCUS C Genes During Vernalization in the Genus Brassica', Frontiers in Plant Science, vol. 11.
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The genusBrassicaincludes oil crops, vegetables, condiments, fodder crops, and ornamental plants.Brassicaspecies underwent a whole genome triplication event after speciation between ancestral species ofBrassicaand closely related genera includingArabidopsis thaliana. Diploid species such asBrassica rapaandBrassica oleraceahave three copies of genes orthologous to eachA. thalianagene, although deletion in one or two of the three homologs has occurred in some genes. The floral transition is one of the crucial events in a plant’s life history, and time of flowering is an important agricultural trait. There is a variation in flowering time within species of the genusBrassica, and this variation is largely dependent on a difference in vernalization requirements. InBrassica, like inA. thaliana, the key gene of vernalization isFLOWERING LOCUS C(FLC). InBrassicaspecies, the vernalization response including the repression ofFLCexpression by cold treatment and the enrichment of the repressive histone modification tri-methylated histone H3 lysine 27 (H3K27me3) at theFLClocus is similar toA. thaliana.B. rapaandB. oleraceaeach have four paralogs ofFLC, and the allotetraploid species,Brassica napus, has nine paralogs. The increased number of paralogs makes the role ofFLCin vernalization more complicated; in a single plant, paralogs vary in the expression level ofFLCbefore and ...
AlAjmi, MF, Khan, S, Choudhury, A, Mohammad, T, Noor, S, Hussain, A, Lu, W, Eapen, MS, Chimankar, V, Hansbro, PM, Sohal, SS, Elasbali, AM & Hassan, MI 2021, 'Impact of Deleterious Mutations on Structure, Function and Stability of Serum/Glucocorticoid Regulated Kinase 1: A Gene to Diseases Correlation', Frontiers in Molecular Biosciences, vol. 8, p. 780284.
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Serum and glucocorticoid-regulated kinase 1 (SGK1) is a Ser/Thr protein kinase involved in regulating cell survival, growth, proliferation, and migration. Its elevated expression and dysfunction are reported in breast, prostate, hepatocellular, lung adenoma, and renal carcinomas. We have analyzed the SGK1 mutations to explore their impact at the sequence and structure level by utilizing state-of-the-art computational approaches. Several pathogenic and destabilizing mutations were identified based on their impact on SGK1 and analyzed in detail. Three amino acid substitutions, K127M, T256A, and Y298A, in the kinase domain of SGK1 were identified and incorporated structurally into original coordinates of SGK1 to explore their time evolution impact using all-atom molecular dynamic (MD) simulations for 200 ns. MD results indicate substantial conformational alterations in SGK1, thus its functional loss, particularly upon T256A mutation. This study provides meaningful insights into SGK1 dysfunction upon mutation, leading to disease progression, including cancer, and neurodegeneration.
Alder, R, Xiao, L & Fu, S 2021, 'Comparison of commercial surface‐enhanced Raman spectroscopy substrates for the analysis of cocaine', Drug Testing and Analysis, vol. 13, no. 5, pp. 944-952.
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AbstractThe use of illicit drugs across the world causes issues for users, healthcare workers and the public. Therefore, rapid and reliable onsite testing methods to detect these drugs are required. In this study, seven commercial surface‐enhanced Raman spectroscopy (SERS) substrates A–G were compared for the analysis of cocaine. These substrates were compared using scanning electron microscopy to study the surface structure and Raman spectroscopy and to determine if there was any enhancement of the cocaine bands. Substrate B provided the best enhancement of known cocaine vibrational bands, allowing the detection down to concentrations of 1 ng/mL in standards and 10 ng/mL extracted from the oral fluid. The results showed that SERS is an ideal method for future rapid onsite analysis of illicit drugs in oral fluid. Commercial SERS substrates were compared for the analysis of cocaine. Substrate B provided the best result and was further tested with lower concentrations and extracts from the oral fluid. The application to oral fluid testing could prove useful for future onsite analysis.
Alderdice, R, Suggett, DJ, Cárdenas, A, Hughes, DJ, Kühl, M, Pernice, M & Voolstra, CR 2021, 'Divergent expression of hypoxia response systems under deoxygenation in reef‐forming corals aligns with bleaching susceptibility', Global Change Biology, vol. 27, no. 2, pp. 312-326.
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AbstractExposure of marine life to low oxygen is accelerating worldwide via climate change and localized pollution. Mass coral bleaching and mortality have recently occurred where reefs have experienced chronic low oxygen events. However, the mechanistic basis of tolerance to oxygen levels inadequate to sustain normal functioning (i.e. hypoxia) and whether it contributes to bleaching susceptibility, remain unknown. We therefore experimentally exposed colonies of the environmentally resilient Acropora tenuis, a common reef‐building coral from the Great Barrier Reef, to deoxygenation–reoxygenation stress that was aligned to their natural night–day light cycle. Specifically, the treatment involved removing the ‘night‐time O2 buffer’ to challenge the inherent hypoxia thresholds. RNA‐Seq analysis revealed that coral possess a complete and active hypoxia‐inducible factor (HIF)‐mediated hypoxia response system (HRS) homologous to other metazoans. As expected, A. tenuis exhibited bleaching resistance and showed a strong inducibility of HIF target genes in response to deoxygenation stress. We applied this same approach in parallel to a colony of Acropora selago, known to be environmnetally susceptible, which conversely exhibited a bleaching phenotype response. This phenotypic divergence of A. selago was accompanied by contrasting gene expression profiles indicative of varied effectiveness of their HIF‐HRS. Based on our RNA‐Seq analysis, we propose (a) that the HIF‐HRS is central for corals to manage deoxygenation stress and (b) that key genes of this system (and the wider gene network) may contribute to variation in coral bleaching susceptibility. Our analysis suggests that heat shock protein (hsp) 70 and 90 are important for low oxygen stress tolerance and further highlights how hsp90 expression might ...
Alemao, CA, Budden, KF, Gomez, HM, Rehman, SF, Marshall, JE, Shukla, SD, Donovan, C, Forster, SC, Yang, IA, Keely, S, Mann, ER, El Omar, EM, Belz, GT & Hansbro, PM 2021, 'Impact of diet and the bacterial microbiome on the mucous barrier and immune disorders', Allergy, vol. 76, no. 3, pp. 714-734.
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AbstractThe prevalence of chronic immune and metabolic disorders is increasing rapidly. In particular, inflammatory bowel diseases, obesity, diabetes, asthma and chronic obstructive pulmonary disease have become major healthcare and economic burdens worldwide. Recent advances in microbiome research have led to significant discoveries of associative links between alterations in the microbiome and health, as well as these chronic supposedly noncommunicable, immune/metabolic disorders. Importantly, the interplay between diet, microbiome and the mucous barrier in these diseases has gained significant attention. Diet modulates the mucous barrier via alterations in gut microbiota, resulting in either disease onset/exacerbation due to a “poor” diet or protection against disease with a “healthy” diet. In addition, many mucosa‐associated disorders possess a specific gut microbiome fingerprint associated with the composition of the mucous barrier, which is further influenced by host‐microbiome and inter‐microbial interactions, dietary choices, microbe immigration and antimicrobials. Our review focuses on the interactions of diet (macronutrients and micronutrients), gut microbiota and mucous barriers (gastrointestinal and respiratory tract) and their importance in the onset and/or progression of major immune/metabolic disorders. We also highlight the key mechanisms that could be targeted therapeutically to prevent and/or treat these disorders.
Alhamami, T, Chowdhury, P, Gomes, N, Carr, M, Veltman, T, Khazandi, M, Mollinger, J, Deutscher, A, Turni, C, Mahdi, L, Venter, H, Abraham, S, Djordjevic, S & Trott, D 2021, 'First Emergence of Resistance to Macrolides and Tetracycline Identified in Mannheimia haemolytica and Pasteurella multocida Isolates from Beef Feedlots in Australia', Microorganisms, vol. 9, no. 6, pp. 1322-1322.
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Bovine respiratory disease (BRD) causes high morbidity and mortality in beef cattle worldwide. Antimicrobial resistance (AMR) monitoring of BRD pathogens is critical to promote appropriate antimicrobial stewardship in veterinary medicine for optimal treatment and control. Here, the susceptibility of Mannheimia haemolytica and Pasteurella multicoda isolates obtained from BRD clinical cases (deep lung swabs at post-mortem) among feedlots in four Australian states (2014–2019) was determined for 19 antimicrobial agents. The M. haemolytica isolates were pan-susceptible to all tested agents apart from a single macrolide-resistant isolate (1/88; 1.1%) from New South Wales (NSW). Much higher frequencies of P. multocida isolates were resistant to tetracycline (18/140; 12.9%), tilmicosin (19/140; 13.6%), tulathromycin/gamithromycin (17/140; 12.1%), and ampicillin/penicillin (6/140; 4.6%). Five P. multocida isolates (3.6%), all obtained from NSW in 2019, exhibited dual resistance to macrolides and tetracycline, and a further two Queensland isolates from 2019 (1.4%) exhibited a multidrug-resistant phenotype to ampicillin/penicillin, tetracycline, and tilmicosin. Random-amplified polymorphic DNA (RAPD) typing identified a high degree of genetic homogeneity among the M. haemolytica isolates, whereas P. multocida isolates were more heterogeneous. Illumina whole genome sequencing identified the genes msr(E) and mph(E)encoding macrolide resistance, tet(R)-tet(H) or tet(Y) encoding tetracycline resistance, and blaROB-1 encoding ampicillin/penicillin resistance in all isolates exhibiting a corresponding resistant phenotype. The exception was the tilmicosin-resistant, tulathromycin/gamithromycin-susceptible phenotype identified in two Queensland isolates, the genetic basis of which could not be determined. These results confirm the first emergence of AMR in M. haemolytica and P. multocida from BRD cases in Australia, which should be closely monitored.
Ali, S, Gupta, A, Shafiei, M & Langford, SJ 2021, 'Recent Advances in Perylene Diimide-Based Active Materials in Electrical Mode Gas Sensing', Chemosensors, vol. 9, no. 2, pp. 30-30.
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This review provides an update on advances in the area of electrical mode sensors using organic small molecule n-type semiconductors based on perylene. Among small organic molecules, perylene diimides (PDIs) are an important class of materials due to their outstanding thermal, chemical, electronic, and optical properties, all of which make them promising candidates for a wide range of organic electronic devices including sensors, organic solar cells, organic field-effect transistors, and organic light-emitting diodes. This is mainly due to their electron-withdrawing nature and significant charge transfer properties. Perylene-based sensors of this type show high sensing performance towards various analytes, particularly reducing gases like ammonia and hydrazine, but there are several issues that need to be addressed including the selectivity towards a specific gas, the effect of relative humidity, and operating temperature. In this review, we focus on the strategies and design principles applied to the gas-sensing performance of PDI-based devices, including resistive sensors, amperometric sensors, and operating at room temperature. The device properties and sensing mechanisms for different analytes, focusing on hydrazine and ammonia, are studied in detail, and some future research perspectives are discussed for this promising field. We hope the discussed results and examples inspire new forms of molecular engineering and begin to open opportunities for other rylene diimide classes to be applied as active materials.
Ali, S, Jameel, MA, Gupta, A, Langford, SJ & Shafiei, M 2021, 'Capacitive humidity sensing performance of naphthalene diimide derivatives at ambient temperature', Synthetic Metals, vol. 275, pp. 116739-116739.
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We report for the first-time the development of capacitive type humidity sensors employing naphthalene diimide derivatives (NDI) as sensing layer. Three different naphthalene diimide derivatives bearing imide side chains of different hydrophilicity were designed, synthesised and characterised. X-ray diffraction and thermogravimetric analyses gave useful information about structural and thermal behaviour of the newly developed materials, indicating their crystallinity and stability. Atomic force microscopy analysis revealed a variety of morphologies in thin films as a result of the structural properties of the NDIs. Devices bearing NDI layers were fabricated on ceramic substrates with gold interdigitated electrodes spaced 200 µm apart. Humidity sensing performance, as a change in capacitance, was studied upon exposure to a wide range of relative humidity levels (0–95%) at ambient temperature. Importantly, an increase in the capacitance of the sensors was recorded with an increase in relative humidity. The developed sensors exhibited high sensitivity, good long-term stability, excellent reproducibility, and low hysteresis. The sensor performance was also tested against different operating frequencies (250 Hz–2 kHz) to improve linearity, illustrating directions for optimised performance. These results confirm that sensors based on NDIs possess better sensing performance to other types of reported capacitive humidity sensors.
Ali, S, Jameel, MA, Harrison, CJ, Gupta, A, Evans, RA, Shafiei, M & Langford, SJ 2021, 'Enhanced Capacitive Humidity Sensing Performance at Room Temperature via Hydrogen Bonding of Cyanopyridone-Based Oligothiophene Donor', Chemosensors, vol. 9, no. 11, pp. 320-320.
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Cyanopyridone-based oligothiophene donors with both hydrophobic and hydrophilic characters have been evaluated as active layers within simple capacitive devices for humidity sensing at room temperature. Surface studies using atomic force microscopy revealed a self-assembled nanofibrous network with a thin needle-like structure for the terminal hydroxy example (CP6), devoid in the methyl example (CP1). The sensing performance of each sensor was investigated over a broad range of relative humidity levels as a function of capacitance at room temperature. The sensor CP6 demonstrated favourable features such as high sensitivity (12.2 pF/%RH), quick response/recovery (13 s/20.7 s), wide working range of relative humidity (10%–95% RH), low hysteresis (0.57%), outstanding recyclability, and excellent long-term stability. From the results obtained, hydrophilicity and hydrogen bonding appear to play a vital role in enhancing humidity sensing performance, leading to possible new design directions for simple organic semiconductor-based sensors.
Alijani, H, Rezk, AR, Khosravi Farsani, MM, Ahmed, H, Halim, J, Reineck, P, Murdoch, BJ, El-Ghazaly, A, Rosen, J & Yeo, LY 2021, 'Acoustomicrofluidic Synthesis of Pristine Ultrathin Ti3C2Tz MXene Nanosheets and Quantum Dots', ACS Nano, vol. 15, no. 7, pp. 12099-12108.
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Allam, VSRR, Faiz, A, Lam, M, Rathnayake, SNH, Ditz, B, Pouwels, SD, Brandsma, C, Timens, W, Hiemstra, PS, Tew, GW, Neighbors, M, Grimbaldeston, M, van den Berge, M, Donnelly, S, Phipps, S, Bourke, JE & Sukkar, MB 2021, 'RAGE and TLR4 differentially regulate airway hyperresponsiveness: Implications for COPD', Allergy, vol. 76, no. 4, pp. 1123-1135.
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AbstractBackgroundThe receptor for advanced glycation end products (RAGE) and Toll‐like receptor 4 (TLR4) is implicated in COPD. Although these receptors share common ligands and signalling pathways, it is not known whether they act in concert to drive pathological processes in COPD. We examined the impact of RAGE and/or TLR4 gene deficiency in a mouse model of COPD and also determined whether expression of these receptors correlates with airway neutrophilia and airway hyperresponsiveness (AHR) in COPD patients.MethodsWe measured airway inflammation and AHR in wild‐type, RAGE−/−, TLR4−/− and TLR4−/−RAGE−/− mice following acute exposure to cigarette smoke (CS). We also examined the impact of smoking status on AGER (encodes RAGE) and TLR4 bronchial gene expression in patients with and without COPD. Finally, we determined whether expression of these receptors correlates with airway neutrophilia and AHR in COPD patients.ResultsRAGE−/− mice were protected against CS‐induced neutrophilia and AHR. In contrast, TLR4−/− mice were not protected against CS‐induced neutrophilia and had more severe CS‐induced AHR. TLR4−/−RAGE−/− mice were not protected against CS‐induced neutrophilia but were partially protected against CS‐induced mediator release and AHR. Current smoking was associated with significantly lower AGER and TLR4 expression irrespective of COPD status, possibly reflecting negative feedback regulation. However, consistent with preclinical findings, AGER expression cor...
Alqudah, A, Eastwood, K-A, Jerotic, D, Todd, N, Hoch, D, McNally, R, Obradovic, D, Dugalic, S, Hunter, AJ, Holmes, VA, McCance, DR, Young, IS, Watson, CJ, Robson, T, Desoye, G, Grieve, DJ & McClements, L 2021, 'FKBPL and SIRT-1 Are Downregulated by Diabetes in Pregnancy Impacting on Angiogenesis and Endothelial Function', Frontiers in Endocrinology, vol. 12.
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Diabetes in pregnancy is associated with adverse pregnancy outcomes including preterm birth. Although the mechanisms leading to these pregnancy complications are still poorly understood, aberrant angiogenesis and endothelial dysfunction play a key role. FKBPL and SIRT-1 are critical regulators of angiogenesis, however, their roles in pregnancies affected by diabetes have not been examined before in detail. Hence, this study aimed to investigate the role of FKBPL and SIRT-1 in pre-gestational (type 1 diabetes mellitus, T1D) and gestational diabetes mellitus (GDM). Placental protein expression of important angiogenesis proteins, FKBPL, SIRT-1, PlGF and VEGF-R1, was determined from pregnant women with GDM or T1D, and in the first trimester trophoblast cells exposed to high glucose (25 mM) and varying oxygen concentrations [21%, 6.5%, 2.5% (ACH-3Ps)]. Endothelial cell function was assessed in high glucose conditions (30 mM) and following FKBPL overexpression. Placental FKBPL protein expression was downregulated in T1D (FKBPL; p<0.05) whereas PlGF/VEGF-R1 were upregulated (p<0.05); correlations adjusted for gestational age were also significant. In the presence of GDM, only SIRT-1 was significantly downregulated (p<0.05) even when adjusted for gestational age (r=-0.92, p=0.001). Both FKBPL and SIRT-1 protein expression was reduced in ACH-3P cells in high glucose conditions associated with 6.5%/2.5% oxygen concentrations compared to experimental normoxia (21%; p<0.05). FKBPL overexpression in endothelial cells (HUVECs) exacerbated reduction in tubule formation compared to empty vector control, in high glucose conditions (junctions; p<0.01, branches; p<0.05). In conclusion, FKBPL and/or SIRT-1 downregulation in response to diabetic pregnancies may have a key role in the development of vascular dysfunction and associated complications affected by impaired placental angiogenesis.
Alqudah, A, Wedyan, M, Qnais, E, Jawarneh, H & McClements, L 2021, 'Plasma Amino Acids Metabolomics' Important in Glucose Management in Type 2 Diabetes', Frontiers in Pharmacology, vol. 12, p. 695418.
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The perturbation in plasma free amino acid metabolome has been observed previously in diabetes mellitus, and is associated with insulin resistance as well as the onset of cardiovascular disease in this population. In this study, we investigated, for the first time, changes in the amino acid profile in a group of people with and without type 2 diabetes (T2D) with normal BMI, from Jordan, who were only managed on metformin. Twenty one amino acids were evaluated in plasma samples from 124 people with T2D and 67 healthy controls, matched for age, gender and BMI, using amino acids analyser. Total amino acids, essential amino acids, non-essential amino acids and semi-essential amino acids were similar in T2D compared to healthy controls. Plasma concentrations of four essential amino acids were increased in the presence of T2D (Leucine, p < 0.01, Lysine, p < 0.001, Phenylalanine, p < 0.01, Tryptophan, p < 0.05). On the other hand, in relation to non-essential amino acids, Alanine and Serine were reduced in T2D (p < 0.01, p < 0.001, respectively), whereas Aspartate and Glutamate were increased in T2D compared to healthy controls (p < 0.001, p < 0.01, respectively). A semi-essential amino acid, Cystine, was also increased in T2D compared to healthy controls (p < 0.01). Citrulline, a metabolic indicator amino acid, demonstrated lower plasma concentration in T2D compared to healthy controls (p < 0.01). These amino acids were also correlated with fasting blood glucose and HbA1c (p < 0.05). Glutamate, glycine and arginine were correlated with the duration of metformin treatment (
Alsahafi, S & Woodcock, S 2021, 'Local analysis for a mutual inhibition in presence of two viruses in a chemostat', Nonlinear Dynamics and Systems Theory, vol. 21, no. 4, pp. 337-359.
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A competition with mutual inhibition is a form of direct competition between the populations of two species where each actively inhibits the other. In this paper, we consider a mathematical system of ordinary differential equations describing two species, with mutual inhibition, competing for a limiting substrate in the presence of two viruses. A detailed local qualitative analysis of the restriction of the system to the attractor set is carried out. We prove that for general nonlinear response functions, the Competitive Exclusion Principle is still fulfilled so that at most one species can survive. Initial species concentrations are important in determining which is the winning species. The results obtained were validated by numerical simulations using Matlab software.
Alsahafi, S & Woodcock, S 2021, 'Mathematical Study for Chikungunya Virus with Nonlinear General Incidence Rate', Mathematics, vol. 9, no. 18, pp. 2186-2186.
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In this article, we examine the dynamics of a Chikungunya virus (CHIKV) infection model with two routes of infection. The model uses four categories, namely, uninfected cells, infected cells, the CHIKV virus, and antibodies. The equilibrium points of the model, which consist of the free point for the CHIKV and CHIKV endemic point, are first analytically determined. Next, the local stability of the equilibrium points is studied, based on the basic reproduction number (R0) obtained by the next-generation matrix. From the analysis, it is found that the disease-free point is locally asymptotically stable if R0≤1, and the CHIKV endemic point is locally asymptotically stable if R0>1. Using the Lyapunov method, the global stability analysis of the steady-states confirms the local stability results. We then describe our design of an optimal recruitment strategy to minimize the number of infected cells, as well as a nonlinear optimal control problem. Some numerical simulations are provided to visualize the analytical results obtained.
Alsahafi, S & Woodcock, S 2021, 'Mutual inhibition in presence of a virus in continuous culture', Mathematical Biosciences and Engineering, vol. 18, no. 4, pp. 3258-3273.
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Al-Sanea, MM, Al-Ansary, GH, Elsayed, ZM, Maklad, RM, Elkaeed, EB, Abdelgawad, MA, Bukhari, SNA, Abdel-Aziz, MM, Suliman, H & Eldehna, WM 2021, 'Development of 3-methyl/3-(morpholinomethyl)benzofuran derivatives as novel antitumor agents towards non-small cell lung cancer cells', Journal of Enzyme Inhibition and Medicinal Chemistry, vol. 36, no. 1, pp. 987-999.
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Alshamrani, R, Arshad, MH, Gull, M, Nawaz, MZ & Malik, S 2021, 'Identification of non-coding RNAs in the hyper thermophilic bacteriumThermotoga maritima MSB8 through comparative genomics and in-silicoanalyses', Asian Journal of Agriculture and Biology, vol. 2022, no. Online First, pp. 1-9.
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Thermotoga maritima is a hyperthermophile with the potential to produce thermostable commercial enzymes which can be used for saccharification of plant biomass for subsequent fermentation to bioproducts. The molecular mechanism involved in the hyper thermostability in this bacterium is still not well-understood. It is known that small noncoding RNAs (ncRNAs) regulate and modulate the gene expression of various biological processes at transcriptional and post-transcriptional levels, hence coordinate the adaptation processes in response to environmental stimuli in both prokaryotes and eukaryotes. To understand the role of small ncRNAs in the hyper thermostability of T. maritima, an in silico-based approach was employed involving the identification of the ncRNAs in this bacterium on a genome-wide scale. A novel pipeline was constructed which involved a combination of various bioinformatics algorithms. In total, 20804 orthologous groups were predicted on the genome of T. maritima and 20 other bacteria (reference genomes) by the OrthoMCL tool. By using the “Perl” and “Bash” languages 258 orthologous IGR datasets were created. Among these datasets, small ncRNAs were identified by employing RNAz and RNA Infernal tools. Total 28 ncRNA candidates were predicted by the RNAz tool and 9 candidates were confirmed as novel cis-regulatory small ncRNAs in T. maritima MSB8 by Infernal tool and were named as Tmn (T. maritima ncRNAs). This work provides novel insights into the role of ncRNAs in the stress adaptability of MSB8 and can give a much better understanding of the lifestyle of this bacterium after validation of the data through wet-lab approaches. Having a clear understanding of the thermo-tolerance mechanism, the MSB8 can be exploited in the future for the commercial production of thermostable compounds and biohydrogen.
al-Zubaidi, Y, Chen, Y, Khalilur Rahman, M, Umashankar, B, Choucair, H, Bourget, K, Chung, L, Qi, Y, Witting, PK, Anderson, RL, O'Neill, GM, Dunstan, CR, Rawling, T & Murray, M 2021, 'PTU, a novel ureido-fatty acid, inhibits MDA-MB-231 cell invasion and dissemination by modulating Wnt5a secretion and cytoskeletal signaling', Biochemical Pharmacology, vol. 192, pp. 114726-114726.
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Migration and invasion promote tumor cell metastasis, which is the leading cause of cancer death. At present there are no effective treatments. Epidemiological studies have suggested that ω-3 polyunsaturated fatty acids (PUFA) may decrease cancer aggressiveness. In recent studies epoxide metabolites of ω-3 PUFA exhibited anti-cancer activity, although increased in vivo stability is required to develop useful drugs. Here we synthesized novel stabilized ureido-fatty acid ω-3 epoxide isosteres and found that one analogue - p-tolyl-ureidopalmitic acid (PTU) - inhibited migration and invasion by MDA-MB-231 breast cancer cells in vitro and in vivo in xenografted nu/nu mice. From proteomics analysis of PTU-treated cells major regulated pathways were linked to the actin cytoskeleton and actin-based motility. The principal finding was that PTU impaired the formation of actin protrusions by decreasing the secretion of Wnt5a, which dysregulated the Wnt/planar cell polarity (PCP) pathway and actin cytoskeletal dynamics. Exogenous Wnt5a restored invasion and Wnt/PCP signalling in PTU-treated cells. PTU is the prototype of a novel class of agents that selectively dysregulate the Wnt/PCP pathway by inhibiting Wnt5a secretion and actin dynamics to impair MDA-MB-231 cell migration and invasion.
Amerizadeh, A, Mashhadian, A, Farahnak-Ghazani, M, Arjmandi, H, Rad, MA, Shamloo, A, Vosoughi, M & Nasiri-Kenari, M 2021, 'Bacterial Receiver Prototype for Molecular Communication Using Rhamnose Operon in a Microfluidic Environment', IEEE Transactions on NanoBioscience, vol. 20, no. 4, pp. 426-435.
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Anburajan, P, Kim, Y, Rice, SA & Oh, H-S 2021, 'Bacterial signaling and signal responses as key factors in water and wastewater treatment', Journal of Water Process Engineering, vol. 44, pp. 102434-102434.
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Andersson, J, Fuller, M, Ashenden, A, Holt, SA & Köper, I 2021, 'Increasing Antibiotic Susceptibility: The Use of Cationic Gold Nanoparticles in Gram-Negative Bacterial Membrane Models', Langmuir, vol. 37, no. 32, pp. 9735-9743.
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Ansari, S, Walsh, JC, Bottomley, AL, Duggin, IG, Burke, C & Harry, EJ 2021, 'A Newly Identified Prophage Gene, ymfM , Causes SOS-Inducible Filamentation in Escherichia coli', Journal of Bacteriology, vol. 203, no. 11.
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Filamentation is an important biological mechanism that aids in the survival, pathogenesis, and antibiotic resistance of bacteria within different environments, including pathogenic bacteria such as uropathogenic Escherichia coli . Here, we have identified a bacteriophage-encoded cell division inhibitor which contributes to the filamentation that occurs during the SOS response.
Argyle, PA, Walworth, NG, Hinners, J, Collins, S, Levine, NM & Doblin, MA 2021, 'Multivariate trait analysis reveals diatom plasticity constrained to a reduced set of biological axes', ISME Communications, vol. 1, no. 1, p. 59.
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Abstract Trait-based approaches to phytoplankton ecology have gained traction in recent decades as phenotypic traits are incorporated into ecological and biogeochemical models. Here, we use high-throughput phenotyping to explore both intra- and interspecific constraints on trait combinations that are expressed in the cosmopolitan marine diatom genus Thalassiosira. We demonstrate that within Thalassiosira, phenotypic diversity cannot be predicted from genotypic diversity, and moreover, plasticity can create highly divergent phenotypes that are incongruent with taxonomic grouping. Significantly, multivariate phenotypes can be represented in reduced dimensional space using principal component analysis with 77.7% of the variance captured by two orthogonal axes, here termed a ‘trait-scape’. Furthermore, this trait-scape can be recovered with a reduced set of traits. Plastic responses to the new environments expanded phenotypic trait values and the trait-scape, however, the overall pattern of response to the new environments was similar between strains and many trait correlations remained constant. These findings demonstrate that trait-scapes can be used to reveal common constraints on multi-trait plasticity in phytoplankton with divergent underlying phenotypes. Understanding how to integrate trait correlational constraints and trade-offs into theoretical frameworks like biogeochemical models will be critical to predict how microbial responses to environmental change will impact elemental cycling now and into the future.
Armstrong, E, Coffin, J, Hersh, D, Katzenellenbogen, JM, Thompson, S, Flicker, L, McAllister, M, Cadilhac, DA, Rai, T, Godecke, E, Hayward, C, Hankey, GJ, Drew, N, Lin, I, Woods, D & Ciccone, N 2021, 'Healing Right Way: study protocol for a stepped wedge cluster randomised controlled trial to enhance rehabilitation services and improve quality of life in Aboriginal Australians after brain injury', BMJ Open, vol. 11, no. 9, pp. e045898-e045898.
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IntroductionDespite higher incidence of brain injury among Aboriginal compared with non-Aboriginal Australians, suboptimal engagement exists between rehabilitation services and Aboriginal brain injury survivors. Aboriginal patients often feel culturally insecure in hospital and navigation of services post discharge is complex. Health professionals report feeling ill-equipped working with Aboriginal patients. This study will test the impact of a research-informed culturally secure intervention model for Aboriginal people with brain injury.Methods and analysisDesign:Stepped wedge cluster randomised control trial design; intervention sequentially introduced at four pairs of healthcare sites across Western Australia at 26-week intervals.Recruitment:Aboriginal participants aged ≥18 years within 4 weeks of an acute stroke or traumatic brain injury.Intervention:(1) Cultural security training for hospital staff and (2) local, trial-specific, Aboriginal Brain Injury Coordinators supporting participants.Primary outcome: Quality-of-life using EuroQOL-5D-3L (European Quality of Life scale, five dimensions, three severity levels) Visual Analogue Scale score at 26 weeks post injury. Recruitment of 312 participants is estimated to detect a difference of 15 points with 80% power at the 5% significance level. A linear mixed model will be used to assess the between-condition difference.Secondary outcome measures: Modified Rankin Scale, Functional Independence Measure, Modified Caregiver Strain Index, Hospital Anxiety and Depression Scale at 12 and 26 weeks post injury, rehabilitation occasions of service received, hospital compliance with minimum care processes by 26 ...
Ashcroft, SP, Fletcher, G, Philp, AM, Jenkinson, C, Das, S, Hansbro, PM, Atherton, PJ & Philp, A 2021, 'Diet-induced vitamin D deficiency reduces skeletal muscle mitochondrial respiration', Journal of Endocrinology, vol. 249, no. 2, pp. 113-124.
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Vitamin D deficiency is associated with symptoms of skeletal muscle myopathy including muscle weakness and fatigue. Recently, vitamin D-related metabolites have been linked to the maintenance of mitochondrial function within skeletal muscle. However, current evidence is limited to in vitro models and the effects of diet-induced vitamin D deficiency upon skeletal muscle mitochondrial function in vivo have received little attention. In order to examine the role of vitamin D in the maintenance of mitochondrial function in vivo, we utilised an established model of diet-induced vitamin D deficiency in C57BL/6J mice. Mice were either fed a control diet (2200 IU/kg i.e. vitamin D replete) or a vitamin D-deplete (0 IU/kg) diet for periods of 1, 2 and 3 months. Gastrocnemius muscle mitochondrial function and ADP sensitivity were assessed via high-resolution respirometry and mitochondrial protein content via immunoblotting. As a result of 3 months of diet-induced vitamin D deficiency, respiration supported via complex I + II (CI + IIP) and the electron transport chain (ETC) were 35 and 37% lower when compared to vitamin D-replete mice (P < 0.05). Despite functional alterations, citrate synthase activity, AMPK phosphorylation, mitofilin, OPA1 and ETC subunit protein content remained unchanged in response to dietary intervention (P > 0.05). In conclusion, we report that 3 months of diet-induced vitamin D deficiency reduced skeletal muscle mitochondrial respiration in C57BL/6J mice. Our data, when combined with previous in vitro observations, suggest that vitamin D-mediated regulation of mitochondrial function may underlie the exacerbated muscle fatigue and performance deficits observed during vitamin D deficiency.
Augustine, R, Dan, P, Hasan, A, Khalaf, IM, Prasad, P, Ghosal, K, Gentile, C, McClements, L & Maureira, P 2021, 'Stem cell-based approaches in cardiac tissue engineering: controlling the microenvironment for autologous cells', Biomedicine & Pharmacotherapy, vol. 138, pp. 111425-111425.
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Augustine, R, Kalva, SN, Ahmad, R, Zahid, AA, Hasan, S, Nayeem, A, McClements, L & Hasan, A 2021, '3D Bioprinted cancer models: Revolutionizing personalized cancer therapy', Translational Oncology, vol. 14, no. 4, pp. 101015-101015.
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After cardiovascular disease, cancer is the leading cause of death worldwide with devastating health and economic consequences, particularly in developing countries. Inter-patient variations in anti-cancer drug responses further limit the success of therapeutic interventions. Therefore, personalized medicines approach is key for this patient group involving molecular and genetic screening and appropriate stratification of patients to treatment regimen that they will respond to. However, the knowledge related to adequate risk stratification methods identifying patients who will respond to specific anti-cancer agents is still lacking in many cancer types. Recent advancements in three-dimensional (3D) bioprinting technology, have been extensively used to generate representative bioengineered tumor in vitro models, which recapitulate the human tumor tissues and microenvironment for high-throughput drug screening. Bioprinting process involves the precise deposition of multiple layers of different cell types in combination with biomaterials capable of generating 3D bioengineered tissues based on a computer-aided design. Bioprinted cancer models containing patient-derived cancer and stromal cells together with genetic material, extracellular matrix proteins and growth factors, represent a promising approach for personalized cancer therapy screening. Both natural and synthetic biopolymers have been utilized to support the proliferation of cells and biological material within the personalized tumor models/implants. These models can provide a physiologically pertinent cell–cell and cell–matrix interactions by mimicking the 3D heterogeneity of real tumors. Here, we reviewed the potential applications of 3D bioprinted tumor constructs as personalized in vitro models in anticancer drug screening and in the establishment of precision treatment regimens.
Awal, MA, Hossain, MS, Debjit, K, Ahmed, N, Nath, RD, Habib, GMM, Khan, MS, Islam, MA & Mahmud, MAP 2021, 'An Early Detection of Asthma Using BOMLA Detector', IEEE Access, vol. 9, pp. 58403-58420.
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Badal, FR, Sarker, SK, Fahim, SR, Das, SK, Islam, MR, Kouzani, AZ & Mahmud, MAP 2021, 'Robust Controller Design for Tracking Enhancement of a Grid-Tied PV-Battery Microgrid Under Industrial Loads', IEEE Transactions on Applied Superconductivity, vol. 31, no. 8, pp. 1-5.
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The concept of microgrid (MG) empowers the application of renewable energy sources (RES) to meet the increasing demand of electrical power, which further inspires us to enable this technology under the study of inverter-based industrial loads (IL). The inclusion of inverter-based IL adds some noises in the MGs dynamics because of the non-linear characteristics of inverter and parametric uncertainty of loads. The above constraints impose extra-challenges to maintain reliable operation of the MGs. In this paper, integral based linear quadratic gaussian (ILQG) controller is proposed to maintain the tracking operation via the control of inverter used with ILs, which is further connected with the dc bus which is regulated by the inverter in grid side and dc-dc converter applied in utility grid, PV and battery, respectively. The proposed ILQG controller is designed based on the proper combination of linear quadratic gaussian (LQG) and integral controller and its performance is evaluated by changing the operating conditions, which includes the switching of supplying power from PV, and both PV and battery. Additionally, the investigation under the variation of the IL parameters and comparison with resonant controller is used to ensure the robust performance of the ILQG controller.
Baffour, B, Brown, JJ & Smith, PWF 2021, 'Latent Class Analysis for Estimating an Unknown Population Size – with Application to Censuses', Journal of Official Statistics, vol. 37, no. 3, pp. 673-697.
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Abstract Estimation of the unknown population size using capture-recapture techniques relies on the key assumption that the capture probabilities are homogeneous across individuals in the population. This is usually accomplished via post-stratification by some key covariates believed to influence individual catchability. Another issue that arises in population estimation from data collected from multiple sources is list dependence, where an individual’s catchability on one list is related to that of another list. The earlier models for population estimation heavily relied upon list independence. However, there are methods available that can adjust the population estimates to account for dependence among lists. In this article, we propose the use of latent class analysis through log-linear modelling to estimate the population size in the presence of both heterogeneity and list dependence. The proposed approach is illustrated using data from the 1988 US census dress rehearsal.
Bagheri, S, Huang, Y, Walker, PD, Zhou, JL & Surawski, NC 2021, 'Strategies for improving the emission performance of hybrid electric vehicles', Science of The Total Environment, vol. 771, pp. 144901-144901.
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Low emission vehicle technologies need widespread adoption in the transport sector to overcome its significant decarbonisation challenges. Hybrid Electric Vehicles (HEVs) represent an intermediate technology between pure electric vehicles and internal combustion engines that have proven capability in reducing petroleum consumption. HEV customers often cite improved fuel economy as a major benefit from adopting this technology; however, outstanding questions remain regarding their respective emission levels. Through an extensive literature study, we show that several issues remain with HEV emissions performance which stem from frequent high-power cold starts, engine calibration issues and inefficient operating conditions for catalytic converters. HEVs have more NOx, HC, CO and particle number emissions compared to conventional vehicles by up to 21.0, 5.8, 9.0 and 23.3 times, respectively. Improved engine control algorithms, after-treatment design and thermal design of three-way catalysts emerge as research priorities for improving the emissions performance of HEVs.
Bake, A, Rezoanur Rahman, M, Evans, PJ, Cortie, M, Nancarrow, M, Abrudan, R, Radu, F, Khaydukov, Y, Causer, G, Callori, S, Livesey, KL, Mitchell, D, Pastuovic, Z, Wang, X & Cortie, D 2021, 'Structure and magnetism of ultra-small cobalt particles assembled at titania surfaces by ion beam synthesis', Applied Surface Science, vol. 570, pp. 151068-151068.
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Bannister, T, Ebert, EE, Silver, J, Newbigin, E, Lampugnani, ER, Hughes, N, Looker, C, Mulvenna, V, Jones, PJ, Davies, JM, Suphioglu, C, Beggs, PJ, Emmerson, KM, Huete, A, Nguyen, H, Williams, T, Douglas, P, Wain, A, Carroll, M & Csutoros, D 2021, 'Breathing Easier in Australia: A Pilot Risk-Assessment System for Epidemic Thunderstorm-induced Asthma', Bulletin of the American Meteorological Society, vol. 102, no. 12, pp. 1173-1180.
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Bannister, T, Ebert, EE, Williams, T, Douglas, P, Wain, A, Carroll, M, Silver, J, Newbigin, E, Lampugnani, ER, Hughes, N, Looker, C, Mulvenna, V, Csutoros, D, Jones, PJ, Davies, JM, Suphioglu, C, Beggs, PJ, Emmerson, KM, Huete, A & Nguyen, H 2021, 'A Pilot Forecasting System for Epidemic Thunderstorm Asthma in Southeastern Australia', Bulletin of the American Meteorological Society, vol. 102, no. 2, pp. E399-E420.
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AbstractIn November 2016, an unprecedented epidemic thunderstorm asthma event in Victoria, Australia, resulted in many thousands of people developing breathing difficulties in a very short period of time, including 10 deaths, and created extreme demand across the Victorian health services. To better prepare for future events, a pilot forecasting system for epidemic thunderstorm asthma (ETSA) risk has been developed for Victoria. The system uses a categorical risk-based approach, combining operational forecasting of gusty winds in severe thunderstorms with statistical forecasts of high ambient grass pollen concentrations, which together generate the risk of epidemic thunderstorm asthma. This pilot system provides the first routine daily epidemic thunderstorm asthma risk forecasting service in the world that covers a wide area, and integrates into the health, ambulance, and emergency management sector. Epidemic thunderstorm asthma events have historically occurred infrequently, and no event of similar magnitude has impacted the Victorian health system since. However, during the first three years of the pilot, 2017–19, two high asthma presentation events and four moderate asthma presentation events were identified from public hospital emergency department records. The ETSA risk forecasts showed skill in discriminating between days with and without health impacts. However, even with hindsight of the actual weather and airborne grass pollen conditions, some high asthma presentation events occurred in districts that were assessed as low risk for ETSA, reflecting the challenge of predicting this unusual phenomenon.
Bao, G, Wen, S, Lin, G, Yuan, J, Lin, J, Wong, K-L, Bünzli, J-CG & Jin, D 2021, 'Learning from lanthanide complexes: The development of dye-lanthanide nanoparticles and their biomedical applications', Coordination Chemistry Reviews, vol. 429, pp. 213642-213642.
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© 2020 Elsevier B.V. Coordination chemistry has been widely studied in lanthanide complexes, where organic ligands are used to chelate individual lanthanide ions, and the complexes are broadly used in analytical, biological, and clinical applications. Significant progress has recently been made to exploit the hybrid structure of lanthanide doped inorganic nanoparticles “coated” with organic dyes. This attributes to the fast developments of nanoscience and technology centred around well-controlled nanocrystal synthesis and engineering, with a variety of shape, size, composition and structures towards the desirable functions. There are a lot of similarities between the two forms of lanthanide materials, waiting for a systematic analysis to guide the emerging field of nanocrystal-dye hybrids. Therefore, we survey here the principles for the design of dye-lanthanide energy transfer systems and analyse the remarkable successes made in hybrid dye-lanthanide nanosystems.
Bao, G, Wen, S, Wang, W, Zhou, J, Zha, S, Liu, Y, Wong, K-L & Jin, D 2021, 'Enhancing Hybrid Upconversion Nanosystems via Synergistic Effects of Moiety Engineered NIR Dyes', Nano Letters, vol. 21, no. 23, pp. 9862-9868.
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Hybrid upconversion nanosystems have been reported to improve the low absorption efficiency of lanthanide-doped upconversion nanoparticles (UCNPs). However, the low quantum yield and poor photostability of NIR dyes pose challenges for practical uses. Here, we introduce a bulky moiety, 4-(1,2,2-triphenylvinyl)-1,1'-biphenyl (TPEO), to enhance its quantum yield by suppressing the bond rotation and improve the stability by deactivating the photoinduced oxidization. Compared with the conventional IR806, the formed NIR dye, TPEO-Cy, has been characterized to deliver three times higher quantum yield and seven times better photostability. Moreover, we take advantage of the strong affinity of sulfonate chains on the TPEO-Cy to bind to the surface of UCNPs. Taking together the synergistic effect, we have achieved a 242-fold upconversion emission enhancement over the benchmark of IR806-sensitized system and an ∼800 000-fold increase than the bare UCNPs. Our design of the NIR dyes suggests a new scope to search for more efficient upconversion nanohybrids.
Bao, T, Damtie, MM, Wei, W, Phong Vo, HN, Nguyen, KH, Hosseinzadeh, A, Cho, K, Yu, ZM, Jin, J, Wei, XL, Wu, K, Frost, RL & Ni, B-J 2021, 'Simultaneous adsorption and degradation of bisphenol A on magnetic illite clay composite: Eco-friendly preparation, characterizations, and catalytic mechanism', Journal of Cleaner Production, vol. 287, pp. 125068-125068.
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Excess bisphenol A (BPA) is a pollutant of concern in different water sources. In this work, magnetic illite clay-composite material (Fe3O4@illite) was synthesized via the coprecipitation method by loading Fe3O4 nanoparticles (nano-Fe3O4) onto the surfaces of illite clay. Results from different characterizations showed that nano-Fe3O4 was embedded into illite clay nanosheets and existed on the surfaces of illite clay, thereby reducing the degree of agglomeration and improving dispersibility. The catalytic BPA degradation of Fe3O4@illite and nano-Fe3O4 confirmed the superior performance of Fe3O4@illite compared with that of nano-Fe3O4. The optimum operating parameters for degradation were 0.3 mL of H2O2 at pH of 3 in the presence of Fe3O4@illite, which provided a maximum degradation capacity up to 816, 364, 113, and 68 mg/g for epoxy BPA concentration of resin wastewater (266 mg/L), synthetic wastewater (80 mg/L), Hefei City swan lake (25 mg/L), and Hefei University lake wastewater (14.94 mg/L), respectively, in 180 min reaction time. The degradation data conformed to the pseudo-first-order kinetic model. The degradation pathways and mineralization study revealed that the adsorption-Fenton-like reaction was the principal mechanism that demonstrated 100% degradation efficiency of Fe3O4@illite even after nine successive runs. The regeneration and reusability tendency analysis ensured that Fe3O4@illite can be easily separated by using magnets. Therefore, Fe3O4@illite composite with H2O2 Fenton-like technology was a promising method for BPA degradation.
Bao, W, Wang, R, Qian, C, Zhang, Z, Wu, R, Zhang, Y, Liu, F, Li, J & Wang, G 2021, 'Porous Heteroatom-Doped Ti3C2Tx MXene Microspheres Enable Strong Adsorption of Sodium Polysulfides for Long-Life Room-Temperature Sodium–Sulfur Batteries', ACS Nano, vol. 15, no. 10, pp. 16207-16217.
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The practical application of Na-S batteries is largely hindered by their low mass loading, inferior rate capability, and poor cycling performance. Herein, we report a design strategy for encapsulation of sodium polysulfides using Ti3C2Tx MXene. Porous nitrogen-doped Ti3C2Tx MXene microspheres have been synthesized by a facile synthesis method. Porous nitrogen-doped Ti3C2Tx MXene microspheres contain abundant pore structures and heteroatom functional groups for structural and chemical synergistic encapsulation of sodium polysulfides. Sodium-sulfur batteries, based on the as-proposed cathode, demonstrated outstanding electrochemical performances, including a high reversible capacity (980 mAh g-1 at 0.5 C rate) and extended cycling stability (450.1 mAh g-1 at 2 C after 1000 cycles at a high areal sulfur loading of 5.5 mg cm-2). This MXene-based hybrid material is a promising cathode host material for polysulfide-retention, enabling high-performance Na-S batteries.
Barnes, JL, Plank, MW, Asquith, K, Maltby, S, Sabino, LR, Kaiko, GE, Lochrin, A, Horvat, JC, Mayall, JR, Kim, RY, Hansbro, PM, Keely, S, Belz, GT, Tay, HL & Foster, PS 2021, 'T-helper 22 cells develop as a distinct lineage from Th17 cells during bacterial infection and phenotypic stability is regulated by T-bet', Mucosal Immunology, vol. 14, no. 5, pp. 1077-1087.
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CD4+ T-helper 22 (Th22) cells are a phenotypically distinct lymphocyte subset that produces high levels of interleukin (IL)-22 without co-production of IL-17A. However, the developmental origin and lineage classification of Th22 cells, their interrelationship to Th17 cells, and potential for plasticity at sites of infection and inflammation remain largely undefined. An improved understanding of the mechanisms underpinning the outgrowth of Th22 cells will provide insights into their regulation during homeostasis, infection, and disease. To address this knowledge gap we generated 'IL-17A-fate-mapping IL-17A/IL-22 reporter transgenic mice' and show that Th22 cells develop in the gastrointestinal tract and lung during bacterial infection without transitioning via an Il17a-expressing intermediate, although in some compartments alternative transition pathways exist. Th22-cell development was not dependent on T-bet; however, this transcription factor functioned as a promiscuous T-cell-intrinsic regulator of IL-17A and IL-22 production, in addition to regulating the outgrowth, phenotypic stability, and plasticity of Th22 cells. Thus, we demonstrate that at sites of mucosal bacterial infection Th22 cells develop as a distinct lineage independently of Th17 cells; though both lineages exhibit bidirectional phenotypic flexibility within infected tissues and their draining lymph nodes, and that T-bet plays a critical regulatory role in Th22-cell function and identity.
Barton, PS, Dawson, BM, Barton, AF, Joshua, S & Wallman, JF 2021, 'Temperature dynamics in different body regions of decomposing vertebrate remains', Forensic Science International, vol. 325, pp. 110900-110900.
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The decomposition of vertebrates is controlled largely by external temperature, yet internal temperatures can also play an important role but are generally poorly documented. In this study, we compared continuous hourly temperature recordings from the mouth, under the head, right chest and right abdomen, and in the rectum of one refrigerated human and one fresh pig cadaver during 29 days of decomposition. Each cadaver differed in its internal starting temperature, thus providing two contrasting case studies for examining temperature dynamics among body regions. We used time-series analysis methods common to hydrology to reveal key differences in internal temperature dynamics. Within both cadavers, the chest region experienced the highest average temperatures, and the mouth experienced the highest maximum hourly temperature. Temperatures exceeded 30 °C inside the pig for between 40% (rectum) and 75% (chest) of the duration of the study, but for only 20% (rectum) and 35% (chest) of the time in the human. Our study provides evidence of the different thermal trajectories occurring in different body regions, and some similarities between two cadavers despite their different starting thermal conditions. These results improve our understanding of why decomposition occurs at different rates within the same cadaver, and that the location of blowfly larvae collections should be noted to improve estimates of the post-mortem interval.
Batistic, F-K, Rhumorbarbe, D, Lefrancois, E, Tettey, J, Raithelhuber, M, Rossy, Q & Morelato, M 2021, 'Analysis of Google Trends to monitor new psychoactive substance. Is there an added value?', Forensic Science International, vol. 326, pp. 110918-110918.
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The past decade has seen an increase in the development and availability of a broad category of drugs, known as new psychoactive substances (NPS). NPS are challenging for public health authorities, therefore the two major drug monitoring bodies – the European Monitoring Centre for Drugs and Drug Addiction (EMCDDA) and the United Nations Office on Drugs and Crime (UNODC) – have implemented the EU Early Warning System (EWS) and Early Warning Advisory (EWA), respectively. While these monitoring systems are informative, it is difficult to keep up with the constant and rapid developmental rate of NPS. The EMCDDA has recognised the need for an alternative and technologically derived early warning system. The aim of this research is to determine whether Google Trends and drug discussion forum data can be used to complement early warning systems for NPS.Forty-eight substances were used in this study and classed into groups based on their chemical structure, following the UNODC classification system. Google Trends data (time range: 2004–2019) and drug forum data (time range: 2003–2018) were extracted for each substance and visual trend profiles were created for class groups as well as individual substances. Analysis was conducted to determine when a substance first appeared on Google Trends and a drug discussion forum as well as their trends over time. This date of first appearance was then compared to the date the substance was first reported to UNODC.Of the three data sources utilised, substances were most likely to appear on Google Trends first. Amongst the different classes of NPS, discernible trends (‘block’, ‘successive’, and ‘generational’ trends) were observed. These trends reflect the evolution of the manufacture of substances or generations of substances that has been observed in the literature. For example, in the synthetic cannabinoids’ category, a generational trend is observed that corresponds to the different generations of synthetic cannabino...
Beltrán, VH, Puill-Stephan, E, Howells, E, Flores-Moya, A, Doblin, M, Núñez-Lara, E, Escamilla, V, López, T & van Oppen, MJH 2021, 'Physiological diversity among sympatric, conspecific endosymbionts of coral (Cladocopium C1acro) from the Great Barrier Reef', Coral Reefs, vol. 40, no. 4, pp. 985-997.
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Bennett, AC, Arndt, SK, Bennett, LT, Knauer, J, Beringer, J, Griebel, A, Hinko‐Najera, N, Liddell, MJ, Metzen, D, Pendall, E, Silberstein, RP, Wardlaw, TJ, Woodgate, W & Haverd, V 2021, 'Thermal optima of gross primary productivity are closely aligned with mean air temperatures across Australian wooded ecosystems', Global Change Biology, vol. 27, no. 19, pp. 4727-4744.
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AbstractGross primary productivity (GPP) of wooded ecosystems (forests and savannas) is central to the global carbon cycle, comprising 67%–75% of total global terrestrial GPP. Climate change may alter this flux by increasing the frequency of temperatures beyond the thermal optimum of GPP (Topt). We examined the relationship between GPP and air temperature (Ta) in 17 wooded ecosystems dominated by a single plant functional type (broadleaf evergreen trees) occurring over a broad climatic gradient encompassing five ecoregions across Australia ranging from tropical in the north to Mediterranean and temperate in the south. We applied a novel boundary‐line analysis to eddy covariance flux observations to (a) derive ecosystem GPP–Ta relationships and Topt (including seasonal analyses for five tropical savannas); (b) quantitatively and qualitatively assess GPP–Ta relationships within and among ecoregions; (c) examine the relationship between Topt and mean daytime air temperature (MDTa) across all ecosystems; and (d) examine how down‐welling short‐wave radiation (Fsd) and vapour pressure deficit (VPD) influence the GPP–Ta relationship. GPP–Ta relationships were convex parabolas with narrow curves in tropical forests, tropical savannas (wet season), and temperate forests, and wider curves in temperate woodlands, Mediterranean woodlands, and tropical savannas (dry season). Ecosystem Topt ranged from 15℃ (temperate forest) to 32℃ (tropical savanna—wet and dry seasons). The shape of GPP–Ta curves was largely determined by daytime Ta range, MDTa, and maximum GPP with the upslope influenced by Fsd and the downslope influenced by VPD. Across all ecosystems, there was a strong positive linear relationship between T
BERDINSKY, D, ELDER, M & TABACK, J 2021, 'BEING CAYLEY AUTOMATIC IS CLOSED UNDER TAKING WREATH PRODUCT WITH VIRTUALLY CYCLIC GROUPS', Bulletin of the Australian Mathematical Society, vol. 104, no. 3, pp. 464-474.
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AbstractWe extend work of Berdinsky and Khoussainov [‘Cayley automatic representations of wreath products’, International Journal of Foundations of Computer Science27(2) (2016), 147–159] to show that being Cayley automatic is closed under taking the restricted wreath product with a virtually infinite cyclic group. This adds to the list of known examples of Cayley automatic groups.
Berlińska, J, Kononov, A & Zinder, Y 2021, 'Two-machine flow shop with dynamic storage space', Optimization Letters, vol. 15, no. 7, pp. 2433-2454.
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AbstractThe publications on two-machine flow shop scheduling problems with job dependent storage requirements, where a job seizes a portion of the storage space for the entire duration of its processing, were motivated by various applications ranging from supply chains of mineral resources to multimedia systems. In contrast to the previous publications that assumed that the availability of the storage space remains unchanged, this paper is concerned with a more general case when the availability is a function of time. It strengthens the previously published result concerning the existence of an optimal permutation schedule, shows that the variable storage space availability leads to the NP-hardness in the strong sense even for unit processing times, and presents a polynomial-time approximation scheme together with several heuristic algorithms. The heuristics are evaluated by means of computational experiments.
Bernhardt, N, Kim, S, Fröch, JE, White, SJU, Duong, NMH, He, Z, Chen, B, Liu, J, Aharonovich, I & Solntsev, AS 2021, 'Large few-layer hexagonal boron nitride flakes for nonlinear optics', Optics Letters, vol. 46, no. 3, pp. 564-564.
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Hexagonal boron nitride (hBN) is a layered dielectric material with a wide range of applications in optics and photonics. In this work, we demonstrate a fabrication method for few-layer hBN flakes with areas up to 5000 µ m 2 . We show that hBN in this form can be integrated with photonic microstructures: as an example, we use a circular Bragg grating (CBG). The layer quality of the exfoliated hBN flake on and off a CBG is confirmed by Raman spectroscopy and second-harmonic generation (SHG) microscopy. We show that the SHG signal is uniform across the hBN sample outside the CBG and is amplified in the center of the CBG.
Berry, IJ, Widjaja, M, Jarocki, VM, Steele, JR, Padula, MP & Djordjevic, SP 2021, 'Protein cleavage influences surface protein presentation in Mycoplasma pneumoniae', Scientific Reports, vol. 11, no. 1, p. 6743.
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AbstractMycoplasma pneumoniae is a significant cause of pneumonia and post infection sequelae affecting organ sites distant to the respiratory tract are common. It is also a model organism where extensive ‘omics’ studies have been conducted to gain insight into how minimal genome self-replicating organisms function. An N-terminome study undertaken here identified 4898 unique N-terminal peptides that mapped to 391 (56%) predicted M. pneumoniae proteins. True N-terminal sequences beginning with the initiating methionine (iMet) residue from the predicted Open Reading Frame (ORF) were identified for 163 proteins. Notably, almost half (317; 46%) of the ORFS derived from M. pneumoniae strain M129 are post-translationally modified, presumably by proteolytic processing, because dimethyl labelled neo-N-termini were characterised that mapped beyond the predicted N-terminus. An analysis of the N-terminome describes endoproteolytic processing events predominately targeting tryptic-like sites, though cleavages at negatively charged residues in P1′ (D and E) with lysine or serine/alanine in P2′ and P3′ positions also occurred frequently. Surfaceome studies identified 160 proteins (23% of the proteome) to be exposed on the extracellular surface of M. pneumoniae. The two orthogonal methodologies used to characterise the surfaceome each identified the same 116 proteins, a 72% (116/160) overlap. Apart from lipoproteins, transporters, and adhesins, 93/160 (58%) of the surface proteins lack signal peptides and have well characterised, canonical functions in the cell. Of the 160 surface proteins identified, 134 were also targets of endo-proteolytic processing. These processing events are likely to have profound implications for how the host immune system recognises and responds to M. pneumoniae.
Bertram, MR, Brito, B, Palinski, RM, Fish, IH, Pauszek, SJ, Hartwig, EJ, Smoliga, GR, Vu, LT, Hoang, BH, Phuong, NT, Hung, VV, Vu, PP, Dung, NK, Tien, NN, Dong, PV, Dung, DH & Arzt, J 2021, 'Novel Recombinant Foot-and-Mouth Disease Virus Circulating in Vietnam', Microbiology Resource Announcements, vol. 10, no. 1.
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We report the genome sequences of 12 recombinant foot-and-mouth disease virus isolates from Vietnam. The recombinant strain has a capsid region from an A/Sea-97 strain and a nonstructural segment from an O/ME-SA/PanAsia strain. The isolates were obtained from two outbreak samples collected in June 2017 and 10 subclinical samples collected between 2017 and 2019.
Birrer, SC, Wemheuer, F, Dafforn, KA, Gribben, PE, Steinberg, PD, Simpson, SL, Potts, J, Scanes, P, Doblin, MA & Johnston, EL 2021, 'Legacy Metal Contaminants and Excess Nutrients in Low Flow Estuarine Embayments Alter Composition and Function of Benthic Bacterial Communities', Frontiers in Microbiology, vol. 12, p. 661177.
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Coastal systems such as estuaries are threatened by multiple anthropogenic stressors worldwide. However, how these stressors and estuarine hydrology shape benthic bacterial communities and their functions remains poorly known. Here, we surveyed sediment bacterial communities in poorly flushed embayments and well flushed channels in Sydney Harbour, Australia, using 16S rRNA gene sequencing. Sediment samples were collected monthly during the Austral summer-autumn 2014 at increasing distance from a large storm drain in each channel and embayment. Bacterial communities differed significantly between sites that varied in proximity to storm drains, with a gradient of change apparent for sites within embayments. We explored this pattern for embayment sites with analysis of RNA-Seq gene expression patterns and found higher expression of multiple genes involved in bacterial stress response far from storm drains, suggesting that bacterial communities close to storm drains may be more tolerant of localised anthropogenic stressors. Several bacterial groups also differed close to and far from storm drains, suggesting their potential utility as bioindicators to monitor contaminants in estuarine sediments. Overall, our study provides useful insights into changes in the composition and functioning of benthic bacterial communities as a result of multiple anthropogenic stressors in differing hydrological conditions.
Bishop, DP, Westerhausen, MT, Barthelemy, F, Lockwood, T, Cole, N, Gibbs, EM, Crosbie, RH, Nelson, SF, Miceli, MC, Doble, PA & Wanagat, J 2021, 'Quantitative immuno-mass spectrometry imaging of skeletal muscle dystrophin', Scientific Reports, vol. 11, no. 1, pp. 1-11.
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AbstractEmerging and promising therapeutic interventions for Duchenne muscular dystrophy (DMD) are confounded by the challenges of quantifying dystrophin. Current approaches have poor precision, require large amounts of tissue, and are difficult to standardize. This paper presents an immuno-mass spectrometry imaging method using gadolinium (Gd)-labeled anti-dystrophin antibodies and laser ablation-inductively coupled plasma-mass spectrometry to simultaneously quantify and localize dystrophin in muscle sections. Gd is quantified as a proxy for the relative expression of dystrophin and was validated in murine and human skeletal muscle sections following k-means clustering segmentation, before application to DMD patients with different gene mutations where dystrophin expression was measured up to 100 µg kg−1 Gd. These results demonstrate that immuno-mass spectrometry imaging is a viable approach for pre-clinical to clinical research in DMD. It rapidly quantified relative dystrophin in single tissue sections, efficiently used valuable patient resources, and may provide information on drug efficacy for clinical translation.
Biswas, SP, Anower, MS, Sheikh, MRI, Islam, MR, Rahman, MA, Mahmud, MAP & Kouzani, AZ 2021, 'A Modified Reference Saturated Third Harmonic Injected Equal Loading PWM for VSC-Based Renewable Energy Systems', IEEE Transactions on Applied Superconductivity, vol. 31, no. 8, pp. 1-5.
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Mitigation of excessive heat due to high frequency switching of voltage source converter (VSC) is always an industrial concern for superconducting magnetic energy storage (SMES) or high temperature superconducting (HTS) material based power conditioning system with grid-tied renewable energy interface. The pulse width modulation (PWM) technique employed for the switching of the VSC has a significant impact on joules heating, switching and conduction power losses, total harmonic distortion (THD) profile of the VSC output, and conversion efficiency in the SMES/HTS based grid-tied power system. In this paper, a modified reference saturated third harmonic injected equal loading PWM technique is proposed for a VSC-based grid-tied photovoltaic (PV) system, which offers lower THD and reduced power conversion losses. The proposed PWM technique employed in the VSC can be used in a PV-based SMES/HTS integrated power system to improve the performance of the power conditioner. To prove the superiority of the proposed PWM technique, a simulation in MATLAB/Simulink was carried out and the simulation results were validated by laboratory tests.
Blomme, EE, Provoost, S, De Smet, EG, De Grove, KC, Van Eeckhoutte, HP, De Volder, J, Hansbro, PM, Bonato, M, Saetta, M, Wijnant, SRA, Verhamme, F, Joos, GF, Bracke, KR, Brusselle, GG & Maes, T 2021, 'Quantification and role of innate lymphoid cell subsets in Chronic Obstructive Pulmonary Disease', Clinical & Translational Immunology, vol. 10, no. 6, pp. 1-16.
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AbstractObjectivesInnate lymphoid cells (ILCs) secrete cytokines, such as IFN‐γ, IL‐13 and IL‐17, which are linked to chronic obstructive pulmonary disease (COPD). Here, we investigated the role of pulmonary ILCs in COPD pathogenesis.MethodsLung ILC subsets in COPD and control subjects were quantified using flow cytometry and associated with clinical parameters. Tissue localisation of ILC and T‐cell subsets was determined by immunohistochemistry. Mice were exposed to air or cigarette smoke (CS) for 1, 4 or 24 weeks to investigate whether pulmonary ILC numbers and activation are altered and whether they contribute to CS‐induced innate inflammatory responses.ResultsQuantification of lung ILC subsets demonstrated that ILC1 frequency in the total ILC population was elevated in COPD and was associated with smoking and severity of respiratory symptoms (COPD Assessment Test [CAT] score). All three ILC subsets localised near lymphoid aggregates in COPD. In the COPD mouse model, CS exposure in C57BL/6J mice increased ILC numbers at all time points, with relative increases in ILC1 in bronchoalveolar lavage (BAL) fluid. Importantly, CS exposure induced increases in neutrophils, monocytes and dendritic cells that remained elevated in Rag2/Il2rg‐deficient mice that lack adaptive immune cells and ILCs. However, CS‐induced CXCL1, IL‐6, TNF‐α and IFN‐γ levels were reduced by ILC deficiency.ConclusionThe ILC1 subset is increased in COPD patients and correlates with smoking and severity of respiratory symptoms. ILCs also increase upon CS exposure in C57BL/6J mice. In the absence of adaptive immunity, ILCs contribute to CS‐induced pro‐inflammatory mediator release, b...
Bogema, DR, Yam, J, Micallef, ML, Gholipourkanani, H, Go, J, Jenkins, C & Dang, C 2021, 'Draft genomes of Perkinsus olseni and Perkinsus chesapeaki reveal polyploidy and regional differences in heterozygosity', Genomics, vol. 113, no. 1, pp. 677-688.
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© 2020 Perkinsus spp. parasites have significant impact on aquaculture and wild mollusc populations. We sequenced the genomes of five monoclonal isolates of Perkinsus olseni and one Perkinsus chesapeaki from international sources. Sequence analysis revealed similar levels of repetitive sequence within species, a polyploid genome structure, and substantially higher heterozygosity in Oceanian-sourced isolates. We also identified tandem replication of the rRNA transcriptional unit, with high strain variation. Characterized gene content was broadly similar amongst all Perkinsus spp. but P. olseni Oceanian isolates contained an elevated number of genes compared to other P. olseni isolates and cox3 could not be identified in any Perkinsus spp. sequence. Phylogenetics and average nucleotide identity scans were consistent with all P. olseni isolates being within one species. These are the first genome sequences generated for both P. olseni and P. chesapeaki and will allow future advances in diagnostic design and population genomics of these important aquatic parasites.
Bohaud, C, Johansen, MD, Jorgensen, C, Ipseiz, N, Kremer, L & Djouad, F 2021, 'The Role of Macrophages During Zebrafish Injury and Tissue Regeneration Under Infectious and Non-Infectious Conditions', Frontiers in Immunology, vol. 12, pp. 1-9.
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The future of regenerative medicine relies on our understanding of the mechanistic processes that underlie tissue regeneration, highlighting the need for suitable animal models. For many years, zebrafish has been exploited as an adequate model in the field due to their very high regenerative capabilities. In this organism, regeneration of several tissues, including the caudal fin, is dependent on a robust epimorphic regenerative process, typified by the formation of a blastema, consisting of highly proliferative cells that can regenerate and completely grow the lost limb within a few days. Recent studies have also emphasized the crucial role of distinct macrophage subpopulations in tissue regeneration, contributing to the early phases of inflammation and promoting tissue repair and regeneration in late stages once inflammation is resolved. However, while most studies were conducted under non-infectious conditions, this situation does not necessarily reflect all the complexities of the interactions associated with injury often involving entry of pathogenic microorganisms. There is emerging evidence that the presence of infectious pathogens can largely influence and modulate the host immune response and the regenerative processes, which is sometimes more representative of the true complexities underlying regenerative mechanics. Herein, we present the current knowledge regarding the paths involved in the repair of non-infected and infected wounds using the zebrafish model.
Bohaud, C, Johansen, MD, Jorgensen, C, Kremer, L, Ipseiz, N & Djouad, F 2021, 'The Role of Macrophages During Mammalian Tissue Remodeling and Regeneration Under Infectious and Non-Infectious Conditions', Frontiers in Immunology, vol. 12, pp. 1-13.
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Several infectious pathologies in humans, such as tuberculosis or SARS-CoV-2, are responsible for tissue or lung damage, requiring regeneration. The regenerative capacity of adult mammals is limited to few organs. Critical injuries of non-regenerative organs trigger a repair process that leads to a definitive architectural and functional disruption, while superficial wounds result in scar formation. Tissue lesions in mammals, commonly studied under non-infectious conditions, trigger cell death at the site of the injury, as well as the production of danger signals favouring the massive recruitment of immune cells, particularly macrophages. Macrophages are also of paramount importance in infected injuries, characterized by the presence of pathogenic microorganisms, where they must respond to both infection and tissue damage. In this review, we compare the processes implicated in the tissue repair of non-infected versus infected injuries of two organs, the skeletal muscles and the lungs, focusing on the primary role of macrophages. We discuss also the negative impact of infection on the macrophage responses and the possible routes of investigation for new regenerative therapies to improve the recovery state as seen with COVID-19 patients.
Bolitho, C, Moscova, M, Baxter, RC & Marsh, DJ 2021, 'Amphiregulin increases migration and proliferation of epithelial ovarian cancer cells by inducing its own expression via PI3-kinase signaling', Molecular and Cellular Endocrinology, vol. 533, pp. 111338-111338.
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Booth, DJ & Beretta, GA 2021, 'Long-term demographics of a coral-reef fish: growth, survival and abundance at several spatial scales', Coral Reefs, vol. 40, no. 4, pp. 1257-1266.
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In marine organisms, pelagic larval dispersal often results in genetic panmixis among widely separated populations; however, local conditions may produce populations of marine organisms that differ in key life history traits. Here, we assess spatial differences in growth, body condition, survivorship and movement over a decade for lemon damselfish Pomacentrus moluccensis. Newly recruited fish were tagged on the southern (One Tree Island, 23°S), and northern Great Barrier Reef (Lizard Island, 15°S), 1200 km apart, and monitored for over a decade to provide direct data on growth and survivorship. New recruit physiological condition (lipid content) had a weak positive influence on early survival, but not on long-term persistence or growth, and the larval supply signal was lost after 2 years, suggesting post-settlement processes were key in long-term population persistence. Fish exhibited extreme site fidelity, with older/larger fish moving most (all less than 7 m). At Lizard Island, under 5% of individuals remained after 3 years, none after 4 years, while at One Tree Island 5% of individuals survived over 5 years, with 1% remaining after a decade, suggesting Lizard Island populations may require more frequent replenishment to persist. Among-site (within location) variation in mortality was high, and not related to density, suggesting local conditions such as wave exposure and predators were important. Surprisingly, mean growth at the two locations, which differ by around 2 °C on average in sea temperature, was practically identical, levelling off after 3 years, but with high variation among nearby sites within each location, which would affect size-based fecundity and time of first reproduction at these smaller spatial scales. Neither early post-settlement growth nor mortality were density-dependent, and early growth was not related to overall longevity. These small reef fishes are highly sedentary and some demographic parameters, but not others, differ at...
Borchhardt, N, Chomérat, N, Bilien, G, Zentz, F, Rhodes, L, Murray, SA & Hoppenrath, M 2021, 'Morphology and molecular phylogeny of Bindiferia gen. nov. (Dinophyceae), a new marine, sand-dwelling dinoflagellate genus formerly classified within Amphidinium', Phycologia, vol. 60, no. 6, pp. 631-643.
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Bouchekara, HREH, Shahriar, MS, Irshad, UB, Sha’ aban, YA, Mahmud, MAP, Javaid, MS, Ramli, MAM & Farjana, SH 2021, 'Optimal sizing of hybrid photovoltaic/diesel/battery nanogrid using a parallel multiobjective PSO-based approach: Application to desert camping in Hafr Al-Batin city in Saudi Arabia', Energy Reports, vol. 7, pp. 4360-4375.
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Bousquet, J, Anto, JM, Czarlewski, W, Haahtela, T, Fonseca, SC, Iaccarino, G, Blain, H, Vidal, A, Sheikh, A, Akdis, CA & Zuberbier, T 2021, 'Cabbage and fermented vegetables: From death rate heterogeneity in countries to candidates for mitigation strategies of severe COVID‐19', Allergy, vol. 76, no. 3, pp. 735-750.
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AbstractLarge differences in COVID‐19 death rates exist between countries and between regions of the same country. Some very low death rate countries such as Eastern Asia, Central Europe, or the Balkans have a common feature of eating large quantities of fermented foods. Although biases exist when examining ecological studies, fermented vegetables or cabbage have been associated with low death rates in European countries. SARS‐CoV‐2 binds to its receptor, the angiotensin‐converting enzyme 2 (ACE2). As a result of SARS‐CoV‐2 binding, ACE2 downregulation enhances the angiotensin II receptor type 1 (AT1R) axis associated with oxidative stress. This leads to insulin resistance as well as lung and endothelial damage, two severe outcomes of COVID‐19. The nuclear factor (erythroid‐derived 2)‐like 2 (Nrf2) is the most potent antioxidant in humans and can block in particular the AT1R axis. Cabbage contains precursors of sulforaphane, the most active natural activator of Nrf2. Fermented vegetables contain many lactobacilli, which are also potent Nrf2 activators. Three examples are: kimchi in Korea, westernized foods, and the slum paradox. It is proposed that fermented cabbage is a proof‐of‐concept of dietary manipulations that may enhance Nrf2‐associated antioxidant effects, helpful in mitigating COVID‐19 severity.
Bowman, S, Casares-de-Cal, M-Á, Alvarez-Dios, J, Gomez Tato, A, Roffey, P, Richardson, A, McNevin, D & Gahan, ME 2021, 'Identification ofBacillusandYersiniaspecies and hoax agents by protein profiling using microfluidic capillary electrophoresis with peak detection algorithms', Australian Journal of Forensic Sciences, vol. 53, no. 1, pp. 2-15.
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© 2019, © 2019 Australian Academy of Forensic Sciences. Bacillus anthracis and Yersinia pestis are biological agents that pose an increasing concern to national security if deliberately disseminated. Hoax agents, including suspicious white powders and environmental bacterial species, can also cause disruption. In either scenario it is of high importance to rapidly and accurately identify any suspicious powder as hazardous or hoax. Protein profiling, using microfluidic capillary electrophoresis, provides a rapid (less than 40 minutes), reliable and field-based screening method. Two commonly encountered hoax agents, three Bacillus species (including B. anthracis Sterne strain), two Yersinia species and E. coli were profiled on the Experion™ System (Bio-Rad). Peak detection algorithms were developed for the identification of protein peaks in electropherograms. Boolean logic paths were then employed to predict the electrophoretic pattern of samples. Parameters assessed included variation within and between Experion™ Pro260 chips and the ability to discriminate between samples over time intervals, between operators and between field and laboratory analyses. Classification with optimal Boolean logic paths reported no misclassification with an accuracy of 100% for B. anthracis Sterne strain, B. thuringiensis (powder and culture-based), B. cereus and plain wheat flour. Overall there was 75% correct identification for the eight sample types tested.
Bradac, C, Xu, Z-Q & Aharonovich, I 2021, 'Quantum Energy and Charge Transfer at Two-Dimensional Interfaces', Nano Letters, vol. 21, no. 3, pp. 1193-1204.
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Bradbury, P, Nader, CP, Cidem, A, Rutting, S, Sylvester, D, He, P, Rezcallah, MC, O’Neill, GM & Ammit, AJ 2021, 'Tropomyosin 2.1 collaborates with fibronectin to promote TGF-β1-induced contraction of human lung fibroblasts', Respiratory Research, vol. 22, no. 1, pp. 1-10.
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AbstractMany lung diseases are characterized by fibrosis, leading to impaired tissue patency and reduced lung function. Development of fibrotic tissue depends on two-way interaction between the cells and the extra-cellular matrix (ECM). Concentration-dependent increased stiffening of the ECM is sensed by the cells, which in turn increases intracellular contraction and pulling on the matrix causing matrix reorganization and further stiffening. It is generally accepted that the inflammatory cytokine growth factor β1 (TGF-β1) is a major driver of lung fibrosis through the stimulation of ECM production. However, TGF-β1 also regulates the expression of members of the tropomyosin (Tm) family of actin associating proteins that mediate ECM reorganization through intracellular-generated forces. Thus, TGF-β1 may mediate the bi-directional signaling between cells and the ECM that promotes tissue fibrosis. Using combinations of cytokine stimulation, mRNA, protein profiling and cellular contractility assays with human lung fibroblasts, we show that concomitant induction of key Tm isoforms and ECM by TGF-β1, significantly accelerates fibrotic phenotypes. Knocking down Tpm2.1 reduces fibroblast-mediated collagen gel contraction. Collectively, the data suggest combined ECM secretion and actin cytoskeleton contractility primes the tissue for enhanced fibrosis. Our study suggests that Tms are at the nexus of inflammation and tissue stiffening. Small molecules targeting specific Tm isoforms have recently been designed; thus targeting Tpm2.1 may represent a novel therapeutic target in lung fibrosis.
Bradfield, L & Balleine, B 2021, 'Editorial overview: Value-based decision making: control, value, and context in action', Current Opinion in Behavioral Sciences, vol. 41, pp. iii-vi.
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Bradfield, LA & Iordanova, MD 2021, 'Threat perception: Fear and the retrorubal field', Current Biology, vol. 31, no. 10, pp. R469-R471.
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A new study has found that neurons within a structure of the rat midbrain known as the retrorubral field show diverse responses to stimuli that signal different levels of threat, as well as a separate pattern of diverse responses to differentially predicted aversive outcomes.
Bradley, DJ, Boada, J, Gladstone, W, Glasby, TM & Gribben, PE 2021, 'Sublethal effects of a rapidly spreading native alga on a key herbivore', Ecology and Evolution, vol. 11, no. 18, pp. 12605-12616.
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AbstractMultiple anthropogenic stressors are causing a global decline in foundation species, including macrophytes, often resulting in the expansion of functionally different, more stressor‐tolerant macrophytes. Previously subdominant species may experience further positive demographic feedback if they are exposed to weaker plant–herbivore interactions, possibly via decreased palatability or being structurally different from the species they are replacing. However, the consequences of the spread of opportunistic macrophytes for the local distribution and life history of herbivores are unknown.The green alga,Caulerpa filiformis, previously a subdominant macrophyte on low intertidal‐shallow subtidal rock shores, is becoming locally more abundant and has spread into warmer waters across the coast of New South Wales, Australia.In this study, we measured (a) the distribution and abundance of a key consumer, the sea urchinHeliocidaris erythrogramma,across a seascape at sites whereC. filiformishas become dominant, (b) performed behavioral field experiments to test the role of habitat selection in determining the local distribution ofH. erythrogramma,and (c) consumer experiments to test differential palatability between previously dominant higher quality species likeEcklonia radiataandSargassumsp. andC. filiformisand the physiological consequences of consuming it.At all sites, urchin densities were positively correlated with distance away fromC. filiformisbeds, and they actively moved away from beds. Feeding experiments showed that, wh...
Bramucci, AR, Focardi, A, Rinke, C, Hugenholtz, P, Tyson, GW, Seymour, JR & Raina, J-B 2021, 'Microvolume DNA extraction methods for microscale amplicon and metagenomic studies', ISME Communications, vol. 1, no. 1, pp. 1-5.
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Abstract Investigating the composition and metabolic capacity of aquatic microbial assemblages usually requires the filtration of multi-litre samples, which are up to 1 million-fold larger than the microenvironments within which microbes are predicted to be spatially organised. To determine if community profiles can be reliably generated from microlitre volumes, we sampled seawater at a coastal and an oceanic site, filtered and homogenised them, and extracted DNA from bulk samples (2 L) and microvolumes (100, 10 and 1 μL) using two new approaches. These microvolume DNA extraction methods involve either physical or chemical lysis (through pH/thermal shock and lytic enzymes/surfactants, respectively), directly followed by the capture of DNA on magnetic beads. Downstream analysis of extracted DNA using both amplicon sequencing and metagenomics, revealed strong correlation with standard large volume approaches, demonstrating the fidelity of taxonomic and functional profiles of microbial communities in as little as 1 μL of seawater. This volume is six orders of magnitude smaller than most standard operating procedures for marine metagenomics, which will allow precise sampling of the heterogenous landscape that microbes inhabit.
Brown, AO, Frankham, GJ, Bond, L, Stuart, BH, Johnson, RN & Ueland, M 2021, 'An overview of risk investment in the transnational illegal wildlife trade from stakeholder perspectives', WIREs Forensic Science, vol. 3, no. 2.
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AbstractThe illegal wildlife trade (IWT) is a lucrative, clandestine trade that endangers animal welfare, damages native biodiversity and undermines the rule of law. Despite enhanced law enforcement focus and increased litigation, the illicit trade of wildlife and wildlife products has continued to flourish. The increase in the IWT can be attributed to a lack of identifiable relationships, risk functions and reward systems specific to each stakeholder in this illicit market. The increase in the IWT indicates that domestic and international regulations are not effective in their intent of preventing the illegal trade of various wildlife species. Without a clear understanding of stakeholder relationships, resources will continue to be wasted on ineffective prevention and detection methods with regards to the IWT. Law enforcement strategies rely on identifying key stakeholders in the IWT as well as their perceived motivations, risks, and relationships. These definitions may provide further insight into the motivations driving these individuals participating in this illicit market and may contribute to more successful interventions. Stakeholders and their associated roles within the IWT have been defined to serve as a tool to understand the various risk/reward utility functions in global markets. This study provides a framework support for policy makers by establishing baseline risk/reward systems for each stakeholder which can be built upon as intelligence surrounding these stakeholders increases.This article is categorized under: Jurisprudence and Regulatory Oversight > Communication Across Science and Law Jurisprudence and Regulatory Oversight > Interdisciplinary Collaboration
Brown, AO, Frankham, GJ, Stuart, BH & Ueland, M 2021, 'Reptile volatilome profiling optimisation: A pathway towards forensic applications', Forensic Science International: Animals and Environments, vol. 1, pp. 100024-100024.
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Reptiles are the most trafficked live taxa in the illegal wildlife trade, in part due to their popularity as an exotic pet. Current methods used to detect these illegally trafficked animals are limited. This study optimised the collection and analysis parameters associated with volatilome collection that will set the foundation for targeted odourant detection methods. This study determined that the dual sorbent type (Tenax® TA and Carbograph 5DT) in combination with 20-min sampling times and 15-min sampling intervals collected the most reproducible reptile volatilome profiles. It was also determined that desorption methods with mid-range desorption flows (20 ml/min), trap temperatures (-15 °C), and mid-range trap desorption (25 ml/min) were most effective in retrieving collected reptile volatilomes. Two-dimensional gas chromatography coupled with time-of-flight mass spectrometry was used for analysis, where combined Rxi-624 Sil MS (mid-polar) first dimension and Stabilwax® (polar) second dimension column sets were selected as the most effective columns for analysing reptile volatilomes. The resultant data collected and analysed using these parameters demonstrated that individual volatilomes from three reptile species were distinct using principal component analysis. In addition, this work highlighted the need for more rigorous statistical methods to determine reptile biomarkers and which compounds most significantly influence volatilome profiles between species.
Brown, AO, Romanis, CS, Dvořák, P, Foss, AJ, Gibson, QA, Villanueva, CD, Durden, WN, Garvey, AD, Jenkins, P, Hašler, P, Johansen, JR, Neilan, BA & Casamatta, DA 2021, 'A new species of cryptic cyanobacteria isolated from the epidermis of a bottlenose dolphin and as a bioaerosol', Phycologia, vol. 60, no. 6, pp. 603-618.
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Brunet, M, de Bettignies, F, Le Duff, N, Tanguy, G, Davoult, D, Leblanc, C, Gobet, A & Thomas, F 2021, 'Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities', Environmental Microbiology, vol. 23, no. 3, pp. 1638-1655.
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SummaryKelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its accumulation and degradation on the seafloor. Kelp tissue, seawater and sediment were sampled during a 6‐month in situ experiment simulating kelp detritus accumulation. Evaluation of the epiphytic bacterial community abundance, structure, taxonomic composition and predicted functional profiles evidenced a biphasic succession. Initially, dominant genera (Hellea, Litorimonas, Granulosicoccus) showed a rapid and drastic decrease in sequence abundance, probably outcompeted by algal polysaccharide‐degraders such as Bacteroidia members which responded within 4 weeks. Acidimicrobiia, especially members of the Sva0996 marine group, colonized the degrading kelp biomass after 11 weeks. These secondary colonizers could act as opportunistic scavenger bacteria assimilating substrates exposed by early degraders. In parallel, kelp accumulation modified bacterial communities in the underlying sediment, notably favouring anaerobic taxa potentially involved in the sulfur and nitrogen cycles. Overall, this study provides insights into the bacterial degradation of algal biomass in situ, an important link in coastal trophic chains.
Brunet, M, Le Duff, N, Fuchs, BM, Amann, R, Barbeyron, T & Thomas, F 2021, 'Specific detection and quantification of the marine flavobacterial genus Zobellia on macroalgae using novel qPCR and CARD-FISH assays', Systematic and Applied Microbiology, vol. 44, no. 6, pp. 126269-126269.
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The flavobacterial genus Zobellia is considered as a model to study macroalgal polysaccharide degradation. The lack of data regarding its prevalence and abundance in coastal habitats constitutes a bottleneck to assess its ecological strategies. To overcome this issue, real-time quantitative PCR (qPCR) and fluorescence in situ hybridization (FISH) methods targeting the 16S rRNA gene were optimized to specifically detect and quantify Zobellia on the surface of diverse macroalgae. The newly designed qPCR primers and FISH probes targeted 98 and 100% of the Zobellia strains in silico and their specificity was confirmed using pure bacterial cultures. The dynamic range of the qPCR assay spanned 8 orders of magnitude from 10 to 108 16S rRNA gene copies and the detection limit was 0.01% relative abundance of Zobellia in environmental samples. Zobellia-16S rRNA gene copies were detected on all surveyed brown, green and red macroalgae, in proportion varying between 0.1 and 0.9% of the total bacterial copies. The absolute and relative abundance of Zobellia varied with tissue aging on the kelp Laminaria digitata. Zobellia cells were successfully visualized in Ulva lactuca and stranded Palmaria palmata surface biofilm using CARD-FISH, representing in the latter 105Zobellia cells·cm-2 and 0.43% of total bacterial cells. Overall, qPCR and CARD-FISH assays enabled robust detection, quantification and localization of Zobellia representatives in complex samples, underlining their ecological relevance as primary biomass degraders potentially cross-feeding other microorganisms.
Bryant, CJ, Burke, C & Huston, WM 2021, 'Cervicovaginal microbiota and women’s health outcomes', Microbiology Australia, vol. 42, no. 2, pp. 65-68.
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The human cervicovaginal microbiome has an important role in the health and homoeostasis of the female reproductive tract. A eubiotic microbiome is typically dominated with lactic acid producing bacteria and is categorised into five community state types. Issues arise when the microbiome becomes dysbiotic, with the microbial composition shifting to contain a greater relative abundance of strict and facultative anaerobes. This shift will lead to several adverse changes in the vaginal environment including compromised epithelial cells, cell death, inflammation, and greater susceptibility to infection. These changes are associated with various adverse outcomes including infections, preterm birth, and infertility. In this review, we discuss how the cervicovaginal microbiome influences these outcomes and possible future directions of treatment and research.
Bulbul, AA-M, Kouzani, AZ, Mahmud, MAP & Nahid, A-A 2021, 'Design and Numerical Analysis of a Novel Rectangular PCF (R-PCF)-Based Biochemical Sensor (BCS) in the THz Regime', International Journal of Optics, vol. 2021, pp. 1-16.
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A novel PCF-based sensor has been presented in this paper to sense different chemicals and biocomponents. The proposed biochemical sensor (BCS) comprises a simple arrangement of rectangular holes. The competence of this BCS in detecting analytes is evaluated employing the full-vector finite element method (FEM). Performance metrics prove the competence of this BCS in sensing various analytes that have a refractive index in the range of 1.33–1.48. The proposed BCS shows ultralower values for both the bulk absorption and confinement loss. This BCS attains a maximum of about 95.82% relative sensitivity at 2.5 THz. Also, the dispersion for this sensor is only 0.12 ± 0.011 ps/THz/cm at the same point of interest. These results prove that the proposed BCS will play a key role in sensing toxic chemicals, illegal drugs, biocomponents, etc. Besides, the simple rectangle-based PCF structure ensures the feasibility of fabrication by practicing the existing fabrication strategies.
Burnett, DL, Jackson, KJL, Langley, DB, Aggarwal, A, Stella, AO, Johansen, MD, Balachandran, H, Lenthall, H, Rouet, R, Walker, G, Saunders, BM, Singh, M, Li, H, Henry, JY, Jackson, J, Stewart, AG, Witthauer, F, Spence, MA, Hansbro, NG, Jackson, C, Schofield, P, Milthorpe, C, Martinello, M, Schulz, SR, Roth, E, Kelleher, A, Emery, S, Britton, WJ, Rawlinson, WD, Karl, R, Schäfer, S, Winkler, TH, Brink, R, Bull, RA, Hansbro, PM, Jäck, H-M, Turville, S, Christ, D & Goodnow, CC 2021, 'Immunizations with diverse sarbecovirus receptor-binding domains elicit SARS-CoV-2 neutralizing antibodies against a conserved site of vulnerability', Immunity, vol. 54, no. 12, pp. 2908-2921.e6.
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Viral mutations are an emerging concern in reducing SARS-CoV-2 vaccination efficacy. Second-generation vaccines will need to elicit neutralizing antibodies against sites that are evolutionarily conserved across the sarbecovirus subgenus. Here, we immunized mice containing a human antibody repertoire with diverse sarbecovirus receptor-binding domains (RBDs) to identify antibodies targeting conserved sites of vulnerability. Antibodies with broad reactivity against diverse clade B RBDs targeting the conserved class 4 epitope, with recurring IGHV/IGKV pairs, were readily elicited but were non-neutralizing. However, rare class 4 antibodies binding this conserved RBD supersite showed potent neutralization of SARS-CoV-2 and all variants of concern. Structural analysis revealed that the neutralizing ability of cross-reactive antibodies was reserved only for those with an elongated CDRH3 that extends the antiparallel beta-sheet RBD core and orients the antibody light chain to obstruct ACE2-RBD interactions. These results identify a structurally defined pathway for vaccine strategies eliciting escape-resistant SARS-CoV-2 neutralizing antibodies.
Butterworth, NJ, White, TE, Byrne, PG & Wallman, JF 2021, 'Love at first flight: wing interference patterns are species‐specific and sexually dimorphic in blowflies (Diptera: Calliphoridae)', Journal of Evolutionary Biology, vol. 34, no. 3, pp. 558-570.
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AbstractWing interference patterns (WIPs) are stable structural colours displayed on insect wings which are only visible at specific viewing geometries and against certain backgrounds. These patterns are widespread among flies and wasps, and growing evidence suggests that they may function as species‐ and sex‐specific mating cues in a range of taxa. As such, it is expected that WIPs should differ between species and show clear sexual dimorphisms. However, the true extent to which WIPs vary between species, sexes and individuals is currently unclear, as previous studies have only taken a qualitative approach, without considering how WIPs might be perceived by the insect. Here, we perform the first quantitative analysis of inter‐ and intra‐specific variation in WIPs across seven Australian species of the blowfly genus Chrysomya. Using multispectral digital imaging and a tentative model of blowfly colour vision, we provide quantitative evidence that WIPs are species‐specific, highlight that the extent of divergence is greater in males than in females and demonstrate sexual dimorphisms in several species. These data suggest that WIPs have diversified substantially in blowflies as a result of either sexual or ecological selection.
Cai, X, Li, JJ, Liu, T, Brian, O & Li, J 2021, 'Infectious disease mRNA vaccines and a review on epitope prediction for vaccine design', Briefings in Functional Genomics, vol. 20, no. 5, pp. 289-303.
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AbstractMessenger RNA (mRNA) vaccines have recently emerged as a new type of vaccine technology, showing strong potential to combat the COVID-19 pandemic. In addition to SARS-CoV-2 which caused the pandemic, mRNA vaccines have been developed and tested to prevent infectious diseases caused by other viruses such as Zika virus, the dengue virus, the respiratory syncytial virus, influenza H7N9 and Flavivirus. Interestingly, mRNA vaccines may also be useful for preventing non-infectious diseases such as diabetes and cancer. This review summarises the current progresses of mRNA vaccines designed for a range of diseases including COVID-19. As epitope study is a primary component in the in silico design of mRNA vaccines, we also survey on advanced bioinformatics and machine learning algorithms which have been used for epitope prediction, and review on user-friendly software tools available for this purpose. Finally, we discuss some of the unanswered concerns about mRNA vaccines, such as unknown long-term side effects, and present with our perspectives on future developments in this exciting area.
Callan, T, Woodcock, S & Huston, WM 2021, 'Ascension of Chlamydia is moderated by uterine peristalsis and the neutrophil response to infection', PLOS Computational Biology, vol. 17, no. 9, pp. e1009365-e1009365.
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Chlamydia trachomatis is a common sexually transmitted infection that is associated with a range of serious reproductive tract sequelae including in women Pelvic Inflammatory Disease (PID), tubal factor infertility, and ectopic pregnancy. Ascension of the pathogen beyond the cervix and into the upper reproductive tract is thought to be necessary for these pathologies. However, Chlamydia trachomatis does not encode a mechanism for movement on its genome, and so the processes that facilitate ascension have not been elucidated. Here, we evaluate the factors that may influence chlamydial ascension in women. We constructed a mathematical model based on a set of stochastic dynamics to elucidate the moderating factors that might influence ascension of infections in the first month of an infection. In the simulations conducted from the stochastic model, 36% of infections ascended, but only 9% had more than 1000 bacteria ascend. The results of the simulations indicated that infectious load and the peristaltic contractions moderate ascension and are inter-related in impact. Smaller initial loads were much more likely to ascend. Ascension was found to be dependent on the neutrophil response. Overall, our results indicate that infectious load, menstrual cycle timing, and the neutrophil response are critical factors in chlamydial ascension in women.
Camaya, I, Mok, TY, Lund, M, To, J, Braidy, N, Robinson, MW, Santos, J, O’Brien, B & Donnelly, S 2021, 'The parasite-derived peptide FhHDM-1 activates the PI3K/Akt pathway to prevent cytokine-induced apoptosis of β-cells', Journal of Molecular Medicine, vol. 99, no. 11, pp. 1605-1621.
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Type 1 diabetes (T1D) is an autoimmune disease characterised by the destruction of the insulin-producing beta (β)-cells within the pancreatic islets. We have previously identified a novel parasite-derived molecule, termed Fasciola hepatica helminth defence molecule 1 (FhHDM-1), that prevents T1D development in non-obese diabetic (NOD) mice. In this study, proteomic analyses of pancreas tissue from NOD mice suggested that FhHDM-1 activated the PI3K/Akt signalling pathway, which is associated with β-cell metabolism, survival and proliferation. Consistent with this finding, FhHDM-1 preserved β-cell mass in NOD mice. Examination of the biodistribution of FhHDM-1 after intraperitoneal administration in NOD mice revealed that the parasite peptide localised to the pancreas, suggesting that it exerted a direct effect on the survival/function of β-cells. This was confirmed in vitro, as the interaction of FhHDM-1 with the NOD-derived β-cell line, NIT-1, resulted in increased levels of phosphorylated Akt, increased NADH and NADPH and reduced activity of the NAD-dependent DNA nick sensor, poly(ADP-ribose) polymerase (PARP-1). As a consequence, β-cell survival was enhanced and apoptosis was prevented in the presence of the pro-inflammatory cytokines that destroy β-cells during T1D pathogenesis. Similarly, FhHDM-1 protected primary human islets from cytokine-induced apoptosis. Importantly, while FhHDM-1 promoted β-cell survival, it did not induce proliferation. Collectively, these data indicate that FhHDM-1 has significant therapeutic applications to promote β-cell survival, which is required for T1D and T2D prevention and islet transplantation. KEY MESSAGES: FhHDM-1 preserves β-cell mass in NOD mice and prevents the development of T1D. FhHDM-1 enhances phosphorylation of Akt in mouse β-cell lines. FhHDM-1 increases levels of NADH/NADPH in mouse β-cell lines in vitro. FhHDM-1 prevents cytokine-induced cell death of mouse β-cell lines and primary human β-cells in vitr...
Castrogiovanni, P, Sanfilippo, C, Imbesi, R, Maugeri, G, Lo Furno, D, Tibullo, D, Castorina, A, Musumeci, G & Di Rosa, M 2021, 'Brain CHID1 Expression Correlates with NRGN and CALB1 in Healthy Subjects and AD Patients', Cells, vol. 10, no. 4, pp. 882-882.
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Alzheimer’s disease is a progressive, devastating, and irreversible brain disorder that, day by day, destroys memory skills and social behavior. Despite this, the number of known genes suitable for discriminating between AD patients is insufficient. Among the genes potentially involved in the development of AD, there are the chitinase-like proteins (CLPs) CHI3L1, CHI3L2, and CHID1. The genes of the first two have been extensively investigated while, on the contrary, little information is available on CHID1. In this manuscript, we conducted transcriptome meta-analysis on an extensive sample of brains of healthy control subjects (n = 1849) (NDHC) and brains of AD patients (n = 1170) in order to demonstrate CHID1 involvement. Our analysis revealed an inverse correlation between the brain CHID1 expression levels and the age of NDHC subjects. Significant differences were highlighted comparing CHID1 expression of NDHC subjects and AD patients. Exclusive in AD patients, the CHID1 expression levels were correlated positively to calcium-binding adapter molecule 1 (IBA1) levels. Furthermore, both in NDHC and in AD patient’s brains, the CHID1 expression levels were directly correlated with calbindin 1 (CALB1) and neurogranin (NRGN). According to brain regions, correlation differences were shown between the expression levels of CHID1 in prefrontal, frontal, occipital, cerebellum, temporal, and limbic system. Sex-related differences were only highlighted in NDHC. CHID1 represents a new chitinase potentially involved in the principal processes underlying Alzheimer’s disease.
Celis-Plá, PSM, Rearte, TA, Neori, A, Masojídek, J, Bonomi-Barufi, J, Álvarez-Gómez, F, Ranglová, K, Carmo da Silva, J, Abdala, R, Gómez, C, Caporgno, M, Torzillo, G, Silva Benavides, AM, Ralph, PJ, Fávero Massocato, T, Atzmüller, R, Vega, J, Chávez, P & Figueroa, FL 2021, 'A new approach for cultivating the cyanobacterium Nostoc calcicola (MACC-612) to produce biomass and bioactive compounds using a thin-layer raceway pond', Algal Research, vol. 59, pp. 102421-102421.
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Chadwick, S, Cvetanovski, M, Ross, M, Sharp, A & Moret, S 2021, 'Comparison of NIR powders to conventional fingerprint powders', Forensic Science International, vol. 328, pp. 111023-111023.
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Fingerprint powders remain one of the most common detection techniques used at the crime scene. However, powder efficiency and contrast can be hindered when applied to highly patterned backgrounds. This problem can be overcome using powders that are luminescent in the near-infrared (NIR) region of the electromagnetic spectrum. Despite being commercially available, those powders have been the focus of only a small number of studies, limited to a few substrates or donors. Their performance and advantages over common techniques are still to be thoroughly investigated. This study aims at assessing the performances of two NIR powder (fpNATURAL 1® and Universal Powder an in-house developed powder) against two conventional powders, a black and a luminescent powder (Sirchie Black, GREENcharge™) under various optical conditions (white light, visible luminescence and NIR luminescence). The powders were compared on four substrates using fingermarks of four different ages from five donors. A total 900 fingermarks were collected for each pairwise comparison. NIR imaging provided good background suppression and a high contrast, however it was shown that conventional powders remained the most effective powdering methods on the substrates tested as sufficient contrast could be achieved under white light or in luminescent mode in the visible region. The results showed that Universal Powder performed similarly to conventional powders, but poor performances were obtained on most substrates with fpNATURAL 1®. Based on the results obtained, it is recommended to use NIR powders only on substrates or conditions where traditional powders are known to perform poorly.
Chai, H, Cheng, W, Jin, D & Miao, P 2021, 'Recent Progress in DNA Hybridization Chain Reaction Strategies for Amplified Biosensing', ACS Applied Materials & Interfaces, vol. 13, no. 33, pp. 38931-38946.
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With the continuous development of DNA nanotechnology, various spatial DNA structures and assembly techniques emerge. Hybridization chain reaction (HCR) is a typical example with exciting features and bright prospects in biosensing, which has been intensively investigated in the past decade. In this Spotlight on Applications, we summarize the assembly principles of conventional HCR and some novel forms of linear/nonlinear HCR. With advantages like great assembly kinetics, facile operation, and an enzyme-free and isothermal reaction, these strategies can be integrated with most mainstream reporters (e.g., fluorescence, electrochemistry, and colorimetry) for the ultrasensitive detection of abundant targets. Particularly, we select several representative studies to better illustrate the novel ideas and performances of HCR strategies. Theoretical and practical utilities are confirmed for a range of biosensing applications. In the end, a deep discussion is provided about the challenges and future tasks of this field.
Chan, SH, Ismail, MH, Tan, CH, Rice, SA & McDougald, D 2021, 'Microbial predation accelerates granulation and modulates microbial community composition', BMC Microbiology, vol. 21, no. 1, pp. 91-91.
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Abstract Background Bacterial communities are responsible for biological nutrient removal and flocculation in engineered systems such as activated floccular sludge. Predators such as bacteriophage and protozoa exert significant predation pressure and cause bacterial mortality within these communities. However, the roles of bacteriophage and protozoan predation in impacting granulation process remain limited. Recent studies hypothesised that protozoa, particularly sessile ciliates, could have an important role in granulation as these ciliates were often observed in high abundance on surfaces of granules. Bacteriophages were hypothesized to contribute to granular stability through bacteriophage-mediated extracellular DNA release by lysing bacterial cells. This current study investigated the bacteriophage and protozoan communities throughout the granulation process. In addition, the importance of protozoan predation during granulation was also determined through chemical killing of protozoa in the floccular sludge. Results Four independent bioreactors seeded with activated floccular sludge were operated for aerobic granulation for 11 weeks. Changes in the phage, protozoa and bacterial communities were characterized throughout the granulation process. The filamentous phage, Inoviridae, increased in abundance at the initiation phase of granulation. However, the abundance shifted towards lytic phages during the maturation phase. In contrast, the abundance and diversity of protozoa decreased initially, possibly due to the reduction in settling time and subsequent washout. Upon the formation of granules, ciliated protozoa from the class Oligohymenophorea were the dominant group of protozoa based on metacommunity analysis. These ...
Chan, Y, Mehta, M, Paudel, KR, Madheswaran, T, Panneerselvam, J, Gupta, G, Su, QP, Hansbro, PM, MacLoughlin, R, Dua, K & Chellappan, DK 2021, 'Versatility of Liquid Crystalline Nanoparticles in Inflammatory Lung Diseases', Nanomedicine, vol. 16, no. 18, pp. 1545-1548.
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Chan, Y, Ng, SW, Chellappan, DK, Madheswaran, T, Zeeshan, F, Kumar, P, Pillay, V, Gupta, G, Wadhwa, R, Mehta, M, Wark, P, Hsu, A, Hansbro, NG, Hansbro, PM, Dua, K & Panneerselvam, J 2021, 'Celastrol-loaded liquid crystalline nanoparticles as an anti-inflammatory intervention for the treatment of asthma', International Journal of Polymeric Materials and Polymeric Biomaterials, vol. 70, no. 11, pp. 754-763.
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The present study aimed to formulate celastrol into liquid crystalline nanoparticles (LCNPs) through ultrasonication to enhance its therapeutic efficacy in the treatment of asthma. The physiochemical characteristics, in-vitro release studies were determined along with molecular simulations. Celastrol-loaded LCNPs showed the mean particle size of 194.1 ± 9.78 nm and high entrapment efficiency of 99.1 ± 0.02%. TEM revealed cubical-like structure of the nanoparticles and in-vitro release study demonstrated sustained drug release. They also demonstrated significant activity in reducing IL-1β production, when evaluated using immortalized human bronchial epithelial cell lines (BCi-NS1.1), that may help alleviate the symptoms of asthma.
Chan, Y, Ng, SW, Singh, SK, Gulati, M, Gupta, G, Chaudhary, SK, Hing, GB, Collet, T, MacLoughlin, R, Löbenberg, R, Oliver, BG, Chellappan, DK & Dua, K 2021, 'Revolutionizing polymer-based nanoparticle-linked vaccines for targeting respiratory viruses: A perspective', Life Sciences, vol. 280, pp. 119744-119744.
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Viral respiratory tract infections have significantly impacted global health as well as socio-economic growth. Respiratory viruses such as the influenza virus, respiratory syncytial virus (RSV), and the recent SARS-CoV-2 infection (COVID-19) typically infect the upper respiratory tract by entry through the respiratory mucosa before reaching the lower respiratory tract, resulting in respiratory disease. Generally, vaccination is the primary method in preventing virus pathogenicity and it has been shown to remarkably reduce the burden of various infectious diseases. Nevertheless, the efficacy of conventional vaccines may be hindered by certain limitations, prompting the need to develop novel vaccine delivery vehicles to immunize against various strains of respiratory viruses and to mitigate the risk of a pandemic. In this review, we provide an insight into how polymer-based nanoparticles can be integrated with the development of vaccines to effectively enhance immune responses for combating viral respiratory tract infections.
Chan, Y, Prasher, P, Löbenberg, R, Gupta, G, Singh, SK, Oliver, BG, Chellappan, DK & Dua, K 2021, 'Applications and Practice of Advanced Drug Delivery Systems for Targeting Toll-Like Receptors in Pulmonary Diseases', Nanomedicine, vol. 16, no. 10, pp. 783-786.
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Chang, JJ-Y, Rawlinson, D, Pitt, ME, Taiaroa, G, Gleeson, J, Zhou, C, Mordant, FL, De Paoli-Iseppi, R, Caly, L, Purcell, DFJ, Stinear, TP, Londrigan, SL, Clark, MB, Williamson, DA, Subbarao, K & Coin, LJM 2021, 'Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection', Cell Reports, vol. 35, no. 6, pp. 109108-109108.
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Charon, J, Murray, S & Holmes, EC 2021, 'Revealing RNA virus diversity and evolution in unicellular algae transcriptomes', Virus Evolution, vol. 7, no. 2, p. veab070.
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Abstract Remarkably little is known about the diversity and evolution of RNA viruses in unicellular eukaryotes. We screened a total of 570 transcriptomes from the Marine Microbial Eukaryote Transcriptome Sequencing Project that encompasses a wide diversity of microbial eukaryotes, including most major photosynthetic lineages (i.e. the microalgae). From this, we identified thirty new and divergent RNA virus species, occupying a range of phylogenetic positions within the overall diversity of RNA viruses. Approximately one-third of the newly described viruses comprised single-stranded positive-sense RNA viruses from the order Lenarviricota associated with fungi, plants, and protists, while another third were related to the order Ghabrivirales, including members of the protist and fungi-associated Totiviridae. Other viral species showed sequence similarity to positive-sense RNA viruses from the algae-associated Marnaviridae, the double-stranded RNA (ds-RNA) Partitiviridae, as well as tentative evidence for one negative-sense RNA virus related to the Qinviridae. Importantly, we were able to identify divergent RNA viruses from distant host taxa, revealing the ancestry of these viral families and greatly extending our knowledge of the RNA viromes of microalgal cultures. Both the limited number of viruses detected per sample and the low sequence identity to known RNA viruses imply that additional microalgal viruses exist that could not be detected at the current sequencing depth or were too divergent to be identified using sequence similarity. Together, these results highlight the need for further investigation of algal-associated RNA viruses as well as the development of new tools to identify RNA viruses that exhibit very high levels of sequence divergence.
Chellappan, DK, Dharwal, V, Paudel, KR, Jha, NK, MacLoughlin, R, Oliver, BG, M Hansbro, P & Dua, K 2021, 'Mitochondrial Dysfunctions Associated With Chronic Respiratory Diseases and Their Targeted Therapies: an Update', Future Medicinal Chemistry, vol. 13, no. 15, pp. 1249-1251.
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Chen, C, Liu, B, Liu, Y, Liao, J, Shan, X, Wang, F & Jin, D 2021, 'Heterochromatic Nonlinear Optical Responses in Upconversion Nanoparticles for Super‐Resolution Nanoscopy', Advanced Materials, vol. 33, no. 23, pp. e2008847-2008847.
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AbstractPoint spread function (PSF) engineering by an emitter's response can code higher‐spatial‐frequency information of an image for microscopy to achieve super‐resolution. However, complexed excitation optics or repetitive scans are needed, which explains the issues of low speed, poor stability, and operational complexity associated with the current laser scanning microscopy approaches. Here, the diverse emission responses of upconversion nanoparticles (UCNPs) are reported for super‐resolution nanoscopy to improve the imaging quality and speed. The method only needs a doughnut‐shaped scanning excitation beam at an appropriate power density. By collecting the four‐photon emission of single UCNPs, the high‐frequency information of a super‐resolution image can be resolved through the doughnut‐emission PSF. Meanwhile, the two‐photon state of the same nanoparticle is oversaturated, so that the complementary lower‐frequency information of the super‐resolution image can be simultaneously collected by the Gaussian‐like emission PSF. This leads to a method of Fourier‐domain heterochromatic fusion, which allows the extended capability of the engineered PSFs to cover both low‐ and high‐frequency information to yield optimized image quality. This approach achieves a spatial resolution of 40 nm, 1/24th of the excitation wavelength. This work suggests a new scope for developing nonlinear multi‐color emitting probes in super‐resolution nanoscopy.
Chen, H, Chhor, M, Rayner, BS, McGrath, K & McClements, L 2021, 'Evaluation of the diagnostic accuracy of current biomarkers in heart failure with preserved ejection fraction: A systematic review and meta-analysis', Archives of Cardiovascular Diseases, vol. 114, no. 12, pp. 793-804.
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Background: A number of circulating biomarkers are currently utilized for the diagnosis of chronic heart failure with preserved ejection fraction (HFpEF). However, due to HFpEF heterogeneity, the accuracy of these biomarkers remains unclear. Aims: This study aimed to systematically determine the diagnostic accuracy of currently available biomarkers for chronic HFpEF. Methods: PubMed, Web of Science, MEDLINE and SCOPUS databases were searched systematically to identify studies assessing the diagnostic accuracy of biomarkers of chronic HFpEF with left ventricular ejection fraction (LVEF) ≥ 50%. All included studies were independently assessed for quality and relevant information was extracted. Random-effects models were used to estimate the pooled diagnostic accuracy of HFpEF biomarkers. Results: The search identified 6145 studies, of which 19 were included. Four biomarkers were available for meta-analysis. The pooled sensitivity of B-type natriuretic peptide (BNP) (0.787, 95% confidence interval [CI] 0.719–0.842) was higher than that of N-terminal pro-BNP (NT-proBNP) (0.696, 95% CI 0.599–0.779) in chronic HFpEF diagnosis. However, NT-proBNP showed improved specificity (0.882, 95% CI 0.778–0.941) compared to BNP (\0.796, 95% CI 0.672–0.882). Galectin-3 (Gal-3) exhibited a reliable diagnostic adequacy for HFpEF (sensitivity 0.760, 95% CI 0.631–0.855; specificity 0.803, 95% CI 0.667–0.893). However, suppression of tumorigenesis-2 (ST2) displayed limited diagnostic performance for chronic HFpEF diagnosis (sensitivity 0.636, 95% CI 0.465–0.779; specificity 0.595, 95% CI 0.427–0.743). Conclusion: NT-proBNP and BNP appear to be the most reliable biomarkers in chronic HFpEF with NT-proBNP showing higher specificity and BNP showing higher sensitivity. Although Gal-3 appears more reliable than ST2 in HFpEF diagnosis, the conclusions are limited as only three studies were included in this meta-analysis.
Chen, H, Wang, B, Li, G, Steele, JR, Stayte, S, Vissel, B, Chan, YL, Yi, C, Saad, S, Machaalani, R & Oliver, BG 2021, 'Brain health is independently impaired by E-vaping and high-fat diet', Brain, Behavior, and Immunity, vol. 92, pp. 57-66.
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Tobacco smoking and high-fat diet (HFD) independently impair short-term memory. E-cigarettes produce e-vapour containing flavourings and nicotine. Here, we investigated whether e-vapour inhalation interacts with HFD to affect short-term memory and neural integrity. Balb/c mice (7 weeks, male) were fed a HFD (43% fat, 20 kJ/g) for 16 weeks. In the last 6 weeks, half of the mice were exposed to tobacco-flavoured e-vapour from nicotine-containing (18 mg/L) or nicotine-free (0 mg/L) e-fluids twice daily. Short-term memory function was measured in week 15. HFD alone did not impair memory function, but increased brain phosphorylated (p)-Tau and astrogliosis marker, while neuron and microglia levels were decreased. E-vapour exposure significantly impaired short-term memory function independent of diet and nicotine. Nicotine free e-vapour induced greater changes compared to the nicotine e-vapour and included, increased systemic cytokines, increased brain p-Tau and decreased postsynaptic density protein (PSD)-95 levels in chow-fed mice, and decreased astrogliosis marker, increased microglia and increased glycogen synthase kinase levels in HFD-fed mice. Increased hippocampal apoptosis was also differentially observed in chow and HFD mice. In conclusion, E-vapour exposure impaired short-term memory independent of diet and nicotine, and was correlated to increased systemic inflammation, reduced PSD-95 level and increased astrogliosis in chow-fed mice, but decreased gliosis and increased microglia in HFD-fed mice, indicating the inflammatory nature of e-vapour leading to short term memory impairment.
Chen, K, Fan, Y, Cao, X, Liu, J, Tian, H & Tian, J 2021, 'Corrigendum to “A novel green enzymatic synthetic route of 2, 3-dihydroxybenzoic acid from glucose and CO2 fixation” [Process Biochem. 94 (2020) 207–212]', Process Biochemistry, vol. 103, pp. 123-123.
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Chen, L-J, Humphrey, SJ, Zhu, J-L, Zhu, F-F, Wang, X-Q, Wang, X, Wen, J, Yang, H-B & Gale, PA 2021, 'A Two-Dimensional Metallacycle Cross-Linked Switchable Polymer for Fast and Highly Efficient Phosphorylated Peptide Enrichment', Journal of the American Chemical Society, vol. 143, no. 22, pp. 8295-8304.
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Chen, P, Bornhorst, J, Patton, S, Bagai, K, Nitin, R, Miah, M, Hare, DJ, Kysenius, K, Crouch, PJ, Xiong, L, Rouleau, GA, Schwerdtle, T, Connor, J, Aschner, M, Bowman, AB & Walters, AS 2021, 'A potential role for zinc in restless legs syndrome', Sleep, vol. 44, no. 4.
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Abstract Study Objectives Evaluate serum and brain noniron metals in the pathology and genetics of restless legs syndrome (RLS). Methods In two independent studies (cohorts 1 and 2), in which subjects either remained on medications or tapered off medications, we analyzed serum levels of iron, calcium, magnesium, manganese, copper, and zinc both in RLS patients and controls, and assessed the prevalence of the MEIS1 and BTBD9 risk alleles previously established through genome-wide association studies. Human brain sections and a nematode genetic model were also quantified for metal levels using mass spectrometry. Results We found a significant enrichment for the BTBD9 risk genotype in the RLS affected group compared to control (p = 0.0252), consistent with previous literature. Serum (p = 0.0458 and p = 0.0139 for study cohorts 1 and 2, respectively) and brain (p = 0.0413) zinc levels were significantly elevated in the RLS patients versus control subjects. Conclusion We show for the first time that serum and brain levels of zinc are elevated in RLS. Further, we confirm the BTBD9 genetic risk factor in a new population, although the zinc changes were not significantly associated with risk genotypes. Zinc and iron homeostasis are interrelated, and zinc biology impacts neurotransmitter systems previously linked to RLS. Given the modest albeit statistically significant increase in serum zinc of ~20%, and the lack of association with two known genetic risk fa...
Chen, S-Y, Beretta, M, Alexopoulos, SJ, Shah, DP, Olzomer, EM, Hargett, SR, Childress, ES, Salamoun, JM, Aleksovska, I, Roseblade, A, Cranfield, C, Rawling, T, Quinlan, KGR, Morris, MJ, Tucker, SP, Santos, WL & Hoehn, KL 2021, 'Mitochondrial uncoupler SHC517 reverses obesity in mice without affecting food intake', Metabolism, vol. 117, pp. 154724-154724.
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Aims
Mitochondrial uncouplers decrease caloric efficiency and have potential therapeutic benefits for the treatment of obesity and related metabolic disorders. Herein we investigate the metabolic and physiologic effects of a recently identified small molecule mitochondrial uncoupler named SHC517 in a mouse model of diet-induced obesity.Methods
SHC517 was administered as an admixture in food. The effect of SHC517 on in vivo energy expenditure and respiratory quotient was determined by indirect calorimetry. A dose-finding obesity prevention study was performed by starting SHC517 treatment concomitant with high fat diet for a period of 12 days. An obesity reversal study was performed by feeding mice western diet for 4 weeks prior to SHC517 treatment for 7 weeks. Biochemical assays were used to determine changes in glucose, insulin, triglycerides, and cholesterol. SHC517 concentrations were determined by mass spectrometry.Results
SHC517 increased lipid oxidation without affecting body temperature. SHC517 prevented diet-induced obesity when administered at 0.05% and 0.1% w/w in high fat diet and reversed established obesity when tested at the 0.05% dose. In the obesity reversal model, SHC517 restored adiposity to levels similar to chow-fed control mice without affecting food intake or lean body mass. SHC517 improved glucose tolerance and fasting glucose levels when administered in both the obesity prevention and obesity reversal modes.Conclusions
SHC517 is a mitochondrial uncoupler with potent anti-obesity and insulin sensitizing effects in mice. SHC517 reversed obesity without altering food intake or compromising lean mass, effects that are highly sought-after in anti-obesity therapeutics.
Chen, X, Yang, L, Liang, S, Dang, P, Jin, D, Cheng, Z & Lin, J 2021, 'Entropy-driven strand displacement reaction for ultrasensitive detection of circulating tumor DNA based on upconversion and Fe3O4 nanocrystals', Science China Materials, vol. 64, no. 10, pp. 2593-2600.
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Early detection of cancer biomarkers applied in real-time disease diagnosis and therapies can increase the survival rate of patients. Circulating tumor DNA (ctDNA) as a typical cancer biomarker plays a great role in the process of tumor disease monitoring, especially in early diagnosis. Unfortunately, most ctDNA detection systems have not been widely used due to their low sensitivity, poor specificity, and high cost. Herein, we developed an alternative ctDNA detection system to present the levels of ctDNA by recording the fluorescence signals of the system containing upconversion nanoparticles (UCNPs), Fe3O4, and entropy-driven strand displacement reaction. The method has a practical sensitivity with a wide linear range from 100 amol L−1 to 1 nmol L−1 and a low detection limit of 1.6 amol L−1. Furthermore, the system demonstrates a practical application in mouse blood serum samples and meets the requirements for rapid, sensitive, specific, and economical diagnosis of cancers. Thus, this ctDNA detection system may have great potential for ctDNA detection and clinical diagnosis.
Chen, Y, Li, C, White, S, Nonahal, M, Xu, Z-Q, Watanabe, K, Taniguchi, T, Toth, M, Tran, TT & Aharonovich, I 2021, 'Generation of High-Density Quantum Emitters in High-Quality, Exfoliated Hexagonal Boron Nitride', ACS Applied Materials & Interfaces, vol. 13, no. 39, pp. 47283-47292.
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Single-photon emitters in hexagonal boron nitride (hBN) are promising constituents for integrated quantum photonics. Specifically, engineering these emitters in large-area, high-quality, exfoliated hBN is needed for their incorporation into photonic devices and two dimensional heterostructures. Here, we report on two different routes to generate high-density quantum emitters with excellent optical properties-including high brightness and photostability. We study in detail high-temperature annealing and plasma treatments as an efficient means to generate dense emitters. We show that both an optimal oxygen flow rate and annealing temperature are required for the formation of high-density quantum emitters. In parallel, we demonstrate that the plasma treatment in various environments, followed by standard annealing is also an effective route for emission engineering. Our work provides vital information for the fabrication of quantum emitters in high-quality, exfoliated hBN flakes and paves the way toward the integration of the quantum emitters with photonic devices.
Chen, Y, Wang, T, Tian, H, Su, D, Zhang, Q & Wang, G 2021, 'Advances in Lithium–Sulfur Batteries: From Academic Research to Commercial Viability', Advanced Materials, vol. 33, no. 29, pp. 1-67.
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AbstractLithium‐ion batteries, which have revolutionized portable electronics over the past three decades, were eventually recognized with the 2019 Nobel Prize in chemistry. As the energy density of current lithium‐ion batteries is approaching its limit, developing new battery technologies beyond lithium‐ion chemistry is significant for next‐generation high energy storage. Lithium–sulfur (Li–S) batteries, which rely on the reversible redox reactions between lithium and sulfur, appears to be a promising energy storage system to take over from the conventional lithium‐ion batteries for next‐generation energy storage owing to their overwhelming energy density compared to the existing lithium‐ion batteries today. Over the past 60 years, especially the past decade, significant academic and commercial progress has been made on Li–S batteries. From the concept of the sulfur cathode first proposed in the 1960s to the current commercial Li–S batteries used in unmanned aircraft, the story of Li–S batteries is full of breakthroughs and back tracing steps. Herein, the development and advancement of Li–S batteries in terms of sulfur‐based composite cathode design, separator modification, binder improvement, electrolyte optimization, and lithium metal protection is summarized. An outlook on the future directions and prospects for Li–S batteries is also offered.
Chen, Y, Westerhausen, MT, Li, C, White, S, Bradac, C, Bendavid, A, Toth, M, Aharonovich, I & Tran, TT 2021, 'Solvent-Exfoliated Hexagonal Boron Nitride Nanoflakes for Quantum Emitters', ACS Applied Nano Materials, vol. 4, no. 10, pp. 10449-10457.
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Quantum emitters in hexagonal boron nitride (hBN) flakes have recently emerged as a promising platform for nanophotonic and quantum applications. The solvent-exfoliation process of these flakes has, however, remained largely unexplored. In this work, we demonstrate a surfactant-assisted exfoliation technique in an aqueous solution to exfoliate a variety of commercially available hBN powders into hBN nanoflakes. We show that the selection of hBN powder greatly impacts the optical properties of the resultant quantum emitters embedded in exfoliated hBN nanoflakes. We find that the sample with the best optical performance also shows the lowest impurity levels in its starting hBN powder. Our study provides further insight into quantum emitter fabrication in hBN and tailoring of their optical properties.
Chen, Y, Xu, X, Li, C, Bendavid, A, Westerhausen, MT, Bradac, C, Toth, M, Aharonovich, I & Tran, TT 2021, 'Bottom‐Up Synthesis of Hexagonal Boron Nitride Nanoparticles with Intensity‐Stabilized Quantum Emitters', Small, vol. 17, no. 17, pp. 1-7.
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AbstractFluorescent nanoparticles are widely utilized in a large range of nanoscale imaging and sensing applications. While ultra‐small nanoparticles (size ≤10 nm) are highly desirable, at this size range, their photostability can be compromised due to effects such as intensity fluctuation and spectral diffusion caused by interaction with surface states. In this article, a facile, bottom‐up technique for the fabrication of sub‐10‐nm hexagonal boron nitride (hBN) nanoparticles hosting photostable bright emitters via a catalyst‐free hydrothermal reaction between boric acid and melamine is demonstrated. A simple stabilization protocol that significantly reduces intensity fluctuation by ≈85% and narrows the emission linewidth by ≈14% by employing a common sol–gel silica coating process is also implemented. This study advances a promising strategy for the scalable, bottom‐up synthesis of high‐quality quantum emitters in hBN nanoparticles.
Cheng, A, Tse, K-H, Chow, H-M, Gan, Y, Song, X, Ma, F, Qian, YXY, She, W & Herrup, K 2021, 'ATM loss disrupts the autophagy-lysosomal pathway', Autophagy, vol. 17, no. 8, pp. 1998-2010.
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Chong, H, Tan, C, Fang, S, Chen, X, Tao, Q, Yuan, X, Li, J, Zhai, C, Fei, C, Yang, D, Fan, H, Shao, H, Qin, A, Wang, G, Shi, Z, Z’hang, T, Yao, H, Li, H & Wang, C 2021, 'BODIPY-Appended Pt(II) Complexes with High Toxicities and Anti-chemoresistance Performances in a Cisplatin Resistant In Vivo Model', Inorganic Chemistry, vol. 60, no. 13, pp. 10047-10055.
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Two novel fluorophore (BODIPY)-bearing complexes, pyriplatin (mCBP) and pyrimidine-chelated cisplatin (dCBP), were synthesized and characterized. The additional BODIPY-pyridine/pyridimine motifs of the two Pt(II) complexes resulted in stronger interactions with DNA in comparison with those of cisplatin. mCBP and cisplatin caused relative decreases in life span and body length in a cisplatin resistant in vivo model, N2 (wild-type) Caenorhabditis elegans. In contrast, dCBP resulted in a dramatic reduction in the two physiological parameters in N2 C. elegans, indicating high toxicity and sensitivity. The resistance factors (RF) of cisplatin, mCBP, and dCBP were determined to be 2.46, 1.04, and 0.91, respectively. The increasing RF folds for mCBP and dCBP against cisplatin were 2.36 and 2.70, respectively. This suggested they were featured with improved anti-chemoresistance capabilities. It is noteworthy that dCBP showed lowest lethal concentration (LC50) values of 0.56 and 0.61 mM in cisplatin resistant and sensitive in vivo models, respectively. Upregulation of several evolutionary conservation genes that regulate cisplatin chemoresistance through cisplatin effluxing, the DNA damage response, the unfolded protein response, and detoxification (asna-1, parp-1, enpl-1, and skn-1) was observed upon exposure to cisplatin but not to mCBP and dCBP. This could explain the improved anti-chemoresistance performances of synthesized Pt(II) complexes.
Chong, H, Zhang, G, Wu, Y, Xu, B, Wang, G & Wang, C 2021, 'Enantioselective recognition of amino acid based on electrochemical deposition and X-ray diffraction technology', Journal of Inorganic Biochemistry, vol. 218, pp. 111398-111398.
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Addition of D-Asp in the electrochemical deposition process of Bismuth film resulted the generation of a new diffraction peak in X-ray diffraction (XRD) spectrum. This phenomenon was not observed in the situation of L-Asp. The new diffraction peak might suggest D-Asp could result in the generation of a specific Bismuth structure. Enantioselective recognition of D- and L-Asp can be realized based on this new XRD peak. The limit of detection was determined to be 3.5 × 10-8 and 1.7 × 10-8 mol L-1 for D- and L-Asp, respectively. The XRD spectra of electrodeposited Copper films fabricated in the presence of D- or L-Asp showed different lattice plane diffraction peak intensity ratios. The reason was believed to be chirality induced different binding capabilities of Asp enantiomers that influenced Copper film growth. Therefore, the combination of electrochemical deposition using Copper as metal source and XRD technology can be used to achieve enantioselective recognition of Asp. The limit of detection for D- and L-Asp were determined to be 1.5 × 10-10 and 1.2 × 10-11 mol L-1, respectively.
Chong, WC, Shastri, MD, Peterson, GM, Patel, RP, Pathinayake, PS, Dua, K, Hansbro, NG, Hsu, AC, Wark, PA, Shukla, SD, Johansen, MD, Schroder, K & Hansbro, PM 2021, 'The complex interplay between endoplasmic reticulum stress and the NLRP3 inflammasome: a potential therapeutic target for inflammatory disorders', Clinical & Translational Immunology, vol. 10, no. 2, p. e1247.
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AbstractInflammation is the result of a complex network of cellular and molecular interactions and mechanisms that facilitate immune protection against intrinsic and extrinsic stimuli, particularly pathogens, to maintain homeostasis and promote tissue healing. However, dysregulation in the immune system elicits excess/abnormal inflammation resulting in unintended tissue damage and causes major inflammatory diseases including asthma, chronic obstructive pulmonary disease, atherosclerosis, inflammatory bowel diseases, sarcoidosis and rheumatoid arthritis. It is now widely accepted that both endoplasmic reticulum (ER) stress and inflammasomes play critical roles in activating inflammatory signalling cascades. Notably, evidence is mounting for the involvement of ER stress in exacerbating inflammasome‐induced inflammatory cascades, which may provide a new axis for therapeutic targeting in a range of inflammatory disorders. Here, we comprehensively review the roles, mechanisms and interactions of both ER stress and inflammasomes, as well as their interconnected relationships in inflammatory signalling cascades. We also discuss novel therapeutic strategies that are being developed to treat ER stress‐ and inflammasome‐related inflammatory disorders.
Chopra, N, Menounos, S, Choi, JP, Hansbro, PM, Diwan, AD & Das, A 2021, 'Blood-Spinal Cord Barrier: Its Role in Spinal Disorders and Emerging Therapeutic Strategies', NeuroSci, vol. 3, no. 1, pp. 1-27.
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The blood-spinal cord barrier (BSCB) has been long thought of as a functional equivalent to the blood-brain barrier (BBB), restricting blood flow into the spinal cord. The spinal cord is supported by various disc tissues that provide agility and has different local immune responses compared to the brain. Though physiologically, structural components of the BSCB and BBB share many similarities, the clinical landscape significantly differs. Thus, it is crucial to understand the composition of BSCB and also to establish the cause–effect relationship with aberrations and spinal cord dysfunctions. Here, we provide a descriptive analysis of the anatomy, current techniques to assess the impairment of BSCB, associated risk factors and impact of spinal disorders such as spinal cord injury (SCI), amyotrophic lateral sclerosis (ALS), peripheral nerve injury (PNI), ischemia reperfusion injury (IRI), degenerative cervical myelopathy (DCM), multiple sclerosis (MS), spinal cavernous malformations (SCM) and cancer on BSCB dysfunction. Along with diagnostic and mechanistic analyses, we also provide an up-to-date account of available therapeutic options for BSCB repair. We emphasize the need to address BSCB as an individual entity and direct future research towards it.
Chotithammakul, S, Cortie, MB & Pissuwan, D 2021, 'Comparison of Single- and Mixed-Sized Gold Nanoparticles on Lateral Flow Assay for Albumin Detection', Biosensors, vol. 11, no. 7, pp. 209-209.
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The sensitivity and reproducibility of the lateral flow assay can be influenced by multiple factors, such as the size of gold nanoparticles (GNPs) employed. Here, we evaluated the analytical performance of single-sized and mixed-sized GNPs using a simple lateral flow assay (LFA) platform. This platform was used as a model assay to diagnose albumin levels and demonstrate the analytical performance of single-sized and mixed-sized GNPs in LFA tests. Two sizes of GNPs@anti-bovine serum albumin (BSA) conjugate proteins were mixed at different ratios. The unique optical properties of the GNPs induced a distinguishing color-shedding effect on the single- and mixed-sized GNPs@anti-BSA conjugates interacting with the target analyte BSA spotted on the test line. The use of mixed-sized GNPs@anti-BSA conjugates enhanced signal relative to the 20 nm GNPs, and provided superior stability compared with solely employing the large GNPs (50 nm). The proposed platform in this study could provide an efficient BSA detection mechanism that can be utilized as a model biomarker for confronting chronic kidney disease.
Chow, WS, Larkum, AWD, Pfündel, E, Ritchie, RJ, Scheer, H & Strid, Å 2021, 'A tribute to Robert John Porra (august 7, 1931–may 16, 2019)', Photosynthesis Research, vol. 147, no. 2, pp. 125-130.
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Chowdhury, MR, Chowdhury, S, Rahman, MA, Islam, MR, Mahmud, MAP & Kouzani, AZ 2021, 'Model Predictive Control Based Advanced Switching Strategy for H-Bridge Converter Used in SMES Applications to Obtain Even Loss Sharing', IEEE Transactions on Applied Superconductivity, vol. 31, no. 8, pp. 1-6.
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Christie, MJ, Irving, AT, Forster, SC, Marsland, BJ, Hansbro, PM, Hertzog, PJ, Nold-Petry, CA & Nold, MF 2021, 'Of bats and men: Immunomodulatory treatment options for COVID-19 guided by the immunopathology of SARS-CoV-2 infection', Science Immunology, vol. 6, no. 63, p. eabd0205.
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SARS-CoV-2 evades immune recognition in humans but not bats, pointing to potential strategies for therapeutic intervention.
Chu, Z, Gao, X, Wang, C, Wang, T & Wang, G 2021, 'Metal–organic frameworks as separators and electrolytes for lithium–sulfur batteries', Journal of Materials Chemistry A, vol. 9, no. 12, pp. 7301-7316.
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This review provides a specialized summary of metal–organic frameworks as separators and electrolytes for lithium–sulfur batteries, including design strategies and applications.
Ciobanu, L & Elder, M 2021, 'The complexity of solution sets to equations in hyperbolic groups', Israel Journal of Mathematics, vol. 245, no. 2, pp. 869-920.
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Clancy, L, Philp, M, Shimmon, R & Fu, S 2021, 'Development and validation of a color spot test method for the presumptive detection of 25‐NBOMe compounds', Drug Testing and Analysis, vol. 13, no. 5, pp. 929-943.
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AbstractThe great increase of new psychoactive substances over the past decade has substantially transformed the illicit drug industry to an ever‐changing dynamic market. 25‐NBOMe compounds are just one of these new substance groups that pose a public health risk in many countries around the world. These highly potent, hallucinogenic phenethylamines have previously been sold as “legal highs” or “synthetic LSD” and the necessity to rapidly identify their presence is crucial. While there are many laboratory‐based analytical methods capable of identifying these compounds, the lack of presumptive test methods indicates the need for a specific and timely test that could be used in the field. Herein we outline the developed chemical spot test that can selectively identify the presence of 25‐NBOMe compounds and related analogs through the reaction with a substituted benzoquinone reagent under basic conditions. This test method has been comprehensively validated showing a high level of selectivity, specificity, and precision with only two other illicit substances producing similar positive results as 25‐NBOMe and few false‐negative results seen. The working limit of detection was determined to be 225 μg and there was no cross‐reactivity from potential adulterants of significance. This test has also been shown to work directly with blotter papers containing 25‐NBOMe compounds, indicating no interference from this common matrix and the ability to differentiate these compounds from LSD. This method shows a high potential to be translated to a field compatible test that is simple, rapid, and selective for 25‐NBOMe compounds.
Clark, AS, Blanco-Redondo, A & Aharonovich, I 2021, 'Special Topic on Integrated Quantum Photonics', APL Photonics, vol. 6, no. 12, pp. 120401-120401.
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The realization of scalable, real world devices in quantum technologies requires myriad new approaches and hardware components. Integrated photonics play a crucial role in many applications in quantum information and quantum sensing, enabling the realization of key components such as new light sources, waveguides, resonators, and detectors. The field of integrated quantum photonics is booming, and an increasing number of research groups are contributing to the accelerating efforts to study fundamental and technological challenges at the intersection of quantum optics, nanophotonics, and hybrid integrated devices. This Special Topic Collection is dedicated to highlighting important progress in the field of integrated quantum photonics and presenting new cutting-edge results, both experimental and theoretical, toward the common goal of exploring quantum photonic phenomena.
Clases, D, Ueland, M, Gonzalez de Vega, R, Doble, P & Pröfrock, D 2021, 'Quantitative speciation of volatile sulphur compounds from human cadavers by GC-ICP-MS', Talanta, vol. 221, pp. 121424-121424.
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This work demonstrates the first forensic application of GC-ICP-MS for improved investigations of volatile organic compounds originating from a decomposing body. Volatile organic compounds were extracted from the headspace of human remains using sorbent tubes over a total time of 39 days. To account for naturally abundant species, control sites were prepared and sampled accordingly. All samples were spiked with an internal standard to minimise drift effects and errors during sample preparation and further analysis. Compound independent quantification was possible from a single chromatogram with a standard mix containing volatile pesticide compounds representing different mass fractions of target elements for calibration. Phosphorus, sulphur and chlorine were investigated as biologically relevant elements, which potentially form detectable volatile species during decomposition. The limits of detection of these elements in the headspace were 0.7, 5.4 and 1.6 ng/L, respectively. For sulphur, we identified abundant species which increased in concentrations of up to 1310 ng/L in the headspace above the remains. The concentrations were time dependent and show potential as forensic markers to determine post-mortem intervals or decomposition states. The universal quantification, standardisation and the high sensitivity of GC-ICP-MS augments traditional GC-MS analyses.
Clases, D, Ueland, M, Gonzalez de Vega, R, Doble, P & Pröfrock, D 2021, 'Quantitative speciation of volatile sulphur compounds from human cadavers by GC-ICP-MS.', Talanta, vol. 221, pp. 1-8.
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This work demonstrates the first forensic application of GC-ICP-MS for improved investigations of volatile organic compounds originating from a decomposing body. Volatile organic compounds were extracted from the headspace of human remains using sorbent tubes over a total time of 39 days. To account for naturally abundant species, control sites were prepared and sampled accordingly. All samples were spiked with an internal standard to minimise drift effects and errors during sample preparation and further analysis. Compound independent quantification was possible from a single chromatogram with a standard mix containing volatile pesticide compounds representing different mass fractions of target elements for calibration. Phosphorus, sulphur and chlorine were investigated as biologically relevant elements, which potentially form detectable volatile species during decomposition. The limits of detection of these elements in the headspace were 0.7, 5.4 and 1.6 ng/L, respectively. For sulphur, we identified abundant species which increased in concentrations of up to 1310 ng/L in the headspace above the remains. The concentrations were time dependent and show potential as forensic markers to determine post-mortem intervals or decomposition states. The universal quantification, standardisation and the high sensitivity of GC-ICP-MS augments traditional GC-MS analyses.
Clases, D, Ueland, M, Gonzalez de Vega, R, Doble, P & Pröfrock, D 2021, 'Quantitative speciation of volatile sulphur compounds from human cadavers by GC-ICP-MS.', Talanta, vol. 221, p. 121424.
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This work demonstrates the first forensic application of GC-ICP-MS for improved investigations of volatile organic compounds originating from a decomposing body. Volatile organic compounds were extracted from the headspace of human remains using sorbent tubes over a total time of 39 days. To account for naturally abundant species, control sites were prepared and sampled accordingly. All samples were spiked with an internal standard to minimise drift effects and errors during sample preparation and further analysis. Compound independent quantification was possible from a single chromatogram with a standard mix containing volatile pesticide compounds representing different mass fractions of target elements for calibration. Phosphorus, sulphur and chlorine were investigated as biologically relevant elements, which potentially form detectable volatile species during decomposition. The limits of detection of these elements in the headspace were 0.7, 5.4 and 1.6 ng/L, respectively. For sulphur, we identified abundant species which increased in concentrations of up to 1310 ng/L in the headspace above the remains. The concentrations were time dependent and show potential as forensic markers to determine post-mortem intervals or decomposition states. The universal quantification, standardisation and the high sensitivity of GC-ICP-MS augments traditional GC-MS analyses.
Clases, D, Ueland, M, Gonzalez, DVR, Doble, P & Pröfrock, D 2021, 'Quantitative speciation of volatile sulphur compounds from human cadavers by GC-ICP-MS.', Talanta, vol. 221, pp. 1-8.
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This work demonstrates the first forensic application of GC-ICP-MS for improved investigations of volatile organic compounds originating from a decomposing body. Volatile organic compounds were extracted from the headspace of human remains using sorbent tubes over a total time of 39 days. To account for naturally abundant species, control sites were prepared and sampled accordingly. All samples were spiked with an internal standard to minimise drift effects and errors during sample preparation and further analysis. Compound independent quantification was possible from a single chromatogram with a standard mix containing volatile pesticide compounds representing different mass fractions of target elements for calibration. Phosphorus, sulphur and chlorine were investigated as biologically relevant elements, which potentially form detectable volatile species during decomposition. The limits of detection of these elements in the headspace were 0.7, 5.4 and 1.6 ng/L, respectively. For sulphur, we identified abundant species which increased in concentrations of up to 1310 ng/L in the headspace above the remains. The concentrations were time dependent and show potential as forensic markers to determine post-mortem intervals or decomposition states. The universal quantification, standardisation and the high sensitivity of GC-ICP-MS augments traditional GC-MS analyses.
Clifton, J, Osman, EO, Suggett, DJ & Smith, DJ 2021, 'Resolving conservation and development tensions in a small island state: A governance analysis of Curieuse Marine National Park, Seychelles', Marine Policy, vol. 127, pp. 103617-103617.
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© 2019 Elsevier Ltd The management and conservation of marine resources in Seychelles, a small island developing state (SIDS) in the western Indian Ocean, is fundamental to maintaining the flow of international visitors which forms the mainstay of the nation's economy. There is an increasing trend towards empowering non-governmental organisations and parastatal entities with protected area management responsibilities, which partly reflects the chronic underfunding of the state protected area management institution. This paper explores these and related issues through a governance analysis of Curieuse Marine National Park, which is the most popular state-owned marine national park in terms of recorded visitor numbers. This demonstrates that the inability to implement economic incentives through not fully capitalising on the use and non-use values of the park has deleterious consequences for managing the combined impacts of tourism and fisheries on the ecological assets of the park. Furthermore, the capacity of the state management institution is being eroded through a focus on the development of an extensive network of new marine protected areas under the direction of an international non-governmental organisation. Suggestions are made that could strengthen economic, participative and interpretative incentives to provide a more sustainable basis for marine national park management.
Coetzee, L-CC, Muller, AJ, Adeyinka, AS, Sonopo, MS & Williams, DBG 2021, 'Synthesis, characterisation and DFT studies of [3,5-bis(2-hydroxyphenyl)-1H-1,2,4-triazol-1-yl](phenyl)methanone derivatives', Results in Chemistry, vol. 3, pp. 100165-100165.
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Coignard, J, Lush, M, Beesley, J, O’Mara, TA, Dennis, J, Tyrer, JP, Barnes, DR, McGuffog, L, Leslie, G, Bolla, MK, Adank, MA, Agata, S, Ahearn, T, Aittomäki, K, Andrulis, IL, Anton-Culver, H, Arndt, V, Arnold, N, Aronson, KJ, Arun, BK, Augustinsson, A, Azzollini, J, Barrowdale, D, Baynes, C, Becher, H, Bermisheva, M, Bernstein, L, Białkowska, K, Blomqvist, C, Bojesen, SE, Bonanni, B, Borg, A, Brauch, H, Brenner, H, Burwinkel, B, Buys, SS, Caldés, T, Caligo, MA, Campa, D, Carter, BD, Castelao, JE, Chang-Claude, J, Chanock, SJ, Chung, WK, Claes, KBM, Clarke, CL, Bertrand, O, Caputo, S, Dupré, A, Le Mentec, M, Belotti, M, Birot, A-M, Buecher, B, Fourme, E, Gauthier-Villars, M, Golmard, L, Houdayer, C, Moncoutier, V, de Pauw, A, Saule, C, Sinilnikova, O, Mazoyer, S, Damiola, F, Barjhoux, L, Verny-Pierre, C, Léone, M, Boutry-Kryza, N, Calender, A, Giraud, S, Caron, O, Guillaud-Bataille, M, Bressac-de-Paillerets, B, Bignon, Y-J, Uhrhammer, N, Lasset, C, Bonadona, V, Berthet, P, Vaur, D, Castera, L, Noguchi, T, Popovici, C, Sobol, H, Bourdon, V, Noguchi, T, Remenieras, A, Noguès, C, Coupier, I, Pujol, P, Dumont, A, Révillion, F, Adenis, C, Muller, D, Barouk-Simonet, E, Bonnet, F, Bubien, V, Sevenet, N, Longy, M, Toulas, C, Guimbaud, R, Gladieff, L, Feillel, V, Leroux, D, Dreyfus, H, Rebischung, C, Peysselon, M, Coron, F, Faivre, L, Baurand, A, Jacquot, C, Bertolone, G, Lizard, S, Prieur, F, Lebrun, M, Kientz, C, Ferrer, SF, Mari, V, Vénat-Bouvet, L, Delnatte, C, Bézieau, S, Mortemousque, I, Coulet, F, Colas, C, Soubrier, F, Warcoin, M, Sokolowska, J, Bronner, M, Collonge-Rame, M-A, Damette, A, Gesta, P, Lallaoui, H, Chiesa, J, Molina-Gomes, D, Ingster, O, Gregory, H, Miedzybrodzka, Z, Morrison, PJ, Ong, K-R, Donaldson, A, Rogers, MT, Kennedy, MJ, Porteous, ME, Brewer, C, Davidson, R, Izatt, L, Brady, A, Barwell, J, Adlard, J, Foo, C, Lalloo, F, Side, LE, Eason, J, Henderson, A, Walker, L, Eeles, RA, Cook, J, Snape, K, Eccles, D, Murray, A, McCann, E, Collée, JM, Conroy, DM, Czene, K, Daly, MB, Devilee, P, Diez, O, Ding, YC, Domchek, SM, Dörk, T, dos-Santos-Silva, I, Dunning, AM, Dwek, M, Eccles, DM, Eliassen, AH, Engel, C, Eriksson, M, Evans, DG, Fasching, PA, Flyger, H, Fostira, F, Friedman, E, Fritschi, L, Frost, D, Gago-Dominguez, M, Gapstur, SM, Garber, J, Garcia-Barberan, V, García-Closas, M, García-Sáenz, JA, Gaudet, MM & et al. 2021, 'A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers', Nature Communications, vol. 12, no. 1.
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AbstractBreast cancer (BC) risk forBRCA1andBRCA2mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases withBRCA1orBRCA2mutations. We identify robust novel associations for 2 variants with BC forBRCA1and 3 forBRCA2mutation carriers,P < 10−8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 whereMADD,SP11andEIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores forBRCA1andBRCA2mutation carriers.
Cole, AJ, Dickson, K-A, Liddle, C, Stirzaker, C, Shah, JS, Clifton-Bligh, R & Marsh, DJ 2021, 'Ubiquitin chromatin remodelling after DNA damage is associated with the expression of key cancer genes and pathways', Cellular and Molecular Life Sciences, vol. 78, no. 3, pp. 1011-1027.
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Cole, VJ, Parker, LM, Scanes, E, Wright, J, Barnett, L & Ross, PM 2021, 'Climate change alters shellfish reef communities: A temperate mesocosm experiment', Marine Pollution Bulletin, vol. 173, pp. 113113-113113.
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Commault, AS, Kuzhiumparambil, U, Herdean, A, Fabris, M, Jaramillo-Madrid, AC, Abbriano, RM, Ralph, PJ & Pernice, M 2021, 'Methyl Jasmonate and Methyl-β-Cyclodextrin Individually Boost Triterpenoid Biosynthesis in Chlamydomonas Reinhardtii UVM4', Pharmaceuticals, vol. 14, no. 2, pp. 125-125.
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The commercialisation of valuable plant triterpenoids faces major challenges, including low abundance in natural hosts and costly downstream purification procedures. Endeavours to produce these compounds at industrial scale using microbial systems are gaining attention. Here, we report on a strategy to enrich the biomass of the biotechnologically-relevant Chlamydomonas reinhardtii strain UVM4 with valuable triterpenes, such as squalene and (S)-2,3-epoxysqualene. C. reinhardtii UVM4 was subjected to the elicitor compounds methyl jasmonate (MeJA) and methyl-β-cyclodextrine (MβCD) to increase triterpene yields. MeJA treatment triggered oxidative stress, arrested growth, and altered the photosynthetic activity of the cells, while increasing squalene, (S)-2,3-epoxysqualene, and cycloartenol contents. Applying MβCD to cultures of C. reinhardtii lead to the sequestration of the two main sterols (ergosterol and 7-dehydroporiferasterol) into the growth medium and the intracellular accumulation of the intermediate cycloartenol, without compromising cell growth. When MβCD was applied in combination with MeJA, it counteracted the negative effects of MeJA on cell growth and physiology, but no synergistic effect on triterpene yield was observed. Together, our findings provide strategies for the triterpene enrichment of microalgal biomass and medium.
Coni, EOC, Booth, DJ & Nagelkerken, I 2021, 'Novel species interactions and environmental conditions reduce foraging competency at the temperate range edge of a range-extending coral reef fish', Coral Reefs, vol. 40, no. 5, pp. 1525-1536.
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Coni, EOC, Nagelkerken, I, Ferreira, CM, Connell, SD & Booth, DJ 2021, 'Ocean acidification may slow the pace of tropicalization of temperate fish communities', Nature Climate Change, vol. 11, no. 3, pp. 249-256.
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Cook, AM, Berry, N, Milner, KV & Leigh, A 2021, 'Water availability influences thermal safety margins for leaves', Functional Ecology, vol. 35, no. 10, pp. 2179-2189.
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AbstractOne application of plant physiological heat tolerance measurements is the assessment of vulnerability to increasing environmental temperatures under climatic change. A thermal safety margin (TSM), the difference between physiological tolerance and environmental temperature, is a common metric for the assessment of plant thermal vulnerability. However, there are biological and methodological aspects to consider when evaluating thermal vulnerability that have the potential to substantially alter the assessments. Two such aspects include the leaf to air temperature relationship and the scale at which air temperature data are collected.We grew plants of a desert species, Myoporum montanum, in situ under water‐stressed and well‐watered conditions, and measured their leaf temperatures and photosynthetic heat tolerance (T50 threshold) every third day over 12 days in summer. Thermal safety margins were calculated based on leaf temperatures and compared to those calculated with local and regional air temperatures.We found that heat tolerance and the thermal vulnerability assessment of a plant changed with water status. When water was readily available, plants maintained wide leaf temperature safety margins and displayed partial homeothermy. When cooling via transpiration was limited, increasing leaf temperature corresponded with occurrences of leaf poikilo‐ and megathermy, higher heat tolerance and narrower safety margins.Our study shows high physiological heat thresholds are not necessarily reflective of wide safety margins, but instead can indicate a greater vulnerability and increased risk of heat stress exposure. Calculating TSMs using air temperatures c...
Coulon, PML, Zlosnik, JEA & Déziel, E 2021, 'Presence of the Hmq System and Production of 4-Hydroxy-3-Methyl-2-Alkylquinolines Are Heterogeneously Distributed between Burkholderia cepacia Complex Species and More Prevalent among Environmental than Clinical Isolates', Microbiology Spectrum, vol. 9, no. 1.
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Environmental bacteria belonging to the various closely related species forming the Burkholderia cepacia complex (Bcc) can infect plants and animals, including humans. Their pathogenicity is regulated by intercellular communication, or quorum sensing, allowing them to collaborate instead of acting individually.
Counoupas, C, Johansen, MD, Stella, AO, Nguyen, DH, Ferguson, AL, Aggarwal, A, Bhattacharyya, ND, Grey, A, Hutchings, O, Patel, K, Siddiquee, R, Stewart, EL, Feng, CG, Hansbro, NG, Palendira, U, Steain, MC, Saunders, BM, Low, JKK, Mackay, JP, Kelleher, AD, Britton, WJ, Turville, SG, Hansbro, PM & Triccas, JA 2021, 'A single dose, BCG-adjuvanted COVID-19 vaccine provides sterilising immunity against SARS-CoV-2 infection', npj Vaccines, vol. 6, no. 1, p. 143.
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AbstractGlobal control of COVID-19 requires broadly accessible vaccines that are effective against SARS-CoV-2 variants. In this report, we exploit the immunostimulatory properties of bacille Calmette-Guérin (BCG), the existing tuberculosis vaccine, to deliver a vaccination regimen with potent SARS-CoV-2-specific protective immunity. Combination of BCG with a stabilised, trimeric form of SARS-CoV-2 spike antigen promoted rapid development of virus-specific IgG antibodies in the blood of vaccinated mice, that was further augmented by the addition of alum. This vaccine formulation, BCG:CoVac, induced high-titre SARS-CoV-2 neutralising antibodies (NAbs) and Th1-biased cytokine release by vaccine-specific T cells, which correlated with the early emergence of T follicular helper cells in local lymph nodes and heightened levels of antigen-specific plasma B cells after vaccination. Vaccination of K18-hACE2 mice with a single dose of BCG:CoVac almost completely abrogated disease after SARS-CoV-2 challenge, with minimal inflammation and no detectable virus in the lungs of infected animals. Boosting BCG:CoVac-primed mice with a heterologous vaccine further increased SARS-CoV-2-specific antibody responses, which effectively neutralised B.1.1.7 and B.1.351 SARS-CoV-2 variants of concern. These findings demonstrate the potential for BCG-based vaccination to protect against major SARS-CoV-2 variants circulating globally.
Cranfield, C, Whelan, D, Cox, C, Shearwin, K, Ho, J, Allen, T, Shibuya, R, Hibino, E, Hayashi, K, dos Remedios, C & Li, A 2021, 'Announcing the call for the Special Issue on “The Australian Society for Biophysics (ASB) – 2021 Meeting”', Biophysical Reviews, vol. 13, no. 4, pp. 485-486.
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This Commentary describes a call for submissions for the upcoming Special Issue focused on the research topics presented at the Australian Society of Biophysics (ASB) in 2020 and 2021. Submissions from past and present ASB members who could not attend these meetings are also welcome as contributions to this special issue.
Cranwell Schaeper, O, Fröch, JE, Kim, S, Mu, Z, Toth, M, Gao, W & Aharonovich, I 2021, 'Fabrication of Photonic Resonators in Bulk 4H‐SiC', Advanced Materials Technologies, vol. 6, no. 11, pp. 2100589-2100589.
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AbstractThe design and engineering of photonic architectures, suitable to enhance, collect and guide light on chip is needed for applications in quantum photonics and quantum optomechanics. In this work, a Faraday cage‐based oblique angle etch method is applied to fabricate various functional photonic devices from 4H Silicon Carbide (SiC)—a material that has attracted attention in recent years, due to its potential in optomechanics, nonlinear optics, and quantum information. The processing conditions are detailed and the geometrical and optical characteristics of the fabricated devices are thoroughly addressed. Employing photoluminescence measurements high‐quality factors are demonstrated for suspended microring resonators of up to 3500 in the visible range. Such devices will be applicable in the future to augment the properties of SiC in integrated on chip quantum photonics.
Cuartas-Villa, S & Webb, JK 2021, 'Nest site selection in a southern and northern population of the velvet gecko (Amalosia lesueurii)', Journal of Thermal Biology, vol. 102, pp. 103121-103121.
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In many oviparous reptiles, thermal conditions inside nests influence phenotypic traits of hatchlings that are linked to survival. Maternal nest-site selection can therefore have long-term implications for offspring and maternal fitness. We studied nest-site selection in a nocturnal lizard (Amalosia lesueurii) from south eastern Australia. Females of this species lay their eggs communally inside rock crevices, and previous studies have shown that maximum daily nest temperatures are positively correlated with maximum daily air temperatures. The incubation period extends for up to 100 d, so during hot summers, embryos may be exposed to stressful thermal conditions. Potentially, mothers could buffer their eggs from thermal extremes via careful selection of nest sites. To evaluate this, we studied nest site selection in a southern population (Morton) and a northern population (Yengo) that experience mild and hot summers respectively. In the field, we measured the physical characteristics, orientation, canopy cover and incident radiation load, and thermal regimes of nest sites and randomly available crevices during one of the hottest Australian summers on record (2018–2019). We found strong inter population differences in the degree of canopy cover and solar radiation loads above nest sites. Nest sites from Morton were more open, and received higher radiation loads, than nest sites from Yengo. Mean nest temperatures were similar in Morton and Yengo, but nests from Yengo experienced higher daily temperatures than those from Morton. During heatwaves, temperatures in some nests exceeded the species critical thermal maximum (39.9 °C) for several hours each day. Our results show that females can adjust nest-site choice to match local environments, but future research is necessary to clarify whether exposure to high temperatures influences hatching success or offspring phenotypes in this species.
Cwiklinski, K, Robinson, MW, Donnelly, S & Dalton, JP 2021, 'Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver', BMC Genomics, vol. 22, no. 1, pp. 1-16.
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AbstractBackgroundThe major pathogenesis associated withFasciola hepaticainfection results from the extensive tissue damage caused by the tunnelling and feeding activity of immature flukes during their migration, growth and development in the liver. This is compounded by the pathology caused by host innate and adaptive immune responses that struggle to simultaneously counter infection and repair tissue damage.ResultsComplementary transcriptomic and proteomic approaches defined theF. hepaticafactors associated with their migration in the liver, and the resulting immune-pathogenesis. Immature liver-stage flukes express ~ 8000 transcripts that are enriched for transcription and translation processes reflective of intensive protein production and signal transduction pathways. Key pathways that regulate neoblast/pluripotent cells, including the PI3K-Akt signalling pathway, are particularly dominant and emphasise the importance of neoblast-like cells for the parasite’s rapid development. The liver-stage parasites display different secretome profiles, reflecting their distinct niche within the host, and supports the view that cathepsin peptidases, cathepsin peptidase inhibitors, saposins and leucine aminopeptidases play a central role in the parasite’s destructive migration, and digestion of host tissue and blood. Immature flukes are also primed for countering immune attack by secreting immunomodulating fatty acid binding proteins (FABP) and helminth defence molecules (FhHDM). Combined with published host microarray data, our results suggest that considerable immune cell infiltration and subsequent fibrosis of the liver tissue exacerbates oxidative stress within parenchyma that compels the expression of a range of antioxidant molecules within both host and parasite.
Cziesielski, MJ, Duarte, CM, Aalismail, N, Al-Hafedh, Y, Anton, A, Baalkhuyur, F, Baker, AC, Balke, T, Baums, IB, Berumen, M, Chalastani, VI, Cornwell, B, Daffonchio, D, Diele, K, Farooq, E, Gattuso, J-P, He, S, Lovelock, CE, Mcleod, E, Macreadie, PI, Marba, N, Martin, C, Muniz-Barreto, M, Kadinijappali, KP, Prihartato, P, Rabaoui, L, Saderne, V, Schmidt-Roach, S, Suggett, DJ, Sweet, M, Statton, J, Teicher, S, Trevathan-Tackett, SM, Joydas, TV, Yahya, R & Aranda, M 2021, 'Investing in Blue Natural Capital to Secure a Future for the Red Sea Ecosystems', Frontiers in Marine Science, vol. 7, p. 603722.
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For millennia, coastal and marine ecosystems have adapted and flourished in the Red Sea’s unique environment. Surrounded by deserts on all sides, the Red Sea is subjected to high dust inputs and receives very little freshwater input, and so harbors a high salinity. Coral reefs, seagrass meadows, and mangroves flourish in this environment and provide socio-economic and environmental benefits to the bordering coastlines and countries. Interestingly, while coral reef ecosystems are currently experiencing rapid decline on a global scale, those in the Red Sea appear to be in relatively better shape. That said, they are certainly not immune to the stressors that cause degradation, such as increasing ocean temperature, acidification and pollution. In many regions, ecosystems are already severely deteriorating and are further threatened by increasing population pressure and large coastal development projects. Degradation of these marine habitats will lead to environmental costs, as well as significant economic losses. Therefore, it will result in a missed opportunity for the bordering countries to develop a sustainable blue economy and integrate innovative nature-based solutions. Recognizing that securing the Red Sea ecosystems’ future must occur in synergy with continued social and economic growth, we developed an action plan for the conservation, restoration, and growth of marine environments of the Red Sea. We then investigated the level of resources for financial and economic investment that may incentivize these activities. This study presents a set of commercially viable financial investment strategies, ecological innovations, and sustainable development opportunities, which can, if implemented strategically, help ensure long-term economic benefits while promoting environmental conservation. We make a case for investing in blue natural capital and propose a strategic development model that relies on maintaining the health of natural ecosystems to ...
D’Agostino, D, Burt, JA, Santinelli, V, Vaughan, GO, Fowler, AM, Reader, T, Taylor, BM, Hoey, AS, Cavalcante, GH, Bauman, AG & Feary, DA 2021, 'Growth impacts in a changing ocean: insights from two coral reef fishes in an extreme environment', Coral Reefs, vol. 40, no. 2, pp. 433-446.
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AbstractDetermining the life-history consequences for fishes living in extreme and variable environments will be vital in predicting the likely impacts of ongoing climate change on reef fish demography. Here, we compare size-at-age and maximum body size of two common reef fish species (Lutjanus ehrenbergii and Pomacanthus maculosus) between the environmentally extreme Arabian/Persian Gulf (‘Arabian Gulf’) and adjacent comparably benign Oman Sea. Additionally, we use otolith increment width profiles to investigate the influence of temperature, salinity and productivity on the individual growth rates. Individuals of both species showed smaller size-at-age and lower maximum size in the Arabian Gulf compared to conspecifics in the less extreme and less variable environment of the Oman Sea, suggesting a life-history trade-off between size and metabolic demands. Salinity was the best environmental predictor of interannual growth across species and regions, with low growth corresponding to more saline conditions. However, salinity had a weaker negative effect on interannual growth of fishes in the Arabian Gulf than in the Oman Sea, indicating Arabian Gulf populations may be better able to acclimate to changing environmental conditions. Temperature had a weak positive effect on the interannual growth of fishes in the Arabian Gulf, suggesting that these populations may still be living within their thermal windows. Our results highlight the potential importance of osmoregulatory cost in impacting growth, and the need to consider the effect of multiple stressors when investigating the consequences of future climate change on fish demography.
Dadd-Daigle, P, Kirkby, K, Chowdhury, PR, Labbate, M & Chapman, TA 2021, 'The Verticillium wilt problem in Australian cotton', Australasian Plant Pathology, vol. 50, no. 2, pp. 129-135.
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© 2021, Australasian Plant Pathology Society Inc. Verticillium dahliae is a soil-borne phytopathogen and the causal agent of Verticillium wilt. It affects many agriculturally important crops around the world, including cotton. In Australia, the billion-dollar cotton industry is increasingly impacted by Verticillium wilt. Internationally it has been reported that the defoliating V. dahliae Vegetative Compatibility Group (VCG) 1A causes severe damage to cotton. In Australia however, the non-defoliating VCG2A is causing more severe damage to crops in fields than the defoliating VCG1A. This review examines the current research to understand the Australian V. dahliae situation, including current classification systems, genetic analyses and management strategies. It appears that virulence cannot be defined solely by VCG in Australian Verticillium dahliae isolates causing disease in cotton, and that the industry must continually adapt their practices in order to keep the disease under control.
Das, A, Lee, DJ, Shandilya, PK, Kim, S, Kang, G, Lake, DP, Behera, B, Sukachev, D, Aharonovich, I, Lee, J-H, Park, J & Barclay, PE 2021, 'Demonstration of Hybrid High-Q Hexagonal Boron Nitride Microresonators', ACS Photonics, vol. 8, no. 10, pp. 3027-3033.
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Hexagonal boron nitride (hBN) is a wide bandgap van der Waals material that is emerging as a powerful platform for quantum optics and nanophotonics. In this work, we demonstrate whispering gallery mode silica microresonators hybridized with thin layers of hBN that exhibit high intrinsic optical quality factor >7 × 105 and a linear absorption coefficient of 9.5 cm-1. Measurements of the effect of hBN thickness on optical Q and comparison with a theoretical model allows the linear optical absorption coefficient of the hBN films to be estimated. These high-Q devices will be useful for applications in quantum and nonlinear optics, and their hybridized geometry provides a sensitive platform for evaluating losses in hBN and other 2D materials.
Dawson, BM, Barton, PS & Wallman, JF 2021, 'Field succession studies and casework can help to identify forensically useful Diptera', Journal of Forensic Sciences, vol. 66, no. 6, pp. 2319-2328.
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AbstractFly development rates, and to a lesser extent succession data, can be used to provide an estimate of a minimum postmortem interval (mPMI). Yet, these data are most useful when a full account of species’ ecology, seasonality, and distribution is known. We conducted succession experiments on human cadavers over different seasons near Sydney, Australia, to document forensically useful information, including the pre‐appearance interval for carrion flies. We also compiled a detailed record of flies identified in casework collected in 156 cases distributed across New South Wales, Australia. We then compared the occurrence of fly species from both field and casework datasets to identify any consistencies or gaps to determine how useful species might be for forensic investigations. In the field experiments, we found differences in species diversity and abundance between seasons, as well as yearly variation between two winter seasons. Most fly species we recorded ovipositing showed a 2‐ or 3‐day delay between adult arrival and oviposition in summer, with a longer delay in winter. Species that were previously encountered in casework, such as Calliphora augur (Fabricius, 1775) and Calliphora ochracea Schiner, 1868, were confirmed as forensically useful, with their colonization behavior and seasonal preferences documented here. Although not encountered in casework, we confirmed Hemipyrellia fergusoni Patton, 1925 as a primary colonizer of human cadavers. Our study emphasizes the need to link field and casework data for a complete understanding of all aspects of a carrion fly's ecology to assist forensic investigators in mPMI estimations.
Dawson, BM, Wallman, JF, Evans, MJ & Barton, PS 2021, 'Is Resource Change a Useful Predictor of Carrion Insect Succession on Pigs and Humans?', Journal of Medical Entomology, vol. 58, no. 6, pp. 2228-2235.
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Abstract Carrion is a dynamic and nutrient-rich resource that attracts numerous insect species that undergo succession due to the rapid change in the carrion resource. Despite this process being well-understood, few studies have examined resource change as a driver of carrion insect succession, and instead have focused on the effects of time per se, or on coarse, qualitative measures such as decay stage. Here we report on three field succession experiments using pig carcasses and human cadavers encompassing two winters and one summer. We quantified the effects of resource change (measured as total body score, TBS), carrion type, initial carrion mass, ambient temperature, and season on insect species richness and community composition. We found that all variables had an effect on different taxonomic or trophic components of the insect community composition, with the exception of initial carrion mass which had no effect. We found significant positive effects of TBS on beetle species richness and composition, while fly species richness was not significantly affected by TBS, but was by ambient temperature. TBS had a significant positive effect on all trophic groups, while ambient temperature also had a significant positive effect on the necrophages and predator/parasitoids. Our study indicates that resource change, as indicated by TBS, is an important driver of carrion insect species turnover and succession on carrion, and that TBS can provide information about insect ecological patterns on carrion that other temporal measures of change cannot.
de Silva, RT, Abdul-Halim, MF, Pittrich, DA, Brown, HJ, Pohlschroder, M & Duggin, IG 2021, 'Improved growth and morphological plasticity of Haloferax volcanii', Microbiology, vol. 167, no. 2.
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Some microbes display pleomorphism, showing variable cell shapes in a single culture, whereas others differentiate to adapt to changed environmental conditions. The pleomorphic archaeon Haloferax volcanii commonly forms discoid-shaped (‘plate’) cells in culture, but may also be present as rods, and can develop into motile rods in soft agar, or longer filaments in certain biofilms. Here we report improvement of H. volcanii growth in both semi-defined and complex media by supplementing with eight trace element micronutrients. With these supplemented media, transient development of plate cells into uniformly shaped rods was clearly observed during the early log phase of growth; cells then reverted to plates for the late log and stationary phases. In media prepared with high-purity water and reagents, without supplemental trace elements, rods and other complex elongated morphologies (‘pleomorphic rods’) were observed at all growth stages of the culture; the highly elongated cells sometimes displayed a substantial tubule at one or less frequently both poles, as well as unusual tapered and highly curved forms. Polar tubules were observed forming by initial mid-cell narrowing or tubulation, causing a dumbbell-like shape, followed by cell division towards one end. Formation of the uniform early...
Dean, S, Razavy, S, Walsh, S, Zaslawski, C, Levett-Jones, T & Cant, R 2021, 'Building empathy awareness in undergraduate traditional Chinese Medicine students via an undercover ‘mystery shopper’ experience', Advances in Integrative Medicine, vol. 8, no. 4, pp. 267-271.
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Objective: To measure empathy within the therapeutic relationship between fourth year Traditional Chinese Medicine (TCM) intern practitioners and their patients, who are first-year students within the same program. Methods: An observational design was used to examine the interns’ empathic communication, evaluated by first year students ‘mystery shoppers’ using the Consultation and Relational Empathy Measure (CARE). First year TCM students went undercover to experience a clinical treatment (acupuncture) by a fourth-year intern in a public Chinese Medicine clinic attached to a metropolitan university in Sydney, Australia. Results: Thirty-nine consultations were assessed by 39 undercover shopper students. The Intern practitioners’ consultation and relational empathy was rated as a mean 76.4% (38.2 points of a possible 50 (median 78%; 39); range 24–50. Significant response differences were found between female and male interns with males rated higher. The underlying elements are presented and discussed. Conclusion: The intern practitioners’ level of empathy averaged 76.4% which is consistent with empathy ratings for international studies of healthcare students. Results showed that males were rated higher for empathy than females, indicating further studies examining the specific behaviours that characterise empathy of different genders would be a useful addition to knowledge and assist teaching.
Dedousis-Wallace, A, Drysdale, SA, McAloon, J & Ollendick, TH 2021, 'Parental and Familial Predictors and Moderators of Parent Management Treatment Programs for Conduct Problems in Youth', Clinical Child and Family Psychology Review, vol. 24, no. 1, pp. 92-119.
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Despite the established efficacy of Parent Management Training (PMT) for conduct problems in youth, evidence suggests that up to half of all treated youth still display clinical levels of disruptive behavior post-treatment. The reasons for these unsatisfactory outcomes are poorly understood. The aim of the present review was to provide an updated analysis of studies from the past 15 years that examined parental and familial predictors and moderators of improvement in PMT for conduct problems. A systematic literature review of indicated prevention (children with conduct problem symptoms) and intervention (children with clinical diagnoses) studies published between 2004 and 2019 was conducted. This 15-year time period was examined since the last systematic reviews were reported in 2006 and summarized studies completed through mid-2004 (see Lundahl et al. in Clin Psychol Rev 26(1):86-104, 2006; Reyno and McGrath in J Child Psychol Psychiatry 47(1):99-111, 2006). Risk of bias indices was also computed (see Higgins et al. in Revised Cochrane risk of bias tool for randomized trials (RoB 2.0), University of Bristol, Bristol, 2016) in our review. A total of 21 studies met inclusion criteria. Results indicated that a positive parent-child relationship was most strongly associated with better outcomes; however, little additional consistency in findings was evident. Future PMT research should routinely examine predictors and moderators that are both conceptually and empirically associated with treatment outcomes. This would further our understanding of factors that are associated with poorer treatment outcome and inform the development of treatment components or modes of delivery that might likely enhance evidence-based treatments and our clinical science. Protocol Registration Number: PROSPERO CRD42017058996.
DeMaere, MZ & Darling, AE 2021, 'qc3C: Reference-free quality control for Hi-C sequencing data', PLOS Computational Biology, vol. 17, no. 10, pp. e1008839-e1008839.
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Hi-C is a sample preparation method that enables high-throughput sequencing to capture genome-wide spatial interactions between DNA molecules. The technique has been successfully applied to solve challenging problems such as 3D structural analysis of chromatin, scaffolding of large genome assemblies and more recently the accurate resolution of metagenome-assembled genomes (MAGs). Despite continued refinements, however, preparing a Hi-C library remains a complex laboratory protocol. To avoid costly failures and maximise the odds of successful outcomes, diligent quality management is recommended. Current wet-lab methods provide only a crude assay of Hi-C library quality, while key post-sequencing quality indicators used have—thus far—relied upon reference-based read-mapping. When a reference is accessible, this reliance introduces a concern for quality, where an incomplete or inexact reference skews the resulting quality indicators. We propose a new, reference-free approach that infers the total fraction of read-pairs that are a product of proximity ligation. This quantification of Hi-C library quality requires only a modest amount of sequencing data and is independent of other application-specific criteria. The algorithm builds upon the observation that proximity ligation events are likely to create k-mers that would not naturally occur in the sample. Our software tool (qc3C) is to our knowledge the first to implement a reference-free Hi-C QC tool, and also provides reference-based QC, enabling Hi-C to be more easily applied to non-model organisms and environmental samples. We characterise the accuracy of the new algorithm on simulated and real datasets and compare it to reference-based methods.
Deng, K, Zhang, X, Liu, Y, Zhang, L, Wang, G, Feng, M, Oliver, BG, Wang, L, Hansbro, PM, Qin, L, Xie, M, Chen, ZH, Simpson, J, Zhang, J, Li, WM, Wang, G & Gibson, PG 2021, 'Heterogeneity of Paucigranulocytic Asthma: A Prospective Cohort Study with Hierarchical Cluster Analysis', The Journal of Allergy and Clinical Immunology: In Practice, vol. 9, no. 6, pp. 2344-2355.
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BACKGROUND: Asthma, a heterogeneous disease, can be divided into 4 inflammatory phenotypes using induced sputum cell counts-eosinophilic asthma (EA), neutrophilic asthma (NA), mixed granulocytic asthma, and paucigranulocytic asthma (PGA). Although research has focused on EA and NA, there is little known about PGA. OBJECTIVE: To study the heterogeneity of PGA and identify possible PGA clusters to guide clinical treatment. METHODS: Patients with PGA were grouped by hierarchical cluster analysis and enrolled into a prospective cohort study to validate the clusters, relative to future risk of asthma exacerbations in a real-world setting. Clusters were validated by tree analysis in a separate population. Finally, we explored PGA stability. RESULTS: Cluster analysis of 145 patients with PGA identified 3 clusters: cluster 1 (n = 110, 75.9%) was 'mild PGA,' cluster 2 (n = 20, 13.8%) was 'PGA with psychological dysfunction and rhinoconjunctivitis and other allergic diseases,' and cluster 3 (n = 15, 10.3%) was 'smoking-associated PGA.' Cluster 3 had significantly increased risk of severe exacerbation (relative risk [RR] = 6.43, P = .01), emergency visit (RR = 8.61, P = .03), and hospitalization (RR = 12.94, P < .01). Results of the cluster analysis were successfully validated in an independent PGA population classified using decision tree analysis. Although PGA can transform into or develop from other phenotypes, 70% were stable over time. CONCLUSIONS: Among 3 identified PGA clusters, cluster 3 had a higher risk of severe exacerbation. PGA heterogeneity indicates the requirement of novel targeted interventions.
Deplazes, E, Tafalla, BD, Murphy, C, White, J, Cranfield, CG & Garcia, A 2021, 'Calcium Ion Binding at the Lipid–Water Interface Alters the Ion Permeability of Phospholipid Bilayers', Langmuir, vol. 37, no. 48, pp. 14026-14033.
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Devkota, HP, Gaire, BP, Hori, K, Subedi, L, Adhikari-Devkota, A, Belwal, T, Paudel, KR, Jha, NK, Singh, SK, Chellappan, DK, Hansbro, PM, Dua, K & Kurauchi, Y 2021, 'The science of matcha: Bioactive compounds, analytical techniques and biological properties', Trends in Food Science & Technology, vol. 118, pp. 735-743.
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Devkota, HP, Paudel, KR, Jha, NK, Gupta, PK, Singh, SK, Chellappan, DK, Hansbro, PM & Dua, K 2021, 'Applications of Drug-Delivery Systems Targeting Inflammasomes in Pulmonary Diseases', Nanomedicine, vol. 16, no. 27, pp. 2407-2410.
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Dhouib, R, Nasreen, M, Othman, DSMP, Ellis, D, Lee, S, Essilfie, A-T, Hansbro, PM, McEwan, AG & Kappler, U 2021, 'The DmsABC Sulfoxide Reductase Supports Virulence in Non-typeable Haemophilus influenzae', Frontiers in Microbiology, vol. 12, pp. 1-11.
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Although molybdenum-containing enzymes are well-established as having a key role in bacterial respiration, it is increasingly recognized that some may also support bacterial virulence. Here, we show that DmsABC, a putative dimethylsulfoxide (DMSO) reductase, is required for fitness of the respiratory pathogen Haemophilus influenzae (Hi) in different models of infection. Expression of the dmsABC operon increased with decreasing oxygen availability, but despite this, a Hi2019ΔdmsA strain did not show any defects in anaerobic growth on chemically defined medium (CDM), and viability was also unaffected. Although Hi2019ΔdmsA exhibited increased biofilm formation in vitro and greater resistance to hypochlorite killing compared to the isogenic wild-type strain, its survival in contact with primary human neutrophils, in infections of cultured tissue cells, or in a mouse model of lung infection was reduced compared to Hi2019WT. The tissue cell infection model revealed a two-fold decrease in intracellular survival, while in the mouse model of lung infection Hi2019ΔdmsA was strongly attenuated and below detection levels at 48 h post-inoculation. While Hi2019WT was recovered in approximately equal numbers from bronchoalveolar lavage fluid (BALF) and lung tissue, survival of Hi2019ΔdmsA was reduced in lung tissue compared to BALF samples, indicating that ...
Di, X, Wang, D, Zhou, J, Zhang, L, Stenzel, MH, Su, QP & Jin, D 2021, 'Quantitatively Monitoring In Situ Mitochondrial Thermal Dynamics by Upconversion Nanoparticles', Nano Letters, vol. 21, no. 4, pp. 1651-1658.
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Temperature dynamics reflect the physiological conditions of cells and organisms. Mitochondria regulate the temperature dynamics in living cells as they oxidize the respiratory substrates and synthesize ATP, with heat being released as a byproduct of active metabolism. Here, we report an upconversion nanoparticle-based thermometer that allows the in situ thermal dynamics monitoring of mitochondria in living cells. We demonstrate that the upconversion nanothermometers can efficiently target mitochondria, and the temperature-responsive feature is independent of probe concentration and medium conditions. The relative sensing sensitivity of 3.2% K-1 in HeLa cells allows us to measure the mitochondrial temperature difference through the stimulations of high glucose, lipid, Ca2+ shock, and the inhibitor of oxidative phosphorylation. Moreover, cells display distinct response time and thermodynamic profiles under different stimulations, which highlight the potential applications of this thermometer to study in situ vital processes related to mitochondrial metabolism pathways and interactions between organelles.
Diaz, D, Vidal, X, Sunna, A & Care, A 2021, 'Bioengineering a Light-Responsive Encapsulin Nanoreactor: A Potential Tool for In Vitro Photodynamic Therapy', ACS Applied Materials & Interfaces, vol. 13, no. 7, pp. 7977-7986.
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DiBattista, JD, West, KM, Hay, AC, Hughes, JM, Fowler, AM & McGrouther, MA 2021, 'Community‐based citizen science projects can support the distributional monitoring of fishes', Aquatic Conservation: Marine and Freshwater Ecosystems, vol. 31, no. 12, pp. 3580-3593.
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AbstractEffective conservation and fisheries management requires data to capture demographic processes and range limits for each species to maximize population health and productivity. This need is constrained by limited funding and resources, particularly for countries with large land areas and coastlines as well as expansive exclusive economic zones. This imbalance means that monitoring efforts are often focused on targets of commercial and recreational fishing, which results in incomplete distributional records for non‐target, small‐bodied, and/or cryptic species.Community‐based citizen science projects offer one potential alternative for scientists and fisheries managers needing this type of information but lacking sufficient resources to gather it.This study investigated whether data sourced from an online citizen science project (iNaturalist: Australasian Fishes) can assist in the distributional monitoring of a subset of fish species. Given the regional focus of this citizen science project, distributional data in the form of occurrence records for abundant, protected, and threatened fish species as assessed by the International Union for Conservation of Nature in Australia and New Zealand were explored. Data for important commercial and recreational fishery targets in New South Wales were also explored, as a case study of a large jurisdiction with extensive monitoring requirements.The occurrence records for some of these categories of fishes were well represented in the quality‐filtered citizen science data set, particularly endemic fishes whose threat status had not yet been assessed and species not currently under any form of management. Despite gaps in coverage between major urban centres, citizen science data for the best r...
Dickson, K-A, Xie, T, Evenhuis, C, Ma, Y & Marsh, DJ 2021, 'PARP Inhibitors Display Differential Efficacy in Models of BRCA Mutant High-Grade Serous Ovarian Cancer', International Journal of Molecular Sciences, vol. 22, no. 16, pp. 8506-8506.
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Several poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors are now in clinical use for tumours with defects in BReast CAncer genes BRCA1 or BRCA2 that result in deficient homologous recombination repair (HRR). Use of olaparib, niraparib or rucaparib for the treatment of high-grade serous ovarian cancer, including in the maintenance setting, has extended both progression free and overall survival for women with this malignancy. While different PARP inhibitors (PARPis) are mechanistically similar, differences are apparent in their chemical structures, toxicity profiles, PARP trapping abilities and polypharmacological landscapes. We have treated ovarian cancer cell line models of known BRCA status, including the paired cell lines PEO1 and PEO4, and UWB1.289 and UWB1.289+BRCA1, with five PARPis (olaparib, niraparib, rucaparib, talazoparib and veliparib) and observed differences between PARPis in both cell viability and cell survival. A cell line model of acquired resistance to veliparib showed increased resistance to the other four PARPis tested, suggesting that acquired resistance to one PARPi may not be able to be rescued by another. Lastly, as a proof of principle, HRR proficient ovarian cancer cells were sensitised to PARPis by depletion of BRCA1. In the future, guidelines will need to emerge to assist clinicians in matching specific PARPis to specific patients and tumours.
Dikshit, A, Pradhan, B & Huete, A 2021, 'An improved SPEI drought forecasting approach using the long short-term memory neural network', Journal of Environmental Management, vol. 283, pp. 111979-111979.
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Droughts are slow-moving natural hazards that gradually spread over large areas and capable of extending to continental scales, leading to severe socio-economic damage. A key challenge is developing accurate drought forecast model and understanding a models' capability to examine different drought characteristics. Traditionally, forecasting techniques have used various time-series approaches and machine learning models. However, the use of deep learning methods have not been tested extensively despite its potential to improve our understanding of drought characteristics. The present study uses a deep learning approach, specifically the Long Short-Term Memory (LSTM) to predict a commonly used drought measure, the Standard Precipitation Evaporation Index (SPEI) at two different time scales (SPEI 1, SPEI 3). The model was compared with other common machine learning method, Random Forests, Artificial Neural Networks and applied over the New South Wales (NSW) region of Australia, using hydro-meteorological variables as predictors. The drought index and predictor data were collected from the Climatic Research Unit (CRU) dataset spanning from 1901 to 2018. We analysed the LSTM forecasted results in terms of several drought characteristics (drought intensity, drought category, or spatial variation) to better understand how drought forecasting was improved. Evaluation of the drought intensity forecasting capabilities of the model were based on three different statistical metrics, Coefficient of Determination (R2), Root Mean Square Error (RMSE), and Mean Absolute Error (MAE). The model achieved R2 value of more than 0.99 for both SPEI 1 and SPEI 3 cases. The variation in drought category forecasted results were studied using a multi-class Receiver Operating Characteristic based Area under Curves (ROC-AUC) approach. The analysis revealed an AUC value of 0.83 and 0.82 for SPEI 1 and SPEI 3 respectively. The spatial variation between observed a...
Ding, L, Zhou, J, Fu, Q, Bao, G, Liu, Y & Jin, D 2021, 'Triplet Fusion Upconversion with Oxygen Resistance in Aqueous Media', Analytical Chemistry, vol. 93, no. 10, pp. 4641-4646.
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Triplet fusion upconversion (also called triplet-triplet annihilation, TTA) arouses much attention due to its potential in the fields of biological imaging, optogenetics, and light harvesting. However, oxygen quenching remains a challenge ahead, restricting its applications in aqueous media. Previous efforts to realize aqueous TTA with oxygen resistance have been focused on core-shell structures and self-assembly, but tedious processes and complicated chemical modification are required. Here, we report a direct and efficient strategy to realize aqueous TTA by controlling the ionic equilibrium of the TTA dyad. We find that the ionized organic dyad in physiological buffers and electrolyte-based media shows a natural aerotolerance without any complicated structure engineering. In particular, the upconversion intensity of this aqueous TTA in Tris buffer under an air-saturated condition is more than twice that under the deaerated condition. We further demonstrate the TTA system for potential applications in pH and temperature sensing with reversible and sensitive performance. We anticipate this facile approach will inspire the development of practical aqueous TTA and broad applications in biological science.
Dirar, AI, Adhikari-Devkota, A, Kunwar, RM, Paudel, KR, Belwal, T, Gupta, G, Chellappan, DK, Hansbro, PM, Dua, K & Devkota, HP 2021, 'Genus Blepharis (Acanthaceae): A review of ethnomedicinally used species, and their phytochemistry and pharmacological activities', Journal of Ethnopharmacology, vol. 265, pp. 113255-113255.
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ETHNOPHARMACOLOGICAL RELEVANCE:Blepharis is an Afro-Asiatic genus belonging to the family Acanthaceae. It comprises 126 species that occur in arid and semi-arid habitats. Some species of Blepharis are used in traditional medicines in different countries mainly for their anti-inflammatory, would healing activities along with treatment of gastrointestinal disorders and bone fractures. AIM OF THE REVIEW:The present review aims to collate and analyze the available data and information on distribution, traditional uses, chemical constituents and pharmacological activities of Blepharis. METHODS:Scientific information of genus Blepharis was retrieved from the online bibliographic databases like MEDLINE/PubMed, SciFinder, Web of Science and Google Scholar and secondary resources including books and proceedings. RESULTS:Seven species of Blepharis were found to be reported frequently as useful in folklore in Asian and African countries. B. maderaspatensis was found to be widely used in Indian traditional medicines whereas the B. ciliaris and B. edulis were common in folklore of Egypt, Jordan, and Arabia. Active phytochemicals of Blepharis are flavonoids from B. ciliaris, alkaloids from B. sindica, phenolic acid derivatives, and phytosterols, and derivatives of hydroxamic acids from B. edulis resulted in possessing diverse biological properties such as anti-microbial, anti-inflammatory, and anti-cancer. CONCLUSION:Various species of Blepharis were found to be used in traditional medicine systems in African and Asian countries. Few of these species were studied for their bioactive chemical constituents however the activity guided isolation studies are not performed. Similarly, detailed pharmacological studies in animal models to explore their mechanism of action are also not reported. Future studies should focus on these aspects related to the medicinally used species of Blepharis. The detailed and comprehensive comparative analysis presented here gives valuable in...
Ditz, B, Sarma, A, Kerstjens, HAM, Liesker, JJW, Bathoorn, E, Vonk, JM, Bernal, V, Horvatovich, P, Guryev, V, Caldera, S, Langelier, C, Faiz, A, Christenson, SA & van den Berge, M 2021, 'The sputum transcriptome better predicts COPD exacerbations after the withdrawal of inhaled corticosteroids than sputum eosinophils', ERJ Open Research, vol. 7, no. 3, pp. 00097-2021.
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IntroductionContinuing inhaled corticosteroid (ICS) use does not benefit all patients with COPD, yet it is difficult to determine which patients may safely sustain ICS withdrawal. Although eosinophil levels can facilitate this decision, better biomarkers could improve personalised treatment decisions.MethodsWe performed transcriptional profiling of sputum to explore the molecular biology and compared the predictive value of an unbiased gene signatureversussputum eosinophils for exacerbations after ICS withdrawal in COPD patients. RNA-sequencing data of induced sputum samples from 43 COPD patients were associated with the time to exacerbation after ICS withdrawal. Expression profiles of differentially expressed genes were summarised to create gene signatures. In addition, we built a Bayesian network model to determine coregulatory networks related to the onset of COPD exacerbations after ICS withdrawal.ResultsIn multivariate analyses, we identified a gene signature (LGALS12,ALOX15,CLC,IL1RL1,CD24,EMR4P) associated with the time to first exacerbation after ICS withdrawal. The addition of this gene signature to a multiple Cox regression model explained more variance of time to exacerbations compared to a model using sputum eosinophils. The gene signature correlated with sputum eosinophil as well as macrophage cell counts. The Bayesian network model identified three coregulatory gene networks as well as sex to be related to an earlyversuslate/nonexacerbation phenotype.ConclusionWe identified a sputum gene expression s...
Doble, PA, de Vega, RG, Bishop, DP, Hare, DJ & Clases, D 2021, 'Laser Ablation–Inductively Coupled Plasma–Mass Spectrometry Imaging in Biology', Chemical Reviews, vol. 121, no. 19, pp. 11769-11822.
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Elemental imaging gives insight into the fundamental chemical makeup of living organisms. Every cell on Earth is comprised of a complex and dynamic mixture of the chemical elements that define structure and function. Many disease states feature a disturbance in elemental homeostasis, and understanding how, and most importantly where, has driven the development of laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) as the principal elemental imaging technique for biologists. This review provides an outline of ICP-MS technology, laser ablation cell designs, imaging workflows, and methods of quantification. Detailed examples of imaging applications including analyses of cancers, elemental uptake and accumulation, plant bioimaging, nanomaterials in the environment, and exposure science and neuroscience are presented and discussed. Recent incorporation of immunohistochemical workflows for imaging biomolecules, complementary and multimodal imaging techniques, and image processing methods is also reviewed.
Dominici, L, Fleck, R, Gill, RL, Pettit, TJ, Irga, PJ, Comino, E & Torpy, FR 2021, 'Analysis of lighting conditions of indoor living walls: Effects on CO2 removal', Journal of Building Engineering, vol. 44, pp. 102961-102961.
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Vertical greening systems, or living walls, are becoming increasingly used indoors for improving the sustainability of buildings, including for the mitigation of excess CO2 levels, derived from human respiration. However, light provision within indoor environments is often insufficient for the efficient functioning of many plant species, leading to low photosynthetic CO2 removal rates, and the need for supplementary light sources. In this study, we investigated the performance of supplementary lighting employed for indoor living wall systems, and whether optimised lighting conditions could lead to improved CO2 removal. In situ trials with several medium-large indoor living walls were performed to sample the lighting scenarios currently employed. We concluded that the majority of plants in existing systems were exposed to suboptimal lighting and will have a net-zero CO2 removal efficiency. Sealed chamber experiments using two common living wall plant species were conducted to explore the effect of varying lighting conditions on CO2 removal efficiency. Comparisons on optimal and “best case” in situ conditions were carried out, showing that CO2 removal efficiency was significantly correlated with both leaf and stem angles, which suggest phototropism may influence in situ CO2 removal. After a ten-day experimental period, the highest CO2 removal efficiency for both test plant species was observed at 200 μmol m−2 s−1 light flux density (~10500 lux) at 15° from the vertical growing surface. Our results indicate that most current lighting systems are inadequate for healthy plant photosynthesis and CO2 removal, and that modified lighting systems could improve this performance. The estimation of the CO2 removal ability of a 5 m2 passive living wall decreases from an ACH of 0.21 h−1, achieved in an optimal light exposure condition, to only 0.03 h−1 when plants are exposed to sub-optimal conditions. To reduce maintenance costs, technical guidelines for indoor livin...
Donnelly, S & Tran, N 2021, 'Commandeering the mammalian Ago2 miRNA network: a newly discovered mechanism of helminth immunomodulation', Trends in Parasitology, vol. 37, no. 12, pp. 1031-1033.
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MicroRNAs (miRNAs) are a class of noncoding RNAs that contribute to a broad range of biological processes through post-transcriptional regulation of gene expression. Helminths exploit this system to target mammalian gene expression, to modulate the host immune response. Recent discoveries have shed new light on the mechanisms involved.
DOOLEY, AH & JARRETT, K 2021, 'Non-singular -actions: an ergodic theorem over rectangles with application to the critical dimensions', Ergodic Theory and Dynamical Systems, vol. 41, no. 12, pp. 3722-3739.
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AbstractWe adapt techniques developed by Hochman to prove a non-singular ergodic theorem for $\mathbb {Z}^d$-actions where the sums are over rectangles with side lengths increasing at arbitrary rates, and in particular are not necessarily balls of a norm. This result is applied to show that the critical dimensions with respect to sequences of such rectangles are invariants of metric isomorphism. These invariants are calculated for the natural action of $\mathbb {Z}^d$ on a product of d measure spaces.
Douglas, ANJ, Morgan, AL, Rogers, EIE, Irga, PJ & Torpy, FR 2021, 'Evaluating and comparing the green wall retrofit suitability across major Australian cities', Journal of Environmental Management, vol. 298, pp. 113417-113417.
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Urban densification continues to present a unique set of economic and environmental challenges. A growing shortage of green space and infrastructure is intrinsically linked with urban growth and development. With this comes the loss of ecosystem services such as urban heat island effects, reduction of air quality and biodiversity loss. Vertical greenery systems (VGS) offer an adaptive solution to space-constrained areas that are characteristic of dense urban areas, and can potentially improve the sustainability of cities. However, in order to promote VGS uptake, methods are required to enable systematic appraisal of whether existing walls can be retrofitted with VGS. Further, feasibility studies that quantify the potential for retrofit suitability of VGS across entire urban areas are lacking. This study established an evaluation tool for green wall constructability in urban areas and validated the assessment tool by determining the quantity of walls in five major Australian cities that could potentially have VGS incorporated into the existing infrastructure. Each wall was analysed using an exclusionary set of criteria that evaluated and ranked a wall based on its suitability to VGS implementation. Sydney and Brisbane recorded the greatest proportional length of walls suitable for VGS, with 33.74% and 34.12% respectively. Conversely, Perth's urban centre was the least feasible site in which to incorporate VGS, with over 97% of surveyed walls excluded, mainly due to the prevalence of <1 m high fence lines and glazed shopfronts. This study aimed to evaluate feasibility assessments of green wall retrofitability in highly urbanised areas with the intention of creating an analytical method that is accessible to all. This method, coupled with the promising number of feasible walls found in this study, emphasises the need for more government policy and incentives encouraging green wall uptake and could play a pivotal role in the expansion of green infrastructur...
Douna, V, Barraza, V, Grings, F, Huete, A, Restrepo-Coupe, N & Beringer, J 2021, 'Towards a remote sensing data based evapotranspiration estimation in Northern Australia using a simple random forest approach', Journal of Arid Environments, vol. 191, pp. 104513-104513.
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In this work we have developed a random forest regressor to predict daily evapotranspiration in three eddy-covariance sites in Northern Australia from in-situ meteorological data and fluxes, and satellite leaf area index and land surface temperature data. The variable analysis for the random forest regressor suggests that leaf area index is the most important one at this temporal scale. A development sample corresponding to the period 2010–2013 was used, while the year 2014 has been separated for testing. Using this approach, we have obtained satisfactory performances in the three sites, with RMSE errors around 1 mm/day (and relative RMSEs ~0.3) in comparison to the measured values. With the final aim of testing the predictive capability of a model that uses remote sensing data as input, regressors that predict evapotranspiration exclusively from leaf area index and land surface temperature, have been trained resulting in reasonable performances. The RMSEs over the test set are ~1.1−1.2 mm/day. In all cases, the errors are comparable to those obtained in previous works that use similar locations and different methods. When compared to the measured values, the random forest predictions of evapotranspiration are more accurate than the global MODIS ET 8-day 1 km product, which was used as benchmark for the performance evaluation of our models, in the three selected locations.
Douraghi, M, Aris, P, To, J, Myers, GSA & Hamidian, M 2021, 'Two carbapenem-resistant ST1:ST231:KL1:OCL1Acinetobacter baumanniistrains recovered in Tehran, Iran, carry AbaR31 in the chromosome and AbaR4 and TnaphA6in a RepAci6 plasmid', JAC-Antimicrobial Resistance, vol. 3, no. 3, p. dlab112.
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AbstractObjectivesTo analyse the context of genes conferring antibiotic resistance in two carbapenem-resistant Acinetobacter baumannii isolates recovered in Tehran, Iran.MethodsThe antibiotic resistance phenotype for 28 antibiotics was determined using disc diffusion. The whole genome sequences of ABH008 and ABS200 were determined using the Illumina HiSeq X Ten platform. Resistance genes were identified using ResFinder and multilocus sequence types were determined using the Oxford and Institut Pasteur schemes.ResultsIsolates ABH008 and ABS200, recovered in 2012 and 2013, respectively, in two different Tehran hospitals, belong to the common global clone 1 lineage, ST1IP and ST231OX. They are resistant to sulfamethoxazole, tetracycline, gentamicin, amikacin, third-generation cephalosporins and carbapenems. Despite being isolated in different hospitals, phylogenetic analysis indicated they are closely related. Consistent with this, both isolates carry catA1, sul1, aacC1 and aadA1 in a novel variant of the AbaR3-type resistance island, named AbaR31. Both isolates are resistant to amikacin and carbapenems owing to aphA6 and oxa23, respectively. The oxa23 gene is located in the AbaR4 resistance island, and aphA6 in TnaphA6, and both mobile elements are in an ∼90 kbp plasmid encoding the putative RepAci6 replication initiation protein. Resistance to third-generation cephalosporins is due to the acquisition by homologous recombination of a 5 kb DNA segment that contains ISAba1-ampC from a ST623 strain.ConclusionsThe resistance gene complements of ABH008 and ABS200 were found in AbaR31 and a plasmid that encodes RepAci6. The close genetic relationship of ABH008 and ABS200, despite each being recovered from dif...
Dowla, R, Murnion, B, Hung, C, Currell, K, Kendig, M, Freeston, J & Rooney, K 2021, 'Exercise Capacity and Acute Effect of Exercise on Affect in a Substance Use Disorder Population', Journal of Clinical Exercise Physiology, vol. 10, no. 4, pp. 142-149.
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ABSTRACT Background It is known that exercise is beneficial to people with substance use disorder, however little evidence exists regarding their exercise capacity. This pilot study investigates the exercise capacity of patients with substance use disorder and effects of an acute bout of exercise on affect. Methods Twenty-nine participants admitted to a withdrawal management facility were recruited to complete a health and exercise assessment (18 females, 11 males; 41 ± 11 years old). Mood was measured before and after exercise assessments using the subjective experience to exercise scale. Data was grouped by sex, and descriptive analyses were performed against age-matched normative data. Within group, before and after subjective experience to exercise scale measures were analyzed using 2-way ANOVA with sex as a between subject factor. Results Participants ranged from having 2 to 6 modifiable cardiovascular risk factors. Participants performed below average compared to age-matched and sex-matched normative data for the 6-minute walk test (females: 539 ± 54 m, males: 606 ± 89 m); and push-up test (females: 22% good, males: 36% good). Of the 29 participants, 29% failed to achieve the average range for sex-matched norms in the sit-to-stand test. However, all participants achieved above average for curl-ups, and 72% achieved an average or above score in the step-up test. Exercise significantly increased wellbeing (P < 0.001, effect size = 1.12) and decreased psychological distress (P = 0.045, effect size = 1.03) and fatigue (P < 0.001, effect size = 1.32). ...
Dua, K, Löbenberg, R, Luzo, ÂCM, Shukla, S & Satija, S 2021, 'Preface', Targeting Cellular Signalling Pathways in Lung Diseases, pp. v-vi.
Dutt, S, Apel, P, Lizunov, N, Notthoff, C, Wen, Q, Trautmann, C, Mota-Santiago, P, Kirby, N & Kluth, P 2021, 'Shape of nanopores in track-etched polycarbonate membranes', Journal of Membrane Science, vol. 638, pp. 119681-119681.
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Eid, B, Islam, MR, Shah, R, Nahid, A-A, Kouzani, AZ & Mahmud, MAP 2021, 'Enhanced Profitability of Photovoltaic Plants By Utilizing Cryptocurrency-Based Mining Load', IEEE Transactions on Applied Superconductivity, vol. 31, no. 8, pp. 1-5.
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Elder, M & Goh, YK 2021, '$k$-Pop Stack Sortable Permutations and $2$-Avoidance', The Electronic Journal of Combinatorics, vol. 28, no. 1.
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We consider permutations sortable by $k$ passes through a deterministic pop stack. We show that for any $k\in\mathbb{N}$ the set is characterised by finitely many patterns, answering a question of Claesson and Guðmundsson. Moreover, these sets of patterns are algorithmically constructible.
Our characterisation demands a more precise definition than in previous literature of what it means for a permutation to avoid a set of barred and unbarred patterns. We propose a new notion called $2$-avoidance.
Ellis, J, Barratt, J, Kaufer, A, Pearn, L, Armstrong, B, Johnson, M, Park, Y, Downey, L, Cao, M, Neill, L, Lee, R, Ellis, B, Tyler, K, Lun, Z-R & Stark, D 2021, 'A new subspecies of Trypanosoma cyclops found in the Australian terrestrial leech Chtonobdella bilineata', Parasitology, vol. 148, no. 10, pp. 1125-1136.
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Abstract
Ellis, J, Ellis, B, Tyler, K & Reichel, MP 2021, 'Recent trends in the use of social media in parasitology and the application of alternative metrics', Current Research in Parasitology & Vector-Borne Diseases, vol. 1, pp. 100013-100013.
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El‐Madany, TS, Reichstein, M, Carrara, A, Martín, MP, Moreno, G, Gonzalez‐Cascon, R, Peñuelas, J, Ellsworth, DS, Burchard‐Levine, V, Hammer, TW, Knauer, J, Kolle, O, Luo, Y, Pacheco‐Labrador, J, Nelson, JA, Perez‐Priego, O, Rolo, V, Wutzler, T & Migliavacca, M 2021, 'How Nitrogen and Phosphorus Availability Change Water Use Efficiency in a Mediterranean Savanna Ecosystem', Journal of Geophysical Research: Biogeosciences, vol. 126, no. 5.
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AbstractNutrient availability, especially of nitrogen (N) and phosphorus (P), is of major importance for every organism and at a larger scale for ecosystem functioning and productivity. Changes in nutrient availability and potential stoichiometric imbalance due to anthropogenic nitrogen deposition might lead to nutrient deficiency or alter ecosystem functioning in various ways. In this study, we present 6 years (2014–2020) of flux‐, plant‐, and remote sensing data from a large‐scale nutrient manipulation experiment conducted in a Mediterranean savanna‐type ecosystem with an emphasis on the effects of N and P treatments on ecosystem‐scale water‐use efficiency (WUE) and related mechanisms. Two plots were fertilized with N (NT, 16.9 Ha) and N + P (NPT, 21.5 Ha), and a third unfertilized plot served as a control (CT). Fertilization had a strong impact on leaf nutrient stoichiometry only within the herbaceous layer with increased leaf N in both fertilized treatments and increased leaf P in NPT. Following fertilization, WUE in NT and NPT increased during the peak of growing season. While gross primary productivity similarly increased in NT and NPT, transpiration and surface conductance increased more in NT than in NPT. The results show that the NPT plot with higher nutrient availability, but more balanced N:P leaf stoichiometry had the highest WUE. On average, higher N availability resulted in a 40% increased leaf area index (LAI) in both fertilized treatments in the spring. Increased LAI reduced aerodynamic conductance and thus evaporation at both fertilized plots in the spring. Despite reduced evaporation, annual evapotranspiration increased by 10% (48.6 ± 28.3 kg H2O m−2), in the NT plot, while NPT remained similar to CT (−1%, −6.7 ± 12.2 kgH2O m−2). Potential causes for increased transpiration at NT could be increased root biomass and thus ...
Enosi Tuipulotu, D, Mathur, A, Ngo, C & Man, SM 2021, 'Bacillus cereus: Epidemiology, Virulence Factors, and Host–Pathogen Interactions', Trends in Microbiology, vol. 29, no. 5, pp. 458-471.
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Estherby, CA, Arnold, MD, Tai, MC & Gentle, AR 2021, 'Dynamic control of polarized thermal emission from VO2 nanofins', Journal of Photonics for Energy, vol. 11, no. 04.
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Facey, JA, Rogers, TA, Apte, SC & Mitrovic, SM 2021, 'Micronutrients as growth limiting factors in cyanobacterial blooms; a survey of freshwaters in South East Australia', Aquatic Sciences, vol. 83, no. 2.
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Fahim, S, Sarker, S, Das, S, Islam, MR, Kouzani, A & Mahmud, MAP 2021, 'A Probabilistic Generative Model for Fault Analysis of a Transmission Line With SFCL', IEEE Transactions on Applied Superconductivity, vol. 31, no. 8, pp. 1-5.
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The fault analysis of a transmission line (TL) are the key factors for the rapid restoration of the power network. Due to the recent expansion of the power system as well as the increased generation capacity, the magnitude of the fault current increases beyond the interruption capability of the existing circuit breaker. In this turn, the superconducting fault current limiters (SFCLs) come in handy which limits the fault current and facilitates the tripping operation without upgrading the breaker rating. Besides, the SFCLs affect the three-phase signals which, in turn, negatively affect the transmission line protection scheme. This paper proposes an unsupervised framework for fault detection and classification of a transmission line with SFCLs. The proposed scheme receives 1/2 cycle post-fault three-phase signals and hierarchically extracts the fault information for fault analyzing purposes. The effectiveness of the proposed approach is justified in terms of overall and individual accuracy. Further assessment of the model's performance against noise and measurement error is also carried out in order to confirm the high reliability of the proposed model.
Fairley, LH, Sahara, N, Aoki, I, Ji, B, Suhara, T, Higuchi, M & Barron, AM 2021, 'Neuroprotective effect of mitochondrial translocator protein ligand in a mouse model of tauopathy', Journal of Neuroinflammation, vol. 18, no. 1.
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Abstract Background The translocator protein (TSPO) has been identified as a positron emission tomography (PET)-visible biomarker of inflammation and promising immunotherapeutic target for the treatment of Alzheimer’s disease (AD). While TSPO ligands have been shown to reduce the accumulation of the toxic Alzheimer’s beta-amyloid peptide, their effect on tau pathology has not yet been investigated. To address this, we analyzed the effects of TSPO ligand, Ro5-4864, on the progression of neuropathology in rTg4510 tau transgenic mice (TauTg). Methods Brain atrophy, tau accumulation, and neuroinflammation were assessed longitudinally using volumetric magnetic resonance imaging, tau-PET, and TSPO-PET, respectively. In vivo neuroimaging results were confirmed by immunohistochemistry for markers of neuronal survival (NeuN), tauopathy (AT8), and inflammation (TSPO, ionized calcium-binding adaptor molecule 1 or IBA-1, and complement component 1q or C1q) in brain sections from scanned mice. Results TSPO ligand treatment attenuated brain atrophy and hippocampal neuronal loss in the absence of any detected effect on tau depositions. Atrophy and neuronal loss were strongly associated with in vivo inflammatory signals measured by TSPO-PET, IBA-1, and levels of C1q, a regulator of the complement cascade. In vitro studies confirmed that the TSPO ligand Ro5-4864 reduces C1q expression in a microglial cell line in response to inflammation, reduction of which has been shown in previous studies to protect synapses and neurons in models of tauopathy. Conclusions ...
Faiz, A, Harkness, LM, Tjin, G, Bernal, V, Horvatovich, P, James, A, Elliot, JG, Burgess, JK & Ashton, AW 2021, 'Angiogenic regulatory influence of extracellular matrix deposited by resting state asthmatic and non‐asthmatic airway smooth muscle cells is similar', Journal of Cellular and Molecular Medicine, vol. 25, no. 13, pp. 6438-6447.
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AbstractThe extracellular matrix (ECM) is the tissue microenvironment that regulates the characteristics of stromal and systemic cells to control processes such as inflammation and angiogenesis. Despite ongoing anti‐inflammatory treatment, low levels of inflammation exist in the airways in asthma, which alters ECM deposition by airway smooth muscle (ASM) cells. The altered ECM causes aberrant behaviour of cells, such as endothelial cells, in the airway tissue. We therefore sought to characterize the composition and angiogenic potential of the ECM deposited by asthmatic and non‐asthmatic ASM. After 72 hours under non‐stimulated conditions, the ECM deposited by primary human asthmatic ASM cells was equal in total protein, collagen I, III and fibronectin content to that from non‐asthmatic ASM cells. Further, the matrices of non‐asthmatic and asthmatic ASM cells were equivalent in regulating the growth, activity, attachment and migration of primary human umbilical vein endothelial cells (HUVECs). Under basal conditions, asthmatic and non‐asthmatic ASM cells intrinsically deposit an ECM of equivalent composition and angiogenic potential. Previous findings indicate that dysregulation of the airway ECM is driven even by low levels of inflammatory provocation. This study suggests the need for more effective anti‐inflammatory therapies in asthma to maintain the airway ECM and regulate ECM‐mediated aberrant angiogenesis.
Falkenberg, LJ, Scanes, E, Ducker, J & Ross, PM 2021, 'Biotic habitats as refugia under ocean acidification', Conservation Physiology, vol. 9, no. 1, p. coab077.
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Abstract Habitat-forming organisms have an important role in ameliorating stressful conditions and may be of particular relevance under a changing climate. Increasing CO2 emissions are driving a range of environmental changes, and one of the key concerns is the rapid acceleration of ocean acidification and associated reduction in pH. Such changes in seawater chemistry are anticipated to have direct negative effects on calcifying organisms, which could, in turn, have negative ecological, economic and human health impacts. However, these calcifying organisms do not exist in isolation, but rather are part of complex ecosystems. Here, we use a qualitative narrative synthesis framework to explore (i) how habitat-forming organisms can act to restrict environmental stress, both now and in the future; (ii) the ways their capacity to do so is modified by local context; and (iii) their potential to buffer the effects of future change through physiological processes and how this can be influenced by management adopted. Specifically, we highlight examples that consider the ability of macroalgae and seagrasses to alter water carbonate chemistry, influence resident organisms under current conditions and their capacity to do so under future conditions, while also recognizing the potential role of other habitats such as adjacent mangroves and saltmarshes. Importantly, we note that the outcome of interactions between these functional groups will be context dependent, influenced by the local abiotic and biotic characteristics. This dependence provides local managers with opportunities to create conditions that enhance the likelihood of successful amelioration. Where individuals and populations are managed effectively, habitat formers could provide local refugia for resident organisms of ecological and economic importance under an acidifying ocean.
Falster, D, Gallagher, R, Wenk, EH, Wright, IJ, Indiarto, D, Andrew, SC, Baxter, C, Lawson, J, Allen, S, Fuchs, A, Monro, A, Kar, F, Adams, MA, Ahrens, CW, Alfonzetti, M, Angevin, T, Apgaua, DMG, Arndt, S, Atkin, OK, Atkinson, J, Auld, T, Baker, A, von Balthazar, M, Bean, A, Blackman, CJ, Bloomfield, K, Bowman, DMJS, Bragg, J, Brodribb, TJ, Buckton, G, Burrows, G, Caldwell, E, Camac, J, Carpenter, R, Catford, JA, Cawthray, GR, Cernusak, LA, Chandler, G, Chapman, AR, Cheal, D, Cheesman, AW, Chen, S-C, Choat, B, Clinton, B, Clode, PL, Coleman, H, Cornwell, WK, Cosgrove, M, Crisp, M, Cross, E, Crous, KY, Cunningham, S, Curran, T, Curtis, E, Daws, MI, DeGabriel, JL, Denton, MD, Dong, N, Du, P, Duan, H, Duncan, DH, Duncan, RP, Duretto, M, Dwyer, JM, Edwards, C, Esperon-Rodriguez, M, Evans, JR, Everingham, SE, Farrell, C, Firn, J, Fonseca, CR, French, BJ, Frood, D, Funk, JL, Geange, SR, Ghannoum, O, Gleason, SM, Gosper, CR, Gray, E, Groom, PK, Grootemaat, S, Gross, C, Guerin, G, Guja, L, Hahs, AK, Harrison, MT, Hayes, PE, Henery, M, Hochuli, D, Howell, J, Huang, G, Hughes, L, Huisman, J, Ilic, J, Jagdish, A, Jin, D, Jordan, G, Jurado, E, Kanowski, J, Kasel, S, Kellermann, J, Kenny, B, Kohout, M, Kooyman, RM, Kotowska, MM, Lai, HR, Laliberté, E, Lambers, H, Lamont, BB, Lanfear, R, van Langevelde, F, Laughlin, DC, Laugier-Kitchener, B-A, Laurance, S, Lehmann, CER, Leigh, A, Leishman, MR, Lenz, T, Lepschi, B, Lewis, JD, Lim, F, Liu, U, Lord, J, Lusk, CH, Macinnis-Ng, C, McPherson, H, Magallón, S, Manea, A, López-Martinez, A, Mayfield, M, McCarthy, JK, Meers, T, van der Merwe, M, Metcalfe, DJ, Milberg, P, Mokany, K, Moles, AT, Moore, BD, Moore, N, Morgan, JW, Morris, W, Muir, A, Munroe, S, Nicholson, Á, Nicolle, D, Nicotra, AB, Niinemets, Ü, North, T, O’Reilly-Nugent, A, O’Sullivan, OS, Oberle, B, Onoda, Y, Ooi, MKJ, Osborne, CP, Paczkowska, G, Pekin, B, Guilherme Pereira, C, Pickering, C, Pickup, M, Pollock, LJ, Poot, P, Powell, JR, Power, SA, Prentice, IC, Prior, L, Prober, SM, Read, J, Reynolds, V, Richards, AE, Richardson, B, Roderick, ML, Rosell, JA, Rossetto, M, Rye, B, Rymer, PD, Sams, MA, Sanson, G, Sauquet, H, Schmidt, S, Schönenberger, J, Schulze, E-D, Sendall, K, Sinclair, S, Smith, B, Smith, R, Soper, F, Sparrow, B, Standish, RJ, Staples, TL, Stephens, R, Szota, C, Taseski, G, Tasker, E, Thomas, F, Tissue, DT, Tjoelker, MG & et al. 2021, 'AusTraits, a curated plant trait database for the Australian flora', Scientific Data, vol. 8, no. 1, p. 254.
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AbstractWe introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.
Fan, J, Liang, L, Gu, Y & Liu, X 2021, '(INVITED) Opposing effects of energy migration and cross-relaxation on surface sensitivity of lanthanide-doped nanocrystals', Optical Materials: X, vol. 12, pp. 100104-100104.
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Fan, J, Zhao, Z, Zhang, J, Peng, C, Tang, X, Li, X & Cui, X 2021, 'Electromagnetic Disturbance Characteristics and Influence Factors of PETT Oscillation in High-Voltage IGBT Devices', IEEE Transactions on Power Electronics, vol. 36, no. 4, pp. 4116-4124.
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Fan, L, Guo, Z, Zhao, D, Zhao, C, Lu, X, Chen, A, Yin, X, Zhang, Y, Sun, B & Zhang, N 2021, 'Stable and Dendrite‐Free Lithium Metal Anodes Enabled by Ionic/Electronic Li2S/Mo Interlayer', Advanced Energy and Sustainability Research, vol. 2, no. 11, pp. 1-8.
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The wide applications of high‐capacity lithium metal anodes for lithium metal batteries are restricted by the uncontrollable lithium dendrite growth caused by the uneven lithium deposition and the infinite volume change of lithium anodes during the plating/stripping process. Herein, the composite ionic/electronic interlayer of Li2S/Mo is deposited on the surface of stainless steel mesh (SSM) by in situ electrochemical conversion reaction from MoS2 nanosheet arrays. The Li2S/Mo interlayer with high ionic conductivity can regulate uniform lithium‐ion flux and promote homogeneous lithium deposition without dendrite growth. The half cells with Li2S/Mo‐modified SSM current collector show stable cycling performance of more than 400 cycles at 1 and 1 mAh cm−2, with the average Coulombic efficiency higher than 96%. By coupling with LiFePO4 cathodes, the assembled full cells demonstrate improved cycling performance. This work provides a new idea for using metal sulfides as a lithiophilic interlayer to facilitate dendrite‐free lithium deposition.
Fan, L, Sun, B, Yan, K, Xiong, P, Guo, X, Guo, Z, Zhang, N, Feng, Y, Sun, K & Wang, G 2021, 'A Dual‐Protective Artificial Interface for Stable Lithium Metal Anodes', Advanced Energy Materials, vol. 11, no. 48, pp. 1-10.
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AbstractConstructing an advanced artificial solid electrolyte interphase (SEI) on lithium metal anodes is a promising strategy to protect Li anodes and enable them to maintain long‐term cycling stability and safety. Herein, the development of a dual‐protective interface as an artificial SEI with high ionic conductivity and appropriate mechanical strength to protect Li anodes from parasitic reactions and dendrite formation is reported. The dual‐protective interface consists of a Prussian blue (PB) inner layer and a reduced graphene oxide (rGO) outer layer. The compact and uniform PB layer with abundant Li‐ion diffusion channels facilitates fast and uniform Li‐ion flux to or from the surface of the Li metal anode, guiding uniform Li deposition without dendrite formation. In addition, the flexible rGO layer on the top of the PB layer enhances the structural integrity of the PB film against severe volume change during repeated Li plating and stripping. As a result, the Li metal anodes with the dual‐protective interfaces show significantly improved cycling stability with high Coulombic efficiency and dendrite‐free morphology. This work provides a new strategy to enhance the stability and safety of Li metal anodes for lithium metal batteries.
Fang, G, Lu, H, Aboulkheyr Es, H, Wang, D, Liu, Y, Warkiani, ME, Lin, G & Jin, D 2021, 'Unidirectional intercellular communication on a microfluidic chip', Biosensors and Bioelectronics, vol. 175, pp. 112833-112833.
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Cell co-culture serves as a standard method to study intercellular communication. However, random diffusion of signal molecules during co-culture may arouse crosstalk among different types of cells and hide directive signal-target responses. Here, a microfluidic chip is proposed to study unidirectional intercellular communication by spatially controlling the flow of the signal molecules. The chip contains two separated chambers connected by two channels where the culture media flows oppositely. A zigzag signal-blocking channel is designed to study the function of a specific signal. The chip is applied to study the unidirectional communication between tumor cells and stromal cells. It shows that the expression of α-smooth muscle actin (a marker of cancer-associated fibroblast (CAF)) of both MRC-5 fibroblasts and mesenchymal stem cells can be up-regulated only by the secreta from invasive MDA-MB-231 cells, but not from non-invasive MCF-7 cells. The proliferation of the tumor cells can be improved by the stromal cells. Moreover, transforming growth factor beta 1 is found as one of the main factors for CAF transformation via the signal-blocking function. The chip achieves unidirectional cell communication along X-axis, signal concentration gradient along Y-axis and 3D cell culture along Z-axis, which provides a useful tool for cell communication studies.
Fang, G, Lu, H, Rodriguez de la Fuente, L, Law, AMK, Lin, G, Jin, D & Gallego‐Ortega, D 2021, 'Mammary Tumor Organoid Culture in Non‐Adhesive Alginate for Luminal Mechanics and High‐Throughput Drug Screening', Advanced Science, vol. 8, no. 21, pp. 1-13.
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AbstractMammary tumor organoids have become a promising in vitro model for drug screening and personalized medicine. However, the dependency on the basement membrane extract (BME) as the growth matrices limits their comprehensive application. In this work, mouse mammary tumor organoids are established by encapsulating tumor pieces in non‐adhesive alginate. High‐throughput generation of organoids in alginate microbeads is achieved utilizing microfluidic droplet technology. Tumor pieces within the alginate microbeads developed both luminal‐ and solid‐like structures and displayed a high similarity to the original fresh tumor in cellular phenotypes and lineages. The mechanical forces of the luminal organoids in the alginate capsules are analyzed with the theory of the thick‐wall pressure vessel (TWPV) model. The luminal pressure of the organoids increase with the lumen growth and can reach 2 kPa after two weeks’ culture. Finally, the mammary tumor organoids are treated with doxorubicin and latrunculin A to evaluate their application as a drug screening platform. It is found that the drug response is related to the luminal size and pressures of organoids. This high‐throughput culture for mammary tumor organoids may present a promising tool for preclinical drug target validation and personalized medicine.
Fang, L, Ruan, M, Yang, S, Qu, X, Chen, H, Zhao, J & Cheng, J 2021, 'Prednisone combined with letrozole reduced risk of ovarian hyperstimulation syndrome (OHSS) in women undergoing long-term gonadotropin-releasing hormone analog treatment', Annals of Palliative Medicine, vol. 10, no. 8, pp. 8837-8847.
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Fatima Shad, K, Soubra, W & Cordato, DJ 2021, 'The role of thymoquinone, a major constituent of Nigella sativa, in the treatment of inflammatory and infectious diseases', Clinical and Experimental Pharmacology and Physiology, vol. 48, no. 11, pp. 1445-1453.
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AbstractNigella sativa (N. sativa) is an annual flowering plant that has been used as a traditional remedy for many centuries. The seed possesses a large variety of compounds with thymoquinone (TQ) considered its major but not sole bioactive constituent. Supercritical fluid extraction, geographical location, and oxidative status of N. sativa produces the highest yield of essential oil content including TQ. Thymoquinone is lipophilic, heat and light sensitive with low oral bioavailability and rapid elimination that have significantly inhibited its pharmacological development. Novel developments in nanoparticulate‐based oral administration, nasal spray and transdermal delivery may allow the clinical development of N. sativa and TQ as therapeutic agents. Animal and human studies indicate a potential role of N. sativa seed oil and TQ for a diverse range of disease processes including hypertension, dyslipidaemia, type 2 diabetes mellitus, arthritis, asthma, bacterial and viral infections, neurological and dermatological disorders, as it belongs to the group of pan‐assay interference compounds. This review outlines the pharmacological properties of N. sativa and TQ and their potential wide application for a large variety of human diseases. The paper will focus on recent studies of the anti‐inflammatory and antiviral properties that make N. sativa and TQ promising therapeutic agents targeting contemporary inflammatory and infectious diseases including Covid 19.
Fernandez, E, Ostrowski, M, Siboni, N, Seymour, JR & Petrou, K 2021, 'Uptake of Dimethylsulfoniopropionate (DMSP) by Natural Microbial Communities of the Great Barrier Reef (GBR), Australia', Microorganisms, vol. 9, no. 9, pp. 1891-1891.
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Dimethylsulfoniopropionate (DMSP) is a key organic sulfur compound that is produced by many phytoplankton and macrophytes and is ubiquitous in marine environments. Following its release into the water column, DMSP is primarily metabolised by heterotrophic bacterioplankton, but recent evidence indicates that non-DMSP producing phytoplankton can also assimilate DMSP from the surrounding environment. In this study, we examined the uptake of DMSP by communities of bacteria and phytoplankton within the waters of the Great Barrier Reef (GBR), Australia. We incubated natural GBR seawater with DMSP and quantified the uptake of DMSP by different fractions of the microbial community (>8 µm, 3–8 µm, <3 µm). We also evaluated how microbial community composition and the abundances of DMSP degrading genes are influenced by elevated dissolved DMSP levels. Our results showed uptake and accumulation of DMSP in all size fractions of the microbial community, with the largest fraction (>8 µm) forming the dominant sink, increasing in particulate DMSP by 44–115% upon DMSP enrichment. Longer-term incubations showed however, that DMSP retention was short lived (<24 h) and microbial responses to DMSP enrichment differed depending on the community carbon and sulfur demand. The response of the microbial communities from inside the reef indicated a preference towards cleaving DMSP into the climatically active aerosol dimethyl sulfide (DMS), whereas communities from the outer reef were sulfur and carbon limited, resulting in more DMSP being utilised by the cells. Our results show that DMSP uptake is shared across members of the microbial community, highlighting larger phytoplankton taxa as potentially relevant DMSP reservoirs and provide new information on sulfur cycling as a function of community metabolism in deeper, oligotrophic GBR waters.
Finkelstein, DI, Billings, JL, Adlard, PA, Ayton, S, Sedjahtera, A, Masters, CL, Wilkins, S, Shackleford, DM, Charman, SA, Bal, W, Zawisza, IA, Kurowska, E, Gundlach, AL, Ma, S, Bush, AI, Hare, DJ, Doble, PA, Crawford, S, Gautier, ECL, Parsons, J, Huggins, P, Barnham, KJ & Cherny, RA 2021, 'Correction to: The novel compound PBT434 prevents iron mediated neurodegeneration and alpha-synuclein toxicity in multiple models of Parkinson’s disease', Acta Neuropathologica Communications, vol. 9, no. 1.
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Following publication of the original article [1], the author identified an error in Fig. 4E. The data and statistics were correct, but the synaptophysin blot was incorrect. The incorrect (Fig. 1) and correct figure (Fig. 2) are shown in this correction article. (Figure presented.).
Fitzpatrick, KJ, Rohlf, HJ, Sutherland, TD, Koo, KM, Beckett, S, Okelo, WO, Keyburn, AL, Morgan, BS, Drigo, B, Trau, M, Donner, E, Djordjevic, SP & De Barro, PJ 2021, 'Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains', ACS Sensors, vol. 6, no. 12, pp. 4283-4296.
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The spread of antimicrobial resistance (AMR) is a rapidly growing threat to humankind on both regional and global scales. As countries worldwide prepare to embrace a One Health approach to AMR management, which is one that recognizes the interconnectivity between human, animal, and environmental health, increasing attention is being paid to identifying and monitoring key contributing factors and critical control points. Presently, AMR sensing technologies have significantly progressed phenotypic antimicrobial susceptibility testing (AST) and genotypic antimicrobial resistance gene (ARG) detection in human healthcare. For effective AMR management, an evolution of innovative sensing technologies is needed for tackling the unique challenges of interconnected AMR across various and different health domains. This review comprehensively discusses the modern state-of-play for innovative commercial and emerging AMR sensing technologies, including sequencing, microfluidic, and miniaturized point-of-need platforms. With a unique view toward the future of One Health, we also provide our perspectives and outlook on the constantly changing landscape of AMR sensing technologies beyond the human health domain.
Flórido, M, Chiu, J & Hogg, PJ 2021, 'Influenza A Virus Hemagglutinin Is Produced in Different Disulfide-Bonded States', Antioxidants & Redox Signaling, vol. 35, no. 13, pp. 1081-1092.
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Fowler, AM, Hall, KC, Liggins, GW & Chick, RC 2021, 'Prioritising fished stocks for monitoring and assessment: A decision analysis approach for diverse fisheries of limited commercial value', Ocean & Coastal Management, vol. 199, pp. 105404-105404.
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Fröch, JE, Spencer, L, Kianinia, M, Totonjian, D, Nguyen, M, Dyakonov, V, Toth, M, Kim, S & Aharonovich, I 2021, 'Coupling spin defects in hexagonal boron nitride to monolithic bullseye cavities', Nano Letters: a journal dedicated to nanoscience and nanotechnology, vol. 21, no. 15, pp. 6549-6555.
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Color centers in hexagonal boron nitride (hBN) are becoming an increasinglyimportant building block for quantum photonic applications. Herein, wedemonstrate the efficient coupling of recently discovered spin defects in hBNto purposely designed bullseye cavities. We show that the all monolithic hBNcavity system exhibits an order of magnitude enhancement in the emission of thecoupled boron vacancy spin defects. In addition, by comparative finitedifference time domain modelling, we shed light on the emission dipoleorientation, which has not been experimentally demonstrated at this point.Beyond that, the coupled spin system exhibits an enhanced contrast in opticallydetected magnetic resonance readout and improved signal to noise ratio. Thus,our experimental results supported by simulations, constitute a first steptowards integration of hBN spin defects with photonic resonators for a scalablespin photon interface.
Fronzi, M, Isayev, O, Winkler, DA, Shapter, JG, Ellis, AV, Sherrell, PC, Shepelin, NA, Corletto, A & Ford, MJ 2021, 'Active Learning in Bayesian Neural Networks for Bandgap Predictions of Novel Van der Waals Heterostructures', Advanced Intelligent Systems, vol. 3, no. 11, pp. 2100080-2100080.
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The bandgap is one of the most fundamental properties of condensed matter. However, an accurate calculation of its value, which could potentially allow experimentalists to identify materials suitable for device applications, is very computationally expensive. Here, active machine learning algorithms are used to leverage a limited number of accurate density functional theory calculations to robustly predict the bandgap of a very large number of novel 2D heterostructures. Using this approach, a database of ≈2.2 million bandgap values for various novel 2D van der Waals heterostructures is produced.
Fujise, L, Suggett, DJ, Stat, M, Kahlke, T, Bunce, M, Gardner, SG, Goyen, S, Woodcock, S, Ralph, PJ, Seymour, JR, Siboni, N & Nitschke, MR 2021, 'Unlocking the phylogenetic diversity, primary habitats, and abundances of free‐living Symbiodiniaceae on a coral reef', Molecular Ecology, vol. 30, no. 1, pp. 343-360.
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AbstractDinoflagellates of the family Symbiodiniaceae form mutualistic symbioses with marine invertebrates such as reef‐building corals, but also inhabit reef environments as free‐living cells. Most coral species acquire Symbiodiniaceae horizontally from the surrounding environment during the larval and/or recruitment phase, however the phylogenetic diversity and ecology of free‐living Symbiodiniaceae on coral reefs is largely unknown. We coupled environmental DNA sequencing and genus‐specific qPCR to resolve the community structure and cell abundances of free‐living Symbiodiniaceae in the water column, sediment, and macroalgae and compared these to coral symbionts. Sampling was conducted at two time points, one of which coincided with the annual coral spawning event when recombination between hosts and free‐living Symbiodiniaceae is assumed to be critical. Amplicons of the internal transcribed spacer (ITS2) region were assigned to 12 of the 15 Symbiodiniaceae genera or genera‐equivalent lineages. Community compositions were separated by habitat, with water samples containing a high proportion of sequences corresponding to coral symbionts of the genus Cladocopium, potentially as a result of cell expulsion from in hospite populations. Sediment‐associated Symbiodiniaceae communities were distinct, potentially due to the presence of exclusively free‐living species. Intriguingly, macroalgal surfaces displayed the highest cell abundances of Symbiodiniaceae, suggesting a key role for macroalgae in ensuring the ecological success of corals through maintenance of a continuum between environmental and symbiotic populations of Symbiodiniaceae.
Gaiani, G, Toldrà, A, Andree, KB, Rey, M, Diogène, J, Alcaraz, C, O’Sullivan, CK & Campàs, M 2021, 'Detection of Gambierdiscus and Fukuyoa single cells using recombinase polymerase amplification combined with a sandwich hybridization assay', Journal of Applied Phycology, vol. 33, no. 4, pp. 2273-2282.
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Gaio, D, DeMaere, MZ, Anantanawat, K, Chapman, TA, Djordjevic, SP & Darling, AE 2021, 'Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes', Microbial Genomics, vol. 7, no. 8.
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Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50 000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5 % of which were classified as >70 % complete with a <10 % contamination rate, and 24.4 % were nearly complete genomes. Here, we describe the generation and analysis of those MAGs using time-series samples. The gut microbial communities of piglets appear to follow a highly structured developmental programme in the weeks following weaning, and this development is robust to treatments including an intramuscular antibiotic treatment and two probiotic treatments. The high resolution we obtained allowed us to identify specific taxonomic ‘signatures’ that characterize the gut microbial development immediately after weaning. Additionally, we characterized the carbohydrate repertoire of the organisms resident in the porcine gut. We tracked the abundance shifts of 294 carbohydrate active enzymes, and identified the species and higher-level taxonomic groups carrying each of these enzymes in their MAGs. This knowledge can contribute to the design of probiotics and prebiotic interventions as a means to modify the piglet gut microbiome.
Gaio, D, DeMaere, MZ, Anantanawat, K, Eamens, GJ, Liu, M, Zingali, T, Falconer, L, Chapman, TA, Djordjevic, SP & Darling, AE 2021, 'A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen', GigaScience, vol. 10, no. 6.
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Abstract Background Early weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. As an alternative to antibiotic treatment, studies have previously investigated the potential of probiotics for the prevention of postweaning diarrhea. In order to describe the post-weaning gut microbiota, and to study the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we sampled and processed over 800 faecal time-series samples from 126 piglets and 42 sows. Results Here we report on the largest shotgun metagenomic dataset of the pig gut lumen microbiome to date, consisting of >8 Tbp of shotgun metagenomic sequencing data. The animal trial, the workflow from sample collection to sample processing, and the preparation of libraries for sequencing, are described in detail. We provide a preliminary analysis of the dataset, centered on a taxonomic profiling of the samples, and a 16S-based beta diversity analysis of the mothers and the piglets in the first 5 weeks after weaning. Conclusions This study was conducted to generate a publicly available databank of the faecal metagenome of weaner piglets aged between 3 and 9 weeks old, treated with different probiotic formulations and intramuscular antibiotic treatment. Besides investigating the effects of the probiotic and intramuscular antibiotic treatment, the dataset ...
Gale, A, Fröch, JE, Kianinia, M, Bishop, J, Aharonovich, I & Toth, M 2021, 'Recoil implantation using gas-phase precursor molecules', Nanoscale, vol. 13, no. 20, pp. 9322-9327.
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Schematic illustration of the recoil implantation process by using gas-phase precursor molecules.
Gao, C, Garren, M, Penn, K, Fernandez, VI, Seymour, JR, Thompson, JR, Raina, J-B & Stocker, R 2021, 'Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen', The ISME Journal, vol. 15, no. 12, pp. 3668-3682.
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Abstract Elevated seawater temperatures have contributed to the rise of coral disease mediated by bacterial pathogens, such as the globally distributed Vibrio coralliilyticus, which utilizes coral mucus as a chemical cue to locate stressed corals. However, the physiological events in the pathogens that follow their entry into the coral host environment remain unknown. Here, we present simultaneous measurements of the behavioral and transcriptional responses of V. coralliilyticus BAA-450 incubated in coral mucus. Video microscopy revealed a strong and rapid chemokinetic behavioral response by the pathogen, characterized by a two-fold increase in average swimming speed within 6 min of coral mucus exposure. RNA sequencing showed that this bacterial behavior was accompanied by an equally rapid differential expression of 53% of the genes in the V. coralliilyticus genome. Specifically, transcript abundance 10 min after mucus exposure showed upregulation of genes involved in quorum sensing, biofilm formation, and nutrient metabolism, and downregulation of flagella synthesis and chemotaxis genes. After 60 min, we observed upregulation of genes associated with virulence, including zinc metalloproteases responsible for causing coral tissue damage and algal symbiont photoinactivation, and secretion systems that may export toxins. Together, our results suggest that V. coralliilyticus employs a suite of behavioral and transcriptional responses to rapidly shift into a distinct infection mode within minutes of exposure to the coral microenvironment.
Gao, X, Pandey, S, Kianinia, M, Ahn, J, Ju, P, Aharonovich, I, Shivaram, N & Li, T 2021, 'Femtosecond Laser Writing of Spin Defects in Hexagonal Boron Nitride', ACS Photonics, vol. 8, no. 4, pp. 994-1000.
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Optically active spin defects in wide-bandgap materials have many potential applications in quantum information and quantum sensing. Spin defects in two-dimensional layered van der Waals materials are just emerging to be investigated. Here we demonstrate that optically addressable spin ensembles in hexagonal boron nitride (hBN) can be generated by femtosecond laser irradiation. We observe optically detected magnetic resonance (ODMR) of hBN spin defects created by laser irradiation. We show that the creation of spin defects in hBN is strongly affected by the pulse energy of the femtosecond laser. When the laser pulse number is less than a few thousand, the pulse number only affects the density of the defects but not the type of defects. With proper laser parameters, spin defects can be generated with a high probability of success. Our work provides a convenient way to create spin defects in hBN by femtosecond laser writing, which shows promising prospects for quantum technologies.
Garces, LPDM & Cheang, GHL 2021, 'A Numerical Approach to Pricing Exchange Options under Stochastic Volatility and Jump-Diffusion Dynamics', Quantitative Finance, vol. 21, no. 12, pp. 2025-2054.
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We consider a method of lines (MOL) approach to determine prices of Europeanand American exchange options when underlying asset prices are modelled withstochastic volatility and jump-diffusion dynamics. As the MOL, as with anyother numerical scheme for PDEs, becomes increasingly complex when higherdimensions are involved, we first simplify the problem by transforming theexchange option into a call option written on the ratio of the yield processesof the two assets. This is achieved by taking the second asset yield process asthe numeraire. We also characterize the near-maturity behavior of the earlyexercise boundary of the American exchange option and analyze how modelparameters affect this behavior. Using the MOL scheme, we conduct a numericalcomparative static analysis of exchange option prices with respect to the modelparameters and investigate the impact of stochastic volatility and jumps tooption prices. We also consider the effect of boundary conditions atfar-but-finite limits of the computational domain on the overall efficiency ofthe MOL scheme. Toward these objectives, a brief exposition of the MOL and howit can be implemented on computing software are provided.
Geange, SR, Arnold, PA, Catling, AA, Coast, O, Cook, AM, Gowland, KM, Leigh, A, Notarnicola, RF, Posch, BC, Venn, SE, Zhu, L & Nicotra, AB 2021, 'The thermal tolerance of photosynthetic tissues: a global systematic review and agenda for future research', New Phytologist, vol. 229, no. 5, pp. 2497-2513.
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SummaryUnderstanding plant thermal tolerance is fundamental to predicting impacts of extreme temperature events that are increasing in frequency and intensity across the globe. Extremes, not averages, drive species evolution, determine survival and increase crop performance. To better prioritize agricultural and natural systems research, it is crucial to evaluate how researchers are assessing the capacity of plants to tolerate extreme events. We conducted a systematic review to determine how plant thermal tolerance research is distributed across wild and domesticated plants, growth forms and biomes, and to identify crucial knowledge gaps. Our review shows that most thermal tolerance research examines cold tolerance of cultivated species; c. 5% of articles consider both heat and cold tolerance. Plants of extreme environments are understudied, and techniques widely applied in cultivated systems are largely unused in natural systems. Lastly, we find that lack of standardized methods and metrics compromises the potential for mechanistic insight. Our review provides an entry point for those new to the methods used in plant thermal tolerance research and bridges often disparate ecological and agricultural perspectives for the more experienced. We present a considered agenda of thermal tolerance research priorities to stimulate efficient, reliable and repeatable research across the spectrum of plant thermal tolerance.
Gertner, DS, Bishop, DP, Oglobline, A & Padula, MP 2021, 'Enhancing Coverage of Phosphatidylinositol Species in Canola Through Specialised Liquid Chromatography-Mass Spectrometry Buffer Conditions', Journal of Chromatography A, vol. 1637, pp. 461860-461860.
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Phosphatidylinositols (PIs) constitute a minor class of phospholipid with wide-spread influence throughout various cellular functions. Monitoring the distribution of these lipids can therefore provide insight as to the state of cellular processes or reveal the development of various pathologies. The speciation of these compounds is often performed either as part of a comprehensive characterisation of lipids, or specifically targeted using the same methods, however, such methods were intended to maximise coverage of lipid classes rather than provide an in-depth analysis of any single class. In the particular case of PIs, the majority of reported molecular diversity is limited to a small proportion of the already minor class, as such the cursory glance enabled by such methods is insufficient. Therefore, this work compared the suitability of both established and novel LC-MS buffers with the aim of maximising the ionisation efficiency of PIs, in an attempt to enhance coverage of the class. Through experimentation, it was determined that a 0.25 mM ammonium fluoride buffer provided up to a 6-fold increase in signal intensity, and on average a 38-fold increase in the signal-to-noise ratio. Using these new conditions, 14 PI species, and 12 PI candidates were identified within a dilute lipid extract sourced from canola seed, compared to 0 species identified using the generalised method. As a result, it is suggested that this procedure has yielded the highest number of PI species identifications for a sample of this concentration. Methods which therefore intend to characterise PI species in dilute quantities, such as those extracted from mammalian cells, are henceforth provided with the means to conduct more comprehensive characterisations.
Gibbs, MC, Parker, LM, Scanes, E, Byrne, M, O’Connor, WA & Ross, PM 2021, 'Adult exposure to ocean acidification and warming leads to limited beneficial responses for oyster larvae', ICES Journal of Marine Science, vol. 78, no. 6, pp. 2017-2030.
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AbstractThere is a need to understand the responses of marine molluscs in this era of rapid climate change. Transgenerational plasticity that results in resilient offspring provides a mechanism for rapid acclimation of marine organisms to climate change. This study tested the hypothesis that adult parental exposure to elevated pCO2 and warming will have transgenerational benefits for offspring in the oysters Saccostrea glomerata and Crassostrea gigas. Adult S. glomerata and C. gigas were exposed to orthogonal treatments of ambient and elevated pCO2, and ambient and elevated temperature for 8 weeks. Gametes were collected and fertilized, larvae were then reared for 9 days under ambient and elevated pCO2. Egg lipidome and larval morphology and lipidome were measured. Parental exposure to warming and elevated pCO2 led to limited beneficial transgenerational responses for eggs and larvae of S. glomerata and C. gigas. Overall, larvae of S. glomerata were more sensitive than C. gigas, and both species had some capacity for transgenerational plasticity. This study supports the idea that transgenerational plasticity acts as an acclimatory mechanism for marine organisms to cope with the stress of climate change, but there are limitations, and it may not be a panacea or act equally in different species.
Gibbs, MC, Parker, LM, Scanes, E, Byrne, M, O’Connor, WA & Ross, PM 2021, 'Adult exposure to ocean acidification and warming remains beneficial for oyster larvae following starvation', ICES Journal of Marine Science, vol. 78, no. 5, pp. 1587-1598.
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Abstract Climate change is expected to warm and acidify oceans and alter the phenology of phytoplankton, creating a mismatch between larvae and their food. Transgenerational plasticity (TGP) may allow marine species to acclimate to climate change; however, it is expected that this may come with elevated energetic demands. This study used the oysters, Saccostrea glomerata and Crassostrea gigas, to test the effects of adult parental exposure to elevated pCO2 and temperature on larvae during starvation and recovery. It was anticipated that beneficial effects of TGP will be limited when larvae oyster are starved. Transgenerational responses and lipid reserves of larvae were measured for 2 weeks. Larvae of C. gigas and S. glomerata from parents exposed to elevated pCO2 had greater survival when exposed to elevated CO2, but this differed between species and temperature. For S. glomerata, survival of larvae was greatest when the conditions experienced by larvae matched the condition of their parents. For C. gigas, survival of larvae was greater when parents and larvae were exposed to elevated pCO2. Larvae of both species used lipids when starved. The total lipid content was dependent on parental exposure and temperature. Against expectations, the beneficial TGP responses of larvae remained, despite starvation.
Gibbs, MC, Parker, LM, Scanes, E, Byrne, M, O'Connor, WA & Ross, PM 2021, 'Energetic lipid responses of larval oysters to ocean acidification', Marine Pollution Bulletin, vol. 168, pp. 112441-112441.
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Climate change will increase energetic demands on marine invertebrate larvae and make planktonic food more unpredictable. This study determined the impact of ocean acidification on larval energetics of the oysters Saccostrea glomerata and Crassostrea gigas. Larvae of both oysters were reared until the 9-day-old, umbonate stage under orthogonal combinations of ambient and elevated p CO 2 (340 and 856 μatm) and food was limited. Elevated p CO 2 reduced the survival, size and larval energetics, larvae of C. gigas being more resilient than S. glomerata. When larvae were fed, elevated p CO 2 reduced lipid levels across all lipid classes. When larvae were unfed elevated p CO 2 resulted in increased lipid levels and mortality. Ocean acidification and food will interact to limit larval energetics. Larvae of S. glomerata will be more impacted than C. gigas and this is of concern given their aquacultural status and ecological function.
Ginés, I, Gaiani, G, Ruhela, A, Skouridou, V, Campàs, M & Masip, L 2021, 'Nucleic acid lateral flow dipstick assay for the duplex detection of and', Harmful Algae, vol. 110, pp. 102135-102135.
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Glushkov, E, Mendelson, N, Chernev, A, Ritika, R, Lihter, M, Zamani, RR, Comtet, J, Navikas, V, Aharonovich, I & Radenovic, A 2021, 'Direct Growth of Hexagonal Boron Nitride on Photonic Chips for High-Throughput Characterization', ACS Photonics, vol. 8, no. 7, pp. 2033-2040.
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Adapting optical microscopy methods for nanoscale characterization of defects in two-dimensional (2D) materials is a vital step for photonic on-chip devices. To increase the analysis throughput, waveguide-based on-chip imaging platforms have been recently developed. Their inherent disadvantage, however, is the necessity to transfer the 2D material from the growth substrate to the imaging chip, which introduces nonuniform material coverage and contamination, potentially altering the characterization results. Here we present a unique approach to circumvent these shortfalls by directly growing a widely used 2D material (hexagonal boron nitride, hBN) on silicon nitride chips and optically characterizing the defects in the intact as-grown material. We compare the direct growth approach to the standard PMMA-assisted wet transfer method and confirm the clear advantages of the direct growth. While demonstrated with hBN in the current work, the method can be extended to other 2D materials.
Godecke, E, Armstrong, E, Rai, T, Ciccone, N, Rose, ML, Middleton, S, Whitworth, A, Holland, A, Ellery, F, Hankey, GJ, Cadilhac, DA & Bernhardt, J 2021, 'A randomized control trial of intensive aphasia therapy after acute stroke: The Very Early Rehabilitation for SpEech (VERSE) study', International Journal of Stroke, vol. 16, no. 5, pp. 556-572.
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Background Effectiveness of early intensive aphasia rehabilitation after stroke is unknown. The Very Early Rehabilitation for SpEech trial (VERSE) aimed to determine whether intensive aphasia therapy, beginning within 14 days after stroke, improved communication recovery compared to usual care. Methods Prospective, randomized, single-blinded trial conducted at 17 acute-care hospitals across Australia/New Zealand from 2014 to 2018. Participants with aphasia following acute stroke were randomized to receive usual care (direct usual care aphasia therapy), or one of two higher intensity regimens (20 sessions of either non-prescribed (usual care-plus or prescribed (VERSE) direct aphasia therapy). The primary outcome was improvement of communication on the Western Aphasia Battery-Revised Aphasia Quotient (AQ) at 12 weeks after stroke. Our pre-planned intention to treat analysis combined high intensity groups for the primary outcome. Findings Among 13,654 acute stroke patients screened, 25% (3477) had aphasia, of whom 25% (866) were eligible and 246 randomized to usual care ( n = 81; 33%), usual care-plus ( n = 82; 33%) or VERSE ( n = 83; 34%). At 12 weeks after stroke, the primary outcome was assessed in 217 participants (88%); 14 had died, 9 had withdrawn, and 6 were too unwell for assessment. Communication recovery was 50.3% (95% CI 45.7–54.8) in the high intensity group ( n = 147) and 52.1% (95% CI 46.1–58.1) in the usual care group ( n = 70; difference −1.8, 95% CI −8.7–5.0). There was no difference between groups in non-fatal or fatal adverse events ( p = 0.72). Interpretation Early, intensive aphasia therapy did not improve communication recovery within 12 weeks post stroke compared to usual care.
Goggins, BJ, Minahan, K, Sherwin, S, Soh, WS, Pryor, J, Bruce, J, Liu, G, Mathe, A, Knight, D, Horvat, JC, Walker, MM & Keely, S 2021, 'Pharmacological HIF-1 stabilization promotes intestinal epithelial healing through regulation of α-integrin expression and function', American Journal of Physiology-Gastrointestinal and Liver Physiology, vol. 320, no. 4, pp. G420-G438.
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HIF-1 plays an important role in epithelial restitution, selectively inducing integrins α6 and α2 to promote migration and proliferation, respectively. HIF-stabilizing prolyl-hydroxylase inhibitors accelerate intestinal mucosal healing by inducing epithelial integrin expression.
Gomez, HM, Pillar, AL, Brown, AC, Kim, RY, Ali, MK, Essilfie, A-T, Vanders, RL, Frazer, DM, Anderson, GJ, Hansbro, PM, Collison, AM, Jensen, ME, Murphy, VE, Johnstone, DM, Reid, D, Milward, EA, Donovan, C & Horvat, JC 2021, 'Investigating the Links between Lower Iron Status in Pregnancy and Respiratory Disease in Offspring Using Murine Models', Nutrients, vol. 13, no. 12, pp. 4461-4461.
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Maternal iron deficiency occurs in 40–50% of all pregnancies and is associated with an increased risk of respiratory disease and asthma in children. We used murine models to examine the effects of lower iron status during pregnancy on lung function, inflammation and structure, as well as its contribution to increased severity of asthma in the offspring. A low iron diet during pregnancy impairs lung function, increases airway inflammation, and alters lung structure in the absence and presence of experimental asthma. A low iron diet during pregnancy further increases these major disease features in offspring with experimental asthma. Importantly, a low iron diet increases neutrophilic inflammation, which is indicative of more severe disease, in asthma. Together, our data demonstrate that lower dietary iron and systemic deficiency during pregnancy can lead to physiological, immunological and anatomical changes in the lungs and airways of offspring that predispose to greater susceptibility to respiratory disease. These findings suggest that correcting iron deficiency in pregnancy using iron supplements may play an important role in preventing or reducing the severity of respiratory disease in offspring. They also highlight the utility of experimental models for understanding how iron status in pregnancy affects disease outcomes in offspring and provide a means for testing the efficacy of different iron supplements for preventing disease.
Gong, Y, Xu, Z-Q, Li, D, Zhang, J, Aharonovich, I & Zhang, Y 2021, 'Two-Dimensional Hexagonal Boron Nitride for Building Next-Generation Energy-Efficient Devices', ACS Energy Letters, vol. 6, no. 3, pp. 985-996.
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Gonzalez de Vega, R, Cameron, A, Clases, D, Dodgen, TM, Doble, PA & Bishop, DP 2021, '“Simultaneous targeted and non-targeted analysis of per- and polyfluoroalkyl substances in environmental samples by liquid chromatography-ion mobility-quadrupole time of flight-mass spectrometry and mass defect analysis”', Journal of Chromatography A, vol. 1653, pp. 462423-462423.
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Per- and polyfluoroalkyl substances (PFAS) represent a large group of synthetic organic compounds which exhibit unique properties and have been extensively used for consumer and industrial products, resulting in a widespread presence in the environment. Regulation requiring PFAS monitoring has been implemented worldwide due to their potential health and eco-toxicological effects. Targeted methods are commonly used to monitor between twenty to forty PFAS compounds, representing only a small fraction of the number of compounds that may be present. Consequently, there is an increasing interest in complementary non-targeted methods to screen and identify unknown PFAS compounds with the aim to improve knowledge and to generate more accurate models regarding their environmental mobility and persistence. This work details the development of a method that simultaneously provided targeted and non-targeted PFAS analysis. Ultra-high performance liquid chromatography (UHPLC) was coupled to ion mobility-quadrupole time of flight-mass spectrometry (IMS-QTOF-MS) and used to quantify known and screen unknown PFAS in environmental samples collected within the greater Sydney basin (Australia). The method was validated for the quantification of 14 sulfonate-based PFAS, and a non-targeted data analysis workflow was developed using a combination of mass defect analysis with common fragment and neutral loss filtering to identify fluorine-containing species. The optimised method was applied to the environmental samples and enabled the determination of 3-7 compounds from the targeted list and the detection of a further 56-107 untargeted PFAS. This simultaneous analysis reduces the complexity of multiple analyses, and allows for greater interrogation of the full PFAS load in environmental samples.
Gonzalez de Vega, R, Goyen, S, Lockwood, TE, Doble, PA, Camp, EF & Clases, D 2021, 'Characterisation of microplastics and unicellular algae in seawater by targeting carbon via single particle and single cell ICP-MS', Analytica Chimica Acta, vol. 1174, pp. 338737-338737.
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The discharge of plastic waste and subsequent formation and global distribution of microplastics (MPs) has caused great concern and highlighted the need for dedicated methods to characterise MPs in complex environmental matrices like seawater. Single particle inductively coupled plasma - mass spectrometry (SP ICP-MS) is an elegant method for the rapid analysis of nano- and microparticles and to characterise number concentrations, mass, and size distributions. However, the analysis of carbon (C)-based microstructures such as MPs by SP ICP-MS is at an early stage. This paper investigates various strategies to improve figures of merit to detect and characterise MPs in complex matrices, such as seawater. Ten methods operating distinct acquisition modes with various collision/reaction gases, tandem MS (ICP-MS/MS) and targeting 12C or 13C were developed and compared for the analysis of polystyrene-based MPs standards in ultra-pure water and seawater. The robust analysis of MPs in seawater was accomplished by on-line aerosol dilution enabling repeatable size calibration while minimising drift effects. However, the direct analysis of seawater decreased ion transmission and required matrix-matching for accurate size calibration. Analysis of the 12C isotope instead of 13C improved the size detection limits (sDL) to 0.62 μm in ultra-pure water and to 0.96 μm in seawater. ICP-MS/MS methods decreased ion transmission but also reduced background signal and increased selectivity, particularly in the presence of spectral interferences. In the second part of this study, it was demonstrated that the developed methods were applicable for the analysis of C in unicellular organisms and allowed calibration of physical dimensions. This is relevant for the investigation and understanding of phenotypical traits associated, for example, with climate change resilience as well as oceanic C storage. SP/SC ICP-MS was employed to target five different intact Symbiodiniaceae algae str...
Goodswen, SJ, Barratt, JLN, Kennedy, PJ, Kaufer, A, Calarco, L & Ellis, JT 2021, 'Machine learning and applications in microbiology', FEMS Microbiology Reviews, vol. 45, no. 5, p. fuab015.
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ABSTRACT To understand the intricacies of microorganisms at the molecular level requires making sense of copious volumes of data such that it may now be humanly impossible to detect insightful data patterns without an artificial intelligence application called machine learning. Applying machine learning to address biological problems is expected to grow at an unprecedented rate, yet it is perceived by the uninitiated as a mysterious and daunting entity entrusted to the domain of mathematicians and computer scientists. The aim of this review is to identify key points required to start the journey of becoming an effective machine learning practitioner. These key points are further reinforced with an evaluation of how machine learning has been applied so far in a broad scope of real-life microbiology examples. This includes predicting drug targets or vaccine candidates, diagnosing microorganisms causing infectious diseases, classifying drug resistance against antimicrobial medicines, predicting disease outbreaks and exploring microbial interactions. Our hope is to inspire microbiologists and other related researchers to join the emerging machine learning revolution.
Goodswen, SJ, Kennedy, PJ & Ellis, JT 2021, 'Applying Machine Learning to Predict the Exportome of Bovine and Canine Babesia Species That Cause Babesiosis', Pathogens, vol. 10, no. 6, pp. 660-660.
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Babesia infection of red blood cells can cause a severe disease called babesiosis in susceptible hosts. Bovine babesiosis causes global economic loss to the beef and dairy cattle industries, and canine babesiosis is considered a clinically significant disease. Potential therapeutic targets against bovine and canine babesiosis include members of the exportome, i.e., those proteins exported from the parasite into the host red blood cell. We developed three machine learning-derived methods (two novel and one adapted) to predict for every known Babesia bovis, Babesia bigemina, and Babesia canis protein the probability of being an exportome member. Two well-studied apicomplexan-related species, Plasmodium falciparum and Toxoplasma gondii, with extensive experimental evidence on their exportome or excreted/secreted proteins were used as important benchmarks for the three methods. Based on 10-fold cross validation and multiple train–validation–test splits of training data, we expect that over 90% of the predicted probabilities accurately provide a secretory or non-secretory indicator. Only laboratory testing can verify that predicted high exportome membership probabilities are creditable exportome indicators. However, the presented methods at least provide those proteins most worthy of laboratory validation and will ultimately save time and money.
Goodswen, SJ, Kennedy, PJ & Ellis, JT 2021, 'Computational Antigen Discovery for Eukaryotic Pathogens Using Vacceed', vol. 2183, pp. 29-42.
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© Springer Science+Business Media, LLC, part of Springer Nature 2021. Bioinformatics programs have been developed that exploit informative signals encoded within protein sequences to predict protein characteristics. Unfortunately, there is no program as yet that can predict whether a protein will induce a protective immune response to a pathogen. Nonetheless, predicting those pathogen proteins most likely from those least likely to induce an immune response is feasible when collectively using predicted protein characteristics. Vacceed is a computational pipeline that manages different standalone bioinformatics programs to predict various protein characteristics, which offer supporting evidence on whether a protein is secreted or membrane -associated. A set of machine learning algorithms predicts the most likely pathogen proteins to induce an immune response given the supporting evidence. This chapter provides step by step descriptions of how to configure and operate Vacceed for a eukaryotic pathogen of the user’s choice.
Gottscholl, A, Diez, M, Soltamov, V, Kasper, C, Krauße, D, Sperlich, A, Kianinia, M, Bradac, C, Aharonovich, I & Dyakonov, V 2021, 'Spin defects in hBN as promising temperature, pressure and magnetic field quantum sensors', Nature Communications, vol. 12, no. 1, pp. 1-8.
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AbstractSpin defects in solid-state materials are strong candidate systems for quantum information technology and sensing applications. Here we explore in details the recently discovered negatively charged boron vacancies (VB−) in hexagonal boron nitride (hBN) and demonstrate their use as atomic scale sensors for temperature, magnetic fields and externally applied pressure. These applications are possible due to the high-spin triplet ground state and bright spin-dependent photoluminescence of the VB−. Specifically, we find that the frequency shift in optically detected magnetic resonance measurements is not only sensitive to static magnetic fields, but also to temperature and pressure changes which we relate to crystal lattice parameters. We show that spin-rich hBN films are potentially applicable as intrinsic sensors in heterostructures made of functionalized 2D materials.
Gottscholl, A, Diez, M, Soltamov, V, Kasper, C, Sperlich, A, Kianinia, M, Bradac, C, Aharonovich, I & Dyakonov, V 2021, 'Room temperature coherent control of spin defects in hexagonal boron nitride', Science Advances, vol. 7, no. 14, pp. 1-6.
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Atomic defects in 2D materials show excellent spin coherence time and become promising contenders for quantum applications.
Green, DW, Watson, JA, Ben-Nissan, B, Watson, GS & Stamboulis, A 2021, 'Synthetic tissue engineering with smart, cytomimetic protocells', Biomaterials, vol. 276, pp. 120941-120941.
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Grottoli, AG, Toonen, RJ, van Woesik, R, Vega Thurber, R, Warner, ME, McLachlan, RH, Price, JT, Bahr, KD, Baums, IB, Castillo, KD, Coffroth, MA, Cunning, R, Dobson, KL, Donahue, MJ, Hench, JL, Iglesias‐Prieto, R, Kemp, DW, Kenkel, CD, Kline, DI, Kuffner, IB, Matthews, JL, Mayfield, AB, Padilla‐Gamiño, JL, Palumbi, S, Voolstra, CR, Weis, VM & Wu, HC 2021, 'Increasing comparability among coral bleaching experiments', Ecological Applications, vol. 31, no. 4.
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AbstractCoral bleaching is the single largest global threat to coral reefs worldwide. Integrating the diverse body of work on coral bleaching is critical to understanding and combating this global problem. Yet investigating the drivers, patterns, and processes of coral bleaching poses a major challenge. A recent review of published experiments revealed a wide range of experimental variables used across studies. Such a wide range of approaches enhances discovery, but without full transparency in the experimental and analytical methods used, can also make comparisons among studies challenging. To increase comparability but not stifle innovation, we propose a common framework for coral bleaching experiments that includes consideration of coral provenance, experimental conditions, and husbandry. For example, reporting the number of genets used, collection site conditions, the experimental temperature offset(s) from the maximum monthly mean (MMM) of the collection site, experimental light conditions, flow, and the feeding regime will greatly facilitate comparability across studies. Similarly, quantifying common response variables of endosymbiont (Symbiodiniaceae) and holobiont phenotypes (i.e., color, chlorophyll, endosymbiont cell density, mortality, and skeletal growth) could further facilitate cross‐study comparisons. While no single bleaching experiment can provide the data necessary to determine global coral responses of all corals to current and future ocean warming, linking studies through a common framework as outlined here, would help increase comparability among experiments, facilitate synthetic insights into the causes and underlying mechanisms of coral bleaching, and reveal unique bleaching responses among genets, species, and regions. Such a collaborative framework that fosters transparency in methods used would strengthen comparisons among studies that can help inform coral reef management and facilitate conserv...
Grzywacz, A, Jarmusz, M, Walczak, K, Skowronek, R, Johnston, NP & Szpila, K 2021, 'DNA Barcoding Identifies Unknown Females and Larvae of Fannia R.-D. (Diptera: Fanniidae) from Carrion Succession Experiment and Case Report', Insects, vol. 12, no. 5, pp. 381-381.
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Application of available keys to European Fanniidae did not facilitate unequivocal species identification for third instar larvae and females of Fannia Robineau-Desvoidy, 1830 collected during a study of arthropod succession on pig carrion. To link these samples to known species, we took the advantage of molecular identification methods and compared newly obtained cytochrome oxidase subunit I (COI) barcode sequences against sequences deposited in reference databases. As an outcome of the results obtained, we describe for the first time a third instar larva of Fannia nigra Malloch, 1910 and Fannia pallitibia (Rondani, 1866) and a female of Fannia collini d’Assis-Fonseca, 1966. We provide combinations of characters allowing for discrimination of described insects from other Fanniidae. We provide an update for the key by Rozkošný et al. 1997, which allows differentiation between females of F. collini and other species of Fanniidae. Additionally, we provide a case of a human cadaver discovered in Southern Poland and insect fauna associated with it as the first report of F. nigra larvae developing on a human body.
Gu, Y, Guo, Z, Yuan, W, Kong, M, Liu, Y, Liu, Y, Gao, Y, Feng, W, Wang, F, Zhou, J, Jin, D & Li, F 2021, 'Author Correction: High-sensitivity imaging of time-domain near-infrared light transducer', Nature Photonics, vol. 15, no. 9, pp. 712-712.
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Guan, M & Jin, D 2021, 'Dark bridge at the interface of hybrid nanosystem: Lanthanide-triplet NIR photosensitization', Chem, vol. 7, no. 6, pp. 1412-1414.
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“Dark” organic triplet states typically require visible light to activate via singlet-triplet intersystem crossing. In this issue of Chem, Deng and co-workers report a new near-infrared photosensitization strategy using lanthanide-doped nanoparticles to directly activate the dark triplet states of organic photosensitizers, significantly reducing the power requirement of irradiance.
Guo, X, Wang, S, Yu, L, Guo, C, Yan, P, Gao, H & Liu, H 2021, 'Dense SnS2 nanoplates vertically anchored on a graphene aerogel for pseudocapacitive sodium storage', Materials Chemistry Frontiers, vol. 6, no. 3, pp. 325-332.
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A 2D heterostructure with dense SnS2 nanoplates vertically anchored on a graphene aerogel (SnS2@GA) was achieved via a controlled self-assembly process followed by a thermally induced sulfidation treatment for high-performance sodium-ion batteries.
Guo, Z, Jasin Arachchige, L, Qiu, S, Zhang, X, Xu, Y, Langford, SJ & Sun, C 2021, 'p-Block element-doped silicon nanowires for nitrogen reduction reaction: a DFT study', Nanoscale, vol. 13, no. 35, pp. 14935-14944.
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B-doping on 1D SiNWs can reduce N2into NH3with an ultralow overpotential of 0.34 V and suppressed HER performance.
Guo, Z, Qiu, S, Li, H, Xu, Y, Langford, SJ & Sun, C 2021, 'Electrocatalytic Nitrogen Reduction Performance of Si‐doped 2D Nanosheets of Boron Nitride Evaluated via Density Functional Theory', ChemCatChem, vol. 13, no. 4, pp. 1239-1245.
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AbstractElectrochemical nitrogen fixation under ambient conditions is proposed as a sustainable alternative to the traditional Haber‐Bosch method to combat both a global energy crisis and climate change. However, effective catalysts for electrocatalytic nitrogen reduction reaction (eNRR) under ambient conditions, a crucial part for the electrocatalysis system, still face large challenges of low Faradic efficiency (FE) and low yield of ammonia. Here, we propose Si‐doped BN 2D nanosheets (BNNS) as a new class of metal‐free catalysts, and computationally study their performance in eNRR by density functional theory (DFT). The calculations show that the Si atom in the boron‐edge site exhibits the highest activity with the over‐potential (η) of 1.06 V from the first hydrogenation step, which is close in value to the benchmark of this reaction, the flat Ru(0001) surface (η=0.92 V). Moreover, Si‐doping can greatly enhance the conductivity of pristine BNNS, making it a good candidate for electrocatalysis. Overall, this research opens up a new direction of designing high‐performance Si‐based 2D catalysts for dinitrogen fixation beyond the hotspot research of boron‐ or transition metal‐based catalysts.
Guo, Z, Qiu, S, Li, H, Xu, Y, Langford, SJ & Sun, C 2021, 'Evaluation of electrocatalytic dinitrogen reduction performance on diamond carbon via density functional theory', Diamond and Related Materials, vol. 111, pp. 108210-108210.
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Carbon-based electrocatalysts for nitrogen fixation under ambient conditions has attracted tremendous attention but still encounter great challenges of low Faradic efficiency (FE) and a sluggish kinetics. Inspired by intrinsic defects (vacancies, edges and dislocation) on graphene showing activity towards oxygen reduction reaction (ORR) and nitrogen reduction reaction (NRR), here, two commonly exposed surfaces of diamond carbon, i.e., C(111) & C(110), were calculated for electrocatalytic nitrogen reduction reaction (eNRR) by the density functional theory (DFT) method, and calculations show that, compared with C(110), C(111) could be highly promising towards eNRR with a low over-potential (η) of 0.57 V (ΔGmax = 0.73 eV, η = 0.57 V), which are distinctly less than that (ΔGmax = 1.08 eV, η = 0.92 V) of flat benchmark Ru(0001) catalysts. Importantly, these two surfaces are shown to exhibit the suppression of hydrogen evolution reaction (HER). This work is the first reported indication that the low-coordinated carbons (LCCs) on sp3-hybridized diamond-carbon framework are active for eNRR, which gives a brand-new direction of designing/synthesizing sp3-configured diamond-carbon-composited catalysts for eNRR.
Gupta, A, Corzo, R, Akmeemana, A, Lambert, K, Jimenez, K, Curran, JM & Almirall, JR 2021, 'Dimensionality reduction of multielement glass evidence to calculate likelihood ratios', Journal of Chemometrics, vol. 35, no. 1.
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AbstractDimensionality reduction of multivariate elemental concentrations of glass is reported for computing likelihood ratios (LRs). TheLRs calculated using principal component analysis (PCA) and a post hoc calibration steps result in very low (<1%) false inclusions when comparing glass samples known to originate from different sources and very low (<1%) false exclusions when comparing glass samples known to originate from the same source. TheLRs calculated using the novel PCA approach are compared with previously reportedLRs calculated using a more computationally intensive Multivariate Kernel (MVK) model followed by a calibration step using a Pool Adjacent Violators (PAV) algorithm. In both cases, the calibratedLRs limited the magnitude of the misleading evidence, providing only weak to moderate support for the incorrect hypotheses. Most of the different pairs that were found to be falsely included were explained by chemical relatedness (same manufacturer of the glass sources in very close time interval between manufacture). The computation ofLRs using dimensionality reduction of elemental concentrations using PCA may transfer to other multivariate data‐generating evidence types.
Gupta, A, Ghosh, S, Thakur, MK, Zhou, J, (Ken) Ostrikov, K, Jin, D & Chattopadhyay, S 2021, 'Up-conversion hybrid nanomaterials for light- and heat-driven applications', Progress in Materials Science, vol. 121, pp. 100838-100838.
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Composites or hybrid materials offer diverse properties not achievable in pure materials. Here we critically review the interesting and controllable fluorescence and photothermal properties of diverse hybrid materials containing up-conversion nanoparticles (UCNPs). These hybrids couple plasmons, photonic crystals, bio-surfaces, and two dimensional (2D) materials to the UCNPs, offering optical non-linearity, and enable effective photo-electro-thermal control leading to new light and heat driven applications. Among the light driven applications, coupling of UCNPs with graphene and molybdenum disulfide (MoS2) enables photodetectors with better photoresponse, and broader spectral range not accessible to individual components. Irradiated MoS2 coupled-UCNPs is a new paradigm in resistive random access memory devices. Conjugation of graphene and perovskites, with the UCNPs, have led to novel optical limiting phenomenon and better solar cells. Examples of new opportunities offered by UCNPs in heat driven applications are photothermal water desalination using solar daylight and photothermal disintegration of fat droplets in obesity treatment. Phonons, manifesting as heat, can also be utilized to enhance fluorescence and translate to high sensitivity nanothermometers. This review covers fundamentals, and applications of the new UCNP-enabled class of hybrid materials in energy harnessing, light sources and detectors, memory devices, nanothermometers, desalination, intracellular pH sensing, and cancer theranostics.
Gupta, G, Chellappan, DK, Singh, SK, Gupta, PK, Kesari, KK, Jha, NK, Thangavelu, L, G Oliver, B & Dua, K 2021, 'Advanced Drug Delivery Approaches in Managing TGF-β-Mediated Remodeling in Lung Diseases', Nanomedicine, vol. 16, no. 25, pp. 2243-2247.
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Guttentag, A, Krishnakumar, K, Cokcetin, N, Hainsworth, S, Harry, E & Carter, D 2021, 'Inhibition of Dermatophyte Fungi by Australian Jarrah Honey', Pathogens, vol. 10, no. 2, pp. 194-194.
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Superficial dermatophyte infections, commonly known as tineas, are the most prevalent fungal ailment and are increasing in incidence, leading to an interest in alternative treatments. Many floral honeys possess antimicrobial activity due to high sugar, low pH, and the production of hydrogen peroxide (H2O2) from the activity of the bee-derived enzyme glucose oxidase. Australian jarrah (Eucalyptus marginata) honey produces particularly high levels of H2O2 and has been found to be potently antifungal. This study characterized the activity of jarrah honey on fungal dermatophyte species. Jarrah honey inhibited dermatophytes with minimum inhibitory concentrations (MICs) of 1.5–3.5% (w/v), which increased to ≥25% (w/v) when catalase was added. Microscopic analysis found jarrah honey inhibited the germination of Trichophyton rubrum conidia and scanning electron microscopy of mature T. rubrum hyphae after honey treatment revealed bulging and collapsed regions. When treated hyphae were stained using REDOX fluorophores these did not detect any internal oxidative stress, suggesting jarrah honey acts largely on the hyphal surface. Although H2O2 appears critical for the antifungal activity of jarrah honey and its action on fungal cells, these effects persisted when H2O2 was eliminated and could not be replicated using synthetic honey spiked with H2O2, indicating jarrah honey contains agents that augment antifungal activity.
Guttentag, A, Krishnakumar, K, Cokcetin, N, Harry, E & Carter, D 2021, 'Factors affecting the production and measurement of hydrogen peroxide in honey samples', Access Microbiology, vol. 3, no. 3.
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Many Australian native honeys possess significant antimicrobial properties due to the production of hydrogen peroxide (H2O2) by glucose oxidase, an enzyme derived from the honeybee. The level of H2O2 produced in different honey samples is highly variable, and factors governing its production and stability are not well understood. In this study, highly active Australian honeys that had been stored for >10 years lost up to 54 % of their antibacterial activity, although almost all retained sufficient activity to be considered potentially therapeutically useful. We used a simple colourimetric assay to quantify H2O2 production. Although we found a significant correlation between H2O2 production and antibacterial activity across diverse honey samples, variation in H2O2 only explained 47 % of the variation observed in activity, limiting the assay as a screening tool and highlighting the complexity of the relationship between H2O2 and the killing power of honey. To further examine this, we tested whether H2O2 detection in honey was being inhibited by pigmented compounds and if H2O2 might be directly degraded in some honey samples. We found no correlation between H2O2 detection and honey colour. Some honey samples rapidly lost endogenous and spiked H2O2, suggesting that components in honey, such as catalase or antioxidant polyphenols, may degrade or quench H2O2. Despite this rapid loss of H2O2, these honeys had significant peroxide-based antibacterial activ...
Hallegraeff, GM, Schweibold, L, Jaffrezic, E, Rhodes, L, MacKenzie, L, Hay, B & Farrell, H 2021, 'Overview of Australian and New Zealand harmful algal species occurrences and their societal impacts in the period 1985 to 2018, including a compilation of historic records', Harmful Algae, vol. 102, pp. 101848-101848.
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© 2020 Elsevier B.V. Similarities and differences between Australia and New Zealand in Harmful Algal species occurrences and Harmful Algal Events impacting on human society (HAEDAT) are reported and factors that explain their differences explored. Weekly monitoring of harmful phytoplankton and biotoxins commenced in Australia in 1986 and in New Zealand in 1993. Anecdotal historic HAB records in both countries are also catalogued. In Australia, unprecedented highly toxic Paralytic Shellfish Toxin (PST)-producing blooms of Alexandrium catenella have impacted the seafood industry along the 200 km east coast of Tasmania from 2012 to present. Toxic blooms in 1986-1993 by Gymnodinium catenatum in Tasmania were effectively mitigated by closing the affected area for shellfish farming, while a bloom by this same species in 2000 in New Zealand caused significant economic damage from restrictions on the movement of greenshell mussel spat. The biggest biotoxin event in New Zealand was an unexpected outbreak of Neurotoxic Shellfish Poisoning (NSP) in 1993 in Hauraki Gulf (putatively due to Karenia cf. mikimotoi) with 180 reported cases of human poisonings as well as reports of respiratory irritation north of Auckland. Strikingly, NSP never recurred in New Zealand since and no NSP events have ever been reported in Australia. In New Zealand, Paralytic Shellfish Poisoning (PSP) was the predominant seafood toxin syndrome, while in Australia Ciguatera Fish Poisoning (CFP) was the major reported seafood toxin syndrome, while no CFP has been recorded from consumption of New Zealand fish. In Australia, Diarrhetic Shellfish Poisoning (DSP) illnesses were recorded from two related outbreaks in 1997/98 following consumption of beach harvested clams (pipis) from a previously non-monitored area, whereas in New Zealand limited DSP illnesses are known. No human illnesses from Amnesic Shellfish Poisoning (ASP) have been reported in either Australia or New Zealand. Selected examples...
Hamidian, M & Hall, RM 2021, 'Dissemination of novel Tn7 family transposons carrying genes for synthesis and uptake of fimsbactin siderophores among Acinetobacter baumannii isolates', Microbial Genomics, vol. 7, no. 3.
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Acinetobacter baumannii is a successful opportunistic pathogen that can compete for iron under iron-limiting conditions. Here, large novel transposons that carry genes for synthesis and transport of the fimsbactin siderophores present in some A. baumannii strains were examined. Tn6171, originally found in the A. baumannii global clone 1 (GC1) lineage 2 isolate D36, includes tns genes encoding proteins related to the TnsA, TnsB, TnsC transposition proteins (50–59 % identity), TnsD targeting protein (43 % identity) and TnsE (31 % identity) of Tn7, and is found in the chromosome downstream of the glmS gene, the preferred location for Tn7, flanked by a 5 bp target site duplication. Tn6171 is bounded by 29 bp inverted repeats and, like Tn7, includes addit...
Hamidian, M, Ambrose, SJ, Blackwell, GA, Nigro, SJ & Hall, RM 2021, 'An outbreak of multiply antibiotic-resistant ST49:ST128:KL11:OCL8Acinetobacter baumanniiisolates at a Sydney hospital', Journal of Antimicrobial Chemotherapy, vol. 76, no. 4, pp. 893-900.
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AbstractObjectivesTo understand the acquisition of resistance genes by a non-GC1, non-GC2 Acinetobacter baumannii strain responsible for a 4 year outbreak at a Sydney hospital.MethodsRepresentative isolates were screened for resistance to antibiotics. Three were subjected to WGS using Illumina HiSeq. One genome was completed with MinION long reads. Resistance regions were compared with known sequences using bioinformatics.ResultsIsolates were resistant to third-generation cephalosporins, gentamicin and tobramycin, sulfamethoxazole and erythromycin. Sequenced isolates were ST49 (Institut Pasteur scheme) and ST128 (Oxford scheme) and carried KL11 at the capsule locus and OCL8 at the lipooligosaccharide outer core locus. The complete genome of isolate J9 revealed that the resistance genes were all in plasmids; pRAY* contained aadB, and a large plasmid, pJ9-3, contained sul2 and floR genes and a dif module containing the mph(E)-msr(E) macrolide resistance genes. Transposon Tn6168, consisting of a second copy of the chromosomal ampC gene region flanked by ISAba1s, confers resistance to third-generation cephalosporins. Tn6168 is located inside the mph(E)-msr(E) dif module. pJ9-3 includes a set of four dif modules and the orientation of the pdif sites, XerC-XerD or XerD-XerC, alternates. A large transposon, Tn6175, containing tniCABDE transposition genes and genes annotated as being involved in heavy metal metabolism, uptake or export was found in the comM gene. Other ST49:ST128:KL11:OCL8 genomes found in the GenBank WGS database carried Tn6175 but neither of the plasmids carrying the resistance genes.ConclusionsAn early carbapenem-susceptible A. baumannii outbreak recorded in Australia was caused by an unus...
Hamilton, LA, Shiraishi, F, Nakajima, D, Boake, M, Lim, RP, Champeau, O & Tremblay, LA 2021, 'Assessment of the efficacy of an advanced tertiary sewage treatment plant to remove biologically active chemicals using endocrine and genotoxicity bioassays', Emerging Contaminants, vol. 7, pp. 124-131.
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Han, YY, Zhang, X, Wang, J, Wang, G, Oliver, BG, Zhang, HP, Kang, DY, Wang, L, Qiu, ZX, Li, WM & Wang, G 2021, 'Multidimensional Assessment of Asthma Identifies Clinically Relevant Phenotype Overlap: A Cross-Sectional Study', The Journal of Allergy and Clinical Immunology: In Practice, vol. 9, no. 1, pp. 349-362.e18.
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BACKGROUND:Asthma is a heterogeneous disease with multiple phenotypes; however, the relevance of phenotype overlap remains largely unexplored. OBJECTIVE:To examine the relationship between phenotype overlap and clinical and inflammatory profiles of asthma. METHODS:In this cross-sectional study, adult participants with stable asthma (n = 522) underwent multidimensional assessments. The 10 most common phenotypes of asthma were defined and then classified into those commonly associated with Type (T) 2 or non-T2 inflammation. Furthermore, phenotype overlap scores (POS), representing the cumulative concomitant phenotypes, were used to analyze its association with clinical and inflammatory asthmatic profiles. RESULTS:Among the 522 participants, 73.4% (n = 383) had phenotype overlap, and mixed T2 and non-T2 inflammation coexisted in 47.5% (n = 248). T2 POS was positively associated with eosinophils, IgE, and fractional exhaled nitric oxide (FeNO), and negatively with Asthma Quality of Life Questionnaire (AQLQ), sputum neutrophils, IL-17A, IL-8, and TNF-α. Non-T2 POS was positively associated with Asthma Control Questionnaire, neutrophils and sputum IL-8, and negatively with AQLQ, forced expiratory volume in 1 s, blood eosinophils, IgE, and FeNO (all P < .05). Patients with phenotypes that are associated with mixed T2 and non-T2 inflammation had elevated T2 inflammation biomarkers but worse asthma control. Both T2 (adjusted β = -0.191, P = .035) and non-T2 (adjusted β = 0.310, P < .001) POS were significantly associated with severe exacerbations. CONCLUSIONS:Phenotype overlap is extremely common in asthmatic patients and significantly associated with clinical and inflammatory profiles. Patients with phenotypes associated with mixed T2 and non-T2 inflammation might be unresponsive to medications owing to increased non-T2 inflammation. Multidimensional asthma assessment identifies clinically relevant phenotype overlap.
Handa, P, Shinde, N, Sivabalan, B, Varma, A, Pathak, M, Singh, S & Varma, PRP 2021, 'APPLICATION OF LIQUISOLID TECHNIQUE FOR ENHANCEMENT OF DISSOLUTION OF WATER INSOLUBLE DRUG CHOLECALCIFEROL', INDIAN DRUGS, vol. 58, no. 01, pp. 64-72.
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The issue of low solubility and bioavailability poses a significant challenge for most of the drug candidates for oral delivery. Liquisolid, a recently evolved technique for dissolution enhancement, can dodge these barriers. The purpose of this research was to increase the solubility of poorly soluble drug cholecalciferol by liquisolid technique. The cholecalciferol’s solubility studies were performed in a mixture of Polysorbate 80 and PEG 400 in different ratios (1:1, 1:2, 2:1, 1:3, and 3:1). Maximum solubility was observed in a 1:2 ratio. There were changes in the X-ray diffractogram and shifting of the endothermic peak in DSC from 85oC to 146oC, which indicated the drug’s conversion into an amorphous form. The liquisolid form was adsorbed on the carrier material and compressed. The optimization was done by using Plackett Burman Design with Design-Expert software. It was observed that the drugs release profile of the optimized formulation was better than the generic product and was comparable to Divisun tablets 2000 I.U (Innovator).
Hanna, CC, Ashhurst, AS, Quan, D, Maxwell, JWC, Britton, WJ & Payne, RJ 2021, 'Synthetic protein conjugate vaccines provide protection against Mycobacterium tuberculosis in mice', Proceedings of the National Academy of Sciences, vol. 118, no. 4.
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Significance Tuberculosis is the leading cause of death worldwide from a single infectious agent, but vaccines developed to date have limited efficacy and pose safety concerns. Protein-based vaccines are a safe option but usually require powerful adjuvants. We present examples of fully synthetic, self-adjuvanted protein vaccine constructs. These vaccines comprise a low-dose immune-stimulating adjuvant, covalently fused to the ESAT6 protein from Mycobacterium tuberculosis , the causative agent of tuberculosis. When administered by inhalation, the vaccines generated powerful immune responses and significant protection from M. tuberculosis in the lungs of mice. The synthetic strategy we describe represents a method that could be used to rapidly generate vaccines for preclinical testing against many diseases, including novel pathogens such as SARS-CoV-2.
Haq, S, Biswas, SP, Jahan, S, Islam, MR, Rahman, MA, Mahmud, MAP & Kouzani, AZ 2021, 'An Advanced PWM Technique for MMC Inverter Based Grid-Connected Photovoltaic Systems', IEEE Transactions on Applied Superconductivity, vol. 31, no. 8, pp. 1-5.
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Recent developments in multilevel inverters have provided impetus for their applications in the medium voltage renewable energy generation processes. This paper proposes an advanced pulse width modulation technique for a modular multilevel cascaded (MMC) inverter based grid integrated solar photovoltaic (PV) system. It offers lower total harmonic distortion (THD) and power losses compared to the existing modulation techniques. This paper shows the design and performance evaluation of the proposed technique using a 3-phase 5-level MMC inverter-based grid connected PV system. The proposed PWM technique offers 12.49% (without filter) and 0.96% (with filter) output line voltage THDs. It also offers 4.64% output current THD, which complies with the IEEE-519 standard for grid integration. Besides THD reduction, it also reduces the switching and conduction power losses of the MMC inverter. Lower losses may help to keep device temperature low, which is essential for power converters used in superconducting magnetic energy storage (SMES) systems. The simulation is performed in MATLAB/Simulink and the proposed technique is experimentally validated with a laboratory test platform.
Hardwick, J, Taylor, J, Mehta, M, Satija, S, Paudel, KR, Hansbro, PM, Chellappan, DK, Bebawy, M & Dua, K 2021, 'Targeting Cancer using Curcumin Encapsulated Vesicular Drug Delivery Systems', Current Pharmaceutical Design, vol. 27, no. 1, pp. 2-14.
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Curcumin is a major curcuminoid present in turmeric. The compound is attributed to various therapeuticproperties, which include anti-oxidant, anti-inflammatory, anti-bacterial, anti-malarial, and neuroprotection.Due to its therapeutic potential, curcumin has been employed for centuries in treating different ailments. Curcuminhas been investigated lately as a novel therapeutic agent in the treatment of cancer. However, the mechanismsby which curcumin exerts its cytotoxic effects on malignant cells are still not fully understood. One of themain limiting factors in the clinical use of curcumin is its poor bioavailability and rapid elimination. Advancementsin drug delivery systems such as nanoparticle-based vesicular drug delivery platforms have improved severalparameters, namely, drug bioavailability, solubility, stability, and controlled release properties. The use ofcurcumin-encapsulated niosomes to improve the physical and pharmacokinetic properties of curcumin is one suchapproach. This review provides an up-to-date summary of nanoparticle-based vesicular drug carriers and theirtherapeutic applications. Specifically, we focus on niosomes as novel drug delivery formulations and their potentialin improving the delivery of challenging small molecules, including curcumin. Overall, the applications ofsuch carriers will provide a new direction for novel pharmaceutical drug delivery, as well as for biotechnology,nutraceutical, and functional food industries.
Hartigan, J, MacNamara, S, Leslie, L & Speer, M 2021, 'High resolution simulations of a tornadic storm affecting Sydney', ANZIAM Journal, vol. 62, pp. C1-C15.
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On 16 December 2015 a severe thunderstorm and associated tornado affected Sydney causing widespread damage and insured losses of $206 million. Severe impacts occurred in Kurnell, requiring repairs to Sydney's desalination plant which supplies up to 15% of Sydney water during drought, with repairs only completed at the end of 2018. Climatologically, this storm was unusual as it occurred during the morning and had developed over the ocean, rather than developing inland during the afternoon as is the case for many severe storms impacting the Sydney region. Simulations of the Kurnell storm were conducted using the Weather Research and Forecasting (WRF) model on a double nested domain using the Morrison microphysics scheme and the NSSL 2-moment 4-ice microphysics scheme. Both simulations produced severe storms that followed paths similar to the observed storm. However, the storm produced under the Morrison scheme did not have the same morphology as the observed storm. Meanwhile, the storm simulated with the NSSL scheme displayed cyclical low- and mid-level mesocyclone development, which was observed in the Kurnell storm, highlighting that the atmosphere supported the development of severe rotating thunderstorms with the potential for tornadogenesis. The NSSL storm also produced severe hail and surface winds, similar to observations. The ability of WRF to simulate general convective characteristics and a storm similar to that observed displays the applicability of this model to study the causes of severe high-impact Australian thunderstorms.ReferencesJ. T. Allen and E. R. Allen. A review of severe thunderstorms in Australia. Atmos. Res., 178:347–366, 2016. doi:10.1016/j.atmosres.2016.03.011.Bureau of Meteorology. Severe Storms Archive, 2020. URL http://www.bom.gov.au/australia/stormarchive/.D. T. Dawson II, M. Xue, J. A. Milbrandt, and M. K. Yau. Comparison of evaporation and cold pool development between single-moment and multimoment bulk microp...
Hasan, J, Islam, MR, Islam, MR, Kouzani, AZ & Mahmud, MAP 2021, 'A Capacitive Bridge-Type Superconducting Fault Current Limiter to Improve the Transient Performance of DFIG/PV/SG-Based Hybrid Power System', IEEE Transactions on Applied Superconductivity, vol. 31, no. 8, pp. 1-5.
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This paper proposes a capacitive bridge-type superconducting fault current limiter (CB-SFCL) to address the most concerning issue with the grid connected hybrid power system by improving the transient performance. The hybrid system incorporates a doubly fed induction generator (DFIG) based wind farm, a solar photovoltaic (PV) system and a synchronous generator (SG) based power system. The CB-SFCL incorporates a high temperature superconductor (HTS) along with a power capacitor to provide adequate reactive power support before and after the fault. The capacitor is kept inactive during normal operation by a control circuit to ensure seamless operation. During fault, the capacitor gets connected in series with the HTS and suppress the fault current. The performance of the CB-SFCL is investigated by proper graphical and mathematical analyses and conclusions are obtained by comparing them with that of the conventional bridge-type superconducting fault current limiter (BSFCL) and the capacitive bridge-type fault current limiter (CBFCL). The analyses support the theoretical superiority of the CB-SFCL over the BSFCL and the CBFCL by a satisfying margin.
Hasan, M, Altaf, M, Zafar, A, Hassan, SG, Ali, Z, Mustafa, G, Munawar, T, Saif, MS, Tariq, T, Iqbal, F, Khan, MW, Mahmood, A, Mahmood, N & Shu, X 2021, 'Bioinspired synthesis of zinc oxide nano-flowers: A surface enhanced antibacterial and harvesting efficiency', Materials Science and Engineering: C, vol. 119, pp. 111280-111280.
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Despite of broad range application, the cost effective, highly stable and reproduceable synthesis of ZnO is needed, especially which can make it biosafe as well. Here, a unique bioinspired synthesis of ZnO nanoflowers (NFs) has been introduced using Withania coagulans extract as reducing agent. Different molar concentrations were assessed to counter the effect of structural, morphological, antibacterial activity and high efficiency of algae harvesting. The UV-spectroscopy authenticates the synthesis of ZnO NFs having Wurtzite hexagonal structure with the size in the range of 360-550 nm. While surface analysis revealed the presence of stabilizing agent like phenolic, amine, etc. on surface of ZnO NFs. These perineum ZnO NFs exhibited a stronger antibacterial with Gram-positive bacteria Staphylococcus aureus as compare to Gram-negative bacteria Pseudomonas aeruginosa and greater harvesting efficiency up to 94% on the account of greater surface area and unique surface chemistry, thus leading a new horizon of more efficient and effective applications for ethanol production.
Hasan, M, Gulzar, H, Zafar, A, ul Haq, A, Mustafa, G, Tariq, T, Khalid, A, Mahmmod, A, Shu, X & Mahmood, N 2021, 'Multiplexing surface anchored functionalized iron carbide nanoparticle: A low molecular weight proteome responsive nano-tracer', Colloids and Surfaces B: Biointerfaces, vol. 203, pp. 111746-111746.
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Häußler, S, Bayer, G, Waltrich, R, Mendelson, N, Li, C, Hunger, D, Aharonovich, I & Kubanek, A 2021, 'Tunable Fiber‐Cavity Enhanced Photon Emission from Defect Centers in hBN', Advanced Optical Materials, vol. 9, no. 17, pp. 1-8.
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AbstractRealization of quantum photonic devices requires coupling single quantum emitters to the mode of optical resonators. In this work, a hybrid system consisting of defect centers in few‐layer hexagonal boron nitride (hBN) grown by chemical vapor deposition and a fiber‐based Fabry–Pérot cavity is presented. The sub 10‐nm thickness of hBN and its smooth surface enable efficient integration into the cavity mode. This hybrid platform is operated over a broad spectral range larger than 30 nm and its tuneability is used to explore different coupling regimes. Consequently, very large cavity‐assisted signal enhancement up to 50‐fold and strongly narrowed linewidths are achieved, which is owing to cavity funneling, a record for hBN‐cavity systems. Additionally, an excitation and readout scheme is implemented for resonant excitation that allows to establish cavity‐assisted photoluminescence excitation (PLE) spectroscopy. This work marks an important milestone for the deployment of 2D materials coupled to fiber‐based cavities in practical quantum technologies.
Haydon, TD, Seymour, JR, Raina, J-B, Edmondson, J, Siboni, N, Matthews, JL, Camp, EF & Suggett, DJ 2021, 'Rapid Shifts in Bacterial Communities and Homogeneity of Symbiodiniaceae in Colonies of Pocillopora acuta Transplanted Between Reef and Mangrove Environments', Frontiers in Microbiology, vol. 12, p. 756091.
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It has been proposed that an effective approach for predicting whether and how reef-forming corals persist under future climate change is to examine populations thriving in present day extreme environments, such as mangrove lagoons, where water temperatures can exceed those of reef environments by more than 3°C, pH levels are more acidic (pH < 7.9, often below 7.6) and O2 concentrations are regularly considered hypoxic (<2 mg/L). Defining the physiological features of these “extreme” corals, as well as their relationships with the, often symbiotic, organisms within their microbiome, could increase our understanding of how corals will persist into the future. To better understand coral-microbe relationships that potentially underpin coral persistence within extreme mangrove environments, we therefore conducted a 9-month reciprocal transplant experiment, whereby specimens of the coral Pocillopora acuta were transplanted between adjacent mangrove and reef sites on the northern Great Barrier Reef. Bacterial communities associated with P. acuta specimens native to the reef environment were dominated by Endozoicomonas, while Symbiodiniaceae communities were dominated by members of the Cladocopium genus. In contrast, P. acuta colonies native to the mangrove site exhibited highly diverse bacterial communities with no dominating members, and Symbiodiniaceae communities dominated by Durusdinium. All corals survived for 9 months after being transplanted from reef-to-mangrove, mangrove-to-reef environments (as well as control within environment transplants), and during this time there were significant changes in the bacterial communities, but not in the Symbiodiniaceae communities or their photo-physiological functioning. In reef-to-mangrove transplanted corals, t...
Hayward, RJ, Humphrys, MS, Huston, WM & Myers, GSA 2021, 'Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells', Scientific Reports, vol. 11, no. 1.
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AbstractDual RNA-seq experiments examining viral and bacterial pathogens are increasing, but vary considerably in their experimental designs, such as infection rates and RNA depletion methods. Here, we have applied dual RNA-seq to Chlamydia trachomatis infected epithelial cells to examine transcriptomic responses from both organisms. We compared two time points post infection (1 and 24 h), three multiplicity of infection (MOI) ratios (0.1, 1 and 10) and two RNA depletion methods (rRNA and polyA). Capture of bacterial-specific RNA were greatest when combining rRNA and polyA depletion, and when using a higher MOI. However, under these conditions, host RNA capture was negatively impacted. Although it is tempting to use high infection rates, the implications on host cell survival, the potential reduced length of infection cycles and real world applicability should be considered. This data highlights the delicate nature of balancing host–pathogen RNA capture and will assist future transcriptomic-based studies to achieve more specific and relevant infection-related biological insights.
He, Y, Zhang, Y, Liao, Y, Dennis, ES, Peacock, WJ & Wu, X 2021, 'Rice hybrid mimics have stable yields equivalent to those of the F1 hybrid and suggest a basis for hybrid vigour', Planta, vol. 254, no. 3.
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Hegarty, A, Stewart, J & Gladstone, W 2021, 'Reproductive strategies of a temperate Australian sciaenid (teraglin, Atractoscion atelodus )', Journal of Applied Ichthyology, vol. 37, no. 5, pp. 735-747.
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Herdean, A, Hall, CC, Pham, LL, Macdonald Miller, S, Pernice, M & Ralph, PJ 2021, 'Action Spectra and Excitation Emission Matrices reveal the broad range of usable photosynthetic active radiation for Phaeodactylum tricornutum', Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol. 1862, no. 9, pp. 148461-148461.
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Hickey, BA, Chalmers, T, Newton, P, Lin, C-T, Sibbritt, D, McLachlan, CS, Clifton-Bligh, R, Morley, J & Lal, S 2021, 'Smart Devices and Wearable Technologies to Detect and Monitor Mental Health Conditions and Stress: A Systematic Review', Sensors, vol. 21, no. 10, pp. 3461-3461.
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Recently, there has been an increase in the production of devices to monitor mental health and stress as means for expediting detection, and subsequent management of these conditions. The objective of this review is to identify and critically appraise the most recent smart devices and wearable technologies used to identify depression, anxiety, and stress, and the physiological process(es) linked to their detection. The MEDLINE, CINAHL, Cochrane Central, and PsycINFO databases were used to identify studies which utilised smart devices and wearable technologies to detect or monitor anxiety, depression, or stress. The included articles that assessed stress and anxiety unanimously used heart rate variability (HRV) parameters for detection of anxiety and stress, with the latter better detected by HRV and electroencephalogram (EGG) together. Electrodermal activity was used in recent studies, with high accuracy for stress detection; however, with questionable reliability. Depression was found to be largely detected using specific EEG signatures; however, devices detecting depression using EEG are not currently available on the market. This systematic review highlights that average heart rate used by many commercially available smart devices is not as accurate in the detection of stress and anxiety compared with heart rate variability, electrodermal activity, and possibly respiratory rate.
Hiscocks, HG, Yit, DL, Pascali, G & Ung, AT 2021, 'Incorporation of the pentafluorosulfanyl group through common synthetic transformations', Monatshefte für Chemie - Chemical Monthly, vol. 152, no. 4, pp. 449-459.
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Hogg, PJ 2021, 'Toxicokinetics of the tumour cell mitochondrial toxin, PENAO, in rodents', Investigational New Drugs, vol. 39, no. 3, pp. 756-763.
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Holland, MM, Everett, JD, Cox, MJ, Doblin, MA & Suthers, IM 2021, 'Pelagic forage fish distribution in a dynamic shelf ecosystem – Thermal demands and zooplankton prey distribution', Estuarine, Coastal and Shelf Science, vol. 249, pp. 107074-107074.
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Honey, R, McLean, C, Murray, BR & Webb, JK 2021, 'Insulated nest boxes provide thermal refuges for wildlife in urban bushland during summer heatwaves', Journal of Urban Ecology, vol. 7, no. 1, pp. 1-8.
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Abstract In urban bushland, the installation of nest boxes is widely used to compensate for the loss of natural tree hollows. However, current nest box designs may not provide thermal refuges for wildlife during summer heatwaves, particularly if internal temperatures exceed the upper critical temperatures of wildlife. We investigated whether the addition of roofing insulation to nest boxes deployed for sugar gliders (Petaurus breviceps) and squirrel gliders (Petaurus norfolcensis) in urban bushland would reduce internal nest box temperatures during summer heatwaves. We measured temperatures of 44 insulated and 47 uninsulated nest boxes during one of the hottest summers on record (2018–2019) in the Lake Macquarie region of NSW, Australia, a period during which several prolonged heatwaves occurred. Over the 90-day study, maximum temperatures were, on average, 3.1°C lower in insulated boxes than in uninsulated boxes. The addition of insulation significantly lowered nest box temperatures regardless of aspect (north or south facing) or day of measurement. Temperatures exceeded the upper critical temperature (35.1°C) of gliders more frequently in uninsulated nest boxes (28% of days) than in insulated nest boxes (8% days). Although the addition of insulation to nest boxes lowered their internal temperatures, during heatwaves spanning 23 days, nest box temperatures exceeded the upper critical temperatures of gliders on 58% and 23% of days in uninsulated and insulated nest boxes respectively. These findings underscore the importance of retaining natural hollows in urban bushland to provide thermally suitable refuges for wildlife during extreme heat events.
Honey, R, McLean, CM, Murray, BR, Callan, MN & Webb, JK 2021, 'Choice of monitoring method can influence estimates of usage of artificial hollows by vertebrate fauna', Australian Journal of Zoology, vol. 69, no. 1, pp. 18-25.
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The loss of hollow-bearing trees is a key threat for many hollow-dependent taxa. Nesting boxes have been widely used to offset tree hollow loss, but they have high rates of attrition, and, often, low rates of usage by target species. To counter these problems, chainsaw carved hollows (artificial cavities cut into trees) have become a popular alternative, yet little research has been published on their effectiveness. We examined the usage of 150 chainsaw carved hollows by cavity-dependent fauna in the central west of New South Wales using observations from traditional inspection methods and remote cameras. Between October 2017 and April 2019, we detected 21 species of vertebrates (two reptile, one amphibian, 10 bird, and eight mammal species) inside chainsaw carved hollows, but the number of species detected was dependent on the chosen monitoring method. We detected six species inside hollows during physical inspections, whereas remote cameras detected 21 species entering hollows. Cameras detected eight species using hollows as breeding sites, whereas physical inspections detected just four species. Cameras detected two threatened mammals (squirrel glider (Petaurus norfolcensis) and greater glider (Petauroides volans)) raising young inside hollows, yet we failed to detect these species during physical inspections. For birds, the two methods yielded equivalent results for detection of breeding events. Overall, our study showed that few cavity-dependent species used chainsaw carved hollows as breeding sites. This highlights how artificial hollows are not a substitute for retaining naturally occurring hollows in large trees and revegetation programs.
Horstmann, M, Gonzalez de Vega, R, Bishop, DP, Karst, U, Doble, PA & Clases, D 2021, 'Determination of gadolinium MRI contrast agents in fresh and oceanic waters of Australia employing micro-solid phase extraction, HILIC-ICP-MS and bandpass mass filtering', Journal of Analytical Atomic Spectrometry, vol. 36, no. 4, pp. 767-775.
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Speciation analysis of Gd-based MRI contrast agents in fresh and oceanic waters employing an automatised micro-solid phase extraction method and HILIC-ICP-MS detection operating an increased mass bandpass.
Hossain, MA, Brito-Rodriguez, B, Sedger, LM & Canning, J 2021, 'A Cross-Disciplinary View of Testing and Bioinformatic Analysis of SARS-CoV-2 and Other Human Respiratory Viruses in Pandemic Settings', IEEE Access, vol. 9, pp. 163716-163734.
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Hossain, MJ, Kendig, MD, Wild, BM, Morris, MJ & Arnold, R 2021, 'Effects of Diet Reversal on Metabolic and Peripheral Neuropathy Endpoints in a Rat Model of Cafeteria Diet-Induced Obesity', Metabolism, vol. 116, pp. 154638-154638.
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Hossain, R, Ahmed, AJ, Yun, FF, Sang, L, Islam, SMKN, Yang, G, Cortie, MB & Wang, X 2021, 'Significant enhancement of electrical conductivity by incorporating carbon fiber into CoSb3 thermoelectric skutterudite fabricated by spark plasma sintering method', Journal of Materials Science, vol. 56, no. 36, pp. 20138-20153.
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Hossain, SI, Luo, Z, Deplazes, E & Saha, SC 2021, 'Shape matters—the interaction of gold nanoparticles with model lung surfactant monolayers', Journal of The Royal Society Interface, vol. 18, no. 183.
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The lung surfactant monolayer (LSM) forms the main biological barrier for any inhaled particles to enter our bloodstream, including gold nanoparticles (AuNPs) present as air pollutants and under investigation for use in biomedical applications. Understanding the interaction of AuNPs with lung surfactant can assist in understanding how AuNPs enter our lungs. In this study, we use coarse-grained molecular dynamics simulations to investigate the effect of four different shape D AuNPs (spherical, box, icosahedron and rod) on the structure and dynamics of a model LSM, with a particular focus on differences resulting from the shape of the AuNP. Monolayer-AuNP systems were simulated in two different states: the compressed state and the expanded state, representing inhalation and exhalation conditions, respectively. Our results indicate that the compressed state is more affected by the presence of the AuNPs than the expanded state. Our results show that in the compressed state, the AuNPs prevent the monolayer from reaching the close to zero surface tension required for normal exhalation. In the compressed state, all four nanoparticles (NPs) reduce the lipid order parameters and cause a thinning of the monolayer where the particles drag surfactant molecules into the water phase. Comparing the different properties shows no trend concerning which shape has the biggest effect on the monolayer, as shape-dependent effects vary among the different properties. Insights from this study might assist future work of how AuNP shapes affect the LSM during inhalation or exhalation conditions.
Hossain, SI, Saha, SC & Deplazes, E 2021, 'Phenolic compounds alter the ion permeability of phospholipid bilayersviaspecific lipid interactions', Physical Chemistry Chemical Physics, vol. 23, no. 39, pp. 22352-22366.
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How phenolic compounds interact with biological membranes and alter the menbrane properties.
Hosseinabadi, F, Soleymani, B, Adib, E, Islam, MR, Farzanehfard, H, Kouzani, AZ & Mahmud, MAP 2021, 'A soft‐switching inverting high step‐down converter with a pair of coupled inductors and self‐driven synchronous rectifier', IET Power Electronics, vol. 14, no. 15, pp. 2441-2451.
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AbstractIn this paper, a non‐isolated coupled‐inductor high step‐down converter with extended duty cycle is proposed, which operates under discontinuous conduction mode. The soft‐switching condition is provided for all the switches and diodes, which results in the reduction of the switching losses, and the losses related to diode reverse recovery problem. Also, a self‐drive circuit is used to automatically generate the ON and OFF gate signals of the synchronous rectifier, which recovers the gate energy and reduces the complexity. In this topology, only a single coupled inductor is proposed which decreases the size and cost of the proposed converter. A 200 W laboratory prototype is implemented, and its results confirm the validity of theoretical analysis and advantages of the proposed converter over previous structures.
Howlett, L, Camp, EF, Edmondson, J, Henderson, N & Suggett, DJ 2021, 'Coral growth, survivorship and return-on-effort within nurseries at high-value sites on the Great Barrier Reef', PLOS ONE, vol. 16, no. 1, pp. e0244961-e0244961.
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Coral reefs are deteriorating worldwide prompting reef managers and stakeholders to increasingly explore new management tools. Following back-to-back bleaching in 2016/2017, multi-taxa coral nurseries were established in 2018 for the first time on the Great Barrier Reef (GBR) to aid reef maintenance and restoration at a “high-value” location–Opal Reef–frequented by the tourism industry. Various coral species (n = 11) were propagated within shallow water (ca. 4-7m) platforms installed across two sites characterised by differing environmental exposure–one adjacent to a deep-water channel (Blue Lagoon) and one that was relatively sheltered (RayBan). Growth rates of coral fragments placed onto nurseries were highly variable across taxa but generally higher at Blue Lagoon (2.1–10.8 cm2 month-1 over 12 months) compared to RayBan (0.6–6.6 cm2 month-1 over 9 months). Growth at Blue Lagoon was largely independent of season, except for Acropora tenuis and Acropora hyacinthus, where growth rates were 15–20% higher for December 2018-July 2019 (“warm season”) compared to August-December 2018 (“cool season”). Survivorship across all 2,536 nursery fragments was ca. 80–100%, with some species exhibiting higher survivorship at Blue Lagoon (Acropora loripes, Porites cylindrica) and others at RayBan (A. hyacinthus, Montipora hispida). Parallel measurements of growth and survivorship were used to determine relative return-on-effort (RRE) scores as an integrated metric of “success” accounting for life history trade-offs, complementing the mutually exclusive assessment of growth or survivorship. RRE scores within sites (across species) were largely driven by growth, whereas RRE scores between sites ...
Huang, H, Zhan, Y, Tao, Y, Ai, C, Ren, D & Jin, D 2021, 'Three-dimensional characterization of bonding features for asphalt pavement interface using a novel interlayer isolation film', Construction and Building Materials, vol. 311, pp. 125301-125301.
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Huang, Q, Jacquelot, N, Preaudet, A, Hediyeh-zadeh, S, Souza-Fonseca-Guimaraes, F, McKenzie, ANJ, Hansbro, PM, Davis, MJ, Mielke, LA, Putoczki, TL & Belz, GT 2021, 'Type 2 Innate Lymphoid Cells Protect against Colorectal Cancer Progression and Predict Improved Patient Survival', Cancers, vol. 13, no. 3, pp. 559-559.
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Chronic inflammation of the gastrointestinal (GI) tract contributes to colorectal cancer (CRC) progression. While the role of adaptive T cells in CRC is now well established, the role of innate immune cells, specifically innate lymphoid cells (ILCs), is not well understood. To define the role of ILCs in CRC we employed complementary heterotopic and chemically-induced CRC mouse models. We discovered that ILCs were abundant in CRC tumours and contributed to anti-tumour immunity. We focused on ILC2 and showed that ILC2-deficient mice developed a higher tumour burden compared with littermate wild-type controls. We generated an ILC2 gene signature and using machine learning models revealed that CRC patients with a high intratumor ILC2 gene signature had a favourable clinical prognosis. Collectively, our results highlight a critical role for ILC2 in CRC, suggesting a potential new avenue to improve clinical outcomes through ILC2-agonist based therapeutic approaches.
Huang, T, Long, M, Xiao, J, Liu, H & Wang, G 2021, 'Recent research on emerging organic electrode materials for energy storage', Energy Materials, vol. 1, no. 1, pp. 100009-100009.
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Due to the growth of the demand for rechargeable batteries in intelligent terminals, electric vehicles, energy storage, and other markets, electrode materials, as the essential of batteries, have attracted tremendous attention. The research of emerging organic electrode materials in batteries has been boosted recently to their advantages of low cost, environmental friendliness, biodegradability, and designability. This manuscript highlights and classifies several recent studies on organic electrode materials and lists their potential applications in various battery systems. Finally, the challenge and perspective of organic electrode materials are also summarized.
Huang, T, Yang, M, Zeng, Y, Huang, X, Wang, N, Chen, Y, Li, P, Yuan, J, Chen, C, Oliver, BG & Yi, C 2021, 'Maternal High Fat Diet Consumption Exaggerates Metabolic Disorders in Mice With Cigarette-Smoking Induced Intrauterine Undernutrition', Frontiers in Nutrition, vol. 8, p. 638576.
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Objectives: Maternal smoking causes fetal underdevelopment and results in births which are small for gestation age due to intrauterine undernutrition, leading to various metabolic disorders in adulthood. Furthermore, postnatal high fat diet (HFD) consumption is also a potent obesogenic factor, which can interact with maternal smoking. In this study, we aimed to determine whether maternal HFD consumption during pregnancy can reverse the adverse impact of maternal smoking and change the response to postnatal HFD consumption.Methods: Female mice were exposed to cigarette smoke (SE, 2 cigarettes/day) or sham exposed for 5 weeks before mating, with half of the SE dams fed HFD (43% fat, SE+HFD). The same treatment continued throughout gestation and lactation. Male offspring from each maternal group were fed the same HFD or chow after weaning and sacrificed at 13 weeks.Results: Maternal SE alone increased body weight and fat mass in HFD-fed offspring, while SE+HFD offspring showed the highest energy intake and glucose metabolic disorder in adulthood. In addition, postnatal HFD increased the body weight and aggravated the metabolic disorder caused by maternal SE and SE+HFD.Conclusions: Maternal HFD consumption could not ameliorate the adverse effect of maternal SE but exaggerate metabolic disorders in adult offspring. Smoking cessation and a healthy diet are needed during pregnancy to optimize the health outcome in the offspring.
Huang, T, Zhang, Y, Wang, Z, Zeng, Y, Wang, N, Fan, H, Huang, Z, Su, Y, Huang, X, Chen, H, Zhang, K & Yi, C 2021, 'Optogenetically Controlled TrkA Activity Improves the Regenerative Capacity of Hair‐Follicle‐Derived Stem Cells to Differentiate into Neurons and Glia', Advanced Biology, vol. 5, no. 5, pp. e2000134-2000134.
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AbstractHair‐follicle‐derived stem cells (HSCs) originating from the bulge region of the mouse vibrissa hair follicle are able to differentiate into neuronal and glial lineage cells. The tropomyosin receptor kinase A (TrkA) receptor that is expressed on these cells plays key roles in mediating the survival and differentiation of neural progenitors as well as in the regulation of the growth and regeneration of different neural systems. In this study, the OptoTrkA system is introduced, which is able to stimulate TrkA activity via blue‐light illumination in HSCs. This allows to determine whether TrkA signaling is capable of influencing the proliferation, migration, and neural differentiation of these somatic stem cells. It is found that OptoTrkA is able to activate downstream molecules such as ERK and AKT with blue‐light illumination, and subsequently able to terminate this kinase activity in the dark. HSCs with OptoTrkA activity show an increased ability for proliferation and migration and also exhibited accelerated neuronal and glial cell differentiation. These findings suggest that the precise control of TrkA activity using optogenetic tools is a viable strategy for the regeneration of neurons from HSCs, and also provides a novel insight into the clinical application of optogenetic tools in cell‐transplantation therapy.
Huang, X, Cai, H, Li, H, Su, Y, Li, H, Li, W, Yi, C, Oliver, BG & Chen, H 2021, 'Cinnamon as Dietary Supplement Caused Hyperlipidemia in Healthy Rats', Evidence-Based Complementary and Alternative Medicine, vol. 2021, pp. 1-7.
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Objective. Cinnamon is a cooking spice and a medicinal herb. It is increasingly used as a health supplement due to its perceived benefit to prevent and or manage type 2 diabetes and metabolic disorders. However, it is unclear if regular consumption of this medicinal plant will interfere with normal physiological functions. Therefore, this study investigated the impact of daily cinnamon supplements on glucose and lipid metabolic profiles in healthy rats. Methods. Male rats (Sprague Dawley, 8 weeks) were supplied with cinnamon in their diet (equivalent to ∼1 g/day in humans) for two weeks. Blood glucose and lipid levels, as well as metabolic markers in both liver and abdominal white adipose tissue, were measured. Results. Cinnamon significantly increased fat mass and blood cholesterol and low-density lipoprotein (LDL) levels, but reduced fasting blood glucose level by 12%. Liver functional enzymes were normal in rats consuming cinnamon. However, several lipid metabolic markers were impaired which may contribute to dyslipidemia, including two main switches for energy metabolism (sirtuin 1 and peroxisome proliferator-activated receptor-gamma coactivator-1α) and the LDL receptor. However, de novo lipid synthesis enzymes and inflammatory markers were also reduced in the liver by cinnamon treatment, which may potentially prevent the development of steatosis. Markers for lipid oxidation were downregulated in fat tissue in cinnamon-treated rats, contributing to increased fat accumulation. Conclusion. Daily low-dose cinnamon supplementation seems to promote abdominal adipose tissue accumulation and disturb lipid homeostasis in healthy rats, raising the concerns regarding daily use in healthy people.
Huang, X, Su, Y, Wang, N, Li, H, Li, Z, Yin, G, Chen, H, Niu, J & Yi, C 2021, 'Astroglial Connexins in Neurodegenerative Diseases', Frontiers in Molecular Neuroscience, vol. 14.
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Astrocytes play a crucial role in the maintenance of the normal functions of the Central Nervous System (CNS). During the pathogenesis of neurodegenerative diseases, astrocytes undergo morphological and functional remodeling, a process called reactive astrogliosis, in response to the insults to the CNS. One of the key aspects of the reactive astrocytes is the change in the expression and function of connexins. Connexins are channel proteins that highly expressed in astrocytes, forming gap junction channels and hemichannels, allowing diffusional trafficking of small molecules. Alterations of astrocytic connexin expression and function found in neurodegenerative diseases have been shown to affect the disease progression by changing neuronal function and survival. In this review, we will summarize the role of astroglial connexins in neurodegenerative diseases including Alzheimer’s disease, Huntington’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis. Also, we will discuss why targeting connexins can be a plausible therapeutic strategy to manage these neurodegenerative diseases.
Hudspith, M, Rix, L, Achlatis, M, Bougoure, J, Guagliardo, P, Clode, PL, Webster, NS, Muyzer, G, Pernice, M & de Goeij, JM 2021, 'Subcellular view of host–microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan–microbe symbiosis', Microbiome, vol. 9, no. 1.
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Abstract Background Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea. Results The two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome. Conclusions Here, we provide empirical evidence indicating that the prokaryotic communities of a high and ...
Hughes, DJ, Giannini, FC, Ciotti, AM, Doblin, MA, Ralph, PJ, Varkey, D, Verma, A & Suggett, DJ 2021, 'Taxonomic Variability in the Electron Requirement for Carbon Fixation Across Marine Phytoplankton', Journal of Phycology, vol. 57, no. 1, pp. 111-127.
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Fast Repetition Rate fluorometry (FRRf) has been increasingly used to measure marine primary productivity by oceanographers to understand how carbon (C) uptake patterns vary over space and time in the global ocean. As FRRf measures electron transport rates through photosystem II (ETRPSII), a critical, but difficult to predict conversion factor termed the “electron requirement for carbon fixation” (Φe,C) is needed to scale ETRPSII to C‐fixation rates. Recent studies have generally focused on understanding environmental regulation of Φe,C, while taxonomic control has been explored by only a handful of laboratory studies encompassing a limited diversity of phytoplankton species. We therefore assessed Φe,C for a wide range of marine phytoplankton (n = 17 strains) spanning multiple taxonomic and size classes. Data mined from previous studies were further considered to determine whether Φe,C variability could be explained by taxonomy versus other phenotypic traits influencing growth and physiological performance (e.g., cell size). We found that Φe,C exhibited considerable variability (~4–10 mol e‐ · [mol C]−1) and was negatively correlated with growth rate (R2 = 0.7, P < 0.01). Diatoms exhibited a lower Φe,C compared to chlorophytes during steady‐state, nutrient‐replete growth. Inclusion of meta‐analysis data did not find significant relationships between Φe,C and class, or growth rate, although confounding factors inherent to methodological inconsistencies between studies likely contributed to this. Knowledge of empirical relationships between Φe,C and growth rate coupled with recent improvements in ...
Hundal, AK, Ali, S, Agarwal, A, Jameel, MA, Jones, LA, Li, J-L, Evans, RA, Langford, SJ & Gupta, A 2021, 'Enhanced Photovoltaic Efficiency via Control of Self-Assembly in Cyanopyridone-Based Oligothiophene Donors', The Journal of Physical Chemistry Letters, vol. 12, no. 2, pp. 919-924.
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The optoelectronic properties of functional π-conjugated organic materials are affected by their ability to self-assemble within thin films of devices. There are limited reports that demonstrate the positive impact of self-assembly on the photovoltaic performance of organic solar cells. Here, we demonstrate that hydrogen-bonded supramolecular arrays of a cyanopyridone-based oligothiophene donor, CP6, show notable improvement in photovoltaic performance upon self-assembly into a nanofibrous network. The honeycomb-like blend network exhibited higher hole mobility, leading to efficient charge generation and transport. The photovoltaic performance of CP6 was superior to that of two structural analogues, CP5 and CP1, and was attributed to the enhanced capability of CP6 to self-assemble into a film morphology favorable for BHJ devices. The BHJ devices comprising CP6 and the conventional fullerene acceptor (PC71BM) exhibited an efficiency of 7.26%, which is greater than that of CP5 (5.19%) and CP1 (3.11%) and is among the best-performing, cyanopyridone-based oligothiophene donors described to date.
Huo, J, Lu, L, Shen, Z, Gao, H & Liu, H 2021, 'Rational design of CoNi alloy and atomic Co/Ni composite as an efficient electrocatalyst', Surface Innovations, vol. 9, no. 1, pp. 37-48.
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Highly efficient, non-precious and stable electrocatalysts for both oxygen (O2) reduction reaction (ORR) and oxygen evolution reaction (OER) have drawn attention as alternatives to noble-metal catalysts. The rational construction of dual-functional catalysts is meaningful because most nanomaterials can perform only a single electrocatalytic activity. Herein, nitrogen (N)-doped carbon (C) nanotubes encapsulating CoNi alloy (CoNi@NCNTs) nanoparticles coupled with a cobalt (Co) and nickel (Ni) dual atom hybrid are successfully designed and synthesized through a simple metal–organic-framework-assisted strategy, which are explored as a catalyst for ORR and OER. The optimized catalyst exhibits highly efficient bifunctional catalytic activity with a low voltage spacing of 0.78 V between an overpotential of 370 mV (at 10 mA/cm2) toward OER and a half-wave potential of 0.822 V toward ORR, as well as high durability. The excellent electrocatalytic performance should be attributed to the advantages of uniformly dispersed CoNi alloy nanoparticles, highly conductive nitrogen-doped carbon nanotubes and the formation of metal–Nxspecies. This work provides a novel strategy for rationally designing bifunctional catalysts for reversible energy conversion.
Hurtado-McCormick, V, Kahlke, T, Petrou, K, Jeffries, T, Ralph, PJ & Seymour, JR 2021, 'Corrigendum: Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome', Frontiers in Microbiology, vol. 12, p. 642964.
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[This corrects the article DOI: 10.3389/fmicb.2019.01011.].
Hurtado-McCormick, V, Krix, D, Tschitschko, B, Siboni, N, Ralph, PJ & Seymour, JR 2021, 'Shifts in the seagrass leaf microbiome associated with wasting disease in', Marine and Freshwater Research, vol. 72, no. 9, pp. 1303-1320.
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Seagrass wasting disease (SWD), an infection believed to be caused by Labyrinthula zosterae, has been linked to seagrass declines in several places around the world. However, there is uncertainty about the mechanisms of disease and the potential involvement of opportunistic colonising microorganisms. Using 16S rRNA gene amplicon sequencing, we compared the microbiome of SWD lesions in leaves of Zostera muelleri with communities in adjacent asymptomatic tissues and healthy leaves. The microbiome of healthy leaf tissues was dominated by Pseudomonas and Burkholderia, whereas the most predominant taxa within adjacent tissues were Pseudomonas and Rubidimonas. Members of the Saprospiraceae, potential macroalgal pathogens, were over-represented within SWD lesions. These pronounced changes in microbiome structure were also apparent when we examined the core microbiome of different tissue types. Although the core microbiome associated with healthy leaves included three operational taxonomic units (OTUs) classified as Burkholderia, Cryomorphaceae and the SAR11 clade, a single core OTU from the Arenicella was found within adjacent tissues. Burkholderia are diazotrophic microorganisms and may play an important role in seagrass nitrogen acquisition. In contrast, some members of the Arenicella have been implicated in necrotic disease in other benthic animals. Moreover, microbiome structure was maintained across sites within healthy tissues, but not within SWD lesions or the tissues immediately adjacent to lesions. Predicted functional profiles revealed increased photoautotrophic functions in SWD tissues relative to healthy leaves, but no increase in pathogenicity or virulence. Notably, we demonstrated the presence of L. zosterae in SWD lesions by polymerase chain reaction, but only in one of the two sampled locations, which indicates that other microbiological factors may be involved in the initiation or development of SWD-like symptoms. This study suggests t...
Hussain, MS, Sharma, P, Dhanjal, DS, Khurana, N, Vyas, M, Sharma, N, Mehta, M, Tambuwala, MM, Satija, S, Sohal, SS, Oliver, BGG & Sharma, HS 2021, 'Nanotechnology based advanced therapeutic strategies for targeting interleukins in chronic respiratory diseases', Chemico-Biological Interactions, vol. 348, pp. 109637-109637.
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Both communicable and non-communicable chronic respiratory conditions have accorded for suffering of millions of people of all ages and stated to be leading cause of death, morbidity, economic and social pressures, and disability-adjusted life-years (DALYs) worldwide. These illnesses impair patient's health and negatively impacts families and society, particularly in low and middle-income countries. Chronic respiratory diseases (CRDs) affect different organs of respiratory system, involving airways, parenchyma, and pulmonary vasculature. As the number of respiratory diseases are exponentially escalating but still the stakeholders are not paying attention towards its serious complications. Currently, the treatment being used primarily focusses only on alleviating symptoms of these illness rather delivering the therapeutic agent at target site for optimal care and/or prevention. Lately, extensive research is being conducted on airways and systemic inflammation, oxidative stress, airway, or parenchymal rehabilitation. From which macrophages, neutrophils, and T cells, as well as structural cells as fibroblasts, epithelial, endothelial, and smooth muscle cells have been found to be active participants that are involved in these chronic respiratory diseases. The pathogenesis of all these chronic respiratory diseases gets caused differently via mediators and proteins, including cytokines, chemokines, growth factors and oxidants. Presently, the target of prescription therapies is to reduce the inflammation of airways and relieve the airway contraction. In all studies, cytokines have been found to play an imperative role in fostering chronic airway inflammation and remodelling. Owing to the limitations of conventional treatments, the current review aims to summarize the current knowledge about the chronic respiratory disease and discuss further about the various conventional methods that can be used for treating this ailment. Additionally, it also highlights and...
Hwang, J, Strange, N, Phillips, MJA, Krause, AL, Heywood, A, Gamble, AB, Huston, WM & Tyndall, JDA 2021, 'Optimization of peptide-based inhibitors targeting the HtrA serine protease in Chlamydia: Design, synthesis and biological evaluation of pyridone-based and N-Capping group-modified analogues', European Journal of Medicinal Chemistry, vol. 224, pp. 113692-113692.
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The obligate intracellular bacterium Chlamydia trachomatis (C. trachomatis) is responsible for the most common bacterial sexually transmitted infection and is the leading cause of preventable blindness, representing a major global health burden. While C. trachomatis infection is currently treatable with broad-spectrum antibiotics, there would be many benefits of a chlamydia-specific therapy. Previously, we have identified a small-molecule lead compound JO146 [Boc-Val-Pro-ValP(OPh)2] targeting the bacterial serine protease HtrA, which is essential in bacterial replication, virulence and survival, particularly under stress conditions. JO146 is highly efficacious in attenuating infectivity of both human (C. trachomatis) as well as koala (C. pecorum) species in vitro and in vivo, without host cell toxicity. Herein, we present our continuing efforts on optimizing JO146 by modifying the N-capping group as well as replacing the parent peptide structure with the 2-pyridone scaffold at P3/P2. The drug optimization process was guided by molecular modelling, enzyme and cell-based assays. Compound 18b from the pyridone series showed improved inhibitory activity against CtHtrA by 5-fold and selectivity over human neutrophil elastase (HNE) by 109-fold compared to JO146, indicating that 2-pyridone is a suitable bioisostere of the P3/P2 amide/proline for developing CtHtrA inhibitors. Most pyridone-based inhibitors showed superior anti-chlamydial potency to JO146 especially at lower doses (25 and 50 μM) in C. trachomatis and C. pecorum cell culture assays. Modifications of the N-capping group of the peptidyl inhibitors did not have much influence on the anti-chlamydial activities, providing opportunities for more versatile alterations and future optimization. In summary, we present 2-pyridone based analogues as a new generation of non-peptidic CtHtrA inhibitors, which hold better promise as anti-chlamydial drug candidates.
Hynen, AL, Lazenby, JJ, Savva, GM, McCaughey, LC, Turnbull, L, Nolan, LM & Whitchurch, CB 2021, 'Multiple holins contribute to extracellular DNA release in Pseudomonas aeruginosa biofilms', Microbiology, vol. 167, no. 2.
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Bacterial biofilms are composed of aggregates of cells encased within a matrix of extracellular polymeric substances (EPS). One key EPS component is extracellular DNA (eDNA), which acts as a ‘glue’, facilitating cell–cell and cell–substratum interactions. We have previously demonstrated that eDNA is produced in Pseudomonas aeruginosa biofilms via explosive cell lysis. This phenomenon involves a subset of the bacterial population explosively lysing, due to peptidoglycan degradation by the endolysin Lys. Here we demonstrate that in P. aeruginosa three holins, AlpB, CidA and Hol, are involved in Lys-mediated eDNA release within both submerged (hydrated) and interstitial (actively expanding) biofilms, albeit to different extents, depending upon the type of biofilm and the stage of biofilm development. We also demonstrate that eDNA release events determine the sites at which cells begin to cluster to initiate microcolony formation during the early stages of submerged biofilm development. Furthermore, our results show that sustained release of eDNA is required for cell cluster consolidation and subsequent microcolony development in submerged biofilms. Overall, this study adds to our understanding of how eDNA release is controlled temporally and spatially within ...
Ibrahim, I, Seo, DH, Angeloski, A, McDonagh, A, Shon, HK & Tijing, LD 2021, '3D microflowers CuS/Sn2S3 heterostructure for highly efficient solar steam generation and water purification', Solar Energy Materials and Solar Cells, vol. 232, pp. 111377-111377.
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Solar-driven interfacial steam generation is a promising method to produce potable water using renewable energy and help solve global clean water scarcity problems. However, the design of photothermal materials (PTMs) with excellent light absorption that can localize heat at the air/water interface, and facilitate water vapor generation remains a key challenge for its practical implementation. In this work, we demonstrate the synthesis of heterostructure microflowers composed of vertically aligned CuS/Sn2S3 nanosheets (3D CSS-NS MF) using a single-step solvothermal method for solar steam generation application. The microflower structures and the abundant nanocavities between the vertically aligned nanosheets resulted in significant sunlight harvesting over the solar spectrum, excellent heat localization through trapping and re-absorbing the heat, and fast escape of water vapor. Under 1 sun (1 kW m-2) illumination, a high water evaporation rate of 1.42 kg m-2 h-1, corresponding to an efficiency of 82.93% was obtained. The 3D CSS-NS MF based solar evaporator exhibited remarkable salt ions rejection efficiency and good reusability over 10 cycles. Furthermore, efficient removal of organic dyes was observed in application geared towards wastewater treatment with a rejection ∼99.9%. Our work demonstrates the potential of using novel semiconductor-based nanocomposites as effective photothermal materials for high-performance solar steam generation in water desalination and wastewater treatment applications.
Ibrahim, I, Seo, DH, McDonagh, AM, Shon, HK & Tijing, L 2021, 'Semiconductor photothermal materials enabling efficient solar steam generation toward desalination and wastewater treatment', Desalination, vol. 500, pp. 114853-114853.
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© 2020 Elsevier B.V. Water scarcity issues around the world have renewed interest in the use of solar water evaporation as a means of providing fresh water. Advances in photothermal materials and thermal management, together with new interfacial system designs, have considerably improved the overall efficiency of solar steam generation (SSG) for desalination and wastewater treatment. Several classes of rationally-designed photothermal materials (PTMs) and nanostructures have enabled effective absorption of broad solar spectrum resulting in improved solar evaporation efficiency. Among several classes of PTMs, semiconductor-based PTMs have demonstrated great potential for SSG. In this review, we highlight the progress and prospects in SSG with emphasis on the use and evolution of advanced semiconductor materials for PTMs and their various designs and engineered architectures. Applications and future prospects for desalination and wastewater treatment are also discussed.
Impellizzeri, FM, Woodcock, S, Coutts, AJ, Fanchini, M, McCall, A & Vigotsky, AD 2021, 'What Role Do Chronic Workloads Play in the Acute to Chronic Workload Ratio? Time to Dismiss ACWR and Its Underlying Theory', Sports Medicine, vol. 51, no. 3, pp. 581-592.
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Aim
The aim of this study was to examine the associations between the injury risk and the acute (AL) to chronic (CL) workload ratio (ACWR) by substituting the original CL with contrived values to assess the role of CL (i.e., the presence and implications of statistical artefacts).
Methods
Using previously published data, we generated a contrived ACWR by dividing the AL by fixed and randomly generated CLs, and we compared these results to real data. We also reproduced previously reported subgroup analyses, including dichotomising players' data above and below the median CL. Our analyses follow the same, previously published modelling approach.
Results
The analyses with original data showed effects compatible with higher injury risk for ACWR only (odd ratios, OR: 2.45, 95% CI 1.28-4.71). However, we observed similar effects by dividing AL by the 'contrived' fixed and randomly generated CLs: OR 1.95 (1.18-3.52) dividing by 1510 (average CL); and OR ranging from 1.16 to 2.07, using random CL 1.53 (mean). Random ACWRs reduced the variance relative to the original AL and further inflated the ORs (mean OR 1.89, from 1.42 to 2.70). ACWR causes artificial reclassification of players compared to AL alone. Finally, neither ACWR nor AL alone confer a meaningful predictive advantage to an intercept-only model, even within the training sample (c-statistic 0.574/0.544 vs. 0.5 in both ACWR/AL and intercept-only models, respectively).
Discussion
ACWR is a rescaling of the explanatory variable (AL, numerator), in turn magnifying its effect estimates and decreasing its variance despite conferring no predictive advantage. Other ratio-related transformations (e.g., reducing the variance of the explanatory variable and unjustified reclassifications) further inflate the OR of AL alone with injury risk. These results also disprove the etiological theory behind this ratio and its components. We suggest ACWR be dismissed as a framework and model, and...
Indigo, NL, Jolly, CJ, Kelly, E, Smith, J, Webb, JK & Phillips, BL 2021, 'Effects of learning and adaptation on population viability', Conservation Biology, vol. 35, no. 4, pp. 1245-1255.
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AbstractCultural adaptation is one means by which conservationists may help populations adapt to threats. A learned behavior may protect an individual from a threat, and the behavior can be transmitted horizontally (within generations) and vertically (between generations), rapidly conferring population‐level protection. Although possible in theory, it remains unclear whether such manipulations work in a conservation setting; what conditions are required for them to work; and how they might affect the evolutionary process. We examined models in which a population can adapt through both genetic and cultural mechanisms. Our work was motivated by the invasion of highly toxic cane toads (Rhinella marina) across northern Australia and the resultant declines of endangered northern quolls (Dasyurus hallucatus), which attack and are fatally poisoned by the toxic toads. We examined whether a novel management strategy in which wild quolls are trained to avoid toads can reduce extinction probability. We used a simulation model tailored to quoll life history. Within simulations, individuals were trained and a continuous evolving trait determined innate tendency to attack toads. We applied this model in a population viability setting. The strategy reduced extinction probability only when heritability of innate aversion was low (<20%) and when trained mothers trained >70% of their young to avoid toads. When these conditions were met, genetic adaptation was slower, but rapid cultural adaptation kept the population extant while genetic adaptation was completed. To gain insight into the evolutionary dynamics (in which we saw a transitory peak in cultural adaptation over time), we also developed a simple analytical model of evolutionary dynamics. This model showed that the strength of natural selection declined as the cultural transmission rate increased and that adaptation procee...
Inomura, K, Masuda, T, Eichner, M, Rabouille, S, Zavřel, T, Červený, J, Vancová, M, Bernát, G, Armin, G, Claquin, P, Kotabová, E, Stephan, S, Suggett, DJ, Deutsch, C & Prášil, O 2021, 'Quantifying Cyanothece growth under DIC limitation', Computational and Structural Biotechnology Journal, vol. 19, pp. 6456-6464.
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The photoautotrophic, unicellular N2-fixer, Cyanothece, is a model organism that has been widely used to study photosynthesis regulation, the structure of photosystems, and the temporal segregation of carbon (C) and nitrogen (N) fixation in light and dark phases of the diel cycle. Here, we present a simple quantitative model and experimental data that together, suggest external dissolved inorganic carbon (DIC) concentration as a major limiting factor for Cyanothece growth, due to its high C-storage requirement. Using experimental data from a parallel laboratory study as a basis, we show that after the onset of the light period, DIC was rapidly consumed by photosynthesis, leading to a sharp drop in the rate of photosynthesis and C accumulation. In N2-fixing cultures, high rates of photosynthesis in the morning enabled rapid conversion of DIC to intracellular C storage, hastening DIC consumption to levels that limited further uptake. The N2-fixing condition allows only a small fraction of fixed C for cellular growth since a large fraction was reserved in storage to fuel night-time N2 fixation. Our model provides a framework for resolving DIC limitation in aquatic ecosystem simulations, where DIC as a growth-limiting factor has rarely been considered, and importantly emphasizes the effect of intracellular C allocation on growth rate that varies depending on the growth environment.
Iranpour, H, Hosseini, SN, Hosseini Far, H, Zhand, S, Mohammadi Ghanbarlu, M, Shahsavarani, H, Bouzari, S & Shokrgozar, MA 2021, 'Self-assembling of chimeric mussel-inspired bio-adhesives originated from Mytilus californianus and Anabaena flos-aquae: A new approach to develop underwater adhesion', International Journal of Adhesion and Adhesives, vol. 110, pp. 102938-102938.
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Bio-adhesives play a pivotal role in a wide range of medical applications. However, there are some problems about their application in different pH values and low adhesion force under wet conditions. Here, we report new recombinant fusion protein achieved by mussel foot proteins (Mfps) of Mytilus Californianus and gas vesicle protein A (GvpA) of Anabaena flos-aquae by genetic engineering methods. Transmission electron microscopy verified that these chimeric proteins self-assembled into β-sheet rich fibres because of GvpA amyloid structure. Also, in comparison to other studies, their adhesion forces were significantly increased, especially in the alkaline environments based on Mfp-3 and Mfp-5, confirmed by the colloidal probe atomic force microscope. This study illustrates that copolymer of Mfp-5-GvpA:GvpA-Mfp-3 can be used as a sturdy underwater adhesive with tolerance to auto-oxidation, especially at basic conditions.
Islam, MR, Hasan, J, Islam, MR, Kouzani, AZ & Mahmud, MAP 2021, 'Transient Performance Augmentation of DFIG Based Wind Farms by Nonlinear Control of Flux-Coupling-Type Superconducting Fault Current Limiter', IEEE Transactions on Applied Superconductivity, vol. 31, no. 8, pp. 1-5.
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Any fault related to grid is a matter of great concern for doubly fed induction generator (DFIG) based power system as DFIG's stator windings are connected to the grid directly. To augment the transient performance of the DFIGs, superconducting fault current limiter (SFCL) is a certified device. To boost the performance of a flux-coupling-type SFCL (FC-SFCL) by ensuing the adaptive use of fault current limiting impedance based on fault severity, rather involving the full impedance unnecessarily, a nonlinear controller (NC) for FC-SFCL (NC-FC-SFCL) is presented in this paper. Reason behind choosing a straightforward NC for this work is to have simple implementation capability with the full flavor of a nonlinear controller. Effectiveness of the NC-FC-SFCL is compared with conventionally controlled FC-SFCL for various fault scenarios. Simulation results suggest that, NC-FC-SFCL can improve the overall fault ride through (FRT) capability which is verified both graphically and numerically. Additionally, this effective use of the fault current limiting impedance guarantees better transient sub-synchronous resonance (SSR) performance, and exhibits better total harmonic distortion responses.
Ismail, MH, Michie, KA, Goh, YF, Noorian, P, Kjelleberg, S, Duggin, IG, McDougald, D & Rice, SA 2021, 'The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression', Viruses, vol. 13, no. 8, pp. 1614-1614.
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It has been shown that the filamentous phage, Pf4, plays an important role in biofilm development, stress tolerance, genetic variant formation and virulence in Pseudomonas aeruginosa PAO1. These behaviours are linked to the appearance of superinfective phage variants. Here, we have investigated the molecular mechanism of superinfection as well as how the Pf4 phage can control host gene expression to modulate host behaviours. Pf4 exists as a prophage in PAO1 and encodes a homologue of the P2 phage repressor C and was recently named Pf4r. Through a combination of molecular techniques, ChIPseq and transcriptomic analyses, we show a critical site in repressor C (Pf4r) where a mutation in the site, 788799A>G (Ser4Pro), causes Pf4r to lose its function as the immunity factor against reinfection by Pf4. X-ray crystal structure analysis shows that Pf4r forms symmetric homo-dimers homologous to the E.coli bacteriophage P2 RepC protein. A mutation, Pf4r*, associated with the superinfective Pf4r variant, found at the dimer interface, suggests dimer formation may be disrupted, which derepresses phage replication. This is supported by multi-angle light scattering (MALS) analysis, where the Pf4r* protein only forms monomers. The loss of dimerisation also explains the loss of Pf4r’s immunity function. Phenotypic assays showed that Pf4r increased LasB activity and was also associated with a slight increase in the percentage of morphotypic variants. ChIPseq and transcriptomic analyses suggest that Pf4r also likely functions as a transcriptional regulator for other host genes. Collectively, these data suggest the mechanism by which filamentous phages play such an important role in P. aeruginosa biofilm development.
Italiano, CJ, Pu, L, Violi, JP, Duggin, IG & Rodgers, KJ 2021, 'Cysteine biosynthesis contributes to β-methylamino-l-alanine tolerance in Escherichia coli', Research in Microbiology, vol. 172, no. 6, pp. 103852-103852.
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In contrast to mammalian cells, bacteria such as Escherichia coli have been shown to display tolerance towards the neurotoxin β-methylamino-l-alanine (BMAA) suggesting that these prokaryotes possess a way to metabolise BMAA or its products, resulting in their export, degradation, or detoxification. Single gene deletion mutants of E. coli K-12 with inactivated amino acid biosynthesis pathways were treated with 500 μg/ml BMAA and the resulting growth was monitored. Wild type E. coli and most of the gene deletion mutants displayed unaltered growth in the presence of BMAA over 12 h. Conversely, deletion of genes in the cysteine biosynthesis pathway, cysE, cysK or cysM resulted in a BMAA dose-dependent growth delay in minimal medium. Through further studies of the ΔcysE strain, we observed increased susceptibility to oxidative stress from H2O2 in minimal medium, and disruptions in glutathione levels and oxidation state. The cysteine biosynthesis pathway is therefore linked to the tolerance of BMAA and oxidative stress in E. coli, which potentially represents a mechanism of BMAA detoxification.
Iwasaki, K, Evenhuis, C, Tamburic, B, Kuzhiumparambil, U, O'Connor, W, Ralph, P & Szabó, M 2021, 'Improving light and CO2 availability to enhance the growth rate of the diatom, Chaetoceros muelleri', Algal Research, vol. 55, pp. 102234-102234.
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Diatoms (Bacillariophyceae) are an important source of feed for juvenile animals in aquaculture hatcheries. Increasing the yield of feed cultures by optimizing illumination and inorganic carbon supply could significantly reduce operational costs for hatcheries. In this study, the growth dynamics and photosynthetic efficiency of the aquaculture-relevant diatom Chaetoceros muelleri were monitored and modelled under four different light and CO2 conditions. By increasing the availability of both light and CO2, a growth rate of 1.59 ± 0.12 (day−1) was achieved for C. muelleri, an increase of approximately 89% compared to 0.84 ± 0.08 (day−1) which was recorded in cultures under light limitation with no CO2 addition. The real-time monitoring and modelling of growth dynamics and photosynthesis rates in different light and CO2 conditions have demonstrated that light availability can be improved by minimizing the path length of light through the culture, and the importance of on-demand CO2 supply. The techniques and results outlined in this study could be used to potentially improve biomass production in hatcheries.
Jackman, JA, Yoon, BK, Mokrzecka, N, Kohli, GS, Valle‐González, ER, Zhu, X, Pumera, M, Rice, SA & Cho, N 2021, 'Graphene Oxide Mimics Biological Signaling Cue to Rescue Starving Bacteria', Advanced Functional Materials, vol. 31, no. 25, pp. 2102328-2102328.
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AbstractThere is extensive debate about how 2D nanomaterials such as graphene oxide (GO) affect bacteria. Various effects of GO are proposed, including bacterial growth inhibition or enhancement, killing, and no activity. Herein, we report that GO protects Staphylococcus aureus bacterial cells from death in starvation conditions with up to a 1000‐fold improvement in cell viability. Transcriptomic profiling reveals that bacterial cells in starvation conditions generally shut down metabolic activity, while only cells incubated with GO increase production of specific enzymes involved in the glyoxalase detoxification pathway along with repressed autolysis. The oxygen‐containing functional groups of GO resemble the molecular structure of methylglyoxal, which bacteria produce to adapt to nutrient imbalances and is detoxified by glyoxalase enzymes. The ability of GO to enable bacterial cell survival in starvation conditions and accompanying cellular responses support that bacterial cells perceive GO as a methylglyoxal‐mimicking nanomaterial cue to reshuffle cellular metabolism and defenses.
Jacobson, JL, Akkaya‐Hocagil, T, Ryan, LM, Dodge, NC, Richardson, GA, Olson, HC, Coles, CD, Day, NL, Cook, RJ & Jacobson, SW 2021, 'Effects of prenatal alcohol exposure on cognitive and behavioral development: Findings from a hierarchical meta‐analysis of data from six prospective longitudinal U.S. cohorts', Alcoholism: Clinical and Experimental Research, vol. 45, no. 10, pp. 2040-2058.
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AbstractBackgroundCognitive and behavioral sequelae of prenatal alcohol exposure (PAE) continue to be prevalent in the United States and worldwide. Because these sequelae are also common in other neurodevelopmental disorders, researchers have attempted to identify a distinct neurobehavioral profile to facilitate the differential diagnosis of fetal alcohol spectrum disorders (FASD). We used an innovative, individual participant meta‐analytic technique to combine data from six large U.S. longitudinal cohorts to provide a more comprehensive and reliable characterization of the neurobehavioral deficits seen in FASD than can be obtained from smaller samples.MethodsMeta‐analyses were performed on data from 2236 participants to examine effects of PAE (measured as oz absolute alcohol/day (AA/day)) on IQ, four domains of cognition function (learning and memory, executive function, reading achievement, and math achievement), sustained attention, and behavior problems, after adjusting for potential confounders using propensity scores.ResultsThe effect sizes for IQ and the four domains of cognitive function were strikingly similar to one another and did not differ at school age, adolescence, or young adulthood. Effect sizes were smaller in the more middle‐class Seattle cohort and larger in the three cohorts that obtained more detailed and comprehensive assessments of AA/day. PAE effect sizes were somewhat weaker for parent‐ and teacher‐reported behavior problems and not significant for sustained attention. In a meta‐analysis of five aspects of executive function, the strongest effect was on set‐shifting.ConclusionsThe similarity in the effect sizes for the four domains of cognitive function suggests that PAE affe...
Jacquelot, N, Seillet, C, Wang, M, Pizzolla, A, Liao, Y, Hediyeh-zadeh, S, Grisaru-Tal, S, Louis, C, Huang, Q, Schreuder, J, Souza-Fonseca-Guimaraes, F, de Graaf, CA, Thia, K, Macdonald, S, Camilleri, M, Luong, K, Zhang, S, Chopin, M, Molden-Hauer, T, Nutt, SL, Umansky, V, Ciric, B, Groom, JR, Foster, PS, Hansbro, PM, McKenzie, ANJ, Gray, DHD, Behren, A, Cebon, J, Vivier, E, Wicks, IP, Trapani, JA, Munitz, A, Davis, MJ, Shi, W, Neeson, PJ & Belz, GT 2021, 'Blockade of the co-inhibitory molecule PD-1 unleashes ILC2-dependent antitumor immunity in melanoma', Nature Immunology, vol. 22, no. 7, pp. 851-864.
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Group 2 innate lymphoid cells (ILC2s) are essential to maintain tissue homeostasis. In cancer, ILC2s can harbor both pro-tumorigenic and anti-tumorigenic functions, but we know little about their underlying mechanisms or whether they could be clinically relevant or targeted to improve patient outcomes. Here, we found that high ILC2 infiltration in human melanoma was associated with a good clinical prognosis. ILC2s are critical producers of the cytokine granulocyte-macrophage colony-stimulating factor, which coordinates the recruitment and activation of eosinophils to enhance antitumor responses. Tumor-infiltrating ILC2s expressed programmed cell death protein-1, which limited their intratumoral accumulation, proliferation and antitumor effector functions. This inhibition could be overcome in vivo by combining interleukin-33-driven ILC2 activation with programmed cell death protein-1 blockade to significantly increase antitumor responses. Together, our results identified ILC2s as a critical immune cell type involved in melanoma immunity and revealed a potential synergistic approach to harness ILC2 function for antitumor immunotherapies.
Jahan, S, Biswas, SP, Haq, S, Islam, MR, Mahmud, MAP & Kouzani, A 2021, 'An Advanced Control Scheme for Voltage Source Inverter Based Grid-Tied PV Systems', IEEE Transactions on Applied Superconductivity, vol. 31, no. 8, pp. 1-5.
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Nowadays, the use of superconductive magnetic energy storage (SMES) devices in grid integration are highly escalated with the technological amelioration of magnetic components. The power quality and energy conversion efficiency of the power conditioning system of the SMES and renewable energy systems depend on the control algorithms of the voltage source inverter (VSI). However, the traditional control schemes cause inferior response and conversion efficiency. In this paper, an advanced control technique named PI+LLC controller is proposed, which is based on the proportional integral (PI) controller and lead-lag compensator (LLC). The proposed control technique offers significant reduction in the total harmonic distortion (THD), superior dynamic response, smooth response against fault, excellent reference tracking capability of grid current and improved power quality performance at both inverter side and grid side for a 5-level neutral point clamped inverter based grid-tied photovoltaic system. It is expected that, the proposed control scheme can also be used to mitigate the excessive heat of the VSI based SMES system by improving the performance of the power conditioning system. The performance of the proposed control technique is evaluated in MATLAB/Simulink environment to validate the excellent features of the proposed control scheme.
Jain, SK, Low, MX, Vashishtha, P, Nirantar, S, Zhu, L, Ton‐That, C, Ahmed, T, Sriram, S, Walia, S, Gupta, G & Bhaskaran, M 2021, 'Influence of Temperature on Photodetection Properties of Honeycomb‐like GaN Nanostructures', Advanced Materials Interfaces, vol. 8, no. 14, pp. 2100593-2100593.
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AbstractBroadband photodetectors operable under harsh temperature conditions are crucial optoelectronic components to support ongoing and futuristic technological advancement. Conventional photodetectors are limited to room temperature operation due to the thermal instability of semiconductors under harsh conditions and incapable of covering the ultraviolet (UV) spectrum due to narrow bandgap properties. Gallium nitride (GaN) is a wide bandgap and thermally stable semiconductor, ideal for addressing the abovementioned limitations. Here, epitaxial honeycomb nanostructured GaN film is grown via a plasma‐assisted molecular beam epitaxy system and deployed for stable broadband photodetectors, which can be operated from −75 to 250 °C. Further, spectral response is investigated for a broad spectrum from UV (280 nm) to near‐infrared (850 nm) region. It displays a peak responsivity at 365 nm associated to the bandgap energy of GaN. Fabricated photodetectors with honeycomb‐like nanostructures drive peak responsivity and external quantum efficiency of 2.41 × 106 AW−1 and 8.18 × 108%, respectively, when illuminated at a power density of 1 mWcm−2 and 365 nm wavelength source under 1 V bias. Temperature‐correlated spectral response presents a quenching of responsivity at higher temperatures in visible spectrum associated with the thermal quenching of defect states. The thermally stable and efficient broadband photodetector based on honeycomb‐like nanostructured GaN is promising for the combustion industry, arctic science, and space explorations.
Jamil, R, Ali, R, Loomba, S, Xian, J, Yousaf, M, Khan, K, Shabbir, B, McConville, CF, Mahmood, A & Mahmood, N 2021, 'The role of nitrogen in transition-metal nitrides in electrochemical water splitting', Chem Catalysis, vol. 1, no. 4, pp. 802-854.
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H2 as a storable fuel can be sustainably generated from direct cleavage of water with a catalytic approach. However, H2 generation is severely affected by poor catalytic activities and the instability of catalyst materials. Recently, transition-metal-based nitrides (TMNs) have been widely explored because of their intrinsic abilities to catalyze water splitting, wide pH stability, high corrosion resistance, and potential for structural modulations. Most investigations have focused on the design of advanced heterostructures for improving catalytic activity. However, identification of the active sites and decoding the inherent mechanisms are often neglected. Here, we investigate the fundamental aspects of H2 production to elucidate the cutting-edge progress of TMNs. First, we explore the engineering of the active sites of ordered and disordered structures and the relation with hydrogen evolution reaction activity. Second, we explain the development of advanced oxygen evolution reaction catalysts by focusing on minimizing autoxidation. Third and finally, we discuss complementary strategies for converting unifunctional TMNs to bifunctional catalysts for overall water splitting.
Jarman, LR, Elliott, JL, Lees, T, Clifton-Bligh, R, Simpson, AM, Nassif, N & Lal, S 2021, 'Heart Rate Variability as a Potential Non-invasive Marker of Blood Glucose Level', Human Physiology, vol. 47, no. 2, pp. 209-218.
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Abstract: Currently, monitoring of blood glucose level (BGL) is constrained by the invasive nature of BGL measures. We investigated heart rate variability (HRV) parameters as potential non-invasive markers of BGL. Healthy volunteers (n = 25; aged 27 ± 9 years) uninhibited by regular medications or chronic illness were recruited for this study. BGL and HRV were assessed during fasting (9:00 am), postprandial (12:00 pm), and postabsorptive (3:00 pm) periods using self-monitoring of blood glucose techniques and ten-minute electrocardiogram, respectively. Frequency-domain HRV measures, which estimate contributions of sympathetic and parasympathetic systems to autonomic modulation of the heart, were correlated against BGL data with the following significant (p < 0.05) findings. The change in BGL from fasting to postprandial levels was negatively correlated with fasting low frequency (LF) power and total power (TP). Postprandial BGL was negatively associated with fasting LF and TP, as well as with postprandial LF, high frequency (HF), and TP. The change in BGL from postprandial to postabsorptive levels was positively correlated with fasting LF power, as well as with postprandial LF, HF, and TP. Frequency-domain HRV parameters may be useful in predicting the magnitude and direction of acute fluctuations in BGL, and further research could develop them as non-invasive markers of BGL.
Jarocki, VM, Heß, S, Anantanawat, K, Berendonk, TU & Djordjevic, SP 2021, 'Multidrug-Resistant Lineage of Enterotoxigenic Escherichia coli ST182 With Serotype O169:H41 in Airline Waste', Frontiers in Microbiology, vol. 12, p. 731050.
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Enterotoxigenic Escherichia coli (ETEC) is the primary aetiologic agent of traveller’s diarrhoea and a significant cause of diarrhoeal disease and death in developing countries. ETEC O169:H41 strains are known to cause both traveller’s diarrhoea and foodborne outbreaks in developed countries and are cause for concern. Here, whole-genome sequencing (WGS) was used to assemble 46 O169:H41 (ST182) E. coli draft genomes derived from two airplane waste samples sourced from a German international airport. The ST182 genomes were compared with all 84 publicly available, geographically diverse ST182 genomes to construct a core genome-based phylogenetic tree. ST182 isolates were all phylogroup E, the majority serotype O169:H41 (n = 121, 93%) and formed five major clades. The airplane waste isolates differed by an average of 15 core SNPs (range 0–45) but their accessory genome content was diverse. While uncommon in other ST182 genomes, all airplane-derived ST182 isolates carried: (i) extended-spectrum β-lactamase gene blaCTX–M–15 notably lacking the typical adjacent ISEcp1; (ii) qnrS1 and the S83L mutation in gyrA, both conferring resistance to fluoroquinolones; and (iii) a class 1 integron structure (IS26-intI1Δ648-dfrA17-aadA5-qacEΔ1-sul1-ORF-srpC-padR-IS6100-mphR-mrx-mphA-IS26) identified previously in major extrain...
Jarvie, S, Worthy, TH, Saltré, F, Scofield, RP, Seddon, PJ & Cree, A 2021, 'Using Holocene fossils to model the future: Distribution of climate suitability for tuatara, the last rhynchocephalian', Journal of Biogeography, vol. 48, no. 6, pp. 1489-1502.
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AbstractAimCorrelative species distribution models (SDMs) are typically trained using only the contemporary distribution of species; however, recent records might reflect an incomplete description of a species' niche, limiting the reliability of predictions. SDMs linking fossil records have the potential to improve conservation decisions under human‐induced climate change. Here, we built SDMs using presence records from contemporary and Holocene records to enable estimations of climatically suitable area under current and future climate scenarios.LocationAotearoa New ZealandTaxonTuatara, Sphenodon punctatusMethodsFor an evolutionary relict found in Aotearoa New Zealand, the tuatara (Sphenodon punctatus), we built SDMs using presence records from contemporary and Holocene records to estimate climatically suitable area under current and future climate scenarios. We also use our detailed knowledge of the Holocene distribution and remnant populations to examine niche shifts following the arrival of humans and associated introduction of mammalian predators. To build SDMs, we use presence records from four sources: (a) remnant populations, (b) radiocarbon‐dated fossil deposits from the Holocene, (c) other fossil deposits containing tuatara bones of Holocene age and iv) islands from which tuatara are known or highly likely to have become extinct.ResultsWe found shifts in the niche of tuatara due to niche unfilling. Incorporating locations of Holocene deposits and/or all past locations in SDMs led to larger areas of climatically suitable area being identified compared to SDMs derived from remna...
Jaumaux, P, Wu, J, Shanmukaraj, D, Wang, Y, Zhou, D, Sun, B, Kang, F, Li, B, Armand, M & Wang, G 2021, 'Non‐Flammable Liquid and Quasi‐Solid Electrolytes toward Highly‐Safe Alkali Metal‐Based Batteries', Advanced Functional Materials, vol. 31, no. 10, pp. 2008644-2008644.
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AbstractRechargeable alkali metal (i.e., lithium, sodium, potassium)‐based batteries are considered as vital energy storage technologies in modern society. However, the traditional liquid electrolytes applied in alkali metal‐based batteries mainly consist of thermally unstable salts and highly flammable organic solvents, which trigger numerous accidents related to fire, explosion, and leakage of toxic chemicals. Therefore, exploring non‐flammable electrolytes is of paramount importance for achieving safe batteries. Although replacing traditional liquid electrolytes with all‐solid‐state electrolytes is the ultimate way to solve the above safety issues, developing non‐flammable liquid electrolytes can more directly fulfill the current needs considering the low ionic conductivities and inferior interfacial properties of existing all‐solid‐state electrolytes. Moreover, the electrolyte leakage concern can be further resolved by gelling non‐flammable liquid electrolytes to obtain quasi‐solid electrolytes. Herein, a comprehensive review of the latest progress in emerging non‐flammable liquid electrolytes, including non‐flammable organic liquid electrolytes, aqueous electrolytes, and deep eutectic solvent‐based electrolytes is provided, and systematically introduce their flame‐retardant mechanisms and electrochemical behaviors in alkali metal‐based batteries. Then, the gelation techniques for preparing quasi‐solid electrolytes are also summarized. Finally, the remaining challenges and future perspectives are presented. It is anticipated that this review will promote a safety improvement of alkali metal‐based batteries.
Jaumaux, P, Yang, X, Zhang, B, Safaei, J, Tang, X, Zhou, D, Wang, C & Wang, G 2021, 'Localized Water‐In‐Salt Electrolyte for Aqueous Lithium‐Ion Batteries', Angewandte Chemie International Edition, vol. 60, no. 36, pp. 19965-19973.
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AbstractWater‐in‐salt (WIS) electrolytes using super‐concentrated organic lithium (Li) salts are of interest for aqueous Li‐ion batteries. However, the high salt cost, high viscosity, poor wettability, and environmental hazards remain a great challenge. Herein, we present a localized water‐in‐salt (LWIS) electrolyte based on low‐cost lithium nitrate (LiNO3) salt and 1,5‐pentanediol (PD) as inert diluent. The addition of PD maintains the solvation structure of the WIS electrolyte, improves the electrolyte stability via hydrogen‐bonding interactions with water and NO3− molecules, and reduces the total salt concentration. By in situ gelling the LWIS electrolyte with tetraethylene glycol diacrylate (TEGDA) monomer, the electrolyte stability window can be further expanded to 3.0 V. The as‐developed Mo6S8|LWIS gel electrolyte|LiMn2O4 (LMO) batteries delivered outstanding cycling performance with an average Coulombic efficiency of 98.53 % after 250 cycles at 1 C.
Jaumaux, P, Yang, X, Zhang, B, Safaei, J, Tang, X, Zhou, D, Wang, C & Wang, G 2021, 'Localized Water‐In‐Salt Electrolyte for Aqueous Lithium‐Ion Batteries', Angewandte Chemie, vol. 133, no. 36, pp. 20118-20126.
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AbstractWater‐in‐salt (WIS) electrolytes using super‐concentrated organic lithium (Li) salts are of interest for aqueous Li‐ion batteries. However, the high salt cost, high viscosity, poor wettability, and environmental hazards remain a great challenge. Herein, we present a localized water‐in‐salt (LWIS) electrolyte based on low‐cost lithium nitrate (LiNO3) salt and 1,5‐pentanediol (PD) as inert diluent. The addition of PD maintains the solvation structure of the WIS electrolyte, improves the electrolyte stability via hydrogen‐bonding interactions with water and NO3− molecules, and reduces the total salt concentration. By in situ gelling the LWIS electrolyte with tetraethylene glycol diacrylate (TEGDA) monomer, the electrolyte stability window can be further expanded to 3.0 V. The as‐developed Mo6S8|LWIS gel electrolyte|LiMn2O4 (LMO) batteries delivered outstanding cycling performance with an average Coulombic efficiency of 98.53 % after 250 cycles at 1 C.
Jerotić, Đ, Matić, M & McClements, L 2021, 'The importance of polymorphisms of regulatory and catalytic antioxidant proteins in chronic kidney disease', Medicinski podmladak, vol. 72, no. 1, pp. 25-33.
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Both excessive production of reactive oxygen species (ROS) and impaired antioxidant function are found in patients with chronic kidney disease (CKD). Therefore, individual susceptibility towards CKD can be induced by functional variations of genes encoding antioxidant regulatory (nuclear factor erythroid 2 - related factor 2 (Nrf2)) and catalytic (superoxide dismutase (SOD2) and glutathione peroxidase (GPX1)) proteins. Several types of single nucleotide polymorphisms (SNPs) have been found within the genes encoding these proteins, with Nrf2 (-617C/A), SOD2 (Ala16Val) and GPX1 (Pro198Leu) conferring impaired catalytic activity. The most unexplored gene polymorphism in CKD susceptibility, progression and survival, with only two original studies published, is the Nrf2 (-617C/A) polymorphism. The results of these studies showed that there was no individual impact of this polymorphism on the susceptibility towards end stage renal disease (ESRD) development, oxidative phenotype and mortality. However, Nrf2 had a significant role in ESRD risk and survival, when combined with other antioxidant genes. The results regarding the impact of SOD2 (Ala16Val) and GPX1 (Pro198Leu) polymorphisms on either CKD or ESRD are still inconclusive. Namely, some studies showed that patients having variant SOD2 (Val) or GPX1 (Leu) allele were at increased risk of CKD development and progression, while other studies reported only weak or no association between these polymorphisms and CKD. Surprisingly, the only study that reported an association of GPX1 polymorphism with overall/cardiovascular survival in ESRD patients showed a significant impact of low activity GPX1 (Leu/Leu) genotype on better survival. In this review, we comprehensively and critically appraise the literature on these polymorphisms related to oxidative stress in CKD patients, in order to identify gaps and provide recommendations for further clinical research and translation. New developments in the field ...
Jerotic, D, Suvakov, S, Matic, M, Alqudah, A, Grieve, DJ, Pljesa-Ercegovac, M, Savic-Radojevic, A, Damjanovic, T, Dimkovic, N, McClements, L & Simic, T 2021, 'GSTM1 Modulates Expression of Endothelial Adhesion Molecules in Uremic Milieu', Oxidative Medicine and Cellular Longevity, vol. 2021, no. 1, pp. 1-12.
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Deletion polymorphism of glutathione S‐transferase M1 (GSTM1), a phase II detoxification and antioxidant enzyme, increases susceptibility to end‐stage renal disease (ESRD) as well as the development of cardiovascular diseases (CVD) among ESRD patients and leads to their shorter cardiovascular survival. The mechanisms by which GSTM1 downregulation contributes to oxidative stress and inflammation in endothelial cells in uremic conditions have not been investigated so far. Therefore, the aim of the present study was to elucidate the effects of GSTM1 knockdown on oxidative stress and expression of a panel of inflammatory markers in human umbilical vein endothelial cells (HUVECs) exposed to uremic serum. Additionally, we aimed to discern whether GSTM1-null genotype is associated with serum levels of adhesion molecules in ESRD patients. HUVECs treated with uremic serum exhibited impaired redox balance characterized by enhanced lipid peroxidation and decreased antioxidant enzyme activities, independently of the GSTM1 knockdown. In response to uremic injury, HUVECs exhibited alteration in the expression of a series of inflammatory cytokines including retinol‐binding protein 4 (RBP4), regulated on activation, normal T cell expressed and secreted (RANTES), C‐reactive protein (CRP), angiogenin, dickkopf‐1 (Dkk‐1), and platelet factor 4 (PF4). GSTM1 knockdown in HUVECs showed upregulation of monocyte chemoattractant protein‐1 (MCP‐1), a cytokine involved in the regulation of monocyte migration and adhesion. These cells also have shown upregulated intracellular and vascular cell adhesion molecules (ICAM‐1 and VCAM‐1). In accordance with these findings, the levels of serum ICAM‐1 and VCAM‐1 (sICAM‐1 and sVCAM‐1) were increased in ESRD patients lacking GSTM1, in comparison with patients with the GSTM1-active genotype. Based on these results, it may be concluded that incubation of endothelial cells in uremic...
Jiang, Q, Zeng, H, Liu, X, Yan, J, Li, A & Zhou, J 2021, 'Superhydrophobic surface of glass powder derived from wet milling with aliphatic chemicals modification', Ceramics International, vol. 47, no. 20, pp. 29091-29098.
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Glass frit has emerged recently as a promising material for incorporation in adhesive of electronic components owing to its high sealing density, environmental stability and easy processing. This requires the glass surface to be hydrophobic to ensure high dispersity, grinding uniformity, and high-temperature sintering performance of the glass frit. However, the glass surface is usually hydrophilic. In this work, we developed a wet milling method to effectively produce hydrophobic glass powder by using aliphatic chemicals modification. We employed a series of aliphatic chemicals containing nucleophilic functional groups to prepare ultrafine lead aluminosilicate electronic glass powders. The nucleophilic substitution reaction of amino groups, carboxylic acid groups, hydroxyl groups and phosphoric acid groups reduces the hydroxyl content on the surface of the glass powder to 0.10 mg/m2, and generates steric hindrance and hydrophobicity (contact angle: 153.0°) through the long carbon chain. The obtained powder therefore shows a uniform particle size distribution, anti-agglomerated property, and maximum 25 °C lower hemispheric point temperature compared to powder prepared by conventional hydrophilic milling method. This work provides a versatile method to simultaneously control the structural and surface properties of glass powders at their formation stage.
Jin, D, Liu, Y, Lv, S, Qi, Q, Li, M, Wang, Y, Wang, X & Wu, H 2021, 'Electroacupuncture and Moxibustion Modulate the BDNF and TrkB Expression in the Colon and Dorsal Root Ganglia of IBS Rats with Visceral Hypersensitivity', Evidence-Based Complementary and Alternative Medicine, vol. 2021, pp. 1-10.
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Objective. To evaluate the effects of electroacupuncture and moxibustion on brain-derived neurotrophic factor (BDNF) and its receptor tyrosine kinase receptor B (TrkB) protein and mRNA expressions in the colon and dorsal root ganglia of IBS rats with visceral hypersensitivity and to explore their underlying therapeutic mechanisms. Method. Forty Sprague Dawley rats were randomly divided into normal, model, model + mild moxibustion (MM), model + electroacupuncture (EA), and model + pinaverium bromide (PB) groups, with eight rats in each group. Chronic visceral hypersensitive IBS rat models were established by colorectal distension (CRD) with mustard oil clyster. Rats in the MM and EA groups, respectively, received moxibustion and electroacupuncture treatments on the Tianshu (ST25) and Shangjuxu (ST37) acupoints once daily for 7 days, and rats in the PB group received pinaverium bromide by oral gavage once daily for 7 consecutive days. After treatment, rats underwent abdominal withdrawal reflex (AWR) scoring under CRD and colon histopathological examination. Immunohistochemistry and real-time quantitative PCR (RT-qPCR) were used to study the protein and mRNA expressions of BDNF and TrkB in the rat colon and dorsal root ganglia. Results. Compared with the normal group, AWR scores and body weight were clearly increased in the model group rats (both P < 0.01 ). The body weights were significantly elevated ( P < 0.01 ...
Johansen, MD, Alcaraz, M, Dedrick, RM, Roquet-Banères, F, Hamela, C, Hatfull, GF & Kremer, L 2021, 'Mycobacteriophage–antibiotic therapy promotes enhanced clearance of drug-resistant Mycobacterium abscessus', Disease Models & Mechanisms, vol. 14, no. 9.
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ABSTRACT Infection by multidrug-resistant Mycobacterium abscessus is increasingly prevalent in cystic fibrosis (CF) patients, leaving clinicians with few therapeutic options. A compassionate study showed the clinical improvement of a CF patient with a disseminated M. abscessus (GD01) infection, following injection of a phage cocktail, including phage Muddy. Broadening the use of phage therapy in patients as a potential antibacterial alternative necessitates the development of biological models to improve the reliability and successful prediction of phage therapy in the clinic. Herein, we demonstrate that Muddy very efficiently lyses GD01 in vitro, an effect substantially increased with standard drugs. Remarkably, this cooperative activity was retained in an M. abscessus model of infection in CFTR-depleted zebrafish, associated with a striking increase in larval survival and reduction in pathological signs. The activity of Muddy was lost in macrophage-ablated larvae, suggesting that successful phage therapy relies on functional innate immunity. CFTR-depleted zebrafish represent a practical model to rapidly assess phage treatment efficacy against M. abscessus isolates, allowing the identification of drug combinations accompanying phage therapy and treatment prediction in patients. This article has an associated First Person interview with the first author of the paper.
Johansen, MD, Shalini, Kumar, S, Raynaud, C, Quan, DH, Britton, WJ, Hansbro, PM, Kumar, V & Kremer, L 2021, 'Biological and Biochemical Evaluation of Isatin-Isoniazid Hybrids as Bactericidal Candidates against Mycobacterium tuberculosis', Antimicrobial Agents and Chemotherapy, vol. 65, no. 8.
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Tuberculosis remains a leading cause of mortality among infectious diseases worldwide, prompting the need to discover new drugs to fight this disease. We report here the design, synthesis, and antimycobacterial activity of isatin-mono/bis-isoniazid hybrids.
Johnson, L, Vekariya, S, Wood, B, Costa, M, Waters, L, Green, S & Marks, DC 2021, 'The in vitro quality of X‐irradiated platelet components in PAS‐E is equivalent to gamma‐irradiated components', Transfusion, vol. 61, no. 11, pp. 3075-3080.
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AbstractBackgroundBlood components are irradiated to inactivate lymphocytes in an effort to prevent transfusion‐associated graft versus host disease. Although gamma irradiators are commonly used, they are subjected to rigorous health, safety, and compliance regulations, compared with X‐irradiators which have the advantage of only emitting radiation while the machine is switched on. While the effects of gamma irradiation on platelet components are well known, there is little or no data comparing the effects of X‐ and gamma‐irradiation on the quality of these components. Therefore, this study examined the in vitro quality of platelet components (pooled and apheresis) following X‐ or gamma‐irradiation.Study design and methodsWhole‐blood‐derived (pooled) and apheresis platelet components in platelet additive solution (n = 20 pairs for each type) were irradiated (X vs. gamma). In vitro platelet quality was tested prior to irradiation (day 1) and subsequently on days 2, 5, and 7. Non‐irradiated components were tested on day 5 in parallel as reference controls. Metabolic parameters, surface expression of glycoproteins and activation markers (CD62P and annexin‐V binding), and agonist‐induced aggregation were measured.ResultsAll components met Council of Europe specifications. There were no statistical differences in any in vitro quality measurements between X‐ and gamma‐irradiated pooled or apheresis platelet components.ConclusionX‐ and gamma‐irradiation have similar effects on the in vitro quality of stored blood components, indicating that either technology represents a suitable option for irradiation of platelet components.
Johnson, L, Vekariya, S, Wood, B, Tan, S, Roan, C & Marks, DC 2021, 'Refrigeration of apheresis platelets in platelet additive solution (PAS‐E) supports in vitro platelet quality to maximize the shelf‐life', Transfusion, vol. 61, no. S1, pp. S58-S67.
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AbstractBackgroundRefrigeration, or cold‐storage, of platelets may be beneficial to extend the limited shelf‐life of conventionally stored platelets and support transfusion protocols in rural and military areas. The aim of this study was to compare the morphologic, metabolic, and functional aspects of apheresis platelets stored at room‐temperature (RT) or cold conditions, in either plasma or supplemented with platelet additive solution (PAS).Study design and methodsDouble‐dose apheresis platelets were collected in either 100% plasma or 40% plasma/60% PAS‐E using the Trima apheresis platform. One component from each group was either stored at RT (20–24°C) or refrigerated (2–6°C). Platelets were tested over a 21‐day period.ResultsThe platelet concentration decreased by approximately 30% in all groups during 21 days of storage (p > .05). Cold‐storage reduced glycolytic metabolism, and the pH was maintained above the minimum specification (>6.4) for 21 days only when platelets were stored in PAS. The surface phenotype and the composition of the supernatant were differentially affected by temperature and storage solution. Functional responses (aggregation, agonist‐induced receptor activation, clotting time) were improved during cold‐storage, and the influence of residual plasma was assay dependent.ConclusionIn vitro platelet quality is differentially affected by storage time, temperature, and solution. Cold‐storage, particularly in PAS, better maintains key metabolic, phenotypic, and functional parameters during prolonged storage.
Johnson, N, Maguire, S, Morra, A, Kapoor, PM, Tomczyk, K, Jones, ME, Schoemaker, MJ, Gilham, C, Bolla, MK, Wang, Q, Dennis, J, Ahearn, TU, Andrulis, IL, Anton-Culver, H, Antonenkova, NN, Arndt, V, Aronson, KJ, Augustinsson, A, Baynes, C, Freeman, LEB, Beckmann, MW, Benitez, J, Bermisheva, M, Blomqvist, C, Boeckx, B, Bogdanova, NV, Bojesen, SE, Brauch, H, Brenner, H, Burwinkel, B, Campa, D, Canzian, F, Castelao, JE, Chanock, SJ, Chenevix-Trench, G, Clarke, CL, Conroy, DM, Couch, FJ, Cox, A, Cross, SS, Czene, K, Dörk, T, Eliassen, AH, Engel, C, Evans, DG, Fasching, PA, Figueroa, J, Floris, G, Flyger, H, Gago-Dominguez, M, Gapstur, SM, García-Closas, M, Gaudet, MM, Giles, GG, Goldberg, MS, González-Neira, A, Guénel, P, Hahnen, E, Haiman, CA, Håkansson, N, Hall, P, Hamann, U, Harrington, PA, Hart, SN, Hooning, MJ, Hopper, JL, Howell, A, Hunter, DJ, Jager, A, Jakubowska, A, John, EM, Kaaks, R, Keeman, R, Khusnutdinova, E, Kitahara, CM, Kosma, V-M, Koutros, S, Kraft, P, Kristensen, VN, Kurian, AW, Lambrechts, D, Le Marchand, L, Linet, M, Lubiński, J, Mannermaa, A, Manoukian, S, Margolin, S, Martens, JWM, Mavroudis, D, Mayes, R, Meindl, A, Milne, RL, Neuhausen, SL, Nevanlinna, H, Newman, WG, Nielsen, SF, Nordestgaard, BG, Obi, N, Olshan, AF, Olson, JE, Olsson, H, Orban, E, Park-Simon, T-W, Peterlongo, P, Plaseska-Karanfilska, D, Pylkäs, K, Rennert, G, Rennert, HS, Ruddy, KJ, Saloustros, E, Sandler, DP, Sawyer, EJ, Schmutzler, RK, Scott, C, Shu, X-O, Simard, J, Smichkoska, S, Sohn, C, Southey, MC, Spinelli, JJ, Stone, J, Tamimi, RM, Taylor, JA, Tollenaar, RAEM, Tomlinson, I, Troester, MA, Truong, T, Vachon, CM, van Veen, EM, Wang, SS, Weinberg, CR, Wendt, C, Wildiers, H, Winqvist, R, Wolk, A, Zheng, W, Ziogas, A, Dunning, AM, Pharoah, PDP, Easton, DF, Howie, AF, Peto, J, dos-Santos-Silva, I, Swerdlow, AJ, Chang-Claude, J, Schmidt, MK, Orr, N & Fletcher, O 2021, 'CYP3A7*1C allele: linking premenopausal oestrone and progesterone levels with risk of hormone receptor-positive breast cancers', British Journal of Cancer, vol. 124, no. 4, pp. 842-854.
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Abstract Background Epidemiological studies provide strong evidence for a role of endogenous sex hormones in the aetiology of breast cancer. The aim of this analysis was to identify genetic variants that are associated with urinary sex-hormone levels and breast cancer risk. Methods We carried out a genome-wide association study of urinary oestrone-3-glucuronide and pregnanediol-3-glucuronide levels in 560 premenopausal women, with additional analysis of progesterone levels in 298 premenopausal women. To test for the association with breast cancer risk, we carried out follow-up genotyping in 90,916 cases and 89,893 controls from the Breast Cancer Association Consortium. All women were of European ancestry. Results For pregnanediol-3-glucuronide, there were no genome-wide significant associations; for oestrone-3-glucuronide, we identified a single peak mapping to the CYP3A locus, annotated by rs45446698. The minor rs45446698-C allele was associated with lower oestrone-3-glucuronide (−49.2%, 95% CI −56.1% to −41.1%, P = 3.1 × 10–18); in follow-up analyses, rs45446698-C was also associated with lower progesterone (−26.7%, 95% CI −39.4% to −11.6%, P = 0.001) and reduced risk of oestrogen and progesterone receptor-positive breast cancer (OR = 0.86, 95% CI 0.82–0.91, P = 6.9 × 10–8). Conclusions The CYP3A7*1C allele is associated with reduced risk of hormone recept...
Johnston, NP & Wallman, JF 2021, 'A new species of carrion-breeding “golden blowfly” from south-eastern Australia (Diptera: Calliphoridae)', Transactions of the Royal Society of South Australia, vol. 145, no. 2, pp. 143-151.
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The adults and third instar larva of Calliphora pryori sp. nov., a new species of Calliphora Robineau-Desvoidy endemic to south-eastern Australia, are described for the first time. This species breeds in carrion and is very closely allied to C. hilli, with which it is found sympatrically. However, it is less frequently encountered and has only been recorded from southern parts of both South Australia and Victoria. The evolutionary affinities of C. pryori with other members of the C. hilli group are discussed.
JOHNSTON, NP, WALLMAN, JF, SZPILA, K & PAPE, T 2021, 'Integrative taxonomy reveals remarkable diversity in Australian Protomiltogramma (Diptera: Sarcophagidae)', Zootaxa, vol. 5043, no. 1, pp. 1-104.
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Protomiltogramma Townsend is the largest and most diverse genus of miltogrammine flesh flies in Australia. However, no comprehensive taxonomic work had been completed on the Australian members of this genus in almost a century. This study presents the first taxonomic revision of all Australian species of Protomiltogramma (Sarcophagidae: Miltogramminae), completed using an integrative approach combining molecular and morphological data. Eight new species endemic to Australia are described: P. dalbiensis sp. n., P. grandis sp. n., P. incana sp. n., P. kapnos sp. n., P. nigrisensa sp. n., P. popularis sp. n., P. rubra sp. n. and P. subtilis sp. n. In addition, P. australis Malloch, 1930 is synonymised with P. cincta Townsend, 1916, syn. n. and P. mallochi Verves, 1987 is synonymised with P. laticeps Malloch, 1930, syn. n. Molecular phylogenetics is used to place the Australian Protomiltogramma among the miltogrammine genera of the world.
Jolly, CJ, Smart, AS, Moreen, J, Webb, JK, Gillespie, GR & Phillips, BL 2021, 'Novel Predators can Elicit Rapid Shifts in Prey Demographics and Behavior', The Bulletin of the Ecological Society of America, vol. 102, no. 4.
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Jolly, CJ, Smart, AS, Moreen, J, Webb, JK, Gillespie, GR & Phillips, BL 2021, 'Trophic cascade driven by behavioral fine‐tuning as naïve prey rapidly adjust to a novel predator', Ecology, vol. 102, no. 7, pp. 1-11.
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AbstractThe arrival of novel predators can trigger trophic cascades driven by shifts in prey numbers. Predators also elicit behavioral change in prey populations, via phenotypic plasticity and/or rapid evolution, and such changes may also contribute to trophic cascades. Here, we document rapid demographic and behavioral changes in populations of a prey species (grassland melomys Melomys burtoni, a granivorous rodent) following the introduction of a novel marsupial predator (northern quoll Dasyurus hallucatus). Within months of quolls appearing, populations of melomys exhibited reduced survival and population declines relative to control populations. Quoll‐invaded populations were also significantly shyer than nearby, quoll‐free populations of conspecifics. This rapid but generalized response to a novel threat was replaced over the following 2 yr with more threat‐specific antipredator behaviors (i.e., predator‐scent aversion). Predator‐exposed populations, however, remained more neophobic than predator‐free populations throughout the study. These behavioral responses manifested rapidly in changed rates of seed predation by melomys across treatments. Quoll‐invaded melomys populations exhibited lower per‐capita seed take rates, and rapidly developed an avoidance of seeds associated with quoll scent, with discrimination playing out over a spatial scale of tens of meters. Presumably the significant and novel predation pressure induced by quolls drove melomys populations to fine‐tune behavioral responses to be more predator specific through time. These behavioral shifts could reflect individual plasticity (phenotypic flexibility) in behavior or may be adaptive shifts from natural selection imposed by quoll predation. Our study provides a rare insight into the rapid ecological and behavioral shifts enacted by prey to mitigate the impacts of a novel predator and shows that tr...
Jolly, CJ, Von Takach, B & Webb, JK 2021, 'Slow life history leaves endangered snake vulnerable to illegal collecting', Scientific Reports, vol. 11, no. 1, p. 5380.
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AbstractGlobal wildlife trade is a multibillion-dollar industry and a significant driver of vertebrate extinction risk. Yet, few studies have quantified the impact of wild harvesting for the illicit pet trade on populations. Long-lived species, by virtue of their slow life history characteristics, may be unable to sustain even low levels of collecting. Here, we assessed the impact of illegal collecting on populations of endangered broad-headed snakes (Hoplocephalus bungaroides) at gated (protected) and ungated (unprotected) sites. Because broad-headed snakes are long-lived, grow slowly and reproduce infrequently, populations are likely vulnerable to increases in adult mortality. Long-term data revealed that annual survival rates of snakes were significantly lower in the ungated population than the gated population, consistent with the hypothesis of human removal of snakes for the pet trade. Population viability analysis showed that the ungated population has a strongly negative population growth rate and is only prevented from ultimate extinction by dispersal of small numbers of individuals from the gated population. Sensitivity analyses showed that the removal of a small number of adult females was sufficient to impose negative population growth and suggests that threatened species with slow life histories are likely to be especially vulnerable to illegal collecting.
Joshi, RV, Gunawan, C & Mann, R 2021, 'We Are One: Multispecies Metabolism of a Biofilm Consortium and Their Treatment Strategies', Frontiers in Microbiology, vol. 12, p. 635432.
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The ecological and medical significance of bacterial biofilms have been well recognized. Biofilms are harder to control than their planktonic free-living counterparts and quite recently, the focus of the study has shifted to the multispecies consortia, which represent the vast majority of real-case infection scenarios. Studies have begun to explore the complex interspecies interactions within these biofilms. However, only little attention is currently given to the role of cellular metabolites in the cell-to-cell communication. The concentration gradients of metabolic substrates and products affect the spatial growth of bacteria in multispecies biofilm. This, if looked into more deeply, can lead to identification of potential therapies targeting the specific metabolites and hence the coordinated protection in the bacterial community. Herein, we review the interspecies communications, including their metabolic cross-talking, in multispecies biofilm, to signify the importance of such interactions on the initial formation and subsequent growth of these biofilms. Multispecies biofilms with their species heterogeneity are more resilient to antimicrobial agents than their single species biofilm counterparts and this characteristic is of particular interest when dealing with pathogenic bacteria. In this Review, we also discuss the treatment options available, to include current and emerging avenues to combat pathogenic multispecies biofilms in the clinical, environmental, as well as industrial settings.
Jun, MY, Karki, R, Paudel, KR, Panth, N, Devkota, HP & Kim, D-W 2021, 'Liensinine Prevents Vascular Inflammation by Attenuating Inflammatory Mediators and Modulating VSMC Function', Applied Sciences, vol. 11, no. 1, pp. 386-386.
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Liensinine is a bisbenzylisoquinoline alkaloid found in various parts of the lotus (Nelumbo nucifera Gaertn.) including seeds. In this study, we explored the preventive activity of liensinine on vascular inflammation via attenuation of inflammatory mediators in macrophage and targeting the proliferation and migration of human vascular smooth muscle cells (VSMC). Anti-oxidative activity was evaluated by using the 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging assay method and measuring the peroxidation of serum lipid. Inflammatory markers were studied by evaluating the release of nitric oxide (NO) and the protein levels of inducible nitric oxide synthase (iNOS) and cyclooxygenase (COX-2) in macrophage cells (RAW264.7) and interleukin (IL)-6 production in VSMC. Similarly, anti-proliferative activity in VSMC was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The enzymatic activity of matrix metalloproteinase (MMP)-9 in VSMC was evaluated by gelatin zymography. Liensinine possesses significant anti-oxidative activity as revealed by the DPPH assay and inhibition of serum lipid peroxidation. Likewise, liensinine decreased NO generation in RAW 264.7 cells. In VSMC, liensinine suppressed platelet-derived growth factor stimulated proliferation and tumor necrosis factor-α (TNF-α) induced MMP-9 enzymatic activity as well as IL-6 expression. Our results revealed the potential preventive effect of liensinine on vascular inflammation, suggesting it as a promising compound for the prevention of vascular inflammation.
Kang, H, Walsh, S, Oliver, B, Royce, T & Cho, BJ 2021, 'Exploring Heart Rate Variability as a Biomedical Diagnostic Tool for the Disympathetic Dimension of Eight-Constitution Medicine', Evidence-Based Complementary and Alternative Medicine, vol. 2021, pp. 1-13.
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Background. Eight-Constitution Medicine (ECM), an extension of Traditional Korean Medicine, divides the population into eight groups based on their physiological characteristics. ECM divides these eight groups into two larger groups based on autonomic reactivity: the Sympathicotonic group and the Vagotonic group (herein referred to as the Disympathetic Dimension). Heart Rate Variability (HRV) is a widely used biomedical tool to assess cardiac autonomic function. This raises the question of the utility of using HRV to correctly diagnose ECM constitutions. Methods. A systematic literature review was conducted to evaluate the correlation between HRV and constitutions in Korean Constitutional Medicine, including Eight-Constitution Medicine (ECM) and Sasang Constitution Medicine (SCM). The articles were obtained from both English (Scopus, PubMed, EMBASE, ProQuest, and Medline) and Korean databases (NDSL and RISS), in addition to Google Scholar, without date restriction. 20 studies met the inclusion criteria, and data were extracted against three aspects: (1) correlation between HRV and constitution, (2) HRV reporting and interpretation, and (3) extraneous factors that were controlled in the studies. Results. 386 articles were initially identified, which was reduced to n = 20 studies which met the inclusion criteria. Of these, 19 were SCM studies and 1 was an ECM study. Sample sizes varied from 10 to 8498 men and women, with an age range of 10–80 years. SCM studies explored HRV differences by constitution, measuring HRV at resting, with controlled breathing, before and after acupuncture stimulation, and by other interventions. SCM studies reported either no significant differences (HRV at resting or with controlled breathing studies) or conflicting data (HRV with acupuncture stimulation studies). The single ECM study measured HRV at resting and after acupuncture stimulation but reported no significant differences between the two groups of Sympathicoto...
Kanodarwala, FK, Leśniewski, A, Olszowska-Łoś, I, Spindler, X, Pieta, IS, Lennard, C, Niedziółka-Jönsson, J, Moret, S & Roux, C 2021, 'Fingermark detection using upconverting nanoparticles and comparison with cyanoacrylate fuming', Forensic Science International, vol. 326, pp. 110915-110915.
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This paper reports the synthesis of high-quality upconverting nanoparticles (UCNPs) - sodium yttrium tetrafluoride doped with ytterbium and erbium (NaYF4:Yb,Er) with a silica shell and capped with phenyl functional groups. The main goal of this research was to design tailor-made UCNPs for fingermark detection, to test and validate a nanoparticle-based detection technique and to compare their performance against a benchmark method to assess potential implementation in routine practice by law enforcement agencies. The water-based UCNPs solution was applied to natural fingermarks on a number of substrates. This is the first ever systematic comparative study between UCNPs and a benchmark fingermark detection technique - cyanoacrylate fuming (CAF) followed by luminescent dye staining. Fingermark detection effectiveness was studied by treating 300 latent fingermark specimens on aluminium foil, polyethylene, polypropylene and glass slides. It was concluded that, on average, CAF performed better across the substrates tested. Nevertheless, UCNPs can be advantageous for fingermark detection on multicoloured, patterned or luminescent substrates due to their unique optical properties. There are, however, shortfalls associated with their synthesis and use that need to be addressed before they can be considered for operational purposes.
Kanodarwala, FK, Moret, S, Spindler, X, Lennard, C & Roux, C 2021, 'Novel upconverting nanoparticles for fingermark detection', Optical Materials, vol. 111, pp. 110568-110568.
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© 2020 This paper reports the synthesis of high-quality upconverter nanoparticles (UCNPs) – sodium yttrium tetrafluoride doped with ytterbium and erbium (NaYF4:Yb,Er) with a silica shell and capped with carboxyl functional groups. The effect of different synthesis methods on the silica capping has been studied in detail. The main goal of this research was to design tailor-made UCNPs for fingermark detection and to validate a NP-based detection technique that is user-friendly, cost-effective and can be implemented in routine practice by law enforcement agencies. UCNP powders and solutions were used as a proof-of-concept to detect latent fingermarks on an aluminium foil substrate. This study not only highlights the potential use of UCNPs as a fingermark detection method but also identifies a number of shortfalls in its application that need to be addressed before such an approach could be implemented as a valid detection technique.
Kar, R, Jha, SK, Ojha, S, Sharma, A, Dholpuria, S, Raju, VSR, Prasher, P, Chellappan, DK, Gupta, G, Kumar Singh, S, Paudel, KR, Hansbro, PM, Kumar Singh, S, Ruokolainen, J, Kesari, KK, Dua, K & Jha, NK 2021, 'The FBXW7‐NOTCH interactome: A ubiquitin proteasomal system‐induced crosstalk modulating oncogenic transformation in human tissues', Cancer Reports, vol. 4, no. 4.
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AbstractBackgroundUbiquitin ligases or E3 ligases are well programmed to regulate molecular interactions that operate at a post‐translational level. Skp, Cullin, F‐box containing complex (or SCF complex) is a multidomain E3 ligase known to mediate the degradation of a wide range of proteins through the proteasomal pathway. The three‐dimensional domain architecture of SCF family proteins suggests that it operates through a novel and adaptable “super‐enzymatic” process that might respond to targeted therapeutic modalities in cancer.Recent findingsSeveral F‐box containing proteins have been characterized either as tumor suppressors (FBXW8, FBXL3, FBXW8, FBXL3, FBXO1, FBXO4, and FBXO18) or as oncogenes (FBXO5, FBXO9, and SKP2). Besides, F‐box members like βTrcP1 and βTrcP2, the ones with context‐dependent functionality, have also been studied and reported. FBXW7 is a well‐studied F‐box protein and is a tumor suppressor. FBXW7 regulates the activity of a range of substrates, such as c‐Myc, cyclin E, mTOR, c‐Jun, NOTCH, myeloid cell leukemia sequence‐1 (MCL1), AURKA, NOTCH through the well‐known ubiquitin‐proteasome system (UPS)‐mediated degradation pathway. NOTCH signaling is a primitive pathway that plays a crucial role in maintaining normal tissue homeostasis. FBXW7 regulates NOTCH protein activity by controlling its half‐life, thereby maintaining optimum protein levels in tissue. However, aberrations in the FBXW7 or NOTCH expression levels can lead to poor prognosis and detrimental outcomes in patients. Therefore, the FBXW7‐NOTCH axis has been a subject of intense study and research over the years, especially around the interactome's role in driving cancer development and progression. Several studies have reported the effect of FBXW7 and NOTCH mutations on normal tissue behavior. The current review attempts to critically analy...
Karacan, I, Cox, N, Dowd, A, Vago, R, Milthorpe, B, Cazalbou, S & Ben-Nissan, B 2021, 'The synthesis of hydroxyapatite from artificially grown Red Sea hydrozoan coral for antimicrobacterial drug delivery system applications', Journal of the Australian Ceramic Society, vol. 57, no. 2, pp. 399-407.
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The hydrozoan Millepora dichotoma (MD) is a typical Red Sea species containing a porous skeleton in the form of aragonite crystalline calcium carbonate. Due to environmental considerations, the artificial production of coralline species under controlled conditions is pertinent and underway. Artificially grown MD was used as a raw material for the production of calcium phosphate, mainly hydroxyapatite bioceramics, to be used in the drug delivery systems as a drug carrier or in the tissue engineering such as bone graft. DTA-TGA, XRD, FT-IR, Raman, and SEM analysis were carried out to analyze both unconverted and converted artificial corals. Hydrothermally converted coral fine powders were loaded with gentamicin (Gm) antibiotic, and the drug-loaded particles were analyzed by SEM. Unconverted coral was mainly aragonite, while hydrothermally treated coral was completely converted to hydroxyapatite. Hydrothermally treated coral was showing agglomerated nodules up to 1-μm size consisting of nanocrystalline hydroxyapatite platelets in the size range of less than 100 nm. The general macropore size of the coral was found to be appropriate for osteoid growth, which is 100 to 600 μm range. These artificially grown corals can be easily produced and used for bone growth and repair and other biomedical applications.
Karunia, J, Niaz, A, Mandwie, M, Thomas Broome, S, Keay, KA, Waschek, JA, Al-Badri, G & Castorina, A 2021, 'PACAP and VIP Modulate LPS-Induced Microglial Activation and Trigger Distinct Phenotypic Changes in Murine BV2 Microglial Cells', International Journal of Molecular Sciences, vol. 22, no. 20, pp. 10947-10947.
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Pituitary adenylate cyclase-activating polypeptide (PACAP) and vasoactive intestinal peptide (VIP) are two structurally related immunosuppressive peptides. However, the underlying mechanisms through which these peptides regulate microglial activity are not fully understood. Using lipopolysaccharide (LPS) to induce an inflammatory challenge, we tested whether PACAP or VIP differentially affected microglial activation, morphology and cell migration. We found that both peptides attenuated LPS-induced expression of the microglial activation markers Iba1 and iNOS (### p < 0.001), as well as the pro-inflammatory mediators IL-1β, IL-6, Itgam and CD68 (### p < 0.001). In contrast, treatment with PACAP or VIP exerted distinct effects on microglial morphology and migration. PACAP reversed LPS-induced soma enlargement and increased the percentage of small-sized, rounded cells (54.09% vs. 12.05% in LPS-treated cells), whereas VIP promoted a phenotypic shift towards cell subpopulations with mid-sized, spindle-shaped somata (48.41% vs. 31.36% in LPS-treated cells). Additionally, PACAP was more efficient than VIP in restoring LPS-induced impairment of cell migration and the expression of urokinase plasminogen activator (uPA) in BV2 cells compared with VIP. These results suggest that whilst both PACAP and VIP exert similar immunosuppressive effects in activated BV2 microglia, each peptide triggers distinctive shifts towards phenotypes of differing morphologies and with differing migration capacities.
Katsnelson, A 2021, 'A Conversation with Maiken Ueland', ACS Central Science, vol. 7, no. 9, pp. 1451-1453.
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Kaur, J, Famta, P, Famta, M, Mehta, M, Satija, S, Sharma, N, Vyas, M, Khatik, GL, Chellappan, DK, Dua, K & Khurana, N 2021, 'Potential anti-epileptic phytoconstituents: An updated review', Journal of Ethnopharmacology, vol. 268, pp. 113565-113565.
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ETHNOPHARMACOLOGICAL RELEVANCE:Epilepsy is one of the most commonly occurring non-communicable neurological disorder that affects people of all age groups. Around 50 million people globally are epileptic, with 80% cases in developing countries due to lack of access to treatments determined by high cost and poor availability or it can be defined by the fraction of active epileptic patients who are not appropriately being treated. The availability of antiepileptic drugs and their adjuvant therapy in such countries is less than 50% and these are highly susceptible to drug interactions and severe adverse effects. As a result, the use of herbal medicine is increasingly becoming popular. AIM OF THE STUDY:To provide pharmacological information on the active constituents evaluated in the preclinical study to treat epilepsy with potential to be used as an alternative therapeutic option in future. It also provides affirmation for the development of novel antiepileptic drugs derived from medicinal plants. MATERIALS AND METHODS:Relevant information on the antiepileptic potential of phytoconstituents in the preclinical study (in-vitro, in-vivo) is provided based on their effect on screening parameters. Besides, relevant information on pharmacology of phytoconstituents, the traditional use of their medicinal plants related to epilepsy and status of phytoconstituents in the clinical study were derived from online databases, including PubMed, Clinicaltrial.gov, The Plant List (TPL, www.theplantlist.org), Science Direct. Articles identified using preset searching syntax and inclusion criteria are presented. RESULTS:More than 70% of the phytoconstituents reviewed in this paper justified the traditional use of their medicinal plant related to epilepsy by primarily acting on the GABAergic system. Amongst the phytoconstituents, only cannabidiol and tetrahydrocannabinol have been explored for clinical application in epilepsy. CONCLUSION:The preclinical and clinical data of t...
Keen, B, Cawley, A, Fouracre, C, Pyke, J & Fu, S 2021, 'Towards an untargeted mass spectrometric approach for improved screening in equine antidoping', Drug Testing and Analysis, vol. 13, no. 5, pp. 1001-1007.
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AbstractThe emergence of novel doping agents is a continuous issue for analysts who aim to maintain the integrity of horseracing together with the well‐being and safety of the animals and riders involved. Untargeted mass spectrometric analysis presents a potential improvement for antidoping as it enables the detection of compounds being indirectly affected by an administered drug. In this study, liquid chromatography–high‐resolution mass spectrometry was used to investigate a 12‐horse administration study of the synthetic opioid, butorphanol. A mass spectrometric workflow capable of detecting metabolic differences for an extended period of time was successfully developed. This proof‐of‐concept study demonstrates the potential of untargeted workflows to provide a list of biomarkers of exposure and effect that are indicative of drug administration which may be implemented into routine testing for improved doping control.
Kelly, E, Jolly, CJ, Indigo, N, Smart, A, Webb, J & Phillips, B 2021, 'No outbreeding depression in a trial of targeted gene flow in an endangered Australian marsupial', Conservation Genetics, vol. 22, no. 1, pp. 23-33.
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© 2020, Springer Nature B.V. Targeted gene flow is a novel conservation strategy that involves translocating individuals with favourable genes to areas where they will have a conservation benefit. One oft-cited risk of the strategy is the potential for outbreeding depression. Here, we used the northern quoll (Dasyurus hallucatus) as a model to test this possibility for the first time in a field setting. Northern quolls are endangered by the spread of the invasive cane toad (Rhinella marina), which they are fatally poisoned by, if they mistakenly attempt to consume them. There are, however, a small number of quolls that are “toad-smart”—they possess a heritable trait that means they innately do not attack toads. It is this trait we hoped to promote through targeted gene flow. We established a hybrid population (54 toad-smart and toad-naïve northern quolls) and introduced this population onto a small offshore, toad-infested island in 2017. Genetic data suggests an increase in the toad-smart proportion of the genome increasing from 29.4% in the release population to 40.2% in the first island generation (F2). Our data demonstrate successful in situ hybridisation between populations, with viable F2 hybrids and backcrosses observed, and some evidence of heterosis (hybrid vigour) in F1 hybrids. The population experienced significant reductions in size over the two years, however, through a combination of toad-mortality, as well as stochastic processes including fire, a cyclone, predation and ineffective breeding, and so small sample sizes hamper our results. Such establishment problems would not occur were we to attempt targeted gene flow into already established quoll populations, and our observation of successful hybridisation suggests targeted gene flow could be a viable strategy in established quoll populations soon to be impacted by toads.
Kendig, MD, Leigh, S-J & Morris, MJ 2021, 'Unravelling the impacts of western-style diets on brain, gut microbiota and cognition', Neuroscience & Biobehavioral Reviews, vol. 128, pp. 233-243.
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Kendig, MD, Martire, SI, Boakes, RA & Rooney, KB 2021, 'Comparable metabolic effects of isocaloric sucrose and glucose solutions in rats', Physiology & Behavior, vol. 229, pp. 113239-113239.
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Ketelaar, ME, Portelli, MA, Dijk, FN, Shrine, N, Faiz, A, Vermeulen, CJ, Xu, CJ, Hankinson, J, Bhaker, S, Henry, AP, Billington, CK, Shaw, DE, Johnson, SR, Benest, AV, Pang, V, Bates, DO, Pogson, ZEK, Fogarty, A, McKeever, TM, Singapuri, A, Heaney, LG, Mansur, AH, Chaudhuri, R, Thomson, NC, Holloway, JW, Lockett, GA, Howarth, PH, Niven, R, Simpson, A, Tobin, MD, Hall, IP, Wain, LV, Blakey, JD, Brightling, CE, Obeidat, M, Sin, DD, Nickle, DC, Bossé, Y, Vonk, JM, van den Berge, M, Koppelman, GH, Sayers, I & Nawijn, MC 2021, 'Phenotypic and functional translation of IL33 genetics in asthma', Journal of Allergy and Clinical Immunology, vol. 147, no. 1, pp. 144-157.
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BACKGROUND:Asthma is a complex disease with multiple phenotypes that may differ in disease pathobiology and treatment response. IL33 single nucleotide polymorphisms (SNPs) have been reproducibly associated with asthma. IL33 levels are elevated in sputum and bronchial biopsies of patients with asthma. The functional consequences of IL33 asthma SNPs remain unknown. OBJECTIVE:This study sought to determine whether IL33 SNPs associate with asthma-related phenotypes and with IL33 expression in lung or bronchial epithelium. This study investigated the effect of increased IL33 expression on human bronchial epithelial cell (HBEC) function. METHODS:Association between IL33 SNPs (Chr9: 5,815,786-6,657,983) and asthma phenotypes (Lifelines/DAG [Dutch Asthma GWAS]/GASP [Genetics of Asthma Severity & Phenotypes] cohorts) and between SNPs and expression (lung tissue, bronchial brushes, HBECs) was done using regression modeling. Lentiviral overexpression was used to study IL33 effects on HBECs. RESULTS:We found that 161 SNPs spanning the IL33 region associated with 1 or more asthma phenotypes after correction for multiple testing. We report a main independent signal tagged by rs992969 associating with blood eosinophil levels, asthma, and eosinophilic asthma. A second, independent signal tagged by rs4008366 presented modest association with eosinophilic asthma. Neither signal associated with FEV1, FEV1/forced vital capacity, atopy, and age of asthma onset. The 2 IL33 signals are expression quantitative loci in bronchial brushes and cultured HBECs, but not in lung tissue. IL33 overexpression in vitro resulted in reduced viability and reactive oxygen species-capturing of HBECs, without influencing epithelial cell count, metabolic activity, or barrier function. CONCLUSIONS:We identify IL33 as an epithelial susceptibility gene for eosinophilia and asthma, provide mechanistic insight, and implicate targeting of the IL33 pathway specifically in eosinophilic asthma.
Khan, M, Willcox, MDP, Rice, SA, Sharma, S & Stapleton, F 2021, 'Development of antibiotic resistance in the ocular Pseudomonas aeruginosa clone ST308 over twenty years', Experimental Eye Research, vol. 205, pp. 108504-108504.
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Corneal infection caused by a bacteria Pseudomonas aeruginosa is common cause of ocular morbidity. Increasing antibiotic resistance by ocular P. aeruginosa is an emerging concern. In this study the resistome of ocular isolates of Pseudomonas aeruginosa clone ST308 isolated in India in 1997 (PA31, PA32, PA33, PA35 and PA37) and 2018 (PA198 and PA219) were investigated. All the isolates of ST308 had >95% nucleotide similarity. The isolates from 2018 had larger genomes, coding sequences, accessory and pan genes compared to the older isolates from 1997. The 2018 isolate PA219 was resistant to all antibiotics except polymyxin B, while the 2018 isolate PA198 was resistant to ciprofloxacin, levofloxacin, gentamicin and tobramycin. Among the isolates from 1997, five were resistant to gentamicin, tobramycin and ciprofloxacin, four were resistant to levofloxacin while two were resistant to polymyxin B. Twenty-four acquired resistance genes were present in the 2018 isolates compared to 11 in the historical isolates. All isolates contained genes encoding for aminoglycoside (aph(6)-Id, aph(3')-lIb, aph(3″)-Ib), beta-lactam (blaPAO), tetracycline (tet(G)), fosfomycin (fosA), chloramphenicol (catB7), sulphonamide (sul1), quaternary ammonium (qacEdelta1) and fluoroquinolone (crpP) resistance. Isolate PA198 possessed aph(3')-VI, rmtD2, qnrVC1, blaOXA-488, blaPME-1, while PA219 possessed aadA1, rmtB, qnrVC1, aac(6')-Ib-cr, blaTEM-1B, blaVIM-2, blaPAO-1, mph(E), mph(A), msr(E). In both recent isolates qnrVC1 was present in Tn3 transposon. In 219 blaTEM-1 was carried on a transposon and blaOXA-10 on a class 1 integron. There were no notable differences in the number of single nucleotide polymorphisms, but recent isolates carried more insertions and deletions in their genes. These findings suggest that genomes of P. aeruginosa ocular clonal strains with >95% nucleotide identity isolated twenty years apart had changed over time with the acquisition of resistance genes. The p...
Khantisitthiporn, O, Shue, B, Eyre, NS, Nash, CW, Turnbull, L, Whitchurch, CB, Van der Hoek, KH, Helbig, KJ & Beard, MR 2021, 'Viperin interacts with PEX19 to mediate peroxisomal augmentation of the innate antiviral response', Life Science Alliance, vol. 4, no. 7, pp. e202000915-e202000915.
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Peroxisomes are recognized as significant platforms for the activation of antiviral innate immunity where stimulation of the key adapter molecule mitochondrial antiviral signaling protein (MAVS) within the RIG-I like receptor (RLR) pathway culminates in the up-regulation of hundreds of ISGs, some of which drive augmentation of multiple innate sensing pathways. However, whether ISGs can augment peroxisome-driven RLR signaling is currently unknown. Using a proteomics-based screening approach, we identified Pex19 as a binding partner of the ISG viperin. Viperin colocalized with numerous peroxisomal proteins and its interaction with Pex19 was in close association with lipid droplets, another emerging innate signaling platform. Augmentation of the RLR pathway by viperin was lost when Pex19 expression was reduced. Expression of organelle-specific MAVS demonstrated that viperin requires both mitochondria and peroxisome MAVS for optimal induction of IFN-β. These results suggest that viperin is required to enhance the antiviral cellular response with a possible role to position the peroxisome at the mitochondrial/MAM MAVS signaling synapse, furthering our understanding of the importance of multiple organelles driving the innate immune response against viral infection.
Kihara, S, Ashenden, A, Kaur, M, Glasson, J, Ghosh, S, van der Heijden, N, Brooks, AES, Mata, JP, Holt, S, Domigan, LJ, Köper, I & McGillivray, DJ 2021, 'Cellular interactions with polystyrene nanoplastics—The role of particle size and protein corona', Biointerphases, vol. 16, no. 4, pp. 041001-041001.
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Plastic waste is ubiquitously spread across the world and its smaller analogs—microplastics and nanoplastics—raise particular health concerns. While biological impacts of microplastics and nanoplastics have been actively studied, the chemical and biological bases for the adverse effects are sought after. This work explores contributory factors by combining results from in vitro and model mammalian membrane experimentation to assess the outcome of cell/nanoplastic interactions in molecular detail, inspecting the individual contribution of nanoplastics and different types of protein coronae. The in vitro study showed mild cytotoxicity and cellular uptake of polystyrene (PS) nanoplastics, with no clear trend based on nanoplastic size (20 and 200 nm) or surface charge. In contrast, a nanoplastic size-dependency on bilayer disruption was observed in the model system. This suggests that membrane disruption resulting from direct interaction with PS nanoplastics has little correlation with cytotoxicity. Furthermore, the level of bilayer disruption was found to be limited to the hydrophilic headgroup, indicating that transmembrane diffusion was an unlikely pathway for cellular uptake—endocytosis is the viable mechanism. In rare cases, small PS nanoplastics (20 nm) were found in the vicinity of chromosomes without a nuclear membrane surrounding them; however, this was not observed for larger PS nanoplastics (200 nm). We hypothesize that the nanoplastics can interact with chromosomes prior to nuclear membrane formation. Overall, precoating PS particles with protein coronae reduced the cytotoxicity, irrespective of the corona type. When comparing the two types, the extent of reduction was more apparent with soft than hard corona.
Kim, RY, Glick, C, Furmanek, S, Ramirez, JA & Cavallazzi, R 2021, 'Association between body mass index and mortality in hospitalised patients with community-acquired pneumonia', ERJ Open Research, vol. 7, no. 1, pp. 00736-2020.
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The obesity paradox postulates that increased body mass index (BMI) is protective in certain patient populations. We aimed to investigate the association of BMI and different weight classes with outcomes in hospitalised patients with community-acquired pneumonia (CAP).This cohort study is a secondary data analysis of the University of Louisville Pneumonia Study database, a prospective study of hospitalised adult patients with CAP from June, 2014, to May, 2016, in Louisville, KY, USA. BMI as a predictor was assessed both as a continuous and categorical variable. Patients were categorised as weight classes based on World Health Organization definitions: BMI of <18.5 kg·m−2(underweight), BMI of 18.5 to <25 kg·m−2(normal weight), BMI of 25.0 to <30 kg·m−2(overweight), BMI of 30 to <35 kg·m−2(obesity class I), BMI of 35 to <40 kg·m−2(obesity class II), and BMI of ≥40 kg·m−2(obesity class III). Study outcomes, including time to clinical stability, length of stay, clinical failure and mortality, were assessed in hospital, at 30 days, at 6 months and at 1 year. Clinical failure was defined as the need for noninvasive ventilation, invasive ventilation or vasopressors within 1 week of admission. Patient characteristics and crude outcomes were stratified by BMI categories, and generalised additive binomial regression models were performed to analyse the impact of BMI as a continuous variable on study outcomes adjusting for possible confounding variables.7449 patients were included in the study. Median time to clinical stability was 2 days for every BMI group. There was no association between BMI as a continuous predictor and length of stay <5 days (chi-squared=1.83, estimated degrees of freedom (EDF)=2.74, p=0.608). Clinical failure was highest in the class III obesity group, and h...
Kim, RY, Sunkara, KP, Bracke, KR, Jarnicki, AG, Donovan, C, Hsu, AC, Ieni, A, Beckett, EL, Galvão, I, Wijnant, S, Ricciardolo, FLM, Di Stefano, A, Haw, TJ, Liu, G, Ferguson, AL, Palendira, U, Wark, PA, Conickx, G, Mestdagh, P, Brusselle, GG, Caramori, G, Foster, PS, Horvat, JC & Hansbro, PM 2021, 'A microRNA-21–mediated SATB1/S100A9/NF-κB axis promotes chronic obstructive pulmonary disease pathogenesis', Science Translational Medicine, vol. 13, no. 621, p. eaav7223.
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Inhibition of cigarette smoke–induced microRNA-21 suppresses chronic obstructive pulmonary disease through effects on a SATB1/S100A9/NF-κB axis.
Kim, T-H, Alraek, T, Bian, Z-X, Birch, S, Bovey, M, Lee, J, Lee, MS, Robinson, N & Zaslawski, C 2021, 'Clinical reasoning in traditional medicine exemplified by the clinical encounter of Korean medicine', Integrative Medicine Research, vol. 10, no. 2, pp. 100641-100641.
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King, WL, Kaestli, M, Siboni, N, Padovan, A, Christian, K, Mills, D, Seymour, J & Gibb, K 2021, 'Pearl Oyster Bacterial Community Structure Is Governed by Location and Tissue-Type, but Vibrio Species Are Shared Among Oyster Tissues', Frontiers in Microbiology, vol. 12, pp. 1-11.
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Diseases of bivalves of aquacultural importance, including the valuable Australian silver-lipped pearl oyster (Pinctada maxima), have been increasing in frequency and severity. The bivalve microbiome is linked to health and disease dynamics, particularly in oysters, with putative pathogens within the Vibrio genus commonly implicated in oyster diseases. Previous studies have been biased toward the Pacific oyster because of its global dominance in oyster aquaculture, while much less is known about the microbiome of P. maxima. We sought to address this knowledge gap by characterizing the P. maxima bacterial community, and we hypothesized that bacterial community composition, and specifically the occurrence of Vibrio, will vary according to the sampled microenvironment. We also predicted that the inside shell swab bacterial composition could represent a source of microbial spillover biofilm into the solid pearl oyster tissues, thus providing a useful predictive sampling environment. We found that there was significant heterogeneity in bacterial composition between different pearl oyster tissues, which is consistent with patterns reported in other bivalve species and supports the hypothesis that each tissue type represents a unique microenvironment for bacterial colonization. We suggest that, based on the strong effect of tissue-type on the pearl oyster bacterial community, future studies should apply caution when attempting to compare microbial patterns from different locations, and when searching for disease agents. The lack of association with water at each farm also supported the unique nature of the microbial communities in oyster tissues. In contrast to the whole bacterial community, there was no significant difference in the Vibrio community among tissue types nor location. These resu...
Kiran, MR, Farrok, O, Islam, MR, Zhu, J, Kouzani, AZ & Mahmud, MAP 2021, 'The High Frequency Magnetic-Link With Distributed HTS YBCO Windings for Power Converter Applications', IEEE Transactions on Applied Superconductivity, vol. 31, no. 8, pp. 1-5.
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Klingberg, J, Cawley, A, Shimmon, R & Fu, S 2021, 'Towards compound identification of synthetic opioids in nontargeted screening using machine learning techniques', Drug Testing and Analysis, vol. 13, no. 5, pp. 990-1000.
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AbstractThe constant evolution of the illicit drug market makes the identification of unknown compounds problematic. Obtaining certified reference materials for a broad array of new analogues can be difficult and cost prohibitive. Machine learning provides a promising avenue to putatively identify a compound before confirmation against a standard. In this study, machine learning approaches were used to develop class prediction and retention time prediction models. The developed class prediction model used a naïve Bayes architecture to classify opioids as belonging to either the fentanyl analogues, AH series or U series, with an accuracy of 89.5%. The model was most accurate for the fentanyl analogues, most likely due to their greater number in the training data. This classification model can provide guidance to an analyst when determining a suspected structure. A retention time prediction model was also trained for a wide array of synthetic opioids. This model utilised Gaussian process regression to predict the retention time of analytes based on multiple generated molecular features with 79.7% of the samples predicted within ±0.1 min of their experimental retention time. Once the suspected structure of an unknown compound is determined, molecular features can be generated and input for the prediction model to compare with experimental retention time. The incorporation of machine learning prediction models into a compound identification workflow can assist putative identifications with greater confidence and ultimately save time and money in the purchase and/or production of superfluous certified reference materials.
Klingberg, J, Cawley, A, Shimmon, R, Fouracre, C, Pasin, D & Fu, S 2021, 'Finding the proverbial needle: Non‐targeted screening of synthetic opioids in equine plasma', Drug Testing and Analysis, vol. 13, no. 5, pp. 977-989.
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AbstractSynthetic opioids are a class of compounds that are of particular concern due to their high potency and potential health impacts. With the relentless emergence of new synthetic opioid derivatives, non‐targeted screening strategies are required that do not rely on the use of library spectra or reference materials. In this study, product ion searching, and Kendrick mass defect analysis were investigated for non‐targeted screening of synthetic opioids. The estimated screening cut‐offs for these techniques ranged between 0.05 and 0.1 ng/mL. These techniques were designed to not be reliant on a particular vendor's software, meaning that they can be applied to existing drug screening protocols, without requiring the development and validation of new analytical procedures. The efficacy of the developed techniques was tested through blind trials, with spiked samples inserted amongst authentic plasma samples, which demonstrated the usefulness of these methods for high‐throughput screening. The use of a non‐targeted screening workflow that contains complementary techniques can increase the likelihood of detecting compounds of interest within a sample, as well as the confidence in detections that are made.
Klionsky, DJ, Abdel-Aziz, AK, Abdelfatah, S, Abdellatif, M, Abdoli, A, Abel, S, Abeliovich, H, Abildgaard, MH, Abudu, YP, Acevedo-Arozena, A, Adamopoulos, IE, Adeli, K, Adolph, TE, Adornetto, A, Aflaki, E, Agam, G, Agarwal, A, Aggarwal, BB, Agnello, M, Agostinis, P, Agrewala, JN, Agrotis, A, Aguilar, PV, Ahmad, ST, Ahmed, ZM, Ahumada-Castro, U, Aits, S, Aizawa, S, Akkoc, Y, Akoumianaki, T, Akpinar, HA, Al-Abd, AM, Al-Akra, L, Al-Gharaibeh, A, Alaoui-Jamali, MA, Alberti, S, Alcocer-Gómez, E, Alessandri, C, Ali, M, Alim Al-Bari, MA, Aliwaini, S, Alizadeh, J, Almacellas, E, Almasan, A, Alonso, A, Alonso, GD, Altan-Bonnet, N, Altieri, DC, Álvarez, ÉMC, Alves, S, Alves da Costa, C, Alzaharna, MM, Amadio, M, Amantini, C, Amaral, C, Ambrosio, S, Amer, AO, Ammanathan, V, An, Z, Andersen, SU, Andrabi, SA, Andrade-Silva, M, Andres, AM, Angelini, S, Ann, D, Anozie, UC, Ansari, MY, Antas, P, Antebi, A, Antón, Z, Anwar, T, Apetoh, L, Apostolova, N, Araki, T, Araki, Y, Arasaki, K, Araújo, WL, Araya, J, Arden, C, Arévalo, M-A, Arguelles, S, Arias, E, Arikkath, J, Arimoto, H, Ariosa, AR, Armstrong-James, D, Arnauné-Pelloquin, L, Aroca, A, Arroyo, DS, Arsov, I, Artero, R, Asaro, DML, Aschner, M, Ashrafizadeh, M, Ashur-Fabian, O, Atanasov, AG, Au, AK, Auberger, P, Auner, HW, Aurelian, L, Autelli, R, Avagliano, L, Ávalos, Y, Aveic, S, Aveleira, CA, Avin-Wittenberg, T, Aydin, Y, Ayton, S, Ayyadevara, S, Azzopardi, M, Baba, M, Backer, JM, Backues, SK, Bae, D-H, Bae, O-N, Bae, SH, Baehrecke, EH, Baek, A, Baek, S-H, Baek, SH, Bagetta, G, Bagniewska-Zadworna, A, Bai, H, Bai, J, Bai, X, Bai, Y, Bairagi, N, Baksi, S, Balbi, T, Baldari, CT, Balduini, W, Ballabio, A, Ballester, M, Balazadeh, S, Balzan, R, Bandopadhyay, R, Banerjee, S, Banerjee, S, Bánréti, Á, Bao, Y, Baptista, MS, Baracca, A, Barbati, C, Bargiela, A, Barilà, D, Barlow, PG, Barmada, SJ, Barreiro, E, Barreto, GE, Bartek, J, Bartel, B, Bartolome, A, Barve, GR, Basagoudanavar, SH, Bassham, DC, Bast, RC, Basu, A, Batoko, H, Batten, I, Baulieu, EE, Baumgarner, BL, Bayry, J, Beale, R, Beau, I, Beaumatin, F, Bechara, LRG, Beck, GR, Beers, MF, Begun, J, Behrends, C, Behrens, GMN, Bei, R, Bejarano, E, Bel, S, Behl, C, Belaid, A, Belgareh-Touzé, N, Bellarosa, C, Belleudi, F, Belló Pérez, M, Bello-Morales, R, Beltran, JSDO, Beltran, S, Benbrook, DM, Bendorius, M, Benitez, BA, Benito-Cuesta, I & et al. 2021, 'Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1', Autophagy, vol. 17, no. 1, pp. 1-382.
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Klont, F, Kwiatkowski, M, Faiz, A, van den Bosch, T, Pouwels, SD, Dekker, FJ, ten Hacken, NHT, Horvatovich, P & Bischoff, R 2021, 'Adsorptive Microtiter Plates As Solid Supports in Affinity Purification Workflows', Journal of Proteome Research, vol. 20, no. 11, pp. 5218-5221.
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Affinity ligands such as antibodies are widely used in (bio)medical research for purifying proteins from complex biological samples. These ligands are generally immobilized onto solid supports which facilitate the separation of a captured protein from the sample matrix. Adsorptive microtiter plates are commonly used as solid supports prior to immunochemical detection (e.g., immunoassays) but hardly ever prior to liquid chromatography-mass spectrometry (LC-MS-)-based detection. Here, we describe the use of adsorptive microtiter plates for protein enrichment prior to LC-MS detection, and we discuss opportunities and challenges of corresponding workflows, based on examples of targeted (i.e., soluble receptor for advanced glycation end-products (sRAGE) in human serum) and discovery-based workflows (i.e., transcription factor p65 (NF-κB) in lysed murine RAW 264.7 macrophages and peptidyl-prolyl cis-trans isomerase FKBP5 (FKBP5) in lysed human A549 alveolar basal epithelial cells). Thereby, we aim to highlight the potential usefulness of adsorptive microtiter plates in affinity purification workflows prior to LC-MS detection, which could increase their usage in mass spectrometry-based protein research.
Kong, M, Gu, Y, Chai, Y, Ke, J, Liu, Y, Xu, X, Li, Z, Feng, W & Li, F 2021, 'Luminescence interference-free lifetime nanothermometry pinpoints in vivo temperature', Science China Chemistry, vol. 64, no. 6, pp. 974-984.
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Koong, J, Johnson, C, Rafei, R, Hamze, M, Myers, GSA, Kenyon, JJ, Lopatkin, AJ & Hamidian, M 2021, 'Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1', Microbial Genomics, vol. 7, no. 12.
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Acinetobacter baumannii is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global lineages, namely global clones 1 and 2 (GC1 and GC2). Here, we used a combination of Illumina short read and MinION (Oxford Nanopore) long-read sequence data with a hybrid assembly approach to complete the genome sequence of two antibiotic-sensitive GC1 strains, Ex003 and Ax270, recovered in Lebanon from water and a rectal swab of a cat, respectively. Phylogenetic analysis of Ax270 and Ex003 with 186 publicly available GC1 genomes revealed two major clades, including five main lineages (L1–L5), and four single-isolate lineages outside of the two clades. Ax270 and Ex003, along with AB307-0294 and MRSN7213 (both predicted antibiotic-susceptible isolates) represent these individual lineages. Antibiotic resistance islands and transposons interrupting the comM gene remain important features in L1–L5, with L1 associated with the AbaR-type resistance islands, L2 with AbaR4, L3 strains containing either AbaR4 or its variants as well as Tn6022::ISAba42, and L4 and L5 associated with Tn6022 or its variants. Analysis of the capsule (KL) and outer core (OCL) polysaccharide loci further revealed a complex evolutionary history probably involving many recombination events. As more genomes become available, more GC1 lineages continue to emerge. However, genome sequence data from more diverse geograp...
Kordzahiya, NE & Novikov, AA 2021, 'On maximal inequalities for Ornstein-Uhlenbeck processes with jumps', Теория вероятностей и ее применения, vol. 66, no. 4, pp. 895-913.
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Получены моментные и экспоненциальные неравенства для максимума обобщенного процесса Орнштейна-Уленбека при некоторых предположениях на хвосты распределения скачкообразной компоненты.
Krishnaswamy, S, Ageno, W, Arabi, Y, Barbui, T, Cannegieter, S, Carrier, M, Cleuren, AC, Collins, P, Panicot‐Dubois, L, Freedman, JE, Freson, K, Hogg, P, James, AH, Kretz, CA, Lavin, M, Leebeek, FWG, Li, W, Maas, C, Machlus, K, Makris, M, Martinelli, I, Medved, L, Neerman‐Arbez, M, O’Donnell, JS, O'Sullivan, J, Rajpurkar, M, Schroeder, V, Spiegel, PC, Stanworth, SJ, Green, L & Undas, A 2021, 'Illustrated State‐of‐the‐Art Capsules of the ISTH 2021 Congress', Research and Practice in Thrombosis and Haemostasis, vol. 5, no. 5, pp. e12532-e12532.
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Królas, W, Ibarra, A, Arbeiter, F, Arranz, F, Bernardi, D, Cappelli, M, Castellanos, J, Dézsi, T, Dzitko, H, Favuzza, P, García, A, Gutiérrez, J, Lewitowicz, M, Maj, A, Martin-Fuertes, F, Micciché, G, Muñoz, A, Nitti, FS, Pinna, T, Podadera, I, Pons, J, Qiu, Y, Román, R, Toth, M & Zsakai, A 2021, 'The IFMIF-DONES fusion oriented neutron source: evolution of the design', Nuclear Fusion, vol. 61, no. 12, pp. 125002-125002.
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Abstract IFMIF-DONES is a powerful neutron irradiation facility for the study and qualification of materials planned as part of the European roadmap to fusion-generated electricity. Its main goal is to study properties of materials under severe irradiation in a neutron field similar to the one in a fusion reactor first wall. It is a key facility to prepare for the construction of the DEMO power plant envisaged to follow ITER. The decision to start the construction of IFMIF-DONES is expected imminent. In this paper we present and discuss several key technical studies and decisions to improve and optimize the engineering design of IFMIF-DONES which were carried out as part of the activities in the framework of the EUROfusion Early Neutron Source work package (2015–2020). The following topics are discussed in this paper: the new layout of the IFMIF-DONES SRF LINAC accelerator and high-energy beam transport line, 7Be impurity management approach for the lithium loop, a maintainable test cell concept, a revised layout of the access cell for the remote maintenance operations, and facilities for complementary experiments.
Kuchibhotla, VNS, Starkey, MR, Reid, AT, Heijink, IH, Nawijn, MC, Hansbro, PM & Knight, DA 2021, 'Inhibition of β-Catenin/CREB Binding Protein Signaling Attenuates House Dust Mite-Induced Goblet Cell Metaplasia in Mice', Frontiers in Physiology, vol. 12.
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Excessive mucus production is a major feature of allergic asthma. Disruption of epithelial junctions by allergens such as house dust mite (HDM) results in the activation of β-catenin signaling, which has been reported to stimulate goblet cell differentiation. β-catenin interacts with various co-activators including CREB binding protein (CBP) and p300, thereby regulating the expression of genes involved in cell proliferation and differentiation, respectively. We specifically investigated the role of the β-catenin/CBP signaling pathway in goblet cell metaplasia in a HDM-induced allergic airway disease model in mice using ICG-001, a small molecule inhibitor that blocks the binding of CBP to β-catenin. Female 6- 8-week-old BALB/c mice were sensitized to HDM/saline on days 0, 1, and 2, followed by intranasal challenge with HDM/saline with or without subcutaneous ICG-001/vehicle treatment from days 14 to 17, and samples harvested 24 h after the last challenge/treatment. Differential inflammatory cells in bronchoalveolar lavage (BAL) fluid were enumerated. Alcian blue (AB)/Periodic acid–Schiff (PAS) staining was used to identify goblet cells/mucus production, and airway hyperresponsiveness (AHR) was assessed using invasive plethysmography. Exposure to HDM induced airway inflammation, goblet cell metaplasia and increased AHR, with increased airway resistance in response to the non-specific spasmogen methacholine. Inhibition of the β-catenin/CBP pathway using treatment with ICG-001 significantly attenuated the HDM-induced goblet cell metaplasia and infiltration of macrophages, but had no effect on eosinophils, neutrophils, lymphocytes or AHR. Increased β-catenin/CBP signaling may promote HDM-induced goblet cell metaplasia in mice.
Kulkarni, MP, Kiran, PSS, Singh, K, Dua, K, Tanwar, S, Satija, S, Singh, V & Kumar, R 2021, 'A Review of Basics and Potential of Liquid Crystalline Nanoparticles as Drug Delivery Systems', Nanoscience & Nanotechnology-Asia, vol. 11, no. 6.
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Aim: For procuring the stable form of drug delivery, tremendous efforts have been made in developing new drug delivery vectors. One such approach that meets the desired stability standards is Liquid Crystalline Nanoparticles (LCNs). Background:The liquid crystals are the intermediate forms of solid and liquid materials, which hold high tolerance to bear the influences of physical parameters. The liquid crystals are employed in nanotechnology to find the best way to produce the intended action of customized targeting drug delivery. The structural alignment is another critical aspect to consider, as these can accommodate wholesome drug amounts. Methods:From the studies, it has been evident that distinct characteristics like the simplicity in structure, self-assembling properties, feasibility of production, efficacy in delivery with low toxic values, have addressed the excellency of LCNs. Conclusion:The current review focusses on key areas regarding the nature of liquid crystal, diverse forms, technologies used to transform them into the desired nanoparticles, and their applications as drug delivery carriers as well as theranostic agent.
Kumar, S, Kumar, M, Chandola, VK, Kumar, V, Saini, RK, Pant, N, Kumari, N, Srivastava, A, Singh, S, Singh, R, Krishan, G, Induwar, SP, Kumar, S, Yadav, BK, Maurya, NS & Chaudhary, A 2021, 'Groundwater Quality Issues and Challenges for Drinking and Irrigation Uses in Central Ganga Basin Dominated with Rice-Wheat Cropping System', Water, vol. 13, no. 17, pp. 2344-2344.
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Increased population and increasing demands for food in the Indo-Gangetic plain are likely to exert pressure on fresh water due to rise in demand for drinking and irrigation water. The study focuses on Bhojpur district, Bihar located in the central Ganga basin, to assess the groundwater quality for drinking and irrigation purpose and discuss the issues and challenges. Groundwater is mostly utilized in the study area for drinking and irrigation purposes (major crops sown in the area are rice and wheat). There were around 45 groundwater samples collected across the study region in the pre-monsoon season (year 2019). The chemical analytical results show that Ca2+, Mg2+ and HCO3− ions are present in abundance in groundwater and governing the groundwater chemistry. Further analysis shows that 66%, 69% and 84% of the samples exceeded the acceptable limit of arsenic (As), Fe and Mn respectively and other trace metals (Cu, Zn, Pb, Cd) are within the permissible limit of drinking water as prescribed by Bureau of Indian Standard for drinking water. Generally, high As concentration has been found in the aquifer (depth ranges from 20 to 40 m below ground surface) located in proximity of river Ganga. For assessing the irrigation water quality, sodium adsorption ratio (SAR) values, residual sodium carbonate (RSC), Na%, permeability index (PI) and calcium alteration index (CAI) were calculated and found that almost all the samples are found to be in good to excellent category for irrigation purposes. The groundwater facie has been classified into Ca-Mg-HCO3 type.
Kumar, U, Srivastava, A, Kumari, N, Rashmi, Sahoo, B, Chatterjee, C & Raghuwanshi, NS 2021, 'Evaluation of Spatio-Temporal Evapotranspiration Using Satellite-Based Approach and Lysimeter in the Agriculture Dominated Catchment', Journal of the Indian Society of Remote Sensing, vol. 49, no. 8, pp. 1939-1950.
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Crop coefficient (Kc) represents the actual crop growth of the crop. It plays an important role in estimating water requirements at the different growth stages of the crop. However, FAO 56 Penman–Monteith Kc method does not account for spatial heterogeneity and uncertainty for regional climatic conditions significantly. Therefore, this study aims to develop the relation between Kc and normalized difference vegetation index (NDVI) using a linear regression and back calculations. These relationships were adjusted to local conditions using information from survey data obtained during Rabi season (2014–2015). The NDVI–Kc model (r2 = 0.86) has developed using NDVI–Kc from a fine resolution Landsat 8 remote sensing data. NDVI–Kc regression equation was utilized for generating crop coefficient for different month of season. The Vegetation Index-based AET estimated was evaluated with lysimeter data for different crop growth stage across the season. The results have shown that NDVI–Kc estimated AET has been better correlated with NDVI–Kc remote sensing model. Thus, the output of this research can help to calculate actual water demand in a command area and be helpful in allocating water from less demand area toward more demand area.
Kumari, N, Srivastava, A & Dumka, UC 2021, 'A Long-Term Spatiotemporal Analysis of Vegetation Greenness over the Himalayan Region Using Google Earth Engine', Climate, vol. 9, no. 7, pp. 109-109.
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The Himalayas constitute one of the richest and most diverse ecosystems in the Indian sub-continent. Vegetation greenness driven by climate in the Himalayan region is often overlooked as field-based studies are challenging due to high altitude and complex topography. Although the basic information about vegetation cover and its interactions with different hydroclimatic factors is vital, limited attention has been given to understanding the response of vegetation to different climatic factors. The main aim of the present study is to analyse the relationship between the spatiotemporal variability of vegetation greenness and associated climatic and hydrological drivers within the Upper Khoh River (UKR) Basin of the Himalayas at annual and seasonal scales. We analysed two vegetation indices, namely, normalised difference vegetation index (NDVI) and enhanced vegetation index (EVI) time-series data, for the last 20 years (2001–2020) using Google Earth Engine. We found that both the NDVI and EVI showed increasing trends in the vegetation greening during the period under consideration, with the NDVI being consistently higher than the EVI. The mean NDVI and EVI increased from 0.54 and 0.31 (2001), respectively, to 0.65 and 0.36 (2020). Further, the EVI tends to correlate better with the different hydroclimatic factors in comparison to the NDVI. The EVI is strongly correlated with ET with r2 = 0.73 whereas the NDVI showed satisfactory performance with r2 = 0.45. On the other hand, the relationship between the EVI and precipitation yielded r2 = 0.34, whereas there was no relationship was observed between the NDVI and precipitation. These findings show that there exists a strong correlation between the EVI and hydroclimatic factors, which shows that changes in vegetation phenology can be better captured using the EVI than the NDVI.
Kumari, N, Srivastava, A, Sahoo, B, Raghuwanshi, NS & Bretreger, D 2021, 'Identification of Suitable Hydrological Models for Streamflow Assessment in the Kangsabati River Basin, India, by Using Different Model Selection Scores', Natural Resources Research, vol. 30, no. 6, pp. 4187-4205.
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The increasing demand for water in developing countries, like India, requires efficient water management and resource allocation. This is crucial to accurately assess and predict hydrological processes such as streamflow, drought, and flood. However, simulations of these hydrologic processes from various hydrological models differ in their accuracy. By analyzing different characteristics of hydrological models, selection scores can be used to select the best model for the intended purpose based on their inherit strengths (i.e., some models are better for streamflow prediction). In this study, 13 different criteria were used for the model selection scores including temporal and spatial resolutions, and processes involved. Thereafter, based on different scores, we selected two different hydrological models for streamflow prediction in the Kangsabati River Basin (KRB) in eastern India, namely (1) Génie Rural à 4 paramètres Journalier (GR4J), a conceptual model, and (2) Variable Infiltration Capacity (VIC), a semi-distributed model. The models were calibrated against the daily observed streamflow at upper KRB (Reservoir) and lower KRB (Mohanpur) from 2000 to 2006 and validated during the period from 2008 to 2010. Despite the differences in model structure and data used, both models simulated streamflow at a daily time scale with Nash–Sutcliffe coefficient of 0.71–0.82 for the VIC model and 0.63–0.71 for the GR4J. Due to the simpler structure, parsimonious nature, fewer parameters, and reasonable accuracy, the results suggest that a conceptual rainfall—runoff model like GR4J can be used in data-deficient conditions.
Labeeuw, L, Commault, AS, Kuzhiumparambil, U, Emmerton, B, Nguyen, LN, Nghiem, LD & Ralph, PJ 2021, 'A comprehensive analysis of an effective flocculation method for high quality microalgal biomass harvesting', Science of The Total Environment, vol. 752, pp. 141708-141708.
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Lagune, M, Petit, C, Sotomayor, FV, Johansen, MD, Beckham, KSH, Ritter, C, Girard-Misguich, F, Wilmanns, M, Kremer, L, Maurer, FP & Herrmann, J-L 2021, 'Conserved and specialized functions of Type VII secretion systems in non-tuberculous mycobacteria', Microbiology, vol. 167, no. 7.
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Non-tuberculous mycobacteria (NTM) are a large group of micro-organisms comprising more than 200 individual species. Most NTM are saprophytic organisms and are found mainly in terrestrial and aquatic environments. In recent years, NTM have been increasingly associated with infections in both immunocompetent and immunocompromised individuals, prompting significant efforts to understand the diverse pathogenic and signalling traits of these emerging pathogens. Since the discovery of Type VII secretion systems (T7SS), there have been significant developments regarding the role of these complex systems in mycobacteria. These specialised systems, also known as Early Antigenic Secretion (ESX) systems, are employed to secrete proteins across the inner membrane. They also play an essential role in virulence, nutrient uptake and conjugation. Our understanding of T7SS in mycobacteria has significantly benefited over the last few years, from the resolution of ESX-3 structure in Mycobacterium smegmatis , to ESX-5 structures in Mycobacterium xenopi and Mycob...
Lai, W-H, Zhang, L, Yan, Z, Hua, W, Indris, S, Lei, Y, Liu, H, Wang, Y-X, Hu, Z, Liu, HK, Chou, S, Wang, G & Dou, SX 2021, 'Activating Inert Surface Pt Single Atoms via Subsurface Doping for Oxygen Reduction Reaction', Nano Letters, vol. 21, no. 19, pp. 7970-7978.
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The performance of single-atom catalysts strongly depends on their particular coordination environments in the near-surface region. Herein, we discover that engineering extra Pt single atoms in the subsurface (Ptsubsurf) can significantly enhance the catalytic efficiency of surface Pt single atoms toward the oxygen reduction reaction (ORR). We experimentally and theoretically investigated the effects of the Ptsubsurf single atoms implanted in different positions of the subsurface of Co particles. The local environments and catalytic properties of surface Pt1 are highly tunable via Ptsubsurf doping. Specifically, the obtained Pt1@Co/NC catalyst displays a remarkable performance for ORR, achieving mass activity of 4.2 mA μgPt-1 (28 times higher than that of commercial Pt/C) at 0.9 V versus reversible hydrogen electrode (RHE) in 0.1 M HClO4 solution with high stability over 30000 cycles.
Laiolo, L, Matear, R, Soja-Woźniak, M, Suggett, DJ, Hughes, DJ, Baird, ME & Doblin, MA 2021, 'Modelling the impact of phytoplankton cell size and abundance on inherent optical properties (IOPs) and a remotely sensed chlorophyll-a product', Journal of Marine Systems, vol. 213, pp. 103460-103460.
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© 2020 Elsevier B.V. Ocean colour data are commonly used to quantify primary production, study phytoplankton dynamics and calibrate marine models, thus understanding the origin of errors in the retrieved chlorophyll-a (Chl-a) product is critical. One source of uncertainty in retrieved Chl-a products can be related to large photosynthetic cells, characterised by lower mass-specific absorption coefficients due to increased packaging effect. Here, we explore the relationship between phytoplankton size structure and an ocean colour product using optical simulations and in situ observations. Specifically, we use an optical model to explore how phytoplankton cell size and abundance influence phytoplankton absorption and backscattering coefficients and the implication this has for water leaving radiance and the estimated Chl-a derived from satellite ocean colour. The optical model simulations show phytoplankton cell size has a significant impact on the remote-sensing reflectance, with Chl-a packaged in 5 to 10 μm cells resulting in about 54 to 76% the simulated ocean colour Chl-a compared to 1 μm cells, as determined by an algorithm that converts reflectances to Chl-a. To support optical simulations, size-fractionated Chl-a samples were collected from several water masses to investigate the phytoplankton size contribution (i.e., < 2 μm, 2–10 μm and > 10 μm) to the total Chl-a. We focused on the offshore eastern Australian ocean region, largely characterised by oligotrophic waters in which phytoplankton dominate the optical properties of the water column. Of the 22 stations sampled, a total of ten in situ size fractionated Chl-a measurements were matched-up with the corresponding clear-sky satellite Chl-a product. The matched-up points revealed a systematic underestimation of in situ Chl-a. With the low amount of data, it was not possible to statistically relate the satellite underestimation to a specific phytoplankton size class, but the observations showed th...
Lapwong, Y, Dejtaradol, A & Webb, JK 2021, 'Plasticity in thermal hardening of the invasive Asian house gecko', Evolutionary Ecology, vol. 35, no. 4, pp. 631-641.
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The Asian house gecko (Hemidactylus frenatus) is a tropical invasive species that has established and spread throughout several temperate regions around the world. In some invasive species, rapid thermal acclimation (thermal hardening) may contribute to their success in occupying a wide range of climates. In this study, we investigated whether invasive house geckos from southeastern Australia show differing thermal hardening responses than individuals from the native range in Thailand. In the laboratory, we measured the basal heat tolerance (CTmax) of the geckos and their heat hardening response after being subjected to the second thermal stress after 1, 3, 5, 7, 9, or 11 h. When geckos had recovered, we measured their basal cold tolerance (CTmin) and cold hardening response over the same time intervals. We then explored whether hardening responses differed between populations or among time intervals. We found that basal heat tolerances did not differ between populations, but geckos from Australia had lower cold tolerance than geckos from Thailand. The magnitude of the heat hardening was similar between populations, but the introduced geckos had a higher magnitude of cold hardening. The native geckos could maximize their cold tolerance capacity for only 0.6 °C, versus 0.9 °C for the introduced geckos. Also, geckos from Australia exhibited faster responses to thermal stress than did geckos from Thailand. Maximum thermal tolerances as a result of hardening responses peaked within three hours after thermal stress in Australian geckos (adjusted means = 44.0 °C for CTmax and 9.9 °C for CTmin) and at five hours after thermal stress in Thailand geckos (adjusted means = 44.2 °C and 10.2 °C, respectively). The plasticity in the thermal hardening of the invasive gecko should enable it to survive rapid temperature fluctuations, especially winter cold snaps that occur in temperate regions.
Lapwong, Y, Dejtaradol, A & Webb, JK 2021, 'Shifts in thermal tolerance of the invasive Asian house gecko (Hemidactylus frenatus) across native and introduced ranges', Biological Invasions, vol. 23, no. 4, pp. 989-996.
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The ability to rapidly adjust thermal tolerance in response to variable temperatures may facilitate the success of invasive species in non-native ranges. The Asian house gecko Hemidactylus frenatus is native to the tropics of South and Southeast Asia. This small lizard has spread across the globe and has also successfully invaded colder regions of Australia. In this study, we investigated whether this species displays plasticity in thermal tolerance in its introduced range. We measured cold tolerance (CTmin) and heat tolerance (CTmax) of H. frenatus from two native tropical populations in Thailand, and two introduced subtropical populations in southeastern Australia. We also explored seasonal variation in the thermal tolerance of the introduced populations. We found that heat tolerance (CTmax) of geckos did not differ among four populations in Thailand and Australia (range = 43.4–43.7 °C). By contrast, geckos from southeastern Australia had lower cold tolerance (CTmin) (mean = 10.43 °C) than geckos from Thailand (mean = 11.57 °C). We also documented seasonal shifts in cold tolerance of H. frenatus from southeastern Australia. Geckos captured in winter had cold tolerances 1–2 °C lower than those captured in summer. Unexpectedly, this shift in cold tolerance was accompanied by a 1–2 °C upward shift in heat tolerance. Our results support a growing body of evidence showing that tropical invaders can adjust cold tolerance downwards via plasticity or acclimation. Such changes may allow tropical invaders to expand their geographic range into colder regions of non-native ranges.
Larkin, BP, Nguyen, LT, Hou, M, Glastras, SJ, Chen, H, Wang, R, Pollock, CA & Saad, S 2021, 'Novel Role of Gestational Hydralazine in Limiting Maternal and Dietary Obesity-Related Chronic Kidney Disease', Frontiers in Cell and Developmental Biology, vol. 9.
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BackgroundMaternal obesity is a risk factor for chronic kidney disease (CKD) in offspring, underpinning the theory of the developmental origins of health and disease. DNA methylation has been implicated in the programming of adult chronic disease by maternal obesity, therefore, DNA demethylating agents may mitigate offspring risk of disease. In rodent models, low-dose hydralazine has previously been shown to reduce renal fibrosis via DNA demethylation. We used mouse models of maternal obesity and offspring obesity to determine whether administration of low-dose hydralazine during gestation can prevent fetal programming of CKD in offspring.MethodsFemale C57BL/6 mice received high fat diet (HFD) or chow prior to mating, during gestation and lactation. During gestation, dams received subcutaneous hydralazine (5 mg/kg) or saline thrice-weekly. Male offspring weaned to HFD or chow, which continued until endpoint at 32 weeks. Biometric and metabolic parameters, renal global DNA methylation, renal functional and structural changes, and renal markers of fibrosis, inflammation and oxidative stress were assessed at endpoint.ResultsOffspring exposed to maternal obesity or diet-induced obesity had significantly increased renal global DNA methylation, together with other adverse renal effects including albuminuria, glomerulosclerosis, renal fibrosis, and oxidative stress. Offspring exposed to gestational hydralazine had significantly reduced renal global DNA methylation. In obese offspring of obese mothers, gestational hydralazine significantly decreased albuminuria, glomerulosclerosis, and serum creatinine. Obese offspring of hydralazine-treated lean mothers displayed reduced markers of renal fibrosis and oxidative stress.ConclusionGesta...
Larkin, BP, Saad, S, Glastras, SJ, Nguyen, LT, Hou, M, Chen, H, Wang, R & Pollock, CA 2021, 'Low-dose hydralazine during gestation reduces renal fibrosis in rodent offspring exposed to maternal high fat diet', PLOS ONE, vol. 16, no. 3, pp. e0248854-e0248854.
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BackgroundMaternal high fat diet (HFD) promotes chronic kidney disease (CKD) in offspring. This is in accordance with the theory of fetal programming, which suggests adverse conditions occurring in utero predispose offspring to chronic conditions later in life. DNA methylation has been proposed as a key mechanism by which fetal programming occurs and is implicated in CKD progression. DNA demethylating drugs may interrupt the fetal programming of CKD by maternal obesity. Hydralazine, an antihypertensive agent, demethylates DNA at low doses which do not reduce blood pressure. We used a mouse model of maternal obesity to determine whether gestational administration of low-dose hydralazine to mothers can prevent CKD in offspring.MethodsC57BL/6 dams received HFD or chow from 6 weeks prior to mating and were administered subcutaneous hydralazine (5mg/kg) or saline thrice weekly during gestation. Male offspring were weaned to chow and were sacrificed at either postnatal week 9 or week 32. Biometric and metabolic parameters, renal global DNA methylation, renal structural and functional changes and markers of fibrosis, oxidative stress and inflammation were measured in offspring at weeks 9 and 32.ResultsIn week 9 offspring, maternal HFD consumption did not significantly alter anthropometric or metabolic parameters, or renal global DNA methylation. Week 32 offspring had increased renal global DNA methylation, together with albuminuria, glomerulosclerosis, renal fibrosis and oxidative stress. Administration of low-dose hydralazine to obese mothers during gestation reduced renal global DNA methylation and renal fibrotic markers in week 32 offspring.Conclusion...
Larkin, MF, Davis, TR, Harasti, D, Cadiou, G, Poulos, DE & Smith, SDA 2021, 'The rapid decline of an Endangered temperate soft coral species', Estuarine, Coastal and Shelf Science, vol. 255, pp. 107364-107364.
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Lawson, CA, Raina, J, Deschaseaux, E, Hrebien, V, Possell, M, Seymour, JR & Suggett, DJ 2021, 'Heat stress decreases the diversity, abundance and functional potential of coral gas emissions', Global Change Biology, vol. 27, no. 4, pp. 879-891.
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AbstractTerrestrial ecosystems emit large quantities of biogenic volatile organic compounds (BVOCs), many of which play important roles in abiotic stress responses, pathogen and grazing defences, inter‐ and intra‐species communications, and climate regulation. Conversely, comparatively little is known about the diversity and functional potential of BVOCs produced in the marine environment, especially in highly productive coral reefs. Here we describe the first ‘volatilomes’ of two common reef‐building corals, Acropora intermedia and Pocillopora damicornis, and how the functional potential of their gaseous emissions is altered by heat stress events that are driving rapid deterioration of coral reef ecosystems worldwide. A total of 87 BVOCs were detected from the two species and the chemical richness of both coral volatilomes—particularly the chemical classes of alkanes and carboxylic acids—decreased during heat stress by 41% and 62% in A. intermedia and P. damicornis, respectively. Across both coral species, the abundance of individual compounds changed significantly during heat stress, with the majority (>86%) significantly decreasing compared to control conditions. Additionally, almost 60% of the coral volatilome (or 52 BVOCs) could be assigned to four key functional groups based on their activities in other species or systems, including stress response, chemical signalling, climate regulation and antimicrobial activity. The total number of compounds assigned to these functions decreased significantly under heat stress for both A. intermedia (by 35%) and P. damicornis (by 64%), with most dramatic losses found for climatically active BVOCs in P. damicornis and antimicrobial BVOCs in A. intermedia. Together...
Leal, E, de Beyer, L, O'Connor, W, Dove, M, Ralph, PJ & Pernice, M 2021, 'Production optimisation of Tisochrysis lutea as a live feed for juvenile Sydney rock oysters, Saccostrea glomerata, using large-scale photobioreactors', Aquaculture, vol. 533, pp. 736077-736077.
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© 2020 Elsevier B.V. The aquaculture industry uses microalgae as a live feed for juvenile oysters in hatcheries to meet their nutritional requirements, including their need for several essential Poly Unsaturated Fatty Acids (PUFAs) such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). The mass culture of microalgae is not only a major bottleneck for the production of juvenile oysters, but also a significant cost, accounting for 20–50% of hatchery operating costs. Currently, low biomass concentrations, high production costs and poor cultivation systems limit the quantity and quality of microalgae feed. This study focused on Tisochrysis lutea, a microalgae species commonly used in aquaculture, and we assessed the potential of photobioreactors with an improved light source and CO2 input to increase biomass production and improve biochemical composition of algal feed. Two photobioreactor systems were compared: the current industry set up (DPI) comprising fluorescent lighting and minimal CO2 input versus an optimized system utilising LEDs and increased CO2. Cultures of T. lutea were monitored over a 12-day growth period and harvested on day 14 for biochemical analysis. Final cell density was significantly higher in the optimized system relative to the conventional culture systems (6.2 × 106 cells / mL versus 3.7 × 106 cells / mL, respectively). The biochemical profile of T. lutea was not significantly different between the two photobioreactors systems. The algal biomass produced during this comparative experiment was used in a feeding trial on oyster spat, Saccostrea glomerata. Spat fed with algae produced in optimized vs conventional photobioreactors showed no significant difference in growth, but oyster spat fed with T. lutea grown in optimized photobioreactors did show a significant increase in their EPA content. Overall, our results contribute to our understanding of how altered culture conditions affect microalgal production and biochemical composit...
Lee, L-Y, Hew, GSY, Mehta, M, Shukla, SD, Satija, S, Khurana, N, Anand, K, Dureja, H, Singh, SK, Mishra, V, Singh, PK, Gulati, M, Prasher, P, Aljabali, AAA, Tambuwala, MM, Thangavelu, L, Panneerselvam, J, Gupta, G, Zacconi, FC, Shastri, M, Jha, NK, Xenaki, D, MacLoughlin, R, Oliver, BG, Chellappan, DK & Dua, K 2021, 'Targeting eosinophils in respiratory diseases: Biological axis, emerging therapeutics and treatment modalities', Life Sciences, vol. 267, pp. 118973-118973.
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Eosinophils are bi-lobed, multi-functional innate immune cells with diverse cell surface receptors that regulate local immune and inflammatory responses. Several inflammatory and infectious diseases are triggered with their build up in the blood and tissues. The mobilization of eosinophils into the lungs is regulated by a cascade of processes guided by Th2 cytokine generating T-cells. Recruitment of eosinophils essentially leads to a characteristic immune response followed by airway hyperresponsiveness and remodeling, which are hallmarks of chronic respiratory diseases. By analysing the dynamic interactions of eosinophils with their extracellular environment, which also involve signaling molecules and tissues, various therapies have been invented and developed to target respiratory diseases. Having entered clinical testing, several eosinophil targeting therapeutic agents have shown much promise and have further bridged the gap between theory and practice. Moreover, researchers now have a clearer understanding of the roles and mechanisms of eosinophils. These factors have successfully assisted molecular biologists to block specific pathways in the growth, migration and activation of eosinophils. The primary purpose of this review is to provide an overview of the eosinophil biology with a special emphasis on potential pharmacotherapeutic targets. The review also summarizes promising eosinophil-targeting agents, along with their mechanisms and rationale for use, including those in developmental pipeline, in clinical trials, or approved for other respiratory disorders.
Lee, S, Xu, H, Rice, SA, Chong, TH & Oh, H-S 2021, 'Development of a quorum quenching-column to control biofouling in reverse osmosis water treatment processes', Journal of Industrial and Engineering Chemistry, vol. 94, pp. 188-194.
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© 2020 The Korean Society of Industrial and Engineering Chemistry Biofouling is recognized as one of the most problematic fouling types in reverse osmosis (RO) processes and lead to high energy requirements and operating costs. Over the past decade, many studies on membrane bioreactor (MBR) systems for wastewater applications demonstrated that disrupting cell-cell communications among bacteria, called quorum quenching (QQ), is a promising approach to inhibit biofouling of membranes. Here, we developed the QQ-column as a novel strategy to control biofouling in RO systems. The QQ-column was prepared by incorporating a recombinant bacterial QQ strain into hydrogel beads and embedding these beads inside a column. The QQ-column was installed upstream of the RO module to degrade N-acyl homoserine lactone, a quorum sensing (QS) signal, from the feed in a laboratory-scale RO system operating in total recycle mode. The QQ-column reduced the concentrations of signal molecules by ∼29% in an RO system and mitigated biofilm formation (38.6% reduction of cell number) on the membrane, consequently reducing the transmembrane pressure by 50.1%. These results demonstrate that integrating QQ bacteria into columns is a practical method to control biofouling in RO systems.
Lee, U, Carroll, RJ, Marder, K, Wang, Y & Garcia, TP 2021, 'Estimating disease onset from change points of markers measured with error', Biostatistics, vol. 22, no. 4, pp. 819-835.
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Summary Huntington disease is an autosomal dominant, neurodegenerative disease without clearly identified biomarkers for when motor-onset occurs. Current standards to determine motor-onset rely on a clinician’s subjective judgment that a patient’s extrapyramidal signs are unequivocally associated with Huntington disease. This subjectivity can lead to error which could be overcome using an objective, data-driven metric that determines motor-onset. Recent studies of motor-sign decline—the longitudinal degeneration of motor-ability in patients—have revealed that motor-onset is closely related to an inflection point in its longitudinal trajectory. We propose a nonlinear location-shift marker model that captures this motor-sign decline and assesses how its inflection point is linked to other markers of Huntington disease progression. We propose two estimating procedures to estimate this model and its inflection point: one is a parametric method using nonlinear mixed effects model and the other one is a multi-stage nonparametric approach, which we developed. In an empirical study, the parametric approach was sensitive to correct specification of the mean structure of the longitudinal data. In contrast, our multi-stage nonparametric procedure consistently produced unbiased estimates regardless of the true mean structure. Applying our multi-stage nonparametric estimator to Neurobiological Predictors of Huntington Disease, a large observational study of Huntington disease, leads to earlier prediction of motor-onset compared to the clinician’s subjective judgment.
Lenzen, M, Li, M & Murray, SA 2021, 'Impacts of harmful algal blooms on marine aquaculture in a low-carbon future', Harmful Algae, vol. 110, pp. 102143-102143.
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The IPCC Special Report on Global Warming of 1.5 °C highlights the potential for dietary shifts to reduce greenhouse gas emissions from livestock. Reductions in the consumption of terrestrial animal protein require increases in the consumption of other food categories, to maintain food security, balanced dietary patterns, and protein intake. Aquaculture has long been suggested as one way to meet future food security needs, and marine and estuarine aquaculture in particular is associated with comparatively low greenhouse gas emissions. However, marine and freshwater aquaculture is affected by factors including harmful algal blooms (HABs), which have been increasingly documented around the world, correlated to increases in worldwide aquaculture. In this study, we applied a global multi-region input-output model to capture the direct effects as well as the indirect and induced effects HABs might pose to a global dietary transition from terrestrial livestock to increased seafood consumption from marine and estuarine aquaculture sources. We found that marine and estuarine aquaculture has a substantial potential to replace meat consumption from terrestrial livestock sources, as increases in CO2 emissions from aquaculture were more than offset by reductions in emissions from mainly cattle grazing and associated land clearing. HABs were found to have a minor monetary impact, but the impact on protein supply was found to be potentially sizeable. For example, in a future setting where 40% of terrestrial protein sources were replaced by aquaculture, a HAB-caused global loss of 5% would set in motion numerous supply-chain cascades, affecting industries auxiliary to aquaculture, indirectly and ultimately reducing protein intake by 10-20%. Such reductions have the potential for pushing parts of Sub-Saharan populations into protein-energy malnutrition. Nevertheless, there remains a significant potential for a dietary transition to increased aquaculture seafood to cont...
Leong, HS, Watanabe, S, Kuzhiumparambil, U, Fong, CY, Moy, HY, Yao, YJ, Witting, PK & Fu, S 2021, 'Monitoring metabolism of synthetic cannabinoid 4F-MDMB-BINACA via high-resolution mass spectrometry assessed in cultured hepatoma cell line, fungus, liver microsomes and confirmed using urine samples', Forensic Toxicology, vol. 39, no. 1, pp. 198-212.
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Abstract Purpose A tert-leucinate derivative synthetic cannabinoid, methyl (2S)-2-([1-(4-fluorobutyl)-1H-indazole-3-carbonyl]amino)-3,3-dimethylbutanoate (4F-MDMB-BINACA, 4F-MDMB-BUTINACA or 4F-ADB) is known to adversely impact health. This study aimed to evaluate the suitability of three different modes of monitoring metabolism: HepG2 liver cells, fungus Cunninghamella elegans (C. elegans) and pooled human liver microsomes (HLM) for comparison with human in-vivo metabolism in identifying suitable urinary marker(s) for 4F-MDMB-BINACA intake. Methods Tentative structure elucidation of in-vitro metabolites was performed on HepG2, C. elegans and HLM using liquid chromatography–tandem mass spectrometry and high-resolution mass spectrometry analysis. In-vivo metabolites obtained from twenty authentic human urine samples were analysed using liquid chromatography–Orbitrap mass spectrometry. Results Incubation with HepG2, C. elegans and HLM yielded nine, twenty-three and seventeen metabolites of 4F-MDMB-BINACA, respectively, formed via ester hydrolysis, hydroxylation, carboxylation, dehydrogenation, oxidative defluorination, carbonylation or reaction combinations. Phase II metabolites of glucosidation and sulfation were also exclusively identified using C. elegans model. Eight in-vivo metabolites tentatively identified were mainly products of ester hydrolysis with or without additional dehydrogenation,
Letendre, H, Séguin, K, Grenier, A, Mousseau, V, Cadola, L & Crispino, F 2021, 'First lessons regarding the data analysis of physicochemical traces at activity level in TTADB', Canadian Society of Forensic Science Journal, vol. 54, no. 3, pp. 139-156.
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Li, C, Fröch, JE, Nonahal, M, Tran, TN, Toth, M, Kim, S & Aharonovich, I 2021, 'Integration of hBN Quantum Emitters in Monolithically Fabricated Waveguides', ACS Photonics, vol. 8, no. 10, pp. 2966-2972.
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Hexagonal boron nitride (hBN) is gaining interest for potential applications in integrated quantum nanophotonics. Yet, to establish hBN as an integrated photonic platform several cornerstones must be established, including the integration and coupling of quantum emitters to photonic waveguides. Supported by simulations, we study the approach of monolithic integration, which is expected to have coupling efficiencies that are ∼4 times higher than those of a conventional hybrid stacking strategy. We then demonstrate the fabrication of such devices from hBN and showcase the successful integration of hBN single photon emitters with a monolithic waveguide. We demonstrate the coupling of single photons from the quantum emitters to the waveguide modes and collection from on-chip grating couplers. Our results build a general framework for monolithically integrated hBN single photon emitter and will facilitate future works toward on-chip integrated quantum photonics with hBN.
Li, C, Mendelson, N, Ritika, R, Chen, Y, Xu, Z-Q, Toth, M & Aharonovich, I 2021, 'Scalable and Deterministic Fabrication of Quantum Emitter Arrays from Hexagonal Boron Nitride', Nano Letters, vol. 21, no. 8, pp. 3626-3632.
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We demonstrate the fabrication of large-scale arrays of single-photon emitters (SPEs) in hexagonal boron nitride (hBN). Bottom-up growth of hBN onto nanoscale arrays of dielectric pillars yields corresponding arrays of hBN emitters at the pillar sites. Statistical analysis shows that the pillar diameter is critical for isolating single defects, and diameters of ∼250 nm produce a near-unity yield of a single emitter at each pillar site. Our results constitute a promising route toward spatially controlled generation of hBN SPEs and provide an effective and efficient method to create large-scale SPE arrays. The results pave the way to scalability and high throughput fabrication of SPEs for advanced quantum photonic applications.
Li, D, Wyrsch, ER, Elankumaran, P, Dolejska, M, Marenda, MS, Browning, GF, Bushell, RN, McKinnon, J, Chowdhury, PR, Hitchick, N, Miller, N, Donner, E, Drigo, B, Baker, D, Charles, IG, Kudinha, T, Jarocki, VM & Djordjevic, SP 2021, 'Genomic comparisons of Escherichia coli ST131 from Australia', Microbial Genomics, vol. 7, no. 12.
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Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from cla...
Li, G, Du, P, Qiang, X, Jin, D, Liu, H, Li, B & Guo, J 2021, 'Retraction notice to “Low-expressed GAS5 injure myocardial cells and progression of chronic heart failure via regulation of miR-223-3P” [Experimental and Molecular Pathology 117C (2020) 104529]', Experimental and Molecular Pathology, vol. 122, pp. 104683-104683.
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Li, H, Chen, H, Morgan, L, Li, W & Oliver, BG 2021, 'A narrative review of clinical studies of herbal treatment of difficult to manage asthma', Complementary Therapies in Clinical Practice, vol. 44, pp. 101433-101433.
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Asthma can be complex and difficult to manage. Patients often seek alternative treatment options, including Traditional Chinese Medicine (TCM). The paradigms that inform TCM treatments include a philosophy focusing on modifying the whole body status ('bian zheng') to treat the lungs. TCM practitioners use personalized treatment plans based on clusters of clinical patterns (eg. cold-related wheezing, kidney insufficiency/energy-deficiency-related wheezing). TCM includes herbal remedies and non-oral therapies such as cupping, acupuncture, and massage. The efficacy of TCM treatments of asthma is not well described as the majority of studies are published only in Chinese literature. We reviewed all available clinical trials in CNKI, Chaoxin, Wanfang, CQVIP, Springer-link, Science Direct, and Pubmed. Papers in Chinese were translated by dual lingual TCM and Western medicine doctors. Based on the identified studies, TCM is a safe additive treatment to Western medicine that can improve both symptoms and quality of life for patients with asthma.
Li, H, Xu, Y, Wang, G, Chen, X, Liang, W & Ni, H 2021, 'Editorial Expression of Concern: Long non-coding RNA Mirt2 relieves lipopolysaccharide-induced injury in PC12 cells by suppressing miR-429', Journal of Physiology and Biochemistry, vol. 77, no. 4, pp. 695-695.
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Li, J, Ding, Z, Li, J, Wang, C, Pan, L & Wang, G 2021, 'Synergistic coupling of NiS1.03 nanoparticle with S-doped reduced graphene oxide for enhanced lithium and sodium storage', Chemical Engineering Journal, vol. 407, pp. 127199-127199.
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© 2020 Elsevier B.V. The interest on developing nickel sulfide based dual-role anode materials for both lithium-ion battery (LIBs) and sodium-ion battery (SIBs) has aroused broad attention. However, increasing their lithium and sodium storage performances necessitates smart structure design and fabrication. Herein, we demonstrate a facile strategy for the rational combination of NiS1.03 nanoparticles with sulfur doped reduced graphene oxide (NiS1.03/S-rGO), with the designed structure of ultrafine NiS1.03 nanoparticles uniformly anchored on or even wrapped in S-rGO. The systematic electrochemical studies demonstrate that the NiS1.03/S-rGO exhibits high reversible capacities of 996.1 mAh g−1 after 100 cycles at 0.1 A g−1 and 337.8 mAh g−1 up to 2000 cycles at 4 A g−1 as an anode material for LIBs. As for SIBs, the NiS1.03/S-rGO also displays high reversible capacities of 345.6 mAh g−1 at 0.1 A g−1 after 100 cycles and 242.1 mAh g−1 at 0.5 A g−1 after 200 cycles. Additionally, detailed structure analysis illustrates that the superior electrochemical performances mainly originate from the robust composite architecture where the NiS1.03 nanoparticles and S-rGO are tightly bridged via the doped sulfur atoms at the hetero-interface through a synergistic coupling effect, simultaneously guaranteeing the electrode integrity and fast diffusion kinetics. More importantly, the combination approach and mechanism understanding at the molecular level presented in this study show good promise on transition oxides/sulfides for high-performance alkali metal ion battery.
Li, J, Ding, Z, Pan, L, Li, J, Wang, C & Wang, G 2021, 'Facile self-templating synthesis of layered carbon with N, S dual doping for highly efficient sodium storage', Carbon, vol. 173, pp. 31-40.
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Nitrogen and sulfur co-doping is emerging as a promising approach to prominently improve the sodium storage performance of carbonaceous materials. However, poisonous chemicals and rigorous conditions are normally involved in their preparation, especially in the sulfidation process. Therefore, developing novel, facile and eco-friendly approaches to construct nitrogen and sulfur co-doped carbon (NSC) is still challenging. In this work, a facile self-templating synthesis method is reported to allow the simple and green preparation of NSC. Particularly, small-molecule dithiooxamide can be directly converted to NSC through a facile thermal condensation process, serving as precursor, template, and self-doping agent simultaneously. In account of its high ionic and electronic conductivity, increased interlayer spacing, unique layers assembled structure and efficient N, S co-doping, the NSC obtained at 800 °C exhibits excellent sodium storage performances, including prominent reversible capacity (316.1 mAh g−1 at 0.1 A g−1 up to 100 cycles), remarkable rate capability (178.3 mAh g−1 at 3 A g−1), and robust stability upon long-term cycling (213.6 mAh g−1 at 1 A g−1 up to 2000 cycles), rendering itself to be a promising candidate for practical sodium-ion battery.
Li, J, Tong, H, Li, D, Jiang, Q, Zhang, Y, Tang, W, Jin, D, Chen, S, Qin, X, Zhang, S & Xue, R 2021, 'The long non-coding RNA DKFZp434J0226 regulates the alternative splicing process through phosphorylation of SF3B6 in PDAC', Molecular Medicine, vol. 27, no. 1.
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Abstract Background Long noncoding RNAs (lncRNAs), a type of pervasive genes that regulates various biological processes, are differentially expressed in different types of malignant tumors. The role of lncRNAs in the carcinogenesis of pancreatic ductal adenocarcinoma (PDAC) remains unclear. Here, we investigated the role of the lncRNA DKFZp434J0226 in PDAC. Methods Aberrantly expressed mRNAs and lncRNAs among six PDAC and paired non-tumorous tissues were profiled using microarray analysis. Quantitative real-time polymerase chain reaction was used to evaluate DKFZp434J0226 expression in PDAC tissues. CCK-8 assay, wound-healing assay, soft agar colony formation assay, and transwell assay were performed to assess the invasiveness and proliferation of PDAC cells. Furthermore, RNA pull-down, immunofluorescence, RNA immunoprecipitation, and western blotting assays were performed to investigate the association between DKFZp434J0226 and SF3B6. Tumor xenografts in mice were used to test for tumor formation in vivo. Results In our study, 222 mRNAs and 128 lncRNAs were aberrantly expressed (≥ twofold change). Of these, 66 mRNAs and 53 lncRNAs were upregulated, while 75 lncRNAs and 156 mRNAs were downregulated. KEGG pathway analysis and the Gene ontology category indicated that these genes were associated with the regulation of mRNA alternative splicing and metabolic balance. Clinical analyses revealed that overexpression of DKFZp434J0226 was associated with worse tumor grading, frequent perineural invasion, advanced tumor-node-metastasis stage...
Li, J, Xie, Y, Zhao, P, Qin, Y, Oliver, BG, Tian, Y, Li, S, Wang, M & Liu, X 2021, 'A chinese herbal formula ameliorates COPD by inhibiting the inflammatory response via downregulation of p65, JNK, and p38', Phytomedicine, vol. 83, pp. 153475-153475.
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BackgroundBufei Yishen formula (BYF), a traditional Chinese medicine (TCM), is an effective therapeutic strategy for patients with chronic obstructive pulmonary disease (COPD).PurposeTo evaluate the efficacy of BYF and investigate its therapeutic mechanisms.MethodsA total of 134 patients completed the study: 68 patients treated by BYF combined with conventional Western medicine in the trial group; and 66 patients treated using conventional Western medicine in the control group. The efficacy of BYF was evaluated by a subgroup analysis of data obtained from a four-center, open-label, randomized controlled trial of comprehensive TCM interventions. A rat model of COPD was treated with the key active molecules (KAM) of BYF for 8 weeks. An in vitro model of COPD was also treated with KAM.ResultsPatients treated with BYF had reduced frequency of acute exacerbation of COPD (p < 0.001) and duration (p = 0.028), dyspnea scale (p = 0.007), 6-min walking distance (p = 0.048). There were no differences observed in forced vital capacity in one second (FVC), forced expiratory volume in one second (FEV1), and FEV1 percentage of the predicted value (FEV1%). The five KAM of BYF (KAM-BYF) improved lung function, including tidal volume, minute ventilation, peak expiratory flow, FVC, FEV0.1, and FEV0.3, and pathological changes in COPD rats. Treatment with KAM-BYF markedly decreased the levels of interleukin 6 (IL6), tumor necrosis factor-α (TNF-α), matrix metalloproteinase 9 (MMP9), and MMP12 in serum and bronchial alveolar lavage fluid. In airway epithelial cells, KAM-BYF decreased the levels of TNF-α-induced IL8 and IL6. Finally, we discovered that the anti-inflammatory effects of KAM-BYF in COPD rats and BEAS-2Bs were mediated through inhibition of nuclear factor-kappaB (NF-κB) p65, c-Jun NH2-terminal kinase (JNK), and p38 mitogen-activated protein kinase signaling.ConclusionsBYF exerts beneficial effects in patients with COPD via inhibition of inflammation.
Li, J, Zhang, H, Luo, L, Li, H, He, J, Zu, H, Liu, L, Liu, H, Wang, F & Song, J 2021, 'Blocking polysulfides with a Janus Fe3C/N-CNF@RGO electrode via physiochemical confinement and catalytic conversion for high-performance lithium–sulfur batteries', Journal of Materials Chemistry A, vol. 9, no. 4, pp. 2205-2213.
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A novel Janus Fe3C/N-CNF@RGO electrode was successfully constructed, which realizes the co-existence of chemical immobilization, catalytic ability, and physical barrier in 3D conductive networks, enabling robust cycling stability of Li–S battery
Li, J, Zheng, M, Shimoni, O, Banks, WA, Bush, AI, Gamble, JR & Shi, B 2021, 'Development of Novel Therapeutics Targeting the Blood–Brain Barrier: From Barrier to Carrier', Advanced Science, vol. 8, no. 16, pp. 1-27.
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AbstractThe blood–brain barrier (BBB) is a highly specialized neurovascular unit, initially described as an intact barrier to prevent toxins, pathogens, and potentially harmful substances from entering the brain. An intact BBB is also critical for the maintenance of normal neuronal function. In cerebral vascular diseases and neurological disorders, the BBB can be disrupted, contributing to disease progression. While restoration of BBB integrity serves as a robust biomarker of better clinical outcomes, the restrictive nature of the intact BBB presents a major hurdle for delivery of therapeutics into the brain. Recent studies show that the BBB is actively engaged in crosstalk between neuronal and the circulatory systems, which defines another important role of the BBB: as an interfacing conduit that mediates communication between two sides of the BBB. This role has been subject to extensive investigation for brain‐targeted drug delivery and shows promising results. The dual roles of the BBB make it a unique target for drug development. Here, recent developments and novel strategies to target the BBB for therapeutic purposes are reviewed, from both barrier and carrier perspectives.
Li, M, Reimers, JR, Ford, MJ, Kobayashi, R & Amos, RD 2021, 'Accurate prediction of the properties of materials using the CAM‐B3LYP density functional', Journal of Computational Chemistry, vol. 42, no. 21, pp. 1486-1497.
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AbstractDensity functionals with asymptotic corrections to the long‐range potential provide entry‐level methods for calculations on molecules that can sustain charge transfer, but similar applications in materials science are rare. We describe an implementation of the CAM‐B3LYP range‐separated functional within the Vienna Ab‐initio Simulation Package (VASP) framework, together with its analytical functional derivatives. Results obtained for eight representative materials: aluminum, diamond, graphene, silicon, NaCl, MgO, 2D h‐BN, and 3D h‐BN, indicate that CAM‐B3LYP predictions embody mean‐absolute deviations (MAD) compared to HSE06 that are reduced by a factor of six for lattice parameters, four for quasiparticle band gaps, three for the lowest optical excitation energies, and six for exciton binding energies. Further, CAM‐B3LYP appears competitive compared to ab initio G0W0 and Bethe‐Salpeter equation approaches. The CAM‐B3LYP implementation in VASP was verified by comparison of optimized geometries and reaction energies for isolated molecules taken from the ACCDB database, evaluated in large periodic unit cells, to analogous results obtained using Gaussian basis sets. Using standard GW pseudopotentials and energy cutoffs for the plane‐wave calculations and the aug‐cc‐pV5Z basis set for the atomic‐basis ones, the MAD in energy for 1738 chemical reactions was 0.34 kcal mol−1, while for 480 unique bond lengths this was 0.0036 Å; these values reduced to 0.28 kcal mol−1 (largest error 0.94 kcal mol−1) and 0.0009 Å by increasing the plane‐wave cutoff energy to 850 eV.
Li, N, Zhao, Z, Liu, P, Zheng, Y, Cai, S, Sun, Y & Wang, B 2021, 'Upregulation of deubiquitinase USP7 by transcription factor FOXO6 promotes EC progression via targeting the JMJD3/CLU axis', Molecular Therapy - Oncolytics, vol. 20, pp. 583-595.
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Li, N, Zhao, Z, Miao, F, Cai, S, Liu, P, Yu, Y & Wang, B 2021, 'Silencing of long non-coding RNA LINC01270 inhibits esophageal cancer progression and enhances chemosensitivity to 5-fluorouracil by mediating GSTP1methylation', Cancer Gene Therapy, vol. 28, no. 5, pp. 471-485.
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Li, P, Guo, X, Zang, R, Wang, S, Zuo, Y, Man, Z, Li, P, Liu, S & Wang, G 2021, 'Nanoconfined SnO2/SnSe2 heterostructures in N-doped carbon nanotubes for high-performance sodium-ion batteries', Chemical Engineering Journal, vol. 418, pp. 129501-129501.
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Tin-based compounds are promising anode materials for sodium-ion batteries (SIBs), owing to their high theoretical capacities and relatively low sodiation potential. However, their high-rate performance and cycle life-span are severely impeded by the inherent sluggish reaction kinetics and large structural change during charging and discharging. Herein, we report a composite anode consisting of SnO2/SnSe2 heterostructure nanoparticles uniformly encapsulated in N-doped carbon nanotubes (SnO2/SnSe2@C) for high-performance SIBs. The hollow tube nano-architecture not only accommodates the volume expansion of SnO2/SnSe2, but also facilitates the electrolyte penetration and shortens Na+ pathways. Meanwhile, the N-doped carbon shells provide highways for electron transport and contribute to the total capacity. More importantly, the construction of heterostructures boosts the charge transfer kinetics and further stabilizes the electrode structure by the additional confining effects of the increased crystalline boundaries. Benefiting from the synergistic effects between the elaborately-designed electrode architecture and the incorporation of heterostructures, the SnO2/SnSe2@C composite delivered a superior rate capability (322 mAh g−1 at 4 A g−1) and remarkable cycling stability with a capacity retention of 87.7% after 1000 cycles at 2 A g−1.
Li, S, Huang, J, Ren, L, Jiang, W, Wang, M, Zhuang, L, Zheng, Q, Yang, R, Zeng, Y, Luu, LDW, Wang, Y & Tai, J 2021, 'A one-step, one-pot CRISPR nucleic acid detection platform (CRISPR-top): Application for the diagnosis of COVID-19', Talanta, vol. 233, pp. 122591-122591.
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The existing CRISPR-mediated diagnostic tests require a two-step procedure (DNA or RNA amplification followed by CRISPR-mediated sequence-specific detection) for nucleic acid detection, which increases complexity and the risk of sample cross-contamination. Here, we report a new CRISPR-mediated test, called CRISPR-top (CRISPR-mediated testing in one-pot), which integrates simultaneous target pre-amplification with CRISPR/cas12b-mediated detection into a one-pot reaction mixture, performed at a constant temperature. The novel CRISPR-top assay was applied to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent for COVID-19 (coronavirus disease 2019). COVID-19 CRISPR-top targets the ORF1ab (opening reading frame 1a/b) and NP (nucleoprotein) genes of SARS-CoV-2, and operates at 59 °C for 40 min with minimal instrument. The COVID-19 CRISPR-top assay can return results within 60-min and is easily interpreted by visual fluorescence or lateral flow readouts. The analytical limit of detection (LoD) for COVID-19 CRISPR-top is 10 copies (for each detection target) per reaction with no cross-reactivity observed from non-SARS-CoV-2 templates. Among clinically collected non-COVID-19 samples, the assay's specificity was 100% (80/80 oropharynx swab samples). Among 52 COVID-19 positive clinical samples collected, the COVID-19 CRISPR-top assay yielded 38 (73.1%) positive results using fluorescence readout and 35 (67.3%) positive results with lateral-flow readout. These diagnostic results were similar to those obtained using RT-PCR (34 positive (65.4%)). These data indicate that COVID-19 CRISPR-top is a simple, rapid, accurate and highly sensitive method for SARS-CoV-2 detection which can be used in the clinic, field laboratories and primary care facilities in resource-challenged settings.
Li, X, Jin, D, Zhu, Y, Liu, L, Qiao, Y, Qian, Y, Tian, J, Jiang, B, Hou, C, Geng, J, Li, X, Gao, X, Ma, Y, Wang, S, Zong, J & Qin, Y 2021, 'Quantitative susceptibility mapping to evaluate brain iron deposition and its correlation with physiological parameters in hypertensive patients', Annals of Translational Medicine, vol. 9, no. 20, pp. 1582-1582.
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Li, Y, Faiz, A, Moshage, H, Schubert, R, Schilling, L & Kamps, JA 2021, 'Comparative transcriptome analysis of inner blood-retinal barrier and blood–brain barrier in rats', Scientific Reports, vol. 11, no. 1.
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AbstractAlthough retinal microvessels (RMVs) and brain microvessels (BMVs) are closely related in their developmental and share similar blood-neural barriers, studies have reported markedly different responses to stressors such as diabetes. Therefore, we hypothesized that RMVs and BMVs will display substantial differences in gene expression levels even though they are of the same embryological origin. In this study, both RMVs and BMVs were mechanically isolated from rats. Full retinal and brain tissue samples (RT, BT) were collected for comparisons. Total RNA extracted from these four groups were processed on Affymetrix rat 2.0 microarray Chips. The transcriptional profiles of these tissues were then analyzed. In the present paper we looked at differentially expressed genes (DEGs) in RMVs (against RT) and BMVs (against BT) using a rather conservative threshold value of ≥ ± twofold change and a false discovery rate corrected for multiple comparisons (p < 0.05). In RMVs a total of 1559 DEGs were found, of which 1004 genes were higher expressed in RMVs than in RT. Moreover, 4244 DEGs between BMVs and BT were identified, of which 1956 genes were ≥ twofold enriched in BMVs. Using these DEGs, we comprehensively analyzed the actual expression levels and highlighted their involvement in critical functional structures in RMVs and BMVs, such as junctional complex, transporters and signaling pathways. Our work provides for the first time the transcriptional profiles of rat RMVs and BMVs. These results may help to understand why retina and brain microvasculature show different susceptibilities to stressors, and they might even provide new insight for pharmacological interventions.
Li, Y, Li, J, Yuan, J, Zhao, Y, Zhang, J, Liu, H, Wang, F, Tang, J & Song, J 2021, '3D CoS2/rGO aerogel as trapping-catalyst sulfur host to promote polysulfide conversion for stable Li-S batteries', Journal of Alloys and Compounds, vol. 873, pp. 159780-159780.
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Li, Y, Yang, W, Yang, W, Huang, Y, Wang, G, Xu, C, Kang, F & Dong, L 2021, 'High-performance zinc-ion batteries enabled by electrochemically induced transformation of vanadium oxide cathodes', Journal of Energy Chemistry, vol. 60, pp. 233-240.
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Rechargeable aqueous zinc-ion batteries (ZIBs) have become a research hotspot in recent years, due to their huge potential for high-energy, fast-rate, safe and low-cost energy storage. To realize good electrochemical properties of ZIBs, cathode materials with prominent Zn2+ storage capability are highly needed. Herein, we report a promising ZIB cathode material based on electrochemically induced transformation of vanadium oxides. Specifically, K2V6O16·1.5H2O nanofibers were synthesized through a simple stirring method at near room temperature and then used as cathode materials for ZIBs in different electrolytes. The cathode presented superior Zn2+ storage capability in Zn(OTf)2 aqueous electrolyte, including high capacity of 321 mAh/g, fast charge/discharge ability (96 mAh/g delivered in 35 s), high energy density of 235 Wh/kg and good cycling performance. Mechanism analysis evidenced that in Zn(OTf)2 electrolyte, Zn2+ intercalation in the first discharge process promoted K2V6O16·1.5H2O nanofibers to transform into Zn3+xV2O7(OH)2·2H2O nanoflakes, and the latter served as the Zn2+-storage host in subsequent charge/discharge processes. Benefiting from open-framework crystal structure and sufficiently exposed surface, the Zn3+xV2O7(OH)2·2H2O nanoflakes exhibited high Zn2+ diffusion coefficient, smaller charge-transfer resistance and good reversibility of Zn2+ intercalation/de-intercalation, thus leading to superior electrochemical performance. While in ZnSO4 aqueous electrolyte, the cathode material cannot sufficiently transform into Zn3+xV2O7(OH)2·2H2O, thereby corresponding to inferior electrochemical behaviors. Underlying mechanism and influencing factors of such a transformation phenomenon was also explored. This work not only reports a high-performance ZIB cathode material based on electrochemically induced transformation of vanadium oxides, but also provides new insights into Zn2+-storage electrochemistry.
Li, Y, Yang, W, Yang, W, Wang, Z, Rong, J, Wang, G, Xu, C, Kang, F & Dong, L 2021, 'Towards High-Energy and Anti-Self-Discharge Zn-Ion Hybrid Supercapacitors with New Understanding of the Electrochemistry', Nano-Micro Letters, vol. 13, no. 1, pp. 1-16.
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AbstractAqueous Zn-ion hybrid supercapacitors (ZHSs) are increasingly being studied as a novel electrochemical energy storage system with prominent electrochemical performance, high safety and low cost. Herein, high-energy and anti-self-discharge ZHSs are realized based on the fibrous carbon cathodes with hierarchically porous surface and O/N heteroatom functional groups. Hierarchically porous surface of the fabricated free-standing fibrous carbon cathodes not only provides abundant active sites for divalent ion storage, but also optimizes ion transport kinetics. Consequently, the cathodes show a high gravimetric capacity of 156 mAh g−1, superior rate capability (79 mAh g−1 with a very short charge/discharge time of 14 s) and exceptional cycling stability. Meanwhile, hierarchical pore structure and suitable surface functional groups of the cathodes endow ZHSs with a high energy density of 127 Wh kg−1, a high power density of 15.3 kW kg−1 and good anti-self-discharge performance. Mechanism investigation reveals that ZHS electrochemistry involves cation adsorption/desorption and Zn4SO4(OH)6·5H2O formation/dissolution at low voltage and anion adsorption/desorption at high voltage on carbon cathodes. The roles of these reactions in energy storage of ZHSs are elucidated. This work not only paves a way for high-performance cathode materials of ZHSs, but also provides a deeper understanding of ZHS electrochemistry.
Liao, J, Zhou, J, Song, Y, Liu, B, Chen, Y, Wang, F, Chen, C, Lin, J, Chen, X, Lu, J & Jin, D 2021, 'Preselectable Optical Fingerprints of Heterogeneous Upconversion Nanoparticles', Nano Letters, vol. 21, no. 18, pp. 7659-7668.
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The control in optical uniformity of single nanoparticles and tuning their diversity in multiple dimensions, dot to dot, holds the key to unlocking nanoscale applications. Here we report that the entire lifetime profile of the single upconversion nanoparticle (τ2 profile) can be resolved by confocal, wide-field, and super-resolution microscopy techniques. The advances in both spatial and temporal resolutions push the limit of optical multiplexing from microscale to nanoscale. We further demonstrate that the time-domain optical fingerprints can be created by utilizing nanophotonic upconversion schemes, including interfacial energy migration, concentration dependency, energy transfer, and isolation of surface quenchers. We exemplify that three multiple dimensions, including the excitation wavelength, emission color, and τ2 profile, can be built into the nanoscale derivative τ2-dots. Creating a vast library of individually preselectable nanotags opens up a new horizon for diverse applications, spanning from sub-diffraction-limit data storage to high-throughput single-molecule digital assays and super-resolution imaging.
Liao, J, Zhou, J, Song, Y, Liu, B, Lu, J & Jin, D 2021, 'Optical Fingerprint Classification of Single Upconversion Nanoparticles by Deep Learning', The Journal of Physical Chemistry Letters, vol. 12, no. 41, pp. 10242-10248.
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Highly controlled synthesis of upconversion nanoparticles (UCNPs) can be achieved in the heterogeneous design, so that a library of optical properties can be arbitrarily produced by depositing multiple lanthanide ions. Such a control offers the potential in creating nanoscale barcodes carrying high-capacity information. With the increasing creation of optical information, it poses more challenges in decoding them in an accurate, high-throughput, and speedy fashion. Here, we reported that the deep-learning approach can recognize the complexity of the optical fingerprints from different UCNPs. Under a wide-field microscope, the lifetime profiles of hundreds of single nanoparticles can be collected at once, which offers a sufficient amount of data to develop deep-learning algorithms. We demonstrated that high accuracies of over 90% can be achieved in classifying 14 kinds of UCNPs. This work suggests new opportunities in handling the diverse properties of nanoscale optical barcodes toward the establishment of vast luminescent information carriers.
Liao, Y, Ithurbide, S, Evenhuis, C, Löwe, J & Duggin, IG 2021, 'Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction', Nature Microbiology, vol. 6, no. 5, pp. 594-605.
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In bacteria, the tubulin homologue FtsZ assembles a cytokinetic ring, termed the Z ring, and plays a key role in the machinery that constricts to divide the cells. Many archaea encode two FtsZ proteins from distinct families, FtsZ1 and FtsZ2, with previously unclear functions. Here, we show that Haloferax volcanii cannot divide properly without either or both FtsZ proteins, but DNA replication continues and cells proliferate in alternative ways, such as blebbing and fragmentation, via remarkable envelope plasticity. FtsZ1 and FtsZ2 colocalize to form the dynamic division ring. However, FtsZ1 can assemble rings independent of FtsZ2, and stabilizes FtsZ2 in the ring, whereas FtsZ2 functions primarily in the constriction mechanism. FtsZ1 also influenced cell shape, suggesting it forms a hub-like platform at midcell for the assembly of shape-related systems too. Both FtsZ1 and FtsZ2 are widespread in archaea with a single S-layer envelope, but archaea with a pseudomurein wall and division septum only have FtsZ1. FtsZ1 is therefore likely to provide a fundamental recruitment role in diverse archaea, and FtsZ2 is required for constriction of a flexible S-layer envelope, where an internal constriction force might dominate the division mechanism, in contrast with the single-FtsZ bacteria and archaea that divide primarily by wall ingrowth.
Liao, Y, Vogel, V, Hauber, S, Bartel, J, Alkhnbashi, OS, Maaß, S, Schwarz, TS, Backofen, R, Becher, D, Duggin, IG & Marchfelder, A 2021, 'CdrS Is a Global Transcriptional Regulator Influencing Cell Division in Haloferax volcanii', mBio, vol. 12, no. 4.
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Cell division is a central mechanism of life and is essential for growth and development. Members of the Bacteria and Eukarya have different mechanisms for cell division, which have been studied in detail.
Lin, G 2021, 'Magnetic particles for multidimensional in vitro bioanalysis', VIEW, vol. 2, no. 5, pp. 20200076-20200076.
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AbstractMultidimensional or multiplex bioanalysis represents a crucial approach to improve diagnostic precision, increase assay throughput and advance fundamental discoveries in analytical industry, life science, and nanomedicine. Along this line, bio‐interfacing magnetic particles have been playing an important role. Fully exploiting the properties of magnetic particles is the key to tailoring recent technology development for better translational outcomes. In this mini‐review, typical magneto‐physical dimensions of magnetic particles are introduced. Recent progress of implementing these dimensions with advanced sensor and actuator technologies in multiplex bioanalysis is discussed. Outlooks on potential biomedical applications and challenges are provided.
Lin, G & Jin, D 2021, 'Responsive Sensors of Upconversion Nanoparticles', ACS Sensors, vol. 6, no. 12, pp. 4272-4282.
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Upconversion nanoparticles are a class of luminescent materials that convert longer-wavelength near-infrared photons into visible and ultraviolet emissions. They can respond to various external stimuli, which underpins many opportunities for developing the next generation of sensing technologies. In this perspective, the unique stimuli-responsive properties of upconverting nanoparticles are introduced, and their recent implementations in sensing are summarized. Promising material development strategies for enhancing the key sensing merits, including intrinsic sensitivity, biocompatibility and modality, are identified and discussed. The outlooks on future technological developments, novel sensing concepts, and applications of nanoscale upconversion sensors are provided.
Lin, G, Liu, Y, Huang, G, Chen, Y, Makarov, D, Lin, J, Quan, Z & Jin, D 2021, '3D Rotation‐Trackable and Differentiable Micromachines with Dimer‐Type Structures for Dynamic Bioanalysis', Advanced Intelligent Systems, vol. 3, no. 2, pp. 2170020-2170020.
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Lin, G, Liu, Y, Huang, G, Chen, Y, Makarov, D, Lin, J, Quan, Z & Jin, D 2021, '3D Rotation‐Trackable and Differentiable Micromachines with Dimer‐Type Structures for Dynamic Bioanalysis', Advanced Intelligent Systems, vol. 3, no. 2, pp. 2000205-2000205.
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Utilizing the magnetic interactions between microparticle building blocks allows creating long‐range ordered structures and constructing smart multifunctional systems at different scales. The elaborate control over the inter‐particle magnetic coupling interaction is entailed to unlock new magnetoactuation functionalities. Herein, dimer‐type microstructures consisting of a pair of magnetic emulsions with tailorable dimension and magnetic coupling strength are fabricated using a microfluidic emulsion‐templated assembly approach. The magnetite nanoparticles dispersed in vinylbenzene monomers are partitioned into a pair of emulsions with conserved volume, which are wrapped by an aqueous hydrogel shell and finally polymerized to form discrete structures. Tunable synchronous–asynchronous rotation over 60 dB is unlocked in magnetic dimers, which is shown to be dependent on the magnetic moments induced. This leads to a new class of magnetic actuators for the parallelized assay of distinctive virus DNAs and the dynamic optical evaluation of 3D cell cultures. The work suggests a new perspective to design smart multifunctional microstructures and devices by exploring their natural variance in magnetic coupling.
Lin, Y, Quan, D, Chang, RYK, Chow, MYT, Wang, Y, Li, M, Morales, S, Britton, WJ, Kutter, E, Li, J & Chan, H-K 2021, 'Synergistic activity of phage PEV20-ciprofloxacin combination powder formulation—A proof-of-principle study in a P. aeruginosa lung infection model', European Journal of Pharmaceutics and Biopharmaceutics, vol. 158, pp. 166-171.
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Ling, C, Marlton, F, Brown, A, Maljuk, A, Büchner, B, Lewis, W, Sale, M & Luck, I 2021, 'Stoichiometric molecular hydration of interstitial sites in a close-packed ionic lattice', Acta Crystallographica Section A Foundations and Advances, vol. 77, no. a2, pp. C751-C751.
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Liu Chung Ming, C, Sesperez, K, Ben-Sefer, E, Arpon, D, McGrath, K, McClements, L & Gentile, C 2021, 'Considerations to Model Heart Disease in Women with Preeclampsia and Cardiovascular Disease', Cells, vol. 10, no. 4, pp. 899-899.
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Preeclampsia is a multifactorial cardiovascular disorder diagnosed after 20 weeks of gestation, and is the leading cause of death for both mothers and babies in pregnancy. The pathophysiology remains poorly understood due to the variability and unpredictability of disease manifestation when studied in animal models. After preeclampsia, both mothers and offspring have a higher risk of cardiovascular disease (CVD), including myocardial infarction or heart attack and heart failure (HF). Myocardial infarction is an acute myocardial damage that can be treated through reperfusion; however, this therapeutic approach leads to ischemic/reperfusion injury (IRI), often leading to HF. In this review, we compared the current in vivo, in vitro and ex vivo model systems used to study preeclampsia, IRI and HF. Future studies aiming at evaluating CVD in preeclampsia patients could benefit from novel models that better mimic the complex scenario described in this article.
Liu, B, Wang, F, Chen, C & McGloin, D 2021, 'Single-Pixel Diffuser Camera', IEEE Photonics Journal, vol. 13, no. 6, pp. 1-5.
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We present a compact, diffuser assisted, single-pixel computational camera. A rotating ground glass diffuser is adopted, in preference to a commonly used digital micro-mirror device (DMD), to encode a two-dimensional (2D) image into single-pixel signals. We retrieve images with an 8.8% sampling ratio after the calibration of the pseudo-random pattern of the diffuser under light-emitting diode (LED) illumination. Furthermore, we demonstrate hyperspectral imaging with line array detection by adding a diffraction grating. As the random and fixed patterns of a rotating diffuser placed in the image plane can serve as 2D modulation patterns in single-pixel imaging, we do not need further calibration for spectral imaging case since we use a parallel recovery strategy for images at all wavelengths. The implementation results in a cost-effective single-pixel camera for high-dimensional imaging, with potential for imaging in non-visible wavebands.
Liu, B, Wang, F, Chen, C, Dong, F & McGloin, D 2021, 'Self-evolving ghost imaging', Optica, vol. 8, no. 10, pp. 1340-1340.
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Ghost imaging captures 2D images with a point detector instead of an array sensor. It could therefore solve the challenge of building cameras in wave bands where sensors are difficult and expensive to produce and could open up more routine THz, near-infrared, lifetime, and hyperspectral imaging simply by using single-pixel detectors. Traditionally, ghost imaging retrieves the image of an object offline by correlating measured light intensities with pre-designed illuminating patterns. Here we present a “self-evolving” ghost imaging (SEGI) strategy for imaging objects bypassing offline post-processing. It also offers the capability to image objects in turbid media. By inspecting the optical feedback, we evaluate the illumination patterns by a cost function and generate offspring illumination patterns that mimic the object’s image, bypassing the reconstruction process. At the initial evolving state, the object’s “genetic information” is stored in the patterns. At the following imaging stage, the object’s image ( 48 × 48 p i x e l s ) can be updated at a 40 Hz imaging rate. We numerically and experimentally demonstrate this concept for static and moving objects. The frame-memory effect between the self-evolving illumination patterns provided by the genetic algorithm enables SEGI imaging through turbid media. We further demonst...
Liu, D, Jin, Y, Dong, X, Liu, L, Jin, D, Capobianco, JA & Shen, D 2021, 'Low-Temperature-Induced Controllable Transversal Shell Growth of NaLnF4 Nanocrystals', Nanomaterials, vol. 11, no. 3, pp. 654-654.
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Highly controllable anisotropic shell growth is essential for further engineering the function and properties of lanthanide-doped luminescence nanocrystals, especially in some of the advanced applications such as multi-mode bioimaging, security coding and three-dimensional (3D) display. However, the understanding of the transversal shell growth mechanism is still limited today, because the shell growth direction is impacted by multiple complex factors, such as the anisotropy of surface ligand-binding energy, anisotropic core–shell lattice mismatch, the size of cores and varied shell crystalline stability. Herein, we report a highly controlled transversal shell growth method for hexagonal sodium rare-earth tetrafluoride (β-NaLnF4) nanocrystals. Exploiting the relationship between reaction temperature and shell growth direction, we found that the shell growth direction could be tuned from longitudinal to transversal by decreasing the reaction temperature from 310 °C to 280 °C. In addition to the reaction temperature, we also discussed the roles of other factors in the transversal shell growth of nanocrystals. A suitable core size and a relative lower shell precursor concentration could promote transversal shell growth, although different shell hosts played a minor role in changing the shell growth direction.
Liu, D, Xu, X, Du, Y, Liao, J, Wen, S, Dong, X, Jin, Y, Liu, L, Jin, D, Capobianco, JA & Shen, D 2021, 'Reconstructing the Surface Structure of NaREF4 Upconversion Nanocrystals with a Novel K+ Treatment', Chemistry of Materials, vol. 33, no. 7, pp. 2548-2556.
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Property of the nanocrystals' surface structure plays a key role in developing novel nanomaterials with high performance and new functionalities. Conventional methods of nanocrystal surface engineering are commonly based on tuning the synthesis reaction parameters or growing core-shell structures, which usually results in increasing the size of the nanoparticles. Here, we report an approach to tailoring the surface crystalline structure of β-NaYF4 nanocrystals by reheating the nanocrystals in a K+-rich environment of the oleic acid-1-octadecene (OA-ODE) system. We found that the crystal surface stability of nanocrystals was decreased in the K+-rich solution, which reconstructs the nanocrystals' surface into a porous surface structure. With a systematic design of experiments, the roles of the cations, such as K+, K+-Gd3+, and Na+-Y3+, are individually identified, which leads to a reformation of the surface structure of the hexagonal NaYF4 nanocrystal into different forms, e.g., a mesostructured, spherical, and diamond surface. The technique of tailoring the surface crystalline structures will provide new insight for the shape and surface-dependent property studies and luminescence enhancement without a size increase.
Liu, G, Philp, AM, Corte, T, Travis, MA, Schilter, H, Hansbro, NG, Burns, CJ, Eapen, MS, Sohal, SS, Burgess, JK & Hansbro, PM 2021, 'Therapeutic targets in lung tissue remodelling and fibrosis', Pharmacology & Therapeutics, vol. 225, pp. 107839-107839.
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Structural changes involving tissue remodelling and fibrosis are major features of many pulmonary diseases, including asthma, chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Abnormal deposition of extracellular matrix (ECM) proteins is a key factor in the development of tissue remodelling that results in symptoms and impaired lung function in these diseases. Tissue remodelling in the lungs is complex and differs between compartments. Some pathways are common but tissue remodelling around the airways and in the parenchyma have different morphologies. Hence it is critical to evaluate both common fibrotic pathways and those that are specific to different compartments; thereby expanding the understanding of the pathogenesis of fibrosis and remodelling in the airways and parenchyma in asthma, COPD and IPF with a view to developing therapeutic strategies for each. Here we review the current understanding of remodelling features and underlying mechanisms in these major respiratory diseases. The differences and similarities of remodelling are used to highlight potential common therapeutic targets and strategies. One central pathway in remodelling processes involves transforming growth factor (TGF)-β induced fibroblast activation and myofibroblast differentiation that increases ECM production. The current treatments and clinical trials targeting remodelling are described, as well as potential future directions. These endeavours are indicative of the renewed effort and optimism for drug discovery targeting tissue remodelling and fibrosis.
Liu, H, Lai, W-H, Yang, H-L, Zhu, Y-F, Lei, Y-J, Zhao, L, Peng, J, Wang, Y-X, Chou, S-L & Liu, H-K 2021, 'Efficient separators with fast Li-ion transfer and high polysulfide entrapment for superior lithium-sulfur batteries', Chemical Engineering Journal, vol. 408, pp. 127348-127348.
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Liu, H, Lai, W-H, Yang, Q, Lei, Y, Wu, C, Wang, N, Wang, Y-X, Chou, S-L, Liu, HK & Dou, SX 2021, 'Understanding Sulfur Redox Mechanisms in Different Electrolytes for Room-Temperature Na–S Batteries', Nano-Micro Letters, vol. 13, no. 1.
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Abstract This work reports influence of two different electrolytes, carbonate ester and ether electrolytes, on the sulfur redox reactions in room-temperature Na–S batteries. Two sulfur cathodes with different S loading ratio and status are investigated. A sulfur-rich composite with most sulfur dispersed on the surface of a carbon host can realize a high loading ratio (72% S). In contrast, a confined sulfur sample can encapsulate S into the pores of the carbon host with a low loading ratio (44% S). In carbonate ester electrolyte, only the sulfur trapped in porous structures is active via ‘solid–solid’ behavior during cycling. The S cathode with high surface sulfur shows poor reversible capacity because of the severe side reactions between the surface polysulfides and the carbonate ester solvents. To improve the capacity of the sulfur-rich cathode, ether electrolyte with NaNO3 additive is explored to realize a ‘solid–liquid’ sulfur redox process and confine the shuttle effect of the dissolved polysulfides. As a result, the sulfur-rich cathode achieved high reversible capacity (483 mAh g−1), corresponding to a specific energy of 362 Wh kg−1 after 200 cycles, shedding light on the use of ether electrolyte for high-loading sulfur cathode.
Liu, Q, Wang, Y, Yang, X, Zhou, D, Wang, X, Jaumaux, P, Kang, F, Li, B, Ji, X & Wang, G 2021, 'Rechargeable anion-shuttle batteries for low-cost energy storage', Chem, vol. 7, no. 8, pp. 1993-2021.
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As promising alternatives to lithium-ion batteries, rechargeable anion-shuttle batteries (ASBs) with anions as charge carriers stand out because of their low cost, long cyclic lifetime, and/or high energy density. In this review, we provide for the first time, comprehensive insights into the anion shuttling mechanisms of ASBs, including anion-based rocking-chair batteries (ARBs), dual-ion batteries (DIBs), including insertion-type, conversion-type, and conversion-insertion-type, and reverse dual-ion batteries (RDIBs). Thereafter, we review the latest progresses and challenges regarding electrode materials and electrolytes for ASBs. In addition, we summarize the existing dilemmas of ASBs and outline the perspective of ASB technology for future grid storage.
Liu, Y, Lin, G & Jin, D 2021, 'Off-axis gyration induces large-area circular motion of anisotropic microparticles in a dynamic magnetic trap', Applied Physics Letters, vol. 119, no. 3, pp. 034102-034102.
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Magnetic tweezers are crucial for single-molecule and atomic characterization and biomedical isolation of microparticle carriers. The trapping component of magnetic tweezing can be reliant on a magnetic potential well that can confine the relevant species to a localized region. Here, we report that magnetic microparticles with tailored anisotropy can transition from localized off-axis gyration to large-area locomotion in a rotating magnetic trap. The microparticles, consisting of assemblies of magnetic cores, are observed to either rotate about its structural geometric center or gyrate about one of the magnetic cores and the switching of which can be modulated by the external field. Raising the magnetic field strength above a threshold, the particles can go beyond the traditional synchronous-rotation and asynchronous-oscillation modes and into a scenario of large-area circular motion. This results in peculiar retrograde locomotion related to the magnetization maxima of the microparticle. Our finding suggests the important role of the microparticle's magnetic morphology in the controlled transport of microparticles and developing smart micro-actuators and micro-robot devices.
Liu, Y, Lin, G, Bao, G, Guan, M, Yang, L, Liu, Y, Wang, D, Zhang, X, Liao, J, Fang, G, Di, X, Huang, G, Zhou, J, Cheng, YY & Jin, D 2021, 'Stratified Disk Microrobots with Dynamic Maneuverability and Proton-Activatable Luminescence for in Vivo Imaging', ACS Nano, vol. 15, no. 12, pp. 19924-19937.
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Microrobots can expand our abilities to access remote, confined, and enclosed spaces. Their potential applications inside our body are obvious, e.g., to diagnose diseases, deliver medicine, and monitor treatment efficacy. However, critical requirements exist in relation to their operations in gastrointestinal environments, including resistance to strong gastric acid, responsivity to a narrow proton variation window, and locomotion in confined cavities with hierarchical terrains. Here, we report a proton-activatable microrobot to enable real-time, repeated, and site-selective pH sensing and monitoring in physiological relevant environments. This is achieved by stratifying a hydrogel disk to combine a range of functional nanomaterials, including proton-responsive molecular switches, upconversion nanoparticles, and near-infrared (NIR) emitters. By leveraging the 3D magnetic gradient fields and the anisotropic composition, the microrobot can be steered to locomote as a gyrating 'Euler's disk', i.e., aslant relative to the surface and along its low-friction outer circumference, exhibiting a high motility of up to 60 body lengths/s. The enhanced magnetomotility can boost the pH-sensing kinetics by 2-fold. The fluorescence of the molecular switch can respond to pH variations with over 600-fold enhancement when the pH decreases from 8 to 1, and the integration of upconversion nanoparticles further allows both the efficient sensitization of NIR light through deep tissue and energy transfer to activate the pH probes. Moreover, the embedded down-shifting NIR emitters provide sufficient contrast for imaging of a single microrobot inside a live mouse. This work suggests great potential in developing multifunctional microrobots to perform generic site-selective tasks in vivo.
Liu, Y, Zhang, L, Li, HL, Liang, BM, Wang, J, Zhang, X, Chen, ZH, Zhang, HP, Xie, M, Wang, L, Wang, G & Oliver, BG 2021, 'Small Airway Dysfunction in Asthma Is Associated with Perceived Respiratory Symptoms, Non-Type 2 Airway Inflammation, and Poor Responses to Therapy', Respiration, vol. 100, no. 8, pp. 767-779.
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<b><i>Background:</i></b> Emerging evidence has indicated that small airway dysfunction (SAD) contributes to the clinical expression of asthma. <b><i>Objectives:</i></b> The aim of the study was to explore the relationships of SAD assessed by forced expiratory flow between 25 and 75% (FEF<sub>25–75</sub>%), with clinical and inflammatory profile and treatment responsiveness in asthma. <b><i>Method:</i></b> In study I, dyspnea intensity (Borg scale), chest tightness, wheezing and cough (visual analog scales, VASs), and pre- and post-methacholine challenge testing (MCT) were analyzed in asthma patients with SAD and non-SAD. In study II, asthma subjects with SAD and non-SAD underwent sputum induction, and inflammatory mediators in sputum were detected. Asthma patients with SAD and non-SAD receiving fixed treatments were prospectively followed up for 4 weeks in study III. Spirometry, Asthma Control Questionnaire (ACQ), and Asthma Control Test (ACT) were carried out to define treatment responsiveness. <b><i>Results:</i></b> SAD subjects had more elevated ΔVAS for dyspnea (<i>p</i> = 0.027) and chest tightness (<i>p</i> = 0.032) after MCT. Asthma patients with SAD had significantly elevated interferon (IFN)-γ in sputum (<i>p</i> < 0.05), and Spearman partial correlation found FEF<sub>25–75</sub>% significantly related to IFN-γ and interleukin-8 (both having <i>p</i> < 0.05). Furthermore, multivariable regression analysis indicated SAD was significantly associated with worse treatment responses (decrease in ACQ ≥0.5 and increase in ACT ≥3) (<i>p</i> = 0.022 and <i>p</i> = 0.032). <b><i>Conclusions:</i></b> This study indicates that SAD in asthma predisposes patients to greater dyspnea intensity and chest tightness during b...
Liu, Y, Zhou, Z, Wang, F, Kewes, G, Wen, S, Burger, S, Ebrahimi Wakiani, M, Xi, P, Yang, J, Yang, X, Benson, O & Jin, D 2021, 'Axial localization and tracking of self-interference nanoparticles by lateral point spread functions', Nature Communications, vol. 12, no. 1, pp. 1-9.
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AbstractSub-diffraction limited localization of fluorescent emitters is a key goal of microscopy imaging. Here, we report that single upconversion nanoparticles, containing multiple emission centres with random orientations, can generate a series of unique, bright and position-sensitive patterns in the spatial domain when placed on top of a mirror. Supported by our numerical simulation, we attribute this effect to the sum of each single emitter’s interference with its own mirror image. As a result, this configuration generates a series of sophisticated far-field point spread functions (PSFs), e.g. in Gaussian, doughnut and archery target shapes, strongly dependent on the phase difference between the emitter and its image. In this way, the axial locations of nanoparticles are transferred into far-field patterns. We demonstrate a real-time distance sensing technology with a localization accuracy of 2.8 nm, according to the atomic force microscope (AFM) characterization values, smaller than 1/350 of the excitation wavelength.
Liu, Z, Li, J, Yang, J, Ma, H, Wang, C, Guo, X & Wang, G 2021, 'Preparation of a Novel g-C3N4/Sn/N-doped Carbon Composite for Sodium Storage', Gaodeng Xuexiao Huaxue Xuebao Chemical Journal of Chinese Universities, vol. 42, no. 2, pp. 633-642.
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Sodium-ion batteries(SIBs) based on Sn-based anodes have attracted increasing attention due to their high theoretical capacity(847 mA•h/g), high electrical conductivity and suitable operation potential. Unfortunately, the huge structural change upon cycling often causes particle pulverization and rapid capacity decay. In this work, ultrafine Sn nanoparticles with dual protection from graphitic carbon nitride(g-C3N4) and polydopamine derived N-doped carbon(g-C3N4/Sn/NC) were successfully fabricated through a designed strategy. Generally, the introduction of g-C3N4 and NC can dramatically accelerate the transport of electrons/ions as well as the reaction dynamics, thus contributing to the alloying reaction between Sn and Na+. Importantly, the ultrafine Sn as well as the dual buffering matrices can efficiently maintain the integrity of electrode upon cycling, guaranteeing the superior electrochemical performance. Benefitting from the structural advantages inhe-rited from the ultrafine Sn nanoparticles and dual protection scaffolds, the as-obtained g-C3N4/Sn/NC displays excellent sodium storage performances, with high reversible capacity(450.7 mA•h/g at 0.5 A/g after 100 cycles), remarkable rate capability(388.3 mA•h/g at 1.0 A/g) and stable long-term cycling stability(363.3 mA•h/g after 400 cycles at 1.0 A/g).
Lockwood, TE, Gonzalez de Vega, R & Clases, D 2021, 'An interactive Python-based data processing platform for single particle and single cell ICP-MS', Journal of Analytical Atomic Spectrometry, vol. 36, no. 11, pp. 2536-2544.
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A data processing platform was developed for the analysis of single particle and single cell ICP-MS data sets. All functions are embedded in a GUI and enable signal recognition, accumulation and calibration via dedicated pathways and filters.
Lockwood, TE, Westerhausen, MT & Doble, PA 2021, 'Pew2: Open-Source Imaging Software for Laser Ablation–Inductively Coupled Plasma–Mass Spectrometry', Analytical Chemistry, vol. 93, no. 30, pp. 10418-10423.
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Open-sourced software is a key component of the mass spectrometry imaging field, where transparency in data processing is vital. Imaging of trace elements and immunohistochemically labeled biomolecules in tissue sections is typically performed using laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). However, efficient and facile processing of images is hampered by a lack of verifiable and user-friendly software that supports multiple LA-ICP-MS platforms. In this technical note, we introduce Pew2, a LA-ICP-MS specific and feature-rich open-source image processing software that is compatible with common ICP-MS vendors. Pew2 is designed to be fast and easy to use and adheres to modern visualization philosophies to maximize productivity and to minimize data interpretation errors and image anomalies.
Lodge, CJ, Lowe, AJ, Milanzi, E, Bowatte, G, Abramson, MJ, Tsimiklis, H, Axelrad, C, Robertson, B, Darling, AE, Svanes, C, Wjst, M, Dharmage, SC & Bode, L 2021, 'Human milk oligosaccharide profiles and allergic disease up to 18 years', Journal of Allergy and Clinical Immunology, vol. 147, no. 3, pp. 1041-1048.
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BACKGROUND:Human milk oligosaccharides (HMO) are a diverse range of sugars secreted in breast milk that have direct and indirect effects on immunity. The profiles of HMOs produced differ between mothers. OBJECTIVE:We sought to determine the relationship between maternal HMO profiles and offspring allergic diseases up to age 18 years. METHODS:Colostrum and early lactation milk samples were collected from 285 mothers enrolled in a high-allergy-risk birth cohort, the Melbourne Atopy Cohort Study. Nineteen HMOs were measured. Profiles/patterns of maternal HMOs were determined using LCA. Details of allergic disease outcomes including sensitization, wheeze, asthma, and eczema were collected at multiple follow-ups up to age 18 years. Adjusted logistic regression analyses and generalized estimating equations were used to determine the relationship between HMO profiles and allergy. RESULTS:The levels of several HMOs were highly correlated with each other. LCA determined 7 distinct maternal milk profiles with memberships of 10% and 20%. Compared with offspring exposed to the neutral Lewis HMO profile, exposure to acidic Lewis HMOs was associated with a higher risk of allergic disease and asthma over childhood (odds ratio asthma at 18 years, 5.82; 95% CI, 1.59-21.23), whereas exposure to the acidic-predominant profile was associated with a reduced risk of food sensitization (OR at 12 years, 0.08; 95% CI, 0.01-0.67). CONCLUSIONS:In this high-allergy-risk birth cohort, some profiles of HMOs were associated with increased and some with decreased allergic disease risks over childhood. Further studies are needed to confirm these findings and realize the potential for intervention.
Loering, S, Cameron, GJM, Bhatt, NP, Belz, GT, Foster, PS, Hansbro, PM & Starkey, MR 2021, 'Differences in pulmonary group 2 innate lymphoid cells are dependent on mouse age, sex and strain', Immunology & Cell Biology, vol. 99, no. 5, pp. 542-551.
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AbstractInnate lymphoid cells (ILCs) are resident in the lung and are involved in both the maintenance of homeostasis and the pathogenesis of respiratory diseases. In this study, murine lung ILCs were characterized using flow cytometry and the impact of mouse age, sex and strain were assessed. Lung ILCs were found as early as postnatal day 4 and numbers peaked at 2 weeks, and then decreased as the lung matured. During postnatal lung development, ILC expressed differential amounts of group 2 ILC (ILC2)‐associated cell surface antigens including ST2, CD90.2 and ICOS. Using Il5venusIl13td‐tomato dual reporter mice, neonates were found to have increased constitutive interleukin (IL)‐13 expression compared with adult mice. Neonates and adults had similar ratios of IL‐5+CD45+ leukocytes; however, these cells were mostly composed of ILCs in neonates and T cells in adults. Sex‐specific differences in ILC numbers were also observed, with females having greater numbers of lung ILCs than males in both neonatal and adult mice. Female lung ILCs also expressed higher levels of ICOS and decreased KLRG1. Mouse strain also impacted on lung ILCs with BALB/c mice having more ILCs in the lung and increased expression of ST2 and ICOS compared with C57BL/6J mice. Collectively, these data show that lung ILC numbers, cell surface antigen expression, IL‐5 and IL‐13 levels differed between neonatal and adult lung ILCs. In addition, cell surface antigens commonly used for ILC2 quantification, such as ST2, CD90.2 and ICOS, differ depending on age, sex and strain and these are important considerations for consistent universal identification of lung ILC2s.
López-Denman, AJ, Tuipulotu, DE, Ross, JB, Trenerry, AM, White, PA & Mackenzie, JM 2021, 'Nuclear localisation of West Nile virus NS5 protein modulates host gene expression', Virology, vol. 559, pp. 131-144.
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Lu, J, Jaumaux, P, Wang, T, Wang, C & Wang, G 2021, 'Recent progress in quasi-solid and solid polymer electrolytes for multivalent metal-ion batteries', Journal of Materials Chemistry A, vol. 9, no. 43, pp. 24175-24194.
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The increasing urgency of the energy source crisis has accelerated the application of polymers in energy storage for renewable energy.
Lu, Z, Van Eeckhoutte, HP, Liu, G, Nair, PM, Jones, B, Gillis, CM, Nalkurthi, BC, Verhamme, F, Buyle-Huybrecht, T, Vandenabeele, P, Vanden Berghe, T, Brusselle, GG, Horvat, JC, Murphy, JM, Wark, PA, Bracke, KR, Fricker, M & Hansbro, PM 2021, 'Necroptosis Signaling Promotes Inflammation, Airway Remodeling, and Emphysema in Chronic Obstructive Pulmonary Disease', American Journal of Respiratory and Critical Care Medicine, vol. 204, no. 6, pp. 667-681.
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Rationale: Necroptosis, mediated by RIPK3 (receptor-interacting protein kinase 3) and MLKL (mixed lineage kinase domain-like), is a form of regulated necrosis that can drive tissue inflammation and destruction; however, its contribution to chronic obstructive pulmonary disease (COPD) pathogenesis is poorly understood. Objectives: To determine the role of necroptosis in COPD. Methods: Total and active (phosphorylated) RIPK3 and MLKL were measured in the lung tissue of patients with COPD and control subjects without COPD. Necroptosis-related mRNA and proteins as well as cell death were examined in lungs and pulmonary macrophages of mice with cigarette smoke (CS)-induced experimental COPD. The responses of Ripk3-/- and Mlkl-/- mice to acute and chronic CS exposure were compared with those of wild-type mice. The combined inhibition of apoptosis (with the pan-caspase inhibitor quinoline-Val-Asp-difluorophenoxymethylketone [qVD-OPh]) and necroptosis (with deletion of Mlkl in mice) was assessed. Measurements and Main Results: The total MLKL protein in the epithelium and macrophages and the pRIPK3 and pMLKL in lung tissue were increased in patients with severe COPD compared with never-smokers or smoker control subjects without COPD. Necroptosis-related mRNA and protein levels were increased in the lungs and macrophages in CS-exposed mice and experimental COPD. Ripk3 or Mlkl deletion prevented airway inflammation upon acute CS exposure. Ripk3 deficiency reduced airway inflammation and remodeling as well as the development of emphysematous pathology after chronic CS exposure. Mlkl deletion and qVD-OPh treatment reduced chronic CS-induced airway inflammation, but only Mlkl deletion prevented airway remodeling and emphysema. Ripk3 or Mlkl deletion and qVD-OPh treatment reduced CS-induced lung-cell death. Conclusions: Necroptosis is induced by CS exposure and is increased in the lungs of patients with COPD and in experimental COPD. Inhibiting necroptosis attenuates ...
Luo, Z, Morey, JR, Deplazes, E, Motygullina, A, Tan, A, Ganio, K, Neville, SL, Eleftheriadis, N, Isselstein, M, Pederick, VG, Paton, JC, Cordes, T, Harmer, JR, Kobe, B & McDevitt, CA 2021, 'A Trap-Door Mechanism for Zinc Acquisition by Streptococcus pneumoniae AdcA', mBio, vol. 12, no. 1, pp. 1-14.
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Zinc is an essential nutrient for the virulence of bacterial pathogens such as Streptococcus pneumoniae . Many Gram-positive bacteria use a two-domain lipoprotein for zinc acquisition, but how this class of metal-recruiting proteins acquire zinc and interact with the uptake machinery has remained poorly defined.
Luu, LDW, Payne, M, Zhang, X, Luo, L & Lan, R 2021, 'Development and comparison of novel multiple cross displacement amplification (MCDA) assays with other nucleic acid amplification methods for SARS-CoV-2 detection', Scientific Reports, vol. 11, no. 1, pp. 1-7.
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AbstractThe development of alternative isothermal amplification assays including multiple cross displacement amplification (MCDA) may address speed and portability limitations of real-time PCR (rt-PCR) methods for SARS-CoV-2 detection. We developed a novel SARS-CoV-2 MCDA assay and compared its speed and sensitivity to loop-mediated isothermal amplification (LAMP) and rt-PCR. Two MCDA assays targeting SARS-CoV-2 N gene and ORF1ab were designed. The fastest time to detection and sensitivity of MCDA was compared to LAMP and rt-PCR using DNA standards and transcribed RNA. For the N gene, MCDA was faster than LAMP and rt-PCR by 10 and 20 min, respectively with fastest time to detection at 5.2 min. rt-PCR had the highest sensitivity with the limit of detection at 10 copies/µl compared with MCDA (100 copies/µl) and LAMP (500 copies/µl). For ORF1ab, MCDA and LAMP had similar speed with fastest time to detection at 9.7 and 8.4 min, respectively. LAMP was more sensitive for ORF1ab detection with 50 copies/µl compared to MCDA (500 copies/µl). In conclusion, different nucleic acid amplification methods provide different advantages. MCDA is the fastest nucleic acid amplification method for SARS-CoV-2 while rt-PCR is the most sensitive. These advantages should be considered when determining the most suitable nucleic acid amplification methods for different applications.
Luu, LDW, Zhong, L, Kaur, S, Raftery, MJ & Lan, R 2021, 'Comparative Phosphoproteomics of Classical Bordetellae Elucidates the Potential Role of Serine, Threonine and Tyrosine Phosphorylation in Bordetella Biology and Virulence', Frontiers in Cellular and Infection Microbiology, vol. 11, p. 660280.
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The Bordetella genus is divided into two groups: classical and non-classical. Bordetella pertussis, Bordetella bronchiseptica and Bordetella parapertussis are known as classical bordetellae, a group of important human pathogens causing whooping cough or whooping cough-like disease and hypothesized to have evolved from environmental non-classical bordetellae. Bordetella infections have increased globally driving the need to better understand these pathogens for the development of new treatments and vaccines. One unexplored component in Bordetella is the role of serine, threonine and tyrosine phosphorylation. Therefore, this study characterized the phosphoproteome of classical bordetellae and examined its potential role in Bordetella biology and virulence. Applying strict identification of localization criteria, this study identified 70 unique phosphorylated proteins in the classical bordetellae group with a high degree of conservation. Phosphorylation was a key regulator of Bordetella metabolism with proteins involved in gluconeogenesis, TCA cycle, amino acid and nucleotide synthesis significantly enriched. Three key virulence pathways were also phosphorylated including type III secretion system, alcaligin synthesis and the BvgAS master transcriptional regulatory system for virulence genes in Bordetella. Seven new phosphosites were identified in BvgA with 6 located in the DNA binding domain. Of the 7, 4 were not present in non-classical bordetellae. This suggests that serine/threonine phosphorylation may play an important role in stabilizing/destabilizing BvgA binding to DNA for fine-tuning of virulence gene expression and that BvgA phosphorylation may be an important factor separa...
Lv, Z, Tang, J, Tian, Y, Hua, Q, Liu, Y, Liu, L & Wang, B 2021, 'Preparation and Characterization of Paraffin@ZnO Microcapsule Phase-Change Material by an in Situ Precipitation Method', Energy & Fuels, vol. 35, no. 21, pp. 17940-17947.
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Ma, H, Li, J, Yang, J, Wang, N, Liu, Z, Wang, T, Su, D, Wang, C & Wang, G 2021, 'Bismuth Nanoparticles Anchored on Ti3C2Tx MXene Nanosheets for High‐Performance Sodium‐Ion Batteries', Chemistry – An Asian Journal, vol. 16, no. 22, pp. 3774-3780.
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AbstractSodium‐ion batteries are promising energy‐storage systems, but they are facing huge challenges for developing fast‐charging anode materials. Bismuth (Bi)‐based anode materials are considered as candidates for fast‐charging anodes of sodium‐ion batteries due to their excellent rate performance. Herein, we designed a two‐dimensional Bi/MXene anode material based on a hydrogen thermal reduction strategy. Benefitting from microstructure advantages, Bi/MXene anodes exhibited an excellent rate capability and superior cycle performance in Na//Bi/MXene half‐batteries and Na3V2(PO4)3/C//Bi/MXene full‐batteries. Moreover, full‐batteries can complete a charge/discharge cycle in 7 min and maintain an excellent cycle life (over 7000 cycles). The electrochemical test results showed that Bi/MXene is a promising anode material with fast charge/discharge capability for sodium‐ion batteries.
Ma, J, Li, Y, Grundish, NS, Goodenough, JB, Chen, Y, Guo, L, Peng, Z, Qi, X, Yang, F, Qie, L, Wang, C-A, Huang, B, Huang, Z, Chen, L, Su, D, Wang, G, Peng, X, Chen, Z, Yang, J, He, S, Zhang, X, Yu, H, Fu, C, Jiang, M, Deng, W, Sun, C-F, Pan, Q, Tang, Y, Li, X, Ji, X, Wan, F, Niu, Z, Lian, F, Wang, C, Wallace, GG, Fan, M, Meng, Q, Xin, S, Guo, Y-G & Wan, L-J 2021, 'The 2021 battery technology roadmap', Journal of Physics D: Applied Physics, vol. 54, no. 18, pp. 183001-183001.
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Abstract Sun, wind and tides have huge potential in providing us electricity in an environmental-friendly way. However, its intermittency and non-dispatchability are major reasons preventing full-scale adoption of renewable energy generation. Energy storage will enable this adoption by enabling a constant and high-quality electricity supply from these systems. But which storage technology should be considered is one of important issues. Nowadays, great effort has been focused on various kinds of batteries to store energy, lithium-related batteries, sodium-related batteries, zinc-related batteries, aluminum-related batteries and so on. Some cathodes can be used for these batteries, such as sulfur, oxygen, layered compounds. In addition, the construction of these batteries can be changed into flexible, flow or solid-state types. There are many challenges in electrode materials, electrolytes and construction of these batteries and research related to the battery systems for energy storage is extremely active. With the myriad of technologies and their associated technological challenges, we were motivated to assemble this 2020 battery technology roadmap.
Mac Aogáin, M, Narayana, JK, Tiew, PY, Ali, NABM, Yong, VFL, Jaggi, TK, Lim, AYH, Keir, HR, Dicker, AJ, Thng, KX, Tsang, A, Ivan, FX, Poh, ME, Oriano, M, Aliberti, S, Blasi, F, Low, TB, Ong, TH, Oliver, B, Giam, YH, Tee, A, Koh, MS, Abisheganaden, JA, Tsaneva-Atanasova, K, Chalmers, JD & Chotirmall, SH 2021, 'Integrative microbiomics in bronchiectasis exacerbations', Nature Medicine, vol. 27, no. 4, pp. 688-699.
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Bronchiectasis, a progressive chronic airway disease, is characterized by microbial colonization and infection. We present an approach to the multi-biome that integrates bacterial, viral and fungal communities in bronchiectasis through weighted similarity network fusion ( https://integrative-microbiomics.ntu.edu.sg ). Patients at greatest risk of exacerbation have less complex microbial co-occurrence networks, reduced diversity and a higher degree of antagonistic interactions in their airway microbiome. Furthermore, longitudinal interactome dynamics reveals microbial antagonism during exacerbation, which resolves following treatment in an otherwise stable multi-biome. Assessment of the Pseudomonas interactome shows that interaction networks, rather than abundance alone, are associated with exacerbation risk, and that incorporation of microbial interaction data improves clinical prediction models. Shotgun metagenomic sequencing of an independent cohort validated the multi-biome interactions detected in targeted analysis and confirmed the association with exacerbation. Integrative microbiomics captures microbial interactions to determine exacerbation risk, which cannot be appreciated by the study of a single microbial group. Antibiotic strategies probably target the interaction networks rather than individual microbes, providing a fresh approach to the understanding of respiratory infection.
Macdonald, PS, Gorrie, N, Brennan, X, Aili, SR, De Silva, R, Jha, SR, Fritis-Lamora, R, Montgomery, E, Wilhelm, K, Pierce, R, Lam, F, Schnegg, B, Hayward, C, Jabbour, A, Kotlyar, E, Muthiah, K, Keogh, AM, Granger, E, Connellan, M, Watson, A, Iyer, A & Jansz, PC 2021, 'The impact of frailty on mortality after heart transplantation', The Journal of Heart and Lung Transplantation, vol. 40, no. 2, pp. 87-94.
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BACKGROUNDFrailty is prevalent in the patients with advanced heart failure; however, its impact on clinical outcomes after heart transplantation (HTx) is unclear. The aim of this study was to assess the impact of pre-transplant frailty on mortality and the duration of hospitalization after HTx.METHODSWe retrospectively reviewed the post-transplant outcomes of 140 patients with advanced heart failure who had undergone frailty assessment within the 6-month interval before HTx: 43 of them were frail (F) and 97 were non-frail (NF).RESULTSPost-transplant survival rates for the NF cohort at 1 and 12 months were 97% (93–100) and 95% (91–99) (95% CI), respectively. In contrast, post-transplant survival rates for the F cohort at the same time points were 86% (76–96) and 74% (60–84) (p < 0.0008 vs NF cohort), respectively. The Cox proportional hazards regression analysis demonstrated that pre-transplant frailty was an independent predictor of post-transplant mortality with a hazard ratio of 3.8 (95% CI: 1.4–10.5). Intensive care unit and hospital length of stay were 2 and 7 days longer in the F cohort (both p < 0.05), respectively, than in the NF cohort.CONCLUSIONSFrailty within 6 months before HTx is independently associated with increased mortality and prolonged hospitalization after transplantation. Future research should focus on the development of strategies to mitigate the adverse effects of pre-transplant frailty.
Maddahfar, M 2021, 'StableandHighlyEfficientAntibody−NanoparticlesConjugation', Bioconjugate Chemistry, vol. 32, no. 6, pp. 1146-1155.
Maddahfar, M, Wen, S, Hosseinpour Mashkani, SM, Zhang, L, Shimoni, O, Stenzel, M, Zhou, J, Fazekas de St Groth, B & Jin, D 2021, 'Stable and Highly Efficient Antibody–Nanoparticles Conjugation', Bioconjugate Chemistry, vol. 32, no. 6, pp. 1146-1155.
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Functional ligands and polymers have frequently been used to yield target-specific bio-nanoconjugates. Herein, we provide a systematic insight into the effect of the chain length of poly(oligo (ethylene glycol) methyl ether acrylate) (POEGMEA) containing polyethylene glycol on the colloidal stability and antibody-conjugation efficiency of nanoparticles. We employed Reversible Addition-Fragmentation Chain Transfer (RAFT) to design diblock copolymers composed of 7 monoacryloxyethyl phosphate (MAEP) units and 6, 13, 35, or 55 OEGMEA units. We find that when the POEGMEA chain is short, the polymer cannot effectively stabilize the nanoparticles, and when the POEGMEA chain is long, the nanoparticles cannot be efficiently conjugated to antibody. In other words, the majority of the carboxylic groups in larger POEGMEA chains are inaccessible to further chemical modification. We demonstrate that the polymer containing 13 OEGMEA units can effectively bind up to 64% of the antibody molecules, while the binding efficiency drops to 50% and 0% for the polymer containing 35 and 55 OEGMEA units. Moreover, flow cytometry assay statistically shows that about 9% of the coupled antibody retained its activity to recognize B220 biomarkers on the B cells. This work suggests a library of stabile, specific, and bioactive lanthanide-doped nanoconjugates for flow cytometry and mass cytometry application.
Maestrini, L & Wand, MP 2021, 'The Inverse G‐Wishart distribution and variational message passing', Australian & New Zealand Journal of Statistics, vol. 63, no. 3, pp. 517-541.
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SummaryMessage passing on a factor graph is a powerful paradigm for the coding of approximate inference algorithms for arbitrarily large graphical models. The notion of a factor graph fragment allows for compartmentalisation of algebra and computer code. We show that the Inverse G‐Wishart family of distributions enables fundamental variational message passing factor graph fragments to be expressed elegantly and succinctly. Such fragments arise in models for which approximate inference concerning covariance matrix or variance parameters is made, and are ubiquitous in contemporary statistics and machine learning.
Mahbub, SB, Nguyen, LT, Habibalahi, A, Campbell, JM, Anwer, AG, Qadri, UM, Gill, A, Chou, A, Wong, MG, Gosnell, ME, Pollock, CA, Saad, S & Goldys, EM 2021, 'Non-invasive assessment of exfoliated kidney cells extracted from urine using multispectral autofluorescence features', Scientific Reports, vol. 11, no. 1.
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AbstractOptimally preserved urinary exfoliated renal proximal tubule cells were assessed by multispectral imaging of cell autofluorescence. We demonstrated different multispectral autofluorescence signals in such cells extracted from the urine of patients with healthy or diseased kidneys. Using up to 10 features, we were able to differentiate cells from individuals with heathy kidneys and impaired renal function (indicated by estimated glomerular filtration rate (eGFR) values) with the receiver operating characteristic area under the curve (AUC) of 0.99. Using the same method, we were also able to discriminate such urine cells from patients with and without renal fibrosis on biopsy, where significant differences in multispectral autofluorescence signals (AUC = 0.90) were demonstrated between healthy and diseased patients (p < 0.05). These findings show that multispectral assessment of the cell autofluorescence in urine exfoliated proximal tubule kidney cells has the potential to be developed as a sensitive, non-invasive diagnostic method for CKD.
Mahbub, SB, Nguyen, LT, Habibalahi, A, Campbell, JM, Anwer, AG, Qadri, UM, Gill, A, Chou, A, Wong, MG, Gosnell, ME, Pollock, CA, Saad, S & Goldys, EM 2021, 'Publisher Correction: Non-invasive assessment of exfoliated kidney cells extracted from urine using multispectral autofluorescence features', Scientific Reports, vol. 11, no. 1.
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Mahmodi, H, Piloni, A, Utama, RH & Kabakova, I 2021, 'Mechanical mapping of bioprinted hydrogel models by brillouin microscopy', Bioprinting, vol. 23, pp. e00151-e00151.
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Three-dimensional (3D) bioprinting has revolutionised the field of biofabrication by delivering precise, cost-effective and a relatively simple way of engineering in vitro living systems in high volume for use in tissue regeneration, biological modelling, drug testing and cell-based diagnostics. The complexity of modern bioprinted systems requires quality control assessment to ensure the resulting product meets the desired criteria of structural design, micromechanical performance and long-term durability. Brillouin microscopy could be an excellent solution for micromechanical assessment of the bioprinted models during or post-fabrication since this technology is non-destructive, label-free and is capable of microscale 3D imaging. In this work, we demonstrate the application of Brillouin microscopy to 3D imaging of hydrogel microstructures created through drop-on-demand bioprinting. In addition, we show that this technology can resolve variations between mechanical properties of the gels with slightly different polymer fractions. This work confirms that Brillouin microscopy can be seen as a characterisation technology complementary to bioprinting, and in the future can be combined within the printer design to achieve simultaneous real-time fabrication and micromechanical characterisation of in vitro biological systems.
Mahmood, A, Yuan, Z, Sui, X, Riaz, MA, Yu, Z, Liu, C, Chen, J, Wang, C, Zhao, S, Mahmood, N, Pei, Z, Wei, L & Chen, Y 2021, 'Foldable and scrollable graphene paper with tuned interlayer spacing as high areal capacity anodes for sodium-ion batteries', Energy Storage Materials, vol. 41, pp. 395-403.
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Mahmud, MA, Pham, HT, Duong, T, Yin, Y, Peng, J, Wu, Y, Liang, W, Li, L, Kumar, A, Shen, H, Walter, D, Nguyen, HT, Mozaffari, N, Tabi, GD, Andersson, G, Catchpole, KR, Weber, KJ & White, TP 2021, 'Combined Bulk and Surface Passivation in Dimensionally Engineered 2D‐3D Perovskite Films via Chlorine Diffusion', Advanced Functional Materials, vol. 31, no. 46.
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AbstractDimensional engineering of perovskite films is a promising pathway to improve the efficiency and stability of perovskite solar cells (PSCs). In this context, surface or bulk passivation of defects in 3D perovskite film by careful introduction of 2D perovskite plays a key role. Here the authors demonstrate a 2D perovskite passivation scheme based on octylammonium chloride, and show that it provides both bulk and surface passivation of 1.6 eV bandgap 3D perovskite film for highly efficient (≈23.62%) PSCs with open‐circuit voltages up to 1.24 V. Surface and depth‐resolved microscopy and spectroscopy analysis reveal that the Cl− anion diffuses into the perovskite bulk, passivating defects, while the octylammonium ligands provide effective, localized surface passivation. The authors find that the Cl− diffusion into the perovskite lattice is independent of the 2D perovskite crystallization process and occurs rapidly during deposition of the 2D precursor solution. The annealing‐induced evaporation of Cl from bulk perovskite is also inhibited in 2D–3D perovskite film as compared to pristine 3D perovskite, ensuring effective bulk passivation in the relevant film.
Mahmud, MAP & Farjana, SH 2021, 'Comparative Eco-Profiles of Polyethylene Terephthalate (PET) and Polymethyl Methacrylate (PMMA) Using Life Cycle Assessment', Journal of Polymers and the Environment, vol. 29, no. 2, pp. 418-428.
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Polyethylene terephthalate (PET) and polymethyl methacrylate (PMMA) are extensively applied to produce nano-energy by harvesting ambient mechanical energy for energizing wearable electronics. Nowadays importance has been given to study on both PET and PMMA due to their growing demand in building Triboelectric Nanogenerators (TENG) to replace small batteries. The manufacturing of both triboelectric polymers from raw materials is hazardous to the environment. However, there has been no comparative evaluation of the probable effects of PET and PMMA production plants yet. This study highlights their comparative eco-profiles. An inclusive Life Cycle Inventory (LCI) model is built for methodical assessment of their impacts. Life Cycle Assessment (LCA) has been done by the ILCD midpoint method, Eco-indicator 99 endpoint method, Raw Material Flow (RMF) method, Greenhouse gas protocol method, and Ecopoints 97 method utilizing the Ecoinvent database and SimaPro software. The effects are assessed and compared for 21 impact categories such as global warming, acidification, eutrophication, terrestrial ecotoxicity, human toxicity, human carcinogenic toxicity, and fine particulate matter formation, marine ecotoxicity etc. The results indicate an estimated 3.01 kg CO2 eq./kg and 8.43 kg CO2 eq./kg of greenhouse gas (GHG) emission to the environment by a PET plant and a PMMA plant, respectively. Moreover, PET plants have the highest effect on land use, ionizing radiation and ozone depletion; whereas PMMA plants have the greatest impact on climate change, acidification, eutrophication and resources. Overall, PMMA polymer production plants are found to be more hazardous to the environment than PET polymer production plants. It is recommended that a better environmental profile from both types of production plants can be achieved through optimization, via abating the effects by replacing the problematic materials, designs, methods and devices with their equivalent environment-friend...
Mahmud, MAP, Tat, T, Xiao, X, Adhikary, P & Chen, J 2021, 'Advances in 4D‐printed physiological monitoring sensors', Exploration, vol. 1, no. 3.
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AbstractPhysiological monitoring sensors have been critical in diagnosing and improving the healthcare industry over the past 30 years, despite various limitations regarding providing differences in signal outputs in response to the changes in the user's body. Four‐dimensional (4D) printing has been established in less than a decade; therefore, it currently offers limited resources and knowledge. Still, the technique paves the way for novel platforms in today's ever‐growing technologies. This innovative paradigm of 4D printing physiological monitoring sensors aspires to provide real‐time and continuous diagnoses. In this perspective, we cover the advancements currently available in the 4D printing industry that has arisen in the last septennium, focusing on the overview of 4D printing, its history, and both wearable and implantable physiological sensing solutions. Finally, we explore the current challenges faced in this field, translational research, and its future prospects. All of these aims highlight key areas of attention that can be applied by future researchers to fully transform 4D printed physiological monitoring sensors into more viable medical products.
Mahmud, MAP, Zolfagharian, A, Gharaie, S, Kaynak, A, Farjana, SH, Ellis, AV, Chen, J & Kouzani, AZ 2021, '3D‐Printed Triboelectric Nanogenerators: State of the Art, Applications, and Challenges', Advanced Energy and Sustainability Research, vol. 2, no. 3.
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Triboelectric nanogenerator (TENG) development is undergoing rapid progress utilizing the state‐of‐the‐art 3D‐printing technologies. Herein a critical analysis of the latest developments in 3D‐printed wearable and implantable TENGs that can be used to energize small portable electronic and biomedical devices is presented. Recent progress in 3D‐printed triboelectric nanogenerator (3DP‐TENG) materials and architectural formations, as well as their performance, is evaluated for powering systems that implement physiological monitoring, multifunctional sensing, electronic energizing, noise canceling, dust filtering, and self‐healing. Furthermore, the review explicitly focuses on the 3D‐printing approaches used to form stable and robust 3DP‐TENGs. In addition, the key challenges to improving the performance of 3DP‐TENGs for optimal energy harvesting are discussed, and a roadmap is given for research and translation to commercial markets in the next decade.
Mai-Prochnow, A, Zhou, R, Zhang, T, Ostrikov, K, Mugunthan, S, Rice, SA & Cullen, PJ 2021, 'Interactions of plasma-activated water with biofilms: inactivation, dispersal effects and mechanisms of action', npj Biofilms and Microbiomes, vol. 7, no. 1, p. 11.
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AbstractBiofilms have several characteristics that ensure their survival in a range of adverse environmental conditions, including high cell numbers, close cell proximity to allow easy genetic exchange (e.g., for resistance genes), cell communication and protection through the production of an exopolysaccharide matrix. Together, these characteristics make it difficult to kill undesirable biofilms, despite the many studies aimed at improving the removal of biofilms. An elimination method that is safe, easy to deliver in physically complex environments and not prone to microbial resistance is highly desired. Cold atmospheric plasma, a lightning-like state generated from air or other gases with a high voltage can be used to make plasma-activated water (PAW) that contains many active species and radicals that have antimicrobial activity. Recent studies have shown the potential for PAW to be used for biofilm elimination without causing the bacteria to develop significant resistance. However, the precise mode of action is still the subject of debate. This review discusses the formation of PAW generated species and their impacts on biofilms. A focus is placed on the diffusion of reactive species into biofilms, the formation of gradients and the resulting interaction with the biofilm matrix and specific biofilm components. Such an understanding will provide significant benefits for tackling the ubiquitous problem of biofilm contamination in food, water and medical areas.
Maire, J, Girvan, SK, Barkla, SE, Perez-Gonzalez, A, Suggett, DJ, Blackall, LL & van Oppen, MJH 2021, 'Correction to: Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs', The ISME Journal, vol. 15, no. 7, pp. 2168-2170.
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Abstract A Correction to this paper has been published: https://doi.org/10.1038/s41396-021-00970-6
Maire, J, Girvan, SK, Barkla, SE, Perez-Gonzalez, A, Suggett, DJ, Blackall, LL & van Oppen, MJH 2021, 'Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs', The ISME Journal, vol. 15, no. 7, pp. 2028-2042.
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Abstract Corals house a variety of microorganisms which they depend on for their survival, including endosymbiotic dinoflagellates (Symbiodiniaceae) and bacteria. While cnidarian–microorganism interactions are widely studied, Symbiodiniaceae–bacteria interactions are only just beginning to receive attention. Here, we describe the localization and composition of the bacterial communities associated with cultures of 11 Symbiodiniaceae strains from nine species and six genera. Three-dimensional confocal laser scanning and electron microscopy revealed bacteria are present inside the Symbiodiniaceae cells as well as closely associated with their external cell surface. Bacterial pure cultures and 16S rRNA gene metabarcoding from Symbiodiniaceae cultures highlighted distinct and highly diverse bacterial communities occur intracellularly, closely associated with the Symbiodiniaceae outer cell surface and loosely associated (i.e., in the surrounding culture media). The intracellular bacteria are highly conserved across Symbiodiniaceae species, suggesting they may be involved in Symbiodiniaceae physiology. Our findings provide unique new insights into the biology of Symbiodiniaceae.
Maitre, M, Chiaravalle, A, Horder, M, Chadwick, S & Beavis, A 2021, 'Evaluating the effect of barrel length on pellet distribution patterns of sawn-off shotguns', Forensic Science International, vol. 320, pp. 110685-110685.
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Malik, S, Shahid, A, Liu, C-G, Zafar Khan, A, Nawaz, MZ, Zhu, H & Mehmood, MA 2021, 'Developing fourth-generation biofuels secreting microbial cell factories for enhanced productivity and efficient product recovery; a review', Fuel, vol. 298, pp. 120858-120858.
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Fourth generation (4G) biofuels have been found compatible with engines, storage systems, and transport facilities. Due to advances in synthetic biology and genetic engineering tools, considerable progress has been made in producing 4G biofuels including high-carbon alcohols, long-chain hydrocarbons, terpenoids-based, and/or fatty-acid derived biofuels using Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lypolytica, and Zymomonas mobilis as microbial cellular factories. However, these microbial platforms face various challenges including low product titers, low product yields, difficult product recovery incurring intensive energy consumption, and discharge of large amounts of wastewater. All these issues make the production and recovery of these biofuels expensive and commercially non-competitive. However, various genetic manipulation approaches including overexpression of heat-shock proteins, enhanced production of precursor molecules, regulating redox-balance, and membrane engineering have been employed to cope with these challenges. This review discusses the progress made in the molecular approaches for the enhanced biosynthesis and easier recovery of these biofuels through employing the secreting microbial cell factories. Besides, based on the data published on membrane transporters in previous fifteen years, selected fungal and bacterial membrane efflux pumps are studied to evaluate their biofuel secretion potential as future targets to be employed in the biofuel secreting microbial cell factories to achieve commercial robustness in the future.
Man, Z, Safaei, J, Zhang, Z, Wang, Y, Zhou, D, Li, P, Zhang, X, Jiang, L & Wang, G 2021, 'Serosa-Mimetic Nanoarchitecture Membranes for Highly Efficient Osmotic Energy Generation', Journal of the American Chemical Society, vol. 143, no. 39, pp. 16206-16216.
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Osmotic energy stored between seawater and freshwater is a clean and renewable energy source. However, developing high-efficiency and durable permselective membranes for harvesting osmotic energy remains a longstanding bottleneck. Herein, we report that a nanocomposite membrane with a biological serosa-mimetic structure can achieve high-performance osmotic energy generation through the coupling of two-dimensional (2D) sulfonated covalent organic framework (COF) nanosheets and anion-grafted aramid nanofibers (ANFs). As verified by theoretical calculations and experimental investigations, the 2D COF nanosheets not only provide abundant one-dimensional (1D)/2D nanofluidic channels to synergistically benefit an ultrafast ion migration but also enable high cation permselectivity via the covalently tethered anions. The grafted ANFs increase the mechanical strength of the membrane and further improve the ion diffusion/rectification. When it was applied in an osmotic power generator, the biomimetic membrane delivered a power density of 9.6 W m-2, far surpassing the commercial benchmark of 5.0 W m-2. This work could boost the viability of osmotic energy conversion toward a sustainable future.
Mandal, PK, Ballerin, G, Nolan, LM, Petty, NK & Whitchurch, CB 2021, 'Bacteriophage infection of Escherichia coli leads to the formation of membrane vesicles via both explosive cell lysis and membrane blebbing', Microbiology, vol. 167, no. 4.
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Membrane vesicles (MVs) are membrane-bound spherical nanostructures that prevail in all three domains of life. In Gram-negative bacteria, MVs are thought to be produced through blebbing of the outer membrane and are often referred to as outer membrane vesicles (OMVs). We have recently described another mechanism of MV formation in Pseudomonas aeruginosa that involves explosive cell-lysis events, which shatters cellular membranes into fragments that rapidly anneal into MVs. Interestingly, MVs are often observed within preparations of lytic bacteriophage, however the source of these MVs and their association with bacteriophage infection has not been explored. In this study we aimed to determine if MV formation is associated with lytic bacteriophage infection. Live super-resolution microscopy demonstrated that explosive cell lysis of Escherichia coli cells infected with either bacteriophage T4 or T7, resulted in the formation of MVs derived from shattered membrane fragments. Infection by either bacteriophage was also associated with the formation of membrane blebs on intact bacteria. TEM revealed multiple classes of MVs within phage lysates, consistent with multiple mechanisms of MV formation. These findings suggest that bacteriophage infection may be a major contributor to the abundance...
Mandigo, AC, Yuan, W, Xu, K, Gallagher, P, Pang, A, Guan, YF, Shafi, AA, Thangavel, C, Sheehan, B, Bogdan, D, Paschalis, A, McCann, JJ, Laufer, TS, Gordon, N, Vasilevskaya, IA, Dylgjeri, E, Chand, SN, Schiewer, MJ, Domingo-Domenech, J, Den, RB, Holst, J, McCue, PA, de Bono, JS, McNair, C & Knudsen, KE 2021, 'RB/E2F1 as a Master Regulator of Cancer Cell Metabolism in Advanced Disease', Cancer Discovery, vol. 11, no. 9, pp. 2334-2353.
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Abstract Loss of the retinoblastoma (RB) tumor suppressor protein is a critical step in reprogramming biological networks that drive cancer progression, although mechanistic insight has been largely limited to the impact of RB loss on cell-cycle regulation. Here, isogenic modeling of RB loss identified disease stage–specific rewiring of E2F1 function, providing the first-in-field mapping of the E2F1 cistrome and transcriptome after RB loss across disease progression. Biochemical and functional assessment using both in vitro and in vivo models identified an unexpected, prominent role for E2F1 in regulation of redox metabolism after RB loss, driving an increase in the synthesis of the antioxidant glutathione, specific to advanced disease. These E2F1-dependent events resulted in protection from reactive oxygen species in response to therapeutic intervention. On balance, these findings reveal novel pathways through which RB loss promotes cancer progression and highlight potentially new nodes of intervention for treating RB-deficient cancers. Significance: This study identifies stage-specific consequences of RB loss across cancer progression that have a direct impact on tumor response to clinically utilized therapeutics. The study herein is the first to investigate the effect of RB loss on global metabolic regulation and link RB/E2F1 to redox control in multiple advanced diseases. This article is highlighted in the In This Issue feature, p. 2113
Mandwie, M, Karunia, J, Niaz, A, Keay, KA, Musumeci, G, Rennie, C, McGrath, K, Al-Badri, G & Castorina, A 2021, 'Metformin Treatment Attenuates Brain Inflammation and Rescues PACAP/VIP Neuropeptide Alterations in Mice Fed a High-Fat Diet', International Journal of Molecular Sciences, vol. 22, no. 24, pp. 13660-13660.
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High-fat diet (HFD)-induced comorbid cognitive and behavioural impairments are thought to be the result of persistent low-grade neuroinflammation. Metformin, a first-line medication for the treatment of type-2 diabetes, seems to ameliorate these comorbidities, but the underlying mechanism(s) are not clear. Pituitary adenylate cyclase-activating peptide (PACAP) and vasoactive intestinal peptide (VIP) are neuroprotective peptides endowed with anti-inflammatory properties. Alterations to the PACAP/VIP system could be pivotal during the development of HFD-induced neuroinflammation. To unveil the pathogenic mechanisms underlying HFD-induced neuroinflammation and assess metformin’s therapeutic activities, (1) we determined if HFD-induced proinflammatory activity was present in vulnerable brain regions associated with the development of comorbid behaviors, (2) investigated if the PACAP/VIP system is altered by HFD, and (3) assessed if metformin rescues such diet-induced neurochemical alterations. C57BL/6J male mice were divided into two groups to receive either standard chow (SC) or HFD for 16 weeks. A further HFD group received metformin (HFD + M) (300 mg/kg BW daily for 5 weeks) via oral gavage. Body weight, fasting glucose, and insulin levels were measured. After 16 weeks, the proinflammatory profile, glial activation markers, and changes within the PI3K/AKT intracellular pathway and the PACAP/VIP system were evaluated by real-time qPCR and/or Western blot in the hypothalamus, hippocampus, prefrontal cortex, and amygdala. Our data showed that HFD causes widespread low-grade neuroinflammation and gliosis, with regional-specific differences across brain regions. HFD also diminished phospho-AKT(Ser473) expression and caused significant disruptions to the PACAP/VIP system. Treatment with metformin attenuated these neuroinflammatory signatures and reversed PI3K/AKT and PACAP/VIP alterations caused by HFD. Altogether, our findings demonstrate that metform...
Mann, R, Holmes, A, McNeilly, O, Cavaliere, R, Sotiriou, GA, Rice, SA & Gunawan, C 2021, 'Evolution of biofilm-forming pathogenic bacteria in the presence of nanoparticles and antibiotic: adaptation phenomena and cross-resistance', Journal of Nanobiotechnology, vol. 19, no. 1, p. 291.
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Abstract Background Treatment of bacterial biofilms are difficult and in many cases, expensive. Bacterial biofilms are naturally more resilient to antimicrobial agents than their free-living planktonic counterparts, rendering the community growth harder to control. The present work described the risks of long-term use of an important alternative antimicrobial, silver nanoparticles (NAg), for the first time, on the dominant mode of bacterial growth. Results NAg could inhibit the formation as well as eradicating an already grown biofilm of Pseudomonas aeruginosa, a pathogen notorious for its resilience to antibiotics. The biofilm-forming bacterium however, evolved a reduced sensitivity to the nanoparticle. Evidence suggests that survival is linked to the development of persister cells within the population. A similar adaptation was also seen upon prolonged exposures to ionic silver (Ag+). The persister population resumed normal growth after subsequent passage in the absence of silver, highlighting the potential risks of recurrent infections with long-term NAg (and Ag+) treatments of biofilm growth. The present study further observed a potential silver/antibiotic cross-resistance, whereby NAg (as well as Ag+) could not eradicate an already growing gentamicin-resistant P. aeruginosa biofilm. The phenomena is thought to result from the hindered biofilm penetration of the silver species. In contrast, both silver formulations inhibited biofilm formation of the resistant strain, presenting a promising avenue for the control of biofilm-forming antibiotic-resistant bacteria.
Mann, R, Mitsidis, D, Xie, Z, McNeilly, O, Ng, YH, Amal, R & Gunawan, C 2021, 'Antibacterial Activity of Reduced Graphene Oxide', Journal of Nanomaterials, vol. 2021, pp. 1-10.
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The increasing biological use of graphene-based materials has prompted research inquiries on their effects on microorganisms. The work herein reported different types of microbiological activity of reduced graphene oxide (RGO). At relatively high concentrations (200 and 400 μg/mL), RGO exhibited antibacterial activity on the model bacterium Escherichia coli, while at lower concentrations (10 and 50 μg/mL), interestingly, no antibacterial effect was observed. Instead, an increase in the viable population after exposure at lower concentrations was observed, verified by colony counting and fluorescence microscopy. Further investigation ruled out the possibility of nutrient release from RGO being responsible for this growth-enhancing effect, whereby a comparable number of viable cells were found in the particle-free RGO leachate systems relative to the control. A before and after exposure X-ray photoelectron spectroscopy (XPS) analysis of the RGO detected less presence of C-C bond on the particle surface, suggesting the ability of the bacterium for the use of the carbon-based materials for growth. This potential RGO-cell interaction is further supported by the observed emergence of C-N bond on the particle surface, the nitrogen moieties most likely of bacterial (cell envelope) origins. Although still an early evidence, such RGO-cell interactions could explain the viable cell increase observed at the lower concentration RGO systems. The present study highlights the concentration-dependent microbiological effects of RGO, clarifying the contradicting reports on the growth enhancing versus antibacterial effect of graphene-based materials. The knowledge is important not only for the antibacterial formulation of carbon-based materials but also when assessing their environmental impact.
Manning, EE, Bradfield, LA & Iordanova, MD 2021, 'Adaptive behaviour under conflict: Deconstructing extinction, reversal, and active avoidance learning', Neuroscience & Biobehavioral Reviews, vol. 120, pp. 526-536.
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In complex environments, organisms must respond adaptively to situations despite conflicting information. Under natural (i.e. non-laboratory) circumstances, it is rare that cues or responses are consistently paired with a single outcome. Inconsistent pairings are more common, as are situations where cues and responses are associated with multiple outcomes. Such inconsistency creates conflict, and a response that is adaptive in one scenario may not be adaptive in another. Learning to adjust responses accordingly is important for species to survive and prosper. Here we review the behavioural and brain mechanisms of responding under conflict by focusing on three popular behavioural procedures: extinction, reversal learning, and active avoidance. Extinction involves adapting from reinforcement to non-reinforcement, reversal learning involves swapping the reinforcement of cues or responses, and active avoidance involves performing a response to avoid an aversive outcome, which may conflict with other defensive strategies. We note that each of these phenomena relies on somewhat overlapping neural circuits, suggesting that such circuits may be critical for the general ability to respond appropriately under conflict.
Marlton, FP, Nayak, S, Venkateshwarlu, S, Chan, NH, Kong, J, Zhang, Y, Tucker, MG, Jørgensen, MRV & Pramanick, A 2021, 'Broad Distribution of Local Polar States Generates Large Electrothermal Properties in Pb-Free Relaxor Ferroelectrics', Chemistry of Materials, vol. 33, no. 22, pp. 8844-8853.
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Marlton, FP, Zhang, Z, Zhang, Y, Proffen, TE, Ling, CD & Kennedy, BJ 2021, 'Lattice Disorder and Oxygen Migration Pathways in Pyrochlore and Defect-Fluorite Oxides', Chemistry of Materials, vol. 33, no. 4, pp. 1407-1415.
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Marlton, FP, Zhang, Z, Zhang, Y, Proffen, TE, Ling, CD & Kennedy, BJ 2021, 'Lattice disorder and oxygen migration pathways in pyrochlore and defect-fluorite oxides', Acta Crystallographica Section A Foundations and Advances, vol. 77, no. a2, pp. C1083-C1084.
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Martins Costa Gomes, G, de Gouveia Belinelo, P, Starkey, MR, Murphy, VE, Hansbro, PM, Sly, PD, Robinson, PD, Karmaus, W, Gibson, PG, Mattes, J & Collison, AM 2021, 'Cord blood group 2 innate lymphoid cells are associated with lung function at 6 weeks of age', Clinical & Translational Immunology, vol. 10, no. 7, p. e1296.
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AbstractObjectiveOffspring born to mothers with asthma in pregnancy are known to have lower lung function which tracks with age. Human group 2 innate lymphoid cells (ILC2) accumulate in foetal lungs, at 10‐fold higher levels compared to adult lungs. However, there are no data on foetal ILC2 numbers and the association with respiratory health outcomes such as lung function in early life. We aimed to investigate cord blood immune cell populations from babies born to mothers with asthma in pregnancy.MethodsCord blood from babies born to asthmatic mothers was collected, and cells were stained in whole cord blood. Analyses were done using traditional gating approaches and computational methodologies (t‐distributed stochastic neighbour embedding and PhenoGraph algorithms). At 6 weeks of age, the time to peak tidal expiratory flow as a percentage of total expiratory flow time (tPTEF/tE%) was determined as well as Lung Clearance Index (LCI), during quiet natural sleep.ResultsOf 110 eligible infants (March 2017 to November 2019), 91 were successfully immunophenotyped (82.7%). Lung function was attempted in 61 infants (67.0%), and 43 of those infants (70.5% of attempted) had technically acceptable tPTEF/tE% measurements. Thirty‐four infants (55.7% of attempted) had acceptable LCI measurements. Foetal ILC2 numbers with increased expression of chemoattractant receptor‐homologous molecule (CRTh2), characterised by two distinct analysis methodologies, were associated with poorer infant lung function at 6 weeks of age.”ConclusionFoetal immune responses may be a surrogate variable for or directly influence lung function outcomes in early life.
Martins Costa Gomes, G, Karmaus, W, Murphy, VE, Gibson, PG, Percival, E, Hansbro, PM, Starkey, MR, Mattes, J & Collison, AM 2021, 'Environmental Air Pollutants Inhaled during Pregnancy Are Associated with Altered Cord Blood Immune Cell Profiles', International Journal of Environmental Research and Public Health, vol. 18, no. 14, pp. 7431-7431.
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Air pollution exposure during pregnancy may be a risk factor for altered immune maturation in the offspring. We investigated the association between ambient air pollutants during pregnancy and cell populations in cord blood from babies born to mothers with asthma enrolled in the Breathing for Life Trial. For each patient (n = 91), daily mean ambient air pollutant levels were extracted during their entire pregnancy for sulfur dioxide (SO2), nitric oxide, nitrogen dioxide, carbon monoxide, ozone, particulate matter <10 μm (PM10) or <2.5 μm (PM2.5), humidity, and temperature. Ninety-one cord blood samples were collected, stained, and assessed using fluorescence-activated cell sorting (FACS). Principal Component (PC) analyses of both air pollutants and cell types with linear regression were employed to define associations. Considering risk factors and correlations between PCs, only one PC from air pollutants and two from cell types were statistically significant. PCs from air pollutants were characterized by higher PM2.5 and lower SO2 levels. PCs from cell types were characterized by high numbers of CD8 T cells, low numbers of CD4 T cells, and by high numbers of plasmacytoid dendritic cells (pDC) and low numbers of myeloid DCs (mDCs). PM2.5 levels during pregnancy were significantly associated with high numbers of pDCs (p = 0.006), and SO2 with high numbers of CD8 T cells (p = 0.002) and low numbers of CD4 T cells (p = 0.011) and mDCs (p = 4.43 × 10−6) in cord blood. These data suggest that ambient SO2 and PM2.5 exposure are associated with shifts in cord blood cell types that are known to play significant roles in inflammatory respiratory disease in childhood.
Masrur, H, Senjyu, T, Islam, MR, Kouzani, AZ & Mahmud, MAP 2021, 'Resilience-Oriented Dispatch of Microgrids Considering Grid Interruptions', IEEE Transactions on Applied Superconductivity, vol. 31, no. 8, pp. 1-5.
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By providing a reliable and economical supply of energy, microgrids (MGs) may play a pivotal role in the case of large grid disruptions. However, the resilience benefits of microgrids in terms of outage survivability that often lead to economic paybacks are not well investigated in the existing literature. To address this concern, this paper optimizes and simulates a grid-connected MG placed at a hospital consisting of a photovoltaic (PV) module and an energy storage unit that can adequately prevent a prolonged blackout. The impact of net energy metering (NEM) and diesel generator (DG) has further been examined for this hybrid system. Four different cases have been optimized and results show that the PV and battery work in tandem, both with and without considering the existing DG and NEM and meets all critical load demand during a grid outage. The findings also indicate that the proposed approach yields significant economic benefits for two cases relative to business as usual case.
Massella, E, Giacometti, F, Bonilauri, P, Reid, CJ, Djordjevic, SP, Merialdi, G, Bacci, C, Fiorentini, L, Massi, P, Bardasi, L, Rubini, S, Savini, F, Serraino, A & Piva, S 2021, 'Antimicrobial Resistance Profile and ExPEC Virulence Potential in Commensal Escherichia coli of Multiple Sources', Antibiotics, vol. 10, no. 4, pp. 351-351.
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We recently described the genetic antimicrobial resistance and virulence profile of a collection of 279 commensal E. coli of food-producing animal (FPA), pet, wildlife and human origin. Phenotypic antimicrobial resistance (AMR) and the role of commensal E. coli as reservoir of extra-intestinal pathogenic Escherichia coli (ExPEC) virulence-associated genes (VAGs) or as potential ExPEC pathogens were evaluated. The most common phenotypic resistance was to tetracycline (76/279, 27.24%), sulfamethoxazole/trimethoprim (73/279, 26.16%), streptomycin and sulfisoxazole (71/279, 25.45% both) among the overall collection. Poultry and rabbit were the sources mostly associated to AMR, with a significant resistance rate (p > 0.01) to quinolones, streptomycin, sulphonamides, tetracycline and, only for poultry, to ampicillin and chloramphenicol. Finally, rabbit was the source mostly associated to colistin resistance. Different pandemic (ST69/69*, ST95, ST131) and emerging (ST10/ST10*, ST23, ST58, ST117, ST405, ST648) ExPEC sequence types (STs) were identified among the collection, especially in poultry source. Both ST groups carried high number of ExPEC VAGs (pandemic ExPEC STs, mean = 8.92; emerging ExPEC STs, mean = 6.43) and showed phenotypic resistance to different antimicrobials (pandemic ExPEC STs, mean = 2.23; emerging ExPEC STs, mean = 2.43), suggesting their role as potential ExPEC pathogens. Variable phenotypic resistance and ExPEC VAG distribution was also observed in uncommon ExPEC lineages, suggesting commensal flora as a potential reservoir of virulence (mean = 3.80) and antimicrobial resistance (mean = 1.69) determinants.
Mathieu, C, Gonzalez, A, Garcia, A, Johow, M, Badia, C, Jara, C, Nuñez, P, Neira, V, Montiel, NA, Killian, ML & Brito, BP 2021, 'H7N6 low pathogenic avian influenza outbreak in commercial turkey farms in Chile caused by a native South American Lineage', Transboundary and Emerging Diseases, vol. 68, no. 1, pp. 2-12.
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© 2019 Blackwell Verlag GmbH In December 2016, low pathogenic avian influenza (LPAI) caused by an H7N6 subtype was confirmed in a grow-out turkey farm located in Valparaiso Region, Chile. Depopulation of exposed animals, zoning, animal movement control and active surveillance were implemented to contain the outbreak. Two weeks later, a second grow-out turkey farm located 70 km north of the first site was also infected by H7N6 LPAI, which subsequently spilled over to one backyard poultry flock. The virus involved in the outbreak shared a close genetic relationship with Chilean aquatic birds’ viruses collected in previous years. The A/turkey/Chile/2017(H7N6) LPAI virus belonged to a native South American lineage. Based on the H7 and most of the internal genes’ phylogenies, these viruses were also closely related to the ones that caused a highly pathogenic avian influenza outbreak in Chile in 2002. Results from this study help to understand the regional dynamics of influenza outbreaks, highlighting the importance of local native viruses circulating in the natural reservoir hosts.
Maugeri, G, D’Agata, V, Magrì, B, Roggio, F, Castorina, A, Ravalli, S, Di Rosa, M & Musumeci, G 2021, 'Neuroprotective Effects of Physical Activity via the Adaptation of Astrocytes', Cells, vol. 10, no. 6, pp. 1542-1542.
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The multifold benefits of regular physical exercise have been largely demonstrated in human and animal models. Several studies have reported the beneficial effects of physical activity, both in peripheral tissues and in the central nervous system (CNS). Regular exercise improves cognition, brain plasticity, neurogenesis and reduces the symptoms of neurodegenerative diseases, making timeless the principle of “mens sana in corpore sano” (i.e., a healthy mind in a healthy body). Physical exercise promotes morphological and functional changes in the brain, acting not only in neurons but also in astrocytes, which represent the most numerous glial cells in the brain. The multiple effects of exercise on astrocytes comprise the increased number of new astrocytes, the maintenance of basal levels of catecholamine, the increase in glutamate uptake, the major release of trophic factors and better astrocytic coverage of cerebral blood vessels. The purpose of this review is to highlight the effects of exercise on brain function, emphasize the role of astrocytes in the healthy CNS, and provide an update for a better understanding of the effects of physical exercise in the modulation of astrocyte function.
Maugeri, G, D'Agata, V, Trovato, B, Roggio, F, Castorina, A, Vecchio, M, Di Rosa, M & Musumeci, G 2021, 'The role of exercise on peripheral nerve regeneration: from animal model to clinical application', Heliyon, vol. 7, no. 11, pp. e08281-e08281.
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McCausland, JW, Yang, X, Squyres, GR, Lyu, Z, Bruce, KE, Lamanna, MM, Söderström, B, Garner, EC, Winkler, ME, Xiao, J & Liu, J 2021, 'Treadmilling FtsZ polymers drive the directional movement of sPG-synthesis enzymes via a Brownian ratchet mechanism', Nature Communications, vol. 12, no. 1, p. 609.
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AbstractThe FtsZ protein is a central component of the bacterial cell division machinery. It polymerizes at mid-cell and recruits more than 30 proteins to assemble into a macromolecular complex to direct cell wall constriction. FtsZ polymers exhibit treadmilling dynamics, driving the processive movement of enzymes that synthesize septal peptidoglycan (sPG). Here, we combine theoretical modelling with single-molecule imaging of live bacterial cells to show that FtsZ’s treadmilling drives the directional movement of sPG enzymes via a Brownian ratchet mechanism. The processivity of the directional movement depends on the binding potential between FtsZ and the sPG enzyme, and on a balance between the enzyme’s diffusion and FtsZ’s treadmilling speed. We propose that this interplay may provide a mechanism to control the spatiotemporal distribution of active sPG enzymes, explaining the distinct roles of FtsZ treadmilling in modulating cell wall constriction rate observed in different bacteria.
McDonald, AG, Murray, BR, Krix, DW & Murray, ML 2021, 'Complex soil contamination severely impacts seed-sown crop viability in Australia', Australian Journal of Crop Science, vol. 15, no. 15(04):2021, pp. 531-537.
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Food security is a critical issue for many global communities. Heavy metal contamination in soils present a major and ongoing ecological risk associated with human activities which may impact the viability and safety of seed-sown crops. To better understand the impacts of soil contamination by heavy metals on seed-sown crop viability, we examined germination responses of eight commercially-important fruit and vegetable crop species to copper, zinc, and lead contamination at levels likely to be found in contaminated regions in Australia. We compared the germination attributes of days to first germination, germination period, and total proportion of seeds germinated under concentration limits of heavy metals detected at degraded sites and current Australian National Environment Protection Measure thresholds for domestic soils (i.e., copper 6,000 mg kg-1, zinc 4,700 mg kg-1, lead 300 mg kg-1). The combined heavy metal treatment (i.e. all three metals) significantly inhibited germination for all edible crop species with only carrots able to germinate under complex, multi-metal-contaminated conditions. Seed viability was significantly decreased in mulberry (M. alba var. tatarica, M. nigra, and M. rubra) and lettuce (L. sativa), with lowered seed germination in all metals compared to carrot (D. carota), radish (R. sativus), tomato (S. lycopersicum) and common bean (P. vulgaris). These results indicate heavy metal contamination is a notable risk to seed-sown crop species, with multi-metal contamination events likely to be severely damaging to lettuce, tomato, radish, common bean, and mulberry crops
McLennan, K, Ruvindy, R, Ostrowski, M & Murray, S 2021, 'Assessing the Use of Molecular Barcoding and qPCR for Investigating the Ecology of Prorocentrum minimum (Dinophyceae), a Harmful Algal Species', Microorganisms, vol. 9, no. 3, pp. 510-510.
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Prorocentrum minimum is a species of marine dinoflagellate that occurs worldwide and can be responsible for harmful algal blooms (HABs). Some studies have reported it to produce tetrodotoxin; however, results have been inconsistent. qPCR and molecular barcoding (amplicon sequencing) using high-throughput sequencing have been increasingly applied to quantify HAB species for ecological analyses and monitoring. Here, we isolated a strain of P. minimum from eastern Australian waters, where it commonly occurs, and developed and validated a qPCR assay for this species based on a region of ITS rRNA in relation to abundance estimates from the cultured strain as determined using light microscopy. We used this tool to quantify and examine ecological drivers of P. minimum in Botany Bay, an estuary in southeast Australia, for over ~14 months in 2016–2017. We compared abundance estimates using qPCR with those obtained using molecular barcoding based on an 18S rRNA amplicon. There was a significant correlation between the abundance estimates from amplicon sequencing and qPCR, but the estimates from light microscopy were not significantly correlated, likely due to the counting method applied. Using amplicon sequencing, ~600 unique actual sequence variants (ASVs) were found, much larger than the known phytoplankton diversity from this region. P. minimum abundance in Botany Bay was found to be significantly associated with lower salinities and higher dissolved CO2 levels.
McNally, R, Alqudah, A, McErlean, EM, Rennie, C, Morshed, N, Short, A, McGrath, K, Shimoni, O, Robson, T, McCarthy, HO & McClements, L 2021, 'Non-Viral Gene Delivery Utilizing RALA Modulates sFlt-1 Secretion, Important for Preeclampsia', Nanomedicine, vol. 16, no. 22, pp. 1999-2012.
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Background: Overexpression of sFlt-1 or modulation of FKBPL, key antiangiogenic proteins, are important in the pathogenesis of preeclampsia. Methods: A newly developed nonviral gene-delivery system, RALA, capable of overexpressing sFlt-1 (e15a isoform) was delivered in vivo in transgenic haploinsufficient ( Fkbpl+/−) mice. RALA was also used in vitro to deliver human Flt1 (hFlt1) in trophoblast cells. Results: Serum stable and nontoxic RALA/DNA-based nanoparticles induced an increase in sFlt-1 protein levels in the blood and total protein in the urine; the effect was more pronounced in Fkbpl+/− mice. In vitro, RALA-hFlt nanoparticles significantly reduced secretion of sFlt-1 in trophoblast cells. Conclusion: The RALA-based genetic nanodelivery system can be safely and effectively applied to emulate preeclampsia-like features or reduce sFlt-1 levels in vitro.
McNaughton, DA, Fares, M, Picci, G, Gale, PA & Caltagirone, C 2021, 'Advances in fluorescent and colorimetric sensors for anionic species', Coordination Chemistry Reviews, vol. 427, pp. 213573-213573.
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McNeilly, O, Mann, R, Hamidian, M & Gunawan, C 2021, 'Emerging Concern for Silver Nanoparticle Resistance in Acinetobacter baumannii and Other Bacteria', Frontiers in Microbiology, vol. 12.
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The misuse of antibiotics combined with a lack of newly developed ones is the main contributors to the current antibiotic resistance crisis. There is a dire need for new and alternative antibacterial options and nanotechnology could be a solution. Metal-based nanoparticles, particularly silver nanoparticles (NAg), have garnered widespread popularity due to their unique physicochemical properties and broad-spectrum antibacterial activity. Consequently, NAg has seen extensive incorporation in many types of products across the healthcare and consumer market. Despite clear evidence of the strong antibacterial efficacy of NAg, studies have raised concerns over the development of silver-resistant bacteria. Resistance to cationic silver (Ag+) has been recognised for many years, but it has recently been found that bacterial resistance to NAg is also possible. It is also understood that exposure of bacteria to toxic heavy metals like silver can induce the emergence of antibiotic resistance through the process of co-selection. Acinetobacter baumannii is a Gram-negative coccobacillus and opportunistic nosocomial bacterial pathogen. It was recently listed as the “number one” critical level priority pathogen because of the significant rise of antibiotic resistance in this species. NAg has proven bactericidal activity towards A. baumannii, even against strains that display multi-drug resistance. However, despite ample evidence of heavy metal (including silver; Ag+) resistance in this bacterium, combined with reports of heavy metal-driven co-selection of antibiotic resistance, little research has been dedicated to assessing the potential for NAg resistance development in A. baumannii. This is worrisome, as the increasingly indiscriminate use of NAg could promote the development of silver resistance in this species, like what has occurred w...
Meakin, GE, Kokshoorn, B, van Oorschot, RAH & Szkuta, B 2021, 'Evaluating forensic DNA evidence: Connecting the dots', WIREs Forensic Science, vol. 3, no. 4.
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AbstractTechnological developments within the field of forensic genetics have enhanced the sensitivity and specificity of DNA testing tremendously and have broadened the applications of biological evidence in criminal investigations. Evaluation and communication of the evidential findings within criminal cases have not maintained the same pace, which has largely stemmed from a failure to adopt a standardized approach within and across the various fields of forensic science. Within forensic biology, this has led to unjustified opinions on the weight of the evidence and occurrences of the association fallacy, when the weight of evidence given propositions at one level of the hierarchy of propositions is inappropriately transposed to a higher level. We further define the association fallacy to include the terms, “source level fallacy” and “activity level fallacy,” to enable the forensic science community to better identify and address issues in biological evidence evaluation. It is important to understand these concepts and their causes, and in doing so, identify potential avenues to avoid these fallacies in forensic science casework. These avenues include training and education of forensic and legal professionals, as well as research into transfer, persistence, prevalence and recovery (TPPR) of DNA and biological evidence in general.This article is categorized under:Forensic Biology > Interpretation of Biological Evidence
Mediati, DG, Lalaouna, D & Tree, JJ 2021, 'Burning the Candle at Both Ends: Have Exoribonucleases Driven Divergence of Regulatory RNA Mechanisms in Bacteria?', mBio, vol. 12, no. 4.
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Regulatory RNAs have emerged as ubiquitous gene regulators in all bacterial species studied to date. The combination of sequence-specific RNA interactions and malleable RNA structure has allowed regulatory RNA to adopt different mechanisms of gene regulation in a diversity of genetic backgrounds.
Mediati, DG, Wu, S, Wu, W & Tree, JJ 2021, 'Networks of Resistance: Small RNA Control of Antibiotic Resistance', Trends in Genetics, vol. 37, no. 1, pp. 35-45.
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Mehraj, H, Takahashi, S, Miyaji, N, Akter, A, Suzuki, Y, Seki, M, Dennis, ES & Fujimoto, R 2021, 'Characterization of Histone H3 Lysine 4 and 36 Tri-methylation in Brassica rapa L.', Frontiers in Plant Science, vol. 12.
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Covalent modifications of histone proteins act as epigenetic regulators of gene expression. We report the distribution of two active histone marks (H3K4me3 and H3K36me3) in 14-day leaves in two lines of Brassica rapa L. by chromatin immunoprecipitation sequencing. Both lines were enriched with H3K4me3 and H3K36me3 marks at the transcription start site, and the transcription level of a gene was associated with the level of H3K4me3 and H3K36me3. H3K4me3- and H3K36me3-marked genes showed low tissue-specific gene expression, and genes with both H3K4me3 and H3K36me3 had a high level of expression and were constitutively expressed. Bivalent active and repressive histone modifications such as H3K4me3 and H3K27me3 marks or antagonistic coexistence of H3K36me3 and H3K27me3 marks were observed in some genes. Expression may be susceptible to changes by abiotic and biotic stresses in genes having both H3K4me3 and H3K27me3 marks. We showed that the presence of H3K36me3 marks was associated with different gene expression levels or tissue specificity between paralogous paired genes, suggesting that H3K36me3 might be involved in subfunctionalization of the subgenomes.
Mehta, M, Malyla, V, Paudel, KR, Chellappan, DK, Hansbro, PM, Oliver, BG & Dua, K 2021, 'Berberine loaded liquid crystalline nanostructure inhibits cancer progression in adenocarcinomic human alveolar basal epithelial cells in vitro', Journal of Food Biochemistry, vol. 45, no. 11, p. e13954.
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Metastasis represents the leading cause of death in lung cancer patients. C-X-C Motif Chemokine Ligand 8 (CXCL-8), Chemokine (C-C motif) ligand 20 (CCL-20) and heme oxygenase -1 (HO-1) play an important role in cancer cell proliferation and migration. Berberine is an isoquinoline alkaloid isolated from several herbs in the Papaveraceae family that exhibits anti-inflammatory, anticancer and antidiabetic properties. Therefore, the aim of present study is to investigate the inhibitory potential of berberine monoolein loaded liquid crystalline nanoparticles (berberine-LCNs) against cancer progression. Berberine-LCNs were prepared by mixing berberine, monoolein and poloxamer 407 (P407) using ultrasonication method. A549 cells were treated with or without 5 µM dose of berberine LCNs for 24 hr and total cellular protein was extracted and further analyzed for the protein expression of CCl-20, CXCL-8 and HO-1 using human oncology array kit. Our results showed that berberine-LCNs significantly reduced the expression of CCl-20, CXCL-8 and HO-1 at dose of 5µM. Collectively, our findings suggest that berberine-LCNs have inhibitory effect on inflammation/oxidative stress related cytokines i.e. CCL20, CXCL-8, and HO-1 which could be a novel therapeutic target for the management of lung cancer. PRACTICAL APPLICATIONS: Berberine is an isoquinoline alkaloid extracted from various plants of Papaveraceae family. CXCL-8, CCL-20 and HO-1 play an important role in cancer progression. Our study showed that Berberine LCNs significantly downregulate the expression of CXCL-8, CCL-20 and HO-1 which suggests that Berberine loaded nanoparticles could be a promising therapeutic alternative for the management of lung cancer.
Mehta, M, Paudel, KR, Panth, N, Xenaki, D, Macloughlin, R, Oliver, BG, Lobenberg, R, Hansbro, PM, Chellappan, DK & Dua, K 2021, 'Drug Delivery Advances in Mitigating Inflammation Via Matrix Metalloproteinases in Respiratory Diseases', Nanomedicine, vol. 16, no. 6, pp. 437-439.
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Mehta, M, Paudel, KR, Shukla, SD, Allam, VSRR, Kannaujiya, VK, Panth, N, Das, A, Parihar, VK, Chakraborty, A, Ali, MK, Jha, NK, Xenaki, D, Su, QP, Wich, PR, Adams, J, Hansbro, PM, Chellappan, DK, Oliver, BGG & Dua, K 2021, 'Recent trends of NFκB decoy oligodeoxynucleotide-based nanotherapeutics in lung diseases', Journal of Controlled Release, vol. 337, pp. 629-644.
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Mehta, M, Paudel, KR, Shukla, SD, Shastri, MD, Satija, S, Singh, SK, Gulati, M, Dureja, H, Zacconi, FC, Hansbro, PM, Chellappan, DK & Dua, K 2021, 'Rutin-Loaded Liquid Crystalline Nanoparticles Attenuate Oxidative Stress in Bronchial Epithelial Cells: A PCR Validation', Future Medicinal Chemistry, vol. 13, no. 6, pp. 543-549.
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Aim: In the present study, the inhibitory potential of rutin-loaded liquid crystalline nanoparticles (LCNs) on oxidative stress was determined in human bronchial epithelial cells (BEAS-2B) by analysing the expression levels of different antioxidant (NADPH quinine oxidoreductase-1 ( NQO1); γ-glutamyl cysteine synthetase catalytic subunit ( GCLC)) and pro-oxidant (NADPH oxidase (Nox)-4; Nox2B) genes. Results: Our findings revealed that the rutin-loaded LCNs inhibited the genes, namely Nox2B and Nox4, which caused oxidative stress. In addition, these nanoparticles demonstrated an upregulation in the expression of the antioxidant genes Gclc and Nqo-1 in a dose-dependent manner. Conclusion: The study indicates the promising potential of rutin-loaded LCNs as an effective treatment strategy in patients with high oxidant loads in various respiratory diseases.
Mehta, M, Satija, S, Paudel, KR, Malyla, V, Kannaujiya, VK, Chellappan, DK, Bebawy, M, Hansbro, PM, Wich, PR & Dua, K 2021, 'Targeting respiratory diseases using miRNA inhibitor based nanotherapeutics: Current status and future perspectives', Nanomedicine: Nanotechnology, Biology and Medicine, vol. 31, pp. 102303-102303.
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MicroRNAs (miRNAs) play a fundamental role in the developmental and physiological processes that occur in both animals and plants. AntagomiRs are synthetic antagonists of miRNA, prevent the target mRNA from suppression. Therapeutic approaches that modulate miRNAs have immense potential in the treatment of chronic respiratory disorders. However, the successful delivery of miRNAs/antagomiRs to the lungs remains a major challenge in clinical applications. A range of materials, namely, polymer nanoparticles, lipid nanocapsules and inorganic nanoparticles have shown promising results for intracellular delivery of miRNA in chronic respiratory disorders. This review discusses the current understanding of miRNA biology, the biological roles of antagomiRs in chronic respiratory disease and the recent advances in the therapeutic utilization of antagomiRs as disease biomarkers. Furthermore our review provides a common platform to debate on the nature of antagomiRs and also address the viewpoint on the new generation of delivery systems that target antagomiRs in respiratory diseases.
Mei, S, Zhou, J, Sun, H, Cai, Y, Sun, L, Jin, D & Yan, C 2021, 'Networking State of Ytterbium Ions Probing the Origin of Luminescence Quenching and Activation in Nanocrystals', Advanced Science, vol. 8, no. 6, pp. 2003325-2003325.
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AbstractAt the organic–inorganic interface of nanocrystals, electron‐phonon coupling plays an important but intricate role in determining the diverse properties of nanomaterials. Here, it is reported that highly doping of Yb3+ ions within the nanocrystal host can form an energy‐migration network. The networking state Yb3+ shows both distinct Stark splitting peak ratios and lifetime dynamics, which allows quantitative investigations of quenching and thermal activation of luminescence, as the high‐dimensional spectroscopy signatures can be correlated to the attaching and de‐attaching status of surface molecules. By in‐situ surface characterizations, it is proved that the Yb‐O coordination associated with coordinated water molecules has significantly contributed to this reversible effect. Moreover, using this approach, the prime quencher OH can be switched to CH in the wet‐chemistry annealing process, resulting in the electron‐phonon coupling probability change. This study provides the molecular level insights and dynamics of the surface dark layer of luminescent nanocrystals.
Mello, MG, Westerhausen, MT, Singh, P, Doble, PA, Wanagat, J & Bishop, DP 2021, 'Assessing the reproducibility of labelled antibody binding in quantitative multiplexed immuno-mass spectrometry imaging', Analytical and Bioanalytical Chemistry, vol. 413, no. 21, pp. 5509-5516.
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Immuno-mass spectrometry imaging (iMSI) uses laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to determine the spatial expression of biomolecules in tissue sections following immunolabelling with antibodies conjugated to a metal reporter. As with all immunolabelling techniques, the binding efficiency of multiplexed staining can be affected by a number of factors including epitope blocking and other forms of steric hindrance. To date, the effects on the binding of metal-conjugated antibodies to their epitopes in a multiplexed analysis have yet to be quantitatively explored by iMSI. Here we describe a protocol to investigate the effects of multiplexing on reproducible binding using the muscle proteins, dystrophin, sarcospan, and myosin as a model, with antibodies conjugated with Maxpar® reagents before histological application to murine quadriceps sections using standard immunolabelling protocols and imaging with LA-ICP-MS. The antibodies were each individually applied to eight sections, and multiplexed to another eight sections. The average concentrations of the lanthanide analytes were determined, before statistical analyses found there was no significant difference between the individual and multiplexed application of the antibodies. These analyses provide a framework for ensuring reproducibility of antibody binding during multiplexed iMSI, which will allow quantitative exploration of protein-protein interactions and provide a greater understanding of fundamental biological processes during healthy and diseased states.
Melo, EM, Oliveira, VLS, Boff, D & Galvão, I 2021, 'Pulmonary macrophages and their different roles in health and disease', The International Journal of Biochemistry & Cell Biology, vol. 141, pp. 106095-106095.
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Mena, J, Ariyama, N, Navarro, C, Quezada, M, Brevis, C, Rojas, D, Medina, RA, Brito, B, Ruiz, Á & Neira, V 2021, 'Ubiquitous influenza A virus in Chilean swine before the H1N1pdm09 introduction', Transboundary and Emerging Diseases, vol. 68, no. 6, pp. 3174-3179.
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Mendelson, N, Chugh, D, Reimers, JR, Cheng, TS, Gottscholl, A, Long, H, Mellor, CJ, Zettl, A, Dyakonov, V, Beton, PH, Novikov, SV, Jagadish, C, Tan, HH, Ford, MJ, Toth, M, Bradac, C & Aharonovich, I 2021, 'Identifying carbon as the source of visible single-photon emission from hexagonal boron nitride', Nature Materials, vol. 20, no. 3, pp. 321-328.
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Single-photon emitters (SPEs) in hexagonal boron nitride (hBN) have garnered increasing attention over the last few years due to their superior optical properties. However, despite the vast range of experimental results and theoretical calculations, the defect structure responsible for the observed emission has remained elusive. Here, by controlling the incorporation of impurities into hBN via various bottom-up synthesis methods and directly through ion implantation, we provide direct evidence that the visible SPEs are carbon related. Room-temperature optically detected magnetic resonance is demonstrated on ensembles of these defects. We perform ion-implantation experiments and confirm that only carbon implantation creates SPEs in the visible spectral range. Computational analysis of the simplest 12 carbon-containing defect species suggest the negatively charged [Formula: see text] defect as a viable candidate and predict that out-of-plane deformations make the defect environmentally sensitive. Our results resolve a long-standing debate about the origin of single emitters at the visible range in hBN and will be key to the deterministic engineering of these defects for quantum photonic devices.
Mendelson, N, Morales‐Inostroza, L, Li, C, Ritika, R, Nguyen, MAP, Loyola‐Echeverria, J, Kim, S, Götzinger, S, Toth, M & Aharonovich, I 2021, 'Grain Dependent Growth of Bright Quantum Emitters in Hexagonal Boron Nitride', Advanced Optical Materials, vol. 9, no. 1, pp. 2001271-2001271.
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AbstractPoint defects in hexagonal boron nitride have emerged as a promising quantum light source due to their bright and photostable room temperature emission. In this work, the incorporation of quantum emitters during chemical vapor deposition growth on a nickel substrate is studied. Combining a range of characterization techniques, it is demonstrated that the incorporation of quantum emitters is limited to (001) oriented nickel grains. Such emitters display improved emission properties in terms of brightness and stability. These emitters are further utilized and integrated with a compact optical antenna enhancing light collection from the sources. The hybrid device yields average saturation count rates of ≈2.9 × 106 cps and an average photon purity of g(2)(0) ≈ 0.1. The results advance the understanding of single photon emitter incorporation during chemical vapor deposition growth and demonstrate a key step towards compact devices for achieving maximum collection efficiency.
Meng, Y, Liu, Y, He, J, Sun, X, Palmieri, A, Gu, Y, Zheng, X, Dang, Y, Huang, X, Mustain, W & Suib, SL 2021, 'Large Scale Synthesis of Manganese Oxide/Reduced Graphene Oxide Composites as Anode Materials for Long Cycle Lithium Ion Batteries', ACS Applied Energy Materials, vol. 4, no. 6, pp. 5424-5433.
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Menounos, S, Hansbro, PM, Diwan, AD & Das, A 2021, 'Pathophysiological Correlation between Cigarette Smoking and Amyotrophic Lateral Sclerosis', NeuroSci, vol. 2, no. 2, pp. 120-134.
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Cigarette smoke (CS) has been consistently demonstrated to be an environmental risk factor for amyotrophic lateral sclerosis (ALS), although the molecular pathogenic mechanisms involved are yet to be elucidated. Here, we propose different mechanisms by which CS exposure can cause sporadic ALS pathogenesis. Oxidative stress and neuroinflammation are widely implicated in ALS pathogenesis, with blood–spinal cord barrier disruption also recognised to be involved in the disease process. In addition, immunometabolic, epigenetic and microbiome alterations have been implicated in ALS recently. Identification of the underlying pathophysiological mechanisms that underpin CS-associated ALS will drive future research to be conducted into new targets for treatment.
Messer, LF, Brown, MV, Van Ruth, PD, Doubell, M & Seymour, JR 2021, 'Temperate southern Australian coastal waters are characterised by surprisingly high rates of nitrogen fixation and diversity of diazotrophs', PeerJ, vol. 9, pp. e10809-e10809.
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Biological dinitrogen (N2) fixation is one mechanism by which specific microorganisms (diazotrophs) can ameliorate nitrogen (N) limitation. Historically, rates of N2 fixation were believed to be limited outside of the low nutrient tropical and subtropical open ocean; however, emerging evidence suggests that N2 fixation is also a significant process within temperate coastal waters. Using a combination of amplicon sequencing, targeting the nitrogenase reductase gene (nifH), quantitative nifH PCR, and 15N2 stable isotope tracer experiments, we investigated spatial patterns of diazotroph assemblage structure and N2 fixation rates within the temperate coastal waters of southern Australia during Austral autumn and summer. Relative to previous studies in open ocean environments, including tropical northern Australia, and tropical and temperate estuaries, our results indicate that high rates of N2 fixation (10–64 nmol L−1 d−1) can occur within the large inverse estuary Spencer Gulf, while comparatively low rates of N2 fixation (2 nmol L−1 d−1) were observed in the adjacent continental shelf waters. Across the dataset, low concentrations of NO3/NO2 were significantly correlated with the highest N2 fixation rates, suggesting that N2 fixation could be an important source of new N in the region as dissolved inorganic N concentrations are typically limiting. Overall, the underlying diazotrophic community was dominated by nifH sequences from Cluster 1 unicellular cyanobacteria of the UCYN-A clade, as well as non-cyanobacterial diazotrophs related to ...
Metia, S, Nguyen, HAD & Ha, QP 2021, 'IoT-Enabled Wireless Sensor Networks for Air Pollution Monitoring with Extended Fractional-Order Kalman Filtering', Sensors, vol. 21, no. 16, pp. 5313-5313.
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This paper presents the development of high-performance wireless sensor networks for local monitoring of air pollution. The proposed system, enabled by the Internet of Things (IoT), is based on low-cost sensors collocated in a redundant configuration for collecting and transferring air quality data. Reliability and accuracy of the monitoring system are enhanced by using extended fractional-order Kalman filtering (EFKF) for data assimilation and recovery of the missing information. Its effectiveness is verified through monitoring particulate matters at a suburban site during the wildfire season 2019–2020 and the Coronavirus disease 2019 (COVID-19) lockdown period. The proposed approach is of interest to achieve microclimate responsiveness in a local area.
Meyer, F, Lesker, T-R, Koslicki, D, Fritz, A, Gurevich, A, Darling, AE, Sczyrba, A, Bremges, A & McHardy, AC 2021, 'Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit', Nature Protocols, vol. 16, no. 4, pp. 1785-1801.
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Computational methods are key in microbiome research, and obtaining a quantitative and unbiased performance estimate is important for method developers and applied researchers. For meaningful comparisons between methods, to identify best practices and common use cases, and to reduce overhead in benchmarking, it is necessary to have standardized datasets, procedures and metrics for evaluation. In this tutorial, we describe emerging standards in computational meta-omics benchmarking derived and agreed upon by a larger community of researchers. Specifically, we outline recent efforts by the Critical Assessment of Metagenome Interpretation (CAMI) initiative, which supplies method developers and applied researchers with exhaustive quantitative data about software performance in realistic scenarios and organizes community-driven benchmarking challenges. We explain the most relevant evaluation metrics for assessing metagenome assembly, binning and profiling results, and provide step-by-step instructions on how to generate them. The instructions use simulated mouse gut metagenome data released in preparation for the second round of CAMI challenges and showcase the use of a repository of tool results for CAMI datasets. This tutorial will serve as a reference for the community and facilitate informative and reproducible benchmarking in microbiome research.
Migliavacca, M, Musavi, T, Mahecha, MD, Nelson, JA, Knauer, J, Baldocchi, DD, Perez-Priego, O, Christiansen, R, Peters, J, Anderson, K, Bahn, M, Black, TA, Blanken, PD, Bonal, D, Buchmann, N, Caldararu, S, Carrara, A, Carvalhais, N, Cescatti, A, Chen, J, Cleverly, J, Cremonese, E, Desai, AR, El-Madany, TS, Farella, MM, Fernández-Martínez, M, Filippa, G, Forkel, M, Galvagno, M, Gomarasca, U, Gough, CM, Göckede, M, Ibrom, A, Ikawa, H, Janssens, IA, Jung, M, Kattge, J, Keenan, TF, Knohl, A, Kobayashi, H, Kraemer, G, Law, BE, Liddell, MJ, Ma, X, Mammarella, I, Martini, D, Macfarlane, C, Matteucci, G, Montagnani, L, Pabon-Moreno, DE, Panigada, C, Papale, D, Pendall, E, Penuelas, J, Phillips, RP, Reich, PB, Rossini, M, Rotenberg, E, Scott, RL, Stahl, C, Weber, U, Wohlfahrt, G, Wolf, S, Wright, IJ, Yakir, D, Zaehle, S & Reichstein, M 2021, 'The three major axes of terrestrial ecosystem function', Nature, vol. 598, no. 7881, pp. 468-472.
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AbstractThe leaf economics spectrum1,2 and the global spectrum of plant forms and functions3 revealed fundamental axes of variation in plant traits, which represent different ecological strategies that are shaped by the evolutionary development of plant species2. Ecosystem functions depend on environmental conditions and the traits of species that comprise the ecological communities4. However, the axes of variation of ecosystem functions are largely unknown, which limits our understanding of how ecosystems respond as a whole to anthropogenic drivers, climate and environmental variability4,5. Here we derive a set of ecosystem functions6 from a dataset of surface gas exchange measurements across major terrestrial biomes. We find that most of the variability within ecosystem functions (71.8%) is captured by three key axes. The first axis reflects maximum ecosystem productivity and is mostly explained by vegetation structure. The second axis reflects ecosystem water-use strategies and is jointly explained by variation in vegetation height and climate. The third axis, which represents ecosystem carbon-use efficiency, features a gradient related to aridity, and is explained primarily by variation in vegetation structure. We show that two state-of-the-art land surface models reproduce the first and most important axis of ecosystem functions. However, the models tend to simulate more strongly correlated functions than those observed, which limits their ability to accurately predict the full range of responses to environmental changes in carbon, water and energy cycling in terrestrial ecosystems7,8.
Mitchell, AB, Li, C-X, Oliver, BGG, Holmes, EC & Glanville, AR 2021, 'High-resolution Metatranscriptomic Characterization of the Pulmonary RNA Virome After Lung Transplantation', Transplantation, vol. 105, no. 12, pp. 2546-2553.
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Background. Lung transplantation provides a unique opportunity to investigate the constituents and temporal dynamics of the human pulmonary microbiome after lung transplantation. For methodological reasons, prior studies using metagenomics have detected DNA viruses but not demonstrated the presence of RNA viruses, including those that are common community acquired. In this proof-of-concept study, we aimed to further characterize the pulmonary microbiome after lung transplantation by using metagenomic next-generation sequencing (mNGS), with a particular focus on the RNA virome. Methods. We performed a single-center longitudinal study of lower respiratory tract RNA viruses and bacteria using bronchoalveolar lavage at postoperative day 1 and week 6 analyzed with total RNA sequencing (metatranscriptomics). Five primary and 5 repeat transplant recipients were recruited. Results. mNGS identified 5 RNA viruses (nil in the normal saline control), including 4 species of human rhinovirus not previously reported in Australia: A7 (HRV-A7), C22 (HRV-C22), B52 (HRV-B52), and B72 (HRV-B72). Overall, 12/20 specimens were virus positive in 7/10 cases. Human parainfluenza virus 3 was the most frequent virus in 7/20 specimens in 5/10 cases. In this small study, we did not detect a significant difference in abundance and diversity of RNA viruses and bacteria at postoperative day 1 and 6 wk, nor differences between retransplant recipients and primary lung transplant recipients. Conclusions. Our study demonstrates how mNGS can also identify RNA viruses within the human pulmonary virome, ...
Miyaji, N, Akter, MA, Suzukamo, C, Mehraj, H, Shindo, T, Itabashi, T, Okazaki, K, Shimizu, M, Kaji, M, Katsumata, M, Dennis, ES & Fujimoto, R 2021, 'Development of a New DNA Marker for Fusarium Yellows Resistance in Brassica rapa Vegetables', Plants, vol. 10, no. 6, pp. 1082-1082.
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In vegetables of Brassica rapa L., Fusarium oxysporum f. sp. rapae (For) or F. oxysporum f. sp. conglutinans (Foc) cause Fusarium yellows. A resistance gene against Foc (FocBr1) has been identified, and deletion of this gene results in susceptibility (focbr1-1). In contrast, a resistance gene against For has not been identified. Inoculation tests showed that lines resistant to Foc were also resistant to For, and lines susceptible to Foc were susceptible to For. However, prediction of disease resistance by a dominant DNA marker on FocBr1 (Bra012688m) was not associated with disease resistance of For in some komatsuna lines using an inoculation test. QTL-seq using four F2 populations derived from For susceptible and resistant lines showed one causative locus on chromosome A03, which covers FocBr1. Comparison of the amino acid sequence of FocBr1 between susceptible and resistant alleles (FocBr1 and FocBo1) showed that six amino acid differences were specific to susceptible lines. The presence and absence of FocBr1 is consistent with For resistance in F2 populations. These results indicate that FocBr1 is essential for For resistance, and changed amino acid sequences result in susceptibility to For. This susceptible allele is termed focbr1-2, and a new DNA marker (focbr1-2m) for detection of the focbr1-2 allele was developed.
Miyaji, N, Shimizu, M, Takasaki-Yasuda, T, Dennis, ES & Fujimoto, R 2021, 'The transcriptional response to salicylic acid plays a role in Fusarium yellows resistance in Brassica rapa L.', Plant Cell Reports, vol. 40, no. 4, pp. 605-619.
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KEY MESSAGE: Fusarium yellows resistant and susceptible lines in Brassica rapa showed different salicylic acid responses; the resistant line showed a similar response to previous reports, but the susceptible line differed. Fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans (Foc) is an important disease. Previous studies showed that genes related to salicylic acid (SA) response were more highly induced following Foc infection in Brassica rapa Fusarium yellows resistant lines than susceptible lines. However, SA-induced genes have not been identified at the whole genome level and it was unclear whether they were up-regulated by Foc inoculation. Transcriptome analysis with and without SA treatment in the B. rapa Fusarium yellows susceptible line 'Misugi' and the resistant line 'Nanane' was performed to obtain insights into the relationship between SA sensitivity/response and Fusarium yellows resistance. 'Nanane's up-regulated genes were related to SA response and down-regulated genes were related to jasmonic acid (JA) or ethylene (ET) response, but differentially expressed genes in 'Misugi' were not. This result suggests that Fusarium yellows resistant and susceptible lines have a different SA response and that an antagonistic transcription between SA and JA/ET responses was found only in a Fusarium yellows resistant line. SA-responsive genes were induced by Foc inoculation in Fusarium yellows resistant (RJKB-T23) and susceptible lines (RJKB-T24). By contrast, 39 SA-induced genes specific to RJKB-T23 might function in the defense response to Foc. In this study, SA-induced genes were identified at the whole genome level, and the possibility, the defense response to Foc observed in a resistant line could be mediated by SA-induced genes, is suggested. These results will be useful for future research concerning the SA importance in Foc or other diseases resistance in B. rapa.
Moecking, J, Laohamonthonkul, P, Chalker, K, White, MJ, Harapas, CR, Yu, C-H, Davidson, S, Hrovat-Schaale, K, Hu, D, Eng, C, Huntsman, S, Calleja, DJ, Horvat, JC, Hansbro, PM, O’Donoghue, RJJ, Ting, JP, Burchard, EG, Geyer, M, Gerlic, M & Masters, SL 2021, 'NLRP1 variant M1184V decreases inflammasome activation in the context of DPP9 inhibition and asthma severity', Journal of Allergy and Clinical Immunology, vol. 147, no. 6, pp. 2134-2145.e20.
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Background
NLRP1 is an innate immune sensor that can form cytoplasmic inflammasome complexes. Polymorphisms in NLRP1 are linked to asthma; however, there is currently no functional or mechanistic explanation for this.Objective
We sought to clarify the role of NLRP1 in asthma pathogenesis.Methods
Results from the GALA II cohort study were used to identify a link between NLRP1 and asthma in Mexican Americans. In vitro and in vivo models for NLRP1 activation were applied to investigate the role of this inflammasome in asthma at the molecular level.Results
We document the association of an NLRP1 haplotype with asthma for which the single nucleotide polymorphism rs11651270 (M1184V) individually is the most significant. Surprisingly, M1184V increases NLRP1 activation in the context of N-terminal destabilization, but decreases NLRP1 activation on dipeptidyl peptidase 9 inhibition. In vitro studies demonstrate that M1184V increases binding to dipeptidyl peptidase 9, which can account for its inhibitory role in this context. In addition, in vivo data from a mouse model of airway inflammation reveal a protective role for NLRP1 inflammasome activation reducing eosinophilia in this setting.Conclusions
Linking our in vitro and in vivo results, we found that the NLRP1 variant M1184V reduces inflammasome activation in the context of dipeptidyl peptidase 9 inhibition and could thereby increase asthma severity. Our studies may have implications for the treatment of asthma in patients carrying this variant of NLRP1.
Moggridge, BJ 2021, 'Indigenous water knowledge and values in an Australasian context', Australasian Journal of Water Resources, vol. 25, no. 1, pp. 1-3.
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Moggridge, BJ & Thompson, RM 2021, 'Cultural value of water and western water management: an Australian Indigenous perspective', Australasian Journal of Water Resources, vol. 25, no. 1, pp. 4-14.
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Mohamed, AMT, Chan, H, Luhur, J, Bauda, E, Gallet, B, Morlot, C, Cole, L, Awad, M, Crawford, S, Lyras, D, Rudner, DZ & Rodrigues, CDA 2021, 'Chromosome Segregation and Peptidoglycan Remodeling Are Coordinated at a Highly Stabilized Septal Pore to Maintain Bacterial Spore Development', Developmental Cell, vol. 56, no. 1, pp. 36-51.e5.
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Asymmetric division, a hallmark of endospore development, generates two cells, a larger mother cell and a smaller forespore. Approximately 75% of the forespore chromosome must be translocated across the division septum into the forespore by the DNA translocase SpoIIIE. Asymmetric division also triggers cell-specific transcription, which initiates septal peptidoglycan remodeling involving synthetic and hydrolytic enzymes. How these processes are coordinated has remained a mystery. Using Bacillus subtilis, we identified factors that revealed the link between chromosome translocation and peptidoglycan remodeling. In cells lacking these factors, the asymmetric septum retracts, resulting in forespore cytoplasmic leakage and loss of DNA translocation. Importantly, these phenotypes depend on septal peptidoglycan hydrolysis. Our data support a model in which SpoIIIE is anchored at the edge of a septal pore, stabilized by newly synthesized peptidoglycan and protein-protein interactions across the septum. Together, these factors ensure coordination between chromosome translocation and septal peptidoglycan remodeling to maintain spore development.
Mohanty, M, Zhang, M, Asghar, MR & Russello, G 2021, 'e-PRNU: Encrypted Domain PRNU-Based Camera Attribution for Preserving Privacy', IEEE Transactions on Dependable and Secure Computing, vol. 18, no. 1, pp. 426-437.
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IEEE Photo Response Non-Uniformity (PRNU) noise-based source camera attribution is a popular digital forensic method. In this method, a camera fingerprint computed from a set of known images of the camera is matched against the extracted noise of an anonymous questionable image to find out if the camera had taken the anonymous image. The possibility of privacy leak, however, is one of the main concerns of the PRNU-based method. Using the camera fingerprint (or the extracted noise), an adversary can identify the owner of the camera by matching the fingerprint with the noise of an image (or with the fingerprint computed from a set of images) crawled from a social media account. In this article, we address this privacy concern by encrypting both the fingerprint and the noise using the Boneh-Goh-Nissim (BGN) encryption scheme, and performing the matching in encrypted domain. To overcome leakage of privacy from the content of an image that is used in the fingerprint calculation, we compute the fingerprint within a trusted environment, such as ARM TrustZone. We present e-PRNU that aims at minimizing privacy loss and allows authorized forensic experts to perform camera attribution. The security analysis shows that the proposed approach is semantically secure.
Mohd Yusop, AY, Xiao, L & Fu, S 2021, 'Fluorescence polarisation for high‐throughput screening of adulterated food products via phosphodiesterase 5 inhibition assay', Drug Testing and Analysis, vol. 13, no. 5, pp. 953-964.
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AbstractThe surge in the consumption of food products containing herbal aphrodisiacs has driven their widespread adulteration. A rapid screening strategy is, therefore, warranted to curb this problem. This study established an enzyme inhibition assay to screen phosphodiesterase 5 (PDE5) inhibitors as adulterants in selected food products. Fluorescein‐labelled cyclic‐3′,5′‐guanosine monophosphate was utilised as substrates for the PDE5A1 enzyme, aided by the presence of nanoparticle phosphate‐binding beads on their fluorescence polarisation. The sample preparation was optimised to improve the enzyme inhibition efficiency and applied to calculate the threshold values of six blank food matrices. The assay was validated using sildenafil, producing an IC50 of 4.2 nM. The applicability of the assay procedure was demonstrated by screening 55 distinct food samples. The results were subsequently verified using confirmatory liquid chromatography–high‐resolution mass spectrometry (LC‐HRMS) analysis. Altogether, 49 samples inhibited the PDE5 enzyme above the threshold values (75.7%–105.5%) and were registered as potentially adulterated samples. The remaining six samples were marked as nonadulterated with percentage inhibition below the threshold values (−3.3%–18.2%). The LC‐HRMS analysis agreed with the assay results for all food products except for the instant coffee premix (ICP) samples. False‐positive results were obtained for the ICP samples at 32% (8/25), due to possible PDE5 inhibition by caffeine. Contrarily, all other food samples were found to produce 0% (0/30) false‐positive or false‐negative results. The broad‐based assay, established via a simple mix‐incubate‐read format, exhibited promising potential for high‐throughput screening of PDE5 inhibitors in various food products, except those with naturally occurring phosphodiesterase inhibitors such as caffeine.
Mohd Yusop, AY, Xiao, L & Fu, S 2021, 'Liquid chromatography-high-resolution mass spectrometry analysis of erectile dysfunction drugs and their analogues in food products', Forensic Science International, vol. 322, pp. 110748-110748.
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The presence of erectile dysfunction (ED) drugs in adulterated dietary supplements, mainly in pharmaceutical dosage forms, is frequently addressed in the literature. Little attention is given to food products despite their increasing adulteration trend. To address this knowledge gap targeted, suspected-target, and non-targeted strategies were utilised to analyse ED drugs and their analogues in powdered drink mix (PDM), honey, jelly, hard candy, and sugar-coated chewing gum using liquid chromatography-high-resolution mass spectrometry (LC-HRMS). The method was optimised and validated using 23 target analytes, representing different ED drugs with structural similarities. The modified quick, easy, cheap, effective, rugged, and safe (QuEChERS) extraction exhibited insignificant matrix effect (ME) within -9.2%–8.8% and provided complete coverage of target analytes with acceptable extraction recovery (RE) within 75.5%–123.9%, except for carbodenafil in the PDM matrix. Based on the ME and RE performance, the analytical method was validated to analyse 25 food samples that claimed to enhance male sexual performance. The method exhibited good specificity and linearity with a limit of detection within 10–70 ng/mL and limit of quantification of 80 ng/mL. Similarly, the accuracy and precision were satisfactory within 77.4%–122.0% and <16.7%RSD, respectively. The LC-HRMS targeted analysis, together with suspected-target and non-targeted screenings, identified and detected ten ED drugs from 24 food samples. The modified QuEChERS extraction with LC-HRMS-based method was demonstrated to be universally applicable to various food products, covering an extensive range of known and potentially novel ED drugs, which is valuable for routine casework.
Mohd Yusop, AY, Xiao, L & Fu, S 2021, 'Suspected‐target and non‐targeted screenings of phosphodiesterase 5 inhibitors in herbal remedies using liquid chromatography–quadrupole time‐of‐flight–mass spectrometry', Drug Testing and Analysis, vol. 13, no. 5, pp. 965-976.
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AbstractThe lucrative market of herbal remedies spurs rampant adulteration, particularly with pharmaceutical drugs and their unapproved analogues. A comprehensive screening strategy is, therefore, warranted to detect these adulterants and, accordingly, to safeguard public health. This study uses the data‐dependent acquisition of liquid chromatography‐quadrupole time‐of‐flight–mass spectrometry (LC–QTOF–MS) to screen phosphodiesterase 5 (PDE5) inhibitors in herbal remedies using suspected‐target and non‐targeted strategies. For the suspected‐target screening, we used a library comprising 95 PDE5 inhibitors. For the non‐targeted screening, we adopted top‐down and bottom‐up approaches to flag novel PDE5 inhibitor analogues based on common fragmentation patterns. LC–QTOF–MS was optimised and validated for capsule and tablet dosage forms using 23 target analytes, selected to represent different groups of PDE5 inhibitors. The method exhibited excellent specificity and linearity with limit of detection and limit of quantification of <40 and 80 ng/mL, respectively. The accuracy ranged from 79.0% to 124.7% with a precision of <14.9% relative standard deviation. The modified, quick, easy, cheap, effective, rugged, and safe extraction provided insignificant matrix effect within −9.1%–8.0% and satisfactory extraction recovery of 71.5%–105.8%. These strategies were used to screen 52 herbal remedy samples that claimed to enhance male sexual performance. The suspected‐target screening resulted in 33 positive samples, revealing 10 target analytes and 2 suspected analytes. Systematic MS and tandem MS interrogations using the non‐targeted screening returned insignificant signals, indicating the absence of potentially novel analogues. The target analytes were quantified from 0.03 to 121.31 mg per dose of each sample. The proposed strategies ensure that all PDE5 inhibitors are comprehensively screened, providing a useful tool to curb ...
Monaco, CJ, Booth, DJ, Figueira, WF, Gillanders, BM, Schoeman, DS, Bradshaw, CJA & Nagelkerken, I 2021, 'Natural and anthropogenic climate variability shape assemblages of range‐extending coral‐reef fishes', Journal of Biogeography, vol. 48, no. 5, pp. 1063-1075.
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AbstractAimClimate change is redistributing species globally, resulting in altered community structures and ecosystem functioning. The current paradigm is that species should track temperature isoclines along latitudinal and depth gradients to remain within their thermal niches. However, the many exceptions to this rule point to complex ecological and environmental processes often overlooked in statistical models predicting species redistributions. We tested the contributions of natural versus anthropogenic climate change to the long‐term spatio‐temporal dynamics of assemblages of range‐shifting tropical fishes at the leading edge of redistribution fronts.LocationEast coast of Australia.TaxonTropical coral‐reef fishes.MethodsWe analysed 16 years (2003–2018) of tropical species occurrences at two temperate locations using traditional diversity metrics (richness, accumulation curves and β‐diversity). We also quantified the role of primary environmental covariates and estimated species associations using joint species distribution models.ResultsWe reveal that tropical species richness has increased in this temperate ecosystem over time. Furthermore, we show that the richness of tropical vagrant species increased with the sea‐surface temperature experienced by both local vagrants and their putative source populations at the southern Great Barrier Reef, which accounted for 23.1% and 22.1% of the explained variance, respectively. We also detected a signal from El Niño‐Southern Oscillation, as species turnover and richness peaked during the strong La Niña event of 2010–2011.Main...
Monaco, CJ, Nagelkerken, I, Booth, DJ, Figueira, WF, Gillanders, BM, Schoeman, DS & Bradshaw, CJA 2021, 'Opposing life stage‐specific effects of ocean warming at source and sink populations of range‐shifting coral‐reef fishes', Journal of Animal Ecology, vol. 90, no. 3, pp. 615-627.
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AbstractClimate change is altering the latitudinal distributions of species, with their capacity to keep pace with a shifting climate depending on the stochastic expression of population growth rates, and the influence of compensatory density feedback on age‐specific survival rates. We use population‐abundance time series at the leading edge of an expanding species’ range to quantify the contribution of stochastic environmental drivers and density feedbacks to the dynamics of life stage‐specific population growth.Using a tropical, range‐shifting Indo‐Pacific damselfish (Abudefduf vaigiensis) as a model organism, we applied variants of the phenomenological Gompertz‐logistic model to a 14‐year dataset to quantify the relative importance of density feedback and stochastic environmental drivers on the separate and aggregated population growth rates of settler and juvenile life stages.The top‐ranked models indicated that density feedback negatively affected the growth of tropical settlers and juveniles. Rates of settlement were negatively linked to temperatures experienced by parents at potential source populations in the tropics, but their subsequent survival and that of juveniles increased with the temperatures experienced at the temperate sink. Including these stochastic effects doubled the deviance explained by the models, corroborating an important role of temperature. By incorporating sea‐surface temperature projections for the remainder of this century into these models, we anticipate improved conditions for the population growth of juvenile coral‐reef fishes, but not for settlers in temperate ecosystems.Previous research has highlighted the association between temperature and the redistribution of spe...
Morris, S, Wright, K, Malyla, V, Britton, WJ, Hansbro, PM, Manuneedhi Cholan, P & Oehlers, SH 2021, 'Exposure to the gut microbiota from cigarette smoke-exposed mice exacerbates cigarette smoke extract-induced inflammation in zebrafish larvae', Current Research in Immunology, vol. 2, pp. 229-236.
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Morshedi Rad, D, Alsadat Rad, M, Razavi Bazaz, S, Kashaninejad, N, Jin, D & Ebrahimi Warkiani, M 2021, 'A Comprehensive Review on Intracellular Delivery', Advanced Materials, vol. 33, no. 13, pp. e2005363-2005363.
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AbstractIntracellular delivery is considered an indispensable process for various studies, ranging from medical applications (cell‐based therapy) to fundamental (genome‐editing) and industrial (biomanufacture) approaches. Conventional macroscale delivery systems critically suffer from such issues as low cell viability, cytotoxicity, and inconsistent material delivery, which have opened up an interest in the development of more efficient intracellular delivery systems. In line with the advances in microfluidics and nanotechnology, intracellular delivery based on micro‐ and nanoengineered platforms has progressed rapidly and held great promises owing to their unique features. These approaches have been advanced to introduce a smorgasbord of diverse cargoes into various cell types with the maximum efficiency and the highest precision. This review differentiates macro‐, micro‐, and nanoengineered approaches for intracellular delivery. The macroengineered delivery platforms are first summarized and then each method is categorized based on whether it employs a carrier‐ or membrane‐disruption‐mediated mechanism to load cargoes inside the cells. Second, particular emphasis is placed on the micro‐ and nanoengineered advances in the delivery of biomolecules inside the cells. Furthermore, the applications and challenges of the established and emerging delivery approaches are summarized. The topic is concluded by evaluating the future perspective of intracellular delivery toward the micro‐ and nanoengineered approaches.
Mote, S, Gupta, V, De, K, Nanajkar, M, Damare, SR & Ingole, B 2021, 'Bacterial diversity associated with a newly described bioeroding sponge, Cliona thomasi, from the coral reefs on the West Coast of India', Folia Microbiologica, vol. 66, no. 2, pp. 203-211.
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Munoz, MA, Fletcher, EK, Skinner, OP, Jurczyluk, J, Kristianto, E, Hodson, MP, Sun, S, Ebetino, FH, Croucher, DR, Hansbro, PM, Center, JR & Rogers, MJ 2021, 'Bisphosphonate drugs have actions in the lung and inhibit the mevalonate pathway in alveolar macrophages', eLife, vol. 10, pp. 1-15.
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Bisphosphonates drugs target the skeleton and are used globally for the treatment of common bone disorders. Nitrogen-containing bisphosphonates act by inhibiting the mevalonate pathway in bone-resorbing osteoclasts but, surprisingly, also appear to reduce the risk of death from pneumonia. We overturn the long-held belief that these drugs act only in the skeleton and show that a fluorescently labelled bisphosphonate is internalised by alveolar macrophages and large peritoneal macrophages in vivo. Furthermore, a single dose of a nitrogen-containing bisphosphonate (zoledronic acid) in mice was sufficient to inhibit the mevalonate pathway in tissue-resident macrophages, causing the build-up of a mevalonate metabolite and preventing protein prenylation. Importantly, one dose of bisphosphonate enhanced the immune response to bacterial endotoxin in the lung and increased the level of cytokines and chemokines in bronchoalveolar fluid. These studies suggest that bisphosphonates, as well as preventing bone loss, may boost immune responses to infection in the lung and provide a mechanistic basis to fully examine the potential of bisphosphonates to help combat respiratory infections that cause pneumonia.
Muus, C, Luecken, MD, Eraslan, G, Sikkema, L, Waghray, A, Heimberg, G, Kobayashi, Y, Vaishnav, ED, Subramanian, A, Smillie, C, Jagadeesh, KA, Duong, ET, Fiskin, E, Torlai Triglia, E, Ansari, M, Cai, P, Lin, B, Buchanan, J, Chen, S, Shu, J, Haber, AL, Chung, H, Montoro, DT, Adams, T, Aliee, H, Allon, SJ, Andrusivova, Z, Angelidis, I, Ashenberg, O, Bassler, K, Bécavin, C, Benhar, I, Bergenstråhle, J, Bergenstråhle, L, Bolt, L, Braun, E, Bui, LT, Callori, S, Chaffin, M, Chichelnitskiy, E, Chiou, J, Conlon, TM, Cuoco, MS, Cuomo, ASE, Deprez, M, Duclos, G, Fine, D, Fischer, DS, Ghazanfar, S, Gillich, A, Giotti, B, Gould, J, Guo, M, Gutierrez, AJ, Habermann, AC, Harvey, T, He, P, Hou, X, Hu, L, Hu, Y, Jaiswal, A, Ji, L, Jiang, P, Kapellos, TS, Kuo, CS, Larsson, L, Leney-Greene, MA, Lim, K, Litviňuková, M, Ludwig, LS, Lukassen, S, Luo, W, Maatz, H, Madissoon, E, Mamanova, L, Manakongtreecheep, K, Leroy, S, Mayr, CH, Mbano, IM, McAdams, AM, Nabhan, AN, Nyquist, SK, Penland, L, Poirion, OB, Poli, S, Qi, C, Queen, R, Reichart, D, Rosas, I, Schupp, JC, Shea, CV, Shi, X, Sinha, R, Sit, RV, Slowikowski, K, Slyper, M, Smith, NP, Sountoulidis, A, Strunz, M, Sullivan, TB, Sun, D, Talavera-López, C, Tan, P, Tantivit, J, Travaglini, KJ, Tucker, NR, Vernon, KA, Wadsworth, MH, Waldman, J, Wang, X, Xu, K, Yan, W, Zhao, W, Ziegler, CGK, Deutsch, GH, Dutra, J, Gaulton, KJ, Holden-Wiltse, J, Huyck, HL, Mariani, TJ, Misra, RS, Poole, C, Preissl, S, Pryhuber, GS, Rogers, L, Sun, X, Wang, A, Whitsett, JA, Xu, Y, Alladina, J, Banovich, NE, Barbry, P, Beane, JE, Bhattacharyya, RP, Black, KE, Brazma, A, Campbell, JD, Cho, JL, Collin, J, Conrad, C, de Jong, K, Desai, T, Ding, DZ, Eickelberg, O, Eils, R, Ellinor, PT, Faiz, A, Falk, CS, Farzan, M, Gellman, A, Getz, G, Glass, IA, Greka, A, Haniffa, M, Hariri, LP, Hennon, MW, Horvath, P, Hübner, N, Hung, DT, Huyck, HL, Janssen, WJ, Juric, D, Kaminski, N, Koenigshoff, M, Koppelman, GH, Krasnow, MA, Kropski, JA, Kuhnemund, M, Lafyatis, R, Lako, M, Lander, ES, Lee, H, Lenburg, ME, Marquette, C-H, Metzger, RJ, Linnarsson, S, Liu, G, Lo, YMD, Lundeberg, J, Marioni, JC, Mazzilli, SA, Medoff, BD, Meyer, KB, Miao, Z, Misharin, AV, Nawijn, MC, Nikolić, MZ, Noseda, M, Ordovas-Montanes, J, Oudit, GY, Pe’er, D, Powell, JE, Quake, SR, Rajagopal, J, Tata, PR, Rawlins, EL, Regev, A, Reid, ME, Reyfman, PA, Rieger-Christ, KM, Rojas, M & et al. 2021, 'Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics', Nature Medicine, vol. 27, no. 3, pp. 546-559.
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Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.
Nair, HAS, Subramoni, S, Poh, WH, Hasnuddin, NTB, Tay, M, Givskov, M, Tolker-Nielsen, T, Kjelleberg, S, McDougald, D & Rice, SA 2021, 'Carbon starvation of Pseudomonas aeruginosa biofilms selects for dispersal insensitive mutants', BMC Microbiology, vol. 21, no. 1, p. 255.
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Abstract Background Biofilms disperse in response to specific environmental cues, such as reduced oxygen concentration, changes in nutrient concentration and exposure to nitric oxide. Interestingly, biofilms do not completely disperse under these conditions, which is generally attributed to physiological heterogeneity of the biofilm. However, our results suggest that genetic heterogeneity also plays an important role in the non-dispersing population of P. aeruginosa in biofilms after nutrient starvation. Results In this study, 12.2% of the biofilm failed to disperse after 4 d of continuous starvation-induced dispersal. Cells were recovered from the dispersal phase as well as the remaining biofilm. For 96 h starved biofilms, rugose small colony variants (RSCV) were found to be present in the biofilm, but were not observed in the dispersal effluent. In contrast, wild type and small colony variants (SCV) were found in high numbers in the dispersal phase. Genome sequencing of these variants showed that most had single nucleotide mutations in genes associated with biofilm formation, e.g. in wspF, pilT, fha1 and aguR. Complementation of those mutations restored starvation-induced dispersal from the biofilms. Because c-di-GMP is linked to biofilm formation and dispersal, we introduced a c-di-GMP reporter into the wild-type P. aeruginosa and monitored green fluorescent protein (GFP) expression before and after starvation-induced dispersal. Post dispersal, the microcolonies were smaller and significantly brighter in GFP intensity, suggesting the relative concentration of c-di-GMP per cell within the microcolonies was also i...
Nair, PC, Gillani, TB, Rawling, T & Murray, M 2021, 'Differential inhibition of human CYP2C8 and molecular docking interactions elicited by sorafenib and its major N-oxide metabolite', Chemico-Biological Interactions, vol. 338, pp. 109401-109401.
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The tyrosine kinase inhibitor sorafenib (SOR) is being used increasingly in combination with other anticancer agents like paclitaxel, but this increases the potential for drug toxicity. SOR inhibits several human CYPs, including CYP2C8, which is a major enzyme in the elimination of oncology drugs like paclitaxel and imatinib. It has been reported that CYP2C8 inhibition by SOR in human liver microsomes is potentiated by NADPH-dependent biotransformation. This implicates a SOR metabolite in enhanced inhibition, although the identity of that metabolite is presently unclear. The present study evaluated the capacity of the major N-oxide metabolite of SOR (SNO) to inhibit CYP2C8-dependent paclitaxel 6α-hydroxylation. The IC50 of SNO against CYP2C8 activity was found to be 3.7-fold lower than that for the parent drug (14 μM versus 51 μM). In molecular docking studies, both SOR and SNO interacted with active site residues in CYP2C8, but four additional major hydrogen and halogen bonding interactions were identified between SNO and amino acids in the B-B' loop region and helixes F' and I that comprise the catalytic region of the enzyme. In contrast, the binding of both SOR and SNO to active site residues in the closely related human CYP2C9 enzyme was similar, as were the IC50s determined against CYP2C9-mediated losartan oxidation. These findings suggest that the active metabolite SNO could impair the elimination of coadministered drugs that are substrates for CYP2C8, and mediate toxic adverse events, perhaps in those individuals in whom SNO is formed extensively.
Nan, J, Guo, X, Xiao, J, Li, X, Chen, W, Wu, W, Liu, H, Wang, Y, Wu, M & Wang, G 2021, 'Nanoengineering of 2D MXene‐Based Materials for Energy Storage Applications', Small, vol. 17, no. 9, pp. 1902085-1902085.
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Abstract2D MXene‐based nanomaterials have attracted tremendous attention because of their unique physical/chemical properties and wide range of applications in energy storage, catalysis, electronics, optoelectronics, and photonics. However, MXenes and their derivatives have many inherent limitations in terms of energy storage applications. In order to further improve their performance for practical application, the nanoengineering of these 2D materials is extensively investigated. In this Review, the latest research and progress on 2D MXene‐based nanostructures is introduced and discussed, focusing on their preparation methods, properties, and applications for energy storage such as lithium‐ion batteries, sodium‐ion batteries, lithium–sulfur batteries, and supercapacitors. Finally, the critical challenges and perspectives required to be addressed for the future development of these 2D MXene‐based materials for energy storage applications are presented.
Naser, IB, Shishir, TA, Faruque, SN, Hoque, MM, Hasan, A & Faruque, SM 2021, 'Environmental prevalence of toxigenic Vibrio cholerae O1 in Bangladesh coincides with V. cholerae non-O1 non-O139 genetic variants which overproduce autoinducer-2', PLOS ONE, vol. 16, no. 7, pp. e0254068-e0254068.
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Prevalence of toxigenic Vibrio cholerae O1 in aquatic reservoirs in Bangladesh apparently increases coinciding with the occurrence of seasonal cholera epidemics. In between epidemics, these bacteria persist in water mostly as dormant cells, known as viable but non-culturable cells (VBNC), or conditionally viable environmental cells (CVEC), that fail to grow in routine culture. CVEC resuscitate to active cells when enriched in culture medium supplemented with quorum sensing autoinducers CAI-1 or AI-2 which are signal molecules that regulate gene expression dependent on cell density. V. cholerae O1 mutant strains with inactivated cqsS gene encoding the CAI-1 receptor has been shown to overproduce AI-2 that enhance CVEC resuscitation in water samples. Since V. cholerae non-O1 non-O139 (non-cholera-vibrios) are abundant in aquatic ecosystems, we identified and characterized naturally occurring variant strains of V. cholerae non-O1 non-O139 which overproduce AI-2, and monitored their co-occurrence with V. cholerae O1 in water samples. The nucleotide sequence and predicted protein products of the cqsS gene carried by AI-2 overproducing variant strains showed divergence from that of typical V. cholerae O1 or non-O1 strains, and their culture supernatants enhanced resuscitation of CVEC in water samples. Furthermore, prevalence of V. cholerae O1 in the aquatic environment was found to coincide with an increase in AI-2 overproducing non-O1 non-O139 strains. These results suggest a possible role of non-cholera vibrios in the environmental biology of the chole...
Nazrul Islam, SMK, Mayank, P, Ouyang, Y, Chen, J, Sagotra, AK, Li, M, Cortie, MB, Mole, R, Cazorla, C, Yu, D, Wang, X, Robinson, RA & Cortie, DL 2021, 'Copper diffusion rates and hopping pathways in superionic Cu2Se', Acta Materialia, vol. 215, pp. 117026-117026.
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Neira, V, Brito, B, Agüero, B, Berrios, F, Valdés, V, Gutierrez, A, Ariyama, N, Espinoza, P, Retamal, P, Holmes, EC, Gonzalez-Reiche, AS, Khan, Z, van de Guchte, A, Dutta, J, Miorin, L, Kehrer, T, Galarce, N, Almonacid, LI, Levican, J, van Bakel, H, García-Sastre, A & Medina, RA 2021, 'A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners', Emerging Microbes & Infections, vol. 10, no. 1, pp. 376-383.
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Nemani, SSP, Vermeulen, CJ, Pech, M, Faiz, A, Oliver, BGG, van den Berge, M, Burgess, JK, Kopp, MV & Weckmann, M 2021, 'COL4A3expression in asthmatic epithelium depends on intronic methylation and ZNF263 binding', ERJ Open Research, vol. 7, no. 2, pp. 00802-2020.
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BackgroundReduction of COL4A3, one of the six isoforms of collagen 4, in asthmatic airways results in increased inflammation and angiogenesis, implicating it as a central part of asthma pathogenesis. However, to date, the path underlying these diminished COL4A3 levels has been elusive. This study investigated a possible mechanism underlying the reduction of COL4A3 expression.MethodsBronchial biopsies of 76 patients with asthma and 83 controls were subjected to RNA-sequencing and DNA methylation bead arrays to identify expression and methylation changes. The binding of ZNF263 was analysed by chromatin-immunoprecipitation sequencing coupled with quantitative (q)PCR. Effects ofZNF263silencing, using small interfering RNA, on theCOL4A3expression were studied using qPCR.ResultsCOL4A3expression was significantly reduced in bronchial biopsies compared to healthy controls, whereas DNA methylation levels at cg11797365 were increased.COL4A3expression levels were significantly low in asthmatics without inhaled corticosteroid (ICS) use, whereas the expression was not statistically different between asthmatics using ICS and controls. Methylation levels at cg11797365in vitrowere increased upon consecutive rhinovirus infections.ConclusionOur data indicate an epigenetic modification as a contributing factor for the loss ofCOL4A3expression in asthmatic airway epithelium.
Nguyen, AQ, Vu, HP, Nguyen, LN, Wang, Q, Djordjevic, SP, Donner, E, Yin, H & Nghiem, LD 2021, 'Monitoring antibiotic resistance genes in wastewater treatment: Current strategies and future challenges', Science of The Total Environment, vol. 783, pp. 146964-146964.
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Antimicrobial resistance (AMR) is a growing threat to human and animal health. Progress in molecular biology has revealed new and significant challenges for AMR mitigation given the immense diversity of antibiotic resistance genes (ARGs), the complexity of ARG transfer, and the broad range of omnipresent factors contributing to AMR. Municipal, hospital and abattoir wastewater are collected and treated in wastewater treatment plants (WWTPs), where the presence of diverse selection pressures together with a highly concentrated consortium of pathogenic/commensal microbes create favourable conditions for the transfer of ARGs and proliferation of antibiotic resistant bacteria (ARB). The rapid emergence of antibiotic resistant pathogens of clinical and veterinary significance over the past 80 years has re-defined the role of WWTPs as a focal point in the fight against AMR. By reviewing the occurrence of ARGs in wastewater and sludge and the current technologies used to quantify ARGs and identify ARB, this paper provides a research roadmap to address existing challenges in AMR control via wastewater treatment. Wastewater treatment is a double-edged sword that can act as either a pathway for AMR spread or as a barrier to reduce the environmental release of anthropogenic AMR. State of the art ARB identification technologies, such as metagenomic sequencing and fluorescence-activated cell sorting, have enriched ARG/ARB databases, unveiled keystone species in AMR networks, and improved the resolution of AMR dissemination models. Data and information provided in this review highlight significant knowledge gaps. These include inconsistencies in ARG reporting units, lack of ARG/ARB monitoring surrogates, lack of a standardised protocol for determining ARG removal via wastewater treatments, and the inability to support appropriate risk assessment. This is due to a lack of standard monitoring targets and agreed threshold values, and paucity of information on the ARG-pat...
Nguyen, HD, Azzi, M, White, S, Salter, D, Trieu, T, Morgan, G, Rahman, M, Watt, S, Riley, M, Chang, LT-C, Barthelemy, X, Fuchs, D, Lieschke, K & Nguyen, H 2021, 'The Summer 2019–2020 Wildfires in East Coast Australia and Their Impacts on Air Quality and Health in New South Wales, Australia', International Journal of Environmental Research and Public Health, vol. 18, no. 7, pp. 3538-3538.
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The 2019–2020 summer wildfire event on the east coast of Australia was a series of major wildfires occurring from November 2019 to end of January 2020 across the states of Queensland, New South Wales (NSW), Victoria and South Australia. The wildfires were unprecedent in scope and the extensive character of the wildfires caused smoke pollutants to be transported not only to New Zealand, but also across the Pacific Ocean to South America. At the peak of the wildfires, smoke plumes were injected into the stratosphere at a height of up to 25 km and hence transported across the globe. The meteorological and air quality Weather Research and Forecasting with Chemistry (WRF-Chem) model is used together with the air quality monitoring data collected during the bushfire period and remote sensing data from the Moderate Resolution Imaging Spectroradiometer (MODIS) and Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) satellites to determine the extent of the wildfires, the pollutant transport and their impacts on air quality and health of the exposed population in NSW. The results showed that the WRF-Chem model using Fire Emission Inventory (FINN) from National Center for Atmospheric Research (NCAR) to simulate the dispersion and transport of pollutants from wildfires predicted the daily concentration of PM2.5 having the correlation (R2) and index of agreement (IOA) from 0.6 to 0.75 and 0.61 to 0.86, respectively, when compared with the ground-based data. The impact on health endpoints such as mortality and respiratory and cardiovascular diseases hospitalizations across the modelling domain was then estimated. The estimated health impact on each of the Australian Bureau of Statistics (ABS) census districts (SA4) of New South Wales was calculated based on epidemiological assumptions of the impact function and incidence rate data from the 2016 ABS and NSW Department of Health statistical health records. Summing up all SA4 census dist...
Nguyen, HM, Bulleri, F, Marín-Guirao, L, Pernice, M & Procaccini, G 2021, 'Photo-physiology and morphology reveal divergent warming responses in northern and southern hemisphere seagrasses', Marine Biology, vol. 168, no. 8.
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Nguyen, HM, Ralph, PJ, Marín‐Guirao, L, Pernice, M & Procaccini, G 2021, 'Seagrasses in an era of ocean warming: a review', Biological Reviews, vol. 96, no. 5, pp. 2009-2030.
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ABSTRACTSeagrasses are valuable sources of food and habitat for marine life and are one of Earth's most efficient carbon sinks. However, they are facing a global decline due to ocean warming and eutrophication. In the last decade, with the advent of new technology and molecular advances, there has been a dramatic increase in the number of studies focusing on the effects of ocean warming on seagrasses. Here, we provide a comprehensive review of the future of seagrasses in an era of ocean warming. We have gathered information from published studies to identify potential commonalities in the effects of warming and the responses of seagrasses across four distinct levels: molecular, biochemical/physiological, morphological/population, and ecosystem/planetary. To date, we know that although warming strongly affects seagrasses at all four levels, seagrass responses diverge amongst species, populations, and over depths. Furthermore, warming alters seagrass distribution causing massive die‐offs in some seagrass populations, whilst also causing tropicalization and migration of temperate species. In this review, we evaluate the combined effects of ocean warming with other environmental stressors and emphasize the need for multiple‐stressor studies to provide a deeper understanding of seagrass resilience. We conclude by discussing the most significant knowledge gaps and future directions for seagrass research.
Nguyen, LN, Vu, MT, Abu Hasan Johir, M, Pernice, M, Ngo, HH, Zdarta, J, Jesionowski, T & Nghiem, LD 2021, 'Promotion of direct interspecies electron transfer and potential impact of conductive materials in anaerobic digestion and its downstream processing - a critical review', Bioresource Technology, vol. 341, pp. 125847-125847.
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Nguyen, LT, Saad, S, Shi, Y, Wang, R, Chou, ASY, Gill, A, Yao, Y, Jarolimek, W & Pollock, CA 2021, 'Lysyl oxidase inhibitors attenuate cyclosporin A-induced nephropathy in mouse', Scientific Reports, vol. 11, no. 1.
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AbstractCalcineurin inhibitors, such as Cyclosporin (CsA), are the mainstay of anti-rejection therapy in solid organ transplants but can paradoxically induce progressive nephropathy characterised by renal dysfunction and interstitial fibrosis. Lysyl oxidases (LOXs), a group of enzymes that catalyse extracellular matrix (ECM) crosslinking, were shown to implicate in tissue scarring. It is hypothesized that inhibition of these enzymes may render therapeutic effects against CsA-induced nephropathy. In this study, 6-to-8 weeks old C57BL/6 J mice were administered saline or CsA (30 mg/kg/day s.c) for 16 weeks. At 8 weeks, CsA-treated animals were divided into 5 groups respectively treated with: (1) vehicle, (2) PXS-5505 (Pan-LOX inhibitor), (3) PXS-5382 (LOX-like 2 inhibitor), (4) PXS-5505 for 4 weeks then PXS-5382 for 4 weeks (sequential therapy), and (5) Telmisartan (standard therapy). Our results indicate that CsA administration significantly increased the levels of blood urea nitrogen, glomerular and tubular injury, tubulointerstitial fibrosis, inflammation and oxidative stress in mouse kidney. These changes were associated with upregulated mRNA expression of LOX and LOXL2. Administration of Pan-LOX or LOXL2 inhibitors or the sequential therapy suppressed the expression of ECM proteins (α-SMA, FN and COL1A), matrix metalloproteases (MMP)2 and 9, inflammatory markers (TNFα and MCP-1) and TGF-β1-Smad3 signalling. Among all regimens including telmisartan, only Pan-LOX inhibitor PXS-5505 was able to attenuate uraemia. Collectively, our study suggests that Pan-LOX and LOXL2 inhibition can attenuate progressive nephropathy due to CsA administration.
Nguyen, MAP, Hite, J, Mastro, MA, Kianinia, M, Toth, M & Aharonovich, I 2021, 'Site control of quantum emitters in gallium nitride by polarity', Applied Physics Letters, vol. 118, no. 2, pp. 1-6.
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Gallium nitride (GaN) is a promising platform for integrated nanophotonic circuitry due to highly versatile growth protocols for the material. With the discovery of quantum emitters hosted by its lattice, potential applications of GaN have expanded to quantum-based technologies, despite the fact that the atomic structures of the emitters are unknown. Thus, we investigate the nature of quantum emitters grown in various samples of differing growth orientations—namely, Ga-polar, N-polar, and a combination of the two in an alternating periodic pattern. We showcase the unique growth technique used to fabricate these samples and characterize the emitters that form as a result. Through measurements of photoluminescence, cathodoluminescence, and Raman spectroscopy, we observe consistent formation of quantum emitters within Ga-polar regions of the grown GaN, attributed to overall defectivity caused by the specific growth procedure used to synthesize Ga-polar GaN. Our findings shed light onto the origins of the quantum emitters and are used to demonstrate site-selective formation of the emitters in GaN.
Nguyen, VK, King, WL, Siboni, N, Mahbub, KR, Rahman, MH, Jenkins, C, Dove, M, O'Connor, W, Seymour, JR & Labbate, M 2021, 'Dynamics of the Sydney rock oyster microbiota before and during a QX disease event', Aquaculture, vol. 541, pp. 736821-736821.
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The Sydney rock oyster (SRO; Saccostrea glomerata) is the most intensively farmed oyster species in Australia however, Queensland unknown (QX) disease has resulted in substantial losses and impeded productivity. QX disease is caused by infection with the parasite Marteilia sydneyi, and like other diseases, outbreaks are driven by a series of complex environmental and host factors such as seasonality, seawater salinity and oyster genetics. A potential but understudied factor in QX disease is the SRO microbiota, which we sought to examine before and during a QX disease outbreak. Using 16S rRNA (V1 – V3 region) amplicon sequencing, we examined the microbiota of SROs deployed in an estuary where QX disease occurs, with sampling conducted fortnightly over 22 weeks. Marteilia sydneyi was detected in the SROs by PCR (QX-positive), 16 weeks after the first sampling event and sporonts were observed in the digestive gland two weeks later on. There were no apparent patterns observed between the microbiota of QX-positive SROs with and without digestive gland sporonts however, the microbiota of QX-positive SROs was significantly different from those sampled prior to detection of M. sydneyi and from those negative for M. sydneyi post detection. As a result, shifts in microbiota structure occurred before sporulation in the digestive gland and either before or shortly after pathogen colonisation. The microbiota shifts associated with QX-positive oysters were principally driven by a relative abundance increase of operational taxonomic units (OTUs) assigned to unclassified species of the Borrelia and Candidatus Hepatoplasma genera and a relative abundance decrease in an OTU assigned to an unclassified species of the Mycoplasma genus. Since Mycoplasma species are common microbiota features of SROs and other oysters, we propose that there may be an important ecological link between Mycoplasma species and the health state of SROs.
Niaz, A, Karunia, J, Mandwie, M, Keay, KA, Musumeci, G, Al-Badri, G & Castorina, A 2021, 'Robust Dopaminergic Differentiation and Enhanced LPS-Induced Neuroinflammatory Response in Serum-Deprived Human SH-SY5Y Cells: Implication for Parkinson’s Disease', Journal of Molecular Neuroscience, vol. 71, no. 3, pp. 565-582.
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Parkinson's disease (PD) is a chronic neurodegenerative condition characterized by motor symptoms such as bradykinesia, resting tremor, and rigidity. PD diagnosis is based on medical history, review of signs, symptoms, neurological and physical examinations. Unfortunately, by the time the disease is diagnosed, dopamine (DA) neuronal loss is often extended, thereby resulting in ineffective therapies. Recent evidence suggests that neuroinflammation may be pivotal during PD onset and progression. However, suitable cellular models and biomarkers to detect early signs of neuroinflammation are still missing. In this study, we developed a well-differentiated DAergic neuronal cell line where we triggered a neuroinflammatory response to assess the temporal expression of the tissue- and urokinase plasminogen activators (tPA and uPA) and their endogenous inhibitor (PAI-1) along with that of pro-inflammatory mediators and the neuronal marker nNOS. Human neuroblastoma cells SH-SY5Y were differentiated into DAergic neuronal-like cells using a combination of 12-O-tetradecanoylphorbol-13-acetate (TPA) and serum depletion. Terminally-differentiated neurons were then exposed to lipopolysaccharide (LPS) for short (up to 24 h) or long term (up to 10 days) to mimic acute or chronic inflammation. Results demonstrated that uPA protein expression was stably upregulated during chronic inflammation, whereas the expression of nNOS protein better reflected the cellular response to acute inflammation. Additional studies revealed that the temporal induction of uPA was associated with increased AKT phosphorylation, but did not seem to involve cAMP-responsive element-binding protein (CREB) activation, nor the mitogen-activated protein kinase (MAPK) pathway. In conclusion, our in vitro data suggests that nNOS and uPA may serve as viable candidate biomarkers of acute and chronic neuroinflammation.
Nielsen, DA, Fierer, N, Geoghegan, JL, Gillings, MR, Gumerov, V, Madin, JS, Moore, L, Paulsen, IT, Reddy, TBK, Tetu, SG & Westoby, M 2021, 'Aerobic bacteria and archaea tend to have larger and more versatile genomes', Oikos, vol. 130, no. 4, pp. 501-511.
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A recent compilation of traits across culturable species of bacteria and archaea allows relationships to be quantified between genome size and other traits and habitat. Cell morphology, size, motility, sporulation and doubling time were not strongly correlated with genome size. Aerobic species averaged ca 35% larger genomes than anaerobic, adjusted for growth temperature. Aerobes had a similar mix of gene functions compared to anaerobes of the same genome size. Shifting proportions of aerobes to anaerobes accounted for about half of previously‐known differences in mean genome size between habitats. One possible factor in these results could be if effective population sizes are larger for aerobes, reducing the potential for gene loss via genetic drift. Larger genomes also confer versatility. They can transport and metabolise a wider range of substrates. More of their genome is engaged in signal detection and response, indicating they benefit from different resources at different times or under different condition. Aerobic habitats might well present opportunities and challenges that vary through time more than anaerobic habitats. The genome size trait‐dimension contributes a useful quantitative descriptor for ecological strategies.
Nieves, OA, Arnold, MD, Schmidt, MK, Steel, MJ & Poulton, CG 2021, 'Noise in Brillouin based information storage', Optics Express, vol. 29, no. 24, pp. 39486-39486.
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We theoretically and numerically study the efficiency of Brillouin-based opto-acoustic data storage in a photonic waveguide in the presence of thermal noise and laser phase noise. We compare the physics of the noise processes and how they affect different storage techniques, examining both amplitude and phase storage schemes. We investigate the effects of storage time and pulse properties on the quality of the retrieved signal and find that phase storage is less sensitive to thermal noise than amplitude storage.
Nieves, OA, Arnold, MD, Steel, MJ, Schmidt, MK & Poulton, CG 2021, 'Numerical simulation of noise in pulsed Brillouin scattering', Journal of the Optical Society of America B, vol. 38, no. 8, pp. 2343-2343.
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We present a numerical method for modeling noise in stimulated Brillouin scattering (SBS). The model applies to dynamic cases such as optical pulses and accounts for both thermal noise and phase noise from the input lasers. Using this model, we compute the statistical properties of the optical and acoustic power in the pulsed spontaneous and stimulated Brillouin cases, and investigate the effects of gain and pulse width on noise levels. We find that thermal noise plays an important role in the statistical properties of the fields and that laser phase noise impacts the SBS interaction when the laser coherence time is close to the time scale of the optical pulses. This algorithm is applicable to arbitrary waveguide geometries and material properties and, thus, presents a versatile way of performing noise-based SBS numerical simulations, which are important in signal processing, sensing, microwave photonics, and opto-acoustic memory storage.
Nikolaeva, A, Frizyuk, K, Olekhno, N, Solntsev, A & Petrov, M 2021, 'Directional emission of down-converted photons from a dielectric nanoresonator', Physical Review A, vol. 103, no. 4, p. 043703.
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Creation of entangled photon pairs is one of the key topics in contemporary quantum optics. In the present article, we theoretically describe the generation of photon pairs in the process of spontaneous parametric down-conversion of light by a resonant spherical nanoparticle made of a dielectric material with bulk ˆχ(2) nonlinearity. We consider the nanoparticle size that satisfies the condition of excitation of resonant eigenmodes described by Mie theory. We demonstrate that a highly directional photon pair generation can be observed utilizing the nonlinear Kerker-type effect, and that this regime provides useful polarization correlations between the emitted photons.
Nolan, RH, Bowman, DMJS, Clarke, H, Haynes, K, Ooi, MKJ, Price, OF, Williamson, GJ, Whittaker, J, Bedward, M, Boer, MM, Cavanagh, VI, Collins, L, Gibson, RK, Griebel, A, Jenkins, ME, Keith, DA, Mcilwee, AP, Penman, TD, Samson, SA, Tozer, MG & Bradstock, RA 2021, 'What Do the Australian Black Summer Fires Signify for the Global Fire Crisis?', Fire, vol. 4, no. 4, pp. 97-97.
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The 2019–20 Australian fire season was heralded as emblematic of the catastrophic harm wrought by climate change. Similarly extreme wildfire seasons have occurred across the globe in recent years. Here, we apply a pyrogeographic lens to the recent Australian fires to examine the range of causes, impacts and responses. We find that the extensive area burnt was due to extreme climatic circumstances. However, antecedent hazard reduction burns (prescribed burns with the aim of reducing fuel loads) were effective in reducing fire severity and house loss, but their effectiveness declined under extreme weather conditions. Impacts were disproportionately borne by socially disadvantaged regional communities. Urban populations were also impacted through prolonged smoke exposure. The fires produced large carbon emissions, burnt fire-sensitive ecosystems and exposed large areas to the risk of biodiversity decline by being too frequently burnt in the future. We argue that the rate of change in fire risk delivered by climate change is outstripping the capacity of our ecological and social systems to adapt. A multi-lateral approach is required to mitigate future fire risk, with an emphasis on reducing the vulnerability of people through a reinvigoration of community-level capacity for targeted actions to complement mainstream fire management capacity.
Nolan, RH, Collins, L, Leigh, A, Ooi, MKJ, Curran, TJ, Fairman, TA, Resco de Dios, V & Bradstock, R 2021, 'Limits to post‐fire vegetation recovery under climate change', Plant, Cell & Environment, vol. 44, no. 11, pp. 3471-3489.
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AbstractRecord‐breaking fire seasons in many regions across the globe raise important questions about plant community responses to shifting fire regimes (i.e., changing fire frequency, severity and seasonality). Here, we examine the impacts of climate‐driven shifts in fire regimes on vegetation communities, and likely responses to fire coinciding with severe drought, heatwaves and/or insect outbreaks. We present scenario‐based conceptual models on how overlapping disturbance events and shifting fire regimes interact differently to limit post‐fire resprouting and recruitment capacity. We demonstrate that, although many communities will remain resilient to changing fire regimes in the short‐term, longer‐term changes to vegetation structure, demography and species composition are likely, with a range of subsequent effects on ecosystem function. Resprouting species are likely to be most resilient to changing fire regimes. However, even these species are susceptible if exposed to repeated short‐interval fire in combination with other stressors. Post‐fire recruitment is highly vulnerable to increased fire frequency, particularly as climatic limitations on propagule availability intensify. Prediction of community responses to fire under climate change will be greatly improved by addressing knowledge gaps on how overlapping disturbances and climate change‐induced shifts in fire regime affect post‐fire resprouting, recruitment, growth rates, and species‐level adaptation capacity.
Nonahal, M, White, SJU, Regan, B, Li, C, Trycz, A, Kim, S, Aharonovich, I & Kianinia, M 2021, 'Bottom‐Up Synthesis of Single Crystal Diamond Pyramids Containing Germanium Vacancy Centers', Advanced Quantum Technologies, vol. 4, no. 7, pp. 1-6.
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AbstractDiamond resonators containing color‐centers are highly sought after for application in quantum technologies. Bottom‐up approaches are promising for the generation of single‐crystal diamond structures with purposely introduced color centers. Here the possibility of using a polycrystalline diamond to grow single‐crystal diamond structures by employing a pattern growth method is demonstrated. For, the possible mechanism of growing a single‐crystal structure with predefined shape and size from a polycrystalline substrate by controlling the growth condition is clarified. Then, by introducing germanium impurities during the growth, localized and enhanced emission from fabricated pyramid shaped single‐crystal diamonds containing germanium vacancy (GeV) color centers is demonstrated. Finally, linewidth of ∼500 MHz at 4 K from a single GeV center in the pyramid shaped diamonds is measured. The method is an important step toward fabrication of 3D structures for integrated diamond photonics.
Nucera, F, Lo Bello, F, Shen, SS, Ruggeri, P, Coppolino, I, Di Stefano, A, Stellato, C, Casolaro, V, Hansbro, PM, Adcock, IM & Caramori, G 2021, 'Role of Atypical Chemokines and Chemokine Receptors Pathways in the Pathogenesis of COPD', Current Medicinal Chemistry, vol. 28, no. 13, pp. 2577-2653.
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Chronic obstructive pulmonary disease (COPD) represents a heightened inflammatory response in the lung generally resulting from tobacco smoking-induced recruitment and activation of inflammatory cells and/or activation of lower airway structural cells. Several mediators can modulate activation and recruitment of these cells, particularly those belonging to the chemokines (conventional and atypical) family. There is emerging evidence for complex roles of atypical chemokines and their receptors (such as high mobility group box 1 (HMGB1), antimicrobial peptides, receptor for advanced glycosylation end products (RAGE) or toll-like receptors (TLRs)) in the pathogenesis of COPD, both in the stable disease and during exacerbations. Modulators of these pathways represent potential novel therapies for COPD and many are now in preclinical development. Inhibition of only a single atypical chemokine or receptor may not block inflammatory processes because there is redundancy in this network. However, there are many animal studies that encourage studies for modulating the atypical chemokine network in COPD. Thus, few pharmaceutical companies maintain a significant interest in developing agents that target these molecules as potential antiinflammatory drugs. Antibody-based (biological) and small molecule drug (SMD)-based therapies targeting atypical chemokines and/or their receptors are mostly at the preclinical stage and their progression to clinical trials is eagerly awaited. These agents will most likely enhance our knowledge about the role of atypical chemokines in COPD pathophysiology and thereby improve COPD management.
O’Rourke, MB, Viengkhou, B, Smith, CC, Sonderegger, L, Padula, MP, Sutherland, GT, Hofer, MJ & Crossett, B 2021, 'Matrix phase fractionation: Investigating the compromise between dynamic range of analyte extraction and spatial resolution in mass spectrometry imaging', Rapid Communications in Mass Spectrometry, vol. 35, no. 13, p. e9106.
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RationaleMatrix‐assisted laser desorption ionisation with mass spectrometry imaging (MSI) has seen rapid development in recent years and as such is becoming an important technique for the mapping of biomolecules from the surface of tissues. One key area of development is the optimisation of analyte extraction by using modified matrices or mixes of common ones.MethodsA series of serial sections were prepared for lipid MSI by either dry coating (sublimation) or by wet spray application of several matrices. These samples were then evaluated for analyte extraction, delocalisation and dynamic range.ResultsWe have shown that the spraying and sublimation methods of matrix application can be used complementarily. This creates large datasets, with each preparation method applied narrowly and then interpreted as a ‘fraction’ of the whole. Once combined, the dynamic range is significantly increased. We have dubbed this technique ‘matrix phase fractionation’.ConclusionsWe have found that, by utilising matrix phase fractionation for the detection of lipids in brain tissue, it is possible to create a significantly more comprehensive dataset than would otherwise be possible with traditional ‘single‐run’ workflows.
O'Connor, C & Booth, DJ 2021, 'Response of estuarine fishes to elevated temperatures within temperate Australia: Implications of climate change on fish growth and foraging performance', Journal of Experimental Marine Biology and Ecology, vol. 544, pp. 151626-151626.
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Olander, A, Lawson, CA, Possell, M, Raina, J-B, Ueland, M & Suggett, DJ 2021, 'Comparative volatilomics of coral endosymbionts from one- and comprehensive two-dimensional gas chromatography approaches', Marine Biology, vol. 168, no. 5, p. 76.
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Volatilomics, the examination of all biogenic volatile organic compounds (BVOCs) emitted by an organism or system, holds potential as a novel screening tool for taxonomy, fitness, and ecological functioning. Volatilomics has been largely applied to terrestrial environments, but highly productive coastal marine systems, which are major sources of specific BVOCs, such as dimethyl sulfide, have been largely neglected. Volatilomic measurements are highly method-dependent, with different instrumentation impacting the diversity of identified BVOCs—therefore, understanding these biases is critical to reconcile studies. Here, we investigated BVOCs emitted by two species of coral endosymbiotic microalgae (Symbiodinium tridacnidorum and Durusdinium trenchii) using gas chromatography–mass spectrometry (GC–MS) and comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (GC × GC–TOFMS). Seven chemical classes were detected by both instruments, the most common being aromatic hydrocarbons. However, GC × GC resolved seven times more BVOCs than GC–MS (290 vs. 40), with a higher proportion of compounds tentatively identified (173 vs. 14). Notably, nine chemical classes were exclusively identified by GC × GC, including alkane, alkene, aldehyde, ester, and nitrile BVOCs—each potentially fulfilling undescribed functions in marine organisms. The microalgal species investigated shared a large proportion of BVOCs, and this result was consistent across instruments (97 and 98% shared compounds via GC × GC and GC–MS, respectively), suggesting consistent retrieval of general patterns between instruments. This method comparison is the first of its kind in marine systems and confirms the greater analytical power of GC × GC, required to help resolve complex BVOC emissions and the identification of their roles in marine systems.
Oliver, BG 2021, 'Food for thought: why is there more airway smooth muscle in asthma?', European Respiratory Journal, vol. 58, no. 5, pp. 2101565-2101565.
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All definitions of asthma include reference to smooth muscle contraction, which manifests as either episodic wheeze, breathlessness, cough, bronchospasm and/or exacerbations. Furthermore, bronchodilators are one of most effective classes of therapeutic for the management of acute exacerbations and long-term treatment of asthma. It is therefore somewhat surprising that the smooth muscle cell is often under researched in comparison to inflammatory and epithelial cells in asthma. This likely relates to the difficulty of obtaining bronchoscopic samples and the expertise required to isolate and grow airway smooth cells in vitro. The in vitro growth of smooth muscle cells from bronchial biopsies was pioneered by the group led by J.L. Black [1]. The first publication from her group characterising airway smooth muscle cells in asthma was published 20 years ago, and described increased proliferation of smooth muscle cells ex vivo from people with asthma. It seems fitting that understanding the cause of this increased proliferation was elegantly investigated by Esteves et al. [2] in this issue of the European Respiratory Journal.
Oliver, TE, Piantavigna, S, Andrews, PC, Holt, SA & Dillon, CT 2021, 'Interactions of Non-steroidal Anti-inflammatory Drugs and Their Bismuth Analogues (BiNSAIDs) with Biological Membrane Mimics at Physiological pH', Langmuir, vol. 37, no. 4, pp. 1337-1352.
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Previous studies have demonstrated the potential for non-steroidal anti-inflammatory drugs (NSAIDs), in particular aspirin, to be used as chemopreventives for colorectal cancer; however, a range of unwanted gastrointestinal side effects limit their effectiveness. Due to the role of bismuth in the treatment of gastrointestinal disorders, it is hypothesized that bismuth-coordinated NSAIDs (BiNSAIDs) could be used to combat the gastrointestinal side effects of NSAIDs while still maintaining their chemopreventive potential. To further understand the biological activity of these compounds, the present study examined four NSAIDs, namely, tolfenamic acid (tolfH), aspirin (aspH), indomethacin (indoH), and mefenamic acid (mefH) and their analogous homoleptic BiNSAIDs ([Bi(L)3]n), to determine how these compounds interact with biological membrane mimics composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) or a mixture of POPC and cholesterol. Electrical impedance spectroscopy studies revealed that each of the NSAIDs and BiNSAIDs influenced membrane conductance, suggesting that temporary pore formation may play a key role in the previously observed cytotoxicity of tolfH and Bi(tolf)3. Quartz crystal microbalance with dissipation monitoring showed that all the compounds were able to interact with membrane mimics composed of solely POPC or POPC/cholesterol. Finally, neutron reflectometry studies showed changes in membrane thickness and composition. The location of the compounds within the bilayer could not be determined with certainty; however, a complex interplay of interactions governs the location of small molecules, such as NSAIDs, within lipid membranes. The charged nature of the parent NSAIDs means that interactions with the polar headgroup region are most likely with larger hydrophobic sections, potentially leading to deeper penetration.
Pacheco Arredondo, G, Holt, SA & He, L 2021, 'Uranyl-Binding Proteins on Silica Nanoparticles for Repeatable Capture of Uranyl Ions', ACS Applied Nano Materials, vol. 4, no. 11, pp. 11801-11808.
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Successful protein-based enrichment of uranyl, the predominant form of uranium from seawater, relies not only on selective binding of uranyl with a high affinity but also on the reusability of protein binder and a supporting matrix that is abundantly available at low cost. In this work, we propose a silica-binding peptide-enabled approach that allows the non-covalent immobilization of super uranyl-binding protein (SUP) onto silica nanoparticles for their repeated use. We first thoroughly examined solution conditions that affect the stability of uranyl-binding proteins and identified suitable physical conditions that are beneficial for the non-covalent SUP immobilization and subsequent capture of uranyl. We found that the molecular linker between SUP and silica binding peptide plays an important role in improving interaction strength between the silica nanoparticles and the engineered proteins. Consequently, we have demonstrated repeatable recovery and enrichment of uranyl ions from synthetic seawater using the engineered protein on silica nanoparticles. Our approach does not require chemical modification of silica nanoparticles, yet offers strong attachment of SUP to the silica interface and thus attractive reusability of protein-silica nanomaterials.
Pacitti, D, Scotton, CJ, Kumar, V, Khan, H, Wark, PAB, Torregrossa, R, Hansbro, PM & Whiteman, M 2021, 'Gasping for Sulfide: A Critical Appraisal of Hydrogen Sulfide in Lung Disease and Accelerated Aging', Antioxidants & Redox Signaling, vol. 35, no. 7, pp. 551-579.
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Hydrogen sulfide (H2S) is a gaseous signaling molecule involved in a plethora of physiological and pathological processes. It is primarily synthesized by cystathionine-β-synthase, cystathionine-γ-lyase, and 3-mercaptopyruvate sulfurtransferase as a metabolite of the transsulfuration pathway. H2S has been shown to exert beneficial roles in lung disease acting as an anti-inflammatory and antiviral and to ameliorate cell metabolism and protect from oxidative stress. H2S interacts with transcription factors, ion channels, and a multitude of proteins via post-translational modifications through S-persulfidation ('sulfhydration'). Perturbation of endogenous H2S synthesis and/or levels have been implicated in the development of accelerated lung aging and diseases, including asthma, chronic obstructive pulmonary disease, and fibrosis. Furthermore, evidence indicates that persulfidation is decreased with aging. Here, we review the use of H2S as a biomarker of lung pathologies and discuss the potential of using H2S-generating molecules and synthesis inhibitors to treat respiratory diseases. Furthermore, we provide a critical appraisal of methods of detection used to quantify H2S concentration in biological samples and discuss the challenges of characterizing physiological and pathological levels. Considerations and caveats of using H2S delivery molecules, the choice of generating molecules, and concentrations are also reviewed. Antioxid. Redox Signal. 35, 551-579.
Padovan, A, Siboni, N, Kaestli, M, King, WL, Seymour, JR & Gibb, K 2021, 'Occurrence and dynamics of potentially pathogenic vibrios in the wet-dry tropics of northern Australia', Marine Environmental Research, vol. 169, pp. 105405-105405.
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Bacteria from the Vibrio genus are a ubiquitous component of coastal and estuarine ecosystems with several pathogenic Vibrio species displaying preferences for warm tropical waters. We studied the spatial and temporal abundance of three key human potential pathogens V. parahaemolyticus, V. cholerae and V. vulnificus in northern tropical Australia, over the wet and dry seasons, to identify environmental parameters influencing their abundance. Quantitative PCR (qPCR) analysis revealed that V. parahaemolyticus occurred more frequently and in higher abundance than V. cholerae and V. vulnificus across all locations examined. All three species were more abundant during the wet season, with V. parahaemolyticus abundance correlated to temperature and conductivity, whereas nutrient concentrations and turbidity best explained V. vulnificus abundance. In addition to these targeted qPCR analyses, we assessed the composition and dynamics of the entire Vibrio community using hsp60 amplicon sequencing. Using this approach, 42 Vibrio species were identified, including a number of other pathogenic species such as V. alginolyticus, V. mimicus and V. fluvialis. The Vibrio community was more diverse in the wet season, with temperature and dissolved oxygen as the key factors governing community composition. Seasonal differences were primarily driven by a greater abundance of V. parahaemolyticus and V. vulnificus during the wet season, while spatial differences were driven by different abundances of V. harveyi, V. campbellii, V. cholerae and V. navarrensis. When we related the abundance of Vibrio to other bacterial taxa, defined using 16S rRNA gene amplicon sequencing, V. parahaemolyticus was negatively correlated to several taxa, including members of the Rickettsiales and Saccharimonadales, while V. vulnificus was negatively correlated to Rhobacteriaceae and Cyanobiaceae. In contrast, V. alginolyticus, V. harveyi and V. mediterranei were all positively correlated to Cyanoba...
Paijmans, KC, Booth, DJ & Wong, MYL 2021, 'Odd one in: Oddity within mixed‐species shoals does not affect shoal preference by vagrant tropical damselfish in the presence or absence of a predator', Ethology, vol. 127, no. 2, pp. 125-134.
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AbstractGrouping behaviour displayed by animals is usually attributed to predation and foraging‐related benefits. The mechanisms of predator protection and foraging efficiency are diverse and often produce conflicting drivers of grouping behaviour. One key conflict is that between group size and phenotypic oddity. Theoretically, individuals should choose the largest available group due to multiple mechanisms associated with “safety in numbers”. However, individuals should also choose the most phenotypically similar group members due to the “predator confusion effect”. This conflict is particularly important within the context of mixed‐species groups because, while their formation may facilitate large group size, phenotypic differences between species may be costly due to oddity. To investigate the interacting effects of shoal size, composition and predator presence on grouping decisions, choice experiments were conducted using displaced tropical damselfish,Abudefduf vaigiensis, settling in temperate south‐eastern Australia (termed vagrants) as a model species. Contrary to predictions,A. vaigiensisdisplayed no preference for single‐ over mixed‐species shoals, with or without a predator present. These results suggest that shoal composition may not be an important driver of shoal choice in this system. Further,A. vaigiensisshowed no preference for larger mixed‐species shoals over smaller single‐species shoals. These outcomes are discussed within the context of climate change‐driven redistribution ofA. vaigiensisin temperate south‐eastern Australia.
Pamphlett, R, Doble, PA & Bishop, DP 2021, 'Mercury in the human thyroid gland: Potential implications for thyroid cancer, autoimmune thyroiditis, and hypothyroidism', PLOS ONE, vol. 16, no. 2, pp. e0246748-e0246748.
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ObjectiveMercury and other toxic metals have been suggested to be involved in thyroid disorders, but the distribution and prevalence of mercury in the human thyroid gland is not known. We therefore used two elemental bio-imaging techniques to look at the distribution of mercury and other toxic metals in the thyroid glands of people over a wide range of ages.Materials and methodsFormalin-fixed paraffin-embedded thyroid tissue blocks were obtained from 115 people aged 1–104 years old, with varied clinicopathological conditions, who had thyroid samples removed during forensic/coronial autopsies. Seven-micron sections from these tissue blocks were used to detect intracellular inorganic mercury using autometallography. The presence of mercury was confirmed using laser ablation-inductively coupled plasma-mass spectrometry which can detect multiple elements.ResultsMercury was found on autometallography in the thyroid follicular cells of 4% of people aged 1–29 years, 9% aged 30–59 years, and 38% aged 60–104 years. Laser ablation-inductively coupled plasma-mass spectrometry confirmed the presence of mercury in samples staining with autometallography, and detected cadmium, lead, iron, nickel and silver in selected samples.ConclusionsThe proportion of people with mercury in their thyroid follicular cells increases with age, until it is present in over one-third of people aged 60 years and over. Other toxic metals in thyroid cells could enhance mercury toxicity. Mercury can trigger genotoxicity, autoimmune reactions, and oxidative damage, which raises the possibility that mercury could play a role in the pathogenesis of thyroid cancers, autoimmune thyroiditis, and hypothyroidism.
Pamphlett, R, Doble, PA & Bishop, DP 2021, 'The Prevalence of Inorganic Mercury in Human Kidneys Suggests a Role for Toxic Metals in Essential Hypertension', Toxics, vol. 9, no. 3, pp. 67-67.
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The kidney plays a dominant role in the pathogenesis of essential hypertension, but the initial pathogenic events in the kidney leading to hypertension are not known. Exposure to mercury has been linked to many diseases including hypertension in epidemiological and experimental studies, so we studied the distribution and prevalence of mercury in the human kidney. Paraffin sections of kidneys were available from 129 people ranging in age from 1 to 104 years who had forensic/coronial autopsies. One individual had injected himself with metallic mercury, the other 128 were from varied clinicopathological backgrounds without known exposure to mercury. Sections were stained for inorganic mercury using autometallography. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was used on six samples to confirm the presence of autometallography-detected mercury and to look for other toxic metals. In the 128 people without known mercury exposure, mercury was found in: (1) proximal tubules of the cortex and Henle thin loops of the medulla, in 25% of kidneys (and also in the man who injected himself with mercury), (2) proximal tubules only in 16% of kidneys, and (3) Henle thin loops only in 23% of kidneys. The age-related proportion of people who had any mercury in their kidney was 0% at 1–20 years, 66% at 21–40 years, 77% at 41–60 years, 84% at 61–80 years, and 64% at 81–104 years. LA-ICP-MS confirmed the presence of mercury in samples staining with autometallography and showed cadmium, lead, iron, nickel, and silver in some kidneys. In conclusion, mercury is found commonly in the adult human kidney, where it appears to accumulate in proximal tubules and Henle thin loops until an advanced age. Dysfunctions of both these cortical and medullary regions have been implicated in the pathogenesis of essential hypertension, so these findings suggest that further studies of the effects of mercury on blood pressure are warranted.
Pamphlett, R, Kum Jew, S, Doble, PA & Bishop, DP 2021, 'Mercury in the human adrenal medulla could contribute to increased plasma noradrenaline in aging', Scientific Reports, vol. 11, no. 1, pp. 1-14.
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AbstractPlasma noradrenaline levels increase with aging, and this could contribute to the sympathetic overactivity that is associated with essential hypertension and the metabolic syndrome. The underlying cause of this rise in noradrenaline is unknown, but a clue may be that mercury increases noradrenaline output from the adrenal medulla of experimental animals. We therefore determined the proportion of people from 2 to 104 years of age who had mercury in their adrenal medulla. Mercury was detected in paraffin sections of autopsied adrenal glands using two methods of elemental bioimaging, autometallography and laser ablation-inductively coupled plasma-mass spectrometry. Mercury first appeared in cells of the adrenal medulla in the 21–40 years group, where it was present in 52% of samples, and increased progressively in frequency in older age groups, until it was detected in 90% of samples from people aged over 80 years. In conclusion, the proportion of people having mercury in their adrenal medulla increases with aging. Mercury could alter the metabolism of catecholamines in the adrenal medulla that leads to the raised levels of plasma noradrenaline in aging. This retrospective autopsy study was not able to provide a definitive link between adrenal mercury, noradrenaline levels and hypertension, but future functional human and experimental studies could provide further evidence for these associations.
Pan, X, Wang, G & Wang, B 2021, 'Ectopic expression of microRNA-874 represses epithelial mesenchymal transition through the NF-κB pathway via CCNE1 in cholangiocarcinoma', Cellular Signalling, vol. 82, pp. 109927-109927.
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Pan, X, Wang, G & Wang, B 2021, 'MicroRNA-1182 and let-7a exert synergistic inhibition on invasion, migration and autophagy of cholangiocarcinoma cells through down-regulation of NUAK1', Cancer Cell International, vol. 21, no. 1.
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Abstract Background Cholangiocarcinoma (CCA) is the second most common primary liver malignancy worldwide. Several microRNAs (miRNAs) have been implicated as potential tumor suppressors in CCA. This study aims to explore the potential effects of miR-1182 and let-7a on CCA development. Methods Bioinformatics analysis was conducted to screen differentially expressed genes in CCA, Western blot analysis detected NUAK1 protein expression and RT-qPCR detected miR-1182, let-7a and NUAK1 expression in CCA tissues and cell lines. Dual luciferase reporter gene assay and RIP were applied to validate the relationship between miR-1182 and NUAK1 as well as between let-7a and NUAK1. Functional experiment was conducted to investigate the role of miR-1182, let-7a and NUAK1 in cell migration, proliferation and autophagy. Then, the CCA cells that received various treatments were implanted to mice to establish animal model, followed by tumor observation and HE staining to evaluate lung metastasis. Results CCA tissues and cells were observed to have a high expression of NUAK1 and poor expression of miR-1182 and let-7a. NUAK1 was indicated as a target gene of miR-1182 and let-7a. Importantly, upregulation of either miR-1182 or let-7a induced autophagy, and inhibited cell progression and in vivo tumor growth and lung metastasis; moreover, combined treatment of miR-1182 and let-7a overexpression presented with enhanced inhibitory effect on NUAK1 expression and CCA progression, but such synergistic effect could be reversed by overexpression of NUAK1. Conclusion
Papanicolaou, M, He, P, Rutting, S, Ammit, A, Xenaki, D, van Reyk, D & Oliver, BG 2021, 'Extracellular Matrix Oxidised by the Granulocyte Oxidants Hypochlorous and Hypobromous Acid Reduces Lung Fibroblast Adhesion and Proliferation In Vitro', Cells, vol. 10, no. 12, pp. 3351-3351.
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Chronic airway inflammation and oxidative stress play crucial roles in the pathogenesis of chronic inflammatory lung diseases, with airway inflammation being a key driving mechanism of oxidative stress in the lungs. Inflammatory responses in the lungs activate neutrophils and/or eosinophils, leading to the generation of hypohalous acids (HOX). These HOX oxidants can damage the extracellular matrix (ECM) structure and may influence cell–ECM interactions. The ECM of the lung provides structural, mechanical, and biochemical support for cells and determines the airway structure. One of the critical cells in chronic respiratory disease is the fibroblast. Thus, we hypothesised that primary human lung fibroblasts (PHLF) exposed to an oxidised cell-derived ECM will result in functional changes to the PHLF. Here, we show that PHLF adhesion, proliferation, and inflammatory cytokine secretion is affected by exposure to HOX-induced oxidisation of the cell-derived ECM. Furthermore, we investigated the impact on fibroblast function from the presence of haloamines in the ECM. Haloamines are chemical by-products of HOX and, like the HOX, haloamines can also modify the ECM. In conclusion, this study revealed that oxidising the cell-derived ECM might contribute to functional changes in PHLF, a key mechanism behind the pathogenesis of inflammatory lung diseases.
Park, S-H, Hwang, I, McNaughton, DA, Kinross, AJ, Howe, ENW, He, Q, Xiong, S, Kilde, MD, Lynch, VM, Gale, PA, Sessler, JL & Shin, I 2021, 'Synthetic Na+/K+ exchangers promote apoptosis by disturbing cellular cation homeostasis', Chem, vol. 7, no. 12, pp. 3325-3339.
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Parker, LM, Scanes, E, O'Connor, WA & Ross, PM 2021, 'Transgenerational plasticity responses of oysters to ocean acidification differ with habitat', Journal of Experimental Biology, vol. 224, no. 12, p. jeb.239269.
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ABSTRACT Transgenerational plasticity (TGP) has been identified as a critical mechanism of acclimation that may buffer marine organisms against climate change, yet whether the TGP response of marine organisms is altered depending on their habitat is unknown. Many marine organisms are found in intertidal zones where they experience episodes of emersion (air exposure) daily as the tide rises and recedes. During episodes of emersion, the accumulation of metabolic carbon dioxide (CO2) leads to hypercapnia for many species. How this metabolic hypercapnia impacts the TGP response of marine organisms to climate change is unknown as all previous transgenerational studies have been done under subtidal conditions, where parents are constantly immersed. Here, we assess the capacity of the ecologically and economically important oyster, Saccostrea glomerata, to acclimate to elevated CO2 dependent on habitat, across its vertical distribution, from the subtidal to intertidal zone. Tidal habitat altered both the existing tolerance and transgenerational response of S. glomerata to elevated CO2. Overall, larvae from parents conditioned in an intertidal habitat had a greater existing tolerance to elevated CO2 than larvae from parents conditioned in a subtidal habitat, but had a lower capacity for beneficial TGP following parental exposure to elevated CO2. Our results suggest that the TGP responses of marine species will not be uniform across their distribution and highlights the need to consider the habitat of a species when assessing TGP responses to climate change stressors.
Pasin, D, Mollerup, CB, Rasmussen, BS, Linnet, K & Dalsgaard, PW 2021, 'Development of a single retention time prediction model integrating multiple liquid chromatography systems: Application to new psychoactive substances', Analytica Chimica Acta, vol. 1184, pp. 339035-339035.
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Database-driven suspect screening has proven to be a useful tool to detect new psychoactive substances (NPS) outside the scope of targeted screening; however, the lack of retention times specific to a liquid chromatography (LC) system can result in a large number of false positives. A singular stream-lined, quantitative structure-retention relationship (QSRR)-based retention time prediction model integrating multiple LC systems with different elution conditions is presented using retention time data (n = 1281) from the online crowd-sourced database, HighResNPS. Modelling was performed using an artificial neural network (ANN), specifically a multi-layer perceptron (MLP), using four molecular descriptors and one-hot encoding of categorical labels. Evaluation of test set predictions (n = 193) yielded coefficient of determination (R2) and mean absolute error (MAE) values of 0.942 and 0.583 min, respectively. The model successfully differentiated between LC systems, predicting 54%, 81% and 97% of the test set within ±0.5, ±1 and ±2 min, respectively. Additionally, retention times for an analyte not previously observed by the model were predicted within ±1 min for each LC system. The developed model can be used to predict retention times for all analytes on HighResNPS for each participating laboratory's LC system to further support suspect screening.
Pastorello, G, Trotta, C, Canfora, E, Chu, H, Christianson, D, Cheah, Y-W, Poindexter, C, Chen, J, Elbashandy, A, Humphrey, M, Isaac, P, Polidori, D, Reichstein, M, Ribeca, A, van Ingen, C, Vuichard, N, Zhang, L, Amiro, B, Ammann, C, Arain, MA, Ardö, J, Arkebauer, T, Arndt, SK, Arriga, N, Aubinet, M, Aurela, M, Baldocchi, D, Barr, A, Beamesderfer, E, Marchesini, LB, Bergeron, O, Beringer, J, Bernhofer, C, Berveiller, D, Billesbach, D, Black, TA, Blanken, PD, Bohrer, G, Boike, J, Bolstad, PV, Bonal, D, Bonnefond, J-M, Bowling, DR, Bracho, R, Brodeur, J, Brümmer, C, Buchmann, N, Burban, B, Burns, SP, Buysse, P, Cale, P, Cavagna, M, Cellier, P, Chen, S, Chini, I, Christensen, TR, Cleverly, J, Collalti, A, Consalvo, C, Cook, BD, Cook, D, Coursolle, C, Cremonese, E, Curtis, PS, D’Andrea, E, da Rocha, H, Dai, X, Davis, KJ, De Cinti, B, de Grandcourt, A, De Ligne, A, De Oliveira, RC, Delpierre, N, Desai, AR, Di Bella, CM, di Tommasi, P, Dolman, H, Domingo, F, Dong, G, Dore, S, Duce, P, Dufrêne, E, Dunn, A, Dušek, J, Eamus, D, Eichelmann, U, ElKhidir, HAM, Eugster, W, Ewenz, CM, Ewers, B, Famulari, D, Fares, S, Feigenwinter, I, Feitz, A, Fensholt, R, Filippa, G, Fischer, M, Frank, J, Galvagno, M, Gharun, M, Gianelle, D, Gielen, B, Gioli, B, Gitelson, A, Goded, I, Goeckede, M, Goldstein, AH, Gough, CM, Goulden, ML, Graf, A, Griebel, A, Gruening, C, Grünwald, T, Hammerle, A, Han, S, Han, X, Hansen, BU, Hanson, C, Hatakka, J, He, Y, Hehn, M, Heinesch, B, Hinko-Najera, N, Hörtnagl, L, Hutley, L, Ibrom, A, Ikawa, H, Jackowicz-Korczynski, M, Janouš, D, Jans, W, Jassal, R, Jiang, S, Kato, T, Khomik, M, Klatt, J, Knohl, A, Knox, S, Kobayashi, H, Koerber, G, Kolle, O, Kosugi, Y, Kotani, A, Kowalski, A, Kruijt, B, Kurbatova, J, Kutsch, WL, Kwon, H, Launiainen, S, Laurila, T, Law, B, Leuning, R, Li, Y, Liddell, M, Limousin, J-M, Lion, M, Liska, AJ, Lohila, A, López-Ballesteros, A, López-Blanco, E, Loubet, B, Loustau, D, Lucas-Moffat, A, Lüers, J, Ma, S, Macfarlane, C, Magliulo, V, Maier, R, Mammarella, I, Manca, G, Marcolla, B, Margolis, HA, Marras, S, Massman, W, Mastepanov, M, Matamala, R, Matthes, JH, Mazzenga, F, McCaughey, H, McHugh, I, McMillan, AMS, Merbold, L, Meyer, W, Meyers, T, Miller, SD, Minerbi, S, Moderow, U, Monson, RK, Montagnani, L, Moore, CE, Moors, E, Moreaux, V, Moureaux, C, Munger, JW, Nakai, T, Neirynck, J, Nesic, Z & et al. 2021, 'Author Correction: The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data', Scientific Data, vol. 8, no. 1, p. 72.
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A Correction to this paper has been published: https://doi.org/10.1038/s41597-021-00851-9.
Pateetin, P, Hutvagner, G, Bajan, S, Padula, MP, McGowan, EM & Boonyaratanakornkit, V 2021, 'Triple SILAC identified progestin-independent and dependent PRA and PRB interacting partners in breast cancer', Scientific Data, vol. 8, no. 1, p. 100.
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AbstractProgesterone receptor (PR) isoforms, PRA and PRB, act in a progesterone-independent and dependent manner to differentially modulate the biology of breast cancer cells. Here we show that the differences in PRA and PRB structure facilitate the binding of common and distinct protein interacting partners affecting the downstream signaling events of each PR-isoform. Tet-inducible HA-tagged PRA or HA-tagged PRB constructs were expressed in T47DC42 (PR/ER negative) breast cancer cells. Affinity purification coupled with stable isotope labeling of amino acids in cell culture (SILAC) mass spectrometry technique was performed to comprehensively study PRA and PRB interacting partners in both unliganded and liganded conditions. To validate our findings, we applied both forward and reverse SILAC conditions to effectively minimize experimental errors. These datasets will be useful in investigating PRA- and PRB-specific molecular mechanisms and as a database for subsequent experiments to identify novel PRA and PRB interacting proteins that differentially mediated different biological functions in breast cancer.
Patel, D, Taudte, RV, Nizio, K, Herok, G, Cranfield, C & Shimmon, R 2021, 'Headspace analysis of E-cigarette fluids using comprehensive two dimensional GC×GC-TOF-MS reveals the presence of volatile and toxic compounds', Journal of Pharmaceutical and Biomedical Analysis, vol. 196, pp. 113930-113930.
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Paudel, KR, Wadhwa, R, Tew, XN, Lau, NJX, Madheswaran, T, Panneerselvam, J, Zeeshan, F, Kumar, P, Gupta, G, Anand, K, Singh, SK, Jha, NK, MacLoughlin, R, Hansbro, NG, Liu, G, Shukla, SD, Mehta, M, Hansbro, PM, Chellappan, DK & Dua, K 2021, 'Rutin loaded liquid crystalline nanoparticles inhibit non-small cell lung cancer proliferation and migration in vitro', Life Sciences, vol. 276, pp. 119436-119436.
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Paul, B, Kysenius, K, Hilton, JB, Jones, MWM, Hutchinson, RW, Buchanan, DD, Rosty, C, Fryer, F, Bush, AI, Hergt, JM, Woodhead, JD, Bishop, DP, Doble, PA, Hill, MM, Crouch, PJ & Hare, DJ 2021, 'An integrated mass spectrometry imaging and digital pathology workflow for objective detection of colorectal tumours by unique atomic signatures', Chemical Science, vol. 12, no. 30, pp. 10321-10333.
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Digital pathology and laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) imaging reveals a unique elemental signature of colorectal cancer.
Paull, NJ, Krix, D, Irga, PJ & Torpy, FR 2021, 'Green wall plant tolerance to ambient urban air pollution', Urban Forestry & Urban Greening, vol. 63, pp. 127201-127201.
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Air pollution exposure can impact plant physiology, morphology and biochemistry, leading to dramatic alterations to plant systems, function and growth. The use of plants for air pollution mitigation is increasing in popularity, particularly in the form of green wall systems, making the identification and classification of pollution sensitive and tolerant species essential. This study aimed to examine the health of common green wall species exposed to ambient air pollution in situ, and thus to identify tolerant species for use in high pollution environments. To do this, 11 plant species were sampled across 15 outdoor green walls, over a 6 month period, and tested for leaf chlorophyll, pH, relative water content and carbon content. Control glasshouse samples were collected simultaneously. Linear mixed models were used to examine patterns in plant health traits across species. Significant differences in plant health between control and in situ samples were observed, however, plant species were not consistent in their responses across health variables. As such, there no clear distinction of the most tolerant species could be made. As most species showed no significant health differences from pollution exposure, it is reasonable to conclude that all test species were able to withstand pollution exposure at the trial sites without any adverse effects.
Payne, M, Bottomley, AL, Och, A, Asmara, AP, Harry, EJ & Ung, AT 2021, 'Synthesis and biological evaluation of 3,5-substituted pyrazoles as possible antibacterial agents', Bioorganic & Medicinal Chemistry, vol. 48, pp. 116401-116401.
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The emergence of multi-drug resistant bacteria has increased the need for novel antibiotics to help overcome what may be considered the greatest threat to modern medicine. Here we report the synthesis of fifteen novel 3,5-diaryl-1H- pyrazoles obtained via one-pot cyclic oxidation of a chalcone and hydrazine-monohydrate. The synthesised pyrazoles were then screened against Staphylococcus aureus and Escherichia coli to determine their antibacterial potential. The results show that compound 7p is bacteriostatic at MIC 8 µg/mL. The compound is non-toxic against healthy mammalian cells, 3T3-L1 at the highest test concentration 50 µg/mL. Furthermore, compound 7p significantly affected bacterial morphogenesis before cell lysis in Bacillus subtilis when treated above the MIC concentration. From the results, a promising lead compound was identified for future development.
Payne, M, Octavia, S, Luu, LDW, Sotomayor-Castillo, C, Wang, Q, Tay, ACY, Sintchenko, V, Tanaka, MM & Lan, R 2021, 'Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds', Microbial Genomics, vol. 7, no. 6.
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Salmonella enterica serovar Typhimurium is the leading cause of salmonellosis in Australia, and the ability to identify outbreaks and their sources is vital to public health. Here, we examined the utility of whole-genome sequencing (WGS), including complete genome sequencing with Oxford Nanopore technologies, in examining 105 isolates from an endemic multi-locus variable number tandem repeat analysis (MLVA) type over 5 years. The MLVA type was very homogeneous, with 90 % of the isolates falling into groups with a five SNP cut-off. We developed a new two-step approach for outbreak detection using WGS. The first clustering at a zero single nucleotide polymorphism (SNP) cut-off was used to detect outbreak clusters that each occurred within a 4 week window and then a second clustering with dynamically increased SNP cut-offs were used to generate outbreak investigation clusters capable of identifying all outbreak cases. This approach offered optimal specificity and sensitivity for outbreak detection and investigation, in particular of those caused by endemic MLVA types or clones with low genetic diversity. We further showed that inclusion of complete genome sequences detected no additional mutational events for genomic outbreak surveillance. Phylogenetic analysis found that the MLVA type was likely to have been derived recently from a single source that persisted over 5 years, and seeded numerous sporadic infections and outbreaks. Our findings suggest that SNP cut-offs for outbreak cluster detection and public-health surveillance should be based on the local diversity of the relevant strains over tim...
Pedersen, JL, Barry, SE, Bokil, NJ, Ellis, M, Yang, Y, Guan, G, Wang, X, Faiz, A, Britton, WJ & Saunders, BM 2021, 'High sensitivity and specificity of a 5‐analyte protein and microRNA biosignature for identification of active tuberculosis', Clinical & Translational Immunology, vol. 10, no. 6, pp. 1-12.
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AbstractObjectivesNon‐sputum‐based tests to accurately identify active tuberculosis (TB) disease and monitor response to therapy are urgently needed. This study examined the biomarker capacity of a panel of plasma proteins alone, and in conjunction with a previously identified miRNA signature, to identify active TB disease.MethodsThe expression of nine proteins (IP‐10, MCP‐1, sTNFR1, RANTES, VEGF, IL‐6, IL‐10, TNF and Eotaxin) was measured in the plasma of 100 control subjects and 100 TB patients, at diagnosis (treatment naïve) and over the course of treatment (1‐, 2‐ and 6‐month intervals). The diagnostic performance of the nine proteins alone, and with the miRNA, was assessed.ResultsSix proteins were significantly up‐regulated in the plasma of TB patients at diagnosis compared to controls. Receiver operator characteristic curve analysis demonstrated that IP‐10 with an AUC = 0.874, sensitivity of 75% and specificity of 87% was the best single biomarker candidate to distinguish TB patients from controls. IP‐10 and IL‐6 levels fell significantly within one month of commencing treatment and may have potential as indicators of a positive response to therapy. The combined protein and miRNA panel gave an AUC of 1.00. A smaller panel of only five analytes (IP‐10, miR‐29a, miR‐146a, miR‐99b and miR‐221) showed an AUC = 0.995, sensitivity of 96% and specificity of 97%.ConclusionsA novel combination of miRNA and proteins significantly improves the sensitivity and specificity as a biosignature over single biomarker candidates and may be useful for the development of a non‐sputum test to aid the diagnosis of active TB disease.
Peel, E, Cheng, Y, Djordjevic, JT, O’Meally, D, Thomas, M, Kuhn, M, Sorrell, TC, Huston, WM & Belov, K 2021, 'Koala cathelicidin PhciCath5 has antimicrobial activity, including against Chlamydia pecorum', PLOS ONE, vol. 16, no. 4, pp. e0249658-e0249658.
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Devastating fires in Australia over 2019–20 decimated native fauna and flora, including koalas. The resulting population bottleneck, combined with significant loss of habitat, increases the vulnerability of remaining koala populations to threats which include disease.Chlamydiais one disease which causes significant morbidity and mortality in koalas. The predominant pathogenic species,Chlamydia pecorum, causes severe ocular, urogenital and reproductive tract disease. In marsupials, including the koala, gene expansions of an antimicrobial peptide family known as cathelicidins have enabled protection of immunologically naïve pouch young during early development. We propose that koala cathelicidins are active againstChlamydiaand other bacteria and fungi. Here we describe ten koala cathelicidins, five of which contained full length coding sequences that were widely expressed in tissues throughout the body. Focusing on these five, we investigate their antimicrobial activity against two koalaC.pecorumisolates from distinct serovars; MarsBar and IPTaLE, as well as other bacteria and fungi. One cathelicidin, PhciCath5, inactivatedC.pecorumIPTaLE and MarsBar elementary bodies and significantly reduced the number of inclusions compared to the control (p<0.0001). Despite evidence of cathelicidin expression within tissues known to be infected byChlamydia, natural PhciCath5 concentrations may be inadequatein vivoto prevent or controlC.pecoruminfections in koalas. PhciCath5 also displayed antimicrobial activity against fungi and Gram negative and positive bacteria, including methicillin-resistantStaphylococcus aureus(MRSA). Electrostatic i...
Peneaux, C, Hansbro, PM & Griffin, AS 2021, 'The potential utility of carotenoid‐based coloration as a biomonitor of environmental change', Ibis, vol. 163, no. 1, pp. 20-37.
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In the past 30 years, carotenoid‐based animal signals have been an intense focus of research because they can potentially broadcast an honest reflection of individual reproductive potential. Our understanding of the underpinning physiological functions of carotenoid compounds is still emerging, however. Here, we argue that wildlife researchers and managers interested in assessing the impact of environmental quality on animal populations should be taking advantage of the signalling function of carotenoid‐based morphological traits. Using birds as a model taxonomic group, we build our argument by first reviewing the strong evidence that the expression of avian carotenoid displays provides an integrated measure of a multitude of diet‐ and health‐related parameters. We then present evidence that human‐induced rapid environmental change (HIREC) impacts the expression of carotenoid signals across different critical periods of a bird’s lifetime. Finally, we argue that variation in signal expression across individuals, populations and species could be quantified relatively easily at a global scale by incorporating such measurements into widespread bird ringing activities. Monitoring the expression of carotenoid‐based coloration could help to identify how the environmental factors linked to HIREC can affect avian populations and allow for potentially detrimental effects on biodiversity to be detected prior to demographic change.
Peng, D, Wang, Y, Xian, G, Huete, AR, Huang, W, Shen, M, Wang, F, Yu, L, Liu, L, Xie, Q, Liu, L & Zhang, X 2021, 'Investigation of land surface phenology detections in shrublands using multiple scale satellite data', Remote Sensing of Environment, vol. 252, pp. 112133-112133.
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Shrublands occupy about 13% of the global land surface, contain about one-third of the biodiversity, store about half of the global terrestrial carbon, and provide many ecosystem services to a large amount of world's human population and livestock. Because phenology is a sensitive indicator of the response of shrubland ecosystems to climate change, the alteration of ecosystems following species invasions, and the dynamics of shrubland ecosystem function, biodiversity, and carbon budgets, it is critical to monitor and assess phenological dynamics in shrubland ecosystems. However, most current land surface phenology (LSP) products derived from satellite data do not provide phenology detections in some semiarid shrublands where the amplitude of seasonal vegetation greenness is small. Therefore, we investigated the LSP detection using multiple spatial resolution satellite data and examined the impacts of spatial scales and shrubland ecosystem components (shrub and herb cover) on LSP detections over the western United States. Specifically, greenup onset date (GUD) in shrublands was detected from 30 m Harmonized Landsat and Sentinel-2 (HLS) data and 500 m Visible Infrared Imaging Radiometer Suite (VIIRS) data to quantify scale effects. The GUD spatial patterns were explored with 30 m pixel variations in shrubland ecosystem components. The results show that GUD values varied with percent vegetation cover and shifted to earlier dates with increasing vegetation cover, demonstrating that satellite observations were not able to capture greenup onset until a threshold of green vegetation cover is reached. GUD was mostly undetectable from both HLS and VIIRS pixels with vegetation cover less than 10% and became fully detectable with vegetation covers larger than 50%. Similarly, the differences of GUD between HLS and VIIRS detections also decreased with increased vegetation cover. As a result of high shrubland heterogeneity, GUD from 30 m HLS pixels could be partially...
Perez Gomez, AA, Karmakar, M, Carroll, RJ, Lawley, KS, Amstalden, K, Young, CR, Threadgill, DW, Welsh, CJ & Brinkmeyer-Langford, C 2021, 'Genetic and immunological contributors to virus-induced paralysis', Brain, Behavior, & Immunity - Health, vol. 18, pp. 100395-100395.
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Petrou, K, Nunn, BL, Padula, MP, Miller, DJ & Nielsen, DA 2021, 'Broad scale proteomic analysis of heat-destabilised symbiosis in the hard coral Acropora millepora', Scientific Reports, vol. 11, no. 1, p. 19061.
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AbstractCoral reefs across the globe are threatened by warming oceans. The last few years have seen the worst mass coral bleaching events recorded, with more than one quarter of all reefs irreversibly impacted. Considering the widespread devastation, we need to increase our efforts to understanding the physiological and metabolic shifts underlying the breakdown of this important symbiotic ecosystem. Here, we investigated the proteome (PRIDE accession # PXD011668) of both host and symbionts of the reef-building coralAcropora milleporaexposed to ambient (~ 28 °C) and elevated temperature (~ 32 °C for 2 days, following a five-day incremental increase) and explored associated biomolecular changes in the symbiont, with the aim of gaining new insights into the mechanisms underpinning the collapse of the coral symbiosis. We identified 1,230 unique proteins (774 host and 456 symbiont) in the control and thermally stressed corals, of which 107 significantly increased and 125 decreased in abundance under elevated temperature relative to the control. Proteins involved in oxidative stress and proteolysis constituted 29% of the host proteins that increased in abundance, with evidence of impairment to endoplasmic reticulum and cytoskeletal regulation proteins. In the symbiont, we detected a decrease in proteins responsible for photosynthesis and energy production (33% of proteins decreased in abundance), yet minimal signs of oxidative stress or proteolysis. Lipid stores increased > twofold despite reduction in photosynthesis, suggesting reduced translocation of carbon to the host. There were significant changes in proteins related to symbiotic state, including proteins linked to nitrogen metabolism in the host and the V-ATPase (-0.6 fold change) known to control symbiosome acidity. These results highlight key differences in host and symbiont proteomic adjustments under elevated temperature and identify tw...
Pettit, T, Torpy, FR, Surawski, NC, Fleck, R & Irga, PJ 2021, 'Effective reduction of roadside air pollution with botanical biofiltration', Journal of Hazardous Materials, vol. 414, pp. 125566-125566.
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Pflugmacher, S, Tallinen, S, Mitrovic, SM, Penttinen, O-P, Kim, Y-J, Kim, S & Esterhuizen, M 2021, 'Case Study Comparing Effects of Microplastic Derived from Bottle Caps Collected in Two Cities on Triticum aestivum (Wheat)', Environments, vol. 8, no. 7, pp. 64-64.
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As plastic has become an integral component of daily life, microplastic has become a ubiquitous, unavoidable constituent of nearly all ecosystems. Besides monitoring the amount and distribution of microplastic in the environment, it is necessary to understand the possible direct effects, especially toxicity and how it is affected by environmental factors where it is discarded. The present study investigated how microplastic derived from high-density polyethylene bottle caps collected in two climatically different cities, i.e., Singapore (tropical rainforest climate) and Lahti, Finland (continental climate), affected the essential agricultural grain crop, Triticum aestivum (L.). Wheat seedlings were exposed to microplastic derived from these collected bottle caps, as well as new and artificially aged caps, for seven days. Morphological parameters, such as root and shoot length and oxidative stress development, were measured. Exposure to microplastic derived from the caps resulted in reduced seedling root and shoot lengths compared to the controls, as well as enhanced lipid peroxidation and catalase activity. With all parameters tested, microplastic derived from Lahti bottle caps exhibited more severe effects than Singapore, which was similar to that elicited by new microplastic. The Singapore microplastic had possibly leached its toxic substances before collection due to accelerated degradation promoted by the prevailing warmer climate conditions.
Pham, AK, Miller, M, Rosenthal, P, Das, S, Weng, N, Jang, S, Kurten, RC, Badrani, J, Doherty, TA, Oliver, B & Broide, DH 2021, 'ORMDL3 expression in ASM regulates hypertrophy, hyperplasia via TPM1 and TPM4, and contractility', JCI Insight, vol. 6, no. 7.
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ORM1-like 3 (ORMDL3) has strong genetic linkage to childhood onset asthma. To determine whether ORMDL3 selective expression in airway smooth muscle (ASM) influences ASM function, we used Cre-loxP techniques to generate transgenic mice (hORMDL3Myh11eGFP-cre), which express human ORMDL3 selectively in smooth muscle cells. In vitro studies of ASM cells isolated from the bronchi of hORMDL3Myh11eGFP-cre mice demonstrated that they developed hypertrophy (quantitated by FACS and image analysis), developed hyperplasia (assessed by BrdU incorporation), and expressed increased levels of tropomysin proteins TPM1 and TPM4. siRNA knockdown of TPM1 or TPM4 demonstrated their importance to ORMDL3-mediated ASM proliferation but not hypertrophy. In addition, ASM derived from hORMDL3Myh11eGFP-cre mice had increased contractility to histamine in vitro, which was associated with increased levels of intracellular Ca2+; increased cell surface membrane Orai1 Ca2+ channels, which mediate influx of Ca2+ into the cytoplasm; and increased expression of ASM contractile genes sarco/endoplasmic reticulum Ca2+ ATPase 2b and smooth muscle 22. In vivo studies of hORMDL3Myh11eGFP-cre mice demonstrated that they had a spontaneous increase in ASM and airway hyperreactivity (AHR). ORMDL3 expression in ASM thus induces changes in ASM (hypertrophy, hyperplasia, increased contractility), which may explain the contribution of ORMDL3 to the development of AHR in childhood onset asthma, which is highly linked to ORMDL3 on chromosome 17q12-21.
Pijning, AE, Blyth, MT, Coote, ML, Passam, F, Chiu, J & Hogg, PJ 2021, 'An alternate covalent form of platelet αIIbβ3 integrin that resides in focal adhesions and has altered function', Blood, vol. 138, no. 15, pp. 1359-1372.
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Abstract The αIIbβ3 integrin receptor coordinates platelet adhesion, activation, and mechanosensing in thrombosis and hemostasis. Using differential cysteine alkylation and mass spectrometry, we have identified a disulfide bond in the αIIb subunit linking cysteines 490 and 545 that is missing in ∼1 in 3 integrin molecules on the resting and activated human platelet surface. This alternate covalent form of αIIbβ3 is predetermined as it is also produced by human megakaryoblasts and baby hamster kidney fibroblasts transfected with recombinant integrin. From coimmunoprecipitation experiments, the alternate form selectively partitions into focal adhesions on the activated platelet surface. Its function was evaluated in baby hamster kidney fibroblast cells expressing a mutant integrin with an ablated C490-C545 disulfide bond. The disulfide mutant integrin has functional outside-in signaling but extended residency time in focal adhesions due to a reduced rate of clathrin-mediated integrin internalization and recycling, which is associated with enhanced affinity of the αIIb subunit for clathrin adaptor protein 2. Molecular dynamics simulations indicate that the alternate covalent form of αIIb requires higher forces to transition from bent to open conformational states that is in accordance with reduced affinity for fibrinogen and activation by manganese ions. These findings indicate that the αIIbβ3 integrin receptor is produced in various covalent forms that have different cell surface distribution and function. The C490, C545 cysteine pair is conserved across all 18 integrin α subunits, and the disulfide bond in the αV and α2 subunits in cultured cells is similarly missing, suggesting that the alternate integrin form and function are also conserved.
Pinkerton, JW, Kim, RY, Koeninger, L, Armbruster, NS, Hansbro, NG, Brown, AC, Jayaraman, R, Shen, S, Malek, N, Cooper, MA, Nordkild, P, Horvat, JC, Jensen, BAH, Wehkamp, J & Hansbro, PM 2021, 'Human β‐defensin‐2 suppresses key features of asthma in murine models of allergic airways disease', Clinical & Experimental Allergy, vol. 51, no. 1, pp. 120-131.
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AbstractBackgroundAsthma is an airway inflammatory disease and a major health problem worldwide. Anti‐inflammatory steroids and bronchodilators are the gold‐standard therapy for asthma. However, they do not prevent the development of the disease, and critically, a subset of asthmatics are resistant to steroid therapy.ObjectiveTo elucidate the therapeutic potential of human β‐defensins (hBD), such as hBD2 mild to moderate and severe asthma.MethodsWe investigated the role of hBD2 in a steroid‐sensitive, house dust mite‐induced allergic airways disease (AAD) model and a steroid‐insensitive model combining ovalbumin‐induced AAD with C muridarum (Cmu) respiratory infection.ResultsIn both models, we demonstrated that therapeutic intranasal application of hBD2 significantly reduced the influx of inflammatory cells into the bronchoalveolar lavage fluid. Furthermore, key type 2 asthma‐related cytokines IL‐9 and IL‐13, as well as additional immunomodulating cytokines, were significantly decreased after administration of hBD2 in the steroid‐sensitive model. The suppression of inflammation was associated with improvements in airway physiology and treatment also suppressed airway hyper‐responsiveness (AHR) in terms of airway resistance and compliance to methacholine challenge.Conclusions and Clinical relevanceThese data indicate that hBD2 reduces the hallmark features and has potential as a new therapeutic agent in allergic and especially steroid‐resistant asthma.
Piotrowski, J, Schmidt, MK, Stiller, B, Poulton, CG & Steel, MJ 2021, 'Picosecond acoustic dynamics in stimulated Brillouin scattering', Optics Letters, vol. 46, no. 12, pp. 2972-2972.
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Recent experiments demonstrating storage of optical pulses in acoustic phonons via stimulated Brillouin scattering raise questions about the spectral and temporal capacities of such protocols and the limitations of the theoretical frameworks routinely used to describe them. We consider the dynamics of photon–phonon scattering induced by optical pulses with temporal widths comparable to the period of acoustic oscillations. We revisit the widely adopted classical formalism of coupled modes and demonstrate its breakdown. We use a simple extension to the formulation and find potentially measurable consequences in the dynamics of Brillouin experiments involving ultrashort pulses.
Platen, E & Tappe, S 2021, 'No-arbitrage concepts in topological vector lattices', Positivity, vol. 25, no. 5, pp. 1853-1898.
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AbstractWe provide a general framework for no-arbitrage concepts in topological vector lattices, which covers many of the well-known no-arbitrage concepts as particular cases. The main structural condition we impose is that the outcomes of trading strategies with initial wealth zero and those with positive initial wealth have the structure of a convex cone. As one consequence of our approach, the concepts NUPBR, NAA$$_1$$1and NA$$_1$$1may fail to be equivalent in our general setting. Furthermore, we derive abstract versions of the fundamental theorem of asset pricing (FTAP), including an abstract FTAP on Banach function spaces, and investigate when the FTAP is warranted in its classical form with a separating measure. We also consider a financial market with semimartingales which does not need to have a numéraire, and derive results which show the links between the no-arbitrage concepts by only using the theory of topological vector lattices and well-known results from stochastic analysis in a sequence of short proofs.
Polerecky, L, Masuda, T, Eichner, M, Rabouille, S, Vancová, M, Kienhuis, MVM, Bernát, G, Bonomi-Barufi, J, Campbell, DA, Claquin, P, Červený, J, Giordano, M, Kotabová, E, Kromkamp, J, Lombardi, AT, Lukeš, M, Prášil, O, Stephan, S, Suggett, D, Zavřel, T & Halsey, KH 2021, 'Temporal Patterns and Intra- and Inter-Cellular Variability in Carbon and Nitrogen Assimilation by the Unicellular Cyanobacterium Cyanothece sp. ATCC 51142', Frontiers in Microbiology, vol. 12, p. 620915.
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Unicellular nitrogen fixing cyanobacteria (UCYN) are abundant members of phytoplankton communities in a wide range of marine environments, including those with rapidly changing nitrogen (N) concentrations. We hypothesized that differences in N availability (N2 vs. combined N) would cause UCYN to shift strategies of intracellular N and C allocation. We used transmission electron microscopy and nanoscale secondary ion mass spectrometry imaging to track assimilation and intracellular allocation of 13C-labeled CO2 and 15N-labeled N2 or NO3 at different periods across a diel cycle in Cyanothece sp. ATCC 51142. We present new ideas on interpreting these imaging data, including the influences of pre-incubation cellular C and N contents and turnover rates of inclusion bodies. Within cultures growing diazotrophically, distinct subpopulations were detected that fixed N2 at night or in the morning. Additional significant within-population heterogeneity was likely caused by differences in the relative amounts of N assimilated into cyanophycin from sources external and internal to the cells. Whether growing on N2 or NO3, cells prioritized cyanophycin synthesis when N assimilation rates were highest. N assimilation in cells growing on NO3 switched from cyanophycin synthesis to protein synthesis, suggesting that once a cyanophycin quota is met, it is bypassed in favor of protein synthesis. Growth on NO3 also revealed that at night, there is a very low level of CO2 assimilation into polysaccharides simultaneous with their catabolism for protein synthesis. This study revealed multiple, detailed mechanisms underlying C and N management in Cyanothece that facilita...
Polonchuk, L, Surija, L, Lee, MH, Sharma, P, Liu Chung Ming, C, Richter, F, Ben-Sefer, E, Rad, MA, Mahmodi Sheikh Sarmast, H, Shamery, WA, Tran, HA, Vettori, L, Haeusermann, F, Filipe, EC, Rnjak-Kovacina, J, Cox, T, Tipper, J, Kabakova, I & Gentile, C 2021, 'Towards engineering heart tissues from bioprinted cardiac spheroids', Biofabrication, vol. 13, no. 4, pp. 045009-045009.
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Abstract Current in vivo and in vitro models fail to accurately recapitulate the human heart microenvironment for biomedical applications. This study explores the use of cardiac spheroids (CSs) to biofabricate advanced in vitro models of the human heart. CSs were created from human cardiac myocytes, fibroblasts and endothelial cells (ECs), mixed within optimal alginate/gelatin hydrogels and then bioprinted on a microelectrode plate for drug testing. Bioprinted CSs maintained their structure and viability for at least 30 d after printing. Vascular endothelial growth factor (VEGF) promoted EC branching from CSs within hydrogels. Alginate/gelatin-based hydrogels enabled spheroids fusion, which was further facilitated by addition of VEGF. Bioprinted CSs contracted spontaneously and under stimulation, allowing to record contractile and electrical signals on the microelectrode plates for industrial applications. Taken together, our findings indicate that bioprinted CSs can be used to biofabricate human heart tissues for long term in vitro testing. This has the potential to be used to study biochemical, physiological and pharmacological features of human heart tissue.
Popkova, AA, Antropov, IM, Fröch, JE, Kim, S, Aharonovich, I, Bessonov, VO, Solntsev, AS & Fedyanin, AA 2021, 'Optical Third-Harmonic Generation in Hexagonal Boron Nitride Thin Films', ACS Photonics, vol. 8, no. 3, pp. 824-831.
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Hexagonal boron nitride (hBN) is a layered material that exhibits remarkable optical features in the UV, visible, and IR ranges, attractive for applications in modern photonics. Being transparent in a wide spectral range, hBN is now considered an important building block for novel integrated photonic platforms, thus requiring the study of its optical properties. In this work, we report on the measurements of hBN optical cubic nonlinearity χ(3) equal to 8.4 × 10-21 m2/V2 by observing the third-harmonic generation for 1080 nm pump wavelength from mechanically exfoliated hBN flakes with thicknesses varying from 5 to 170 nm. The third-order susceptibility of hBN is close to that of Si3N4 highlighting the potential of hBN for nonlinear applications.
Popovic, A, Morelato, M, Roux, C & Beavis, A 2021, 'Interpreting the link value of similarity scores between illicit drug specimens through a dual approach, featuring deterministic and Bayesian frameworks', Forensic Science International, vol. 319, pp. 110651-110651.
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Illicit drug trafficking and in particular amphetamine-type stimulants continue to be a major problem in Australia. With the constant evolution of illicit drugs markets, it is necessary to gain as much knowledge about them to disrupt or reduce their impact. Illicit drug specimens can be analysed to generate forensic intelligence and understand criminal activities. Part of this analysis involves the evaluation of similarity scores between illicit drug profiles to interpret the link value. Most studies utilise one of two prominent score evaluation approaches, i.e. deterministic or Bayesian. In previous work, the notion of a dual approach was suggested, which emphasised the complementary nature of the two mentioned approaches. The aim of this study was to assess the operational capability of a dual approach in evaluating similarity scores between illicit drug profiles. Utilising a practical example, link values were generated individually from both approaches, then compared in parallel. As a result, it was possible to generate more informed hypotheses, relating to specimen linkage, due to the greater wealth of information available from the two approaches working concurrently. Additionally, it was shown that applying only one approach led to less information being generated during analysis as well as potentially important links between illicit drug specimens being missed.
Pouwels, SD, Hesse, L, Wu, X, Allam, VSRR, van Oldeniel, D, Bhiekharie, LJ, Phipps, S, Oliver, BG, Gosens, R, Sukkar, MB & Heijink, IH 2021, 'LL-37 and HMGB1 induce alveolar damage and reduce lung tissue regeneration via RAGE', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 321, no. 4, pp. L641-L652.
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The receptor for advanced glycation end-products (RAGE) has been implicated in the pathophysiology of chronic obstructive pulmonary disease (COPD). However, it is still unknown whether RAGE directly contributes to alveolar epithelial damage and abnormal repair responses. We hypothesize that RAGE activation not only induces lung tissue damage but also hampers alveolar epithelial repair responses. The effects of the RAGE ligands LL-37 and HMGB1 were examined on airway inflammation and alveolar tissue damage in wild-type and RAGE-deficient mice and on lung damage and repair responses using murine precision cut lung slices (PCLS) and organoids. In addition, their effects were studied on the repair response of human alveolar epithelial A549 cells, using siRNA knockdown of RAGE and treatment with the RAGE inhibitor FPS-ZM1. We observed that intranasal installation of LL-37 and HMGB1 induces RAGE-dependent inflammation and severe alveolar tissue damage in mice within 6 h, with stronger effects in a mouse strain susceptible for emphysema compared with a nonsusceptible strain. In PCLS, RAGE inhibition reduced the recovery from elastase-induced alveolar tissue damage. In organoids, RAGE ligands reduced the organoid-forming efficiency and epithelial differentiation into pneumocyte-organoids. Finally, in A549 cells, we confirmed the role of RAGE in impaired repair responses upon exposure to LL-37. Together, our data indicate that activation of RAGE by its ligands LL-37 and HMGB1 induces acute lung tissue damage and that this impedes alveolar epithelial repair, illustrating the therapeutic potential of RAGE inhibitors for lung tissue repair in emphysema.
Pouwels, SD, Wiersma, VR, Fokkema, IE, Berg, M, ten Hacken, NHT, van den Berge, M, Heijink, I & Faiz, A 2021, 'Acute cigarette smoke‐induced eQTL affects formyl peptide receptor expression and lung function', Respirology, vol. 26, no. 3, pp. 233-240.
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ABSTRACTBackground and objectiveCigarette smoking is one of the most prevalent causes of preventable deaths worldwide, leading to chronic diseases, including chronic obstructive pulmonary disease (COPD). Cigarette smoke is known to induce significant transcriptional modifications throughout the respiratory tract. However, it is largely unknown how genetic profiles influence the smoking‐related transcriptional changes and how changes in gene expression translate into altered alveolar epithelial repair responses.MethodsWe performed a candidate‐based acute cigarette smoke‐induced eQTL study, investigating the association between SNP and differential gene expression of FPR family members in bronchial epithelial cells isolated 24 h after smoking and after 48 h without smoking. The effects FPR1 on lung epithelial integrity and repair upon damage in the presence and absence of cigarette smoke were studied in CRISPR‐Cas9‐generated lung epithelial knockout cells.ResultsOne significant (FDR < 0.05) inducible eQTL (rs3212855) was identified that induced a >2‐fold change in gene expression. The minor allele of rs3212855 was associated with significantly higher gene expression of FPR1, FPR2 and FPR3 upon smoking. Importantly, the minor allele of rs3212855 was also associated with lower lung function. Alveolar epithelial FPR1 knockout cells were protected against CSE‐induced reduction in repair capacity upon wounding.ConclusionWe identified a novel smoking‐related inducible eQTL that is associated with a smoke‐induced increase in the expression of FPR1, FPR2 and FPR3, and with lowered lung function. in vitro FPR1 down‐regulation protects against smoke‐induced reduction in lung epithelial repair.
Pradhan, NC, Sahoo, PK, Kushwaha, DK, Mani, I, Srivastava, A, Sagar, A, Kumari, N, Sarkar, SK & Makwana, Y 2021, 'A Novel Approach for Development and Evaluation of LiDAR Navigated Electronic Maize Seeding System Using Check Row Quality Index', Sensors, vol. 21, no. 17, pp. 5934-5934.
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Crop geometry plays a vital role in ensuring proper plant growth and yield. Check row planting allows adequate space for weeding in both direction and allowing sunlight down to the bottom of the crop. Therefore, a light detection and ranging (LiDAR) navigated electronic seed metering system for check row planting of maize seeds was developed. The system is comprised of a LiDAR-based distance measurement unit, electronic seed metering mechanism and a wireless communication system. The electronic seed metering mechanism was evaluated in the laboratory for five different cell sizes (8.80, 9.73, 10.82, 11.90 and 12.83 mm) and linear cell speed (89.15, 99.46, 111.44, 123.41 and 133.72 mm·s−1). The research shows the optimised values for the cell size and linear speed of cell were found to be 11.90 mm and 99.46 mm·s−1 respectively. A light dependent resistor (LDR) and light emitting diode (LED)-based seed flow sensing system was developed to measure the lag time of seed flow from seed metering box to bottom of seed tube. The average lag time of seed fall was observed as 251.2 ± 5.39 ms at an optimised linear speed of cell of 99.46 mm·s−1 and forward speed of 2 km·h−1. This lag time was minimized by advancing the seed drop on the basis of forward speed of tractor, lag time and targeted position. A check row quality index (ICRQ) was developed to evaluate check row planter. While evaluating the developed system at different forward speeds (i.e., 2, 3 and 5 km·h−1), higher standard deviation (14.14%) of check row quality index was observed at forward speed of 5 km·h−1.
Prasad, E, Barash, M, Hitchcock, C, van Oorschot, RAH, Raymond, J, McNevin, D & Gunn, P 2021, 'Evaluation of soaking to recover trace DNA from fired cartridge cases', Australian Journal of Forensic Sciences, vol. 53, no. 5, pp. 512-522.
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© 2020, © 2020 Australian Academy of Forensic Sciences. The recovery of trace DNA from cartridge cases is of common interest across many jurisdictions. Soaking offers improved profiling success rates over traditional methods. We evaluated the effects of firing, calibre, and metal composition on controlled and handled DNA samples utilizing a soaking method. Our results show that firing decreases the quantities of DNA recoverable from cartridge cases and higher quantities of DNA are recoverable from nickel ammunition compared to brass. In spiked samples, calibre of ammunition had no significant effect on DNA recovery. Despite slight to moderate DNA degradation and variable profiling success rates, spiked unfired and fired nickel cartridges resulted in more usable profiles than brass cartridges. These findings can aid in triaging the types of ammunition subjected to DNA testing.
Prasher, P, Sharma, M, Mehta, M, Satija, S, Aljabali, AA, Tambuwala, MM, Anand, K, Sharma, N, Dureja, H, Jha, NK, Gupta, G, Gulati, M, Singh, SK, Chellappan, DK, Paudel, KR, Hansbro, PM & Dua, K 2021, 'Current-status and applications of polysaccharides in drug delivery systems', Colloid and Interface Science Communications, vol. 42, pp. 100418-100418.
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The polysaccharide-based advanced drug delivery system owing to their biocompatibility, ability to encapsulate the drug molecules in their interspaces, and ability to achieve a controlled release of the cargo drug molecules result in improved drug pharmacokinetics. The drug-loaded polysaccharides possess ability to evade the multidrug-resistant microbial efflux pumps by aggregation effect, whereas the drug loaded polysaccharide-fabricated metal nanoparticles present an exceptional candidature for effectively transporting the drug molecules across the membrane barriers while enabling the theranostic applications at the same time. The biodegradability of polysaccharide based drug delivery systems ensure a sustained release of the encapsulated drug molecules, which minimizes the side effects caused by a burst release of the cargo therapeutics. These drug delivery systems proved highly beneficial for the NSAIDs that otherwise manifest ulcerogenic effect in the gastrointestinal tract. The large surface area of polysaccharides further provide a higher drug-loading capacity, which maintains the optimal concentration of the cargo drug at the target sites. The emerging applications of biodegradable polysaccharides in the designing of multicompartmental microspheres revolutionized tissue engineering, multi drug delivery, and cell culturing technologies. The present review deals with the current-status of polysaccharides as advanced drug delivery systems.
Prates-Syed, WA, Chaves, LCS, Crema, KP, Vuitika, L, Lira, A, Côrtes, N, Kersten, V, Guimarães, FEG, Sadraeian, M, Barroso da Silva, FL, Cabral-Marques, O, Barbuto, JAM, Russo, M, Câmara, NOS & Cabral-Miranda, G 2021, 'VLP-Based COVID-19 Vaccines: An Adaptable Technology against the Threat of New Variants', Vaccines, vol. 9, no. 12, pp. 1409-1409.
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Virus-like particles (VLPs) are a versatile, safe, and highly immunogenic vaccine platform. Recently, there are developmental vaccines targeting SARS-CoV-2, the causative agent of COVID-19. The COVID-19 pandemic affected humanity worldwide, bringing out incomputable human and financial losses. The race for better, more efficacious vaccines is happening almost simultaneously as the virus increasingly produces variants of concern (VOCs). The VOCs Alpha, Beta, Gamma, and Delta share common mutations mainly in the spike receptor-binding domain (RBD), demonstrating convergent evolution, associated with increased transmissibility and immune evasion. Thus, the identification and understanding of these mutations is crucial for the production of new, optimized vaccines. The use of a very flexible vaccine platform in COVID-19 vaccine development is an important feature that cannot be ignored. Incorporating the spike protein and its variations into VLP vaccines is a desirable strategy as the morphology and size of VLPs allows for better presentation of several different antigens. Furthermore, VLPs elicit robust humoral and cellular immune responses, which are safe, and have been studied not only against SARS-CoV-2 but against other coronaviruses as well. Here, we describe the recent advances and improvements in vaccine development using VLP technology.
Prosser, C, Gresty, K, Ellis, J, Meyer, W, Anderson, K, Lee, R & Cheng, Q 2021, 'Plasmodium falciparum Histidine-Rich Protein 2 and 3 Gene Deletions in Strains from Nigeria, Sudan, and South Sudan', Emerging Infectious Diseases, vol. 27, no. 2, pp. 471-479.
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Deletion of histidine-rich protein genes pfhrp2/3 in Plasmodium falciparum causes infections to go undetected by HRP2-based malaria rapid diagnostic tests. We analyzed P. falciparum malaria cases imported to Australia (n = 210, collected 2010-2018) for their pfhrp2/3 status. We detected gene deletions in patients from 12 of 25 countries. We found >10% pfhrp2-deletion levels in those from Nigeria (13.3%, n = 30), Sudan (11.2%, n = 39), and South Sudan (17.7%, n = 17) and low levels of pfhrp3 deletion from Sudan (3.6%) and South Sudan (5.9%). No parasites with pfhrp2/3 double deletions were detected. Microsatellite typing of parasites from Nigeria, Sudan, and South Sudan revealed low relatedness among gene-deleted parasites, indicating independent emergences. The gene deletion proportions signify a risk of false-negative HRP2-RDT results. This study's findings warrant surveillance to determine whether the prevalence of gene-deleted parasites justifies switching malaria rapid diagnostic tests in Nigeria, Sudan, and South Sudan.
Qadir, Z, Khan, SI, Khalaji, E, Munawar, HS, Al-Turjman, F, Mahmud, MAP, Kouzani, AZ & Le, K 2021, 'Predicting the energy output of hybrid PV–wind renewable energy system using feature selection technique for smart grids', Energy Reports, vol. 7, pp. 8465-8475.
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In the current technological era, predicting the power and energy output based on the changing weather factors play an important role in the economic growth of the renewable energy sector. Unlike traditional fossil fuel-based resources, renewable energy sources potentially play a pivotal role in sustaining a country's economy and improving the quality of life. As our planet is nowadays facing serious challenges due to climate change and global warming, this research could be effective to achieve good prediction accuracy in smart grids using different weather conditions. In the current study, different machine learning models are compared to estimate power and energy of hybrid photovoltaic (PV)-wind renewable energy systems using seven weather factors that have a significant impact on the output of the PV–wind renewable energy system. This study classified the machine learning model which could be potentially useful and efficient to predict energy and power. The historic hourly data is processed with and without data manipulation. While data manipulations are carried out using recursive feature elimination using cross-validation (RFECV). The data is trained using artificial neural network (ANN) regressors and correlations between different features within the dataset are identified. The main aim is to find meaningful patterns that could help statistical learning models train themselves based on these usage patterns. The results suggest that opting feature selection technique using linear regression model outperforms all the other models in all evaluation metrics having to mean squared error (MSE) of 0.000000104, mean absolute error (MAE) of 0.00083, R2 of 99.6%, and computation time of 0.02 s The results investigated depict that the sustainable computational scheme introduced has vast potential to enhance smart grids efficiency by predicting the energy produced by renewable energy systems.
Qamar, A, Iqbal, S, Ahmad, S, Kouzani, AZ & Mahmud, MAP 2021, 'Configuration Detection of Grounding Grid: Static Electric Field Based Nondestructive Technique', IEEE Access, vol. 9, pp. 132888-132896.
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Qashlan, A, Nanda, P, He, X & Mohanty, M 2021, 'Privacy-Preserving Mechanism in Smart Home Using Blockchain', IEEE Access, vol. 9, pp. 103651-103669.
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The IoT, or Internet of Things has been a major talking point amongst technology enthusiasts in recent years. The internet of thing (IoT) has been emerged and evolved rapidly, making the world's fabric around us smarter and more responsive. The smart home uses one such transformation of IoT, which seems to be the wave of the future. However, with the increasing wide adoption of IoT, data security, and privacy concerns about how our data is collected and shared with others, has also risen. To solve these challenges, an approach to data privacy and security in a smart home using blockchain technology is proposed in this paper. We propose authentication scheme that combines attribute-based access control with smart contracts and edge computing to create a secure framework for IoT devices in smart home systems. The edge server adds scalability to the system by offloading heavy processing activities and using a differential privacy method to aggregate data to the cloud securely and privately. We present several aspects of testing and implementing smart contracts, the differential private stochastic gradient descent algorithm, and system architecture and design. We demonstrate the efficacy of our proposed system by fully examining its security and privacy goals in terms of confidentiality, integrity, and availability. Our framework achieves desired security and privacy goals and is resilient against modification, DoS attacks, data mining and linkage attacks. Finally, we undertake a performance evaluation to demonstrate the proposed scheme's feasibility and efficiency.
Qi, Y, Li, Q-J, Wu, Y, Bao, S-J, Li, C, Chen, Y, Wang, G & Xu, M 2021, 'A Fe3N/carbon composite electrocatalyst for effective polysulfides regulation in room-temperature Na-S batteries', Nature Communications, vol. 12, no. 1, p. 6347.
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AbstractThe practical application of room-temperature Na-S batteries is hindered by the low sulfur utilization, inadequate rate capability and poor cycling performance. To circumvent these issues, here, we propose an electrocatalyst composite material comprising of N-doped nanocarbon and Fe3N. The multilayered porous network of the carbon accommodates large amounts of sulfur, decreases the detrimental effect of volume expansion, and stabilizes the electrodes structure during cycling. Experimental and theoretical results testify the Fe3N affinity to sodium polysulfides via Na-N and Fe-S bonds, leading to strong adsorption and fast dissociation of sodium polysulfides. With a sulfur content of 85 wt.%, the positive electrode tested at room-temperature in non-aqueous Na metal coin cell configuration delivers a reversible capacity of about 1165 mA h g−1 at 167.5 mA g−1, satisfactory rate capability and stable capacity of about 696 mA h g−1 for 2800 cycles at 8375 mA g−1.
Quan, DH, Counoupas, C, Nagalingam, G, Pinto, R, Petrovsky, N, Britton, WJ & Triccas, JA 2021, 'Advax adjuvant formulations promote protective immunity against aerosol Mycobacterium tuberculosis in the absence of deleterious inflammation and reactogenicity', Vaccine, vol. 39, no. 14, pp. 1990-1996.
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Quince, C, Nurk, S, Raguideau, S, James, R, Soyer, OS, Summers, JK, Limasset, A, Eren, AM, Chikhi, R & Darling, AE 2021, 'STRONG: metagenomics strain resolution on assembly graphs', Genome Biology, vol. 22, no. 1, p. 214.
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AbstractWe introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.
Quinn, AW, Phillips, CR, Violi, JP, Steele, JR, Johnson, MS, Westerhausen, MT & Rodgers, KJ 2021, 'β-Methylamino-L-alanine-induced protein aggregation in vitro and protection by L-serine', Amino Acids, vol. 53, no. 9, pp. 1351-1359.
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The cyanobacterial non-protein amino acid α-amino-β-methylaminopropionic acid, more commonly known as BMAA, was first discovered in the seeds of the ancient gymnosperm Cycad circinalis (now Cycas micronesica Hill). BMAA was linked to the high incidence of neurological disorders on the island of Guam first reported in the 1950s. BMAA still attracts interest as a possible causative factor in amyotrophic lateral sclerosis (ALS) following the identification of ALS disease clusters associated with living in proximity to lakes with regular cyanobacterial blooms. Since its discovery, BMAA toxicity has been the subject of many in vivo and in vitro studies. A number of mechanisms of toxicity have been proposed including an agonist effect at glutamate receptors, competition with cysteine for transport system xc_ and other mechanisms capable of generating cellular oxidative stress. In addition, a wide range of studies have reported effects related to disturbances in proteostasis including endoplasmic reticulum stress and activation of the unfolded protein response. In the present studies we examine the effects of BMAA on the ubiquitin-proteasome system (UPS) and on chaperone-mediated autophagy (CMA) by measuring levels of ubiquitinated proteins and lamp2a protein levels in a differentiated neuronal cell line exposed to BMAA. The BMAA induced increases in oxidised proteins and the increase in CMA activity reported could be prevented by co-administration of L-serine but not by the two antioxidants examined. These data provide further evidence of a protective role for L-serine against the deleterious effects of BMAA.
Quiroz, M, Tran, M-N, Villani, M, Kohn, R & Dang, K-D 2021, 'The Block-Poisson Estimator for Optimally Tuned Exact Subsampling MCMC', Journal of Computational and Graphical Statistics, vol. 30, no. 4, pp. 877-888.
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R. Cardoso, B, Hare, DJ & Macpherson, H 2021, 'Sex-dependent association between selenium status and cognitive performance in older adults', European Journal of Nutrition, vol. 60, no. 2, pp. 1153-1159.
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Rabouille, S, Campbell, DA, Masuda, T, Zavřel, T, Bernát, G, Polerecky, L, Halsey, K, Eichner, M, Kotabová, E, Stephan, S, Lukeš, M, Claquin, P, Bonomi-Barufi, J, Lombardi, AT, Červený, J, Suggett, DJ, Giordano, M, Kromkamp, JC & Prášil, O 2021, 'Electron & Biomass Dynamics of Cyanothece Under Interacting Nitrogen & Carbon Limitations', Frontiers in Microbiology, vol. 12, pp. 1-21.
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Marine diazotrophs are a diverse group with key roles in biogeochemical fluxes linked to primary productivity. The unicellular, diazotrophic cyanobacterium Cyanothece is widely found in coastal, subtropical oceans. We analyze the consequences of diazotrophy on growth efficiency, compared to NO3–-supported growth in Cyanothece, to understand how cells cope with N2-fixation when they also have to face carbon limitation, which may transiently affect populations in coastal environments or during blooms of phytoplankton communities. When grown in obligate diazotrophy, cells face the double burden of a more ATP-demanding N-acquisition mode and additional metabolic losses imposed by the transient storage of reducing potential as carbohydrate, compared to a hypothetical N2 assimilation directly driven by photosynthetic electron transport. Further, this energetic burden imposed by N2-fixation could not be alleviated, despite the high irradiance level within the cultures, because photosynthesis was limited by the availability of dissolved inorganic carbon (DIC), and possibly by a constrained capacity for carbon storage. DIC limitation exacerbates the costs on growth imposed by nitrogen fixation. Therefore, the competitive efficiency of diazotrophs could be hindered in areas with insufficient renewal of dissolved gases and/or with intense phytoplankton biomass that both decrease available light energy and draw the DIC level down.
Rädecker, N, Pogoreutz, C, Gegner, HM, Cárdenas, A, Roth, F, Bougoure, J, Guagliardo, P, Wild, C, Pernice, M, Raina, J-B, Meibom, A & Voolstra, CR 2021, 'Heat stress destabilizes symbiotic nutrient cycling in corals', Proceedings of the National Academy of Sciences, vol. 118, no. 5, pp. e2022653118-e2022653118.
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Significance Ocean warming is causing repeated mass coral bleaching, leading to catastrophic losses of coral reefs worldwide. Our ability to slow or revert this decline is hampered by an incomplete understanding of the processes underlying the breakdown of the coral–algal symbiosis. Here, we show that heat stress destabilizes the nutrient cycling between corals and their endosymbiotic algae long before bleaching becomes apparent. Notably, increased metabolic energy demands shift the coral–algal symbiosis from a nitrogen- to a carbon-limited state, reducing translocation and recycling of photosynthetic carbon. This effectively undermines the ecological advantage of harboring algal symbionts and directly contributes to the breakdown of the coral–algal symbiosis during heat stress.
Radfar, P, Bazaz, SR, Mirakhorli, F & Warkiani, ME 2021, 'The Role of 3D Printing in the Fight Against Covid-19 Outbreak', Journal of 3D Printing in Medicine, vol. 5, no. 1, pp. 51-60.
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Along with the COVID-19 pandemic, urgent needs for medical and specialized products, especially personal protective equipment, has been overwhelming. The conventional production line of medical devices has been challenged by excessive global demand, and the need for an easy, low-cost and rapid fabrication method is felt more than ever. In a scramble to address this shortfall, manufacturers referred to additive manufacturing or 3D printing to fill the gap and increase the production line of medical devices. Various previously/conventionally fabricated designs have been modified and redesigned to suit the 3D printing requirement to fight against COVID-19. In this perspective, various designs accommodated for the current worldwide outbreak of COVID-19 are discussed and how 3D printing could help the global community against the current and future conditions has been explored.
Raes, EJ, Karsh, K, Sow, SLS, Ostrowski, M, Brown, MV, van de Kamp, J, Franco-Santos, RM, Bodrossy, L & Waite, AM 2021, 'Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries', Nature Communications, vol. 12, no. 1, pp. 11-12.
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AbstractGlobal oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.
Rafeek, AD, Choi, G & Evans, LA 2021, 'Controlled synthesis of dicalcium phosphate dihydrate (DCPD) from metastable solutions: insights into pathogenic calcification', Journal of Materials Science: Materials in Medicine, vol. 32, no. 12.
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AbstractCalcium phosphate (CaP) compounds may occur in the body as abnormal pathogenic phases in addition to their normal occurrence as bones and teeth. Dicalcium phosphate dihydrate (DCPD; CaPO4·2H2O), along with other significant CaP phases, have been observed in pathogenic calcifications such as dental calculi, kidney stones and urinary stones. While other studies have shown that polar amino acids can inhibit the growth of CaPs, these studies have mainly focused on hydroxyapatite (HAp; Ca10(PO4)6(OH)2) formation from highly supersaturated solutions, while their effects on DCPD nucleation and growth from metastable solutions have been less thoroughly explored. By further elucidating the mechanisms of DCPD formation and the influence of amino acids on those mechanisms, insights may be gained into ways that amino acids could be used in treatment and prevention of unwanted calcifications. The current study involved seeded growth of DCPD from metastable solutions at constant pH in the presence of neutral, acidic and phosphorylated amino acid side chains. As a comparison, solutions were also seeded with calcium pyrophosphate (CPP; Ca2P2O7), a known calcium phosphate inhibitor. The results show that polar amino acids inhibit DCPD growth; this likely occurs due to electrostatic interactions between amino acid side groups and charged DCPD surfaces. Phosphoserine had the greatest inhibitory ability of the amino acids tested, with an effect equal to that of CPP. Clustering of DCPD crystals giving rise to a “chrysanthemum-like” morphology was noted with glutamic acid. This study concludes that molecules containing an increased number of polar side groups will enhance the inhibition of DCPD seeded growth from metastable solutions.
Rafi, MAA, Jaman, MSK, Hasan, MN, Islam, MR, Mahmud, MAP, Kouzani, AZ & Nahid, A-A 2021, 'Renewable Energy-based Hybrid Microgrid for Economically Effective Coastal Electrification', IEEE Transactions on Applied Superconductivity, vol. 31, no. 8, pp. 1-5.
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Rahman, MA, Islam, MJ, Islam, MR & Mahmud, MAP 2021, 'Strain Dependent Performance Analysis of InGaN Multi-junction Solar Cell', Transactions on Electrical and Electronic Materials, vol. 22, no. 6, pp. 833-842.
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Rangsinth, P, Sillapachaiyaporn, C, Nilkhet, S, Tencomnao, T, Ung, AT & Chuchawankul, S 2021, 'Mushroom-derived bioactive compounds potentially serve as the inhibitors of SARS-CoV-2 main protease: An in silico approach', Journal of Traditional and Complementary Medicine, vol. 11, no. 2, pp. 158-172.
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Raoufi, MA, Joushani, HAN, Razavi Bazaz, S, Ding, L, Asadnia, M & Ebrahimi Warkiani, M 2021, 'Effects of sample rheology on the equilibrium position of particles and cells within a spiral microfluidic channel', Microfluidics and Nanofluidics, vol. 25, no. 9, pp. 1-13.
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Elasto-inertial migration in non-Newtonian fluids is a rapidly growing field with tremendous potentials for manipulating micron to submicron particles. Previous research attempts were mainly carried out in straight channels due to the complexity of particle migration, solution tuning, and data analysis in elasto-inertial microfluidics. Consequently, the combined effects of Dean drag force and solution rheology on coupled Dean drag elasto-inertial focusing phenomena have not been carefully analyzed. This study delved thoroughly into the combined effects of solution rheology and Dean drag force on elasto-inertial focusing of particles and cells within a spiral microchannel. Polyethylene oxide (PEO) of 1MDa, 2MDa, and 4MDa molecular weights were used to prepare 250, 500, and 1000 ppm non-Newtonian solutions to investigate the focusing behavior of particles and cells over a wide range of flow rates and solution rheologies. Dean coupled elasto-inertial effects were systematically investigated to demonstrate its potentials for position-adjustable and size-tunable particle and cell focusing phenomenon. Various cells and microbeads with diameters ranging from 1 to 17 μm were employed to carefully study the equilibrium position, focusing band, and migration behavior under different elastic, inertial, and Dean conditions. Following the focusing, cell viability, morphology, and growth rate were evaluated which showed cells remained undamaged from viscosity, shear rate, and chemical properties of PEO solutions. We are of the opinion that the current study can provide scientists with a better understanding of focusing phenomena in viscoelastic fluids within spiral microfluidic channels.
Raymond, JS, Rehn, S, Hoyos, CM & Bowen, MT 2021, 'The influence of oxytocin-based interventions on sleep-wake and sleep-related behaviour and neurobiology: A systematic review of preclinical and clinical studies', Neuroscience & Biobehavioral Reviews, vol. 131, pp. 1005-1026.
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The oxytocin (OXT) system has garnered considerable interest due to its influence on diverse behaviours. However, scant research has considered the influence of oxytocin on sleep-wake and sleep-related behaviour and neurobiology. Consequently, the objective of this systematic review was to assess the extant preclinical and clinical evidence for the influence of oxytocin-based interventions on sleep-wake outcomes. The primary search was conducted on 22/7/2020 using six electronic databases; 30 studies (19 preclinical, 11 clinical) were included based on inclusion criteria. Studies were evaluated for risk of bias using the SYRCLE tool and the Cochrane risk of bias tools for preclinical and clinical studies, respectively. Results indicated manipulation of the OXT system can influence sleep-wake outcomes. Preclinical evidence suggests a wake-promoting influence of OXT system activation whereas the clinical evidence suggests little or no sleep-promoting influence of OXT. OXT dose was identified as a likely modulatory factor of OXT-induced effects on sleep-wake behaviour. Future studies are necessary to validate and strengthen these tentative conclusions about the influence of OXT on sleep-wake behaviour.
Reddy, KD & Oliver, BGG 2021, 'Sex-specific effects of in utero and adult tobacco smoke exposure', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 320, no. 1, pp. L63-L72.
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Tobacco smoke has harmful effects on a multiorgan level. Exposure to smoke, whether in utero or environmental, significantly increases susceptibility. This susceptibility has been identified to be divergent between males and females. However, there remains a distinct lack of thorough research into the relationship between sex and exposure to tobacco. Females tend to generate a more significant response than males during adulthood exposure. The intrauterine environment is meticulously controlled, and exposure to tobacco presents a significant factor that contributes to poor health outcomes and susceptibility later in life. Analysis of these effects in relation to the sex of the offspring is yet to be holistically reviewed and summarized. In this review, we will delineate the time-dependent relationship between tobacco smoke exposure and sex-specific disease susceptibility. We further outline possible biological mechanisms that may contribute to the identified pattern.
Reddy, KD, Lan, A, Boudewijn, IM, Rathnayake, SNH, Koppelman, GH, Aliee, H, Theis, F, Oliver, BG, van den Berge, M & Faiz, A 2021, 'Current Smoking Alters Gene Expression and DNA Methylation in the Nasal Epithelium of Patients with Asthma', American Journal of Respiratory Cell and Molecular Biology, vol. 65, no. 4, pp. 366-377.
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Current smoking contributes to worsened asthma prognosis and more severe symptoms and limits the beneficial effects of corticosteroids. As the nasal epithelium can reflect smoking-induced changes in the lower airways, it is a relevant source to investigate changes in gene expression and DNA methylation. This study explores gene expression and DNA methylation changes in current and ex-smokers with asthma. Matched gene expression and epigenome-wide DNA methylation samples collected from nasal brushings of 55 patients enrolled in a clinical trial investigation of current and ex-smoker patients with asthma were analyzed. Differential gene expression and DNA methylation analyses were conducted comparing current smokers with ex-smokers. Expression quantitative trait methylation (eQTM) analysis was completed to explore smoking-relevant genes by CpG sites that differ between current and ex-smokers. To investigate the relevance of the smoking-associated DNA methylation changes for the lower airways, significant CpG sites were explored in bronchial biopsies from patients who had stopped smoking. A total of 809 genes and 18,814 CpG sites were differentially associated with current smoking in the nose. The cis-eQTM analysis uncovered 171 CpG sites with a methylation status associated with smoking-related gene expression, including AHRR, ALDH3A1, CYP1A1, and CYP1B1. The methylation status of CpG sites altered by current smoking reversed with 1 year of smoking cessation. We confirm that current smoking alters epigenetic patterns and affects gene expression in the nasal epithelium of patients with asthma, which is partially reversible in bronchial biopsies after smoking cessation. We demonstrate the ability to discern molecular changes in the nasal epithelium, presenting this as a tool in future investigations into disease-relevant effects of tobacco smoke.
Regan, B, Trycz, A, Fröch, JE, Schaeper, OC, Kim, S & Aharonovich, I 2021, 'Nanofabrication of high Q, transferable diamond resonators', Nanoscale, vol. 13, no. 19, pp. 8848-8854.
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Schematic illustration of a 1D diamond nanobeam cavity.
Rehn, S & Boakes, RA 2021, 'Persistence of binge-like sucrose intake in rats', Appetite, vol. 157, pp. 104949-104949.
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Rehn, S, Boakes, RA, Badolato, CJ & Rooney, KB 2021, 'Sex differences in recovery from cognitive and metabolic impairments induced by supplementary sucrose in rats.', Physiology & Behavior, vol. 239, pp. 113515-113515.
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Consumption of beverages containing around 10% sucrose contributes to worldwide obesity. Studies using rats can increase understanding of the consequences of such consumption. The present experiment aimed to compare male and female rats, first, in terms of cognitive and metabolic impairments produced by excessive intakes of 10% sucrose solution (Stage 1:8 weeks) and, second, with regard to recovery once access to sucrose ceased (Stage 2:4 weeks). All animals had unrestricted access to chow and water throughout. The primary cognitive outcome was performance on a place recognition task. The primary metabolic outcome was retroperitoneal fat pad mass/kg bodyweight at cull, with body weight and glucose tolerance as secondary outcomes. In a 3 × 2 between-subject factorial design the first factor was whether rats had: (1) unlimited access to a 10% sucrose solution and water throughout both stages (Suc-Suc); (2) were switched from sucrose in the 8-week Stage 1 to water only in the 4-week Stage 2 (Suc-Water); or (3) had no access to sucrose in either stage (Water-Water). The second factor was sex. A major metabolic outcome was that of persistent adiposity in both males and females in the Suc-Water condition. As for place recognition, females in the Suc-Suc condition showed greater long-term resistance than males to the impact of excessive sucrose on spatial memory impairment. Overall, few sex differences were found in secondary metabolic outcomes.
Reid, G, Klebe, S, van Zandwijk, N & George, AM 2021, 'Asbestos and Zeolites: from A to Z via a Common Ion', Chemical Research in Toxicology, vol. 34, no. 4, pp. 936-951.
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Reimers, JR, Yang, J, Darwish, N & Kosov, DS 2021, 'Silicon – single molecule – silicon circuits', Chemical Science, vol. 12, no. 48, pp. 15870-15881.
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Single-molecule circuits using silicon contacts are robust, conductive, controllable, and highly reproducible in blinking experiments, with enhanced conductance in break-junctions owing to residual dangling bonds.
Rennie, C, Fernandez, R, Donnelly, S & McGrath, KCY 2021, 'The Impact of Helminth Infection on the Incidence of Metabolic Syndrome: A Systematic Review and Meta-Analysis', Frontiers in Endocrinology, vol. 12, p. 728396.
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BackgroundThere are a growing number of publications that report an absence of inflammatory based disease among populations that are endemic to parasitic worms (helminths) demonstrating the ability of these parasites to potentially regulate human immune responses. The aim of this systematic review and meta-analysis was to determine the impact of helminth infection on metabolic outcomes in human populations.MethodsUsing PRISMA guidelines, six databases were searched for studies published up to August 2020. Random effects meta-analysis was performed to estimate pooled proportions with 95% confidence intervals using the Review Manager Software version 5.4.1.ResultsFourteen studies were included in the review. Fasting blood glucose was significantly lower in persons with infection (MD -0.22, 95% CI -0.40- -0.04, P=0.02), HbA1c levels were lower, although not significantly, and prevalence of the metabolic syndrome (P=0.001) and type 2 diabetes was lower (OR 1.03, 95% CI 0.34-3.09, P<0.0001). Infection was negatively associated with type 2 diabetes when comparing person with diabetes to the group without diabetes (OR 0.44, 95% CI 0.29-0.67, P=0.0001).ConclusionsWhile infection with helminths was generally associated with improved metabolic function, there were notable differences in efficacy between parasite species. Based on the data assessed, live infection with S. mansoni resulted in the most significant positive changes to metabolic outcomes.Systematic Review RegistrationWebsite: PROSPERO Identified: CRD42021227619.
Rezaei, M, Radfar, P, Winter, M, McClements, L, Thierry, B & Warkiani, ME 2021, 'Simple-to-Operate Approach for Single Cell Analysis Using a Hydrophobic Surface and Nanosized Droplets', Analytical Chemistry, vol. 93, no. 10, pp. 4584-4592.
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Microfluidics-based technologies for single-cell analysis are becoming increasingly important tools in biological studies. With the increasing sophistication of microfluidics, cellular barcoding techniques, and next-generation sequencing, a more detailed picture of cellular subtype is emerging. Unfortunately, the majority of the methods developed for single-cell analysis are high-throughput and not suitable for rare cell analysis as they require a high input cell number. Here, we report a low-cost and reproducible method for rare single-cell analysis using a highly hydrophobic surface and nanosized static droplets. Our method allows rapid and efficient on-chip single-cell lysis and subsequent collection of genetic materials in nanoliter droplets using a micromanipulator or a laboratory pipette before subsequent genetic analysis. We show precise isolation of single cancer cells with high purity using two different strategies (i- cytospin and ii- static droplet array) for subsequent RNA analysis using droplet digital polymerase chain reaction (PCR) and real-time PCR. Our highly controlled isolation method opens a new avenue for the study of subcellular functional mechanisms, enabling the identification of rare cells of potential functional or pathogenic consequence.
Rezaei, M, Razavi Bazaz, S, Morshedi Rad, D, Shimoni, O, Jin, D, Rawlinson, W & Ebrahimi Warkiani, M 2021, 'A Portable RT-LAMP/CRISPR Machine for Rapid COVID-19 Screening', Biosensors, vol. 11, no. 10, pp. 369-369.
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The COVID-19 pandemic has changed people’s lives and has brought society to a sudden standstill, with lockdowns and social distancing as the preferred preventative measures. To lift these measurements and reduce society’s burden, developing an easy-to-use, rapid, and portable system to detect SARS-CoV-2 is mandatory. To this end, we developed a portable and semi-automated device for SARS-CoV-2 detection based on reverse transcription loop-mediated isothermal amplification followed by a CRISPR/Cas12a reaction. The device contains a heater element mounted on a printed circuit board, a cooler fan, a proportional integral derivative controller to control the temperature, and designated areas for 0.2 mL Eppendorf® PCR tubes. Our system has a limit of detection of 35 copies of the virus per microliter, which is significant and has the capability of being used in crisis centers, mobile laboratories, remote locations, or airports to diagnose individuals infected with SARS-CoV-2. We believe the current methodology that we have implemented in this article is beneficial for the early screening of infectious diseases, in which fast screening with high accuracy is necessary.
Rezcallah, MC, Al-mazi, T & Ammit, AJ 2021, 'Cataloguing the phosphorylation sites of tristetraprolin (TTP): Functional implications for inflammatory diseases', Cellular Signalling, vol. 78, pp. 109868-109868.
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Tristetraprolin (TTP) is a destabilizing mRNA binding protein known to regulate gene expression of a wide variety of targets, including those that control inflammation. TTP expression, regulation and function is controlled by phosphorylation. While the importance of key serine (S) sites (S52 and S178 in mice and S186 in humans) has been recognized, other sites on the hyperphosphorylated TTP protein have more recently emerged as playing an important role in regulating cellular signalling and downstream functions of TTP. In order to propel investigation of TTP and fully exploit its potential as a drug target in inflammatory disease, this review will catalogue TTP phosphorylation sites in both the murine and human TTP protein, the known and unknown roles and functions of these sites, the kinases and phosphatases that act upon TTP and overview methodological approaches to increase our knowledge of this important protein regulated by phosphorylation.
Ricafrente, A, Nguyen, H, Tran, N & Donnelly, S 2021, 'An Evaluation of the Fasciola hepatica miRnome Predicts a Targeted Regulation of Mammalian Innate Immune Responses', Frontiers in Immunology, vol. 11, p. 608686.
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Understanding mechanisms by which parasitic worms (helminths) control their hosts’ immune responses is critical to the development of effective new disease interventions. Fasciola hepatica, a global scourge of humans and their livestock, suppresses host innate immune responses within hours of infection, ensuring that host protective responses are quickly incapacitated. This allows the parasite to freely migrate from the intestine, through the liver to ultimately reside in the bile duct, where the parasite establishes a chronic infection that is largely tolerated by the host. The recent identification of micro(mi)RNA, small RNAs that regulate gene expression, within the extracellular vesicles secreted by helminths suggest that these non-coding RNAs may have a role in the parasite-host interplay. To date, 77 miRNAs have been identified in F. hepatica comprising primarily of ancient conserved species of miRNAs. We hypothesized that many of these miRNAs are utilized by the parasite to regulate host immune signaling pathways. To test this theory, we first compiled all of the known published F. hepatica miRNAs and critically curated their sequences and annotations. Then with a focus on the miRNAs expressed by the juvenile worms, we predicted gene targets within human innate immune cells. This approach revealed the existence of targets within every immune cell, providing evidence for the universal management of host immunology by this parasite. Notably, there was a high degree of redundancy in the potential for the parasite to regulate the activation of dendritic cells, eosinophils and neutrophils, with multiple miRNAs predicted to act on singular gene targets within these cells. This original exploration of the Fasciola miRnome offers the first molecular insight into mechanisms by which F. hepatica can regulate the hos...
Richards, C, Sesperez, K, Chhor, M, Ghorbanpour, S, Rennie, C, Ming, CLC, Evenhuis, C, Nikolic, V, Orlic, NK, Mikovic, Z, Stefanovic, M, Cakic, Z, McGrath, K, Gentile, C, Bubb, K & McClements, L 2021, 'Characterisation of cardiac health in the reduced uterine perfusion pressure model and a 3D cardiac spheroid model, of preeclampsia', Biology of Sex Differences, vol. 12, no. 1.
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Abstract Background Preeclampsia is a dangerous cardiovascular disorder of pregnancy that leads to an increased risk of future cardiovascular and metabolic disorders. Much of the pathogenesis and mechanisms involved in cardiac health in preeclampsia are unknown. A novel anti-angiogenic protein, FKBPL, is emerging as having a potential role in both preeclampsia and cardiovascular disease (CVD). Therefore, in this study we aimed to characterise cardiac health and FKBPL regulation in the rat reduced uterine perfusion pressure (RUPP) and a 3D cardiac spheroid model of preeclampsia. Methods The RUPP model was induced in pregnant rats and histological analysis performed on the heart, kidney, liver and placenta (n ≥ 6). Picrosirius red staining was performed to quantify collagen I and III deposition in rat hearts, placentae and livers as an indicator of fibrosis. RT-qPCR was used to determine changes in Fkbpl, Icam1, Vcam1, Flt1 and Vegfa mRNA in hearts and/or placentae and ELISA to evaluate cardiac brain natriuretic peptide (BNP45) and FKBPL secretion. Immunofluorescent staining was also conducted to analyse the expression of cardiac FKBPL. Cardiac spheroids were generated using human cardiac fibroblasts and human coronary artery endothelial cells and treated with patient plasma from normotensive controls, early-onset preeclampsia (EOPE) and late-onset preeclampsia (LOPE); n = 3. FKBPL and CD31 expression was quantified by immunofluorescent labelling. Results The RUPP procedure induced ...
Roberts, L, Kutay, C, Melbourne-Thomas, J, Petrou, K, Benson, TM, Fiore, D, Fletcher, P, Johnson, E, Silk, M, Taberner, S, Filgueira, VV & Constable, AJ 2021, 'Enabling Enduring Evidence-Based Policy for the Southern Ocean Through Cultural Arts Practices', Frontiers in Ecology and Evolution, vol. 9.
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This paper provides a perspective on how art and cross-cultural conversations can facilitate understanding of important scientific processes, outcomes and conclusions, using the Marine Ecosystem Assessment for the Southern Ocean (MEASO) as a case study. First, we reflect on our rationale and approach, describing the importance of deeper communication, such as through the arts, to the policy process; more enduring decisions are possible by engaging and obtaining perspectives through more than just a utilitarian lens. Second, we draw on the LivingData Website [http://www.livingdata.net.au] where art in all its forms is made to bridge differences in knowledge systems and their values, provide examples of how Indigenous knowledge and Western science can be complementary, and how Indigenous knowledge can show the difference between historical natural environmental phenomena and current unnatural phenomena, including how the Anthropocene is disrupting cultural connections with the environment that ultimately impact everyone. Lastly, we document the non-linear process of our experience and draw lessons from it that can guide deeper communication between disciples and cultures, to potentially benefit decision-making. Our perspective is derived as a collective from diverse backgrounds, histories, knowledge systems and values.
Rodrigo, N, Chen, H, Pollock, C & Glastras, S 2021, 'Pre-Conception Weight Loss Improves Reproductive, Metabolic and Kidney Health in Obese Mice and Their Offspring', Journal of the Endocrine Society, vol. 5, no. Suppl 1, pp. A322-A323.
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Abstract Background and Aims: An alarming 40% of women of reproductive age have obesity and during pregnancy obesity adversely impacts metabolic health in mothers and offspring. Maternal complications include diabetes, preeclampsia and chronic kidney disease (CKD). Our previous work showed that offspring have increased risks of obesity, diabetes, and CKD. While pre-pregnancy weight optimisation is advocated, evidence of benefits for mother and offspring are lacking. We aimed to determine if weight loss prior to pregnancy, either with diet modification or liraglutide, improves maternal and offspring metabolic outcomes, and reduces kidney complications in obese mothers and the offspring. Methods: C57BL/6 female mice were fed a high-fat-diet (HFD) for 8 weeks and compared to lean chow-fed controls. HFD-fed dams were administered liraglutide (0.3mg/kg, s.c., for 4weeks) or switched to chow, to induce pre-conception weight loss. Pregnancy rates were observed after mating. Maternal anthropometry and glucose tolerance were measured before and after intervention, and at late gestation. Pregnant dams were either culled at gestational day 18–20 with blood and kidney harvested, or allowed to deliver their offspring. Offspring anthropometry, and glucose tolerance were assessed at postnatal week 12 after either HFD or chow feeding. Immunohistochemistry (IHC), western blotting and RT-PCR were used to measure kidney metabolic (FAS, SREBP) and inflammatory markers (CD-68,TGF-b). Results: HFD-fed dams had reduced glucose tolerance compared to chow-fed dams (p<0.0001), and higher expression of renal metabolic and inflammatory markers in late gestation (eg FAS <0.05, TGFb <0.05). Intervention with liraglutide or diet lowered body weight, improving glucose tolerance (both p<0.001), and fecundity. Markers of kidney damage, namely albuminuria and fibronectin (by RT-PCR and IHC) were reduced (both p<0.05). Liraglutide treated mice exhibited greater gestational weight gain than mice swi...
Ros, M, Suggett, DJ, Edmondson, J, Haydon, T, Hughes, DJ, Kim, M, Guagliardo, P, Bougoure, J, Pernice, M, Raina, J-B & Camp, EF 2021, 'Symbiont shuffling across environmental gradients aligns with changes in carbon uptake and translocation in the reef-building coral Pocillopora acuta', Coral Reefs, vol. 40, no. 2, pp. 595-607.
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Rose, ML, Rai, T, Copland, D, Nickels, L, Togher, L, Meinzer, M, Godecke, E, Kim, J, Cadilhac, DA, Hurley, M, Wilcox, C & Carragher, M 2021, 'Statistical analysis plan for the COMPARE trial: a 3-arm randomised controlled trial comparing the effectiveness of Constraint-induced Aphasia Therapy Plus and Multi-modality Aphasia Therapy to usual care in chronic post-stroke aphasia (COMPARE)', Trials, vol. 22, no. 1, p. 303.
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Abstract Background While high-quality meta-analyses have confirmed the effectiveness of aphasia therapy after stroke, there is limited evidence for the comparative effectiveness of different aphasia interventions. Two commonly used interventions, Constraint-induced Aphasia Therapy Plus (CIAT Plus) and Multi-modality Aphasia Therapy (M-MAT), are hypothesised to rely on diverse underlying neural mechanisms for recovery and may be differentially responsive to aphasia severity. COMPARE is a prospective randomised open-blinded end-point trial designed to determine whether, in people with chronic post-stroke aphasia living in the community, CIAT Plus and M-MAT provide greater therapeutic benefit compared to usual care, are differentially effective according to aphasia severity, and are cost-effective. This paper details the statistical analysis plan for the COMPARE trial developed prior to data analysis. Methods Participants (n = 216) are randomised to one of three arms, CIAT Plus, M-MAT or usual care, and undertake therapy with a study trained speech pathologist in groups of three participants stratified by aphasia severity. Therapy occurs for 3 h blocks per day for 10 days across 2 weeks. The primary clinical outcome is aphasia severity as measured by the Western Aphasia Battery-Revised Aphasia Quotient (WAB-R-AQ) immediately post intervention. Secondary outcomes include WAB-R-AQ at 12-week follow-up, and functional communication, discourse efficiency, multimodal communication, and health-related quality of life immediately post intervention and at 12-week follow-up. Results Linear mixed models (LMMs) will be used t...
Rosset, SL, Oakley, CA, Ferrier-Pagès, C, Suggett, DJ, Weis, VM & Davy, SK 2021, 'The Molecular Language of the Cnidarian–Dinoflagellate Symbiosis', Trends in Microbiology, vol. 29, no. 4, pp. 320-333.
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The cnidarian-dinoflagellate symbiosis is of huge importance as it underpins the success of coral reefs, yet we know very little about how the host cnidarian and its dinoflagellate endosymbionts communicate with each other to form a functionally integrated unit. Here, we review the current knowledge of interpartner molecular signaling in this symbiosis, with an emphasis on lipids, glycans, reactive species, biogenic volatiles, and noncoding RNA. We draw upon evidence of these compounds from recent omics-based studies of cnidarian-dinoflagellate symbiosis and discuss the signaling roles that they play in other, better-studied symbioses. We then consider how improved knowledge of interpartner signaling might be used to develop solutions to the coral reef crisis by, for example, engineering more thermally resistant corals.
Rouhi, O, Razavi Bazaz, S, Niazmand, H, Mirakhorli, F, Mas-hafi, S, A. Amiri, H, Miansari, M & Ebrahimi Warkiani, M 2021, 'Numerical and Experimental Study of Cross-Sectional Effects on the Mixing Performance of the Spiral Microfluidics', Micromachines, vol. 12, no. 12, pp. 1470-1470.
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Mixing at the microscale is of great importance for various applications ranging from biological and chemical synthesis to drug delivery. Among the numerous types of micromixers that have been developed, planar passive spiral micromixers have gained considerable interest due to their ease of fabrication and integration into complex miniaturized systems. However, less attention has been paid to non-planar spiral micromixers with various cross-sections and the effects of these cross-sections on the total performance of the micromixer. Here, mixing performance in a spiral micromixer with different channel cross-sections is evaluated experimentally and numerically in the Re range of 0.001 to 50. The accuracy of the 3D-finite element model was first verified at different flow rates by tracking the mixing index across the loops, which were directly proportional to the spiral radius and were hence also proportional to the Dean flow. It is shown that higher flow rates induce stronger vortices compared to lower flow rates; thus, fewer loops are required for efficient mixing. The numerical study revealed that a large-angle outward trapezoidal cross-section provides the highest mixing performance, reaching efficiencies of up to 95%. Moreover, the velocity/vorticity along the channel length was analyzed and discussed to evaluate channel mixing performance. A relatively low pressure drop (<130 kPa) makes these passive spiral micromixers ideal candidates for various lab-on-chip applications.
Roux, C & Weyermann, C 2021, 'From Research Integrity to Research Relevance to Advance Forensic Science', Forensic Sciences Research, vol. 6, no. 4, pp. 292-294.
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Roux, C, Willis, S & Weyermann, C 2021, 'Shifting forensic science focus from means to purpose: A path forward for the discipline?', Science & Justice, vol. 61, no. 6, pp. 678-686.
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Forensic science is facing a persistent crisis that is often addressed by organizational responses, with a strong focus on the improvement and standardisation of means and processes. However, organisations and processes are highly dependent on the political, economical and legal structures in which they operate. This may explain why most proposed solutions had difficulties in addressing the crisis up to now, as they could hardly be applied transversally to all forensic science models. Moreover, new tools and technologies are continuously developed by a quasi-infinite number of different scientific disciplines, thus leading to further diversity and fragmentation of forensic science. In this paper, it is proposed to shift the focus from means to purpose and consider forensic science current challenges in terms of discipline, before addressing organisations’ specific issues. As a distinct discipline, forensic science can refocus research and development on shared principles and purposes, such as reconstructing, monitoring, and preventing crime and security issues. This focus change will facilitate a better understanding of the trace as the object of study of forensic science and eventually lead to a more impactful and long-lasting effect. This approach will also foster the development of a forensic science culture (instead of a primarily technological culture) unified by purpose rather than means through more relevant education and research.
Rouzé, H, Galand, PE, Medina, M, Bongaerts, P, Pichon, M, Pérez-Rosales, G, Torda, G, Moya, A, Bardout, G, Périé-Bardout, E, Marivint, E, Lagarrigue, G, Leblond, J, Gazzola, F, Pujolle, S, Mollon, N, Mittau, A, Fauchet, J, Paulme, N, Pete, R, Peyrusse, K, Ferucci, A, Magnan, A, Horlaville, M, Breton, C, Gouin, M, Markocic, T, Jubert, I, Herrmann, P, Raina, J-B & Hédouin, L 2021, 'Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth)', The ISME Journal, vol. 15, no. 5, pp. 1564-1568.
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Abstract The symbiosis between scleractinian corals and photosynthetic algae from the family Symbiodiniaceae underpins the health and productivity of tropical coral reef ecosystems. While this photosymbiotic association has been extensively studied in shallow waters (<30 m depth), we do not know how deeper corals, inhabiting large and vastly underexplored mesophotic coral ecosystems, modulate their symbiotic associations to grow in environments that receive less than 1% of surface irradiance. Here we report on the deepest photosymbiotic scleractinian corals collected to date (172 m depth), and use amplicon sequencing to identify the associated symbiotic communities. The corals, identified as Leptoseris hawaiiensis, were confirmed to host Symbiodiniaceae, predominantly of the genus Cladocopium, a single species of endolithic algae from the genus Ostreobium, and diverse communities of prokaryotes. Our results expand the reported depth range of photosynthetic scleractinian corals (0–172 m depth), and provide new insights on their symbiotic associations at the lower depth extremes of tropical coral reefs.
Roy, S, Tiang, J-J, Roslee, MB, Ahmed, MT & Mahmud, MAP 2021, 'A Quad-Band Stacked Hybrid Ambient RF-Solar Energy Harvester With Higher RF-to-DC Rectification Efficiency', IEEE Access, vol. 9, pp. 39303-39321.
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This article addresses the design and implementation of a novel quad-band electromagnetic (EM) and solar energy scavenging system, ensuring energy harvesting from ambient RF environment with excellent 'cold start' power level. The proposed scavenger consists of a single port quad-band rectangular slot antenna, power film solar cell, a quad-band RF- to-DC converter, a microcell power management module, and a battery. The harmonic balance of EM solver is used to design and maximize the RF- to - DC rectification efficiency with the combination of the antenna and the solar cell. The power film solar cell is placed in the middle of the antenna with positive and negative edges connected to the top and bottom layer of the antenna so that total harvested energy passes through the rectifier and forms an ambient hybrid energy harvesting system. One significant benefit of this method is the utilization of the antenna free space for the effective area of the power film. Another important contribution is the employment of multiband antennas for increasing the total ambient RF scavenged energy. Besides, a cost-effective and flexible FR4 substrate and a micropower film solar cell are used to make it conformal and cheaper. The prototype of hybrid harvester demonstrated that with 360 lux ambient light intensity, at the solar cell can generate 0.109 V energy while the harvester can attain an extra 5% - 48% energy with ambient RF input level variation from -15 to -20 dBm. The rectifier circuit achieves 74.5% RF-to-DC rectification efficiency for the value of load resistance 2.7 kΩ. These performances depict that the proposed multiband ambient hybrid RF-solar power scavenger can raise the scavenged power level and offer energy multiplicity.
Roy, S, Tiang, RJ-J, Roslee, MB, Ahmed, MT & Mahmud, MAP 2021, 'Quad-Band Multiport Rectenna for RF Energy Harvesting in Ambient Environment', IEEE Access, vol. 9, pp. 77464-77481.
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This article proposes a quad-band multiport harvester that can scavenge ambient radio frequency (RF) energy of available frequency bands (i.e. GSM-900, GSM-1800, 3G and Wi-Fi) efficiently. This design's novelty is the use of frequency-dependent multiple antenna ports that enables the harvester to fully exploit all available frequency bands, spatial diversity, and polarization for maximizing the harvested RF energy at a lower power density level in an ambient environment. Indistinctly, the proposed antenna consists of 8-port which maintain 0.33lambda times 0.33lambda (i.e. wavelength lambda calculated at 0.9 GHz in free space) average area per port and has achieved more than 35% relative bandwidth (BW) with a maximum gain of 6.5 dBi to cover the selected frequency bands. Besides, the proposed quad-band rectifier with a multi-stub impedance matching network is feasible for RF harvesting over the available ambient frequency bands. The proposed rectenna's measurement results show that the generated average dc output voltage is increased up to 0.750 V at a low RF input power density of -27 dBm for a load resistance of 2.11 text{k}Omega . The overall dc rectification efficiency of the 8-port pixel harvester is also assessed and depicted to be 66.52% when the resultant RF input power density level is -27 dBm. Measurement in an ambient outdoor and controlled indoor environment is also conducted, demonstrating that the new 8-port pixel RF harvester can produce a dc output voltage of 0.797 V which is greater than some of the reference RF harvesters.
Rudd, R, McWalter, T, Kienitz, J & Platen, E 2021, 'Robust Product Markovian Quantization', Journal of Computational Finance, vol. 25.
Ruprecht, JE, Birrer, SC, Dafforn, KA, Mitrovic, SM, Crane, SL, Johnston, EL, Wemheuer, F, Navarro, A, Harrison, AJ, Turner, IL & Glamore, WC 2021, 'Wastewater effluents cause microbial community shifts and change trophic status', Water Research, vol. 200, pp. 117206-117206.
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Widespread wastewater pollution is one of the greatest challenges threatening the sustainable management of rivers globally. Understanding microbial responses to gradients in environmental stressors, such as wastewater pollution, is crucial to identify thresholds of community change and to develop management strategies that protect ecosystem integrity. This study used multiple lines of empirical evidence, including a novel combination of microbial ecotoxicology methods in the laboratory and field to link pressure-stressor-response relationships. Specifically, community-based whole effluent toxicity (WET) testing and environmental genomics were integrated to determine real-world community interactions, shifts and functional change in response to wastewater pollution. Here we show that wastewater effluents above moderate (>10%) concentrations caused consistent significant shifts in bacterial community structure and function. These thresholds of community shifts were also linked to changes in the trophic state of receiving waters in terms of nutrient concentrations. Differences in the community responses along the effluent concentration gradient were primarily driven by two globally relevant bacterial indicator taxa, namely Malikia spp. (Burkholderiales) and hgcI_clade (Frankiales). Species replacement occurred above moderate effluent concentrations with abundances of Malikia spp. increasing, while abundances of hgcI_clade decreased. The responses of Malikia spp. and hgcI_clade matched gene patterns associated with globally important nitrogen cycling pathways, such as denitrification and nitrogen fixation, which linked the core individual taxa to putative function and ecosystem processes, rarely achieved in previous studies. This study has identified potential indicators of change in trophic status and the functional consequences of wastewater pollution. These findings have immediate implications for both the management of environmental stressors and prote...
Ryan, ST, Hosseini-Beheshti, E, Afrose, D, Ding, X, Xia, B, Grau, GE, Little, CB, McClements, L & Li, JJ 2021, 'Extracellular Vesicles from Mesenchymal Stromal Cells for the Treatment of Inflammation-Related Conditions', International Journal of Molecular Sciences, vol. 22, no. 6, pp. 3023-3023.
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Over the past two decades, mesenchymal stromal cells (MSCs) have demonstrated great potential in the treatment of inflammation-related conditions. Numerous early stage clinical trials have suggested that this treatment strategy has potential to lead to significant improvements in clinical outcomes. While promising, there remain substantial regulatory hurdles, safety concerns, and logistical issues that need to be addressed before cell-based treatments can have widespread clinical impact. These drawbacks, along with research aimed at elucidating the mechanisms by which MSCs exert their therapeutic effects, have inspired the development of extracellular vesicles (EVs) as anti-inflammatory therapeutic agents. The use of MSC-derived EVs for treating inflammation-related conditions has shown therapeutic potential in both in vitro and small animal studies. This review will explore the current research landscape pertaining to the use of MSC-derived EVs as anti-inflammatory and pro-regenerative agents in a range of inflammation-related conditions: osteoarthritis, rheumatoid arthritis, Alzheimer’s disease, cardiovascular disease, and preeclampsia. Along with this, the mechanisms by which MSC-derived EVs exert their beneficial effects on the damaged or degenerative tissues will be reviewed, giving insight into their therapeutic potential. Challenges and future perspectives on the use of MSC-derived EVs for the treatment of inflammation-related conditions will be discussed.
Sabir, S, Suresh, D, Subramoni, S, Das, T, Bhadbhade, M, Black, DS, Rice, SA & Kumar, N 2021, 'Thioether-linked dihydropyrrol-2-one analogues as PqsR antagonists against antibiotic resistant Pseudomonas aeruginosa', Bioorganic & Medicinal Chemistry, vol. 31, pp. 115967-115967.
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Sadique, JJ, Ullah, SE, Islam, MR, Raad, R, Kouzani, AZ & Mahmud, MAP 2021, 'Transceiver Design for Full-Duplex UAV Based Zero-Padded OFDM System With Physical Layer Security', IEEE Access, vol. 9, pp. 59432-59445.
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In this paper, multi-antenna transceiver for zero-padded orthogonal frequency division multiplexing (OFDM) system is designed at mmWave by integrating full-duplex unmanned aerial vehicle (UAV) into the terrestrial cellular networks. Assuming that there exist no direct communication links between the ground base station (GBS) and the mobile users due to unexpected blockages from high storied buildings in urban area, the UAV applies decode-and-forward cooperative strategy on the received OFDM signals transmitted from GBS and re-transmits to the ground mobile users and passive eavesdropper. In this proposed system, intertwining logistic map (ILM)-cosine transform aided encryption algorithm combined with artificial noise enhancing physical layer security (PLS) is introduced. Also walsh-hadamard transform technique integrated with QR-decomposition based zero forcing (ZF) block diagonalization (QR-ZF-BD) precoding for multi-user interference reduction and non-iterative clipping and filtering technique for peak to average power ratio (PAPR) reduction are utilized. In addition, Low density parity check (LDPC) and repeat and accumulate (RA) channel coding with cholesky decomposition based ZF and minimum mean square error signal detection schemes for improved bit error rate (BER) are also introduced. Numerical results demonstrate the effectiveness of the proposed system in terms of PLS for color image transmission at high order digital modulation (16-PSK and 16-QAM). At the complementary cumulative distribution function of probability level 1-6%, the estimated PAPR is found to have value of 6 dB.The three users achieve BER $= 1\times {10}^{-4}$ at signal-to-noise ratio of 1.5 dB, 4 dB and 6 dB under RA channel coding and 16-QAM digital modulation.
Sadraeian, M, da Cruz, EF, Boyle, RW, Bahou, C, Chudasama, V, Janini, LMR, Diaz, RS & Guimarães, FEG 2021, 'Photoinduced Photosensitizer–Antibody Conjugates Kill HIV Env-Expressing Cells, Also Inactivating HIV', ACS Omega, vol. 6, no. 25, pp. 16524-16534.
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Safaei, J, Mashkani, SMH, Tian, H, Ye, C, Xiong, P & Wang, G 2021, 'Self-Assembled NbOPO4 Nanosheet/Reduced Graphene Oxide Heterostructure for Capacitive Desalination', ACS Applied Nano Materials, vol. 4, no. 11, pp. 12629-12639.
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Capacitive deionization (CDI) is a promising and energy-efficient technology for desalination. The development of high-performance capacitive electrodes is essential for enhancing the CDI properties for practical applications. Here, a 2D heterostructure was rationally designed and synthesized by face-to-face restacking of NbOPO4 nanosheets and reduced graphene oxide (rGO) via an electrostatic self-assembly process. The as-prepared 2D NbOPO4/rGO heterostructure achieved an excellent ion storage capacity, electronic conductivity, and unimpeded ion kinetics. When applied as electrodes for CDI, the 2D NbOPO4/rGO heterostructure delivered a high specific capacitance of 258.3 F g-1 and an electrosorption capacity of 73 mg g-1 for NaCl solution of 10 000 mg L-1 at an applied voltage of 1.2 V, which is more than five times larger than that of activated carbon. The heterostructure electrode also showed high desalination stability for up to 50 adsorption/desorption cycles. The high CDI performance is attributed to the strong 2D/2D coupling between NbOPO4 nanosheets and rGO. The strong 2D/2D coupling reduced the charge transfer resistance, affirmed via the electrochemical impedance spectroscopy technique, attesting to the enhanced charge transportation across the heterointerface. The robust 2D/2D coupling was affirmed via the uniform and identical Raman shifts at various random regions, and larger XPS binding energy shifts for the self-assembled NbOPO4/rGO heterostructure. This work demonstrated the potential of self-assembled nanoheterostructures for water desalination via capacitive deionization.
Saini, V, Joglekar, MV, Wong, WKM, Jiang, G, Nassif, NT, Simpson, AM, Ma, RCW, Dalgaard, LT & Hardikar, AA 2021, 'Manipulating cellular microRNAs and analyzing high-dimensional gene expression data using machine learning workflows', STAR Protocols, vol. 2, no. 4, pp. 100910-100910.
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Samardzic, K, Steele, JR, Violi, JP, Colville, A, Mitrovic, SM & Rodgers, KJ 2021, 'Toxicity and bioaccumulation of two non-protein amino acids synthesised by cyanobacteria, β-N-Methylamino-L-alanine (BMAA) and 2,4-diaminobutyric acid (DAB), on a crop plant', Ecotoxicology and Environmental Safety, vol. 208, pp. 111515-111515.
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In order to study the toxicity of the cyanobacterial non-protein amino acids (NPAAs) L-β-N-methylamino-L-alanine (BMAA) and its structural isomer L-2,4-diaminobutyric acid (DAB) in the forage crop plant alfalfa (Medicago sativa), seedlings were exposed to NPAA-containing media for four days. Root growth was significantly inhibited by both treatments. The content of derivatised free and protein-bound BMAA and DAB in seedlings was then analysed by LC-MS/MS. Both NPAAs were detected in free and protein-bound fractions with higher levels detected in free fractions. Compared to shoots, there was approximately tenfold more BMAA and DAB in alfalfa roots. These results suggest that NPAAs might be taken up into crop plants from contaminated irrigation water and enter the food chain. This may present an exposure pathway for NPAAs in humans.
Sarkar, A, Pati, D, Mallick, BK & Carroll, RJ 2021, 'Bayesian Copula Density Deconvolution for Zero-Inflated Data in Nutritional Epidemiology', Journal of the American Statistical Association, vol. 116, no. 535, pp. 1075-1087.
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© 2020, © 2020 American Statistical Association. Estimating the marginal and joint densities of the long-term average intakes of different dietary components is an important problem in nutritional epidemiology. Since these variables cannot be directly measured, data are usually collected in the form of 24-hr recalls of the intakes, which show marked patterns of conditional heteroscedasticity. Significantly compounding the challenges, the recalls for episodically consumed dietary components also include exact zeros. The problem of estimating the density of the latent long-time intakes from their observed measurement error contaminated proxies is then a problem of deconvolution of densities with zero-inflated data. We propose a Bayesian semiparametric solution to the problem, building on a novel hierarchical latent variable framework that translates the problem to one involving continuous surrogates only. Crucial to accommodating important aspects of the problem, we then design a copula based approach to model the involved joint distributions, adopting different modeling strategies for the marginals of the different dietary components. We design efficient Markov chain Monte Carlo algorithms for posterior inference and illustrate the efficacy of the proposed method through simulation experiments. Applied to our motivating nutritional epidemiology problems, compared to other approaches, our method provides more realistic estimates of the consumption patterns of episodically consumed dietary components. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
Sarkar, S, Tran, B, Horvath, L, Lam, M, Savas, P, Grimison, P, Whittle, JR, Kuo, JC, Signal, N, Edmonds, D, Hogg, P, Rischin, D, Desai, J & Hamilton, A 2021, 'A phase 1 trial of 4-(N-(S-penicillaminylacetyl)amino)-phenylarsonous acid (PENAO) in patients with advanced solid tumours', Cancer Chemotherapy and Pharmacology, vol. 87, no. 5, pp. 613-620.
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Sarkar, TR, McNeal, CJ, Meininger, CJ, Niu, Y, Mallick, BK, Carroll, RJ & Wu, G 2021, 'Dietary Intakes of Amino Acids and Other Nutrients by Adult Humans', pp. 211-227.
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Sarker, SK, Fahim, SR, Sarker, N, Tayef, KZ, Siddique, AB, Datta, D, Mahmud, MAP, Ishraque, MF, Das, SK, Sarker, MRI, Shezan, SA & Rahman, Z 2021, 'Ancillary Voltage Control Design for Adaptive Tracking Performance of Microgrid Coupled With Industrial Loads', IEEE Access, vol. 9, pp. 143690-143706.
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Satija, S, Kaur, H, Tambuwala, MM, Sharma, P, Vyas, M, Khurana, N, Sharma, N, Bakshi, HA, Charbe, NB, Zacconi, FC, Aljabali, AA, Nammi, S, Dureja, H, Singh, TG, Gupta, G, Dhanjal, DS, Dua, K, Chellappan, DK & Mehta, M 2021, 'Hypoxia-Inducible Factor (HIF): Fuel for Cancer Progression', Current Molecular Pharmacology, vol. 14, no. 3, pp. 321-332.
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Hypoxia is an integral part of the tumor microenvironment, caused primarily due to rapidly multiplying tumor cells and a lack of proper blood supply. Among the major hypoxic pathways, HIF-1 transcription factor activation is one of the widely investigated pathways in the hypoxic tumor microenvironment (TME). HIF-1 is known to activate several adaptive reactions in response to oxygen deficiency in tumor cells. HIF-1 has two subunits, HIF-1β (constitutive) and HIF-1α (inducible). The HIF-1α expression is largely regulated via various cytokines (through PI3K-ACT-mTOR signals), which involves the cascading of several growth factors and oncogenic cascades. These events lead to the loss of cellular tumor suppressant activity through changes in the level of oxygen via oxygen-dependent and oxygen-independent pathways. The significant and crucial role of HIF in cancer progression and its underlying mechanisms have gained much attention lately among the translational researchers in the fields of cancer and biological sciences, which have enabled them to correlate these mechanisms with various other disease modalities. In the present review, we have summarized the key findings related to the role of HIF in the progression of tumors.
Satija, S, Sharma, P, Kaur, H, Dhanjal, DS, Chopra, RS, Khurana, N, Vyas, M, Sharma, N, Tambuwala, MM, Bakshi, HA, Charbe, NB, Zacconi, FC, Chellappan, DK, Dua, K & Mehta, M 2021, 'Perfluorocarbons Therapeutics in Modern Cancer Nanotechnology for Hypoxiainduced Anti-tumor Therapy', Current Pharmaceutical Design, vol. 27, no. 43, pp. 4376-4387.
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:With an estimated failure rate of about 90%, immunotherapies that are intended for the treatment ofsolid tumors have caused an anomalous rise in the mortality rate over the past decades. It is apparent that resistancetowards such therapies primarily occurs due to elevated levels of HIF-1 (Hypoxia-induced factor) intumor cells, which are caused by disrupted microcirculation and diffusion mechanisms. With the advent of nanotechnology,several innovative advances were brought to the fore; and, one such promising direction is the useof perfluorocarbon nanoparticles in the management of solid tumors. Perfluorocarbon nanoparticles enhance theresponse of hypoxia-based agents (HBAs) within the tumor cells and have been found to augment the entry ofHBAs into the tumor micro-environment. The heightened penetration of HBAs causes chronic hypoxia, thusaiding in the process of cell quiescence. In addition, this technology has also been applied in photodynamictherapy, where oxygen self-enriched photosensitizers loaded perfluorocarbon nanoparticles are employed. Theresulting processes initiate a cascade, depleting tumour oxygen and turning it into a reactive oxygen specieseventually to destroy the tumour cell. This review elaborates on the multiple applications of nanotechnologybased perfluorocarbon formulations that are being currently employed in the treatment of tumour hypoxia.
Sayyadi, N, Zhand, S, Razavi Bazaz, S & Warkiani, ME 2021, 'Affibody Functionalized Beads for the Highly Sensitive Detection of Cancer Cell-Derived Exosomes', International Journal of Molecular Sciences, vol. 22, no. 21, pp. 12014-12014.
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Exosomes belong to the class of extracellular vesicles of endocytic origin, which are regarded as a promising source of cancer biomarkers in liquid biopsy. As a result, an accurate, sensitive, and specific quantification of these nano-sized particles is of significant importance. Affinity-based approaches are recognized as the most valuable technique for exosome isolation and characterization. Indeed, Affibody biomolecules are a type of protein scaffold engineered with small size and enjoy the features of high thermal stability, affinity, and specificity. While the utilization of antibodies, aptamers, and other biologically active substances for exosome detection has been reported widely, there are no reports describing Affibody molecules’ usage for exosome detection. In this study, for the first time, we have proposed a novel strategy of using Affibody functionalized microbeads (AffiBeads) for exosome detection with a high degree of efficiency. As a proof-of-concept, anti-EGFR-AffiBeads were fabricated and applied to capture and detect human lung A549 cancer cell-derived EGFR-positive exosomes using flow cytometry and fluorescent microscopy. Moreover, the capture efficiency of the AffiBeads were compared with its counterpart antibody. Our results showed that the Affibody probe had a detection limit of 15.6 ng exosomes per mL (~12 exosomes per AffiBead). The approach proposed in the current study can be used for sensitive detection of low expression level markers on tumor-derived exosomes, providing a basis for early-stage cancer diagnosis.
Scanes, E, Parker, LM, Seymour, JR, Siboni, N, Dove, MC, O’Connor, WA & Ross, PM 2021, 'Microbiomes of an oyster are shaped by metabolism and environment', Scientific Reports, vol. 11, no. 1.
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AbstractMicrobiomes can both influence and be influenced by metabolism, but this relationship remains unexplored for invertebrates. We examined the relationship between microbiome and metabolism in response to climate change using oysters as a model marine invertebrate. Oysters form economies and ecosystems across the globe, yet are vulnerable to climate change. Nine genetic lineages of the oyster Saccostrea glomerata were exposed to ambient and elevated temperature and PCO2 treatments. The metabolic rate (MR) and metabolic by-products of extracellular pH and CO2 were measured. The oyster-associated bacterial community in haemolymph was characterised using 16 s rRNA gene sequencing. We found a significant negative relationship between MR and bacterial richness. Bacterial community composition was also significantly influenced by MR, extracellular CO2 and extracellular pH. The effects of extracellular CO2 depended on genotype, and the effects of extracellular pH depended on CO2 and temperature treatments. Changes in MR aligned with a shift in the relative abundance of 152 Amplicon Sequencing Variants (ASVs), with 113 negatively correlated with MR. Some spirochaete ASVs showed positive relationships with MR. We have identified a clear relationship between host metabolism and the microbiome in oysters. Altering this relationship will likely have consequences for the 12 billion USD oyster economy.
Scanes, E, Parker, LM, Seymour, JR, Siboni, N, King, WL, Danckert, NP, Wegner, KM, Dove, MC, O'Connor, WA & Ross, PM 2021, 'Climate change alters the haemolymph microbiome of oysters', Marine Pollution Bulletin, vol. 164, pp. 111991-111991.
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The wellbeing of marine organisms is connected to their microbiome. Oysters are a vital food source and provide ecological services, yet little is known about how climate change such as ocean acidification and warming will affect their microbiome. We exposed the Sydney rock oyster, Saccostrea glomerata, to orthogonal combinations of temperature (24, 28 °C) and pCO2 (400 and 1000 μatm) for eight weeks and used amplicon sequencing of the 16S rRNA (V3-V4) gene to characterise the bacterial community in haemolymph. Overall, elevated pCO2 and temperature interacted to alter the microbiome of oysters, with a clear partitioning of treatments in CAP ordinations. Elevated pCO2 was the strongest driver of species diversity and richness and elevated temperature also increased species richness. Climate change, both ocean acidification and warming, will alter the microbiome of S. glomerata which may increase the susceptibility of oysters to disease.
Scanes, E, Parker, LM, Seymour, JR, Siboni, N, King, WL, Wegner, KM, Dove, MC, O'Connor, WA & Ross, PM 2021, 'Microbiome response differs among selected lines of Sydney rock oysters to ocean warming and acidification', FEMS Microbiology Ecology, vol. 97, no. 8, pp. 1-13.
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ABSTRACTOyster microbiomes are integral to healthy function and can be altered by climate change conditions. Genetic variation among oysters is known to influence the response of oysters to climate change and may ameliorate any adverse effects on oyster microbiome; however, this remains unstudied. Nine full-sibling selected breeding lines of the Sydney rock oyster (Saccostrea glomerata) were exposed to predicted warming (ambient = 24°C, elevated = 28°C) and ocean acidification (ambient pCO2 = 400, elevated pCO2 = 1000 µatm) for 4 weeks. The haemolymph bacterial microbiome was characterized using 16S rRNA (V3–V4) gene sequencing and varied among oyster lines in the control (ambient pCO2, 24°C) treatment. Microbiomes were also altered by climate change dependent on oyster lines. Bacterial α-diversity increased in response to elevated pCO2 in two selected lines, while bacterial β-diversity was significantly altered by combinations of elevated pCO2 and temperature in four selected lines. Climate change treatments caused shifts in the abundance of multiple amplicon sequence variants driving change in the microbiome of some selected lines. We show that oyster genetic background may influence the Sydney rock oyster haemolymph microbiome under climate change and that future assisted evolution breeding programs to enhance resilience should consider the oyster microbiome.
Schanin, J, Gebremeskel, S, Korver, W, Falahati, R, Butuci, M, Haw, TJ, Nair, PM, Liu, G, Hansbro, NG, Hansbro, PM, Evensen, E, Brock, EC, Xu, A, Wong, A, Leung, J, Bebbington, C, Tomasevic, N & Youngblood, BA 2021, 'A monoclonal antibody to Siglec-8 suppresses non-allergic airway inflammation and inhibits IgE-independent mast cell activation', Mucosal Immunology, vol. 14, no. 2, pp. 366-376.
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In addition to their well characterized role in mediating IgE-dependent allergic diseases, aberrant accumulation and activation of mast cells (MCs) is associated with many non-allergic inflammatory diseases, whereby their activation is likely triggered by non-IgE stimuli (e.g., IL-33). Siglec-8 is an inhibitory receptor expressed on MCs and eosinophils that has been shown to inhibit IgE-mediated MC responses and reduce allergic inflammation upon ligation with a monoclonal antibody (mAb). Herein, we evaluated the effects of an anti-Siglec-8 mAb (anti-S8) in non-allergic disease models of experimental cigarette-smoke-induced chronic obstructive pulmonary disease and bleomycin-induced lung injury in Siglec-8 transgenic mice. Therapeutic treatment with anti-S8 inhibited MC activation and reduced recruitment of immune cells, airway inflammation, and lung fibrosis. Similarly, using a model of MC-dependent, IL-33-induced inflammation, anti-S8 treatment suppressed neutrophil influx, and cytokine production through MC inhibition. Transcriptomic profiling of MCs further demonstrated anti-S8-mediated downregulation of MC signaling pathways induced by IL-33, including TNF signaling via NF-κB. Collectively, these findings demonstrate that ligating Siglec-8 with an antibody reduces non-allergic inflammation and inhibits IgE-independent MC activation, supporting the evaluation of an anti-Siglec-8 mAb as a therapeutic approach in both allergic and non-allergic inflammatory diseases in which MCs play a role.
Schuback, N, Tortell, PD, Berman-Frank, I, Campbell, DA, Ciotti, A, Courtecuisse, E, Erickson, ZK, Fujiki, T, Halsey, K, Hickman, AE, Huot, Y, Gorbunov, MY, Hughes, DJ, Kolber, ZS, Moore, CM, Oxborough, K, Prášil, O, Robinson, CM, Ryan-Keogh, TJ, Silsbe, G, Simis, S, Suggett, DJ, Thomalla, S & Varkey, DR 2021, 'Single-Turnover Variable Chlorophyll Fluorescence as a Tool for Assessing Phytoplankton Photosynthesis and Primary Productivity: Opportunities, Caveats and Recommendations', Frontiers in Marine Science, vol. 8, pp. 1-24.
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Phytoplankton photosynthetic physiology can be investigated through single-turnover variable chlorophyll fluorescence (ST-ChlF) approaches, which carry unique potential to autonomously collect data at high spatial and temporal resolution. Over the past decades, significant progress has been made in the development and application of ST-ChlF methods in aquatic ecosystems, and in the interpretation of the resulting observations. At the same time, however, an increasing number of sensor types, sampling protocols, and data processing algorithms have created confusion and uncertainty among potential users, with a growing divergence of practice among different research groups. In this review, we assist the existing and upcoming user community by providing an overview of current approaches and consensus recommendations for the use of ST-ChlF measurements to examine in-situ phytoplankton productivity and photo-physiology. We argue that a consistency of practice and adherence to basic operational and quality control standards is critical to ensuring data inter-comparability. Large datasets of inter-comparable and globally coherent ST-ChlF observations hold the potential to reveal large-scale patterns and trends in phytoplankton photo-physiology, photosynthetic rates and bottom-up controls on primary productivity. As such, they hold great potential to provide invaluable physiological observations on the scales relevant for the development and validation of ecosystem models and remote sensing algorithms.
Séguin, K, Falardeau, M, Mousseau, V, Ducharme, N, Cadola, L & Crispino, F 2021, 'First lessons regarding the data analysis of gunshot residue traces at activity level in TTADB', Canadian Society of Forensic Science Journal, vol. 54, no. 4, pp. 196-209.
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Semisch-Dieter, OK, Choi, AH, Ben-Nissan, B & Stewart, MP 2021, 'Modifying an Implant: A Mini-review of Dental Implant Biomaterials', BIO Integration, vol. 2, no. 1, pp. 12-21.
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AbstractDental implants have been used as far back as 2000BC, and since then have developed into highly sophisticated solutions for tooth replacement. It is becoming increasingly important for the materials used in dental implants to exhibit and maintain favorable long-term mechanical, biological and more recently, aesthetic properties. This review aims to assess the biomaterials used in modern dental implants, introducing their properties, and concentrating on modifications to improve these biomaterials. Focus is drawn to the prominent biomaterials, titanium (Ti) and zirconia due to their prevalence in implant dentistry. Additionally, novel coatings and materials with potential use as viable improvements or alternatives are reviewed. An effective dental biomaterial should osseointegrate, maintain structural integrity, resist corrosion and infection, and not cause systemic toxicity or cytotoxicity. Current materials such as bioactive glass offer protection against biofilm formation, and when combined with a titanium–zirconium (TiZr) alloy, provide a reliable combination of properties to represent a competitive alternative. Further long-term clinical studies are needed to inform the development of next-generation materials.Significance StatementBiomaterials have become essential for modern implants. A suitable implant biomaterial integrates into the body to perform a key function, whilst minimizing negative immune response. Focusing on dentistry, the use of dental implants for tooth replacement requires a balance between bodily response, mechanical structure and performance, and aesthetics. This mini-review addresses the use of biomaterials in dental implants with significant comparisons drawn between Ti and zirconia. Attention is drawn to optimizing surface modification processes and the additional use of coatings. Alternatives and novel developments are addressed,...
Senanayake, S, Pradhan, B, Huete, A & Brennan, J 2021, 'Proposing an ecologically viable and economically sound farming system using a matrix-based geo-informatics approach', Science of The Total Environment, vol. 794, pp. 148788-148788.
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Healthy farming systems play a vital role in improving agricultural productivity and sustainable food production. The present study aimed to propose an efficient framework to evaluate ecologically viable and economically sound farming systems using a matrix-based analytic hierarchy process (AHP) and weighted linear combination method with geo-informatics tools. The proposed framework has been developed and tested in the Central Highlands of Sri Lanka. Results reveal that more than 50% of farming systems demonstrated moderate status in terms of ecological and economic aspects. However, two vulnerable farming systems on the western slopes of the Central Highlands, named WL1a and WM1a, were identified as very poor status. These farming systems should be a top priority for restoration planning and soil conservation to prevent further deterioration. Findings indicate that a combination of ecologically viable (nine indicators) and economical sound (four indicators) criteria are a practical method to scrutinize farming systems and decision making on soil conservation and sustainable land management. In addition, this research introduces a novel approach to delineate the farming systems based on agro-ecological regions and cropping areas using geo-informatics technology. This framework and methodology can be employed to evaluate the farming systems of other parts of the country and elsewhere to identify ecologically viable and economically sound farming systems concerning soil erosion hazards. The proposed approach addresses a new dimension of the decision-making process by evaluating the farming systems relating to soil erosion hazards and suggests introducing policies on priority-based planning for conservation with low-cost strategies for sustainable land management.
Seviour, T, Winnerdy, FR, Wong, LL, Shi, X, Mugunthan, S, Foo, YH, Castaing, R, Adav, SS, Subramoni, S, Kohli, GS, Shewan, HM, Stokes, JR, Rice, SA, Phan, AT & Kjelleberg, S 2021, 'The biofilm matrix scaffold of Pseudomonas aeruginosa contains G-quadruplex extracellular DNA structures', npj Biofilms and Microbiomes, vol. 7, no. 1, p. 27.
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AbstractExtracellular DNA, or eDNA, is recognised as a critical biofilm component; however, it is not understood how it forms networked matrix structures. Here, we isolate eDNA from static-culture Pseudomonas aeruginosa biofilms using ionic liquids to preserve its biophysical signatures of fluid viscoelasticity and the temperature dependency of DNA transitions. We describe a loss of eDNA network structure as resulting from a change in nucleic acid conformation, and propose that its ability to form viscoelastic structures is key to its role in building biofilm matrices. Solid-state analysis of isolated eDNA, as a proxy for eDNA structure in biofilms, reveals non-canonical Hoogsteen base pairs, triads or tetrads involving thymine or uracil, and guanine, suggesting that the eDNA forms G-quadruplex structures. These are less abundant in chromosomal DNA and disappear when eDNA undergoes conformation transition. We verify the occurrence of G-quadruplex structures in the extracellular matrix of intact static and flow-cell biofilms of P. aeruginosa, as displayed by the matrix to G-quadruplex-specific antibody binding, and validate the loss of G-quadruplex structures in vivo to occur coincident with the disappearance of eDNA fibres. Given their stability, understanding how extracellular G-quadruplex structures form will elucidate how P. aeruginosa eDNA builds viscoelastic networks, which are a foundational biofilm property.
Sezginer, Y, Suggett, DJ, Izett, RW & Tortell, PD 2021, 'Irradiance and nutrient-dependent effects on photosynthetic electron transport in Arctic phytoplankton: A comparison of two chlorophyll fluorescence-based approaches to derive primary photochemistry', PLOS ONE, vol. 16, no. 12, pp. e0256410-e0256410.
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We employed Fast Repetition Rate fluorometry for high-resolution mapping of marine phytoplankton photophysiology and primary photochemistry in the Lancaster Sound and Barrow Strait regions of the Canadian Arctic Archipelago in the summer of 2019. Continuous ship-board analysis of chlorophyll a variable fluorescence demonstrated relatively low photochemical efficiency over most of the cruise-track, with the exception of localized regions within Barrow Strait, where there was increased vertical mixing and proximity to land-based nutrient sources. Along the full transect, we observed strong non-photochemical quenching of chlorophyll fluorescence, with relaxation times longer than the 5-minute period used for dark acclimation. Such long-term quenching effects complicate continuous underway acquisition of fluorescence amplitude-based estimates of photosynthetic electron transport rates, which rely on dark acclimation of samples. As an alternative, we employed a new algorithm to derive electron transport rates based on analysis of fluorescence relaxation kinetics, which does not require dark acclimation. Direct comparison of kinetics- and amplitude-based electron transport rate measurements demonstrated that kinetic-based estimates were, on average, 2-fold higher than amplitude-based values. The magnitude of decoupling between the two electron transport rate estimates increased in association with photophysiological diagnostics of nutrient stress. Discrepancies between electron transport rate estimates likely resulted from the use of different photophysiological parameters to derive the kinetics- and amplitude-based algorithms, and choice of numerical model used to fit variable fluorescence curves and analyze fluorescence kinetics under actinic light. Our results highlight environmental and methodological influences on fluorescence-based photochemistry estimates, and prompt discussion of best-practices for future underway fl...
Shad, KF, Soubra, W & Cordato, D 2021, 'The role of thymoquinone, a major constituent of Nigella sativa, in the treatment of inflammatory and infectious diseases'.
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Nigella sativa (N. sativa) is an annual flowering plant that has been used as a traditional remedy for many centuries. The seed possesses a large variety of compounds with thymoquinone (TQ) considered its major but not sole bioactive constituent. Supercritical fluid extraction, geographical location, and oxidative status of N. sativa produces the highest yield of essential oil content including TQ. Thymoquinone is lipophilic, heat and light sensitive with low oral bioavailability and rapid elimination that have significantly inhibited its pharmacological development. Novel developments in nanoparticulate-based oral administration, nasal spray and transdermal delivery may allow the clinical development of N. sativa and TQ as therapeutic agents. Animal and human studies indicate a potential role of N. sativa seed oil and TQ for a diverse range of disease processes including hypertension, dyslipidaemia, type 2 diabetes mellitus, arthritis, asthma, bacterial and viral infections, neurological and dermatological disorders, as it belongs to the group of pan-assay interference compounds. This review outlines the pharmacological properties of N. sativa and TQ and their potential wide application for a large variety of human diseases. The paper will focus on recent studies of the anti-inflammatory and antiviral properties that make N. sativa and TQ promising therapeutic agents targeting contemporary inflammatory and infectious diseases including Covid 19.
Shahcheraghi, SH, Ayatollahi, J, Aljabali, AAA, Shastri, MD, Shukla, SD, Chellappan, DK, Jha, NK, Anand, K, Katari, NK, Mehta, M, Satija, S, Dureja, H, Mishra, V, Almutary, AG, Alnuqaydan, AM, Charbe, N, Prasher, P, Gupta, G, Dua, K, Lotfi, M, Bakshi, HA & Tambuwala, MM 2021, 'An Overview of Vaccine Development for COVID-19', Therapeutic Delivery, vol. 12, no. 3, pp. 235-244.
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The COVID-19 pandemic continues to endanger world health and the economy. The causative SARS-CoV-2 coronavirus has a unique replication system. The end point of the COVID-19 pandemic is either herd immunity or widespread availability of an effective vaccine. Multiple candidate vaccines – peptide, virus-like particle, viral vectors (replicating and nonreplicating), nucleic acids (DNA or RNA), live attenuated virus, recombinant designed proteins and inactivated virus – are presently under various stages of expansion, and a small number of vaccine candidates have progressed into clinical phases. At the time of writing, three major pharmaceutical companies, namely Pfizer and Moderna, have their vaccines under mass production and administered to the public. This review aims to investigate the most critical vaccines developed for COVID-19 to date.
Shahid, A, Khan, AZ, Malik, S, Liu, C-G, Mehmood, MA, Syafiuddin, A, Wang, N, Zhu, H & Boopathy, R 2021, 'Advances in Green Technologies for the Removal of Effluent Organic Matter from the Urban Wastewater', Current Pollution Reports, vol. 7, no. 4, pp. 463-475.
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Purpose of Review: Effluent organic matter (EfOM) is a blend of organic matter, microbial constituents, biological metabolites, and synthetic chemicals which is originated mainly due to anthropogenic activities and is a matter of emerging environmental concern. The presence of EfOM poses a major challenge in the wastewater treatment processes. This review is aimed to assess the recent progress in developing innovative green approaches for the biotransformation of EfOM into ecofriendly products which is vital to attain the “zero-waste” paradigm to achieve wastewater reclamation and environmental sustainability under the umbrella of circular bioeconomy. Recent Findings: Characteristics of EfOM and its impact on wastewater treatment processes have been evaluated. The potential and shortcomings of the traditional, advanced, and biological approaches for the EfOM removal have been described. Recent strategies which are based on the combination of two or more of these technologies (hybrid systems) have been discussed to address the challenges/shortcomings of the standalone technologies and to improve the process efficiency. Microalgae and cyanobacteria-based removal of EfOM along with its subsequent utilization as a soil amender is proposed as a novel trend in the future. Summary: Assessment of the previously employed technologies provided an insight into their working mechanisms which have suggested several improvements in the processes. Besides, hybrid systems could be an ecofriendly removal of EfOM via biosorption.
Shahid, A, Malik, S, Liu, C-G, Musharraf, SG, Siddiqui, AJ, Khan, F, Tarbiah, NI, Gull, M, Rashid, U & Mehmood, MA 2021, 'Characterization of a newly isolated cyanobacterium Plectonema terebrans for biotransformation of the wastewater-derived nutrients to biofuel and high-value bioproducts', Journal of Water Process Engineering, vol. 39, pp. 101702-101702.
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Cultivating photosynthetic microbes in city wastewater may help to achieve environmental sustainability owing to concomitant pollutant removal, biological transformation of the nutrients into bioproducts, and atmospheric carbon fixation. Cyanobacteria are the most efficient photosynthetic fixers of atmospheric carbon along with the microalgae. The present study was focused on optimizing the growth conditions for a newly isolated filamentous cyanobacterium Plectonema terebrans BERC10 to achieve enhanced biomass and metabolite productivity for a multiproduct biorefinery using various compositions of synthetic wastewaters. Higher biomass productivity of 140 mg L−1 d−1 (dried mass) with CO2 sequestration rate of 250 mg L−1 day−1 was achieved by mimicking the summer (32 ± 2 °C) cultivation conditions, which was further favored by the wastewater-derived alkalinity (pH 10.0–11.0). The biomass produced was rich in carbohydrates and lipids, having 58.68 mgg−1d−1 and 39.25 mgg−1d−1 of carbohydrate and lipid productivities, respectively. While winter cultivation conditions (22 ± 2 °C) favored higher protein productivity (34.49 mgg−1d−1) when compared to summer conditions. Additionally, in response to excessive nutrients and alkalinity (pH 10.0), it produced 180-198 mgg-1 of phycobilins. Considering the multiproduct concept, the phycobilins were extracted and lipids from the residual biomass were converted to biodiesel and analyzed by gas chromatography-mass spectrometry (GC–MS). Intrestingly, phycobilin extraction had no negative impact on the quality and content of the biodiesel in the residual biomass. These features make the Plectonema terebrans BERC10 a promising candidate for the biological transformation of wastewater derived nutrients to biofuels and bioproducts.
Shahid, A, Usman, M, Atta, Z, Musharraf, SG, Malik, S, Elkamel, A, Shahid, M, Abdulhamid Alkhattabi, N, Gull, M & Mehmood, MA 2021, 'Impact of wastewater cultivation on pollutant removal, biomass production, metabolite biosynthesis, and carbon dioxide fixation of newly isolated cyanobacteria in a multiproduct biorefinery paradigm', Bioresource Technology, vol. 333, pp. 125194-125194.
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The impact of wastewater cultivation was studied on pollutant removal, biomass production, and biosynthesis of high-value metabolites by newly isolated cyanobacteria namely Acaryochloris marina BERC03, Oscillatoria sp. BERC04, and Pleurocapsa sp. BERC06. During cultivation in urabn wastewater, its pH used to adjust from pH 8.0 to 11, offering contamination-free cultivation, and flotation-based easy harvesting. Besides, wastewater cultivation improved biomass production by 1.3-fold when compared to control along with 3.54-4.2 gL-1 of CO2 fixation, concomitantly removing suspended organic matter, total nitrogen, and phosphorus by 100%, 53%, and 88%, respectively. Biomass accumulated 26-36% carbohydrates, 15-28% proteins, 38-43% lipids, and 6.3-9.5% phycobilins, where phycobilin yield was improved by 1.6-fold when compared to control. Lipids extracted from the pigment-free biomass were trans-esterified to biodiesel where pigment extraction showed no negative impact on quality of the biodiesel. These strains demonstrated the potential to become feedstock of an integrated biorefinery using urban wastewater as low-cost growth media.
Shan, X, Wang, F, Wang, D, Wen, S, Chen, C, Di, X, Nie, P, Liao, J, Liu, Y, Ding, L, Reece, PJ & Jin, D 2021, 'Optical tweezers beyond refractive index mismatch using highly doped upconversion nanoparticles', Nature Nanotechnology, vol. 16, no. 5, pp. 531-537.
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Optical tweezers are widely used in materials assembly1, characterization2, biomechanical force sensing3,4 and the in vivo manipulation of cells5 and organs6. The trapping force has primarily been generated through the refractive index mismatch between a trapped object and its surrounding medium. This poses a fundamental challenge for the optical trapping of low-refractive-index nanoscale objects, including nanoparticles and intracellular organelles. Here, we report a technology that employs a resonance effect to enhance the permittivity and polarizability of nanocrystals, leading to enhanced optical trapping forces by orders of magnitude. This effectively bypasses the requirement of refractive index mismatch at the nanoscale. We show that under resonance conditions, highly doping lanthanide ions in NaYF4 nanocrystals makes the real part of the Clausius-Mossotti factor approach its asymptotic limit, thereby achieving a maximum optical trap stiffness of 0.086 pN μm-1 mW-1 for 23.3-nm-radius low-refractive-index (1.46) nanoparticles, that is, more than 30 times stronger than the reported value for gold nanoparticles of the same size. Our results suggest a new potential of lanthanide doping for the optical control of the refractive index of nanomaterials, developing the optical force tag for the intracellular manipulation of organelles and integrating optical tweezers with temperature sensing and laser cooling7 capabilities.
Shariev, A, Menounos, S, Laos, AJ, Laxman, P, Lai, D, Hua, S, Zinger, A, McRae, CR, Casbolt, LS, Combes, V, Smith, G, Hung, T-T, Dixon, KM, Thordarson, P, Mason, RS & Das, A 2021, 'Skin protective and regenerative effects of RM191A, a novel superoxide dismutase mimetic', Redox Biology, vol. 38, pp. 101790-101790.
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Superoxide dismutase (SOD) is known to be protective against oxidative stress-mediated skin dysfunction. Here we explore the potential therapeutic activities of RM191A, a novel SOD mimetic, on skin. RM191A is a water-soluble dimeric copper (Cu2+-Cu3+)-centred polyglycine coordination complex. It displays 10-fold higher superoxide quenching activity compared to SOD as well as significant antioxidant, anti-inflammatory and immunomodulatory activities through beneficial modulation of several significant inflammatory cytokines in vitro and in vivo. We tested the therapeutic potential of RM191A in a topical gel using a human skin explant model and observed that it significantly inhibits UV-induced DNA damage in the epidermis and dermis, including cyclobutane pyrimidine dimers (CPD), 8-oxo-guanine (8-oxoG) and 8-nitroguanine (8NGO). RM191A topical gel is found to be non-toxic, non-teratogenic and readily distributed in the body of mice. Moreover, it significantly accelerates excisional wound healing, reduces 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced inflammation and attenuates age-associated oxidative stress in skin, demonstrating both skin regenerative and geroprotective properties of RM191A.
Sharif, HMA, Li, T, Mahmood, N, Ahmad, M, Xu, J, Mahmood, A, Djellabi, R & Yang, B 2021, 'Thermally activated epoxy-functionalized carbon as an electrocatalyst for efficient NOx reduction', Carbon, vol. 182, pp. 516-524.
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Large toxic emissions like nitrogen and sulphur oxides (NOx, SO2) are causing serious environmental and health issues. Catalytic reduction of NOx and SOx into friendly gases is considered one of the best approaches. However, regeneration of catalyst, higher bond-dissociation energy for NOx, i.e., 150.7 kcal/mol, escape of intermediate gas (N2O, a greenhouse gas) with treated flue-gas, and limited activity of catalyst remains a great challenge. Here, a cheap, binderless naturally-extracted bass-wood thin carbon electrode (TCE) was fabricated, which shows excellent catalytic activity towards NOx reduction. The bass-wood carbonization was carried out at 900 °C followed by thermal activation in the presence of CO2 gas at 750 °C. The thermal activation resulted in increased epoxy groups on the surface of the TCE and enhancement in the surface area as well as the degree of graphitization. The TCE unique 3D strongly inter-connected network through hierarchical micro/meso/macro pores that allow large electrode/electrolyte interface. Owing to these characteristics, the TCE exhibited excellent catalytic efficiency towards NOx (∼83.3%) under ambient conditions and enhanced catalytic response around neutral pH and sulphite exposure as well as excellent stability up to 168 h. Moreover, a temperature-dependent activity trend was found where the highest catalytic activity was achieved at 80 °C beyond which the electrolyte became evaporative and resulted in performance decrease. The designed electrocatalyst is low-cost, sustainable and showed great potential for effective NOx-reduction, which might be used for NOx abatement at large scale.
Sharif, HMA, Mahmood, A, Djellabi, R, Cheng, H-Y, Dong, H, Ajibade, FO, Ali, I, Yang, B & Wang, A-J 2021, 'Utilization of electrochemical treatment and surface reconstruction to achieve long lasting catalyst for NOx removal', Journal of Hazardous Materials, vol. 401, pp. 123440-123440.
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The development of catalysts has seen tremendous growth recently but most strategies only report utilization of catalysts for a few initial cycles without taking into account the influence of oxygen poisoning. Here, the magnetic Fe3O4@EDTA-Fe (MEFe, having a core Fe3O4 particle with EDTA-Fe coating) was investigated as a model catalyst for long-term recycling for the removal of nitrogen oxide (NOx) from NO/O2 mixture, followed by N2O recovery. The concentration of oxygen in the flue gas was found to have a strong impact on NOx absorption and catalytic response. To circumvent the oxygen poisoning, the MEFe was subjected to electrochemical treatment in the presence of neutral red (N.R.) and NO removal efficiency was ∼95 % noted. Furthermore, the surface of the catalyst degraded significantly (p < 0.05) after 6-7 repetitive cycling due to surface catalytic reactions, surface poisoning, oxidation of metallic species as well as residual stresses. The MEFe surface was reconstructed after 7 cycles using EDTA solution and Fe source to achieve similar surface coating as the fresh MEFe catalyst. The reconstructed MEFe exhibited similar NOx absorption capability as the fresh MEFe and the reconstruction loop was repeated several times to achieve long term cycling, which make the catalyst cost-effective. Hence, it is proposed that a successful regeneration process can be employed for promising, sustainable and long-lasting catalytic treatment of air pollutants.
Shastri, MD, Allam, VSRR, Shukla, SD, Jha, NK, Paudel, KR, Peterson, GM, Patel, RP, Hansbro, PM, Chellappan, DK & Dua, K 2021, 'Interleukin-13: A pivotal target against influenza-induced exacerbation of chronic lung diseases', Life Sciences, vol. 283, pp. 119871-119871.
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Non-communicable, chronic respiratory diseases (CRDs) affect millions of individuals worldwide. The course of these CRDs (asthma, chronic obstructive pulmonary disease, and cystic fibrosis) are often punctuated by microbial infections that may result in hospitalization and are associated with increased risk of morbidity and mortality, as well as reduced quality of life. Interleukin-13 (IL-13) is a key protein that regulates airway inflammation and mucus hypersecretion. There has been much interest in IL-13 from the last two decades. This cytokine is believed to play a decisive role in the exacerbation of inflammation during the course of viral infections, especially, in those with pre-existing CRDs. Here, we discuss the common viral infections in CRDs, as well as the potential role that IL-13 plays in the virus-induced disease pathogenesis of CRDs. We also discuss, in detail, the immune-modulation potential of IL-13 that could be translated to in-depth studies to develop IL-13-based therapeutic entities.
Shastri, MD, Chong, WC, Dua, K, Peterson, GM, Patel, RP, Mahmood, MQ, Tambuwala, M, Chellappan, DK, Hansbro, NG, Shukla, SD & Hansbro, PM 2021, 'Emerging concepts and directed therapeutics for the management of asthma: regulating the regulators', Inflammopharmacology, vol. 29, no. 1, pp. 15-33.
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Asthma is a common, heterogeneous and serious disease, its prevalence has steadily risen in most parts of the world, and the condition is often inadequately controlled in many patients. Hence, there is a major need for new therapeutic approaches. Mild-to-moderate asthma is considered a T-helper cell type-2-mediated inflammatory disorder that develops due to abnormal immune responses to otherwise innocuous allergens. Prolonged exposure to allergens and persistent inflammation results in myofibroblast infiltration and airway remodelling with mucus hypersecretion, airway smooth muscle hypertrophy, and excess collagen deposition. The airways become hyper-responsive to provocation resulting in the characteristic wheezing and obstructed airflow experienced by patients. Extensive research has progressed the understanding of the underlying mechanisms and the development of new treatments for the management of asthma. Here, we review the basis of the disease, covering new areas such as the role of vascularisation and microRNAs, as well as associated potential therapeutic interventions utilising reports from animal and human studies. We also cover novel drug delivery strategies that are being developed to enhance therapeutic efficacy and patient compliance. Potential avenues to explore to improve the future of asthma management are highlighted.
Shaukat, MA, Shaukat, HR, Qadir, Z, Munawar, HS, Kouzani, AZ & Mahmud, MAP 2021, 'Cluster Analysis and Model Comparison Using Smart Meter Data', Sensors, vol. 21, no. 9, pp. 3157-3157.
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Load forecasting plays a crucial role in the world of smart grids. It governs many aspects of the smart grid and smart meter, such as demand response, asset management, investment, and future direction. This paper proposes time-series forecasting for short-term load prediction to unveil the load forecast benefits through different statistical and mathematical models, such as artificial neural networks, auto-regression, and ARIMA. It targets the problem of excessive computational load when dealing with time-series data. It also presents a business case that is used to analyze different clusters to find underlying factors of load consumption and predict the behavior of customers based on different parameters. On evaluating the accuracy of the prediction models, it is observed that ARIMA models with the (P, D, Q) values as (1, 1, 1) were most accurate compared to other values.
Shi, X, Zuo, Y, Zhai, P, Shen, J, Yang, Y, Gao, Z, Liao, M, Wu, J, Wang, J, Xu, X, Tong, Q, Zhang, B, Wang, B, Sun, X, Zhang, L, Pei, Q, Jin, D, Chen, P & Peng, H 2021, 'Large-area display textiles integrated with functional systems', Nature, vol. 591, no. 7849, pp. 240-245.
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Displays are basic building blocks of modern electronics1,2. Integrating displays into textiles offers exciting opportunities for smart electronic textiles—the ultimate goal of wearable technology, poised to change the way in which we interact with electronic devices3,4,5,6. Display textiles serve to bridge human–machine interactions7,8,9, offering, for instance, a real-time communication tool for individuals with voice or speech difficulties. Electronic textiles capable of communicating10, sensing11,12 and supplying electricity13,14 have been reported previously. However, textiles with functional, large-area displays have not yet been achieved, because it is challenging to obtain small illuminating units that are both durable and easy to assemble over a wide area. Here we report a 6-metre-long, 25-centimetre-wide display textile containing 5 × 105 electroluminescent units spaced approximately 800 micrometres apart. Weaving conductive weft and luminescent warp fibres forms micrometre-scale electroluminescent units at the weft–warp contact points. The brightness between electroluminescent units deviates by less than 8 per cent and remains stable even when the textile is bent, stretched or pressed. Our display textile is flexible and breathable and withstands repeated machine-washing, making it suitable for practical applications. We show that an integrated textile system consisting of display, keyboard and power supply can serve as a communication tool, demonstrating the system’s potential within the ‘internet of things’ in various areas, including healthcare. Our approach unifies the fabrication and function of electronic devices with textiles, and we expect that woven-fibre materials will shape the next generation of electronics.
Shrestha, J, Ryan, ST, Mills, O, Zhand, S, Razavi Bazaz, S, Hansbro, PM, Ghadiri, M & Ebrahimi Warkiani, M 2021, 'A 3D-printed microfluidic platform for simulating the effects of CPAP on the nasal epithelium', Biofabrication, vol. 13, no. 3, pp. 035028-035028.
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Abstract Obstructive sleep apnea (OSA) is a chronic disorder that involves a decrease or complete cessation of airflow during sleep. It occurs when the muscles supporting the soft tissues in the throat relax during sleep, causing narrowing or closure of the upper airway. Sleep apnea is a serious medical condition with an increased risk of cardiovascular complications and impaired quality of life. Continuous positive airway pressure (CPAP) is the most effective treatment for moderate to severe cases of OSA and is effective in mild sleep apnea. However, CPAP therapy is associated with the development of several nasal side effects and is inconvenient for the user, leading to low compliance rates. The effects of CPAP treatment on the upper respiratory system, as well as the pathogenesis of side effects, are incompletely understood and not adequately researched. To better understand the effects of CPAP treatment on the upper respiratory system, we developed an in vitro 3D-printed microfluidic platform. A nasal epithelial cell line, RPMI 2650, was then exposed to certain conditions to mimic the in vivo environment. To create these conditions, the microfluidic device was utilized to expose nasal epithelial cells grown and differentiated at the air–liquid interface. The airflow was similar to what is experienced with CPAP, with pressure ranging between 0 and 20 cm of H2O. Cells exposed to pressure showed decreased barrier integrity, change in cellular shape, and increased cell death (lactate dehydrogenase release into media) compared to unstressed cells. Stressed cells also showed increased secretions of inflammatory markers IL-6 and IL-8 and had increased production of ATP. Our results suggest that stress induced by airflow leads to structural, metabolic, and inflammatory changes in the nasal epithelium, which may be responsible for develo...
Sillapachaiyaporn, C, Rangsinth, P, Nilkhet, S, Ung, AT, Chuchawankul, S & Tencomnao, T 2021, 'Neuroprotective Effects against Glutamate-Induced HT-22 Hippocampal Cell Damage and Caenorhabditis elegans Lifespan/Healthspan Enhancing Activity of Auricularia polytricha Mushroom Extracts', Pharmaceuticals, vol. 14, no. 10, pp. 1001-1001.
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Oxidative stress is associated with several diseases, particularly neurodegenerative diseases, commonly found in the elderly. The attenuation of oxidative status is one of the alternatives for neuroprotection and anti-aging. Auricularia polytricha (AP), an edible mushroom, contains many therapeutic properties, including antioxidant properties. Herein, we report the effects of AP extracts on antioxidant, neuroprotective, and anti-aging activities. The neuroprotective effect of AP extracts against glutamate-induced HT-22 neuronal damage was determined by evaluating the cytotoxicity, intracellular reactive oxygen species (ROS) accumulation, and expression of antioxidant enzyme genes. Lifespan and healthspan assays were performed to examine the effects of AP extracts from Caenorhabditis elegans. We found that ethanolic extract (APE) attenuated glutamate-induced HT-22 cytotoxicity and increased the expression of antioxidant enzyme genes. Moreover, APE promoted in the longevity and health of the C. elegans. Chemical analysis of the extracts revealed that APE contains the highest quantity of flavonoids and a reasonable percentage of phenols. The lipophilic compounds in APE were identified by gas chromatography/mass spectrometry (GC/MS), revealing that APE mainly contains linoleic acid. Interestingly, linoleic acid suppressed neuronal toxicity and ROS accumulation from glutamate induction. These results indicate that AP could be an exciting natural source that may potentially serves as neuroprotective and anti-aging agents.
Sim, DZH, Mowe, MAD, Song, Y, Lu, J, Tan, HTW, Mitrovic, SM, Roelke, DL & Yeo, DCJ 2021, 'Tropical macrophytes promote phytoplankton community shifts in lake mesocosms: relevance for lake restoration in warm climates', Hydrobiologia, vol. 848, no. 20, pp. 4861-4884.
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Sintov, E, Gerace, D & Melton, DA 2021, 'A human ESC line for efficient CRISPR editing of pluripotent stem cells', Stem Cell Research, vol. 57, pp. 102591-102591.
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Skerrett‐Byrne, DA, Bromfield, EG, Murray, HC, Jamaluddin, MFB, Jarnicki, AG, Fricker, M, Essilfie, AT, Jones, B, Haw, TJ, Hampsey, D, Anderson, AL, Nixon, B, Scott, RJ, Wark, PAB, Dun, MD & Hansbro, PM 2021, 'Time‐resolved proteomic profiling of cigarette smoke‐induced experimental chronic obstructive pulmonary disease', Respirology, vol. 26, no. 10, pp. 960-973.
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AbstractBackground and objectiveChronic obstructive pulmonary disease (COPD) is the third leading cause of illness and death worldwide. Current treatments aim to control symptoms with none able to reverse disease or stop its progression. We explored the major molecular changes in COPD pathogenesis.MethodsWe employed quantitative label‐based proteomics to map the changes in the lung tissue proteome of cigarette smoke‐induced experimental COPD that is induced over 8 weeks and progresses over 12 weeks.ResultsQuantification of 7324 proteins enabled the tracking of changes to the proteome. Alterations in protein expression profiles occurred in the induction phase, with 18 and 16 protein changes at 4‐ and 6‐week time points, compared to age‐matched controls, respectively. Strikingly, 269 proteins had altered expression after 8 weeks when the hallmark pathological features of human COPD emerge, but this dropped to 27 changes at 12 weeks with disease progression. Differentially expressed proteins were validated using other mouse and human COPD bronchial biopsy samples. Major changes in RNA biosynthesis (heterogeneous nuclear ribonucleoproteins C1/C2 [HNRNPC] and RNA‐binding protein Musashi homologue 2 [MSI2]) and modulators of inflammatory responses (S100A1) were notable. Mitochondrial dysfunction and changes in oxidative stress proteins also occurred.ConclusionWe provide a detailed proteomic profile, identifying proteins associated with the pathogenesis and disease progression of COPD establishing a platform to develop effective new treatment strategies.
Skinnider, MA, Wang, F, Pasin, D, Greiner, R, Foster, LJ, Dalsgaard, PW & Wishart, DS 2021, 'A deep generative model enables automated structure elucidation of novel psychoactive substances', Nature Machine Intelligence, vol. 3, no. 11, pp. 973-984.
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Smith, C, Cokcetin, N, Truong, T, Harry, E, Hutvagner, G & Bajan, S 2021, 'Cataloguing the small RNA content of honey using next generation sequencing', Food Chemistry: Molecular Sciences, vol. 2, pp. 100014-100014.
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Solntsev, AS, Agarwal, GS & Kivshar, YS 2021, 'Metasurfaces for quantum photonics', Nature Photonics, vol. 15, no. 5, pp. 327-336.
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Rapid progress in the development of metamaterials and metaphotonics allowed bulky optical assemblies to be replaced with thin nanostructured films, often called metasurfaces, opening a broad range of novel and superior applications of flat optics to the generation, manipulation and detection of classical light. Recently, these developments started making headway in quantum photonics, where novel opportunities arose for the control of non-classical nature of light, including photon statistics, quantum state superposition, quantum entanglement and single-photon detection. In this Perspective, we review recent progress in the emerging field of quantum-photonics applications of metasurfaces, focusing on innovative and promising approaches to create, manipulate and detect non-classical light.
Songsom, V, Koedsin, W, Ritchie, RJ & Huete, A 2021, 'Mangrove Phenology and Water Influences Measured with Digital Repeat Photography', Remote Sensing, vol. 13, no. 2, pp. 307-307.
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The intertidal habitat of mangroves is very complex due to the dynamic roles of land and sea drivers. Knowledge of mangrove phenology can help in understanding mangrove growth cycles and their responses to climate and environmental changes. Studies of phenology based on digital repeat photography, or phenocams, have been successful in many terrestrial forests and other ecosystems, however few phenocam studies in mangrove forests showing the influence and interactions of water color and tidal water levels have been performed in sub-tropical and equatorial environments. In this study, we investigated the diurnal and seasonal patterns of an equatorial mangrove forest area at an Andaman Sea site in Phuket province, Southern Thailand, using two phenocams placed at different elevations and with different view orientations, which continuously monitored vegetation and water dynamics from July 2015 to August 2016. The aims of this study were to investigate fine-resolution, in situ mangrove forest phenology and assess the influence and interactions of water color and tidal water levels on the mangrove–water canopy signal. Diurnal and seasonal patterns of red, green, and blue chromatic coordinate (RCC, GCC, and BCC) indices were analyzed over various mangrove forest and water regions of interest (ROI). GCC signals from the water background were found to positively track diurnal water levels, while RCC signals were negatively related with tidal water levels, hence lower water levels yielded higher RCC values, reflecting brownish water colors and increased soil and mud exposure. At seasonal scales, the GCC profiles of the mangrove forest peaked in the dry season and were negatively related with the water level, however the inclusion of the water background signal dampened this relationship. We also detected a strong lunar tidal water periodicity in seasonal GCC values that was not only present in the water background, but was also detected in the mangrove–wa...
Songsomboon, K, Brenton, Z, Heuser, J, Kresovich, S, Shakoor, N, Mockler, T & Cooper, EA 2021, 'Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation', G3 Genes|Genomes|Genetics, vol. 11, no. 7.
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Abstract Genomic structural mutations, especially deletions, are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum [Sorghum bicolor (L.) Moench] is one of the most widely grown cereal crops in the world. It has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity. In this study, we identified genome-wide SVs in the Biomass Association Panel, a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. Using Illumina-based, short-read whole-genome resequencing data from every genotype, we found a total of 24,648 SVs, including 22,359 deletions. The global site frequency spectrum of deletions and other types of SVs fit a model of neutral evolution, suggesting that the majority of these mutations were not under any types of selection. Clustering results based on single nucleotide polymorphisms separated the genotypes into eight clusters which largely corresponded with geographic origins, with many of the large deletions we uncovered being unique to a single cluster. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic and abiotic stress responses, supporting the possibility that at least some of these deletions contribute to local adaptation in sorghum.
Speer, M, Leslie, L, Hartigan, J & MacNamara, S 2021, 'Changes in Frequency and Location of East Coast Low Pressure Systems Affecting Southeast Australia', Climate, vol. 9, no. 3, pp. 44-44.
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Low pressure systems off the southeast coast of Australia can generate intense rainfall and associated flooding, destructive winds, and coastal erosion, particularly during the cool season (April–September). Impacts depend on coastal proximity, strength and latitude. Therefore, it is important to investigate changes in frequency, duration, location, and intensity of these systems. First, an existing observation-based database of these low pressure systems, for 1970–2006, is extended to 2019, focusing on April–September and using archived Australian Bureau of Meteorology MSLP charts. Second, data consistency between 1970 and 2006 and 2007 and 2019 is confirmed. Third, permutation testing is performed on differences in means and variances between the two 25-year intervals 1970–1994 and 1995–2019. Additionally, trends in positions, durations and central pressures of the systems are investigated. p-values from permutation tests reveal statistically significant increases in mean low pressure system frequencies. Specifically, a greater frequency of both total days and initial development days only, occurred in the latter period. Statistically significant lower variance for both latitude and longitude in systems that developed in both subtropical easterly and mid-latitude westerly wind regimes indicate a shift south and east in the latter period. Furthermore, statistically significant differences in variance of development location of explosive low pressure systems that develop in a low level easterly wind regime indicate a shift further south and east. These changes are consistent with fewer systems projected to impact the east coast. Finally, important changes are suggested in the large scale atmospheric dynamics of the eastern Australian/Tasman Sea region.
Speer, MS, Leslie, LM, MacNamara, S & Hartigan, J 2021, 'From the 1990s climate change has decreased cool season catchment precipitation reducing river heights in Australia’s southern Murray-Darling Basin', Scientific Reports, vol. 11, no. 1, p. 16136.
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AbstractThe Murray-Darling Basin (MDB) is Australia’s major agricultural region. The southern MDB receives most of its annual catchment runoff during the cool season (April–September). Focusing on the Murrumbidgee River measurements at Wagga Wagga and further downstream at Hay, cool season river heights are available year to year. The 27-year period April–September Hay and Wagga Wagga river heights exhibit decreases between 1965 and 1991 and 1992–2018 not matched by declining April-September catchment rainfall. However, permutation tests of means and variances of late autumn (April–May) dam catchment precipitation and net inflows, produced p-values indicating a highly significant decline since the early 1990s. Consequently, dry catchments in late autumn, even with average cool season rainfall, have reduced dam inflows and decreased river heights downstream from Wagga Wagga, before water extraction for irrigation. It is concluded that lower April–September mean river heights at Wagga Wagga and decreased river height variability at Hay, since the mid-1990s, are due to combined lower April–May catchment precipitation and increased mean temperatures. Machine learning attribute detection revealed the southern MDB drivers as the southern annular mode (SAM), inter-decadal Pacific oscillation (IPO), Indian Ocean dipole (IOD) and global sea-surface temperature (GlobalSST). Continued catchment drying and warming will drastically reduce future water availability.
Srivastava, A, Rodriguez, JF, Saco, PM, Kumari, N & Yetemen, O 2021, 'Global Analysis of Atmospheric Transmissivity Using Cloud Cover, Aridity and Flux Network Datasets', Remote Sensing, vol. 13, no. 9, pp. 1716-1716.
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Atmospheric transmissivity (τ) is a critical factor in climatology, which affects surface energy balance, measured at a limited number of meteorological stations worldwide. With the limited availability of meteorological datasets in remote areas across different climatic regions, estimation of τ is becoming a challenging task for adequate hydrological, climatic, and crop modeling studies. The availability of solar radiation data is comparatively less accessible on a global scale than the temperature and precipitation datasets, which makes it necessary to develop methods to estimate τ. Most of the previous studies provided region specific datasets of τ, which usually provide local assessments. Hence, there is a necessity to give the empirical models for τ estimation on a global scale that can be easily assessed. This study presents the analysis of the τ relationship with varying geographic features and climatic factors like latitude, aridity index, cloud cover, precipitation, temperature, diurnal temperature range, and elevation. In addition to these factors, the applicability of these relationships was evaluated for different climate types. Thus, empirical models have been proposed for each climate type to estimate τ by using the most effective factors such as cloud cover and aridity index. The cloud cover is an important yet often overlooked factor that can be used to determine the global atmospheric transmissivity. The empirical relationship and statistical indicator provided the best performance in equatorial climates as the coefficient of determination (r2) was 0.88 relatively higher than the warm temperate (r2 = 0.74) and arid regions (r2 = 0.46). According to the results, it is believed that the analysis presented in this work is applicable for estimating the τ in different ecosystems across the globe.
Srivastava, A, Saco, PM, Rodriguez, JF, Kumari, N, Chun, KP & Yetemen, O 2021, 'The role of landscape morphology on soil moisture variability in semi‐arid ecosystems', Hydrological Processes, vol. 35, no. 1, pp. 1-19.
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AbstractPrevious studies on semi‐arid ecosystems have shown high values of soil moisture variability (SMV) primarily induced by the combined effects of non‐uniform precipitation, incoming solar radiation, and soil and vegetation properties. However, the relative impact of these various factors on SMV has been difficult to evaluate due to limited availability of field data. In addition, only a limited number of studies have analysed the role of landscape morphology on SMV. Here we use numerical simulations of a simple hydrological model, the Bucket Grassland Model, to systematically analyse the effect of each contributing factor on SMV on two different landscape morphologies. The two different landform morphologies represent landscapes dominated respectively by either diffusive erosion or fluvial erosion processes. We conducted various simulations driven by a stochastically generated 100‐year climate time series, which is long enough to capture climatic fluctuations, in order to understand the effect of various soil moisture controlling factors on the spatiotemporal SMV. Our modelling results show that the fluvial dominated landscapes promote higher spatial SMV than the diffusive dominated ones. Further, the role of landform morphology on SMV is more pronounced in regions where the spatial variability of incoming solar radiation and precipitation is high.
Srivastava, P, Gunawan, C, Soeriyadi, A, Amal, R, Hoehn, K & Marquis, C 2021, 'In vitrocoronal protein signatures and biological impact of silver nanoparticles synthesized with different natural polymers as capping agents', Nanoscale Advances, vol. 3, no. 15, pp. 4424-4439.
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Biopolymer-capped silver nanoparticle synthesis. Compositional and stability analysis of synthesised particles. Proteomic analysis of particles following serum exposure.In vitrohemolytic assays. Organ distribution following administration in mice.
Stayte, S, Dhungana, A, Vissel, B & Bradfield, LA 2021, 'Parafascicular Thalamic and Orbitofrontal Cortical Inputs to Striatum Represent States for Goal-Directed Action Selection', Frontiers in Behavioral Neuroscience, vol. 15, p. 655029.
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Several lines of evidence accrued over the last 5–10 years have converged to suggest that the parafascicular nucleus of the thalamus and the lateral orbitofrontal cortex each represent or contribute to internal state/context representations that guide action selection in partially observable task situations. In rodents, inactivations of each structure have been found to selectively impair performance in paradigms testing goal-directed action selection, but only when that action selection relies on state representations. Electrophysiological evidence has suggested that each structure achieves this function via inputs onto cholinergic interneurons (CINs) in the dorsomedial striatum. Here, we briefly review these studies, then point to anatomical evidence regarding the afferents of each structure and what they suggest about the specific features that each contribute to internal state representations. Finally, we speculate as to whether this role might be achieved interdependently through direct PF→OFC projections, or through the convergence of independent direct orbitofrontal cortex (OFC) and parafascicular nucleus of the thalamus (PF) inputs onto striatal targets.
Steel, KA, Anderson, DI, Smith, CA, Ellem, E, Liu, KPY, Morrison-Gurza, A, Dune, T & Fairley, LH 2021, 'Potential Value of Customized Video Self-Modelling for Motor Skill Learning in Individuals with Cerebral Palsy: A Case-Study Approach', Perceptual and Motor Skills, vol. 128, no. 4, pp. 1464-1484.
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Cerebral Palsy (CP) is a common physical disability that is managed with a variety of strategies. One non-invasive intervention for people living with CP is a type of video self-modelling (VSM) referred to as positive self-review (PSR). PSR involves watching a video of oneself performing only the best examples of a desired task; this technique has been associated with improved performance and learning for people without disabilities and for those in various clinical populations, including children with spina bifida and stroke patients. PSR may have similar benefits for people living with CP. In this study we examined the effectiveness of PSR for improving a self-selected movement task among individuals living with CP. In this case study approach, eight participants completed a pre-, post-, and second post-test measuring and recording well-being, movement self-consciousness and tendency to consciously monitor movements. Results were mixed, with some participants improving their movement time, well-being ratings and tendency toward self-consciousness and conscious monitoring of movements and others showing no changes or regressions. The effectiveness of VSM appears to depend upon the match between type of task and disability and/or the length of practice. More study is needed.
Steele, JR, Italiano, CJ, Phillips, CR, Violi, JP, Pu, L, Rodgers, KJ & Padula, MP 2021, 'Misincorporation Proteomics Technologies: A Review', Proteomes, vol. 9, no. 1, pp. 2-2.
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Proteinopathies are diseases caused by factors that affect proteoform conformation. As such, a prevalent hypothesis is that the misincorporation of noncanonical amino acids into a proteoform results in detrimental structures. However, this hypothesis is missing proteomic evidence, specifically the detection of a noncanonical amino acid in a peptide sequence. This review aims to outline the current state of technology that can be used to investigate mistranslations and misincorporations whilst framing the pursuit as Misincorporation Proteomics (MiP). The current availability of technologies explored herein is mass spectrometry, sample enrichment/preparation, data analysis techniques, and the hyphenation of approaches. While many of these technologies show potential, our review reveals a need for further development and refinement of approaches is still required.
Steele, JR, Strange, N, Rodgers, KJ & Padula, MP 2021, 'A Novel Method for Creating a Synthetic L-DOPA Proteome and In Vitro Evidence of Incorporation', Proteomes, vol. 9, no. 2, pp. 24-24.
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Proteinopathies are protein misfolding diseases that have an underlying factor that affects the conformation of proteoforms. A factor hypothesised to play a role in these diseases is the incorporation of non-protein amino acids into proteins, with a key example being the therapeutic drug levodopa. The presence of levodopa as a protein constituent has been explored in several studies, but it has not been examined in a global proteomic manner. This paper provides a proof-of-concept method for enzymatically creating levodopa-containing proteins using the enzyme tyrosinase and provides spectral evidence of in vitro incorporation in addition to the induction of the unfolded protein response due to levodopa.
Stevens, MT & Saunders, BM 2021, 'Targets and regulation of microRNA-652-3p in homoeostasis and disease', Journal of Molecular Medicine, vol. 99, no. 6, pp. 755-769.
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Stevens, MT, Nagaria, BD, Britton, WJ & Saunders, BM 2021, 'Macrophages of different tissue origin exhibit distinct inflammatory responses to mycobacterial infection', Immunology & Cell Biology, vol. 99, no. 10, pp. 1085-1092.
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AbstractMacrophages display marked plasticity with functions in both inflammation and tissue repair. Evidence demonstrates that this spectrum of macrophage phenotypes is influenced by their local microenvironment and tissue origin. However, in vitro macrophage experiments often do not or cannot readily use macrophages from the most relevant tissue of origin. This study investigated if the origin of two C57BL/6 mouse macrophage cell lines of alveolar (AMJ2‐C11) and peritoneal (IC‐21) origin may influence their response to mycobacterial infection. Both cell lines equally controlled the growth of Mycobacterium bovis BCG and Mycobacterium tuberculosis, although the expression of all proinflammatory cytokines and chemokines measured (TNF, IL‐6, MCP‐1, MIP‐1α, MIP‐1β, and RANTES) was significantly higher in AMJ2‐C11 cells than in IC‐21 cells. During M. tuberculosis infection, IL‐6, MCP‐1, and RANTES expression increased 5‐fold, and MIP‐1β expression increased 30‐fold. Additionally, AMJ2‐C11 cells exhibited significantly higher inducible nitric oxide synthase activity than IC‐21 cells, indicative of a more polarized M1 response. The expression of multiple surface markers was also assessed by flow cytometry. CD80 and CD86 were significantly upregulated in AMJ2‐C11 cells and downregulated in IC‐21 cells during M. tuberculosis infection. The results support the notion that the origin of tissue‐resident macrophages influences their phenotype and antimicrobial response and demonstrate hereto unrecognized potential for these cell lines in in vitro studies.
Stewart, J, Hegarty, A-M & Gladstone, W 2021, 'The influence of climatic and lunar drivers on landings cycles of the temperate Australian sciaenid (Atractoscion atelodus) at two temporal scales: A working hypothesis for future management of this resource', Marine Environmental Research, vol. 171, pp. 105456-105456.
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Commercial line-fishing catch rates of the endemic sciaenid Atractoscion atelodus in eastern-Australia were significantly affected by lunar phase. Periodic regression analysis indicated that catch rates were greatest during the full moon period and lowest during the new moon period. It is hypothesized that this observation is the result of the visual nocturnal feeding nature of A. atelodus, with schools of fish using the increased ambient light in the water column during the brighter part of the lunar phase to feed intensively. Increased feeding intensity during the brighter phase of the lunar month may also be related to spawning activity during the new moon phase; however this hypothesis remains to be tested. Annual commercial landings through a 71 year dataset (1950–2020) showed an approximately exponential decline, overlaid with periodic years of higher and lower landings. Such periods of higher landings were significantly positively correlated with coastal rainfall two and three years earlier, but not with rainfall in the same year or one, four or five years earlier. We hypothesize that increased coastal rainfall, likely in combination with unknown co-occurring factors, promotes increased recruitment success of A. atelodus, potentially through increased primary productivity in the nearshore marine environment. This translates into an increase in the fishable stock mainly two and three years later. If our hypothesis is correct, climate predictions of reduced rainfall in eastern Australia suggest a pessimistic outlook for this fishery.
Su, L, Zhang, J, Chen, Y, Yang, W, Wang, J, Ma, Z, Shao, G & Wang, G 2021, 'Cobalt-embedded hierarchically-porous hollow carbon microspheres as multifunctional confined reactors for high-loading Li-S batteries', Nano Energy, vol. 85, pp. 105981-105981.
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The shuttle effect of dissolved polysulfides migrating to and depositing on anodes often leads to low round-trip efficiency and short cycle life for lithium-sulfur (Li-S) batteries. Herein, we report the rational design of cobalt-embedded nitrogen-doped hollow carbon microspheres (Co@N-HCMSs) as a multifunctional sulfur host for Li-S batteries. The hollow carbon microspheres exhibit large central cavities wrapped by a hierarchically porous shell, showing a large surface area of 1954 m2 g−1. Furthermore, the carbon shells display a unique porous architecture, in which small pores are scattered on the outside and large pores are inside, thereby functioning as a selection barrier to confine polysulfides and diffuse Li+ simultaneously. Moreover, the highly dispersed cobalt nanoparticles in the porous shell activate the surrounding N-doped carbon layer, which not only promote chemical adsorption of polysulfides but also catalyze polysulfide conversion. This facilitation effect has been confirmed by Bader charge and density function theory (DFT) calculations. When applied in Li-S batteries, the sulfur-impregnated Co@N-HCMSs cathode material exhibits excellent electrochemical performances, especially with a high sulfur content of 90.5 wt% and a high areal sulfur loading of 5.1 mg cm−2.
Su, Q, Wei, H-L, Liu, Y, Chen, C, Guan, M, Wang, S, Su, Y, Wang, H, Chen, Z & Jin, D 2021, 'Six-photon upconverted excitation energy lock-in for ultraviolet-C enhancement', Nature Communications, vol. 12, no. 1, pp. 1-9.
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AbstractPhoton upconversion of near-infrared (NIR) irradiation into ultraviolet-C (UVC) emission offers many exciting opportunities for drug release in deep tissues, photodynamic therapy, solid-state lasing, energy storage, and photocatalysis. However, NIR-to-UVC upconversion remains a daunting challenge due to low quantum efficiency. Here, we report an unusual six-photon upconversion process in Gd3+/Tm3+-codoped nanoparticles following a heterogeneous core-multishell architecture. This design efficiently suppresses energy consumption induced by interior energy traps, maximizes cascade sensitizations of the NIR excitation, and promotes upconverted UVC emission from high-lying excited states. We realized the intense six-photon-upconverted UV emissions at 253 nm under 808 nm excitation. This work provides insight into mechanistic understanding of the upconversion process within the heterogeneous architecture, while offering exciting opportunities for developing nanoscale UVC emitters that can be remotely controlled through deep tissues upon NIR illumination.
Sun, J, Zhu, D & Platen, E 2021, 'DYNAMIC ASSET ALLOCATION FOR TARGET DATE FUNDS UNDER THE BENCHMARK APPROACH', ASTIN Bulletin, vol. 51, no. 2, pp. 449-474.
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ABSTRACTTarget date funds (TDFs) are becoming increasingly popular investment choices among investors with long-term prospects. Examples include members of superannuation funds seeking to save for retirement at a given age. TDFs provide efficient risk exposures to a diversified range of asset classes that dynamically match the risk profile of the investment payoff as the investors age. This is often achieved by making increasingly conservative asset allocations over time as the retirement date approaches. Such dynamically evolving allocation strategies for TDFs are often referred to as glide paths. We propose a systematic approach to the design of optimal TDF glide paths implied by retirement dates and risk preferences and construct the corresponding dynamic asset allocation strategy that delivers the optimal payoffs at minimal costs. The TDF strategies we propose are dynamic portfolios consisting of units of the growth-optimal portfolio (GP) and the risk-free asset. Here, the GP is often approximated by a well-diversified index of multiple risky assets. We backtest the TDF strategies with the historical returns of the S&P500 total return index serving as the GP approximation.
Sun, X, Yang, J, Su, D, Wang, C & Wang, G 2021, 'Highly Efficient Adsorption of Bilirubin by Ti3C2Tx MXene', Chemistry – An Asian Journal, vol. 16, no. 14, pp. 1949-1955.
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AbstractWe discovered that the 2D Ti3C2Tx MXene sheet displays an ultra‐high removal capability for bilirubin (BR). In particular, MXene shows 47.6 times higher removal efficiency over traditional activated carbon absorbents. The effect of MXene on the removal rate of BR in BR solution containing different concentrations of bovine serum albumin (BSA) was studied. The adsorption capacity of BSA for BR at high concentration of 5 g L−1 was about 85% of the best adsorption capacity. The MXene before and after adsorption was characterized by SEM, FT‐IR and XPS. Furthermore, MXene beads were prepared, and the hemoperfusion simulation experiment was carried out. The results show that the adsorption capacity of MXene for bilirubin can reach 1192.9 mg g−1. This study suggests that MXene may be promising in the treatment of hyperbilirubinemia.
Supasri, K, Kumar, M, Mathew, M, Signal, B, Padula, M, Suggett, D & Ralph, P 2021, 'Evaluation of Filter, Paramagnetic, and STAGETips Aided Workflows for Proteome Profiling of Symbiodiniaceae Dinoflagellate', Processes, vol. 9, no. 6, pp. 983-983.
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The integrity of coral reef ecosystems worldwide rests on a fine-tuned symbiotic interaction between an invertebrate and a dinoflagellate microalga from the family Symbiodiniaceae. Recent advances in bottom-up shotgun proteomic approaches and the availability of vast amounts of genetic information about Symbiodiniaceae have provided a unique opportunity to better understand the molecular mechanisms underpinning the interactions of coral-Symbiodiniaceae. However, the resilience of this dinoflagellate cell wall, as well as the presence of polyanionic and phenolics cell wall components, requires the optimization of sample preparation techniques for successful implementation of bottom-up proteomics. Therefore, in this study we compare three different workflows—filter-aided sample preparation (FASP), single-pot solid-phase-enhanced sample preparation (SP3), and stop-and-go-extraction tips (STAGETips, ST)—to develop a high-throughput proteotyping protocol for Symbiodiniaceae algal research. We used the model isolate Symbiodinium tridacnidorum. We show that SP3 outperformed ST and FASP with regard to robustness, digestion efficiency, and contaminant removal, which led to the highest number of total (3799) and unique proteins detected from 23,593 peptides. Most of these proteins were detected with ≥2 unique peptides (73%), zero missed tryptic peptide cleavages (91%), and hydrophilic peptides (>70%). To demonstrate the functionality of this optimized SP3 sample preparation workflow, we examined the proteome of S. tridacnidorum to better understand the molecular mechanism of peridinin-chlorophyll-protein complex (PCP, light harvesting protein) accumulation under low light (LL, 30 μmol photon m−2 s−1). Cells exposed to LL for 7 days upregulated various light harvesting complex (LHCs) proteins through the mevalonate-independent pathway; proteins of this pathway were at 2- to 6-fold higher levels than the control of 120 μmol photon m−2 s−1. Potentially, L...
Supasri, KM, Kumar, M, Segečová, A, McCauley, JI, Herdean, A, Padula, MP, O’Meara, T & Ralph, PJ 2021, 'Characterisation and Bioactivity Analysis of Peridinin-Chlorophyll a-Protein (PCP) Isolated from Symbiodinium tridacnidorum CS-73', Journal of Marine Science and Engineering, vol. 9, no. 12, pp. 1387-1387.
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Peridinin-Chlorophyll a-Proteins (PCP) are the major light harvesting proteins in photosynthetic dinoflagellates. PCP shows great variation in protein length, pigment ratio, sequence, and spectroscopic properties. PCP conjugates (PerCP) are widely used as fluorescent probes for cellular and tissue analysis in the biomedical field. PCP consists of a peridinin carotenoid; thereby, it can potentially be used as a bioactive compound in pharmaceutical applications. However, the biological activities of PCP are yet to be explored. In this study, we extracted, purified, and partially characterised the PCP from Symbiodinium tridacnidorum (CS-73) and explored its antioxidant, anti-cancer and anti-inflammation bioactivities. The PCP was purified using an ÄKTA™ PURE system and predicted to be of 17.3 kDa molecular weight (confirmed as a single band on SDS-PAGE) with an isoelectric point (pI) 5.6. LC-MS/MS and bioinformatic analysis of purified PCP digested with trypsin indicated it was 164 amino acids long with >90% sequence similarity to PCP of SymA3.s6014_g3 (belonging to clade A of Symbiodinium sp.) confirmed with 59 peptide combinations matched across its protein sequence. The spectroscopic properties of purified PCP showed a slight shift in absorption and emission spectra to previously documented analysis in Symbiodinium species possibly due to variation in amino acid sequences that interact with chl a and peridinin. Purified PCP consisted of a 19-amino-acid-long signal peptide at its N terminal and nine helixes in its secondary structure, with several protein binding sites and no DNA/RNA binding site. Furthermore, purified PCP exhibited antioxidant and in vitro anti-inflammation bioactivities, and anti-cancer activities against human metastatic breast adenocarcinoma (MDA-MB-231) and human colorectal (HTC-15) cancer cell lines. Together, all these findings present PCP as a promising candidate for continued investigations for pharmaceutical applicat...
Sutherland, DL & Ralph, PJ 2021, 'Differing growth responses in four related microalgal genera grown under autotrophic, mixotrophic and heterotrophic conditions', Journal of Applied Phycology, vol. 33, no. 6, pp. 3539-3553.
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Sutherland, DL & Ralph, PJ 2021, 'Productivity and community response along an ammonia gradient in cultured wild marine microalgae, using wastewater-derived nutrients for cost-effective feedstock production', Journal of Applied Phycology, vol. 33, no. 5, pp. 2933-2945.
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Sutherland, DL & Ralph, PJ 2021, 'Shortening hydraulic retention time through effluent recycling: impacts on wastewater treatment and biomass production in microalgal treatment systems', Journal of Applied Phycology, vol. 33, no. 6, pp. 3873-3884.
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Sutherland, DL, Burke, J & Ralph, PJ 2021, 'High-throughput screening for heterotrophic growth in microalgae using the Biolog Plate assay', New Biotechnology, vol. 65, pp. 61-68.
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Sutherland, DL, Burke, J & Ralph, PJ 2021, 'Trade-offs between effluent quality and ammonia volatilisation with CO2 augmented microalgal treatment of anaerobically digested food-waste centrate', Journal of Environmental Management, vol. 277, pp. 111398-111398.
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Diversion of food waste from landfill disposal to waste-to-energy facilities has become both an environmentally and economically viable option to support the circular bioeconomy. However, the liquid centrate produced during anaerobic digestion is high in total ammonia, with concentrations ~2000 g m-3, and can release gaseous emissions, including ammonia, methane, CO2 and nitrous oxide, to the atmosphere. Further treatment is required before discharge to sewer, or to the environment. Microalgal wastewater treatment systems augmented with CO2 offer a promising and cost-effective treatment solution for reducing both total ammonia concentrations and ammonia volatilisation. In this study, we investigate the effects of augmenting CO2 on nutrient removal and specifically nitrogen losses, as well as biomass productivity under two difference hydraulic retention times (HRT). Both CO2 addition and HRT affect nitrogen losses, with the percentage removal of total ammonia significantly lower (p < 0.01) when CO2 was added to the treatments, while increased HRT significantly increased (p < 0.05) total ammonia percentage removal. Total nitrogen budgets showed significantly lower (p < 0.01) abiotic nitrogen losses from the system when CO2 was added to the culture but at the expense of effluent quality. Both total suspended solids and volatile suspended solids significantly increased (p < 0.01) under longer HRT (8 days), with CO2 addition, while chlorophyll-a biomass significantly increased (p < 0.01) on longer HRT, regardless of CO2 addition. These results demonstrate that, while CO2 augmentation helped to mitigate ammonia losses to atmosphere, the trade-off was poorer effluent quality. Coupling CO2 augmentation with longer HRT increased biomass production and nutrient removal efficiency. This study provides an insight into how simple operational changes can alleviate some of the trade-offs between atmospheric losses and effluent quality. However, in order to manage the trade-off ...
Sutherland, DL, McCauley, J, Labeeuw, L, Ray, P, Kuzhiumparambil, U, Hall, C, Doblin, M, Nguyen, LN & Ralph, PJ 2021, 'How microalgal biotechnology can assist with the UN Sustainable Development Goals for natural resource management', Current Research in Environmental Sustainability, vol. 3, pp. 100050-100050.
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Sutherland, DL, Park, J, Ralph, PJ & Craggs, R 2021, 'Ammonia, pH and dissolved inorganic carbon supply drive whole pond metabolism in full-scale wastewater high rate algal ponds', Algal Research, vol. 58, pp. 102405-102405.
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Sutherland, TC, Ricafrente, A, Gomola, K, O’Brien, BA & Gorrie, CA 2021, 'Neonatal Rats Exhibit a Predominantly Anti-Inflammatory Response following Spinal Cord Injury', Developmental Neuroscience, vol. 43, no. 1, pp. 18-26.
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It has been reported that children may respond better than adults to a spinal cord injury (SCI) of similar severity. There are known biomechanical differences in the developing spinal cord that may contribute to this “infant lesion effect,” but the underlying mechanisms are unknown. Using immunohistochemistry, we have previously demonstrated a different injury progression and immune cell response after a mild thoracic contusion SCI in infant rats, as compared to adult rats. Here, we investigated the acute inflammatory responses using flow cytometry and ELISA at 1 h, 24 h, and 1 week after SCI in neonatal (P7) and adult (9 weeks) rats, and locomotor recovery was examined for 6 weeks after injury. Adult rats exhibited a pronounced pro-inflammatory response characterized by neutrophils and M1-like macrophage infiltration and Th1 cytokine secretion. Neonatal rats exhibited a decreased pro-inflammatory response characterized by a higher proportion of M2-like macrophages and reduced Th1 cytokine responses, as compared to adults. These results suggest that the initial inflammatory response to SCI is predominantly anti-inflammatory in very young animals.
Szpila, K, Walczak, K, Johnston, NP, Pape, T & Wallman, JF 2021, 'First instar larvae of endemic Australian Miltogramminae (Diptera: Sarcophagidae)', Scientific Reports, vol. 11, no. 1, pp. 1-12.
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AbstractThe first instar larva of a species of the Australian endemic genus Aenigmetopia Malloch is described for the first time, along with the first instar larvae of three other Australian species representing the genera Amobia Robineau-Desvoidy and Protomiltogramma Townsend. Larval morphology was analysed using a combination of light microscopy, confocal laser scanning microscopy and scanning electron microscopy. The following morphological structures are documented: pseudocephalon, antennal complex, maxillary palpus, facial mask, modifications of thoracic and abdominal segments, anal region, spiracular field, posterior spiracles and details of the cephaloskeleton. Substantial morphological differences are observed between the three genera, most notably in the labrum and mouthhooks of the cephaloskeleton, sensory organs of the pseudocephalon, spinulation, sculpture of the integument and form of the spiracular field. The first instar larval morphology of Aenigmetopia amissa Johnston, Wallman, Szpila & Pape corroborates the close phylogenetic affinity of Aenigmetopia Malloch with Metopia Meigen, inferred from recent molecular analysis. The larval morphology of Amobia auriceps (Baranov), Protomiltogramma cincta Townsend and Protomiltogramma plebeia Malloch is mostly congruent with the morphology of Palaearctic representatives of both genera.
Tan, CH, Yeo, YP, Hafiz, M, Ng, NKJ, Subramoni, S, Taj, S, Tay, M, Chao, X, Kjelleberg, S & Rice, SA 2021, 'Functional metagenomic analysis of quorum sensing signaling in a nitrifying community', npj Biofilms and Microbiomes, vol. 7, no. 1.
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AbstractQuorum sensing (QS) can function to shape the microbial community interactions, composition, and function. In wastewater treatment systems, acylated homoserine lactone (AHL)-based QS has been correlated with the conversion of floccular biomass into microbial granules, as well as EPS production and the nitrogen removal process. However, the role of QS in such complex communities is still not fully understood, including the QS-proficient taxa and the functional QS genes involved. To address these questions, we performed a metagenomic screen for AHL genes in an activated sludge microbial community from the Ulu Pandan wastewater treatment plant (WWTP) in Singapore followed by functional validation of luxI activity using AHL biosensors and LC–MSMS profiling. We identified 13 luxI and 30 luxR homologs from the activated sludge metagenome. Of those genes, two represented a cognate pair of luxIR genes belonging to a Nitrospira spp. and those genes were demonstrated to be functionally active. The LuxI homolog synthesized AHLs that were consistent with the dominant AHLs in the activated sludge system. Furthermore, the LuxR homolog was shown to bind to and induce expression of the luxI promoter, suggesting this represents an autoinduction feedback system, characteristic of QS circuits. Additionally, a second, active promoter was upstream of a gene encoding a protein with a GGDEF/EAL domain, commonly associated with modulating the intracellular concentration of the secondary messenger, c-di-GMP. Thus, the metagenomic approach used here was demonstrated to effectively identify functional QS genes and suggests that Nitrospira spp. maybe QS is active in the activated sludge community.
Tang, X, Zhou, D, Zhang, B, Wang, S, Li, P, Liu, H, Guo, X, Jaumaux, P, Gao, X, Fu, Y, Wang, C, Wang, C & Wang, G 2021, 'A universal strategy towards high–energy aqueous multivalent–ion batteries', Nature Communications, vol. 12, no. 1, p. 2857.
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AbstractRechargeable multivalent metal (e.g., Ca, Mg or, Al) batteries are ideal candidates for large–scale electrochemical energy storage due to their intrinsic low cost. However, their practical application is hampered by the low electrochemical reversibility, dendrite growth at the metal anodes, sluggish multivalent–ion kinetics in metal oxide cathodes and, poor electrode compatibility with non–aqueous organic–based electrolytes. To circumvent these issues, here we report various aqueous multivalent–ion batteries comprising of concentrated aqueous gel electrolytes, sulfur–containing anodes and, high-voltage metal oxide cathodes as alternative systems to the non–aqueous multivalent metal batteries. This rationally designed aqueous battery chemistry enables satisfactory specific energy, favorable reversibility and improved safety. As a demonstration model, we report a room–temperature calcium-ion/sulfur| |metal oxide full cell with a specific energy of 110 Wh kg–1 and remarkable cycling stability. Molecular dynamics modeling and experimental investigations reveal that the side reactions could be significantly restrained through the suppressed water activity and formation of a protective inorganic solid electrolyte interphase. The unique redox chemistry of the multivalent–ion system is also demonstrated for aqueous magnesium–ion/sulfur||metal oxide and aluminum–ion/sulfur||metal oxide full cells.
Tangella, LP, Arooj, M, Deplazes, E, Gray, ES & Mancera, RL 2021, 'Identification and characterisation of putative drug binding sites in human ATP-binding cassette B5 (ABCB5) transporter', Computational and Structural Biotechnology Journal, vol. 19, pp. 691-704.
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Tao, S, Wang, T, Wu, Y, Wang, C & Wang, G 2021, 'Removal of extremely low concentration cobalt by intercalation composite material of carbon nitride/titanium dioxide', Journal of Hazardous Materials, vol. 415, pp. 125680-125680.
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Due to the high toxicity and the great harm of radioactive cobalt to the human body and the environment, the removal of heavy metal cobalt ions from radioactive wastewater had attracted more and more scientific researchers. In this paper, the intercalation composite material of carbon nitride itanium dioxide (g-C3N4/TiO2) composite material which combined the advantages of the two materials was prepared and its actual effect of removing Co (Ⅱ) from wastewater was evaluated. Batch experimental method was employed for the investigation of the impact of solution pH during adsorption, adsorption kinetics, adsorption thermodynamics and adsorption isotherms. In this experiment, the saturation adsorption capacity of the composite material to Co (Ⅱ) was 91.55 mg/g, while the bulk g-C3N4 was only 13.2 mg/g. The adsorption kinetics showed that the adsorption process followed a pseudo-second-order kinetic model. The adsorption thermodynamic showed that the adsorption of Co (Ⅱ) was a spontaneous endothermic process. The Langmuir isotherm adsorption model was more consistent with the adsorption isotherm than the Freundlich model. The experimental results proved that g-C3N4/TiO2 composite material had a good adsorption and removal effect on extremely low concentration of Co (II) and was a promising adsorbent for removal radioactive Co (II) from nuclear industrial wastewater.
Tarabai, H, Wyrsch, ER, Bitar, I, Dolejska, M & Djordjevic, SP 2021, 'Epidemic HI2 Plasmids Mobilising the Carbapenemase Gene blaIMP-4 in Australian Clinical Samples Identified in Multiple Sublineages of Escherichia coli ST216 Colonising Silver Gulls', Microorganisms, vol. 9, no. 3, pp. 567-567.
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Escherichia coli ST216, including those that carry blaKPC-2, blaFOX-5, blaCTX-M-15 and mcr-1, have been linked to wild and urban-adapted birds and the colonisation of hospital environments causing recalcitrant, carbapenem-resistant human infections. Here we sequenced 22 multiple-drug resistant ST216 isolates from Australian silver gull chicks sampled from Five Islands, of which 21 carried nine or more antibiotic resistance genes including blaIMP-4 (n = 21), blaTEM-1b (n = 21), aac(3)-IId (n = 20), mph(A) (n = 20), catB3 (n = 20), sul1 (n = 20), aph(3”)-Ib (n = 18) and aph(6)-Id (n = 18) on FIB(K) (n = 20), HI2-ST1 (n = 11) and HI2-ST3 (n = 10) plasmids. We show that (i) all HI2 plasmids harbour blaIMP-4 in resistance regions containing In809 flanked by IS26 (HI2-ST1) or IS15DI (HI2-ST3) and diverse metal resistance genes; (ii) HI2-ST1 plasmids are highly related to plasmids reported in diverse Enterobacteriaceae sourced from humans, companion animals and wildlife; (iii) HI2 were a feature of the Australian gull isolates and were not observed in international ST216 isolates. Phylogenetic analyses identified close relationships between ST216 from Australian gull and clinical isolates from overseas. E. coli ST216 from Australian gulls harbour HI2 plasmids encoding resistance to clinically important antibiotics and metals. Our studies underscore the importance of adopting a one health approach to AMR and pathogen surveillance.
Taras, AK, Tuniz, A, Bajwa, MA, Ng, V, Dawes, JM, Poulton, CG & De Sterke, CM 2021, 'Shortcuts to adiabaticity in waveguide couplers–theory and implementation', Advances in Physics: X, vol. 6, no. 1.
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Taudte, RV, Roux, C, Bishop, DP, Fouracre, C & Beavis, A 2021, 'High-throughput screening for target compounds in smokeless powders using online-SPE tandem mass spectrometry', Australian Journal of Forensic Sciences, vol. 53, no. 1, pp. 16-26.
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© 2019, © 2019 Australian Academy of Forensic Sciences. The detection and quantification of compounds present in smokeless powders plays an important role in various fields such as environmental and forensic science. Often, time and labour consuming sample preparation techniques such as solid phase extraction (SPE) are required to facilitate either pre-concentration or sample clean-up with complex matrices. This paper describes the first application of the completely automated online SPE system RapidFire® connected to a triple quadrupole mass spectrometer for smokeless powder/gunshot residue analysis. The optimized method involved sample loading during 2000 ms using UP water (0.1% formic acid) at a flowrate of 1.25 mL/min on a Type C C18 cartridge followed by elution of the target compounds for 3000 ms using IPA (0.1% formic acid) at 0.75 mL/min. Target compounds were detected in soil (DPA, 2-NDPA, EC, NG, 2,4-DNT) and cotton swabs (NG) in only 8 seconds per sample with detection limits of 0.223 ppm (DPA), 0.104 ppm (2-NDPA), 0.0949 ppm (EC), 0.187 ppm (NG) and 0.128 ppm (2,4-DNT). The presented method showed promising results for the analysis of five target analytes in soil samples. Further optimisations can extend the analysis to other sample matrices and include more analytes potentially present in smokeless powders and GSR.
Thomas Broome, S, Fisher, T, Faiz, A, Keay, KA, Musumeci, G, Al-Badri, G & Castorina, A 2021, 'Assessing the Anti-Inflammatory Activity of the Anxiolytic Drug Buspirone Using CRISPR-Cas9 Gene Editing in LPS-Stimulated BV-2 Microglial Cells', Cells, vol. 10, no. 6, pp. 1312-1312.
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Buspirone is an anxiolytic drug with robust serotonin receptor 1A (Htr1a) agonist activities. However, evidence has demonstrated that this drug also targets the dopamine D3 receptor (Drd3), where it acts as a potent antagonist. In vivo, Drd3 blockade is neuroprotective and reduces inflammation in models of Parkinson’s disease. To test if buspirone also elicited anti-inflammatory activities in vitro, we generated stable Drd3−/− and Htr1a−/− BV2 microglial cell lines using CRISPR-Cas9 technology and then tested the effects of buspirone after lipopolysaccharide (LPS) challenge. We found that LPS exposure had no effect on cell viability, except in Htr1a−/− cells, where viability was reduced (p < 0.001). Drug treatment reduced viability in Drd3−/− cells, but not in WT or Htr1a−/− cells. Buspirone counteracted LPS-induced NO release, NOS2, IL-1β and TNF-α gene expression in WT cells, whereas it exerted limited effects in Drd3−/− or Htr1a−/− microglia. In summary, our findings indicate that buspirone attenuates microglial polarization after LPS challenge. These results also highlight some major effects of Drd3 or Htr1a genetic ablation on microglial biology, raising important questions on the complex role of neurotransmitters in regulating microglia functions.
Thomas, M, Lawrence, A, Kroon, S, Vodstrcil, LA, Phillips, S, Hocking, JS, Timms, P & Huston, WM 2021, 'Chlamydial clinical isolates show subtle differences in persistence phenotypes and growth in vitro', Access Microbiology, vol. 3, no. 3.
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Urogenital Chlamydia trachomatis infection is the most common sexually transmitted bacterial infection throughout the world. While progress has been made to better understand how type strains develop and respond to environmental stress in vitro, very few studies have examined how clinical isolates behave under similar conditions. Here, we examined the development and persistence phenotypes of several clinical isolates, to determine how similar they are to each other, and the type strain C. trachomatis D/UW-3/Cx. The type strain was shown to produce infectious progeny at a higher magnitude than each of the clinical isolates, in each of the six tested cell lines. All chlamydial strains produced the highest number of infectious progeny at 44 h post-infection in the McCoy B murine fibroblast cell line, yet showed higher levels of infectivity in the MCF-7 human epithelial cell line. The clinical isolates were shown to be more susceptible than the type strain to the effects of penicillin and iron deprivation persistence models in the MCF-7 cell line. While subtle differences between clinical isolates were observed throughout the experiments conducted, no significant differences were identified. This study reinforces the importance of examining clinical isolates wh...
Tian, H, Song, A, Tian, H, Liu, J, Shao, G, Liu, H & Wang, G 2021, 'Single-atom catalysts for high-energy rechargeable batteries', Chemical Science, vol. 12, no. 22, pp. 7656-7676.
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Single-atom catalysts are reviewed, aiming to achieve optimized properties to boost electrochemical performances of high-energy batteries.
Tian, H, Tian, H, Yang, W, Zhang, F, Yang, W, Zhang, Q, Wang, Y, Liu, J, Silva, SRP, Liu, H & Wang, G 2021, 'Stable Hollow‐Structured Silicon Suboxide‐Based Anodes toward High‐Performance Lithium‐Ion Batteries', Advanced Functional Materials, vol. 31, no. 25, pp. 1-14.
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AbstractSilicon has been regarded as an attractive high‐capacity anode material for next‐generation lithium‐ion batteries (LIBs). However, Si anodes suffer from huge volume variation during cycling, which poses a critical challenge for stable battery operation. Compared with Si, Si suboxide (SiOx) is one of the most promising candidates for high‐energy‐density LIBs because of its alleviated swelling and highly stable cycling performance. Whereas, the poor electronic conductivity and low (initial) Coulombic efficiency of SiOx anodes severely hinder practical applications for LIBs. Herein, for the first time, these issues are successfully solved through rationally designing hollow‐structured SiOx@carbon nanotubes (CNTs)/C architectures with graphitic carbon coatings and in situ growth of CNTs. When applied as anodes in LIBs, the SiOx@CNTs/C anodes exhibit high reversible capacity, high initial Coulombic efficiency (88%), outstanding cycling performance, and extraordinary mechanical strength during the calendaring process (200 MPa). This work paves the way for developing SiOx‐based anode materials for high‐energy‐density LIBs.
Tiotiu, A, Badi, Y, Kermani, N, Hansbro, P, Wheelock, C, Dahlen, SE, Guo, YK, Sterk, P, Djukanovic, R, Adcock, I & Chung, KF 2021, 'Rôle des mastocytes dans l’asthme sévère : analyse de données transcriptomiques dans la cohorte U-BIOPRED', Revue des Maladies Respiratoires Actualités, vol. 13, no. 1, pp. 68-68.
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Tiotiu, A, Zounemat Kermani, N, Badi, Y, Pavlidis, S, Hansbro, PM, Guo, Y, Chung, KF & Adcock, IM 2021, 'Sputum macrophage diversity and activation in asthma: Role of severity and inflammatory phenotype', Allergy, vol. 76, no. 3, pp. 775-788.
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AbstractBackgroundMacrophages control innate and acquired immunity, but their role in severe asthma remains ill‐defined. We investigated gene signatures of macrophage subtypes in the sputum of 104 asthmatics and 16 healthy volunteers from the U‐BIOPRED cohort.MethodsForty‐nine gene signatures (modules) for differentially stimulated macrophages, one to assess lung tissue‐resident cells (TR‐Mφ) and two for their polarization (classically and alternatively activated macrophages: M1 and M2, respectively) were studied using gene set variation analysis. We calculated enrichment scores (ES) across severity and previously identified asthma transcriptome‐associated clusters (TACs).ResultsMacrophage numbers were significantly decreased in severe asthma compared to mild‐moderate asthma and healthy volunteers. The ES for most modules were also significantly reduced in severe asthma except for 3 associated with inflammatory responses driven by TNF and Toll‐like receptors via NF‐κB, eicosanoid biosynthesis via the lipoxygenase pathway and IL‐2 biosynthesis (all P < .01). Sputum macrophage number and the ES for most macrophage signatures were higher in the TAC3 group compared to TAC1 and TAC2 asthmatics. However, a high enrichment was found in TAC1 for 3 modules showing inflammatory pathways linked to Toll‐like and TNF receptor activation and arachidonic acid metabolism (P < .001) and in TAC2 for the inflammasome and interferon signalling pathways (P < .001). Data were validated in the ADEPT cohort. Module analysis provides additional information compared to conventional M1 and M2 classification. TR‐Mφ were enriched in TAC3 and associat...
Tkacheva, A, Sun, B, Zhang, J, Wang, G & McDonagh, AM 2021, 'Nitronyl Nitroxide-Based Redox Mediators for Li-O2 Batteries', The Journal of Physical Chemistry C, vol. 125, no. 5, pp. 2824-2830.
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Electrochemical processes in Li-O2 batteries benefit from the action of soluble electrocatalysts (redox mediators, RMs) that can facilitate charge or discharge reactions and minimize the blockage of the cathode with the insoluble discharge product Li2O2. In this work, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) analogues (RPTIOs) as new redox mediators for Li-O2 batteries have been investigated. Cyclic voltammetry, scanning electron microscopy, X-ray diffraction studies, and the galvanostatic cycling of the Li-O2 batteries showed that the RPTIOs could effectively catalyze the charge process while having a low impact on the discharge reaction. A direct connection was observed between the character of the substituent on the 2-position of the imidazoline ring, the oxidation redox potential of the RPTIO, and the value of the charge voltage of the battery with this RM, paving a path for further optimization.
Todd, N, McNally, R, Alqudah, A, Jerotic, D, Suvakov, S, Obradovic, D, Hoch, D, Hombrebueno, JR, Campos, GL, Watson, CJ, Gojnic-Dugalic, M, Simic, TP, Krasnodembskaya, A, Desoye, G, Eastwood, K-A, Hunter, AJ, Holmes, VA, McCance, DR, Young, IS, Grieve, DJ, Kenny, LC, Garovic, VD, Robson, T & McClements, L 2021, 'Role of A Novel Angiogenesis FKBPL-CD44 Pathway in Preeclampsia Risk Stratification and Mesenchymal Stem Cell Treatment', The Journal of Clinical Endocrinology & Metabolism, vol. 106, no. 1, pp. 26-41.
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Abstract Context Preeclampsia is a leading cardiovascular complication in pregnancy lacking effective diagnostic and treatment strategies. Objective To investigate the diagnostic and therapeutic target potential of the angiogenesis proteins, FK506-binding protein like (FKBPL) and CD44. Design and Intervention FKBPL and CD44 plasma concentration or placental expression were determined in women pre- or postdiagnosis of preeclampsia. Trophoblast and endothelial cell function was assessed following mesenchymal stem cell (MSC) treatment and in the context of FKBPL signaling. Settings and Participants Human samples prediagnosis (15 and 20 weeks of gestation; n ≥ 57), or postdiagnosis (n = 18 for plasma; n = 4 for placenta) of preeclampsia were used to determine FKBPL and CD44 levels, compared to healthy controls. Trophoblast or endothelial cells were exposed to low/high oxygen, and treated with MSC-conditioned media (MSC-CM) or a FKBPL overexpression plasmid. Main Outcome Measures Preeclampsia risk stratification and diagnostic potential of FKBPL and CD44 were investigated. MSC treatment effects and FKBPL-CD44 signaling in trophoblast and endothelial cells were assessed. Results The CD44/FKBPL ratio...
Tran, N, Ricafrente, A, To, J, Lund, M, Marques, TM, Gama-Carvalho, M, Cwiklinski, K, Dalton, JP & Donnelly, S 2021, 'Fasciola hepatica hijacks host macrophage miRNA machinery to modulate early innate immune responses', Scientific Reports, vol. 11, no. 1, p. 6712.
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AbstractFasciola hepatica, a global worm parasite of humans and their livestock, regulates host innate immune responses within hours of infection. Host macrophages, essential to the first-line defence mechanisms, are quickly restricted in their ability to initiate a classic protective pro-inflammatory immune response. We found that macrophages from infected animals are enriched with parasite-derived micro(mi)RNAs. The most abundant of these miRNAs, fhe-miR-125b, is released by the parasite via exosomes and is homologous to a mammalian miRNA, hsa-miR-125b, that is known to regulate the activation of pro-inflammatory M1 macrophages. We show that the parasite fhe-miR-125b loads onto the mammalian Argonaut protein (Ago-2) within macrophages during infection and, therefore, propose that it mimics host miR-125b to negatively regulate the production of inflammatory cytokines. The hijacking of the miRNA machinery controlling innate cell function could be a fundamental mechanism by which worm parasites disarm the early immune responses of their host to ensure successful infection.
Tran, TN, Kim, S, White, SJU, Nguyen, MAP, Xiao, L, Strauf, S, Yang, T, Aharonovich, I & Xu, Z 2021, 'Enhanced Emission from Interlayer Excitons Coupled to Plasmonic Gap Cavities', Small, vol. 17, no. 45, pp. 1-7.
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AbstractThe emergence of interlayer excitons (IEs) from atomic layered transition metal dichalcogenides (TMDCs) heterostructures has drawn tremendous attention due to their unique and exotic optoelectronic properties. Coupling the IEs into optical cavities provides distinctive electromagnetic environments which plays an important role in controlling multiple optical processes such as optical nonlinear generation or photoluminescence enhancement. Here, the integration of IEs in TMDCs into plasmonic nanocavities based on a nanocube on a metallic mirror is reported. Spectroscopic studies reveal an order of magnitude enhancement of the IE at room temperature and a 5‐time enhancement in fluorescence at cryogenic temperatures. Cavity modeling reveals that the enhancement of the emission is attributed to both increased excitation efficiency and Purcell effect from the cavity. The results show a novel method to control the excitonic processes in TMDC heterostructures to build high performance photonics and optoelectronics devices.
Tran, W, Kusay, AS, Hawkins, PME, Cheung, C-Y, Nagalingam, G, Pujari, V, Ford, DJ, Stoye, A, Ochoa, JL, Audette, RE, Hortle, E, Oehlers, SH, Charman, SA, Linington, RG, Rubin, EJ, Dowson, CG, Roper, DI, Crick, DC, Balle, T, Cook, GM, Britton, WJ & Payne, RJ 2021, 'Synthetic Sansanmycin Analogues as Potent Mycobacterium tuberculosis Translocase I Inhibitors', Journal of Medicinal Chemistry, vol. 64, no. 23, pp. 17326-17345.
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Travis, G, Haddadi, N, Simpson, AM, Marsh, DJ, McGowan, EM & Nassif, NT 2021, 'Studying the Oncosuppressive Functions of PTENP1 as a ceRNA', Methods in molecular biology (Clifton, N.J.), vol. 2324, pp. 165-185.
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PTENP1 is a processed pseudogene of the tumour suppressor phosphatase and tensin homolog deleted on chromosome 10 (PTEN). It functions posttranscriptionally to regulate PTEN by acting as a sponge for microRNAs that target PTEN. PTENP1 therefore functions as a competitive endogenous RNA (ceRNA), competing with PTEN for binding of microRNAs (miRNA) and thereby modulating PTEN cellular abundance. Studies of the overexpression of PTENP1 all confirm its oncosuppressive function to be mediated through the suppression of cell proliferation, induction of apoptosis, and inhibition of cell migration and invasion of cancer cells of differing types. These oncosuppressive functions are a direct consequence of miRNA binding by PTENP1 and the subsequent liberation of PTEN from miRNA induced suppression. In this chapter, we will focus initially on the description of a high efficiency transient transfection method to introduce and overexpress PTENP1 in the cell type of interest, followed by accurate methodologies to measure transfection efficiency by flow cytometry. We will then continue to describe two methods to analyze cell proliferation, namely the CCK-8 assay and Click-iT® EdU assay. Due to commonalities in the manifestation of the oncosuppressive effects of PTENP1, mediated through its role as a ceRNA, the methods presented in this chapter will have wide applicability to a variety of different cell types.
Trist, BG, Hilton, JB, Hare, DJ, Crouch, PJ & Double, KL 2021, 'Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic', Angewandte Chemie International Edition, vol. 60, no. 17, pp. 9215-9246.
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AbstractCu/Zn superoxide dismutase (SOD1) is a frontline antioxidant enzyme catalysing superoxide breakdown and is important for most forms of eukaryotic life. The evolution of aerobic respiration by mitochondria increased cellular production of superoxide, resulting in an increased reliance upon SOD1. Consistent with the importance of SOD1 for cellular health, many human diseases of the central nervous system involve perturbations in SOD1 biology. But far from providing a simple demonstration of how disease arises from SOD1 loss‐of‐function, attempts to elucidate pathways by which atypical SOD1 biology leads to neurodegeneration have revealed unexpectedly complex molecular characteristics delineating healthy, functional SOD1 protein from that which likely contributes to central nervous system disease. This review summarises current understanding of SOD1 biology from SOD1 genetics through to protein function and stability.
Trouve, J, Zapun, A, Arthaud, C, Durmort, C, Di Guilmi, AM, Söderström, B, Pelletier, A, Grangeasse, C, Bourgeois, D, Wong, Y-S & Morlot, C 2021, 'Nanoscale dynamics of peptidoglycan assembly during the cell cycle of Streptococcus pneumoniae', Current Biology, vol. 31, no. 13, pp. 2844-2856.e6.
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Dynamics of cell elongation and septation are key determinants of bacterial morphogenesis. These processes are intimately linked to peptidoglycan synthesis performed by macromolecular complexes called the elongasome and the divisome. In rod-shaped bacteria, cell elongation and septation, which are dissociated in time and space, have been well described. By contrast, in ovoid-shaped bacteria, the dynamics and relationships between these processes remain poorly understood because they are concomitant and confined to a nanometer-scale annular region at midcell. Here, we set up a metabolic peptidoglycan labeling approach using click chemistry to image peptidoglycan synthesis by single-molecule localization microscopy in the ovoid bacterium Streptococcus pneumoniae. Our nanoscale-resolution data reveal spatiotemporal features of peptidoglycan assembly and fate along the cell cycle and provide geometrical parameters that we used to construct a morphogenesis model of the ovoid cell. These analyses show that septal and peripheral peptidoglycan syntheses first occur within a single annular region that later separates in two concentric regions and that elongation persists after septation is completed. In addition, our data reveal that freshly synthesized peptidoglycan is remodeled all along the cell cycle. Altogether, our work provides evidence that septal peptidoglycan is synthesized from the beginning of the cell cycle and is constantly remodeled through cleavage and insertion of material at its periphery. The ovoid-cell morphogenesis would thus rely on the relative dynamics between peptidoglycan synthesis and cleavage rather than on the existence of two distinct successive phases of peripheral and septal synthesis.
Truong, VK, Truong, NP & Rice, SA 2021, 'Antibacterial Activity of Nanoparticles', Nanomaterials, vol. 11, no. 6, pp. 1391-1391.
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Antimicrobial resistance (AMR) is predicted to soon become one of the most serious threats to human and animal health [...]
Tu, X, Donovan, C, Kim, RY, Wark, PAB, Horvat, JC & Hansbro, PM 2021, 'Asthma-COPD overlap: current understanding and the utility of experimental models', European Respiratory Review, vol. 30, no. 159, pp. 190185-190185.
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Pathological features of both asthma and COPD coexist in some patients and this is termed asthma-COPD overlap (ACO). ACO is heterogeneous and patients exhibit various combinations of asthma and COPD features, making it difficult to characterise the underlying pathogenic mechanisms. There are no controlled studies that define effective therapies for ACO, which arises from the lack of international consensus on the definition and diagnostic criteria for ACO, as well as scantin vitroandin vivodata. There remain unmet needs for experimental models of ACO that accurately recapitulate the hallmark features of ACO in patients. The development and interrogation of such models will identify underlying disease-causing mechanisms, as well as enabling the identification of novel therapeutic targets and providing a platform for assessing new ACO therapies. Here, we review the current understanding of the clinical features of ACO and highlight the approaches that are best suited for developing representative experimental models of ACO.
Turkewitz, DR, Moghaddasi, S, Alghalayini, A, D'Amario, C, Ali, HM, Wallach, M & Valenzuela, SM 2021, 'Comparative study of His- and Non-His-tagged CLIC proteins, reveals changes in their enzymatic activity', Biochemistry and Biophysics Reports, vol. 26, pp. 101015-101015.
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The chloride intracellular ion channel protein (CLIC) family are a unique set of ion channels that can exist as soluble and integral membrane proteins. New evidence has emerged that demonstrates CLICs' possess oxidoreductase enzymatic activity and may function as either membrane-spanning ion channels or as globular enzymes. To further characterize the enzymatic profile of members of the CLIC family and to expand our understanding of their functions, we expressed and purified recombinant CLIC1, CLIC3, and a non-functional CLIC1-Cys24A mutant using a Histidine tag, bacterial protein expression system. We demonstrate that the presence of the six-polyhistidine tag at the amino terminus of the proteins led to a decrease in their oxidoreductase enzymatic activity compared to their non-His-tagged counterparts, when assessed using 2-hydroxyethyl disulfide as a substrate. These results strongly suggest the six-polyhistidine tag alters CLIC's structure at the N-terminus, which also contains the enzyme active site. It also raises the need for caution in use of His-tagged proteins when assessing oxidoreductase protein enzymatic function.
Turnbull, L, Leigh, R, Cavaliere, R, Osvath, SR, Nolan, LM, Smyth, D, Verhoeven, K, Chole, RA & Whitchurch, CB 2021, 'Device Design Modifications Informed by In Vitro Testing of Bacterial Attachment Reduce Infection Rates of Cochlear Implants in Clinical Practice', Microorganisms, vol. 9, no. 9, pp. 1809-1809.
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Recalcitrant chronic infections of implanted medical devices are often linked to the presence of biofilms. The prevention and treatment of medical device-associated infections is a major source of antibiotic use and driver of antimicrobial resistance globally. Lowering the incidence of infection in patients that receive implanted medical devices could therefore significantly improve antibiotic stewardship and reduce patient morbidity. Here we determined if modifying the design of an implantable medical device to reduce bacterial attachment, impacted the incidence of device-associated infections in clinical practice. Since the 1980s cochlear implants have provided long-term treatment of sensorineural hearing deficiency in hundreds of thousands of patients world-wide. Nonetheless, a relatively small number of devices are surgically explanted each year due to unresolvable infections. Features associated with the accumulation of bacteria on the Cochlear™ Nucleus® CI24RE™ model of cochlear implant devices were identified using both in vitro bacterial attachment assays and examination of explanted devices. Macro-scale design modifications that reduced bacterial attachment in vitro were incorporated into the design of the CI500™ and Profile™ series of Nucleus implant. Analyses of mandatory post-market vigilance data of 198,757 CI24RE and 123,084 CI500/Profile series implantation surgeries revealed that these design modifications correlated with significantly reduced infection rates. This study demonstrates that a design-centric approach aimed at mitigating bacterial attachment was a simple, and effective means of reducing infections associated with Cochlear Nucleus devices. This approach is likely to be applicable to improving the designs of other implantable medical devices to reduce device-associated infections.
Turner, KM, Balleine, BW & Bradfield, LA 2021, 'Does disrupting the orbitofrontal cortex alter sensitivity to punishment? A potential mechanism of compulsivity.', Behavioral Neuroscience, vol. 135, no. 2, pp. 174-181.
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Abnormal orbitofrontal cortex (OFC) activity is one of the most common findings from neuroimaging studies of individuals with compulsive disorders such as substance use disorder and obsessive-compulsive disorder. The nature of this abnormality is complex, however, with some studies reporting the OFC to be over-active in compulsive individuals relative to controls, whereas other studies report it being under-active, and a further set of studies reporting OFC abnormality in both directions within the same individuals. The OFC has been implicated in a broad range of cognitive processes such as decision-making and goal-directed action. OFC dysfunction could thus impair decision-making and goal-directed action, leading to the kinds of cognitive/behavioral deficits observed in individuals with compulsive disorders. One such deficit that could arise as a result of OFC dysfunction is an altered sensitivity to punishment, which is one of the core characteristics displayed by individuals across multiple types of compulsive disorders. It is, therefore, the aim of the current review to assess the evidence implicating the OFC in adaptation to punishment and to attempt to identify the critical factors that determine this relationship. We distill from this analysis some guidelines for future studies attempting to determine the precise role of the OFC in punishment. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
Turner, KM, Ganesan, K & Bradfield, LA 2021, 'Evidence That Compulsive Reward Seeking Has Been Hiding in the Central Dorsal Striatum', Biological Psychiatry, vol. 90, no. 12, pp. 800-802.
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Ueland, M, Collins, S, Maestrini, L, Forbes, SL & Luong, S 2021, 'Fresh vs. frozen human decomposition – A preliminary investigation of lipid degradation products as biomarkers of post-mortem interval', Forensic Chemistry, vol. 24, pp. 100335-100335.
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Traditionally, the post-mortem interval (PMI) is determined using methods such as forensic entomology or forensic pathology, however, these techniques are often limited to a particular post-mortem window of up to 72 – 120 h after death. In this study, lipids extracted from decomposing human tissue were investigated as potential soft-tissue biomarkers of PMI. Tissue samples were collected from two whole human donors (n = 2), one frozen and one fresh, placed at the Australian Facility for Taphonomic Experimental Research (AFTER) over the course of 69 days post-placement. These samples were analysed using gas chromatography coupled with tandem mass spectrometry (GC–MS/MS), demonstrating statistically significant differences for most fatty acid analytes and further highlighting the well-known stability of sterol compounds over time. Differences were observed between the fresh and frozen donor, with the fresh donor displaying more distinct stages of decomposition. Chemical differences between the donors were more distinct in the fatty acids than the sterols. The fatty acid profiles over time were further investigated and target analytes comprising saturated fatty acids (stearic acid and palmitic acid) and unsaturated fatty acids (oleic acid and linoleic acid) were found to be of particular importance due to their potential as indicators of PMI.
Ueland, M, Harris, S & Forbes, SL 2021, 'Detecting volatile organic compounds to locate human remains in a simulated collapsed building', Forensic Science International, vol. 323, pp. 110781-110781.
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The occurrence of mass disasters has increased worldwide due to changing environments from global warming and a heightened threat of terrorism acts. When these disasters strike, it is imperative to rapidly locate and recover human victims, both the living and deceased. While search and rescue dogs are used to locate the living, cadaver detection dogs are typically tasked with locating the dead. This can prove challenging because commingling of victims is likely to occur during disasters in populated areas which will impact the decomposition process and the resulting odour produced. To date, there has been no research to investigate the process of human decomposition in a mass disaster scenario or to understand which compounds are detectable by cadaver detection dogs. Hence, the current study investigated the human decomposition process and subsequent volatile organic compound (VOC) production in two simulated building collapse scenarios with six human donors placed in each scenario. The human remains were only recovered after a period of one month, during which time VOC samples were collected and analysed using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry. A considerable degree of differential decomposition was observed upon recovery of the human remains, which was carried out as a part of a police disaster victim recovery training exercise. The location of the bodies in the disaster area was found to impact the decomposition process. The VOC profile was found to correlate with the decomposition process. Fifteen days following the simulated disaster, the VOC profile changed showing that a detectable change in the decomposition process had occurred. Overall, the changing VOC profile can inform the training of cadaver detection dogs for these unique scenarios.
Umar, MD, Ishida, K, Murayama, R, Puspita Sari, D, Widyaiswari, U, Fronzi, M, Rozak, H, Zaharim, WN, Watanabe, I & Iwasaki, M 2021, 'Muon spin motion at the crossover regime between Gaussian and Lorentzian distribution of magnetic fields', Progress of Theoretical and Experimental Physics, vol. 2021, no. 8.
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Abstract The muon spin relaxation method is a powerful microscopic tool for probing the electronic states of materials by observing local magnetic field distributions on the muon. It often happens that a distribution of local magnetic fields shows an intermediate state between Gaussian and Lorentzian shapes. In order to generally describe these intermediate field distributions, we considered the convolution of two isotropic distributions in three dimensions and derived exact muon-spin relaxation functions which can be applied to all crossover regimes between Gaussian and Lorentzian.
Ungolo, F, Garces, LP, Sherris, M & Zhou, Y 2021, 'AffineMortality: An R Package for Estimation, Analysis and Projection of Affine Mortality Models'.
Valiate, BVS, Queiroz‐Junior, CM, Levi‐Schaffer, F, Galvão, I & Teixeira, MM 2021, 'CD300a contributes to the resolution of articular inflammation triggered by MSU crystals by controlling neutrophil apoptosis', Immunology, vol. 164, no. 2, pp. 305-317.
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AbstractGout is an inflammatory disease triggered by deposition of monosodium urate (MSU) crystals in the joints, resulting in high neutrophil influx and pain. Here, we studied the role of the inhibitory receptor CD300a in the resolution process in a murine model of gout. We found increased CD300a expression on neutrophils emigrated to the joint. When compared to WT mice, CD300a−/− mice had persistent neutrophil influx till 24 hr after MSU injection. This was associated with increased concentration of IL‐1β and greater tissue damage in the joints of CD300a−/− mice. There was an increase in the percentage of apoptotic neutrophils in the synovial lavage of WT mice, as compared to CD300a−/− mice. This difference was reflected in the decline of efferocytic events in the synovial cavity of CD300a−/− mice 24 hr after MSU injection. A CD300a agonistic antibody was shown, for the first time, to increase apoptosis of human neutrophils, and this was associated with cleavage of caspase‐8. In conclusion, our results reveal an important role of CD300a in the control of leucocyte infiltration, IL‐1β production and caspase‐8 cleavage in neutrophils, contributing to the resolution of inflammation triggered by MSU injection.
van der Molen, MC, Hartman, JE, Vermeulen, CJ, van den Berge, M, Faiz, A, Kerstjens, HAM, Charbonnier, J-P, Vanfleteren, LEGW & Slebos, D-J 2021, 'Determinants of Lung Fissure Completeness', American Journal of Respiratory and Critical Care Medicine, vol. 204, no. 7, pp. 807-816.
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van Oorschot, RAH, Meakin, GE, Kokshoorn, B, Goray, M & Szkuta, B 2021, 'DNA Transfer in Forensic Science: Recent Progress towards Meeting Challenges', Genes, vol. 12, no. 11, pp. 1766-1766.
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Understanding the factors that may impact the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR), and the availability of data to assign probabilities to DNA quantities and profile types being obtained given particular scenarios and circumstances, is paramount when performing, and giving guidance on, evaluations of DNA findings given activity level propositions (activity level evaluations). In late 2018 and early 2019, three major reviews were published on aspects of DNA-TPPR, with each advocating the need for further research and other actions to support the conduct of DNA-related activity level evaluations. Here, we look at how challenges are being met, primarily by providing a synopsis of DNA-TPPR-related articles published since the conduct of these reviews and briefly exploring some of the actions taken by industry stakeholders towards addressing identified gaps. Much has been carried out in recent years, and efforts continue, to meet the challenges to continually improve the capacity of forensic experts to provide the guidance sought by the judiciary with respect to the transfer of DNA.
Vardi, T, Hoot, WC, Levy, J, Shaver, E, Winters, RS, Banaszak, AT, Baums, IB, Chamberland, VF, Cook, N, Gulko, D, Hein, MY, Kaufman, L, Loewe, M, Lundgren, P, Lustic, C, MacGowan, P, Matz, MV, McGonigle, M, McLeod, I, Moore, J, Moore, T, Pivard, S, Pollock, FJ, Rinkevich, B, Suggett, DJ, Suleiman, S, Viehman, TS, Villalobos, T, Weis, VM, Wolke, C & Montoya‐Maya, PH 2021, 'Six priorities to advance the science and practice of coral reef restoration worldwide', Restoration Ecology, vol. 29, no. 8.
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Coral reef restoration is a rapidly growing movement galvanized by the accelerating degradation of the world's tropical coral reefs. The need for concerted and collaborative action focused on the recovery of coral reef ecosystems coalesced in the creation of the Coral Restoration Consortium (CRC) in 2017. In March 2020, the CRC leadership team met for a biennial review of international coral reef restoration efforts and a discussion of perceived knowledge and implementation bottlenecks that may impair scalability and efficacy. Herein we present six priorities wherein the CRC will foster scientific advancement and collaboration to: (1) increase restoration efficiency, focusing on scale and cost‐effectiveness of deployment; (2) scale up larval‐based coral restoration efforts, emphasizing recruit health, growth, and survival; (3) ensure restoration of threatened coral species proceeds within a population‐genetics management context; (4) support a holistic approach to coral reef ecosystem restoration; (5) develop and promote the use of standardized terms and metrics for coral reef restoration; and (6) support coral reef restoration practitioners working in diverse geographic locations. These priorities are not exhaustive nor do we imply that accomplishing these tasks alone will be sufficient to restore coral reefs globally; rather these are topics where we feel the CRC community of practice can make timely and significant contributions to facilitate the growth of coral reef restoration as a practical conservation strategy. The goal for these collective actions is to provide tangible, local‐scale advancements in reef condition that offset declines resulting from local and global stressors including climate change.
Vasilescu, SA, Khorsandi, S, Ding, L, Bazaz, SR, Nosrati, R, Gook, D & Warkiani, ME 2021, 'A microfluidic approach to rapid sperm recovery from heterogeneous cell suspensions', Scientific Reports, vol. 11, no. 1, pp. 1-11.
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AbstractThe isolation of sperm cells from background cell populations and debris is an essential step in all assisted reproductive technologies. Conventional techniques for sperm recovery from testicular sperm extractions stagnate at the sample processing stage, where it can take several hours to identify viable sperm from a background of collateral cells such as white bloods cells (WBCs), red blood cells (RBCs), epithelial cells (ECs) and in some cases cancer cells. Manual identification of sperm from contaminating cells and debris is a tedious and time-consuming operation that can be suitably addressed through inertial microfluidics. Microfluidics has proven an effective technology for high-quality sperm selection based on motility. However, motility-based selection methods cannot cater for viable, non-motile sperm often present in testicular or epididymal sperm extractions and aspirations. This study demonstrates the use of a 3D printed inertial microfluidic device for the separation of sperm cells from a mixed suspension of WBCs, RBCs, ECs, and leukemic cancer cells. This technology presents a 36-fold time improvement for the recovery of sperm cells (> 96%) by separating sperm, RBCS, WBCs, ECs and cancer cells into tight bands in less than 5 min. Furthermore, microfluidic processing of sperm has no impact on sperm parameters; vitality, motility, morphology, or DNA fragmentation of sperm. Applying inertial microfluidics for non-motile sperm recovery can greatly improve the current processing procedure of testicular sperm extractions, simplifying the fertility outcomes for severe forms of male infertility that warrant the surgery.
Venning, KRW, Saltré, F & Bradshaw, CJA 2021, 'Predicting targets and costs for feral‐cat reduction on large islands using stochastic population models', Conservation Science and Practice, vol. 3, no. 8.
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AbstractFeral cats are some of the most destructive invasive predators worldwide, particularly in insular environments; hence, density‐reduction campaigns are often applied to alleviate the predation mortality they add to native fauna. Density‐reduction and eradication efforts are costly procedures with important outcomes for native fauna recovery, so they require adequate planning to be successful. These plans should include empirical density‐reduction models that can guide yearly culling quotas, and resource roll‐out for the duration of the culling period. This ensures densities are reduced over the long term and that resources are not wasted. We constructed a stochastic population model with cost estimates to test the relative effectiveness and cost‐efficiency of two main culling scenarios for a 10‐year eradication campaign of cats on Kangaroo Island, Australia: (a) constant proportional annual cull (one‐phase), and (b) high initial culling followed by a constant proportional maintenance cull (two‐phase). A one‐phase cull of at least 0.35 of the annual population size would reduce the final population to 0.1 of its original size, while a two‐phase cull with an initial cull of minimum 0.6 and minimum 0.5 maintenance cull would reduce the final population to 0.01 of its initial size within the 10‐year time frame. Cost estimates varied widely depending on the methods applied (shooting, trapping, aerial poison baits, Felixer™ poison‐delivery system), but using baiting, trapping and Felixers with additional shooting to meet culling quotas was the most cost‐effective combination (minimum cost: AU$19.56 million; range: AU$16.87 million–AU$20.69 million). Our model provides an adaptable and general assessment tool for cat reductions in Australia and potentially elsewhere, and provides relative culling costs for the Kangaroo Island campaign specifically.
Vicedomini, R, Quince, C, Darling, AE & Chikhi, R 2021, 'Strainberry: automated strain separation in low-complexity metagenomes using long reads', Nature Communications, vol. 12, no. 1, p. 4485.
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AbstractHigh-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 20-118% additional genomic material than conventional metagenome assemblies on individual strain genomes. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements on strain-resolved metagenome assembly in environments of higher complexities.
Violi, JP, Bishop, DP, Padula, MP, Westerhausen, MT & Rodgers, KJ 2021, 'Acetonitrile adduct analysis of underivatised amino acids offers improved sensitivity for hydrophilic interaction liquid chromatography tandem mass-spectrometry', Journal of Chromatography A, vol. 1655, pp. 462530-462530.
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LC-MS/MS method development for native amino acid detection can be problematic due to low ionisation efficiencies, in source fragmentation, potential for cluster ion formation and incorrect application of chromatography techniques. This has led to the majority of the scientific community derivatising amino acids for more sensitive analysis. Derivatisation has several benefits including reduced signal-to-noise ratios, more efficient ionisation, and a change in polarity, allowing the use of reverse phase chromatography. However, derivatisation of amino acids can be expensive, requires additional sample preparation steps, is more time consuming and increases sample instability, due to the most derivatised amino acids only be stable for finite amount of time. While showing initial promise, development of reliable hydrophilic interaction liquid chromatography (HILIC) separation methods has presented difficulties for the analyst including irreproducible separation and poor sensitivity. This study aimed to find a means to improve the detection sensitivity of the 20 protein amino acids by HILIC-MS/MS. We describe the use of previously undescribed amino acid-acetonitrile (ACN) adducts to improve detection of 16 out of the 20 amino acids. While all amino acids examined did form an ACN adduct, 4 had low intensity adduct formation compared to their protonated state, 3 of which are classified as basic amino acids. For 15 of the 20 amino acids tested, we used the ACN adduct for both quantification and qualification ions and demonstrated a significant enhancement in signal-to-noise ratio, ranging from 23 to 1762% improvement. Lower LODs, LOQs and lower ranges of linearity were also achieved for these amino acids. The optimised method was applied to a human neuroblastoma cell line (SH-SY5Y) with the potential to be applied to other complex sample types. The improved sensitivity this method offers simplifies sample preparation and reduces the costs of amino acid analysi...
Vo, HNP, Ngo, HH, Guo, W, Nguyen, KH, Chang, SW, Nguyen, DD, Cheng, D, Bui, XT, Liu, Y & Zhang, X 2021, 'Effect of calcium peroxide pretreatment on the remediation of sulfonamide antibiotics (SMs) by Chlorella sp.', Science of The Total Environment, vol. 793, pp. 148598-148598.
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This study investigated the effect of CaO2 pretreatment on sulfonamide antibiotics (SMs) remediation by Chlorella sp. Results showed that a CaO2 dose ranging from 0.05 to 0.1 g/g biomass was the best and led to higher SMs removal efficacy 5-10% higher than the control. The contributions made by cometabolism and CaO2 in SMs remediation were very similar. Bioassimilation could remove 24% of sulfadiazine (SDZ) and sulfamethazine (SMZ), and accounted for 38% of sulfamethoxazole (SMX) remediation. Pretreatment by CaO2 wielded a positive effect on microalgae. The extracellular polymeric substances (EPS) level of the CaO2 pretreatment microalgae was three times higher when subjected to non-pretreatment. For the long-term, pretreatment microalgae removed SMs 10-20% more than the non-pretreatment microalgae. Protein fractions of EPS in continuous operation produced up to 90 mg/L for cometabolism. For bioassimilation, SMX intensity of the pretreatment samples was 160-fold less than the non-treatment one. It indicated the CaO2 pretreatment has enhanced the biochemical function of the intracellular environment of microalgae. Peroxidase enzyme involved positively in the cometabolism and degradation of SMs to several metabolites including ring cleavage, hydroxylation and pterin-related conjugation.
Voolstra, CR, Quigley, KM, Davies, SW, Parkinson, JE, Peixoto, RS, Aranda, M, Baker, AC, Barno, AR, Barshis, DJ, Benzoni, F, Bonito, V, Bourne, DG, Buitrago-López, C, Bridge, TCL, Chan, CX, Combosch, DJ, Craggs, J, Frommlet, JC, Herrera, S, Quattrini, AM, Röthig, T, Reimer, JD, Rubio-Portillo, E, Suggett, DJ, Villela, H, Ziegler, M & Sweet, M 2021, 'Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition', Frontiers in Marine Science, vol. 8, pp. 1-12.
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Coral research is being ushered into the genomic era. To fully capitalize on the potential discoveries from this genomic revolution, the rapidly increasing number of high-quality genomes requires effective pairing with rigorous taxonomic characterizations of specimens and the contextualization of their ecological relevance. However, to date there is no formal framework that genomicists, taxonomists, and coral scientists can collectively use to systematically acquire and link these data. Spurred by the recently announced “Coral symbiosis sensitivity to environmental change hub” under the “Aquatic Symbiosis Genomics Project” - a collaboration between the Wellcome Sanger Institute and the Gordon and Betty Moore Foundation to generate gold-standard genome sequences for coral animal hosts and their associated Symbiodiniaceae microalgae (among the sequencing of many other symbiotic aquatic species) - we outline consensus guidelines to reconcile different types of data. The metaorganism nature of the coral holobiont provides a particular challenge in this context and is a key factor to consider for developing a framework to consolidate genomic, taxonomic, and ecological (meta)data. Ideally, genomic data should be accompanied by taxonomic references, i.e., skeletal vouchers as formal morphological references for corals and strain specimens in the case of microalgal and bacterial symbionts (cultured isolates). However, exhaustive taxonomic characterization of all coral holobiont member species is currently not feasible simply because we do not have a comprehensive understanding of all the organisms that constitute the coral holobiont. Nevertheless, guidelines on minimal, recommended, and ideal-case descriptions for the major coral holobiont constituents (coral animal, Symbiodiniaceae microalgae, and prokaryotes) will undoubtedly help in future referencing and will facilitate comparative studies. We hope that the guidelines outlined here, which we will ad...
Voolstra, CR, Suggett, DJ, Peixoto, RS, Parkinson, JE, Quigley, KM, Silveira, CB, Sweet, M, Muller, EM, Barshis, DJ, Bourne, DG & Aranda, M 2021, 'Extending the natural adaptive capacity of coral holobionts', Nature Reviews Earth & Environment, vol. 2, no. 11, pp. 747-762.
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Anthropogenic climate change and environmental degradation destroy coral reefs, the ecosystem services they provide, and the livelihoods of close to a billion people who depend on these services. Restoration approaches to increase the resilience of corals are therefore necessary to counter environmental pressures relevant to climate change projections. In this Review, we examine the natural processes that can increase the adaptive capacity of coral holobionts, with the aim of preserving ecosystem functioning under future ocean conditions. Current approaches that centre around restoring reef cover can be integrated with emerging approaches to enhance coral stress resilience and, thereby, allow reefs to regrow under a new set of environmental conditions. Emerging approaches such as standardized acute thermal stress assays, selective sexual propagation, coral probiotics, and environmental hardening could be feasible and scalable in the real world. However, they must follow decision-making criteria that consider the different reef, environmental, and ecological conditions. The implementation of adaptive interventions tailored around nature-based solutions will require standardized frameworks, appropriate ecological risk–benefit assessments, and analytical routines for consistent and effective utilization and global coordination.
Vu, HP, Nguyen, LN, Emmerton, B, Wang, Q, Ralph, PJ & Nghiem, LD 2021, 'Factors governing microalgae harvesting efficiency by flocculation using cationic polymers', Bioresource Technology, vol. 340, pp. 125669-125669.
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This study aims to elucidate the mechanisms governing the harvesting efficiency of Chlorella vulgaris by flocculation using a cationic polymer. Flocculation efficiency increased as microalgae culture matured (i.e. 35-45, 75, and > 97% efficiency at early, late exponential, and stationary phase, respectively. Unlike the negative impact of phosphate on flocculation in traditional wastewater treatment; here, phosphorous residue did not influence the flocculation efficiency of C. vulgaris. The observed dependency of flocculation efficiency on growth phase was driven by changes in microalgal cell properties. Microalgal extracellular polymeric substances (EPS) in both bound and free forms at stationary phase were two and three times higher than those at late and early exponential phase, respectively. Microalgae cells also became more negatively charged as they matured. Negatively charged and high EPS content together with the addition of high molecular weight and positively charged polymer could facilitate effective flocculation via charge neutralisation and bridging.
Vu, HP, Nguyen, LN, Vu, MT, Labeeuw, L, Emmerton, B, Commault, AS, Ralph, PJ, Mahlia, TMI & Nghiem, LD 2021, 'Harvesting Porphyridium purpureum using polyacrylamide polymers and alkaline bases and their impact on biomass quality', Science of The Total Environment, vol. 755, no. Pt 1, pp. 142412-142412.
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This study aims to examine the flocculation efficiency of Porphyridium purpureum (i.e. a red marine microalga with high content of pigments and fatty acids) grown in seawater medium using polyacrylamide polymers and alkaline flocculation. Polymers Flopam™ and FO3801 achieved the highest flocculation efficiency of over 99% at the optimal dose of 21 mg per g of dry biomass through charge neutralisation and bridging mechanism. The addition of sodium hydroxide, potassium hydroxide, and sodium carbonate also achieved flocculation efficiency of 98 and 91%, respectively, but high doses were required (i.e. > 500 mg per g of dry biomass). Calcium hydroxide was not as effective and could only achieve 75% flocculation efficiency. Precipitation of magnesium hydroxide was identified as the major cause of hydroxide-induced flocculation. On the other hand, sodium carbonate addition induced flocculation via both magnesium and calcium carbonate co-precipitation. The large mass of precipitates caused a sweeping effect and enmeshed the microalgal cells to trigger sedimentation. Cell membrane integrity analysis of flocculated P. purpureum indicated that polyacrylamide polymers led to significant compromised cells (i.e. 96%), compared to the alkaline bases (70-96% compromised cells). These results appear to be the first to demonstrate the high efficiency of polyacrylamide polymer and alkaline flocculation of P. purpureum but at the expense of the biomass quality.
Wadhwa, R, Paudel, KR, Chin, LH, Hon, CM, Madheswaran, T, Gupta, G, Panneerselvam, J, Lakshmi, T, Singh, SK, Gulati, M, Dureja, H, Hsu, A, Mehta, M, Anand, K, Devkota, HP, Chellian, J, Chellappan, DK, Hansbro, PM & Dua, K 2021, 'Anti‐inflammatory and anticancer activities of Naringenin‐loaded liquid crystalline nanoparticles in vitro', Journal of Food Biochemistry, vol. 45, no. 1, p. e13572.
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In this study, we had developed Naringenin-loaded liquid crystalline nanoparticles (LCNs) and investigated the anti-inflammatory and anticancer activities of Naringenin-LCNs against human airway epithelium-derived basal cells (BCi-NS1.1) and human lung epithelial carcinoma (A549) cell lines, respectively. The anti-inflammatory potential of Naringenin-LCNs evaluated by qPCR revealed a decreased expression of IL-6, IL-8, IL-1β, and TNF-α in lipopolysaccharide-induced BCi-NS1.1 cells. The activity of LCNs was comparable to the positive control drug Fluticasone propionate (10 nM). The anticancer activity was studied by evaluating the antiproliferative (MTT and trypan blue assays), antimigratory (scratch wound healing assay, modified Boyden chamber assay, and immunoblot), and anticolony formation activity in A549 cells. Naringenin LCNs showed promising antiproliferative, antimigratory, and anticolony formation activities in A549 cells, in vitro. Therefore, based on our observations and results, we conclude that Naringenin-LCNs may be employed as a potential therapy-based intervention to ameliorate airway inflammation and to inhibit the progression of lung cancer. PRACTICAL APPLICATIONS: Naringenin was encapsulated into liquid crystalline nanoparticles, thus, attributing to their sustained-release nature. In addition, Naringenin-loaded LCNs efficiently reduced the levels of pro-inflammatory markers, namely, IL-1β, IL-6, TNF-α, and IL-8. In addition, the Naringenin-loaded LCNs also possess potent anticancer activity, when tested in the A549 cell line, as revealed by the inhibition of proliferation and migration of cells. They also attenuated colony formation and induced apoptosis in the A549 cells. The findings from our study could form the basis for future research that may be translated into an in vivo model to validate the possible therapeutic alternative for lung cancer using Naringenin-loaded LCNs. In addition, the applications of Naringenin-loaded LCNs a...
Walker, AP, De Kauwe, MG, Bastos, A, Belmecheri, S, Georgiou, K, Keeling, RF, McMahon, SM, Medlyn, BE, Moore, DJP, Norby, RJ, Zaehle, S, Anderson‐Teixeira, KJ, Battipaglia, G, Brienen, RJW, Cabugao, KG, Cailleret, M, Campbell, E, Canadell, JG, Ciais, P, Craig, ME, Ellsworth, DS, Farquhar, GD, Fatichi, S, Fisher, JB, Frank, DC, Graven, H, Gu, L, Haverd, V, Heilman, K, Heimann, M, Hungate, BA, Iversen, CM, Joos, F, Jiang, M, Keenan, TF, Knauer, J, Körner, C, Leshyk, VO, Leuzinger, S, Liu, Y, MacBean, N, Malhi, Y, McVicar, TR, Penuelas, J, Pongratz, J, Powell, AS, Riutta, T, Sabot, MEB, Schleucher, J, Sitch, S, Smith, WK, Sulman, B, Taylor, B, Terrer, C, Torn, MS, Treseder, KK, Trugman, AT, Trumbore, SE, van Mantgem, PJ, Voelker, SL, Whelan, ME & Zuidema, PA 2021, 'Integrating the evidence for a terrestrial carbon sink caused by increasing atmospheric CO2', New Phytologist, vol. 229, no. 5, pp. 2413-2445.
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SummaryAtmospheric carbon dioxide concentration ([CO2]) is increasing, which increases leaf‐scale photosynthesis and intrinsic water‐use efficiency. These direct responses have the potential to increase plant growth, vegetation biomass, and soil organic matter; transferring carbon from the atmosphere into terrestrial ecosystems (a carbon sink). A substantial global terrestrial carbon sink would slow the rate of [CO2] increase and thus climate change. However, ecosystem CO2 responses are complex or confounded by concurrent changes in multiple agents of global change and evidence for a [CO2]‐driven terrestrial carbon sink can appear contradictory. Here we synthesize theory and broad, multidisciplinary evidence for the effects of increasing [CO2] (iCO2) on the global terrestrial carbon sink. Evidence suggests a substantial increase in global photosynthesis since pre‐industrial times. Established theory, supported by experiments, indicates that iCO2 is likely responsible for about half of the increase. Global carbon budgeting, atmospheric data, and forest inventories indicate a historical carbon sink, and these apparent iCO2 responses are high in comparison to experiments and predictions from theory. Plant mortality and soil carbon iCO2 responses are highly uncertain. In conclusion, a range of evidence supports a positive terrestrial carbon sink in response to iCO2, albeit with uncertain magnitude and strong suggestion of a role for additional agents of global change.
Walker, GJ, Naing, Z, Ospina Stella, A, Yeang, M, Caguicla, J, Ramachandran, V, Isaacs, SR, Agapiou, D, Bull, RA, Stelzer-Braid, S, Daly, J, Gosbell, IB, Hoad, VC, Irving, DO, Pink, JM, Turville, S, Kelleher, AD & Rawlinson, WD 2021, 'SARS Coronavirus-2 Microneutralisation and Commercial Serological Assays Correlated Closely for Some but Not All Enzyme Immunoassays', Viruses, vol. 13, no. 2, pp. 247-247.
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Serological testing for SARS-CoV-2-specific antibodies provides important research and diagnostic information relating to COVID-19 prevalence, incidence and host immune response. A greater understanding of the relationship between functionally neutralising antibodies detected using microneutralisation assays and binding antibodies detected using scalable enzyme immunoassays (EIA) is needed in order to address protective immunity post-infection or vaccination, and assess EIA suitability as a surrogate test for screening of convalescent plasma donors. We assessed whether neutralising antibody titres correlated with signal cut-off ratios in five commercially available EIAs, and one in-house assay based on expressed spike protein targets. Sera from recovered patients or convalescent plasma donors who reported laboratory-confirmed SARS-CoV-2 infection (n = 200), and negative control sera collected prior to the COVID-19 pandemic (n = 100), were assessed in parallel. Performance was assessed by calculating EIA sensitivity and specificity with reference to microneutralisation. Neutralising antibodies were detected in 166 (83%) samples. Compared with this, the most sensitive EIAs were the Cobas Elecsys Anti-SARS-CoV-2 (98%) and Vitros Immunodiagnostic Anti-SARS-CoV-2 (100%), which detect total antibody targeting the N and S1 antigens, respectively. The assay with the best quantitative relationship with microneutralisation was the Euroimmun IgG. These results suggest the marker used (total Ab vs. IgG vs. IgA) and the target antigen are important determinants of assay performance. The strong correlation between microneutralisation and some commercially available assays demonstrates their potential for clinical and research use in assessing protection following infection or vaccination, and use as a surrogate test to assess donor suitability for convalescent plasma donation.
Walworth, NG, Hinners, J, Argyle, PA, Leles, SG, Doblin, MA, Collins, S & Levine, NM 2021, 'The evolution of trait correlations constrains phenotypic adaptation to high CO2in a eukaryotic alga', Proceedings of the Royal Society B: Biological Sciences, vol. 288, no. 1953, pp. 1-9.
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Microbes form the base of food webs and drive biogeochemical cycling. Predicting the effects of microbial evolution on global elemental cycles remains a significant challenge due to the sheer number of interacting environmental and trait combinations. Here, we present an approach for integrating multivariate trait data into a predictive model of trait evolution. We investigated the outcome of thousands of possible adaptive walks parameterized using empirical evolution data from the algaChlamydomonasexposed to high CO2. We found that the direction of historical bias (existing trait correlations) influenced both the rate of adaptation and the evolved phenotypes (trait combinations). Critically, we use fitness landscapes derived directly from empirical trait values to capture known evolutionary phenomena. This work demonstrates that ecological models need to represent both changes in traits and changes in the correlation between traits in order to accurately capture phytoplankton evolution and predict future shifts in elemental cycling.
Wang, B, Chan, Y-L, Li, G, Ho, KF, Anwer, AG, Smith, BJ, Guo, H, Jalaludin, B, Herbert, C, Thomas, PS, Liao, J, Chapman, DG, Foster, PS, Saad, S, Chen, H & Oliver, BG 2021, 'Maternal Particulate Matter Exposure Impairs Lung Health and Is Associated with Mitochondrial Damage', Antioxidants, vol. 10, no. 7, pp. 1029-1029.
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Relatively little is known about the transgenerational effects of chronic maternal exposure to low-level traffic-related air pollution (TRAP) on the offspring lung health, nor are the effects of removing such exposure before pregnancy. Female BALB/c mice were exposed to PM2.5 (PM2.5, 5 µg/day) for 6 weeks before mating and during gestation and lactation; in a subgroup, PM was removed when mating started to model mothers moving to cleaner areas during pregnancy to protect their unborn child (Pre-exposure). Lung pathology was characterised in both dams and offspring. A subcohort of female offspring was also exposed to ovalbumin to model allergic airways disease. PM2.5 and Pre-exposure dams exhibited airways hyper-responsiveness (AHR) with mucus hypersecretion, increased mitochondrial reactive oxygen species (ROS) and mitochondrial dysfunction in the lungs. Female offspring from PM2.5 and Pre-exposure dams displayed AHR with increased lung inflammation and mitochondrial ROS production, while males only displayed increased lung inflammation. After the ovalbumin challenge, AHR was increased in female offspring from PM2.5 dams compared with those from control dams. Using an in vitro model, the mitochondria-targeted antioxidant MitoQ reversed mitochondrial dysfunction by PM stimulation, suggesting that the lung pathology in offspring is driven by dysfunctional mitochondria. In conclusion, chronic exposure to low doses of PM2.5 exerted transgenerational impairment on lung health.
Wang, B, Chen, H, Xenaki, D, Liao, J, Cowie, C & Oliver, BG 2021, 'Differential inflammatory and toxic effects in-vitro of wood smoke and traffic-related particulate matter from Sydney, Australia', Chemosphere, vol. 272, pp. 129616-129616.
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Background
It is well known that PM
2.5 generated by traffic or burning wood is pro-inflammatory and induces various adverse health outcomes in humans. In Sydney, New South Wales, Australia, the main anthropogenic contributors to particulate matter (PM) air pollution are wood combustion heaters, on-road vehicles, and coal-fired power stations. However, the relative toxicity of these local sources has not to date been investigated.
Method
PM
2.5 was collected on filters from the same sampling site in Liverpool, one suburb of Sydney. According to the positive matrix factorisation and collection season, filters were representative of either day with high traffic-related air pollution (TRAP), wood smoke, or both TRAP and woodsmoke (mixed air pollution). The elemental composition of the PM was assessed by accelerator-based ion beam analysis techniques (i.e. PIXE & PIGE) and size by Dynamic Light Scattering. Toxicity and inflammation were assessed in-vitro in human bronchial epithelial cells by measuring interleukin-6 (IL-6), interleukin-8 (IL-8) release, and MTT.
Results
Mixed air pollution (TRAP/wood smoke) PM had more nanometer (nm) sized PM than the other two groups. Using an in-vitro model of the lungs, the mixed air pollution PM was the most toxic, whereas the PM from woodsmoke induced greater IL-6 release than TRAP PM. There was no difference in the induction of IL-8 between the three sources of PM.
Conclusion
Marked differences occur in the cellular response to PM from different sources, with differences in both toxicity and inflammation.
WANG, B, CHEN, X, ZHU, X & MA, D 2021, 'MicroRNA-217 inhibits proliferation and promotes apoptosis of small cell lung cancer cells via targeting PCDH8', Panminerva Medica, vol. 63, no. 1.
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Wang, D, Tang, K, Xiao, J, Li, X, Long, M, Chen, J, Gao, H, Chen, W, Liu, C & Liu, H 2021, 'Advances of electrospun Mo-based nanocomposite fibers as anode materials for supercapacitors', Sustainable Materials and Technologies, vol. 29, pp. e00302-e00302.
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Wang, F, Langford, S & Nakai, H 2021, 'Robust design of D-π-A model compounds using digital structures for organic DSSC applications', Journal of Molecular Graphics and Modelling, vol. 102, pp. 107798-107798.
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Wang, JJJ & Weatherburn, D 2021, 'The effect of police searches and move-on directions on property and violent crime in New South Wales', Journal of Criminology, vol. 54, no. 3, pp. 383-401.
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The New South Wales (NSW) Law Enforcement (Powers and Responsibilities) Act 2002 gave the NSW Police the power in certain circumstances the power to stop, search and detain a person without warrant. The same legislation gave the police the power to direct a person to move on from a place if they believe on reasonable grounds that the person in question is obstructing traffic or another person; engaging in behaviour that is considered harassment or intimidation to another person (or people); behaving in a way that is causing or likely to cause fear to a reasonable person or present in the place in order to unlawfully supply or cause another person to unlawfully supply drugs. The exercise of these powers has attracted considerable controversy, but little is known about their effectiveness in controlling crime. We investigate the relationship between police activity and crime using panel data of 17 Local Area Command for the period 2001 to 2013. We find a significant and strongly negative long-run relationship between both indices of police activity and each of break and enter, motor vehicle theft and robbery. No significant long-run relationship is found between assault and move-on directions. The person search activity is negatively related to assault, but the effect is weak; with a 10% increase in person search only resulting in a 0.5% fall in assaults. The implications for the exercise of police move-on and search powers are discussed.
Wang, JJJ, Fung, T & Weatherburn, D 2021, 'The impact of the COVID-19, social distancing, and movement restrictions on crime in NSW, Australia', Crime Science, vol. 10, no. 1, pp. 1-14.
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AbstractThe spread of COVID-19 has prompted Governments around the world to impose draconian restrictions on business activity, public transport, and public freedom of movement. The effect of these restrictions appears to vary from country to country and, in some cases, from one area to another within a country. This paper examines the impact of the COVID-19 restrictions imposed in New South Wales (NSW) by the State Government. We examine week-to-week changes in 13 categories of crime (and four aggregated categories) from 2 January 2017 to 28 June 2020. Rather than using the pre-intervention data to make a forecast and then comparing that with what is actually observed, we use a Box–Jenkins (ARIMA) approach to model the entire time series. Our results are broadly in accord with those of other studies, but we find no effect of the lockdown (upward or downward) on domestic assault.
Wang, P, Wu, X & Gale, PA 2021, 'Carbazole-based bis-ureas and thioureas as electroneutral anion transporters', Supramolecular Chemistry, vol. 33, no. 4, pp. 143-149.
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Wang, Q, Guan, YF, Hancock, SE, Wahi, K, van Geldermalsen, M, Zhang, BK, Pang, A, Nagarajah, R, Mak, B, Freidman, N, Horvath, LG, Turner, N & Holst, J 2021, 'Inhibition of guanosine monophosphate synthetase (GMPS) blocks glutamine metabolism and prostate cancer growth', The Journal of Pathology, vol. 254, no. 2, pp. 135-146.
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AbstractGlutamine is a critical nutrient in cancer; however, its contribution to purine metabolism in prostate cancer has not previously been determined. Guanosine monophosphate synthetase (GMPS) acts in the de novo purine biosynthesis pathway, utilizing a glutamine amide to synthesize the guanine nucleotide. This study demonstrates that GMPS mRNA expression correlates with Gleason score in prostate cancer samples, while high GMPS expression was associated with decreased rates of overall and disease/progression‐free survival. Pharmacological inhibition or knockdown of GMPS significantly decreased cell growth in both LNCaP and PC‐3 prostate cancer cells. We utilized [15N‐(amide)]glutamine and [U‐13C5]glutamine metabolomics to dissect the pathways involved and despite similar growth inhibition by GMPS knockdown, we show unique metabolic effects across each cell line. Using a PC‐3 xenograft mouse model, tumor growth was also significantly decreased after GMPS knockdown, highlighting the importance of glutamine metabolism and providing support for GMPS as a therapeutic target in prostate cancer. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Wark, PAB, MacIntyre, CR, Bell, S, Oliver, B & Marks, GB 2021, 'We are not doing enough to prevent the spread of COVID‐19 and other respiratory viruses in Australian hospitals', Medical Journal of Australia, vol. 215, no. 4, pp. 152-152.
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The health care community has been accused of not taking the nosocomial spread of respiratory virus infection to health care workers and patients seriously enough. The evidence from the coronavirus disease 2019 (COVID-19) pandemic has demonstrated that our current approach to controlling respiratory viruses is not sufficient. The overrepresentation of health care workers among those acquiring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in workplace settings is a clear testament to this with an adjusted hazard ratio of 3.40 (95% CI, 3.37–3.43).1 This issue needs to be critically examined in light of the emerging evidence from the COVID-19 pandemic.
Wark, PAB, Pathinayake, PS, Kaiko, G, Nichol, K, Ali, A, Chen, L, Sutanto, EN, Garratt, LW, Sohal, SS, Lu, W, Eapen, MS, Oldmeadow, C, Bartlett, N, Reid, A, Veerati, P, Hsu, AC, Looi, K, Iosifidis, T, Stick, SM, Hansbro, PM & Kicic, A 2021, 'ACE2 expression is elevated in airway epithelial cells from older and male healthy individuals but reduced in asthma', Respirology, vol. 26, no. 5, pp. 442-451.
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ABSTRACTBackground and objectiveCOVID‐19 is complicated by acute lung injury, and death in some individuals. It is caused by SARS‐CoV‐2 that requires the ACE2 receptor and serine proteases to enter AEC. We determined what factors are associated with ACE2 expression particularly in patients with asthma and COPD.MethodsWe obtained lower AEC from 145 people from two independent cohorts, aged 2–89 years, Newcastle (n = 115) and Perth (n = 30), Australia. The Newcastle cohort was enriched with people with asthma (n = 37) and COPD (n = 38). Gene expression for ACE2 and other genes potentially associated with SARS‐CoV‐2 cell entry was assessed by qPCR, and protein expression was confirmed with immunohistochemistry on endobronchial biopsies and cultured AEC.ResultsIncreased gene expression of ACE2 was associated with older age (P = 0.03) and male sex (P = 0.03), but not with pack‐years smoked. When we compared gene expression between adults with asthma, COPD and healthy controls, mean ACE2 expression was lower in asthma patients (P = 0.01). Gene expression of furin, a protease that facilitates viral endocytosis, was also lower in patients with asthma (P = 0.02), while ADAM‐17, a disintegrin that cleaves ACE2 from the surface, was increased (P = 0.02). ACE2 protein expression was also reduced in endobronchial biopsies from asthma patients.ConclusionIncreased ACE2 expression occurs in older people and males. Asthma patients have reduced expression. Altered ACE2 expression ...
Watherston, J, Watson, J, Bruce, D, Ward, J & McNevin, D 2021, 'Efficient DNA Profiling Protocols for Disaster Victim Identification', Forensic Sciences, vol. 1, no. 3, pp. 148-170.
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Advances in forensic biology have increased the options for the collection, sampling, preservation and processing of human remains for DNA-based identification. Combined with a plethora of commercial DNA testing kits that are far more forgiving of inhibited and degraded samples, efficient DNA approaches to post-mortem samples are explored here for DNA-based identification of compromised human remains. Approaches which preserve sample and reduce analytical turnaround times whilst saving resources also have the potential to expedite the identification process, to provide answers to grieving families sooner, or to provide leads in a criminal investigation. Targeting sample types that are minimally-invasive and do not require extensive preparation and testing protocols also has benefit for disaster victim identification (DVI) by facilitating field sampling. We have assessed minimally-invasive and simple to collect sample types compatible with minimal pre-treatment and efficient DNA profiling approaches. Incubating nail, distal phalanges and whole digits in 500 µL of PrepFiler™ Lysis Buffer for 2 h was an efficient and simple method, limiting or removing sample preparation. A reduced 15 min incubation also yielded DNA profiles suggesting a shorter incubation may lyse sufficient DNA. Preservative solutions offer an even simpler process in some cases. Furthermore, the efficient approaches described in this study offer storage solutions and are compatible with backend automated processing. This study will inform further research to develop and optimise efficient protocols. These DNA approaches should not be pursued for every sample; more compromised samples may best be submitted to the laboratory for more effective extraction and genotyping.
Watson, CJ, Ueland, M, Schotsmans, EMJ, Sterenberg, J, Forbes, SL & Blau, S 2021, 'Detecting grave sites from surface anomalies: A longitudinal study in an Australian woodland', Journal of Forensic Sciences, vol. 66, no. 2, pp. 479-490.
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AbstractForensic investigations of single and mass graves often use surface anomalies, including changes to soil and vegetation conditions, to identify potential grave locations. Though numerous resources describe surface anomalies in grave detection, few studies formally investigate the rate at which the surface anomalies return to a natural state; hence, the period the grave is detectable to observers. Understanding these processes can provide guidance as to when ground searches will be an effective strategy for locating graves. We studied three experimental graves and control plots in woodland at the Australian Facility for Taphonomic Experimental Research (Sydney, Australia) to monitor the rate at which surface anomalies change following disturbance. After three years, vegetation cover on all grave sites and control plots had steadily increased but remained substantially less than undisturbed surroundings. Soil anomalies (depressions and cracking) were more pronounced at larger grave sites versus the smaller grave and controls, with leaf litterfall rendering smaller graves difficult to detect beyond 20 months. Similar results were observed in two concurrent burial studies, except where accelerated revegetation appeared to be influenced by mummified remains. Extreme weather events such as heatwaves and heavy rainfall may prolong the detection window for grave sites by hindering vegetation establishment. Observation of grave‐indicator vegetation, which exhibited abnormally strong growth 10 months after commencement, suggests that different surface anomalies may have different detection windows. Our findings are environment‐specific, but the concepts are applicable globally.
Waziri, I, Isa, MA, Sonopo, M, Williams, DBG & Muller, A 2021, 'Synthesis, anti-microbial, toxicity and molecular docking studies of N-nitroso-N-phenylhydroxylamine (cupferron) and its derivatives', Bioorganic & Medicinal Chemistry Letters, vol. 52, pp. 128381-128381.
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Weckmann, M, Bahmer, T, Sand, JM, Rank Rønnow, S, Pech, M, Vermeulen, C, Faiz, A, Leeming, DJ, Karsdal, MA, Lunding, L, Oliver, BGG, Wegmann, M, Ulrich-Merzenich, G, Juergens, UR, Duhn, J, Laumonnier, Y, Danov, O, Sewald, K, Zissler, U, Jonker, M, König, I, Hansen, G, von Mutius, E, Fuchs, O, Dittrich, A-M, Schaub, B, Happle, C, Rabe, KF, van de Berge, M, Burgess, JK & Kopp, MV 2021, 'COL4A3 is degraded in allergic asthma and degradation predicts response to anti-IgE therapy', European Respiratory Journal, vol. 58, no. 6, pp. 2003969-2003969.
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BackgroundAsthma is a heterogeneous syndrome substantiating the urgent requirement for endotype-specific biomarkers. Dysbalance of fibrosis and fibrolysis in asthmatic lung tissue leads to reduced levels of the inflammation-protective collagen 4 (COL4A3).ObjectiveTo delineate the degradation of COL4A3 in allergic airway inflammation and evaluate the resultant product as a biomarker for anti-IgE therapy response.MethodsThe serological COL4A3 degradation marker C4Ma3 (Nordic Bioscience, Denmark) and serum cytokines were measured in the ALLIANCE cohort (paediatric cases/controls: n=134/n=35; adult cases/controls: n=149/n=31). Exacerbation of allergic airway disease in mice was induced by sensitising to ovalbumin (OVA), challenge with OVA aerosol and instillation of poly(cytidylic-inosinic). Fulacimstat (chymase inhibitor; Bayer) was used to determine the role of mast cell chymase in COL4A3 degradation. Patients with cystic fibrosis (n=14) and cystic fibrosis with allergic bronchopulmonary aspergillosis (ABPA; n=9) as well as patients with severe allergic uncontrolled asthma (n=19) were tested for COL4A3 degradation. Omalizumab (anti-IgE) treatment was assessed using the Asthma Control Test.ResultsSerum levels of C4Ma3 were increased in asthma in adults and children alike and linked to a more severe, exacerbating allergic asthma phenotype. In an experimental asthma mouse model, C4Ma3 was dependent on mast cell chymase. Serum C4Ma3 was significantly elevated in cystic fibrosis plus ABPA and at baseline predicted the success of the anti-IgE therapy in allergic, uncontrolled asthmatics (diagnostic OR 31.5).ConclusionC4Ma3 levels depend on lung mast cell chymase and are i...
Wei, Z, Dong, Z, Jia, J, Liang, X, Wang, T, Hu, M, Fu, S & Yun, K 2021, 'Application of Q-TOF–MS based metabonomics techniques to analyze the plasma metabolic profile changes on rats following death due to acute intoxication of phorate', International Journal of Legal Medicine, vol. 135, no. 4, pp. 1437-1447.
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Wei, Z, lan, Y, Zhang, C, Jia, J, Niu, W, Wei, Y, Fu, S & Yun, K 2021, 'A label-free Exonuclease I-assisted fluorescence aptasensor for highly selective and sensitive detection of silver ions', Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol. 260, pp. 119927-119927.
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Westermann, T, Jenkins, C, Onizawa, E, Gestier, S, McNally, J, Kirkland, P, Zhang, J, Bogema, D, Manning, LK, Walker, K & Pinczowski, P 2021, 'Chlamydia pecorum–Associated Sporadic Ovine Abortion', Veterinary Pathology, vol. 58, no. 1, pp. 114-122.
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Despite previous detection of Chlamydia pecorum in sporadic ovine abortions, published descriptions of naturally occurring infections with fetoplacental lesions are lacking. This report provides the first descriptions of severe necrosuppurative chorionitis with vasculitis, and fetal pyelonephritis and enteritis in late-term abortions of maiden ewes. Chlamydial infection was detected using a Chlamydia genus-specific qPCR (quantitative polymerase chain reaction) on tissue extracts from 3 fetuses. C. pecorum was identified using a targeted qPCR assay, which also determined infectious load within fetal tissues. The presence of viable C. pecorum in fetal samples was confirmed by cell culture. Multilocus sequence typing (MLST) data indicated that the C. pecorum strains from each fetus were identical and of sequence type (ST) 23. Chlamydia sp. immunohistochemistry showed strong positive immunolabeling of fetoplacental lesions. Other infectious abortigenic agents were excluded with specific testing. This report confirms C. pecorum as a likely cause of ovine abortion and provides the first descriptions of associated fetoplacental lesions in naturally infected sheep.
Westoby, M, Gillings, MR, Madin, JS, Nielsen, DA, Paulsen, IT & Tetu, SG 2021, 'Trait dimensions in bacteria and archaea compared to vascular plants', Ecology Letters, vol. 24, no. 7, pp. 1487-1504.
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AbstractBacteria and archaea have very different ecology compared to plants. One similarity, though, is that much discussion of their ecological strategies has invoked concepts such as oligotrophy or stress tolerance. For plants, so‐called ‘trait ecology’—strategy description reframed along measurable trait dimensions—has made global syntheses possible. Among widely measured trait dimensions for bacteria and archaea three main axes are evident. Maximum growth rate in association with rRNA operon copy number expresses a rate‐yield trade‐off that is analogous to the acquisitive–conservative spectrum in plants, though underpinned by different trade‐offs. Genome size in association with signal transduction expresses versatility. Cell size has influence on diffusive uptake and on relative wall costs. These trait dimensions, and potentially others, offer promise for interpreting ecology. At the same time, there are very substantial differences from plant trait ecology. Traits and their underpinning trade‐offs are different. Also, bacteria and archaea use a variety of different substrates. Bacterial strategies can be viewed both through the facet of substrate‐use pathways, and also through the facet of quantitative traits such as maximum growth rate. Preliminary evidence shows the quantitative traits vary widely within substrate‐use pathways. This indicates they convey information complementary to substrate use.
Westoby, M, Nielsen, DA, Gillings, MR, Gumerov, VM, Madin, JS, Paulsen, IT & Tetu, SG 2021, 'Strategic traits of bacteria and archaea vary widely within substrate-use groups', FEMS Microbiology Ecology, vol. 97, no. 11.
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ABSTRACT Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here, we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal transduction protein count, histidine kinase count, growth temperature, temperature-adjusted maximum growth rate, cell radial diameter and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate-use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely, this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared with substrate use.
Westoby, M, Nielsen, DA, Gillings, MR, Litchman, E, Madin, JS, Paulsen, IT & Tetu, SG 2021, 'Cell size, genome size, and maximum growth rate are near‐independent dimensions of ecological variation across bacteria and archaea', Ecology and Evolution, vol. 11, no. 9, pp. 3956-3976.
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AbstractAmong bacteria and archaea, maximum relative growth rate, cell diameter, and genome size are widely regarded as important influences on ecological strategy. Via the most extensive data compilation so far for these traits across all clades and habitats, we ask whether they are correlated and if so how. Overall, we found little correlation among them, indicating they should be considered as independent dimensions of ecological variation. Nor was correlation evident within particular habitat types. A weak nonlinearity (6% of variance) was found whereby high maximum growth rates (temperature‐adjusted) tended to occur in the midrange of cell diameters. Species identified in the literature as oligotrophs or copiotrophs were clearly separated on the dimension of maximum growth rate, but not on the dimensions of genome size or cell diameter.
Weyermann, C & Roux, C 2021, 'A different perspective on the forensic science crisis', Forensic Science International, vol. 323, pp. 110779-110779.
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Recurrent mentions of a forensic science crisis are reported in the literature. Some 15 years ago, the discussion was focused on the backlog problem. Other issues have been regularly debated since then, including the risk of error, need for independence, importance and risk of contextualisation, increasing fragmentation into separate processes and specialisations. Proposed solutions to solve one problem often led to other issues in other parts of the process. This paper attempts to address the apparent crisis using a different perspective, through a comparison with established disciplines, namely material science, medicine and historical science. The comparison with material science shows that, despite the varied organisational and legal models and the interdisciplinary nature of the field, a common element to all forensic science endeavours exists: the trace. A greater focus on the trace might thus help the development of a holistic approach in forensic science. The comparison with medicine demonstrates that, through the overall process, the main risk shifts from the risk to overlook important hypotheses or traces at the beginning of the process (e.g. problems in the detection of traces/symptoms and formulation of hypotheses) to the risk of supporting the wrong hypothesis at the end of the process (e.g. erroneous test of the hypotheses/diagnostic). Further, in medicine, symptoms are rarely evaluated in isolation, while traces are often evaluated separately. By analogy, epidemiology illustrates forensic science's critical role in preventing crime through forensic intelligence, supporting a more extensive and more collaborative application of forensic science in security issues. The comparison with historical science also indicates that a single trace (i.e. the observed effect) is rarely sufficient to reason on its cause. Retrodiction (abduction) is proposed as an alternative reasoning approach to reconstruct events from the past based on signs uncovered...
White, S, Stewart, C, Solntsev, AS, Li, C, Toth, M, Kianinia, M & Aharonovich, I 2021, 'Phonon dephasing and spectral diffusion of quantum emitters in hexagonal boron nitride', Optica, vol. 8, no. 9, pp. 1153-1153.
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Quantum emitters in hexagonal boron nitride (hBN) are emerging as bright and robust sources of single photons for applications in quantum optics. In this work we present detailed studies on the limiting factors to achieve Fourier transform limited spectral lines. Specifically, we study phonon dephasing and spectral diffusion of quantum emitters in hBN via resonant excitation spectroscopy at cryogenic temperatures. We show that the linewidths of hBN quantum emitters are phonon broadened, even at 5 K, with typical values of the order of ∼ 1 G H z . While spectral diffusion dominates at increasing pump powers, it can be minimized by working well below saturation excitation power. Our results are important for future utilization of quantum emitters in hBN for quantum interference experiments.
White, SJU, Klauck, F, Trong Tran, T, Schmitt, N, Kianinia, M, Steinfurth, A, Heinrich, M, Toth, M, Szameit, A, Aharonovich, I & Solntsev, AS 2021, 'Quantum random number generation using a hexagonal boron nitride single photon emitter', Journal of Optics, vol. 23, no. 1, pp. 01LT01-01LT01.
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Abstract Quantum random number generation (QRNG) harnesses the intrinsic randomness of quantum mechanical phenomena. On-chip photonic circuitry provides a robust and versatile platform that can address and explore fundamental questions in quantum as well as classical physics. Likewise, integrated waveguide-based architectures hold the potential for intrinsically scalable, efficient and compact implementations of photonic QRNG. Here, we harness the quantum emission from the two-dimensional material hexagonal boron nitride an emerging atomically thin medium that can generate single photons on demand while operating at room temperature. By means of a customized splitter arrangement, we achieve true random number generation through the measurement of single photons exiting one of four designated output ports, and subsequently verify the randomness of the sequences in accordance with the National Institute of Standards and Technology benchmark suite. Our results clearly demonstrate the viability and efficiency of this approach to on-chip deterministic random number generators.
Williams, DBG & Bodachivskyi, I 2021, 'Comment on ‘Chitosan dissolution with sulfopropyl imidazolium Brønsted acidic ionic liquids’', Journal of Molecular Liquids, vol. 328, pp. 115403-115403.
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Wilson, KA, Mostyn, SN, Frangos, ZJ, Shimmon, S, Rawling, T, Vandenberg, RJ & O’Mara, ML 2021, 'The allosteric inhibition of glycine transporter 2 by bioactive lipid analgesics is controlled by penetration into a deep lipid cavity', Journal of Biological Chemistry, vol. 296, pp. 100282-100282.
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The role of lipids in modulating membrane protein function is an emerging and rapidly growing area of research. The rational design of lipids that target membrane proteins for the treatment of pathological conditions is a novel extension in this field and provides a step forward in our understanding of membrane transporters. Bioactive lipids show considerable promise as analgesics for the treatment of chronic pain and bind to a high-affinity allosteric binding site on the human glycine transporter 2 (GlyT2 or SLC6A5). Here we use a combination of medicinal chemistry, electrophysiology, and computational modelling to develop a rational structure activity relationship for lipid inhibitors and demonstrate the key role of the lipid tail interactions for GlyT2 inhibition. Specifically, we examine how lipid inhibitor head group stereochemistry, tail length and double bond position promote enhanced inhibition. Overall, the L-stereoisomer is generally a better inhibitor than the D-stereoisomer, longer tail length correlates with greater potency, and the position of the double bond influences the activity of the inhibitor. We propose that the binding of the lipid inhibitor deep into the allosteric binding pocket is critical for inhibition. Furthermore, this provides insight into the mechanism of inhibition of GlyT2 and highlights how lipids can modulate the activity of membrane proteins by binding to cavities between helices. The principles identified in this work have broader implications for the development of a larger class of compounds that could target SLC6 transporters for disease treatment.
Windhagauer, M, Abbriano, RM, Ashworth, J, Barolo, L, Jaramillo-Madrid, AC, Pernice, M & Doblin, MA 2021, 'Characterisation of novel regulatory sequences compatible with modular assembly in the diatom Phaeodactylum tricornutum', Algal Research, vol. 53, pp. 102159-102159.
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Woldhuis, RR, Heijink, IH, van den Berge, M, Timens, W, Oliver, BGG, de Vries, M & Brandsma, C-A 2021, 'COPD-derived fibroblasts secrete higher levels of senescence-associated secretory phenotype proteins', Thorax, vol. 76, no. 5, pp. 508-511.
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COPD-derived fibroblasts have increased cellular senescence. Senescent cell accumulation can induce tissue dysfunction by their senescence-associated secretory phenotype (SASP). We aimed to determine the SASP of senescent fibroblasts and COPD-derived lung fibroblasts, including severe, early-onset (SEO)-COPD. SASP protein secretion was measured after paraquat-induced senescence in lung fibroblasts using Olink Proteomics and compared between (SEO-)COPD-derived and control-derived fibroblasts. We identified 124 SASP proteins of senescent lung fibroblasts, of which 42 were secreted at higher levels by COPD-derived fibroblasts and 35 by SEO-COPD-derived fibroblasts compared with controls. Interestingly, the (SEO-)COPD-associated SASP included proteins involved in chronic inflammation, which may contribute to (SEO-)COPD pathogenesis.
Wolff, C, Smith, MJA, Stiller, B & Poulton, CG 2021, 'Brillouin scattering—theory and experiment: tutorial', Journal of the Optical Society of America B, vol. 38, no. 4, pp. 1243-1243.
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Brillouin scattering is an important and interesting nonlinear effect involving the interaction between optical and acoustic fields in optical waveguides. It is increasingly useful in the field of photonics, where it supplies a tunable ultra-narrow linewidth response that can be used for applications including sensing, filtering, and lasing, as well as the acoustic storage of optical pulses. This tutorial gives an overview of the fundamentals of Brillouin scattering aimed at newcomers to the field, and covers the physics underlying the interaction, the mathematical theory, and setup details of foundational Brillouin experiments.
Wong, WKM, Joglekar, MV, Saini, V, Jiang, G, Dong, CX, Chaitarvornkit, A, Maciag, GJ, Gerace, D, Farr, RJ, Satoor, SN, Sahu, S, Sharangdhar, T, Ahmed, AS, Chew, YV, Liuwantara, D, Heng, B, Lim, CK, Hunter, J, Januszewski, AS, Sørensen, AE, Akil, ASA, Gamble, JR, Loudovaris, T, Kay, TW, Thomas, HE, O'Connell, PJ, Guillemin, GJ, Martin, D, Simpson, AM, Hawthorne, WJ, Dalgaard, LT, Ma, RCW & Hardikar, AA 2021, 'Machine learning workflows identify a microRNA signature of insulin transcription in human tissues', iScience, vol. 24, no. 4, pp. 102379-102379.
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Wood, B, Padula, MP, Marks, DC & Johnson, L 2021, 'Cryopreservation alters the immune characteristics of platelets', Transfusion, vol. 61, no. 12, pp. 3432-3442.
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AbstractBackgroundCryopreserved platelets are under clinical evaluation as they offer improvements in shelf‐life and potentially hemostatic effectiveness. However, the effect of cryopreservation on characteristics related to the immune function of platelets has not been examined.Study Design and MethodsBuffy coat derived platelets were cryopreserved at −80°C using 5%–6% dimethylsulfoxide (DMSO, n = 8). Paired testing was conducted pre‐freeze (PF), post‐thaw (PT0), and after 24 h of post‐thaw storage at room temperature (PT24). The concentration of biological response modifiers (BRMs) in the supernatant was measured using commercial ELISAs and surface receptor abundance was assessed by flow cytometry.ResultsCryopreservation resulted in increased RANTES, PF4, and C3a but decreased IL‐1β, OX40L, IL‐13, IL‐27, CD40L, and C5a concentrations in the supernatant, compared to PF samples. C4a, endocan, and HMGB1 concentrations were similar between the PF and PT0 groups. The abundance of surface‐expressed P‐selectin, siglec‐7, TLR3, TLR7, and TLR9 was increased PT0; while CD40, CLEC2, ICAM‐2, and MHC‐I were decreased, compared to PF. The surface abundance of CD40L, B7‐2, DC‐SIGN, HCAM, TLR1, TLR2, TLR4, and TLR6 was unchanged by cryopreservation. Following 24 h of post‐thaw storage, all immune associated receptors and TLRs increased to levels higher than observed on PF and PT0 platelets.ConclusionCryopreservation alters the immune phenotype of platelets. Understanding the clinical implications of the observed changes in BRM release and receptor abundance are essential, as they may influence the likelihood of adverse events.
Wood, B, Padula, MP, Marks, DC & Johnson, L 2021, 'The immune potential of ex vivo stored platelets: a review', Vox Sanguinis, vol. 116, no. 5, pp. 477-488.
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AbstractPlatelets are now acknowledged as key regulators of the immune system, as they are capable of mediating inflammation, leucocyte recruitment and activation. This activity is facilitated through platelet activation, which induces significant changes in the surface receptor profile and triggers the release of a range of soluble biological response modifiers (BRMs). In the field of transfusion medicine, the immune function of platelets has gained considerable attention as this may be linked to the development of adverse transfusion reactions. Further, component manufacturing and storage methodologies may impact the immunoregulatory role of platelets, and an understanding of this impact is crucial and should be considered alongside their haemostatic characteristics. This review highlights the key interactions between platelets and traditional immune modulators. Further, the potential impact of current and novel component storage methodologies, such as refrigeration and cryopreservation, on this functional capacity is examined, highlighting why further knowledge in this area would be of benefit.
Wood, MP, Jones, CI, Lippy, A, Oliver, BG, Walund, B, Fancher, KA, Fisher, BS, Wright, PJ, Fuller, JT, Murapa, P, Habib, J, Mavigner, M, Chahroudi, A, Sather, DN, Fuller, DH & Sodora, DL 2021, 'Rapid progression is associated with lymphoid follicle dysfunction in SIV-infected infant rhesus macaques', PLOS Pathogens, vol. 17, no. 5, pp. e1009575-e1009575.
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HIV-infected infants are at an increased risk of progressing rapidly to AIDS in the first weeks of life. Here, we evaluated immunological and virological parameters in 25 SIV-infected infant rhesus macaques to understand the factors influencing a rapid disease outcome. Infant macaques were infected with SIVmac251 and monitored for 10 to 17 weeks post-infection. SIV-infected infants were divided into either typical (TypP) or rapid (RP) progressor groups based on levels of plasma anti-SIV antibody and viral load, with RP infants having low SIV-specific antibodies and high viral loads. Following SIV infection, 11 out of 25 infant macaques exhibited an RP phenotype. Interestingly, TypP had lower levels of total CD4 T cells, similar reductions in CD4/CD8 ratios and elevated activation of CD8 T cells, as measured by the levels of HLA-DR, compared to RP. Differences between the two groups were identified in other immune cell populations, including a failure to expand activated memory (CD21-CD27+) B cells in peripheral blood in RP infant macaques, as well as reduced levels of germinal center (GC) B cells and T follicular helper (Tfh) cells in spleens (4- and 10-weeks post-SIV). Reduced B cell proliferation in splenic germinal GCs was associated with increased SIV+ cell density and follicular type 1 interferon (IFN)-induced immune activation. Further analyses determined that at 2-weeks post SIV infection TypP infants exhibited elevated levels of the GC-inducing chemokine CXCL13 in plasma, as well as significantly lower levels of viral envelope diversity compared to RP infants. Our findings provide evidence that early viral and immunologic events following SIV infection contributes to impairment of B cells, Tfh cells and germinal center formation, ultimately impeding the development of SIV-specific antibody responses in rapidly progressing infant macaques.
Wright, K, de Silva, K, Plain, KM, Purdie, AC, Blair, TA, Duggin, IG, Britton, WJ & Oehlers, SH 2021, 'Mycobacterial infection-induced miR-206 inhibits protective neutrophil recruitment via the CXCL12/CXCR4 signalling axis', PLOS Pathogens, vol. 17, no. 4, pp. e1009186-e1009186.
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Pathogenic mycobacteria actively dysregulate protective host immune signalling pathways during infection to drive the formation of permissive granuloma microenvironments. Dynamic regulation of host microRNA (miRNA) expression is a conserved feature of mycobacterial infections across host-pathogen pairings. Here we examine the role of miR-206 in the zebrafish model ofMycobacterium marinuminfection, which allows investigation of the early stages of granuloma formation. We find miR-206 is upregulated following infection by pathogenicM.marinumand that antagomir-mediated knockdown of miR-206 is protective against infection. We observed striking upregulation ofcxcl12aandcxcr4bin infected miR-206 knockdown zebrafish embryos and live imaging revealed enhanced recruitment of neutrophils to sites of infection. We used CRISPR/Cas9-mediated knockdown ofcxcl12aandcxcr4bexpression and AMD3100 inhibition of Cxcr4 to show that the enhanced neutrophil response and reduced bacterial burden caused by miR-206 knockdown was dependent on the Cxcl12/Cxcr4 signalling axis. Together, our data illustrate a pathway through which pathogenic mycobacteria induce host miR-206 expression to suppress Cxcl12/Cxcr4 signalling and prevent protective neutrophil recruitment to granulomas.
Wu, J, Wang, X, Liu, Q, Wang, S, Zhou, D, Kang, F, Shanmukaraj, D, Armand, M, Rojo, T, Li, B & Wang, G 2021, 'A synergistic exploitation to produce high-voltage quasi-solid-state lithium metal batteries', Nature Communications, vol. 12, no. 1, p. 5746.
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AbstractThe current Li-based battery technology is limited in terms of energy contents. Therefore, several approaches are considered to improve the energy density of these energy storage devices. Here, we report the combination of a heteroatom-based gel polymer electrolyte with a hybrid cathode comprising of a Li-rich oxide active material and graphite conductive agent to produce a high-energy “shuttle-relay” Li metal battery, where additional capacity is generated from the electrolyte’s anion shuttling at high voltages. The gel polymer electrolyte, prepared via in situ polymerization in an all-fluorinated electrolyte, shows adequate ionic conductivity (around 2 mS cm−1 at 25 °C), oxidation stability (up to 5.5 V vs Li/Li+), compatibility with Li metal and safety aspects (i.e., non-flammability). The polymeric electrolyte allows for a reversible insertion of hexafluorophosphate anions into the conductive graphite (i.e., dual-ion mechanism) after the removal of Li ions from Li-rich oxide (i.e., rocking-chair mechanism).
Wu, WW, Zhang, X, Li, M, Liu, Y, Chen, ZH, Xie, M, Zhao, SZ, Wang, G, Zhang, HP, Wang, T, Qin, L, Wang, L, Oliver, BG, Wan, HJ, Zhang, J, McDonald, VM, Marks, GB, Li, WM, Birring, SS, Wang, G & Gibson, PG 2021, 'Treatable Traits in Elderly Asthmatics from the Australasian Severe Asthma Network: A Prospective Cohort Study', The Journal of Allergy and Clinical Immunology: In Practice, vol. 9, no. 7, pp. 2770-2782.
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BACKGROUND: Data on treatable traits (TTs) in different populations are limited. OBJECTIVE: To assess TTs in elderly patients with asthma and compare them to younger patients, to evaluate the association of TTs with future exacerbations, and to develop an exacerbation prediction model. METHODS: We consecutively recruited 521 participants at West China Hospital, Sichuan University based on the Australasian Severe Asthma Network, classified as elderly (n = 62) and nonelderly (n = 459). Participants underwent a multidimensional assessment to characterize the TTs and were then followed up for 12 months. TTs and their relationship with future exacerbations were described. Based on the TTs and asthma control levels, an exacerbation prediction model was developed, and the overall performance was externally validated in an independent cohort. RESULTS: A total of 38 TTs were assessed. Elderly patients with asthma had more chronic metabolic diseases, fixed airflow limitation, emphysema, and neutrophilic inflammation, whereas nonelderly patients with asthma exhibited more allergic characteristics and psychiatric diseases. Nine traits were associated with increased future exacerbations, of which exacerbation prone, upper respiratory infection-induced asthma attack, cardiovascular disease, diabetes, and depression were the strongest. A model including exacerbation prone, psychiatric disease, cardiovascular disease, upper respiratory infection-induced asthma attack, noneosinophilic inflammation, cachexia, food allergy, and asthma control was developed to predict exacerbation risk and showed good performance. CONCLUSIONS: TTs can be systematically assessed in elderly patients with asthma, some of which are associated with future exacerbations, proving their clinical utility of evaluating them. A model based on TTs can be used to predict exacerbation risk in people with asthma.
Wu, X, Macreadie, LK & Gale, PA 2021, 'Anion binding in metal-organic frameworks', Coordination Chemistry Reviews, vol. 432, pp. 213708-213708.
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Wu, Z, Zhou, J, Li, D, Ao, Z, An, T & Wang, G 2021, 'Density functional theory study on the enhanced adsorption mechanism of gaseous pollutants on Al-doped Ti2CO2 monolayer', Sustainable Materials and Technologies, vol. 29, pp. e00294-e00294.
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Inorganic toxic gases (ITGs) and volatile organic compounds (VOCs) are two kinds of typical hazardous gaseous pollutants harming human health. The removal of them is still an enormous challenge. Based on density functional theory (DFT) calculations in this work, Al-doped Ti2CO2 (ATCO), a single-atom-decorated MXene, is expected to be a more effective adsorbent for these gases than pristine Ti2CO2 (TCO) due to the outstanding adsorption capacity and superb electrical properties. We then shed light on the mechanism of enhanced adsorption by ATCO. The results of Mulliken charge analysis, partial density of states (PDOS) and deformation charge density (DCD) confirm the change of charge distribution on ATCO surface after the decoration of Al atom. Obviously, Al atom can act as a bridge to promote the formation of chemical bonds between the adsorbed gases and ATCO substrate. This work not only provides a promising material for the adsorption of gaseous pollutants, but also explores a new avenue for designing and fabricating MXene-based non-noble metal materials in the area of gas adsorbents.
Xiao, J, Li, X, Tang, K, Wang, D, Long, M, Gao, H, Chen, W, Liu, C, Liu, H & Wang, G 2021, 'Recent progress of emerging cathode materials for sodium ion batteries', Materials Chemistry Frontiers, vol. 5, no. 10, pp. 3735-3764.
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We summarized the recent progress of cathode materials used for SIBs and modified strategies, expecting to give an inspiration for the development of high-performance cathode materials.
Xiong, P, Zhang, F, Zhang, X, Liu, Y, Wu, Y, Wang, S, Safaei, J, Sun, B, Ma, R, Liu, Z, Bando, Y, Sasaki, T, Wang, X, Zhu, J & Wang, G 2021, 'Atomic-scale regulation of anionic and cationic migration in alkali metal batteries', Nature Communications, vol. 12, no. 1, pp. 1-15.
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AbstractThe regulation of anions and cations at the atomic scale is of great significance in membrane-based separation technologies. Ionic transport regulation techniques could also play a crucial role in developing high-performance alkali metal batteries such as alkali metal-sulfur and alkali metal-selenium batteries, which suffer from the non-uniform transport of alkali metal ions (e.g., Li+ or Na+) and detrimental shuttling effect of polysulfide/polyselenide anions. These drawbacks could cause unfavourable growth of alkali metal depositions at the metal electrode and irreversible consumption of cathode active materials, leading to capacity decay and short cycling life. Herein, we propose the use of a polypropylene separator coated with negatively charged Ti0.87O2 nanosheets with Ti atomic vacancies to tackle these issues. In particular, we demonstrate that the electrostatic interactions between the negatively charged Ti0.87O2 nanosheets and polysulfide/polyselenide anions reduce the shuttling effect. Moreover, the Ti0.87O2-coated separator regulates the migration of alkali ions ensuring a homogeneous ion flux and the Ti vacancies, acting as sub-nanometric pores, promote fast alkali-ion diffusion.
Xu, X, Gu, Y, Kong, M, Feng, W & Li, F 2021, 'NaYF4:Nd3+, Yb3+ Nanocrystals for Temperature Measurement in Biological Environment', Zhongguo Xitu Xuebao Journal of the Chinese Rare Earth Society, vol. 39, no. 1, pp. 181-187.
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Nd3+-sensitized NIR-emissive NaYF4: Nd3+, Yb3+ nanocrystals were synthesized by solvothermal method. A decrease in the intensity ratio of 865 nm/980 nm peak was observed as temperature increased tuning the Nd3+ and Yb3+ doping ratio, and comprehensively considering the luminescent intensity and temperature sensitivity, 2% Nd and 20% Yb were found to be the optimal doping concentration. The thermal sensitivity can be increased with Yb3+ doping ratio, with a thermal sensitivity (Sr) of 1.9%•K-1 in cyclohexane and 0.46%•K-1 in aqueous phase. Through the demonstrations of covering meat slices and in vivo laser heating, no obvious change in the intensity ratio was found before and after tissue attenuation, which preliminarily verified the feasibility of using the nanothermometer for measuring temperature in biological systems.
Xu, X, Xu, Y, Ma, J, Yin, Y, Fronzi, M, Wang, X & Bi, L 2021, 'Tailoring electronic structure of perovskite cathode for proton-conducting solid oxide fuel cells with high performance', Journal of Power Sources, vol. 489, pp. 229486-229486.
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Tailoring the electronic structure of the perovskite oxide could potentially allow dramatic improvements in the properties of cathode materials in proton-conducting solid oxide fuel cells (SOFCs). This has been demonstrated in the case of Mo-doped La0.5Sr0.5FeO3-δ, where the electronic structure of the La0.5Sr0.5FeO3-δ oxide has been changed with the Mo-doping, leading to a less strong metal-oxygen bond as well as a more active surface towards oxygen reduction. As a result, the more active oxygen atoms make the formation of oxygen vacancy and hydration that are critical for protonation more feasible. Furthermore, the electric field induced by Mo-doping provides an additional driving force for the movement of protons, accelerating the proton migrations in the oxide and thus improving the cathode performance. With the Mo-doped La0.5Sr0.5FeO3-δ as the cathode, a proton-conducting SOFC exhibits an impressive fuel cell output of 1174 mW cm−2 at 700 °C that surpasses most of the cells using similar types of cathodes. This study not only provides a proper cathode material without involving cobalt and barium elements but also gives an understanding of the design of the cathode by tailoring the electronic structures.
Xu, Y, Xu, X, Cao, N, Wang, X, Liu, X, Fronzi, M & Bi, L 2021, 'Perovskite ceramic oxide as an efficient electrocatalyst for nitrogen fixation', International Journal of Hydrogen Energy, vol. 46, no. 17, pp. 10293-10302.
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The electrochemical conversion of N2 to NH3 is an interesting research topic as it provided an alternative and energy-saving method compared with the traditional way of NH3 production. Although different materials have been proposed for N2 reduction, the use of defects in oxides was only reported recently and the relevant working mechanism was not fully revealed. In this study, Sr was used as the dopant for LaFeO3 to create oxygen vacancies, forming the Sr-doped LFO (La0.5Sr0.5FeO3-δ) perovskite oxide. The La0.5Sr0.5FeO3-δ ceramic oxide used as a catalyst achieves an NH3 yield of 11.51 μgh−1 mg−1 and the desirable faradic efficiency (F.E.) of 0.54% at −0.6 V vs reversible hydrogen electrode (RHE), which surpassed that of LaFeO3 nanoparticles. The 15N isotope labeling method was employed to prove the La0.5Sr0.5FeO3-δ catalyst had the function of converting N2 into NH3 under the electrolysis condition. The first principle calculations were used to investigate the mechanism at the atomistic level, revealing that the free energy barriers changed significantly with the introduction of oxygen vacancies that accelerated the overall nitrogen reduction reaction (NRR) procedure.
Yan, J, Kuzhiumparambil, U, Bandodkar, A, Bandodkar, S, Dale, RC & Fu, S 2021, 'Cerebrospinal fluid metabolites in tryptophan‐kynurenine and nitric oxide pathways: biomarkers for acute neuroinflammation', Developmental Medicine & Child Neurology, vol. 63, no. 5, pp. 552-559.
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AimTo explore the cerebrospinal fluid (CSF) metabolite features in acute neuroinflammatory diseases and identify potential biomarkers to diagnose and monitor neuroinflammation.MethodA cohort of 14 patients (five females, nine males; mean [median] age 7y 9mo [9y], range 6mo–13y) with acute encephalitis (acute disseminated encephalomyelitis n=6, unknown suspected viral encephalitis n=3, enteroviral encephalitis n=2, seronegative autoimmune encephalitis n=2, herpes simplex encephalitis n=1) and age‐matched non‐inflammatory neurological disease controls (n=14) were investigated using an untargeted metabolomics approach. CSF metabolites were analyzed with liquid chromatography coupled to high resolution mass spectrometry, followed by subsequent multivariate and univariate statistical methods.ResultsA total of 35 metabolites could be discriminated statistically between the groups using supervised orthogonal partial least squares discriminant analysis and analysis of variance. The tryptophan‐kynurenine pathway contributed nine key metabolites. There was a statistical increase of kynurenine, quinolinic acid, and anthranilic acid in patients with encephalitis, whereas tryptophan, 3‐hydroxyanthrnailic acid, and kynurenic acid were decreased. The nitric oxide pathway contributed four metabolites, with elevated asymmetric dimethylarginine and argininosuccinic acid, and decreased arginine and citrulline in patients with encephalitis. An increase in the CSF kynurenine/tryptophan ratio (p<0.001), anthranilic acid/3‐hydroxyanthranilic acid ratio (p<0.001), asymmetric dimethylarginine/a...
Yan, J, Kuzhiumparambil, U, Bandodkar, S, Dale, RC & Fu, S 2021, 'Cerebrospinal fluid metabolomics: detection of neuroinflammation in human central nervous system disease', Clinical & Translational Immunology, vol. 10, no. 8.
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AbstractThe high morbidity and mortality of neuroinflammatory diseases drives significant interest in understanding the underlying mechanisms involved in the innate and adaptive immune response of the central nervous system (CNS). Diagnostic biomarkers are important to define treatable neuroinflammation. Metabolomics is a rapidly evolving research area offering novel insights into metabolic pathways, and elucidation of reliable metabolites as biomarkers for diseases. This review focuses on the emerging literature regarding the detection of neuroinflammation using cerebrospinal fluid (CSF) metabolomics in human cohort studies. Studies of classic neuroinflammatory disorders such as encephalitis, CNS infection and multiple sclerosis confirm the utility of CSF metabolomics. Additionally, studies in neurodegeneration and neuropsychiatry support the emerging potential of CSF metabolomics to detect neuroinflammation in common CNS diseases such as Alzheimer's disease and depression. We demonstrate metabolites in the tryptophan–kynurenine pathway, nitric oxide pathway, neopterin and major lipid species show moderately consistent ability to differentiate patients with neuroinflammation from controls. Integration of CSF metabolomics into clinical practice is warranted to improve recognition and treatment of neuroinflammation.
Yang, H, Zhou, S, Zhang, B, Chu, S, Guo, H, Gu, Q, Liu, H, Lei, Y, Konstantinov, K, Wang, Y, Chou, S, Liu, H & Dou, S 2021, 'Architecting Freestanding Sulfur Cathodes for Superior Room‐Temperature Na–S Batteries', Advanced Functional Materials, vol. 31, no. 32, pp. 2102280-2102280.
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AbstractRoom‐temperature sodium–sulfur (RT Na–S) batteries have attracted extensive attention because of their low cost and high specific energy. RT Na–S batteries, however, usually suffer from sluggish reaction kinetics, low reversible capacity, and short lifespans. Herein, it is shown that chain‐mail catalysts, consisting of porous nitrogen doped carbon nanofibers (PCNFs) encapsulating Co nanoparticles (Co@PCNFs), can activate sulfur via electron engineering. The chain‐mail catalysts Co@PCNFs with a micrograde hierarchical structure as a freestanding sulfur cathode (Co@PCNFs/S) can provide space for high mass loading of sulfur and polysulfides. The electrons can rapidly transfer from chain‐mail catalysts to sulfur and polysulfides during discharge–charge processes, therefore boosting its conversion kinetics. As a result, this freestanding Co@PCNFs/S cathode achieves a high sulfur loading of 2.1 ± 0.2 mg cm−2, delivering a high reversible capacity of 398 mA h g−1 at 0.5 C (1 C = 1675 mA g−1) over 600 cycles and superior rate capability of an average capacity of 240 mA h g−1 at 5 C. Experimental results, combined with density functional theory calculations, demonstrate that the Co@PCNFs/S can efficiently improve the conversion kinetics between the polysulfides and Na2S via transferring electrons from Co to them, thereby realizing efficient sulfur redox reactions.
YANG, J, KOSOV, DS & REIMERS, JR 2021, 'Electron transport properties of molecular devices based on silicon-1, 6-hexanedithiol-silicon', Journal of Shenzhen University Science and Engineering, vol. 38, no. 06, pp. 636-642.
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Self-assembly of a single-molecule membrane (Self-assembled monolayers,SAMs) has been widely used in nanotechnology, biological sensors, and molecular electronics in the past two decades. However, the microscopic geometric information on the electrode-molecular-electrode conformation is inaccessible experimentally, and the connection between the microstructure of the silicon electrode surface in the real chemical environment and the connection mode of the silicon-sulfur and the electrical transport properties is not clear, and the theoretical calculations will be the main means of clarifying these problems. In this paper, based on the experimental reported silicon-1-6-hexadithiol-silicon molecular devices of density functional theory (DFT), combined with the nonequilibrium Green function (NE GF) method, we perform quantum transport calculations for the zero bias conductance of the model and electron transmission spectra. It is shown that silicon-sulfur molecular junctions have some significantly different properties compared to metal-based molecular junctions. The structural details of silicon-sulfur molecular junctions have a crucial influence on their electrical transport properties
Yang, J, Krix, ZE, Kim, S, Tang, J, Mayyas, M, Wang, Y, Watanabe, K, Taniguchi, T, Li, LH, Hamilton, AR, Aharonovich, I, Sushkov, OP & Kalantar-Zadeh, K 2021, 'Near-Field Excited Archimedean-like Tiling Patterns in Phonon-Polaritonic Crystals', ACS Nano, vol. 15, no. 5, pp. 9134-9142.
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Yang, J, Li, J, Wang, T, Notten, PHL, Ma, H, Liu, Z, Wang, C & Wang, G 2021, 'Novel hybrid of amorphous Sb/N-doped layered carbon for high-performance sodium-ion batteries', Chemical Engineering Journal, vol. 407, pp. 127169-127169.
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© 2020 Elsevier B.V. Antimony (Sb) based materials, which have been proved to be promising anodes to fabricate high-performance sodium-ion batteries (SIBs), have attracted considerable interest owing to its large theoretical capacity (660 mAh g−1), appropriate inserting potential of sodium (0.5–0.8 V vs Na+/Na), and moderate electrode polarization (~0.35 V). Unfortunately, fast capacity decay and serious structure pulverization resulting from large volume variation upon cycling are often observed for Sb-based anodes, and further structure design is needed. In this work, a novel hybrid of amorphous Sb/N-doped layered carbon (a-Sb/NC) was fabricated through a facile bottom-up method, where ultrafine amorphous Sb nanoparticles are uniformly anchored on layered N-doped carbon (NC). When applied as anode material for SIBs, this hybrid exhibits a large reversible capacity (479.6 mAh g−1 at 0.1 A g−1 up to 100 cycles), robust rate capability (298.7 mAh g−1 at current density of 2 A g−1), and remarkable stability upon long-term cycling (280.5 mAh g−1 at 1.0 A g−1 up to 500 cycles), outperforming most of the reported amorphous anodes for SIBs. In principle, such impressive sodium storage properties of a-Sb/NC should be mainly ascribed to the amorphous feature of Sb nanoparticles as well as the synergistic effect between amorphous Sb and layered NC, thereby endowing the composite with improved electron/ion dynamics and efficient self-buffering ability.
Yang, J, Yu, G, Sessler, JL, Shin, I, Gale, PA & Huang, F 2021, 'Artificial transmembrane ion transporters as potential therapeutics', Chem, vol. 7, no. 12, pp. 3256-3291.
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Yang, W, Yang, W, Dong, L, Shao, G, Wang, G & Peng, X 2021, 'Hierarchical ZnO nanorod arrays grown on copper foam as an advanced three-dimensional skeleton for dendrite-free sodium metal anodes', Nano Energy, vol. 80, pp. 105563-105563.
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Na metal is regarded as a potential anode material for next-generation Na metal batteries owing to its high theoretical capacity and low cost. However, the severe dendrite growth and infinitely volume changes of Na limit its practical applications as an anode material. In this study, a three-dimensional (3D) Cu foam skeleton with hierarchical ZnO nanorod arrays (CF@ZnO) was prepared as a stable host for dendrite-free Na metal anodes. Commercially available Cu foam was treated via a simple chemical precipitation method to grow hierarchical ZnO nanorod arrays, exhibiting a 3D porous structure with a cylindrical core-shell skeleton. The highly “sodiophilic” ZnO nanorod arrays provided abundant Na nucleation sites and exhibited low nucleation overpotential, which facilitated the homogeneous nucleation and uniform growth of Na on the electrode. Moreover, the 3D porous core-shell cylindrical structure of the nanorod arrays efficiently reduced the local effective current density, thus suppressing the growth of Na dendrites, as indicated by COMSOL Multiphysics simulations. As a result, the CF@ZnO electrode exhibited dendrite-free morphology during repeated Na plating/striping and excellent cycling stability with very small voltage hysteresis even at high current densities. When paired with a Na3V2(PO4)3 cathode, the CF@ZnO/Na electrode showed significant potential for application in full cells. This study provides a facile approach to design 3D sodiophilic hosts for high-energy-density Na metal batteries.
Yang, X, Liu, Y, Lv, Z, Hua, Q, Liu, L, Wang, B & Tang, J 2021, 'Synthesis of high latent heat lauric acid/silica microcapsules by interfacial polymerization method for thermal energy storage', Journal of Energy Storage, vol. 33, pp. 102059-102059.
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Ye, W, van Dijk, AIJM, Huete, A & Yebra, M 2021, 'Global trends in vegetation seasonality in the GIMMS NDVI3g and their robustness', International Journal of Applied Earth Observation and Geoinformation, vol. 94, pp. 102238-102238.
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Analysing changes in vegetation seasonality of terrestrial ecosystems is important to understand ecological responses to global change. Based on over three decades of observations by the series of Advanced Very High Resolution Radiometer (AVHRR) sensors, the Global Inventory Modelling and Mapping Studies (GIMMS) Normalized Difference Vegetation Index (NDVI) dataset has been widely used for monitoring vegetation trends. However, it is not well known how robust long-term trends in vegetation seasonality derived from GIMMS NDVI are, given inevitable influences from sensor and processing artefacts. Here we analyse long-term seasonality trends in the GIMMS third generation (NDVI3g) record (1982–2013). Changes in vegetation seasonality are decomposed into changes in duration (related to growing season length) and timing (related to peak growing season). We compare seasonality trends from the previous version (NDVI3g v0) with those in the subsequently released version (NDVI3g v1) and, for their common period, with those derived from MODerate Resolution Imaging Spectroradiometer (MODIS) collection 6 NDVI. We find that NDVI3g v0 shows marked seasonality trends for 1982–2013 over more than one-third of the global vegetated area. Long-term trends based on v1 are generally consistent with v0, but v1 shows a strong trend towards earlier timing across the Arctic regions that is absent in v0. NDVI3g v0, v1, and MODIS all point towards an increased duration across the tundra of North Asia and later timing across North Africa. However, several discrepancies are also found between the NDVI datasets. For example, for the North-American tundra, MODIS shows earlier and v0 later timing, while MODIS shows an increased duration and v1 a reduced duration. For North Africa, v0 and v1 exhibit a reduced duration that is absent in MODIS. We conclude that both the primary observations and the subsequent processing can have a marked influence on inferred seasonality trends, and propo...
Ying, L, Sinutok, S, Pramneechote, P, Aiyarak, P, Ralph, PJ & Chotikarn, P 2021, 'Physiological Responses of Pocillopora acuta and Porites lutea Under Plastic and Fishing Net Stress', Frontiers in Marine Science, vol. 8, pp. 1-13.
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Marine debris has become a global problem affecting coral health around the globe. However, the photophysiological responses of corals to marine debris stress remain unclear. Therefore, this study firstly investigated transparent and opaque plastic bag shading and fishing nets directly contacting the coral. Photosynthetic performance, pigment content, symbiont density, and calcification rate of a branching coral Pocillopora acuta and a massive coral Porites lutea were investigated after 4 weeks of exposure to marine debris. The results show that the maximum quantum yield of PSII significantly decreased in P. lutea with all treatments, while P. acuta showed no effect on the maximum quantum yield of PSII from any treatments. Transparent plastic bag shading does not affect P. acuta, but significantly affected the maximum photochemical efficiency of P. lutea. Photoacclimation of cellular pigment content was also observed under opaque plastic bag shading for both species at week 2. Fishing nets had the strongest effect and resulted in P. acuta bleaching and P. lutea partial mortality as well as a decline in zooxanthellae density. Calcification rate of P. acuta significantly decreased with treatments using opaque plastic bag and fishing net, but for P. lutea only the treatment with fishing net gave any observable effects. This study suggests that the sensitivities of corals to marine debris differ strongly by species and morphology of the coral.
Young, KP, Murray, BR, Martin, LJ & Murray, ML 2021, 'Lost but Not Forgotten: Identifying Unmapped and Unlisted Environmental Hazards including Abandoned Mines', Sustainability, vol. 13, no. 19, pp. 11011-11011.
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Environmental databases play an essential role in the management of land and communities, including mapping and monitoring environmental hazards over time (i.e., abandoned mines). Over the last century, mines have closed for many reasons, but there has been no comprehensive database of the locations of closed and abandoned mine sites kept for many regions of the world. As such, the locations of many mines have been lost from public knowledge, with no way for managers to assess the risks of land and water contamination, as well as subsidence. To address this knowledge gap, we present an integrated framework for identifying abandoned mine sites using a combination of satellite imagery, historical records, geographic evidence, and local knowledge. We tested this framework within the Newcastle, Illawarra, and Lithgow regions of NSW, Australia. We identified 61 abandoned coal mines which are currently unaccounted for in mine registries, with 56% of all mines in the Newcastle region being unmarked (N = 32), 36% in the Illawarra region (N = 22), and 20% in the Lithgow region (N = 7). These findings demonstrate that our framework has promising utility in identifying historic and unmarked environmental hazards in both national and international contexts.
Yu, L, Feng, Y, Zheng, S, Li, J, Liu, R & Jin, D 2021, 'Cloning and characterization of a novel DNase gene from Trichogramma pretiosum', Protein Expression and Purification, vol. 185, pp. 105896-105896.
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Yuan, YL, Zhang, X, Liu, L, Wang, G, Chen-Yu Hsu, A, Huang, D, Wang, G & Oliver, BG 2021, 'Total IgE Variability Is Associated with Future Asthma Exacerbations: A 1-Year Prospective Cohort Study', The Journal of Allergy and Clinical Immunology: In Practice, vol. 9, no. 7, pp. 2812-2824.
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BACKGROUND: Few prospective studies have investigated the relationship between IgE variability and risk for asthma exacerbations (AEs). OBJECTIVE: To explore the relationship between IgE variability and AEs. METHODS: Recruited patients with stable asthma underwent two serum total IgE tests within a month (at screening [baseline IgE] and at 1 month) to obtain the coefficient of variation (CV) of base 10 log-transformed IgE. Patients with IgE CV were divided into IgE CV-high and IgE CV-low cohorts based on the CV median and were observed within 12 months, during which the association between IgE variability and AEs was explored using a negative binomial regression model. RESULTS: The IgE CV levels obtained from 340 patients classified patients into two groups (n = 170 for the IgE CV-high and IgE CV-low groups, respectively) based on the serum total IgE CV median of 2.12% (quartiles 1 and 3: 0.98% and 3.91%, respectively). The IgE CV-high patients exhibited worse asthma control and lung function and more marked airway inflammation, and received more intensive medication use compared with IgE CV-low patients. The IgE CV-high patients exhibited increased rates of moderate-to-severe (adjusted rate ratio = 2.88; 95% confidence interval, 1.65-5.03; P < .001) and severe (adjusted rate ratio = 2.16; 95% confidence interval, 1.08-4.32; P = .029) AEs during the follow-up year compared with IgE CV-low patients. Furthermore, sputum IL-6 partially mediated the associations between IgE CV with moderate-to-severe and severe AEs. CONCLUSIONS: Variability in total serum IgE levels is an easily obtained and practical measure for predicting AEs. Future studies are needed to investigate whether IgE variability can be used to guide precision medicine in asthma.
Yuen, ZW-S, Srivastava, A, Daniel, R, McNevin, D, Jack, C & Eyras, E 2021, 'Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing', Nature Communications, vol. 12, no. 1.
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AbstractDNA methylation plays a fundamental role in the control of gene expression and genome integrity. Although there are multiple tools that enable its detection from Nanopore sequencing, their accuracy remains largely unknown. Here, we present a systematic benchmarking of tools for the detection of CpG methylation from Nanopore sequencing using individual reads, control mixtures of methylated and unmethylated reads, and bisulfite sequencing. We found that tools have a tradeoff between false positives and false negatives and present a high dispersion with respect to the expected methylation frequency values. We described various strategies to improve the accuracy of these tools, including a consensus approach, METEORE (https://github.com/comprna/METEORE), based on the combination of the predictions from two or more tools that shows improved accuracy over individual tools. Snakemake pipelines are also provided for reproducibility and to enable the systematic application of our analyses to other datasets.
Zajaczkowski, P, Lee, R, Fletcher-Lartey, SM, Alexander, K, Mahimbo, A, Stark, D & Ellis, JT 2021, 'The controversies surrounding Giardia intestinalis assemblages A and B', Current Research in Parasitology & Vector-Borne Diseases, vol. 1, pp. 100055-100055.
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Zakarya, R, Chan, YL, Rutting, S, Reddy, K, Bozier, J, Woldhuis, RR, Xenaki, D, Van Ly, D, Chen, H, Brandsma, C-A, Adcock, IM & Oliver, BG 2021, 'BET proteins are associated with the induction of small airway fibrosis in COPD', Thorax, vol. 76, no. 7, pp. 647-655.
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RationaleIn COPD, small airway fibrosis occurs due to increased extracellular matrix (ECM) deposition in and around the airway smooth muscle (ASM) layer. Studies of immune cells and peripheral lung tissue have shown that epigenetic changes occur in COPD but it is unknown whether airway mesenchymal cells are reprogrammed.ObjectivesDetermine if COPD ASM cells have a unique epigenetic response to profibrotic cytokine transforming growth factor β1 (TGF-β1).MethodsPrimary human ASM cells from COPD and non-COPD smoking patients were stimulated with TGF-β1. Gene array analysis performed to identify differences in ECM expression. Airway accumulation of collagen 15α1 and tenascin-C proteins was assessed. Aforementioned ASM cells were stimulated with TGF-β1 ± epigenetic inhibitors with qPCR quantification ofCOL15A1andTNC. Global histone acetyltransferase (HAT) and histone deacetylase (HDAC) activity were assessed. chromatin immunoprecipitation (ChIP)-qPCR for histone H3 and H4 acetylation atCOL15A1andTNCpromoters was carried out. Effects of bromoterminal and extraterminal domain (BET) inhibitor JQ1(+) on expression and acetylation of ECM target genes were assessed.Measurements and main resultsCOPD ASM show significantly higherCOL15A1andTNCexpression in vitro and the same trend for higher levels of collagen 15α1 and tenascin-c deposited in COPD airways in vivo. Epigenetic screening indicated differential response to HDAC inhibition. ChIP-qPCR revealed histone H4 acetylation atCOL15A1andTNCpro...
Zalogina, A, Savelev, R, Zuev, D & Shadrivov, I 2021, 'Comparison of GaP and Si nanoantennas for optical emission control', Journal of the Optical Society of America B, vol. 38, no. 7, pp. 2201-2201.
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Nanostructures made of high-refractive-index materials present a novel technological platform for efficient light manipulation at the nanoscale. Among all materials compatible with the currently available fabrication techniques, Si and GaP are the most suitable for the visible spectral range. Here, we consider a system consisting of a luminescent diamond nanoparticle with embedded color centers emitting light, placed on top of a Si or GaP cylindrical nanoantenna. We study theoretically how dielectric nanoantennas affect the emission properties of the system and predict a several-fold enhancement of the spontaneous emission rate of a single emitter located inside an optically small diamond nanoparticle. We compare performance of the two considered materials in different parts of the visible spectrum and find that for single dipole sources that emit at the blue end of the spectrum, it is beneficial to use GaP nanoantennas, while silicon becomes the material of choice for emitters at the red end of the spectrum.
Zalogina, A, Wang, L, Melik-Gaykazyan, E, Kivshar, Y, Shadrivov, I & Kruk, S 2021, 'Mid-infrared cylindrical vector beams enabled by dielectric metasurfaces', APL Materials, vol. 9, no. 12.
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Over the last decade, photonics in the mid-infrared (mid-IR) frequency range had major advances in both generation and detection of light. However, efficient manipulation of the mid-IR light still faces many challenges. Spatially inhomogeneous control over the wavefront and polarization of mid-IR radiation is particularly difficult. Many standard techniques used for visible and near-infrared frequencies, such as liquid crystal-based spatial light modulation, are not applicable in the mid-IR due to unfavorable material properties in that spectral range. Here, we demonstrate spatially inhomogeneous polarization control of the mid-infrared light using custom-designed vortex retarders. Vortex retarders, while being widely used in the near-infrared and visible spectral ranges for generation of cylindrical vector beams, have been missing in the mid-infrared spectral range. Our implementation of mid-infrared vortex retarders is based on the concept of metasurfaces. We demonstrate metasurface-based vortex retarders at the wavelengths of 2.9 and 3.5 μm. We compare the performance of all-dielectric metasurface vortex retarders with the elements arranged in square and hexagonal lattices [Arbabi et al., Nat. Nanotechnol. 10, 937–943 (2015) and Arbabi et al., Nat. Commun. 6, 7069 (2015)]. Our work could accelerate the adoption of metasurfaces for the development of novel classes of mid-infrared optical components.
Zavafer, A, Bates, H, Labeeuw, L, Kofler, JR & Ralph, PJ 2021, 'Normalized chlorophyll fluorescence imaging: A method to determine irradiance and photosynthetically active radiation in phytoplankton cultures', Algal Research, vol. 56, pp. 102309-102309.
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Zavřel, T, Schoffman, H, Lukeš, M, Fedorko, J, Keren, N & Červený, J 2021, 'Monitoring fitness and productivity in cyanobacteria batch cultures', Algal Research, vol. 56, pp. 102328-102328.
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Zeng, Y, Huang, T, Wang, N, Xu, Y, Sun, C, Huang, M, Chen, C, Oliver, BG, Yi, C & Chen, H 2021, 'L-Leucine Improves Metabolic Disorders in Mice With in-utero Cigarette Smoke Exposure', Frontiers in Physiology, vol. 12, p. 700246.
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Objectives: Maternal cigarette smoke exposure (SE) causes intrauterine undernutrition, resulting in increased risk for metabolic disorders and type 2 diabetes in the offspring without sex differences. L-leucine supplementation has been shown to reduce body weight and improve glucose metabolism in both obese animals and humans. In this study, we aimed to determine whether postnatal L-leucine supplementation in female offspring can ameliorate the detrimental impact of maternal SE.Methods: Female Balb/c mice (6-week) were exposed to cigarette smoke (SE, 2 cigarettes/day) prior to mating for 5 weeks until the pups weaned. Sham dams were exposed to air during the same period. Half of the female offspring from the SE and SHAM dams were supplied with L-leucine via drinking water (1.5% w/w) after weaning (21-day) for 10 weeks and sacrificed at 13 weeks (adulthood).Results: Maternal SE during pregnancy resulted in smaller body weight and glucose intolerance in the offspring. L-leucine supplement in Sham offspring reduced body weight, fat mass, and fasting blood glucose levels compared with their untreated littermates; however somatic growth was not changed. L-leucine supplement in SE offspring improved glucose tolerance and reduced fat mass compared with untreated littermates.Conclusions: Postnatal L-leucine supplement could reduce fat accumulation and ameliorate glucose metabolic disorder caused by maternal SE. The application of leucine may provide a potential strategy for reducing metabolic disorders in offspring from mothers who continued to smoke during pregnancy.
Zhand, S, Xiao, K, Razavi Bazaz, S, Zhu, Y, Bordhan, P, Jin, D & Warkiani, ME 2021, 'Improving capture efficiency of human cancer cell derived exosomes with nanostructured metal organic framework functionalized beads', Applied Materials Today, vol. 23, pp. 100994-100994.
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Extracellular vesicles (EVs) have emerged as an invaluable tool for analyzing the physiological processes and an alternative source of disease diagnostic and prognostic biomarkers in liquid biopsies. Exosomes are a subset of EVs offer a window into altered cellular or tissue states, and their detection potentially offers a multicomponent early-stage diagnostic readout. Immunocapture and flow cytometry analysis of exosomes using micron-sized beads has been reported to be a reproducible technique for analysis of exosome surface markers. Nevertheless, the capture capacity remains poor due to limited available surface area. In this study, we have proposed a nanocoating strategy using metal-organic framework (MOF) materials, in particular, Zeolitic Imidazolate Framework-8 (ZIF-8), for highly efficient capturing of low concentration of exosomes from minimally processed samples. In this method, a ZIF-8 thin film was formed on polydopamine-polyethyleneimine (PDA-PEI) coated polystyrene microbeads to improve antibody immobilization due to the larger surface area provided by the MOF microstructures. This novel coating enabled us to detect as little as 50 exosomes per 10 µm polystyrene bead functionalized with ZIF-8/PDA-PEI, which is 180 times higher than the previously reported methods using naked microbeads. This coating requires a lower concentration of antibody to capture exosomes on the surface of microbeads compared to the standard protocols. More importantly, the higher concentration of exosomes on each bead surface provides the opportunity (i.e., higher signal intensity) to sort the beads using fluorescence-activated cell sorting, facilitating molecular analysis of post fractionation exosomes. Additionally, the exosomes can easily be detached from the coated microbeads using EDTA, limiting the usage of harsh chemicals. The procedure described here can be easily reproduced and employed regardless of the biological sample used to obtain exosomes.
Zhang, G, Morrison, D, Bao, G, Yu, H, Yoon, CW, Song, T, Lee, J, Ung, AT & Huang, Z 2021, 'An Amine–Borane System Featuring Room‐Temperature Dehydrogenation and Regeneration', Angewandte Chemie International Edition, vol. 60, no. 21, pp. 11725-11729.
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AbstractAmine–borane complexes have been extensively studied as hydrogen storage materials. Herein, we report a new amine–borane system featuring a reversible dehydrogenation and regeneration at room temperature. In addition to high purity H2, the reaction between ethylenediamine bisborane (EDAB) and ethylenediamine (ED) leads to unique boron–carbon–nitrogen 5‐membered rings in the dehydrogenation product where one boron is tricoordinated by three nitrogen atoms. Owing to the unique cyclic structure, the dehydrogenation product can be efficiently converted back to EDAB by NaBH4 and H2O at room temperature. This finding could lead to the discovery of new amine boranes with potential usage as hydrogen storage materials.
Zhang, G, Morrison, D, Bao, G, Yu, H, Yoon, CW, Song, T, Lee, J, Ung, AT & Huang, Z 2021, 'An Amine–Borane System Featuring Room‐Temperature Dehydrogenation and Regeneration', Angewandte Chemie, vol. 133, no. 21, pp. 11831-11835.
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AbstractAmine–borane complexes have been extensively studied as hydrogen storage materials. Herein, we report a new amine–borane system featuring a reversible dehydrogenation and regeneration at room temperature. In addition to high purity H2, the reaction between ethylenediamine bisborane (EDAB) and ethylenediamine (ED) leads to unique boron–carbon–nitrogen 5‐membered rings in the dehydrogenation product where one boron is tricoordinated by three nitrogen atoms. Owing to the unique cyclic structure, the dehydrogenation product can be efficiently converted back to EDAB by NaBH4 and H2O at room temperature. This finding could lead to the discovery of new amine boranes with potential usage as hydrogen storage materials.
Zhang, H, Li, J, Chen, Y, Wu, J, Wang, K, Chen, L, Wang, Y, Jiang, X, Liu, Y, Wu, Y, Jin, D & Bu, W 2021, 'Magneto‐Electrically Enhanced Intracellular Catalysis of FePt‐FeC Heterostructures for Chemodynamic Therapy', Advanced Materials, vol. 33, no. 17, pp. 1-10.
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AbstractIntracellular catalytic reactions can tailor tumor cell plasticity toward high‐efficiency treatments, but the application is hindered by the low efficiency of intracellular catalysis. Here, a magneto‐electronic approach is developed for efficient intracellular catalysis by inducing eddy currents of FePt‐FeC heterostructures in mild alternating magnetic fields (frequency of f = 96 kHz and amplitude of B ≤ 70 mT). Finite element simulation shows a high density of induced charges gathering at the interface of FePt‐FeC heterostructure in the alternating magnetic field. As a result, the concentration of an essential coenzyme—β‐nicotinamide adenine dinucleotide—in cancer cells is significantly reduced by the enhanced catalytic hydrogenation reaction of FePt‐FeC heterostructures under alternating magnetic stimulation, leading to over 80% of senescent cancer cells—a vulnerable phenotype that facilitates further treatment. It is further demonstrated that senescent cancer cells can be efficiently killed by the chemodynamic therapy based on the enhanced Fenton‐like reaction. By promoting intracellular catalytic reactions in tumors, this approach may enable precise catalytic tumor treatment.
Zhang, H, Li, J, Luo, L, Zhao, J, He, J, Zhao, X, Liu, H, Qin, Y, Wang, F & Song, J 2021, 'Hierarchically porous MXene decorated carbon coated LiFePO4 as cathode material for high-performance lithium-ion batteries', Journal of Alloys and Compounds, vol. 876, pp. 160210-160210.
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As a promising cathode material for high-power lithium-ion batteries, LiFePO4 (LFP) suffers from low lithium-ion diffusivity and poor electronic conductivity. In this work, hierarchically porous Ti3C2Tx MXene decorated LFP@C (LFP@C/MXene) composite was successfully synthesized by a facile and efficient electrostatic self-assemble method at room temperature with the help of CTAB to regulate charge state. The introduction of MXene sheets realized the formation of hierarchically porous structure and “dot-to-surface” conductive network, enabling the fast ion and electrons transfer for redox reactions, meanwhile, MXene will be partially oxidized into TiO2 and carbon during cycling, which further improved the diffusion of lithium-ion. Together with the optimized structure of LFP@C nanoplates, the resulting LFP@C/MXene exhibits robust high-rate capability (139 mAh·g−1 at 20 C) as well as a long-life cycling stability (156.6 mAh·g−1 at 1 C with superior capacity retention of 94.8% for 500 cycles). This ingenious design highlights the great potential of 2D MXene for facilely constructing multifunctional electrode materials for application in high-rate Li-ion batteries.
Zhang, L, Chen, C, Tay, SS, Wen, S, Cao, C, Biro, M, Jin, D & Stenzel, MH 2021, 'Optimizing the Polymer Cloak for Upconverting Nanoparticles: An Evaluation of Bioactivity and Optical Performance', ACS Applied Materials & Interfaces, vol. 13, no. 14, pp. 16142-16154.
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The ability of upconversion nanoparticles (UCNPs) to convert low-energy near-infrared (NIR) light into high-energy visible-ultraviolet light has resulted in their development as novel contrast agents for biomedical imaging. However, UCNPs often succumb to poor colloidal stability in aqueous media, which can be conquered by decorating the nanoparticle surface with polymers. The polymer cloak, therefore, plays an instrumental role in ensuring good stability in biological media. This study aims to understand the relationship between the length and grafting density of the polymer shell on the physicochemical and biological properties of these core-shell UCNPs. Poly(ethylene glycol) methyl ether methacrylate block ethylene glycol methacrylate phosphate (PPEGMEMAn-b-PEGMP3) with different numbers of PEGMEMA repeating units (26, 38, and 80) was prepared and attached to the UCNPs via the phosphate ligand of the poly(ethylene glycol methacrylate phosphate) (PEGMP) block at different polymer densities. The in vitro and in vivo protein corona, cellular uptake in two-dimensional (2D) monolayer and three-dimensional (3D) multicellular tumor spheroid (MCTS) models, and in vivo biodistribution in mice were evaluated. Furthermore, the photoluminescence of single-polymer-coated UCNPs was compared in solid state and cancer cells using laser scanning confocal microscopy (LSCM). Our results showed that the bioactivity and luminescence properties are chain length and grafting density dependent. The UCNPs coated with the longest PPEGMEMA chain, grafted at low brush density, were able to reduce the formation of the protein corona in vitro and in vivo, while these UCNPs also showed the brightest upconversion luminescence in the solid state. Moreover, these particular polymer-coated UCNPs showed enhanced cellular uptake, extended in vivo blood circulation time, and more accumulation in the liver, brain, and heart.
Zhang, L, Jin, D & Stenzel, MH 2021, 'Polymer-Functionalized Upconversion Nanoparticles for Light/Imaging-Guided Drug Delivery', Biomacromolecules, vol. 22, no. 8, pp. 3168-3201.
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The strong upconversion luminescence (UCL) of upconversion nanoparticles (UCNPs) endows the nanoparticles with attractive features for combined imaging and drug delivery. UCNPs convert near-infrared (NIR) light into light of shorter wavelengths such as light in the ultraviolet (UV) and visible regions, which can be used for light-guided drug delivery. Although light-responsive drug delivery systems as such have been known for many years, their application in medicine is limited, as strong UV-light can be damaging to tissue; moreover, UV light will not penetrate deeply into the skin, an issue that UCNPs can now address. However, UCNPs, as obtained after synthesis, are usually hydrophobic and require further surface functionalization to be stable in plasma. Polymers can serve as versatile surface coatings, as they can provide good colloidal stability, prevent the formation of a protein corona, provide a matrix for drugs, and be stimuli-responsive. In this Review, we provide a brief overview of the most recent progress in the synthesis of UCNPs with different shapes/sizes. We will then discuss the purpose of polymer coating for drug delivery before summarizing the strategies to coat UCNPs with various polymers. We will introduce the different polymers that have so far been used to coat UCNPs with the purpose to create a drug delivery system, focusing in detail on light-responsive polymers. To expand the application of UCNPs to allow photothermal therapy or magnetic resonance imaging (MRI) or to simply enhance the loading capacity of drugs, UCNPs were often combined with other materials to generate multifunctional nanoparticles such as carbon-based NPs and nanoMOFs. We then conclude with a discussion on drug loading and release and summarize the current knowledge on the toxicity of these polymer-coated UCNPs.
Zhang, T, Li, H, Liu, M, Zhou, H, Zhang, Z, Yu, C, Wang, C & Wang, G 2021, 'Improved the specificity of peroxidase-like carbonized polydopamine nanotubes with high nitrogen doping for glutathione detection', Sensors and Actuators B: Chemical, vol. 341, pp. 129987-129987.
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The introduction of nitrogen heteroatoms into enzyme-like carbon materials is an effective strategy to enhance both catalytic activity and specificity. Herein, we described the preparation of the carbonized polydopamine nanotubes (C-DPANTs) using sacrificial halloysite nanotubes (HNTs) templates. The resulting nitrogen doped C-PDANTs (N-doped C-PDANTs) exhibit solely the peroxidase-like activity owing to the high N doping. N-doped C-PDANTs could catalyze the reduction of H2O2 to produce OH● radicals, which contributed to the oxidation of 3,3’, 5,5’-tetramethylbenzidine (TMB) substrates. Moreover, the catalytic mechanism of N-doped C-PDANTs was further revealed by electrochemical measurements. N-doped C-PDANTs with pyridinic N and graphitic N compositions possess the capability to accelerate the electron transfer, thus facilitating the reduction of H2O2. The application of N-doped C-PDANTs were demonstrated in the sensitive detection of glutathione (GSH) in serum samples. Therefore, the present study provides a facile way to prepared peroxidase-like nanomaterials with high specificity.
Zhang, Y, Wang, Q, Li, L, Le, Y, Liu, L, Yang, J, Li, Y, Bao, G & Yan, L 2021, 'Synthesis and preliminary structure-activity relationship study of 3-methylquinazolinone derivatives as EGFR inhibitors with enhanced antiproliferative activities against tumour cells', Journal of Enzyme Inhibition and Medicinal Chemistry, vol. 36, no. 1, pp. 1205-1216.
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In this paper, a set of 3-methylquniazolinone derivatives were designed, synthesised, and studied the preliminary structure-activity relationship for antiproliferative activities. All target compounds performed significantly inhibitory effects against wild type epidermal growth factor receptor tyrosine kinase (EGFRwt-TK) and tumour cells (A431, A549, MCF-7, and NCI-H1975). In particular, compound 4d 3-fluoro-N-(4-((3-methyl-4-oxo-3,4-dihydroquinazolin-2-yl)methoxy)phenyl)benzamide showed higher antiproliferative activities against all tumour cells than Gefitinib (IC50 of 3.48, 2.55, 0.87 and 6.42 μM, respectively). Furthermore, compound 4d could induce apoptosis of MCF-7 cells and arrest in G2/M phase at the tested concentration. Molecular docking and ADMET studies showed that compound 4d could closely form many hydrogen bonds with EGFRwt-TK. Therefore, compound 4d is potential to develop as novel anti-cancer drug.
Zhang, Y, Xu, Y, Wang, D, Kuang, T, Wu, W, Xu, X, Jin, D & Lou, W 2021, 'Prognostic value of preoperative glucose to lymphocyte ratio in patients with resected pancreatic cancer', International Journal of Clinical Oncology, vol. 26, no. 1, pp. 135-144.
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Zhao, S, Guo, Z, Yan, K, Guo, X, Wan, S, He, F, Sun, B & Wang, G 2021, 'The Rise of Prussian Blue Analogs: Challenges and Opportunities for High‐Performance Cathode Materials in Potassium‐Ion Batteries', Small Structures, vol. 2, no. 1, pp. 2000054-2000054.
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Potassium‐ion batteries (PIBs) are emerging as one of the potential alternatives to lithium‐ion batteries for next‐generation rechargeable battery systems. Nevertheless, the lack of suitable cathode materials with high capacity hinders their practical applications. Recently, Prussian blue analogs (PBAs) cathode materials stand out as promising candidates for PIBs. Their unique crystal structure with open 3D frameworks and large interstitial voids favors fast K+ intercalation without causing drastic volume expansion, which is the prerequisite for high‐rate and long‐term battery operation. Herein, a fundamental review on the development and advance of PBAs cathode materials is presented for PIBs with in‐depth elucidation of their crystal structures, chemical compositions, and electrochemical performances. Particularly, the unique and prominent advantages of PBAs in both aqueous and nonaqueous PIBs are highlighted. In addition, to bridge the current gap from the laboratory to future commercialization, potential improvement strategies are proposed to overcome the present drawbacks. Finally, perspectives and new insights are provided for further exploration and research in PBAs for better PIBs.
Zhao, S, Guo, Z, Yan, K, Wan, S, He, F, Sun, B & Wang, G 2021, 'Towards high-energy-density lithium-ion batteries: Strategies for developing high-capacity lithium-rich cathode materials', Energy Storage Materials, vol. 34, pp. 716-734.
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With the growing demand for high-energy-density lithium-ion batteries, layered lithium-rich cathode materials with high specific capacity and low cost have been widely regarded as one of the most attractive candidates for next-generation lithium-ion batteries. However, issues such as voltage decay, capacity loss and sluggish reaction kinetics have hindered their further commercialization for decades. Intensive investigations have been devoted to developing high-performance lithium-rich cathode materials, highlighting the importance of improvement strategies as a potential approach. Herein, we summarize various strategies for improving performances of layered lithium-rich cathode materials for next-generation high-energy-density lithium-ion batteries. These include surface engineering, elemental doping, composition optimization, structure engineering and electrolyte additives, with emphasis on the effect and functional mechanism of corresponding techniques. In the subsequent section, we illustrate opportunities and challenges for designing high-performance lithium-rich cathode materials and bridging the gap between the laboratory and practical applications.
Zhao, S, Guo, Z, Yang, J, Wang, C, Sun, B & Wang, G 2021, 'Nanoengineering of Advanced Carbon Materials for Sodium‐Ion Batteries', Small, vol. 17, no. 48, pp. 1-5.
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AbstractRecent research shows that the continuing importance of carbon anode materials plays an important role in the development of sodium‐ion batteries. Nevertheless, the practical deployment of sodium‐ion batteries still faces many challenges such as mediocre sodium storage capability and short cycle life. Therefore, it is imperative to explore improvement methods to boost their competitiveness. Herein, various nanoengineering strategies, including nanostructure design, defect and heteroatom doping, and nanocomposite optimization, are proposed as reliable and effective approaches to improve electrochemical performances and structural stability of carbon‐based anode materials for sodium‐ion batteries (SIBs). The feasibility of nanoengineering is highlighted as a promising approach to develop next‐generation carbon materials for sodium‐ion batteries.
Zhao, S, Liu, Z, Xie, G, Guo, X, Guo, Z, Song, F, Li, G, Chen, C, Xie, X, Zhang, N, Sun, B, Guo, S & Wang, G 2021, 'Achieving High‐Performance 3D K+‐Pre‐intercalated Ti3C2Tx MXene for Potassium‐Ion Hybrid Capacitors via Regulating Electrolyte Solvation Structure', Angewandte Chemie, vol. 133, no. 50, pp. 26450-26457.
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AbstractThe development of high‐performance anode materials for potassium‐based energy storage devices with long‐term cyclability requires combined innovations from rational material design to electrolyte optimization. A three‐dimensional K+‐pre‐intercalated Ti3C2Tx MXene with enlarged interlayer distance was constructed for efficient electrochemical potassium‐ion storage. We found that the optimized solvation structure of the concentrated ether‐based electrolyte leads to the formation of a thin and inorganic‐rich solid electrolyte interphase (SEI) on the K+‐pre‐intercalated Ti3C2Tx electrode, which is beneficial for interfacial stability and reaction kinetics. As a proof of concept, 3D K+‐Ti3C2Tx//activated carbon (AC) potassium‐ion hybrid capacitors (PIHCs) were assembled, which exhibited promising electrochemical performances. These results highlight the significant roles of both rational structure design and electrolyte optimization for highly reactive MXene‐based anode materials in energy storage devices.
Zhao, S, Liu, Z, Xie, G, Guo, X, Guo, Z, Song, F, Li, G, Chen, C, Xie, X, Zhang, N, Sun, B, Guo, S & Wang, G 2021, 'Achieving High‐Performance 3D K+‐Pre‐intercalated Ti3C2Tx MXene for Potassium‐Ion Hybrid Capacitors via Regulating Electrolyte Solvation Structure', Angewandte Chemie International Edition, vol. 60, no. 50, pp. 26246-26253.
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AbstractThe development of high‐performance anode materials for potassium‐based energy storage devices with long‐term cyclability requires combined innovations from rational material design to electrolyte optimization. A three‐dimensional K+‐pre‐intercalated Ti3C2Tx MXene with enlarged interlayer distance was constructed for efficient electrochemical potassium‐ion storage. We found that the optimized solvation structure of the concentrated ether‐based electrolyte leads to the formation of a thin and inorganic‐rich solid electrolyte interphase (SEI) on the K+‐pre‐intercalated Ti3C2Tx electrode, which is beneficial for interfacial stability and reaction kinetics. As a proof of concept, 3D K+‐Ti3C2Tx//activated carbon (AC) potassium‐ion hybrid capacitors (PIHCs) were assembled, which exhibited promising electrochemical performances. These results highlight the significant roles of both rational structure design and electrolyte optimization for highly reactive MXene‐based anode materials in energy storage devices.
Zhao, S, Yan, K, Liang, J, Yuan, Q, Zhang, J, Sun, B, Munroe, P & Wang, G 2021, 'Phosphorus and Oxygen Dual‐Doped Porous Carbon Spheres with Enhanced Reaction Kinetics as Anode Materials for High‐Performance Potassium‐Ion Hybrid Capacitors', Advanced Functional Materials, vol. 31, no. 31, pp. 1-12.
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AbstractHard carbons with low cost and high specific capacity hold great potential as anode materials for potassium‐based energy storage. However, their sluggish reaction kinetics and inevitable volume expansion degrade their electrochemical performance. Through rational nanostructure design and a heteroatom doping strategy, herein, the synthesis of phosphorus/oxygen dual‐doped porous carbon spheres is reported, which possess expanded interlayer distances, abundant redox active sites, and oxygen‐rich defects. The as‐developed battery‐type anode material shows high discharge capacity (401 mAh g−1 at 0.1 A g−1), outstanding rate capability, and ultralong cycling stability (89.8% after 10 000 cycles). In situ Raman spectroscopy and density functional theory calculations further confirm that the formation of PC and PO/POH bonds not only improves structural stability, but also contributes to a rapid surface‐controlled potassium adsorption process. As a proof of concept, a potassium‐ion hybrid capacitor is assembled by a dual‐doped porous carbon sphere anode and an activated carbon cathode. It shows superior electrochemical performance, which opens a new avenue to innovative potassium‐based energy storage technology.
Zhao, S, Yan, K, Zhang, J, Sun, B & Wang, G 2021, 'Reaction Mechanisms of Layered Lithium‐Rich Cathode Materials for High‐Energy Lithium‐Ion Batteries', Angewandte Chemie International Edition, vol. 60, no. 5, pp. 2208-2220.
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AbstractLayered lithium‐rich cathode materials have attracted extensive interest owing to their high theoretical specific capacity (320–350 mA h g−1). However, poor cycling stability and sluggish reaction kinetics inhibit their practical applications. After many years of quiescence, interest in layered lithium‐rich cathode materials is expected to revive in answer to our increasing dependence on high‐energy‐density lithium‐ion batteries. Herein, we review recent research progress and in‐depth descriptions of the structure characterization and reaction mechanisms of layered lithium‐rich manganese‐based cathode materials. In particular, we comprehensively summarize the proposed reaction mechanisms of both the cationic redox reaction of transition‐metal ions and the anionic redox reaction of oxygen species. Finally, we discuss opportunities and challenges facing the future development of lithium‐rich cathode materials for next‐generation lithium‐ion batteries.
Zhao, Y, Jiang, W, Zhang, J, Lovell, EC, Amal, R, Han, Z & Lu, X 2021, 'Anchoring Sites Engineering in Single‐Atom Catalysts for Highly Efficient Electrochemical Energy Conversion Reactions', Advanced Materials, vol. 33, no. 41, pp. 2102801-2102801.
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AbstractSingle‐atom catalysts (SACs) have been at the frontier of research field in catalysis owing to the maximized atomic utilization, unique structures and properties. The atomically dispersed and catalytically active metal atoms are necessarily anchored by surrounding atoms. As such, the structure and composition of anchoring sites significantly influence the catalytic performance of SACs even with the same metal element. Significant progress has been made to understand structure–activity relationships at an atomic level, but in‐depth understanding in precisely designing highly efficient SACs for the targeted reactions is still required. In this review, various anchoring sites in SACs are summarized and classified into five different types (doped heteroatoms, defect sites, surface atoms, metal sites, and cavity sites). Then, their impacts on catalytic performance are elucidated for electrochemical reactions based on their distance from the metal center (first coordination shell and beyond). Further, SACs anchored on two typical types of hosts, carbon‐ and metal‐based materials, are highlighted, and the effects of anchoring points on achieving the desirable atomic structure, catalytic performance, and reaction pathways are elaborated. At last, insights and outlook to the SAC field based on current achievements and challenges are presented.
Zhao, Y, Zhang, J, Xie, Y, Sun, B, Jiang, J, Jiang, W-J, Xi, S, Yang, HY, Yan, K, Wang, S, Guo, X, Li, P, Han, Z, Lu, X, Liu, H & Wang, G 2021, 'Constructing Atomic Heterometallic Sites in Ultrathin Nickel-Incorporated Cobalt Phosphide Nanosheets via a Boron-Assisted Strategy for Highly Efficient Water Splitting', Nano Letters, vol. 21, no. 1, pp. 823-832.
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Identification of active sites for highly efficient catalysts at the atomic scale for water splitting is still a great challenge. Herein, we fabricate ultrathin nickel-incorporated cobalt phosphide porous nanosheets (Ni-CoP) featuring an atomic heterometallic site (NiCo16-xP6) via a boron-assisted method. The presence of boron induces a release-and-oxidation mechanism, resulting in the gradual exfoliation of hydroxide nanosheets. After a subsequent phosphorization process, the resultant Ni-CoP nanosheets are implanted with unsaturated atomic heterometallic NiCo16-xP6 sites (with Co vacancies) for alkaline hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). The optimized Ni-CoP exhibits a low overpotential of 88 and 290 mV at 10 mA cm-2 for alkaline HER and OER, respectively. This can be attributed to reduced free energy barriers, owing to the direct influence of center Ni atoms to the adjacent Co/P atoms in NiCo16-xP6 sites. These provide fundamental insights on the correlation between atomic structures and catalytic activity.
Zhou, D, Tang, X, Zhang, X, Zhang, F, Wu, J, Kang, F, Li, B & Wang, G 2021, 'Multi-ion Strategy toward Highly Durable Calcium/Sodium–Sulfur Hybrid Battery', Nano Letters, vol. 21, no. 8, pp. 3548-3556.
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Nonlithium (Li) metal-sulfur batteries are a viable technology for large-scale energy storage due to their relative high energy densities and low cost. However, their practical application is still hindered by the insufficient reversibility and/or limited cycling stability. Herein, we report a high-performance calcium/sodium-sulfur (Ca/Na-S) hybrid battery enabled by a multi-ion chemistry. The introduction of Na ions in the electrolyte greatly boosts the conversion of Ca polysulfides, which has been verified by theoretical calculation and experimental investigation. Meanwhile, the presence of Ca ions constructs a protective electrostatic shield around the initial protrusions on the Na metal anode without prereduction, thus efficiently suppressing the Na dendrite growth. The as-developed Ca/Na-S cell exhibited a high reversible capacity of 947 mAh g-1 at 0.1 C with long cycle life, clearly demonstrating the feasibility of this multi-ion strategy for developing low-cost non-Li metal-sulfur batteries.
Zhou, J, Zheng, G, Liu, X, Dong, G & Qiu, J 2021, 'Defect engineering in lanthanide doped luminescent materials', Coordination Chemistry Reviews, vol. 448, pp. 214178-214178.
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Lanthanides doped luminescent materials (LLMs) have recently gained considerable attention in the areas of bioimaging, sensing, display, and lasers, benefitting from the intriguing optical characters of lanthanides. In LLMs, defect creates intermediate energy levels within the bandgap, which tailors the excited-state dynamics of lanthanides in photophysics and manipulates the spectroscopic characteristics of the lanthanides with much enhanced precision, and thus defect engineering could be a powerful tool in designing LLMs. In this review, we first discuss the creation and characterization of defects in LLMs, which are especially facilitated by the rapid development in nanofabrication, the state-of-the-art instrumental techniques and computation methods. This advances have pushed the manipulation, understanding and utilization of defects in LLMs to a whole new-level and the tailoring of LLMs with desinged performance to meet the requirements of specific application has been dramatically improved in recent years. We then review the emerging applications of the defect-involved LLMs ranging from colour displays, energy utilization, radiation detection to biological applications. Finally, we envision future potential directions in the research of defect engineerin of LLMs and highlight the unsolved problems in this rapidly growing field.
Zhou, K, Zhang, J, Xu, L & Lim, CED 2021, 'Chinese herbal medicine for subfertile women with polycystic ovarian syndrome', Cochrane Database of Systematic Reviews, vol. 2021, no. 6, p. CD007535.
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BACKGROUND: Polycystic ovarian syndrome (PCOS) is characterised by both metabolic and reproductive disorders, and affects 5% to 15% of women of reproductive age. Different western medicines have been proposed for PCOS-related subfertility, such as oral contraceptives, insulin sensitisers and laparoscopic ovarian drilling (LOD). Chinese herbal medicines (CHM) have also been used for subfertility caused by PCOS for decades, and are expected to become an alternative treatment for subfertile women with PCOS. OBJECTIVES: To assess the efficacy and safety of Chinese herbal medicine (CHM) for subfertile women with polycystic ovarian syndrome (PCOS). SEARCH METHODS: We searched the Cochrane Gynaecology and Fertility Group Specialised Register, CENTRAL, MEDLINE, Embase and six other databases, from inception to 2 June 2020. In addition, we searched three trials registries, the reference lists of included trials and contacted experts in the field to locate trials. SELECTION CRITERIA: We included randomised controlled trials (RCTs) comparing CHM versus placebo, no treatment or conventional (western) therapies for the treatment of subfertile women with PCOS. DATA COLLECTION AND ANALYSIS: Two review authors independently screened trials for inclusion, assessed the risk of bias in included studies and extracted data. We contacted primary study authors for additional information. We conducted meta-analyses. We used the odds ratios (ORs) to report dichotomous data, with 95% confidence intervals (CIs). We assessed the certainty of the evidence using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) methods. MAIN RESULTS: We included eight RCTs with 609 participants. The comparisons in the included trials were as follows: CHM versus clomiphene, CHM plus clomiphene versus clomiphene (with or without ethinyloestradiol cyproterone acetate (EE/CPA)), CHM plus follicle aspiration plus ovulation induction versus follicle aspiration plus ovulation in...
Zhou, M, Zhang, H, Li, F, Yu, Z, Yuan, C, Oliver, B & Li, J 2021, 'Pulmonary Daoyin as a traditional Chinese medicine rehabilitation programme for patients with IPF: A randomized controlled trial', Respirology, vol. 26, no. 4, pp. 360-369.
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ABSTRACTBackground and objectiveIPF is a chronic progressive lung disease in which PR provides benefit for patients. PD, a TCM PR programme, has known effectiveness in COPD, but its utility in IPF is unknown. We investigated its effectiveness and safety in patients with IPF.MethodsA 6‐month randomized controlled trial (RCT) was conducted in three Chinese clinics. Ninety‐six participants diagnosed with IPF were randomly assigned to one of the three groups: the PD group received a PD programme two times a day, 5 days/week for 2 months, and the exercise group exercised via a stationary cycle ergometer, 30 min/day, 5 days/week for 2 months. Volunteers in the control group were advised to maintain their usual activities. Primary outcomes were changes from baseline in the 6MWD and HRQoL score on the SGRQ‐I at 1 and 2 months (at the end of the intervention) and at 6 months (4 months after the intervention). Secondary outcomes measures included FVC, DLCO (% predicted) and the changes in mMRC.ResultsThe 6MWD was increased in the PD group compared to exercise and control groups. 6MWD increased by 60.44 m in the PD group, 32.16 m in the exercise group and 12.42 m in controls after the 2 months of rehabilitation programme. The between‐group differences in the change from baseline were 28.78 m (95% CI: 0.54 to 56.01; P = 0.044) and 48.02 m (95% CI: 23.04 to 73.00; P < 0.001) at 2 months, and 25.61 m (95% CI: −0.67 to 51.89; P = 0.058) and 50.93 m (95% CI: 25.47 to 76.40; P < 0.001) at 6 months, respectively, including a difference exceeding the MCID. There was no significant change in the SGRQ‐I score, the mMRC dyspnoea score, FVC and DL
Zhou, X, Wang, T, Liu, H, Gao, X, Wang, C & Wang, G 2021, 'Desulfurization through Photocatalytic Oxidation: A Critical Review', ChemSusChem, vol. 14, no. 2, pp. 492-511.
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AbstractFuel oil, the most important strategic resource, has been widely used in industrial applications. However, the sulfur‐containing compounds in fuel oil also present humanity with huge environmental issues and health concerns due to the hazardous combustion waste. To address this problem, the low vulcanization of fuel production technology has been intensively explored. Compared with traditional hydrodesulfurization technology, the newly emerged photocatalytic desulfurization has the advantages of milder operating conditions, lower energy consumption, and higher efficiency, holding great prospect to achieve deep desulfurization. Though great efforts have been made, the desulfurization catalysts still suffer from inferior light absorption, fast recombination of photocarriers, and poor structure modification. This Review summarizes recent development of photocatalytic desulfurization, including the desulfurization principle, current desulfurization challenges, and corresponding solutions. Particularly, the roles of defect engineering, hybrid coupling, and structure modifications in the enhancement of photocatalytic performance are emphasized. In addition, the photocatalytic desulfurization mechanism is also introduced with the .OH and .O2− radicals as main active species. Finally, some perspectives on the photocatalytic desulfurization are provided, which can further optimize the desulfurization efficiency and guide future photocatalyst design.
Zhou, Y, Zhang, L, Suo, H, Hua, W, Indris, S, Lei, Y, Lai, W, Wang, Y, Hu, Z, Liu, H, Chou, S & Dou, S 2021, 'Atomic Cobalt Vacancy‐Cluster Enabling Optimized Electronic Structure for Efficient Water Splitting', Advanced Functional Materials, vol. 31, no. 26, pp. 2101797-2101797.
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AbstractVacancies created on a surface can alter the local electronic structure, thus enabling a higher intrinsic activity for the evolution of hydrogen and oxygen. Conventional strategies for vacancy engineering, however, have a strong focus on non‐metal sulfur/oxygen defects, which have often overlooked metallic vacancies. Herein, evidence is provided that cobalt vacancies can be atomically tuned to have different sizes to achieve cobalt vacancy clusters through controlling the migration of iridium single atoms. The coalescence of Co vacancy clusters at the surface of an IrCo alloy results in an increased d‐band level and eventually compromises H adsorption, leading to enhanced electrocatalytic activity toward the hydrogen evolution reaction. In addition, the Co vacancy clusters can improve the electronic conductivity with respect to the oxidized Co surface, which substantially aids in strengthening the adsorption of oxygen intermediates toward an effective oxygen evolution reaction at a low overpotential. These collective effects originate from the Co vacancy cluster and specifically enable highly efficient and stable water splitting with a low total overpotential of 384 mV in alkaline media and 365 mV in an acidic environment, achieving a current density of 10 mA cm–2.
Zhu, WJ, Liu, Y, Wang, G, Deng, K, Liu, L, Wang, J, Oliver, BG, Wang, T, Kang, DY, Wang, L, Li, WM & Wang, G 2021, 'Interaction effects of asthma and rhinitis control on work productivity and activity impairment: A cross-sectional study', Allergy and Asthma Proceedings, vol. 42, no. 5, pp. 409-416.
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Background: Symptomatic asthma and rhinitis negatively impact patients' work productivity and activity. However, little is known about the potential interaction effect of both asthma and rhinitis control on work productivity and activity impairment. Objective: This study aimed to explore whether there are interaction effects of asthma and rhinitis control on work productivity and activity impairment in patients with asthma and with rhinitis. Methods: A total of 206 adult patients were prospectively recruited and were divided into four groups: both poorly controlled (BPC) n = 53), poorly controlled asthma (PCA) with controlled rhinitis (CR) (n = 38), well controlled asthma with uncontrolled rhinitis (n = 43), and both well controlled (BWC) (n = 72) based on the symptom control status of asthma and rhinitis. Work productivity loss and activity impairment, asthma control, and rhinitis control were assessed by using work productivity and activity impairment questionnaire: general health, the asthma control test, and the rhinitis control assessment test, respectively. General linear regression models were used to study the contribution of asthma control, rhinitis control, and the interaction effect on work productivity and activity impairment. Results: Work productivity loss was most frequently reported in patients in the BPC group. Compared with the patients in the BWC group, the patients in the PCA-CR group had significantly higher activity impairment and worse asthma-related quality of life (both p < 0.001). There were significant interaction effects of asthma and rhinitis control, which accounted for the increase in presenteeism, work productivity loss, and activity impairment (all p < 0.001). Although differences in absenteeism were not significant among the groups, there was a significant interaction effect of control levels accounted for ...
Ziegler, M, Anton, A, Klein, SG, Rädecker, N, Geraldi, NR, Schmidt‐Roach, S, Saderne, V, Mumby, PJ, Cziesielski, MJ, Martin, C, Frölicher, TL, Pandolfi, JM, Suggett, DJ, Aranda, M, Duarte, CM & Voolstra, CR 2021, 'Integrating environmental variability to broaden the research on coral responses to future ocean conditions', Global Change Biology, vol. 27, no. 21, pp. 5532-5546.
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AbstractOur understanding of the response of reef‐building corals to changes in their physical environment is largely based on laboratory experiments, analysis of long‐term field data, and model projections. Experimental data provide unique insights into how organisms respond to variation of environmental drivers. However, an assessment of how well experimental conditions cover the breadth of environmental conditions and variability where corals live successfully is missing. Here, we compiled and analyzed a globally distributed dataset of in‐situ seasonal and diurnal variability of key environmental drivers (temperature, pCO2, and O2) critical for the growth and livelihood of reef‐building corals. Using a meta‐analysis approach, we compared the variability of environmental conditions assayed in coral experimental studies to current and projected conditions in their natural habitats. We found that annual temperature profiles projected for the end of the 21st century were characterized by distributional shifts in temperatures with warmer winters and longer warm periods in the summer, not just peak temperatures. Furthermore, short‐term hourly fluctuations of temperature and pCO2 may regularly expose corals to conditions beyond the projected average increases for the end of the 21st century. Coral reef sites varied in the degree of coupling between temperature, pCO2, and dissolved O2, which warrants site‐specific, differentiated experimental approaches depending on the local hydrography and influence of biological processes on the carbonate system and O2 availability. Our analysis highlights that a large portion of the natural environmental variability at short and long timescales is underexplored in experimental designs,...
Zinder, Y, Kononov, A & Fung, J 2021, 'A 5-parameter complexity classification of the two-stage flow shop scheduling problem with job dependent storage requirements', Journal of Combinatorial Optimization, vol. 42, no. 2, pp. 276-309.
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Župan, ML, Luo, Z, Ganio, K, Pederick, VG, Neville, SL, Deplazes, E, Kobe, B & McDevitt, CA 2021, 'Conformation of the Solute-Binding Protein AdcAII Influences Zinc Uptake in Streptococcus pneumoniae', Frontiers in Cellular and Infection Microbiology, vol. 11, p. 729981.
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Streptococcus pneumoniae scavenges essential zinc ions from the host during colonization and infection. This is achieved by the ATP-binding cassette transporter, AdcCB, and two solute-binding proteins (SBPs), AdcA and AdcAII. It has been established that AdcAII serves a greater role during initial infection, but the molecular details of how the protein selectively acquires Zn(II) remain poorly understood. This can be attributed to the refractory nature of metal-free AdcAII to high-resolution structural determination techniques. Here, we overcome this issue by separately mutating the Zn(II)-coordinating residues and performing a combination of structural and biochemical analyses on the variant proteins. Structural analyses of Zn(II)-bound AdcAII variants revealed that specific regions within the protein underwent conformational changes via direct coupling to each of the metal-binding residues. Quantitative in vitro metal-binding assays combined with affinity determination and phenotypic growth assays revealed that each of the four Zn(II)-coordinating residues contributes to metal binding by AdcAII. Intriguingly, the phenotypic growth impact of the mutant adcAII alleles was, in general, independent of affinity, suggesting that the Zn(II)-bound conformation of the SBP is crucial for efficacious metal uptake. Collectively, these data highlight the intimate coupling of ligand affinity with protein conformational change in ligand-receptor proteins and provide a putative mechanism for AdcAII. These findings provide further mechanistic insight into the structural and functional diversity of SBPs that is broadly applicable to other prokaryotes.
