Publications

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. 1-32.
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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. 1-10.
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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.

Aliee, H, Massip, F, Qi, C, Stella, DBM, van, NJ, Kersten, ETG, Kermani, NZ, Khuder, B, Vonk, JM, Vermeulen, RCH, U-BIOPRED, SG, Cambridge, LCEDP, INER-Ciencias, MLP, Neighbors, M, Tew, GW, Grimbaldeston, MA, Ten, HNHT, Hu, S, Guo, Y, Zhang, X, Sun, K, Hiemstra, PS, Ponder, BA, Mäkelä, MJ, Malmström, K, Rintoul, RC, Reyfman, PA, Theis, FJ, Brandsma, C-A, Adcock, IM, Timens, W, Xu, C-J, van, DBM, Schwarz, RF, Koppelman, GH, Nawijn, MC & Faiz, A 2021, 'Determinants of expression of SARS-CoV-2 entry-related genes in upper and lower airways.', Allergy, vol. 77, no. 2, pp. 10.1111/all.15152-694.
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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 correlated wi...

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.

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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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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Anderson, GE, Bell, ME, Stevens, J, Aksulu, MD, Miller-Jones, JCA, van der Horst, AJ, Wijers, RAMJ, Rowlinson, A, Bahramian, A, Hancock, PJ, Macquart, J-P, Ryder, SD & Plotkin, RM 2021, 'Rapid-response radio observations of short GRB 181123B with the Australia Telescope Compact Array', Monthly Notices of the Royal Astronomical Society, vol. 503, no. 3, pp. 4372-4386.
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ABSTRACT We introduce the Australia Telescope Compact Array (ATCA) rapid-response mode by presenting the first successful trigger on the short-duration gamma-ray burst (GRB) 181123B. Early-time radio observations of short GRBs may provide vital insights into the radio afterglow properties of Advanced LIGO- and Virgo-detected gravitational wave events, which will in turn inform follow-up strategies to search for counterparts within their large positional uncertainties. The ATCA was on target within 12.6 h post-burst, when the source had risen above the horizon. While no radio afterglow was detected during the 8.3 h observation, we obtained force-fitted flux densities of 7 ± 12 and $15 \pm 11\, \mu$Jy at 5.5 and 9 GHz, respectively. Afterglow modelling of GRB 181123B showed that the addition of the ATCA force-fitted radio flux densities to the Swift X-ray Telescope detections provided more stringent constraints on the fraction of thermal energy in the electrons (log $\epsilon _e = -0.75^{+0.39}_{-0.40}$ rather than log $\epsilon _e = -1.13^{+0.82}_{-1.2}$ derived without the inclusion of the ATCA values), which is consistent with the range of typical ϵe derived from GRB afterglow modelling. This allowed us to predict that the forward shock may have peaked in the radio band ∼10 d post-burst, producing detectable radio emission ≳3–4 d post-burst. Overall, we demonstrate the potential for extremely rapid radio follow-up of transients and the importance of triggered radio observations for constraining GRB blast wave properties, regardless of whether there is a detection, via the inclusion of force-fitted radio flux densities in afterglow modelling efforts.

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.
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AbstractTrait-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 weeks post...

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.

Augustine, R, S, A, Nayeem, A, Salam, SA, Augustine, P, Dan, P, Monteiro, P, Mraiche, F, Gentile, C, Hansbro, PM, McClements, L & Hasan, A 2021, 'Increased complications of COVID-19 in people with cardiovascular disease: Role of the renin-angiotensin-aldosterone system (RAAS) dysregulation.', Chemico-biological interactions, vol. 351, pp. 109738-109738.
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The rapid spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19), has had a dramatic negative impact on public health and economies worldwide. Recent studies on COVID-19 complications and mortality rates suggest that there is a higher prevalence in cardiovascular diseases (CVD) patients. Past investigations on the associations between pre-existing CVDs and susceptibility to coronavirus infections including SARS-CoV and the Middle East Respiratory Syndrome coronavirus (MERS-CoV), have demonstrated similar results. However, the underlying mechanisms are poorly understood. This has impeded adequate risk stratification and treatment strategies for CVD patients with SARS-CoV-2 infections. Generally, dysregulation of the expression of angiotensin-converting enzyme (ACE) and the counter regulator, angiotensin-converting enzyme 2 (ACE2) is a hallmark of cardiovascular risk and CVD. ACE2 is the main host receptor for SARS-CoV-2. Although further studies are required, dysfunction of ACE2 after virus binding and dysregulation of the renin-angiotensin-aldosterone system (RAAS) signaling may worsen the outcomes of people affected by COVID-19 and with preexisting CVD. Here, we review the current knowledge and outline the gaps related to the relationship between CVD and COVID-19 with a focus on the RAAS. Improved understanding of the mechanisms regulating viral entry and the role RAAS may direct future research with the potential to improve the prevention and management of COVID-19.

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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Bai, X, Chen, H & Oliver, BG 2021, 'The health effects of traffic-related air pollution: A review focused the health effects of going green', Chemosphere, vol. 289, pp. 133082-133082.
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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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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 Lett, 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, VHN, Nguyen, KH, Hosseinzadeh, A, Cho, K, Yu, ZM, Jin, J, Wei, XL, Wu, K, Frost, RL & Ni, BJ 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. 1-14.
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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.

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.

Barratt, J, Houghton, K, Richins, T, Straily, A, Threlkel, R, Bera, B, Kenneally, J, Clemons, B, Madison-Antenucci, S, Cebelinski, E, Whitney, BM, Kreil, KR, Cama, V, Arrowood, MJ & Qvarnstrom, Y 2021, 'Investigation of US Cyclospora cayetanensis outbreaks in 2019 and evaluation of an improved Cyclospora genotyping system against 2019 cyclosporiasis outbreak clusters', Epidemiology and Infection, vol. 149, p. e214.
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Abstract Cyclosporiasis is an illness characterised by watery diarrhoea caused by the food-borne parasite Cyclospora cayetanensis. The increase in annual US cyclosporiasis cases led public health agencies to develop genotyping tools that aid outbreak investigations. A team at the Centers for Disease Control and Prevention (CDC) developed a system based on deep amplicon sequencing and machine learning, for detecting genetically-related clusters of cyclosporiasis to aid epidemiologic investigations. An evaluation of this system during 2018 supported its robustness, indicating that it possessed sufficient utility to warrant further evaluation. However, the earliest version of CDC's system had some limitations from a bioinformatics standpoint. Namely, reliance on proprietary software, the inability to detect novel haplotypes and absence of a strategy to select an appropriate number of discrete genetic clusters would limit the system's future deployment potential. We recently introduced several improvements that address these limitations and the aim of this study was to reassess the system's performance to ensure that the changes introduced had no observable negative impacts. Comparison of epidemiologically-defined cyclosporiasis clusters from 2019 to analogous genetic clusters detected using CDC's improved system reaffirmed its excellent sensitivity (90%) and specificity (99%), and confirmed its high discriminatory power. This C. cayetanensis genotyping system is robust and with ongoing improvement will form the basis of a US-wide C. cayetanensis genotyping network for clinical specimens.

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. 1-7.
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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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Behary, J, Amorim, N, Jiang, X-T, Raposo, A, Gong, L, McGovern, E, Ibrahim, R, Chu, F, Stephens, C, Jebeili, H, Fragomeli, V, Koay, YC, Jackson, M, O'Sullivan, J, Weltman, M, McCaughan, G, El-Omar, E & Zekry, A 2021, 'Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma.', Nature Communications, vol. 12, no. 1, pp. 1-14.
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The gut microbiota is reported to modulate the immune response in hepatocellular carcinoma (HCC). Here, we employ metagenomic and metabolomic studies to characterise gut microbiota in patients with non-alcoholic fatty liver disease (NAFLD) related cirrhosis, with or without HCC, and evaluate its effect on the peripheral immune response in an ex vivo model. We find that dysbiosis characterises the microbiota of patients with NAFLD-cirrhosis, with compositional and functional shifts occurring with HCC development. Gene function of the microbiota in NAFLD-HCC supports short chain fatty acid production, and this is confirmed by metabolomic studies. Ex vivo studies show that bacterial extracts from the NAFLD-HCC microbiota, but not from the control groups, elicit a T cell immunosuppressive phenotype, characterised by expansion of regulatory T cells and attenuation of CD8 + T cells. Our study suggest that the gut microbiota in NAFLD-HCC is characterised by a distinctive microbiome/metabolomic profile, and can modulate the peripheral immune response.

Behary, J, Raposo, AE, Amorim, NML, Zheng, H, Gong, L, McGovern, E, Chen, J, Liu, K, Beretov, J, Theocharous, C, Jackson, MT, Seet-Lee, J, McCaughan, GW, El-Omar, EM & Zekry, A 2021, 'Defining the temporal evolution of gut dysbiosis and inflammatory responses leading to hepatocellular carcinoma in Mdr2 −/− mouse model', BMC Microbiology, vol. 21, no. 1.
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Abstract Background Emerging evidence implicates the gut microbiome in liver inflammation and hepatocellular carcinoma (HCC) development. We aimed to characterize the temporal evolution of gut dysbiosis, in relation to the phenotype of systemic and hepatic inflammatory responses leading to HCC development. In the present study, Mdr2 −/− mice were used as a model of inflammation-based HCC. Gut microbiome composition and function, in addition to serum LPS, serum cytokines/chemokines and intrahepatic inflammatory genes were measured throughout the course of liver injury until HCC development. Results Early stages of liver injury, inflammation and cirrhosis, were characterized by dysbiosis. Microbiome functional pathways pertaining to gut barrier dysfunction were enriched during the initial phase of liver inflammation and cirrhosis, whilst those supporting lipopolysaccharide (LPS) biosynthesis increased as cirrhosis and HCC ensued. In parallel, serum LPS progressively increased during the course of liver injury, corresponding to a shift towards a systemic Th1/Th17 proinflammatory phenotype. Alongside, the intrahepatic inflammatory gene profile transitioned from a proinflammatory phenotype in the initial phases of liver injury to an immunosuppressed one in HCC. In established HCC, a switch in microbiome function from carbohydrate to amino acid metabolism occurred. Conclusion In Mdr2 −/− mice, dysbiosis precedes HCC development, with temporal evolution of microbiome function to support gut barrier dysfunction, LPS biosynthesis, and redirection of energy source utilization. A corresponding shift in systemic and intrahepatic inflammatory responses occurred ...

Belfiore, L, Aghaei, B, Law, AMK, Dobrowolski, JC, Raftery, LJ, Tjandra, AD, Yee, C, Piloni, A, Volkerling, A, Ferris, CJ & Engel, M 2021, 'Generation and analysis of 3D cell culture models for drug discovery', European Journal of Pharmaceutical Sciences, vol. 163, pp. 105876-105876.
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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 Topt

Berdinsky, D, Elder, M & Kruengthomya, P 2021, 'Cayley polynomial–time computable groups', Information and Computation, vol. 288, pp. 104768-104768.
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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.', Opt Lett, vol. 46, no. 3, pp. 564-567.
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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 5000µm2. 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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Mycoplasma 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.', Front Microbiol, 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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Emerging 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.

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, 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.
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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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Bonnin, L, Mouillot, D, Boussarie, G, Robbins, WD, Kiszka, JJ, Dagorn, L & Vigliola, L 2021, 'Recent expansion of marine protected areas matches with home range of grey reef sharks', Scientific Reports, vol. 11, no. 1.
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AbstractDramatic declines in reef shark populations have been documented worldwide in response to human activities. Marine Protected Areas (MPAs) offer a useful mechanism to protect these species and their roles in coral reef ecosystems. The effectiveness of MPAs notably relies on compliance together with sufficient size to encompass animal home range. Here, we measured home range of 147 grey reef sharks,Carcharhinus amblyrhynchos, using acoustic telemetry in New Caledonia. The distribution of home range was then compared to local MPA sizes. We report a home range of 12 km2of reef for the species with strong differences between adult males (21 km2), adult females (4.4 km2) and juveniles (6.2 km2for males, 2.7 km2for females). Whereas local historic MPA size seemed adequate to protect reef shark home range in general, these were clearly too small when considering adult males only, which is consistent with the reported failure of MPAs to protect sharks in New Caledonia. Fortunately, the recent implementation of several orders of magnitude larger MPAs in New Caledonia and abroad show that recent Indo-Pacific MPAs are now sufficiently large to protect the home ranges of this species, including males, across its geographical range. However, protection efforts are concentrated in a few regions and cannot provide adequate protection at a global scale.

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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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. 1-13.
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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 of Bacillus and Yersinia species 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.
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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 : CB, 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, while urchin...

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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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', Animals and Environments, vol. 1, pp. 1-10.
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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.

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.

Burke, C 2021, 'An exploration of liminal pockets of contestation and delight in school spaces', Paedagogica Historica, vol. 57, no. 1-2, pp. 11-22.
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Burke, C & Whyte, W 2021, 'The spaces and places of schooling: historical perspectives', Oxford Review of Education, vol. 47, no. 5, pp. 549-555.
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Burnett, DL, Jackson, KJL, Langley, DB, Aggrawal, 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. elab027-303.
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Messenger 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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Cant, J, Salguero‐Gómez, R, Kim, SW, Sims, CA, Sommer, B, Brooks, M, Malcolm, HA, Pandolfi, JM & Beger, M 2021, 'The projected degradation of subtropical coral assemblages by recurrent thermal stress', Journal of Animal Ecology, vol. 90, no. 1, pp. 233-247.
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Abstract Subtropical coral assemblages are threatened by similar extreme thermal stress events to their tropical counterparts. Yet, the mid‐ and long‐term thermal stress responses of corals in subtropical environments remain largely unquantified, limiting our capacity to predict their future viability. The annual survival, growth and recruitment of 311 individual corals within the Solitary Islands Marine Park (Australia) was recorded over a 3‐year period (2016–2018), including the 2015/2016 thermal stress event. These data were used to parameterise integral projection models quantifying the effect of thermal stress within a subtropical coral assemblage. Stochastic simulations were also applied to evaluate the implications of recurrent thermal stress scenarios predicted by four different Representative Concentration Pathways. We report differential shifts in population growth rates (λ) among coral populations during both stress and non‐stress periods, confirming contrasting bleaching responses among taxa. However, even during non‐stress periods, the observed dynamics for all taxa were unable to maintain current community composition, highlighting the need for external recruitment sources to support the community structure. Across all coral taxa, projected stochastic growth rates (λs) were found to be lowest under higher emissions scenarios. Correspondingly, predicted increases in recurrent thermal stress regimes may accelerate the loss of coral coverage, species diversity and structural complexity within subtropical regions. We suggest that these trends are primarily due to the susceptibility of subtropical specialists an...

Cardoso, BR, Hare, DJ & Macpherson, H 2021, 'Correction to: Sex‑dependent association between selenium status and cognitive performance in older adults', European Journal of Nutrition, vol. 60, no. 2, pp. 1161-1161.
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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 and 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 protozoa h...

Chan, Y, Mehta, M, Paudel, KR, Madheswaran, T, Panneerselvam, J, Gupta, G, Su, QP, Hansbro, PM, McLoughlin, 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. 1-10.
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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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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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Point 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, C-H, Chao, K-M, Hwang, F-J, Han, C & Pu, L 2021, 'Editorial', International Journal of Distributed Sensor Networks, vol. 17, no. 2, pp. 155014772199288-155014772199288.
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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, Lin, Y, Chen, Y, Chen, S, Nassif, N & McGowan, E 2021, 'P-86 The importance of sphingosine kinase 1 isoform expression in the gut-liver axis', Annals of Oncology, vol. 32, pp. S127-S127.
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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 factors, zin...

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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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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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 and 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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Lithium-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 Material, 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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Fluorescent 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.

Choi, JP, Yang, X, He, S, Song, R, Xu, Z-R, Foley, M, Wong, JJ-L, Xu, C-R & Zheng, X 2021, 'CCM2L (Cerebral Cavernous Malformation 2 Like) Deletion Aggravates Cerebral Cavernous Malformation Through Map3k3-KLF Signaling Pathway', Stroke, vol. 52, no. 4, pp. 1428-1436.
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Background and Purpose: Cerebral cavernous malformation (CCM) is a common cerebrovascular disease. CCMs are major causes of stroke, cerebral hemorrhage, and neurological deficits in young individuals. Loss-of-function mutations in CCM1 , CCM2 , and CCM3 have been identified to cause CCM in humans. Ccm2-like ( Ccm2l ) is a paralog of Ccm2 and is predominantly expressed in endothelial cells (ECs). CCM2L (CCM2-like) competes with CCM2 for binding to CCM1 and has been shown to have an antagonistic function to that of CCM2 during vascular development. The role of CCM2L in CCM pathogenesis is unknown. Methods: We isolated brain ECs from the inducible-CCM mouse models for gene expression analysis. Micro-computed tomography imaging was used to analyze CCM lesion burden from the genetic cross of Ccm2l knockout mice ( Ccm2l −/− ) with Ccm1 or Ccm2 -deficient mice to determine the role of Ccm2l in CCM pathogenesis. Genetic crosses with Map3k3 fl/fl mice were used to determine the role...

Chong, H, Xu, Y, Han, Y, Yan, C, Su, D & Wang, C 2021, 'Pillar[5]arene‐based “Three‐components” Supramolecular Assembly and the Performance of Nitrobenzene‐based Explosive Fluorescence Sensing', ChemistrySelect, vol. 6, no. 34, pp. 9363-9367.
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AbstractA “three‐components” supramolecular assembly has been fabricated by mixing 2, 2’: 6’, 2”‐terpyridine attached pillar[5]arene, cyano and triazole bearing alkyl chain and Zn2+ in solvent of CHCl3 and CH3CN. The driving forces for the assembly were believed to be host‐guest and metal chelating interactions as characterized by 1H NMR, UV‐vis and fluorescence spectra. The supramolecular organo‐gel formed upon the concentration of components amount to 1 M. The supramolecular displayed nitrobenzene based explosive sensing capability using picric acid, ortho‐nitrobenzene and phenol as samples. The assembly was most sensitive towards picric acid among the three analytes. The limit of detection for picric acid was determined to be 1.66 × 10−4 M.

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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Inflammation 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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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.

Clarke, C, Singh, M, Tawfik, SA, Xu, X, Spencer, MJS, Ramanathan, R, Reineck, P, Bansal, V & Ton-That, C 2021, 'Mono- to few-layer non-van der Waals 2D lanthanide-doped NaYF(4)nanosheets with upconversion luminescence', 2D MATERIALS, vol. 8, no. 1, pp. 015005-015005.
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AbstractNaYF4is an efficient host material for lanthanide-based upconversion luminescence and has attracted immense interest for potential applications in photovoltaics, lasers and bioimaging. However, being a non-van der Waals (non-vdW) material, there have been thus far no reports on exfoliation of bulk NaYF4to nanosheets and their upconversion luminescence properties. Here, we demonstrate for the first time the fabrication of lanthanide-containing NaYF42D nanosheets using a soft liquid-phase exfoliation method and report on their optical, electronic and chemical characteristics. The nanosheets exfoliated from NaYF4:Yb,Er microcrystals consisting mainly ofβ-NaYF4become enriched inα-NaYF4post exfoliation and have a large micron-sized planar area with a preferential (100) surface orientation. X-ray absorption spectroscopy confirms that both Yb and Er doping ions are retained in the exfoliated nanosheets. Through centrifugation, NaYF42D nanosheets are successfully obtained with thicknesses ranging from a monolayer to tens of layers. Optical analysis of individual nanosheets shows that they exhibit both optical down-conversion and upconversion properties, albeit with reduced emission intensities compared with the parent microparticles. Further exploration of their electronic structure by density functional theory (DFT) calculations and photoelectron spectroscopy reveals the formation of surface F atom defects and a shrinkage of the electronic bandgap in ultrathin nanosheets. Our findings will trigger further interest in non-vdW 2D upconversion nanomaterials.

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.

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 for BRCA1 and BRCA2 mutation 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 with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P < 10−8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD, SP11 and EIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers.

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, 'Author Correction: 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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A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-23162-4

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. 1-12.
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Coni, EOC, Booth, DJ, Ferreira, CM & Nagelkerken, I 2021, 'Behavioural generalism could facilitate co-existence of tropical and temperate fishes under climate change.', The Journal of animal ecology, vol. 91, no. 1, pp. 86-100.
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Coral-reef fishes are shifting their distributions poleward in response to human-mediated ocean warming, yet the consequences for recipient temperate fish communities remain poorly understood. Behavioural modification is often the first response of species to environmental change, but we know little about how this might shape the ongoing colonisation by tropical fishes of temperate-latitude ecosystems under climate change. In a global hotspot of ocean warming (southeast Australia), we quantified 14 behavioural traits of invading tropical and local co-occurring temperate fishes at 10 sites across a 730 km latitudinal gradient as a proxy of species behavioural niche space in different climate ranges (subtropical, warm-temperate, cold-temperate). We found that tropical fishes (4 species) modified their behavioural niches as well as increased their overall behavioural niche breadth in their novel temperate ranges where temperate species predominate, but maintained a moderate to high niche segregation with native temperate species across latitudinal range position. Temperate species (3 co-occurring species) also modified their niches, but in contrast to tropical species, experienced an increased niche breadth towards subtropical ranges. Alterations to feeding and shoaling behaviours contributed most to niche modifications in tropical and temperate species, while behaviours related to alertness and escape from potential threats contributed least. We here show that at warmer and colder range edges where community structures are being reshuffled due to climate change, behavioural generalism and niche modification are potential mechanisms adopted by tropical range extenders and native-temperate fishes to adjust to novel species interactions under climate change.

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. 1-8.
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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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Abstract One 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 can also su...

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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Global 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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Cvitanovic, C, Mackay, M, Kelly, R, Wilson, SK, Waples, K, Nash, KL, van Putten, EI, Field, S, Botterill-James, T, Austin, BJ, Beckley, LE, Boschetti, F, Depczynski, M, Dobbs, RJ, Evans, RD, Feng, M, Goater, RK, Halford, AR, Kendrick, A, Kendrick, GA, Lincoln, GDB, Ludgerus, LJ, Lowe, RJ, McMahon, K, Munro, JK, Newman, SJ, Nutt, C, Pearson, L, O'Leary, MJ, Richards, ZT, Robbins, WD, Rogers, DI, Salgado Kent, CP, Schoepf, V, Travers, MJ, Thums, M, Tucker, AD, Underwood, JN, Whiting, S & Mathews, D 2021, 'Thirty critical research needs for managing an ecologically and culturally unique remote marine environment: The Kimberley region of Western Australia', Ocean & Coastal Management, vol. 212, pp. 105771-105771.
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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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BackgroundThe major pathogenesis associated with Fasciola hepatica infection 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 the F. hepatica factors 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.ConclusionsThe migration of immature F. hepatica parasites within the liver is associated with an increase in protein production, expression of signalling pathways and neoblast proliferation tha...

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.
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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 safeguard ...

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.

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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Dawson, BM, Barton, PS & Wallman, JF 2021, 'Field succession studies and casework can help to identify forensically useful Diptera.', J Forensic Sci, vol. 66, no. 6, pp. 2319-2328.
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Fly 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?', J Med Entomol, vol. 58, no. 6, pp. 2228-2235.
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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, SRT, Abdul-Halim, MF, Pittrich, DA, Brown, HJ, Pohlschroder, M & Duggin, IG 2021, 'Improved growth and morphological plasticity of Haloferax volcanii.', Microbiology (Reading, England), 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 log-phase rods, as well as the pleomorphic rods and tubules were dependent on the function of the tubulin-like cytoskeletal protein, CetZ1. Our results reveal the remarkable morphological plasticity of H. volcanii cells in response to multiple culture conditions, and should facilitate the use of this species in further studies of archaeal biology.

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 Comput Biol, 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.', J Allergy Clin Immunol Pract, 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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Desbiens, AA, Roff, G, Robbins, WD, Taylor, BM, Castro‐Sanguino, C, Dempsey, A & Mumby, PJ 2021, 'Revisiting the paradigm of shark‐driven trophic cascades in coral reef ecosystems', Ecology, vol. 102, no. 4.
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AbstractGlobal overfishing of higher‐level predators has caused cascading effects to lower trophic levels in many marine ecosystems. On coral reefs, which support highly diverse food webs, the degree to which top‐down trophic cascades can occur remains equivocal. Using extensive survey data from coral reefs across the relatively unfished northern Great Barrier Reef (nGBR), we quantified the role of reef sharks in structuring coral reef fish assemblages. Using a structural equation modeling (SEM) approach, we explored the interactions between shark abundance and teleost mesopredator and prey functional group density and biomass, while explicitly accounting for the potentially confounding influence of environmental variation across sites. Although a fourfold difference in reef shark density was observed across our survey sites, this had no impact on either the density or biomass of teleost mesopredators or prey, providing evidence for a lack of trophic cascading across nGBR systems. Instead, many functional groups, including sharks, responded positively to environmental drivers. We found reef sharks to be positively associated with habitat complexity. In turn, physical processes such as wave exposure and current velocity were both correlated well with multiple functional groups, reflecting how changes to energetic conditions and food availability, or modification of habitat affect fish distribution. The diversity of species within coral reef food webs and their associations with bottom‐up drivers likely buffers against trophic cascading across GBR functional guilds when reef shark assemblages are depleted, as has been demonstrated in other complex ecosystems.

Devkota, HP, Gaire, BP, Hori, K, Subedi, L, Adhikari-Devkota, A, Belwal, T, Paudel, KR, Jha, NK, Singh, SK, Chellapan, 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 Hi2019Δd msA strain did not show any defects in anaerobic growth on chemically defined medium (CDM), and viability was also unaffected. Although Hi2019Δd msA 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 Hi2019Δd msA 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 Hi2019Δd msA was reduced in lung tissue compared to BALF samples, indicating that Hi2019Δd msA had reduced access to or survival in the intracellular niche. Our data clearly indicate for the first time a role for DmsABC in H. influenzae infection and that the conditions under which DmsABC is required in this bacterium are closely linked to interactions with the host.

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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Effective 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 represented endemic fishes were qualitatively comparable to the available geographic distributions for these species. We suggest that quality-filtered citizen science data can in fact be used to improve taxonomic representation a...

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, Moloudi, R & Warkiani, ME 2021, 'Bioreactor-Based Adherent Cells Harvesting from Microcarriers with 3D Printed Inertial Microfluidics', pp. 257-266.
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Ding, L, Radfar, P, Rezaei, M & Warkiani, ME 2021, 'An easy-to-operate method for single-cell isolation and retrieval using a microfluidic static droplet array.', Microchimica Acta: an international journal on micro and trace analysis, vol. 188, no. 8, pp. 1-11.
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In-depth study of cellular heterogeneity of rare cells (e.g. circulating tumour cells (CTCs) and circulating foetal cells (CFCs)) is greatly needed in disease management but has never been completely explored due to the current technological limitations. We have developed a retrieval method for single-cell detection using a static droplet array (SDA) device through liquid segmentation with almost no sample loss. We explored the potential of using SDA for low sample input and retrieving the cells of interest using everyday laboratory equipment for downstream molecular analysis. This single-cell isolation and retrieval method is low-cost, rapid and provides a solution to the remaining challenge for single rare cell detection. The entire process takes less than 15 min, is easy to fabricate and allows for on-chip analysis of cells in nanolitre droplets and retrieval of desired droplets. To validate the applicability of our device and method, we mimicked detection of single CTCs by isolating and retrieving single cells and perform real-time PCR on their mRNA contents.

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.

Ditz, B, Boekhoudt, JG, Aliee, H, Theis, FJ, Nawijn, M, Brandsma, C-A, Hiemstra, PS, Timens, W, Tew, GW, Grimbaldeston, MA, Neighbors, M, Guryev, V, van den Berge, M & Faiz, A 2021, 'Comparison of genome-wide gene expression profiling by RNA Sequencing versus microarray in bronchial biopsies of COPD patients before and after inhaled corticosteroid treatment: does it provide new insights?', ERJ Open Research, vol. 7, no. 2, pp. 00104-2021.
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Doble, PA, de, VRG, 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 living wall lig...

Dong, Z-J, Sun, B, Zhu, H, Yuan, G-M, Li, B-L, Guo, J-G, Li, X-K, Cong, Y & Zhang, J 2021, 'A review of aligned carbon nanotube arrays and carbon/carbon composites: fabrication, thermal conduction properties and applications in thermal management', New Carbon Materials, vol. 36, no. 5, pp. 873-892.
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Donnelly, S & Tran, N 2021, 'Commandeering the mammalian Ago2 miRNA network: a newly discovered mechanism of helminth immunomodulation.', Trends Parasitol, 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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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. 1-15.
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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:OCL1 Acinetobacter baumannii strains recovered in Tehran, Iran, carry AbaR31 in the chromosome and AbaR4 and TnaphA6 in a RepAci6 plasmid.', JAC-antimicrobial resistance, vol. 3, no. 3, p. dlab112.
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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 &lt; 0.001, effect size = 1.12) and decreased psychological distress (P = 0.045, effect size = 1.03) and fatigue (P &lt; 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.

Duncan, RJ, Andrew, ME & Forchhammer, MC 2021, 'Snow mediates climatic impacts on Arctic herbivore populations', Polar Biology, vol. 44, no. 7, pp. 1251-1271.
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AbstractArctic ecosystems are particularly vulnerable to impacts of climate change; however, the complex relationships between climate and ecosystems make incorporating effects of climate change into population management difficult. This study used structural equation modelling (SEM) and a 24-year multifaceted monitoring data series collected at Zackenberg, North-East Greenland, to untangle the network of climatic and local abiotic and biotic drivers, determining their direct and indirect effects on two herbivores: musk ox (Ovibos moschatus) and collared lemming (Dicrostonyx groenlandicus). Snow conditions were determined to be the central driver within the system, mediating the effects of climate on herbivore abundance. Under current climate change projections, snow is expected to decrease in the region. Snow had an indirect negative effect on musk ox, as decreased snow depth led to an earlier start to the Arctic willow growing season, shown to increase fecundity and decrease mortality. Musk ox are therefore expected to be more successful under future conditions, within a certain threshold. Snow had both positive and negative effects on lemming, with lemming expected to ultimately be less successful under climate change, as reduction in snow increases their vulnerability to predation. Through their capacity to determine effects of climatic and local drivers within a hierarchy, and the relative strength and direction of these effects, SEMs were demonstrated to have the potential to be valuable in guiding population management.

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. 1-12.
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Previously, it was suggested that haemadipsid leeches represent an important vector of trypanosomes amongst native animals in Australia. Consequently, Chtonobdella bilineata leeches were investigated for the presence of trypanosome species by polymerase chain reaction (PCR), DNA sequencing and in vitro isolation. Phylogenetic analysis ensued to further define the populations present. PCR targeting the 28S rDNA demonstrated that over 95% of C. bilineata contained trypanosomes; diversity profiling by deep amplicon sequencing of 18S rDNA indicated the presence of four different clusters related to the Trypanosoma (Megatrypanum) theileri. Novy–MacNeal–Nicolle slopes with liquid overlay were used to isolate trypanosomes into culture that proved similar in morphology to Trypanosoma cyclops in that they contained a large numbers of acidocalcisomes. Phylogeny of 18S rDNA/GAPDH/ND5 DNA sequences from primary cultures and subclones showed the trypanosomes were monophyletic, with T. cyclops as a sister group. Blood-meal analysis of leeches showed that leeches primarily contained blood from swamp wallaby (Wallabia bicolour), human (Homo sapiens) or horse (Equus sp.). The leech C. bilineata is a host for at least five lineages of Trypanosoma sp. and these are monophyletic with T. cyclops; we propose Trypanosoma cyclops australiensis as a subspecies of T. cyclops based on genetic similarity and biogeography considerations.

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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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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Ewart, KM, Johnson, RN, Joseph, L, Ogden, R, Frankham, GJ & Lo, N 2021, 'Phylogeography of the iconic Australian pink cockatoo,Lophochroa leadbeateri', Biological Journal of the Linnean Society, vol. 132, no. 3, pp. 704-723.
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AbstractThe pink cockatoo (Lophochroa leadbeateri; or Major Mitchell’s cockatoo) is one of Australia’s most iconic bird species. Two subspecies based on morphology are separated by a biogeographical divide, the Eyrean Barrier. Testing the genetic basis for this subspecies delineation, clarifying barriers to gene flow and identifying any cryptic genetic diversity will likely have important implications for conservation and management. Here, we used genome-wide single nucleotide polymorphisms (SNPs) and mitochondrial DNA data to conduct the first range-wide genetic assessment of the species. The aims were to investigate the phylogeography of the pink cockatoo, to characterize conservation units and to reassess subspecies boundaries. We found consistent but weak genetic structure between the two subspecies based on nuclear SNPs. However, phylogenetic analysis of nuclear SNPs and mitochondrial DNA sequence data did not recover reciprocally monophyletic groups, indicating incomplete evolutionary separation between the subspecies. Consequently, we have proposed that the two currently recognized subspecies be treated as separate management units rather than evolutionarily significant units. Given that poaching is suspected to be a threat to this species, we assessed the utility of our data for wildlife forensic applications. We demonstrated that a subspecies identification test could be designed using as few as 20 SNPs.

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 ...

Faisal, SN, Amjadipour, M, Izzo, K, Singer, JA, Bendavid, A, Lin, C-T & Iacopi, F 2021, 'Non-invasive on-skin sensors for brain machine interfaces with epitaxial graphene.', J Neural Eng, vol. 18, no. 6, pp. 066035-066035.
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Objective. Brain-machine interfaces are key components for the development of hands-free, brain-controlled devices. Electroencephalogram (EEG) electrodes are particularly attractive for harvesting the neural signals in a non-invasive fashion.Approach.Here, we explore the use of epitaxial graphene (EG) grown on silicon carbide on silicon for detecting the EEG signals with high sensitivity.Main results and significance.This dry and non-invasive approach exhibits a markedly improved skin contact impedance when benchmarked to commercial dry electrodes, as well as superior robustness, allowing prolonged and repeated use also in a highly saline environment. In addition, we report the newly observed phenomenon of surface conditioning of the EG electrodes. The prolonged contact of the EG with the skin electrolytes functionalize the grain boundaries of the graphene, leading to the formation of a thin surface film of water through physisorption and consequently reducing its contact impedance more than three-fold. This effect is primed in highly saline environments, and could be also further tailored as pre-conditioning to enhance the performance and reliability of the EG sensors.

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.

Faiz, A, Rathnayake, SNH, ten Hacken, NHT, Guryev, V, van den Berge, M & Pouwels, SD 2021, 'Single-nucleotide polymorphism rs2070600 regulates AGER splicing and the sputum levels of the COPD biomarker soluble receptor for advanced glycation end-products', ERJ Open Research, vol. 7, no. 2, pp. 00947-2020.
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The COPD susceptibility SNP rs2070600 affects the levels of the COPD biomarker sRAGE in sputum as well as splicing of AGER. Moreover, @PouwelsScience et al. demonstrate large differences in sRAGE levels between serum and sputum. https://bit.ly/3t0pJtK.

Falkenberg, LJ, Scanes, E, Ducker, J & Ross, PM 2021, 'Biotic habitats as refugia under ocean acidification', Conservation Physiology, vol. 9, no. 1.
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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, BM, 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, LF, 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, DMM, 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, PC, 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, Tng, DYP, de, TF, Tomlinson, K, Turner, NC & 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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We 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, 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. 2102242-2102242.
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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, Rodriguez, DLFL, 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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Mammary 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.

Fernandez-Nieto, G, Martinez-Maldonado, R, Echeverria, V, Kitto, K, An, P & Buckingham Shum, S 2021, 'What Can Analytics for Teamwork Proxemics Reveal About Positioning Dynamics In Clinical Simulations?', Proceedings of the ACM on Human-Computer Interaction, vol. 5, no. CSCW1, pp. 1-24.
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Effective teamwork is critical to improve patient outcomes in healthcare. However, achieving this capabilityrequires that pre-service nurses develop the spatial abilities they will require in their clinical placements, suchas: learning when to remain close to the patient and to other team members; positioning themselves correctlyat the right time; and deciding on specific team formations (e.g. face-to-face or side-by-side) to enable effectiveinteraction or avoid disrupting clinical procedures. However, positioning dynamics are ephemeral and caneasily become occluded by the multiple tasks nurses have to accomplish. Digital traces automatically capturedby indoor positioning sensors can be used to address this problem for the purpose of improving nurses' reflection, learning and professional development. This paper presents; i) a qualitative study that illustrateshow to elicit spatial behaviours from educators' pedagogical expectations, and ii) a modelling approachthat transforms nurses' low-level position traces into higher-order proxemics constructs, informed by sucheducatos' expectations, in the context of simulation-based teamwork training. To illustrate our modellingapproach, we conducted an in-the-wild study with 55 undergraduate students and five educators from whompositioning traces were captured in eleven authentic nursing education classes. Low-levelx-ydata was usedto model three proxemic constructs: i) co-presence in interactional spaces, ii) socio-spatial formations (i.e.f-formations), and ii) presence in spaces of interest. Through a number of vignettes, we illustrate how indoorpositioning analytics can be used to address questions that educators and researchers have about teamwork inhealthcare simulation settings.

Fernandez-Nieto, GM, Echeverria, V, Shum, SB, Mangaroska, K, Kitto, K, Palominos, E, Axisa, C & Martinez-Maldonado, R 2021, 'Storytelling With Learner Data: Guiding Student Reflection on Multimodal Team Data', IEEE Transactions on Learning Technologies, vol. 14, no. 5, pp. 695-708.
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Ferrari, R, Lachs, L, Pygas, DR, Humanes, A, Sommer, B, Figueira, WF, Edwards, AJ, Bythell, JC & Guest, JR 2021, 'Photogrammetry as a tool to improve ecosystem restoration', Trends in Ecology & Evolution, vol. 36, no. 12, pp. 1093-1101.
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Ecosystem restoration has been practiced for over a century and is increasingly supported by the emergent applied science of restoration ecology. A prerequisite for successful ecosystem restoration is determining meaningful and measurable goals. This requires tools to monitor success in a standardized way. Photogrammetry uses images to reconstruct landscapes and organisms in three dimensions, enabling non-invasive measurement of key success indicators with unprecedented accuracy. We propose photogrammetry can improve restoration success by: (i) facilitating measurable goals; (ii) innovating and standardizing indicators of success; and (iii) standardizing monitoring. While the case we present is specific to coral reefs, photogrammetry has enormous potential to improve restoration practice in a wide range of ecosystems.

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, BPJ 2021, 'Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains.', ACS Sens, 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.

Flaherty, BR, Barratt, J, Lane, M, Talundzic, E & Bradbury, RS 2021, 'Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing', Microbiome, vol. 9, no. 1.
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Abstract Background Targeted amplicon deep sequencing (TADS) has enabled characterization of diverse bacterial communities, yet the application of TADS to communities of parasites has been relatively slow to advance. The greatest obstacle to this has been the genetic diversity of parasitic agents, which include helminths, protozoa, arthropods, and some acanthocephalans. Meanwhile, universal amplification of conserved loci from all parasites without amplifying host DNA has proven challenging. Pan-eukaryotic PCRs preferentially amplify the more abundant host DNA, obscuring parasite-derived reads following TADS. Flaherty et al. (2018) described a pan-parasitic TADS method involving amplification of eukaryotic 18S rDNA regions possessing restriction sites only in vertebrates. Using this method, host DNA in total DNA extracts could be selectively digested prior to PCR using restriction enzymes, thereby increasing the number of parasite-derived reads obtained following NGS. This approach showed promise though was only as sensitive as conventional PCR. Results Here, we expand on this work by designing a second set of pan-eukaryotic primers flanking the priming sites already described, enabling nested PCR amplification of the established 18S rDNA target. This nested approach facilitated introduction of a second restriction digestion between the first and second PCR, reducing the proportional mass of amplifiable host-derived DNA while increasing the number of PCR amplification cycles. We applied this method to blood specimens containing Babesia, Plasmodium, various kinetoplastids, and filarial nematodes and confirmed its limit of detection (LOD) to be approximately 10-fold lower than previously described, falling...

Ford, BA, Sullivan, GJ, Moore, L, Varkey, D, Zhu, H, Ostrowski, M, Mabbutt, BC, Paulsen, IT & Shah, BS 2021, 'Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria.', Biochem Soc Trans, vol. 49, no. 6, pp. 2465-2481.
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Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation.

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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Franzen, TMO, Seymour, N, Sadler, EM, Mauch, T, White, SV, Jackson, CA, Chhetri, R, Quici, B, Bell, ME, Callingham, JR, Dwarakanath, KS, For, B, Gaensler, BM, Hancock, PJ, Hindson, L, Hurley-Walker, N, Johnston-Hollitt, M, Kapińska, AD, Lenc, E, McKinley, B, Morgan, J, Offringa, AR, Procopio, P, Staveley-Smith, L, Wayth, RB, Wu, C & Zheng, Q 2021, 'The GLEAM 200-MHz local radio luminosity function for AGN and star-forming galaxies', Publications of the Astronomical Society of Australia, vol. 38, p. e041.
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Abstract The GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) is a radio continuum survey at 76–227 MHz of the entire southern sky (Declination $<\!{+}30^{\circ}$ ) with an angular resolution of ${\approx}2$ arcmin. In this paper, we combine GLEAM data with optical spectroscopy from the 6dF Galaxy Survey to construct a sample of 1 590 local (median $z \approx 0.064$ ) radio sources with $S_{200\,\mathrm{MHz}} > 55$ mJy across an area of ${\approx}16\,700\,\mathrm{deg}^{2}$ . From the optical spectra, we identify the dominant physical process responsible for the radio...

Fröch, JE, Spencer, LP, Kianinia, M, Totonjian, DD, Nguyen, M, Gottscholl, A, 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 increasingly important building block for quantum photonic applications. Herein, we demonstrate the efficient coupling of recently discovered spin defects in hBN to purposely designed bullseye cavities. We show that boron vacancy spin defects couple to the monolithic hBN cavity system and exhibit a 6.5-fold enhancement. In addition, by comparative finite-difference time-domain modeling, we shed light on the emission dipole orientation, which has not been experimentally demonstrated at this point. Beyond that, the coupled spin system exhibits an enhanced contrast in optically detected magnetic resonance readout and improved signal-to-noise ratio. Thus, our experimental results, supported by simulations, constitute a first step toward integration of hBN spin defects with photonic resonators for a scalable spin–photon interface.

Froehlich, CYM, Klanten, OS, Hing, ML, Dowton, M & Wong, MYL 2021, 'Uneven declines between corals and cryptobenthic fish symbionts from multiple disturbances', Scientific Reports, vol. 11, no. 1.
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AbstractWith the onset and increasing frequency of multiple disturbances, the recovery potential of critical ecosystem-building species and their mutual symbionts is threatened. Similar effects to both hosts and their symbionts following disturbances have been assumed. However, we report unequal declines between hosts and symbionts throughout multiple climate-driven disturbances in reef-building Acropora corals and cryptobenthic coral-dwelling Gobiodon gobies. Communities were surveyed before and after consecutive cyclones (2014, 2015) and heatwaves (2016, 2017). After cyclones, coral diameter and goby group size (i.e., the number of gobies within each coral) decreased similarly by 28–30%. After heatwave-induced bleaching, coral diameter decreased substantially (47%) and gobies mostly inhabited corals singly. Despite several coral species persisting after bleaching, all goby species declined, leaving 78% of corals uninhabited. These findings suggest that gobies, which are important mutual symbionts for corals, are unable to cope with consecutive disturbances. This disproportionate decline could lead to ecosystem-level disruptions through loss of key symbiont services to corals.

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.

Fu, X, Qiang, Y, Wang, J, Zhao, X, Hwang, F-J & Chen, C-H 2021, 'Urban Public Transport Accessibility to Medical Services From the Perspective of Residents’ Travel: A Hybrid Assessment Based on the Whole Process', IEEE Access, vol. 9, pp. 8977-8989.
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Equitable access to efficient medical services via public transport has always been one of the most important issues of healthcare in urban development. To accurately measure the urban public transport accessibility to medical services (PTAMS), this research proposes a hybrid assessment method based on multiple public-transport related indicators, including time, cost, and walking rate, which considers the whole process of residents’ public transport travel. The presented assessment technique is then applied in a case of Xi’an, China. Through the classification of medical facilities and PTAMS levels, the results show that: (a) PTAMS value of 3,080 residential areas in Xi’an are highly consistent with the standard normal distribution; (b) More than 80% of residential areas can obtain high PTAMS when considering the use of Class 1 (large-scale) hospitals, while the high PTAMS of Class 2 (small-scale) ones can only cover less than 40% residential areas; (c) There is obvious spatial heterogeneity in the distribution of PTAMS in Class 2 hospitals and a serious lack of medical equity; (d) Among large hospitals, the private ones retain higher PTAMS and equitability, making themselves best choice for residents, which is opposed to the government’s purpose of establishing public hospitals; (e) PTAMS of most residents substantially dropped about 4% during the morning peak-hour. However, subway protects PTAMS of nearby residents. This research provides references and suggestions on how to improve residents’ PTAMS under the existing public transport network and medical facilities layout.

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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Background

Results

Conclusions

Gale, A, Froech, J, 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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Ion implantation underpins a vast range of devices and technologies that require precise control over the physical, chemical, electronic, magnetic and optical properties of materials. A variant termed “recoil implantation” – in which a precursor is deposited onto a substrate as a thin film and implanted via momentum transfer from incident energetic ions – has a number of compelling advantages, particularly when performed using an inert ion nano-beam [Fröch et al., Nat. Commun., 2020, 11, 5039]. However, a major drawback of this approach is that the implant species are limited to the constituents of solid thin films. Here we overcome this limitation by demonstrating recoil implantation using gas-phase precursors. Specifically, we fabricate nitrogen-vacancy (NV) color centers in diamond using an Ar+ ion beam and the nitrogen-containing precursor gases N2, NH3 and NF3. Our work expands the applicability of recoil implantation with the potential to be suitable to a larger portion of the periodic table, and to applications in which thin film deposition/removal is impractical.

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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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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Gao, Y-H, Nan, X, Yang, Y, Sun, B, Xu, W-L, Dasilva, WDL, Li, X-K, Li, Y-J & Zhang, Q 2021, 'Non-layered transition metal carbides for energy storage and conversion', New Carbon Materials, vol. 36, no. 4, pp. 751-778.
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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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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.

Gellert, K & Schlögl, E 2021, 'Parameter Learning and Change Detection Using a Particle Filter with Accelerated Adaptation', Risks, vol. 9, no. 12, pp. 228-228.
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This paper presents the construction of a particle filter, which incorporates elements inspired by genetic algorithms, in order to achieve accelerated adaptation of the estimated posterior distribution to changes in model parameters. Specifically, the filter is designed for the situation where the subsequent data in online sequential filtering does not match the model posterior filtered based on data up to a current point in time. The examples considered encompass parameter regime shifts and stochastic volatility. The filter adapts to regime shifts extremely rapidly and delivers a clear heuristic for distinguishing between regime shifts and stochastic volatility, even though the model dynamics assumed by the filter exhibit neither of those features.

Gellert, K & Schlögl, E 2021, 'Short Rate Dynamics: A Fed Funds and SOFR perspective'.

Gellert, K & Schlögl, E 2021, 'Short Rate Dynamics: A Fed Funds and SOFR perspective'.
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The Secured Overnight Funding Rate (SOFR) is becoming the main Risk-Free Rate benchmark in US dollars, thus interest rate term structure models need to be updated to reflect the key features exhibited by the dynamics of SOFR and the forward rates implied by SOFR futures. Historically, interest rate term structure modelling has been based on rates of substantially longer time to maturity than overnight, but with SOFR the overnight rate now is the primary market observable. This means that the empirical idiosyncrasies of the overnight rate cannot be ignored when constructing interest rate models in a SOFR-based world. As a rate reflecting transactions in the Treasury overnight repurchase market, the dynamics of SOFR are closely linked to the dynamics of the Effective Federal Funds Rate (EFFR), which is the interest rate most directly impacted by US monetary policy target rate decisions. Therefore, these rates feature jumps at known times (Federal Open Market Committee meeting dates), and market expectations of these jumps are reflected in prices for futures written on these rates. On the other hand, forward rates implied by Fed Funds and SOFR futures continue to evolve diffusively. The model presented in this paper reflects the key empirical features of SOFR dynamics and is calibrated to futures prices. In particular, the model reconciles diffusive forward rate dynamics with piecewise constant paths of the target short rate.

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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Gilchrist, AM, Wang, P, Carreira-Barral, I, Alonso-Carrillo, D, Wu, X, Quesada, R & Gale, PA 2021, 'Supramolecular methods: the 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS) transport assay', Supramolecular Chemistry, vol. 33, no. 7, pp. 325-344.
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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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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, DVR, 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, DVR, 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. 1-10.
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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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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.
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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.
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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 conservation stra...

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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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, 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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Electrochemical 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). The LRs 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. The LRs calculated using the novel PCA approach are compared with previously reported LRs 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 calibrated LRs 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 of LRs 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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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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Gupta, KD, Nag, AK, Rahman, ML, Mahmud, MAP & Sadman, N 2021, 'Utilizing Computational Complexity to Protect Cryptocurrency Against Quantum Threats: A Review', IT Professional, vol. 23, no. 5, pp. 50-55.
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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 (Basel, Switzerland), 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 of HABs a...

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 additional TnsB binding sites at each end. Tn6171 or minor variants were detected in the equivalent location in complete or draft genomes of several further A. baumannii isolates belonging to GC1 [sequence type (ST) 1, ST81, ST94, ST328, ST623, ST717], GC2 (ST2) and ST10. However, in some of these isolates the surrounding glmS region was clearly derived from a different A. baumannii lineage, indicating that the transposon may have been acquired by replacement of a segment of the chromosome. A recombination-free phylogeny revealed that there were several transposon acquisition events in GC1. The GC1 isolates were mainly lineage 2, but a potential third lineage was also detected. A related transposon, designated Tn6552, was detected in ATCC 17978 (ST437) and other ST437 isolates. However, the Tn6552 tnsD targeting gene was interrupted by an ISAba12, and Tn6552 is not downstream of glmS.

Hamidian, M, Ambrose, SJ, Blackwell, GA, Nigro, SJ & Hall, RM 2021, 'An outbreak of multiply antibiotic-resistant ST49:ST128:KL11:OCL8 Acinetobacter baumannii isolates at a Sydney hospital.', The Journal of antimicrobial chemotherapy, vol. 76, no. 4, pp. 893-900.
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Objectives

Methods

Results

Conclusions

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.

Hansbro, P, Ashcroft, SP, Fletcher, G, Philp, AM, Jenkinson, C, Handelsman, DJ, Das, S, 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.

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.

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.', Mater Sci Eng C Mater Biol Appl, 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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Hasselerharm, CD, Yanco, E, McManus, JS, Smuts, BH & Ramp, D 2021, 'Wildlife-friendly farming recouples grazing regimes to stimulate recovery in semi-arid rangelands', Science of The Total Environment, vol. 788, pp. 147602-147602.
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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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Realization 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 &lt; 7.9, often below 7.6) and O2 concentrations are regularly considered hypoxic (&lt;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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Hem, S, Jarocki, VM, Baker, DJ, Charles, IG, Drigo, B, Aucote, S, Donner, E, Burnard, D, Bauer, MJ, Harris, PNA, Wyrsch, ER & Djordjevic, SP 2021, 'Genomic analysis of Elizabethkingia species from aquatic environments: evidence for potential clinical transmission', Current Research in Microbial Sciences, vol. 3, pp. 100083-100083.
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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. 1-17.
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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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Hocagil, TA, 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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Propensity 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 from the Detroit Longitudinal Cohort Stud...

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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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 & Cooper, P 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.

Hoque, MM, Noorian, P, Espinoza-Vergara, G, Manuneedhi, CP, Kim, M, Rahman, MH, Labbate, M, Rice, SA, Pernice, M, Oehlers, SH & McDougald, D 2021, 'Adaptation to an amoeba host drives selection of virulence-associated traits in Vibrio cholerae.', The ISME journal, vol. 16, no. 3, pp. 1-12.
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Predation by heterotrophic protists drives the emergence of adaptive traits in bacteria, and often these traits lead to altered interactions with hosts and persistence in the environment. Here we studied adaptation of the cholera pathogen, Vibrio cholerae during long-term co-incubation with the protist host, Acanthamoeba castellanii. We determined phenotypic and genotypic changes associated with long-term intra-amoebal host adaptation and how this impacts pathogen survival and fitness. We showed that adaptation to the amoeba host leads to temporal changes in multiple phenotypic traits in V. cholerae that facilitate increased survival and competitive fitness in amoeba. Genome sequencing and mutational analysis revealed that these altered lifestyles were linked to non-synonymous mutations in conserved regions of the flagellar transcriptional regulator, flrA. Additionally, the mutations resulted in enhanced colonisation in zebrafish, establishing a link between adaptation of V. cholerae to amoeba predation and enhanced environmental persistence. Our results show that pressure imposed by amoeba on V. cholerae selects for flrA mutations that serves as a key driver for adaptation. Importantly, this study provides evidence that adaptive traits that evolve in pathogens in response to environmental predatory pressure impact the colonisation of eukaryotic organisms by these pathogens.

Horstmann, M, Gonzalez, DVR, 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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Gd-based contrast agents (GBCAs) are frequently administered to patients for magnetic resonance imaging to enhance tissue contrasts. After examination, they are excreted and enter surface waters via local wastewater treatment plants' effluents where they lead to anthropogenic Gd anomalies in the environment of metropolitan areas with developed healthcare. This work presents the speciation analysis of GBCAs in water samples from Australia by targeting individual GBCAs in effluent, river and seawater samples obtained from New South Wales (Sydney area), the Northern Territory (Alice Springs) and Victoria (Melbourne area). A method based on hydrophilic interaction liquid chromatography (HILIC) coupled to inductively coupled plasma-mass spectrometry (ICP-MS) provided rapid separation and quantification of four common GBCAs in under three minutes. To improve the sensitivity, ion extraction and transport processes were optimised and the quadrupole mass filter was operated with an increased mass bandpass, decreasing limits of detection to between 18 and 24 ng L-1 for individual GBCAs. This allowed detection of Gd-DOTA, Gd-BT-DO3A and Gd-DTPA-BMA at concentrations of up to 160 ng L-1 in water samples collected from rivers within the proximity of effluents of local wastewater treatment plants. The analysis of GBCAs in oceanic sea water required the development of a novel automated micro-solid phase extraction (μSPE) method for matrix elimination and analyte pre-concentration enabling the detection of Gd-DOTA and Gd-BT-DO3A.

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.

Hosseini, F, Lotfalizadeh, H, Rakhshani, E, Norouzi, M, Butterworth, NJ & Dadpour, M 2021, 'Significance of wing interference patterns as taxonomic characters in Aphidiinae (Hymenoptera: Braconidae)', Journal of Zoological Systematics and Evolutionary Research, vol. 59, no. 7, pp. 1481-1490.
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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 were largely driven by survivorship. The initial nursery phase of coral propagation therefore appears useful to supplement coral material naturally available for stewardship of frequently visited Great Barrier Reef tourism (high-value) sites, but further assessment is needed to ev...

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, 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.
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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. 2000134-2000134.
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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 a low micr...

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 quantifyin...

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.', J Phys Chem Lett, 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 Zostera muelleri', 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 that the ...

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 discusses...

Hwang, FJ & Huang, Y-H 2021, 'An effective logarithmic formulation for piecewise linearization requiring no inequality constraint', Computational Optimization and Applications, vol. 79, no. 3, pp. 601-631.
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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 in line with this, injury frameworks, ...

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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Cultural 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 proceeded only when the rate of cultural transmission was below a critical value determined by the relative...

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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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.

Islam, MZ, Hossain, SI, Deplazes, E & Saha, SC 2021, 'The steroid mometasone alters protein containing lung surfactant monolayers in a concentration-dependent manner.', J Mol Graph Model, vol. 111, pp. 108084-108084.
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Mometasone is an investigational anti-inflammatory steroidal drug to treat inflammation via pulmonary administration. For steroid drugs to be effective they need to be adsorbed by lung surfactants, a thin monolayer at the air-water interface in alveoli that reduces surface tension. Information on the molecular-level interactions of the drug with lung surfactants is useful to understand the mechanism of adsorption. In this study, we use coarse-grained molecular dynamics simulation to understand the concentration-dependent effect of mometasone on a lung surfactant monolayer (LSM) composed of lipids and surfactant proteins, under two different breathing conditions (exhalation, at surface tension 0 mNm-1 and inhalation, surface tension 20-25 mNm-1). A series of fixed-APL and fixed-surface tension simulations were used to demonstrate that in the absence of drugs, the model LSM reproduces the surface tensions for the compressed and expanded states, as well as compressibility at different surface tensions. In-depth analysis of simulations of a LSM in the presence of five different drug concentrations shows that mometasone alters the structure and dynamics of the LSM in a concentration-dependent manner. Mometasone induces a collapse in the monolayer that is affected by the surfactant protein and surface tension. Overall, these findings suggest that the surfactant proteins, surface tension and drug concentration are all critical components affecting monolayer stability and drug adsorption. The outcomes of this study may be beneficial for a more in-depth understanding of how mometasone is adsorbed by lung surfactants.

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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Iwasaki, K, Szabó, M, Tamburic, B, Evenhuis, C, Zavafer, A, Kuzhiumparambil, U & Ralph, P 2021, 'Investigating the impact of light quality on macromolecular of', Functional Plant Biology, vol. 49, no. 6, pp. 554-564.
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Diatoms (Bacillariophyceae) are important to primary productivity of aquatic ecosystems. This algal group is also a valuable source of high value compounds that are utilised as aquaculture feed. The productivity of diatoms is strongly driven by light and CO2 availability, and macro- and micronutrient concentrations. The light dependency of biomass productivity and metabolite composition is well researched in diatoms, but information on the impact of light quality, particularly the productivity return on energy invested when using different monochromatic light sources, remains scarce. In this work, the productivity return on energy invested of improving growth rate, photosynthetic activity, and metabolite productivity of the diatom Chaetoceros muelleri under defined wavelengths (blue, red, and green) as well as while light is analysed. By adjusting the different light qualities to equal photosynthetically utilisable radiation, it was found that the growth rate and photosynthetic oxygen evolution was unchanged under white, blue, and green light, but it was lower under red light. Blue light improved the productivity return on energy invested for biomass, total protein, total lipid, total carbohydrate, and in fatty acids production, which would suggest that blue light should be used for aquaculture feed production.

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.', Alcohol Clin Exp Res, vol. 45, no. 10, pp. 2040-2058.
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BACKGROUND: Cognitive 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. METHODS: Meta-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. RESULTS: The 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. CONCLUSIONS: The similarity in the effect sizes for the four domains of cognitive function suggests that PAE affects an underlying component or components of cognition involving learning and memory and executive function that are reflected in IQ and academic achievement scores. The weaker effects in the more middle-class cohort may reflect a more cognitively stimul...

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, GCA, 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.', Nat Immunol, 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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Broadband 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.', Front Microbiol, 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 bla CTX-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-intI1 Δ 648-dfrA17-aadA5-qacEΔ1-sul1-ORF-srpC-padR-IS6100-mphR-mrx-mphA-IS26) identified previously in major extraintestinal pathogenic E. coli STs but not in ETEC. ST182 isolates carried ETEC-specific virulence factors STp + CS6. Adhesin/invasin tia was identified in 89% of aircraft ST182 isolates (vs 23%) and was located on a putative genomic island within a hotspot region for various insertions including PAI I536 and plasmid-associated transposons. The most common plasmid replicons in this collection were IncFII (100%; F2:A-:B-) and IncB/O/K/Z (89%). Our data suggest that potentially through travel, E. coli ST182 are evolving a multidrug-resistant profile through the acquisition of class 1 integrons and different plasmids.

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 of antioxi...

Jerotic, D, Suvakov, S, Alqudah, A, Savic-Radojevic, A, Pljesa-Ercegovac, M, Coric, V, McClements, L, Simic, T & Matic, M 2021, 'The influence of uremic serum and GSTM1 knockdown on redox homeostasis in HUVECs', Free Radical Biology and Medicine, vol. 177, pp. S82-S83.
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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, 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 serum induces redox imbalance accompanied with altered expressi...

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.

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 herein, the design, synthesis and anti-mycobacterial activity of isatin-mono/bis-isoniazid hybrids. Most of the compounds exhibited very high activity against Mycobacterium tuberculosis with minimal inhibitory concentrations in the range of 0.195-0.39 μg/mL and exerted a more potent bactericidal effect than the standard anti-tubercular drug isoniazid (INH). Importantly, these compounds were found to be well tolerated at high doses (>200 μg/mL) on Vero kidney cells, leading to high selectivity indices. Two of the most promising hybrids were evaluated for activity in THP-1 macrophages infected with M. tuberculosis, among which 11e was found to be slightly more effective than INH. Overexpression of InhA along with cross-resistance determination of the most potent compounds, selection of resistant mutants and biochemical analysis allowed us to decipher their mode of action. These compounds effectively inhibited mycolic acid biosynthesis and required KatG to exert their biological effects. Collectively, this suggests that the synthesized isatin-INH hybrids are promising anti-tubercular molecules for further evaluation in pre-clinical settings.

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.
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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, Floris, G, Flyger, H, Gago-Dominguez, M, Gapstur, SM, García-Closas, M, Gaudet, MM, Giles, GG, Goldberg, MS, González-Neira, A, AOCS, G, Nordestgaard, BG, Guénel, P, Hahnen, E, Haiman, CA, Håkansson, N, Hall, P, Hamann, U, Harrington, PA, Hart, SN, Hooning, MJ, Hopper, JL, Obi, N, Howell, A, Hunter, DJ, ABCTB, I, kConFab, I, Jager, A, Jakubowska, A, John, EM, Kaaks, R, Keeman, R, Khusnutdinova, E, Olshan, AF, Kitahara, CM, Kosma, V-M, Koutros, S, Kraft, P, Kristensen, VN, Kurian, AW, Lambrechts, D, Le, ML, Linet, M, Lubiński, J, Olson, JE, Mannermaa, A, Manoukian, S, Margolin, S, Martens, JWM, Mavroudis, D, Mayes, R, Meindl, A, Milne, RL, Neuhausen, SL, Nevanlinna, H, Olsson, H, Newman, WG, Nielsen, SF, Orban, E, Park-Simon, T-W, Peterlongo, P, Plaseska-Karanfilska, D, Pylkäs, K, Ahearn, TU, Rennert, G, Rennert, HS, Ruddy, KJ, Saloustros, E, Sandler, DP, Sawyer, EJ, Schmutzler, RK, Scott, C, Shu, X-O, Simard, J, Andrulis, IL, Smichkoska, S, Sohn, C, Southey, MC, Spinelli, JJ, Stone, J, Tamimi, RM, Taylor, JA, Tollenaar, RAEM, Tomlinson, I, Troester, MA, Anton-Culver, H, Truong, T, Vachon, CM, van, VEM, Wang, SS, Weinberg, CR, Wendt, C, Wildiers, H, Winqvist, R, Wolk, A, Zheng, W, Antonenkova, NN, Ziogas, A, Dunning, AM, Pharoah, PDP, Easton, DF, Howie, AF, Peto, J, Dos-Santos-Silva, I, Swerdlow, AJ, Chang-Claude, J, Schmidt, MK, Arndt, V, Orr, N, Fletcher, O, 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, NBCS, C, Conroy, DM, Couch, FJ, Cox, A, Cross, SS, Czene, K, Dörk, T, Eliassen, AH, Engel, C, Evans, DG, Fasching, PA & Figueroa, J 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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Background

Methods

Results

Conclusions

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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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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The 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 trophic cascades can be strongly influenced by behavioral as well as numerical responses.

Jolly, CJ, Von, TB & Webb, JK 2021, 'Slow life history leaves endangered snake vulnerable to illegal collecting.', Sci Rep, vol. 11, no. 1, p. 5380.
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Global 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.

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 Sympathicotonia and Va...

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 Sci Int, 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.

Kar, R, Jha, SK, Ojha, S, Sharma, A, Dholpuria, S, Raju, VSR, Prasher, P, Chellappan, DK, Gupta, G, Singh, S, Paudel, KR, Hansbro, PM, 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 analyze these m...

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, BS, 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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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.

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 pattern of ...

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, HJ, Wang, K, Chen, C, Lin, Y, Tam, PPL, Lin, DM, Yang, JYH & Yang, P 2021, 'Uncovering cell identity through differential stability with Cepo', Nature Computational Science, vol. 1, no. 12, pp. 784-790.
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Kim, RY, Oliver, BG, Wark, PAB, Hansbro, PM & Donovan, C 2021, 'COPD exacerbations: targeting IL-33 as a new therapy.', Lancet Respir Med, vol. 9, no. 11, pp. 1213-1214.
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Kim, RY, Sunkara, KP, Bracke, KR, Jarnicki, AG, Donovan, C, Hsu, AC, Ieni, A, Beckett, EL, Galvão, I, Wijnant, S, Ricciardolo, FL, Di, SA, 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.', Sci Transl Med, vol. 13, no. 621, p. eaav7223.
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[Figure: see text].

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 results suggest that Vibrio species are shared among different pearl oyster tissues. In particular, the similarity between the haemolymph, inside shell and solid tissues, sug...

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.

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 geographical regions are needed to draw a more accurate population structure of this globally distributed clone.

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 (Switzerland), 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 spatio-temporal 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 precipi-tation. 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 & Kumar, S 2021, 'Hydrological Analysis Using Observed and Satellite-Based Estimates: Case Study of a Lake Catchment in Raipur, India', Journal of the Indian Society of Remote Sensing, vol. 50, no. 1, pp. 115-128.
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Rainfall plays an essential role in different water management sectors ranging from industries, farming, livestock, and domestic utilization both in rural and urban areas. The surface water bodies like rivers, lakes, ponds, and reservoirs hold a huge proportion of the rainfall. However, due to spatio-temporal variability of rainfall and limited availability of meteorological stations, accurate estimation of the hydrological components such as surface runoff, evaporation, and baseflow is a challenging task. In this study, we have used hydrological information, Soil Conservation Service Curve Number method to develop an empirical relationship between rainfall and runoff in the Telibandha Lake Catchment (TLC), situated in Raipur district of Chhattisgarh, central India. Further, we have used Landsat derived remote sensing product, Normalized Difference Water Index (NDWI) to understand its temporal variation of water spread in the TLC over the fifteen years (2001–2015). The water spread areas are assessed by using the mean monthly NDWI data set and analyzing its seasonal and annual patterns. It is found that Telibandha Lake has a maximum depth of 2.9 m and its surface area is 0.12 km2. Apart from that, the annual runoff is around 232.28 mm, which accounts for almost 22% of the estimated rainfall. The monthly runoff coefficient varies from 0 to 0.25 in TLC. Both the temporal and spatial NDWI plots show that July–September months have high NDWI values in the TLC. The seasonal NDWI showed a good relationship with mean monthly rainfall data and depicts r2 = 0.78. The findings from this study helps in determining the temporal changes of water spread within the TLC and supports in understanding the lake characteristics.

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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Lachs, L, Sommer, B, Cant, J, Hodge, JM, Malcolm, HA, Pandolfi, JM & Beger, M 2021, 'Linking population size structure, heat stress and bleaching responses in a subtropical endemic coral', Coral Reefs, vol. 40, no. 3, pp. 777-790.
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AbstractAnthropocene coral reefs are faced with increasingly severe marine heatwaves and mass coral bleaching mortality events. The ensuing demographic changes to coral assemblages can have long-term impacts on reef community organisation. Thus, understanding the dynamics of subtropical scleractinian coral populations is essential to predict their recovery or extinction post-disturbance. Here we present a 10-yr demographic assessment of a subtropical endemic coral, Pocillopora aliciae (Schmidt-Roach et al. in Zootaxa 3626:576–582, 2013) from the Solitary Islands Marine Park, eastern Australia, paired with long-term temperature records. These coral populations are regularly affected by storms, undergo seasonal thermal variability, and are increasingly impacted by severe marine heatwaves. We examined the demographic processes governing the persistence of these populations using inference from size-frequency distributions based on log-transformed planar area measurements of 7196 coral colonies. Specifically, the size-frequency distribution mean, coefficient of variation, skewness, kurtosis, and coral density were applied to describe population dynamics. Generalised Linear Mixed Effects Models were used to determine temporal trends and test demographic responses to heat stress. Temporal variation in size-frequency distributions revealed various population processes, from recruitment pulses and cohort growth, to bleaching impacts and temperature dependencies. Sporadic recruitment pulses likely support population persistence, illustrated in 2010 by strong positively skewed size-frequency distributions and the highest density of juvenile corals measured during the study. Increasing mean colony size over the following 6 yr indicates further cohort growth of these recruits. Severe heat stress in 2016 resulted in mass bleaching mortality and a 51% decline in coral density. Moderate heat stress in the following yea...

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 Mycobacterium t...

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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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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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.ConclusionGestational hyd...

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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Background Maternal 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. Methods C57BL/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. Results In 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 G...

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, N

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: a journal dedicated to nanoscience and nanotechnology, 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, Wen, S, Kong, M, Liu, Y, Hu, W, Shi, B, Shi, X & Jin, D 2021, 'Correction to Highly Doped Upconversion Nanoparticles for In Vivo Applications Under Mild Excitation Power', Analytical Chemistry, vol. 93, no. 32, pp. 11346-11346.
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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.', Microb Genom, 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 clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron-integrase intI1, 128 (45 %) isolates harboured a truncated intI1 (462-1014 bp), highlighting the ongoing evolution of this element. The module intI1-dfrA17-aadA5-qacEΔ1-sul1-ORF-chrA-padR-IS1600-mphR-mrx-mphA, conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically bla CTX-M-15 and bla CTX-M-27. Notably, dual parC-1aAB and gyrA-1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. The results of this study indicate ...

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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Li, H, Wu, Z, Yang, Z, Zhanghao, K, Xi, P & Jin, D 2021, 'Axially overlapped multi-focus light sheet with enlarged field of view', Applied Physics Letters, vol. 118, no. 22, pp. 223701-223701.
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Light sheet fluorescence microscopy provides optical sectioning and is widely used in volumetric imaging of large specimens. However, the axial resolution and the lateral Field of View (FoV) of the system, defined by the light sheet, typically limit each other due to the spatial band product of the excitation objective. Here, we develop a simple multi-focus scheme to extend the FoV, where a Gaussian light sheet can be focused at three or more consecutive positions. Axially overlapped multiple light sheets significantly enlarge the FoV with improved uniformity and negligible loss in axial resolution. By measuring the point spread function of fluorescent beads, we demonstrated that the obtained light sheet has a FoV of 450 μm and a maximum axial FWHM of 7.5 μm. Compared with the conventional single-focus one, the multi-focus Gaussian light sheet displays a significantly improved optical sectioning ability over the full FoV when imaging cells and zebrafish.

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, and decr...

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 electrodeviaphysiochemical 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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Lithium-sulfur batteries (LSBs) have shown great potential for application in high-density energy storage systems. However, the performance of LSBs is severely hindered by the shuttle effect and the sluggish reaction kinetics of lithium polysulfides (LiPSs). Here, a Janus Fe3C/N-CNF@RGO electrode consisting of a 1D Fe3C-decorated N-doped carbon nanofibers (Fe3C/N-CNFs) side and a 2D reduced graphene oxide (RGO) side was applied as a free-standing carrier for the Li2S6catholyte to improve the overall electrochemical performance of LSBs. The Fe3C/N-CNF layer endows the cathode with strong chemisorption abilities for LiPSs and accelerated the redox kineticsviacatalyzing the conversion of LiPSs. The 2D RGO sheets serve as a microscopic physical barrier and further resist the shuttling of LiPSs. Like a hunter's trap, behind the trap lies a net. Moreover, the 3D hierarchical conductive network based on 1D N-CNF and 2D RGO sheets enables fast electron transfer. Based on the synergetic effects of chemical immobilization, catalytic abilities, and a physical barrier in a 3D conductive network, LSBs with optimal Fe3C/N-CNF@RGO electrodes exhibit robust long-term cycling stability (a decay rate of only 0.0089% per cycle at 0.5C for 300 cycles), superior rate capabilities (821.7 mA h g−1at 2.0C), and stable cycling performance at high sulfur loading (6.29 mg cm−2). This work defines an emerging viewpoint relating to the design of novel sulfur carriers with multiple synergistic effects for application in LSBs.

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. 2101090-2101090.
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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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Density 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 G₀ W₀ 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, 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. 1-9.
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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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Aqueous 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 Lett, 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.', 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.

Liepa, R, Mann, R, Osman, M, Hamze, M, Gunawan, C & Hamidian, M 2021, 'Cl415, a carbapenem-resistant Acinetobacter baumannii isolate containing four AbaR4 and a new variant of AbGRI2, represents a novel global clone 2 strain.', The Journal of antimicrobial chemotherapy, vol. 77, no. 2, pp. 345-350.
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Objectives

Methods

Results

Conclusions

Lin, C, Wang, K & Mueller, S 2021, 'MCVIS: A New Framework for Collinearity Discovery, Diagnostic, and Visualization', Journal of Computational and Graphical Statistics, vol. 30, no. 1, pp. 125-132.
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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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Liu, B, Zhang, F & Hwang, F-J 2021, 'Comfort Value of Water: Natural-artificial Dual-structured Analytical Framework for Comfort Assessment of Regional Water Environment and Landscape System', Water Resources Management, vol. 35, no. 14, pp. 4747-4768.
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Liu, CMC, 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, 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 NaREF4Upconversion 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 and Therapeutics, vol. 225, pp. 1-34.
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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, 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_25–75%), 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> &#x3c; 0.05), and Spearman partial correlation found FEF_25–75% significantly related to IFN-γ and interleukin-8 (both having <i>p</i> &#x3c; 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 bronchocons...

Liu, Y, Zhou, Z, Wang, F, Kewes, G, Wen, S, Burger, S, Ebrahimi, WM, 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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Sub-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, 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.

Lu, Z, Van, EHP, Liu, G, Nair, PM, Jones, B, Gillis, CM, Nalkurthi, BC, Verhamme, F, Buyle-Huybrecht, T, Vandenabeele, P, Vanden, BT, 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.', Am J Respir Crit Care Med, 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 element in all domains of life. Nonetheless, how prokaryotes achieve selective acquisition of zinc from the extracellular environment remains poorly understood. Here, we elucidate a novel mechanism for zinc-binding in AdcA, a solute-binding protein of Streptococcus pneumoniae. Crystal structure analyses reveal the two-domain organization of the protein and show that only the N-terminal domain (AdcAN) is necessary for zinc import. Zinc binding induces only minor changes in the global protein conformation of AdcA and stabilizes a highly mobile loop within the AdcAN domain. This loop region, which is conserved in zinc-specific solute-binding proteins, facilitates closure of the AdcAN binding site and is crucial for zinc acquisition. Collectively, these findings elucidate the structural and functional basis of selective zinc uptake in prokaryotes.IMPORTANCE 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. We report the first structure of a two-domain lipoprotein, AdcA from S. pneumoniae, and use computational, spectroscopic, and microbiological approaches to provide new insights into the functional basis of zinc recruitment. Our findings reveal that AdcA employs a novel mechanism for zinc binding that we have termed the “trap-door” mechanism, and we show how the static metal-binding site of the protein, which confers its selectivity for zinc ions, is combined with a dynamic surface element to facilitate zinc recruitment and import into the bacterium. Together, these findings expand our understanding of how bacteria acquire zinc from the environment and provide a foundation for inhibiting this process, through antimicrobial targeting of the dynamic structural elements to block ...

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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The 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.', Front Cell Infect Microbiol, 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 separating classical from non-classical bordetellae. This study provides the first insight into the phosphoproteome of classical Bordetella species and the role that Ser/Thr/Tyr phosphorylation may play in Bordetella biology and virulence.

Ma, H, Li, J, Yang, J, Wang, N, Liu, Z, Wang, T, Su, D, Wang, C & Wang, G 2021, 'Bismuth Nanoparticles Anchored on Ti₃C₂T_x 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, H, Wang, T, Li, J, Yang, J, Liu, Z, Wang, N, Su, D & Wang, C 2021, 'Nitrogen Doped Carbon Coated Bi Microspheres as High‐performance Anode for Half and Full Sodium Ion Batteries', Chemistry – An Asian Journal, vol. 16, no. 16, pp. 2314-2320.
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AbstractAs two‐dimensional (2D) materials, bismuth (Bi) has large interlayer spacing along c‐axis (0.395 nm) which provides rich active sites for sodium ions, thus guaranteeing high sodium ion storage activity. However, its poor electrical conductivity, combined with its degraded cycling performance, restricts its practical application. Herein, Bi microsphere coated with nitrogen‐doped carbon (Bi@NC) was synthesized. Owing to the unique Bi crystals and nitrogen‐doped carbon layer, the obtained Bi@NC anode exhibited satisfactory cycling stability and superior rate capability. Moreover, after assembling Bi@NC anode with Na3V2(PO4)3@C cathode to full battery, excellent sodium storage performance was obtained (57 mA h g−1 after 2000 cycles at 1.0 A g−1).

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. 1-44.
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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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Macdonald, PS, Gorrie, N, Brennan, X, Aili, SR, De, SR, 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.', 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, MSM, Zhang, L, Shimoni, O, Stenzel, M, Zhou, J, Fazekas, DSGB & 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 and New Zealand Journal of Statistics, vol. 63, no. 3, pp. 517-541.
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Message 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. 1-8.
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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, 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...

Mahony, EK, Allison, JR, Sadler, EM, Ellison, SL, Mao, SA, Morganti, R, Moss, VA, Seta, A, Tadhunter, CN, Weng, S, Whiting, MT, Yoon, H, Bell, M, Bunton, JD, Harvey-Smith, L, Kimball, A, Koribalski, BS & Voronkov, MA 2021, 'H i absorption at z ∼ 0.7 against the lobe of the powerful radio galaxy PKS 0409−75', Monthly Notices of the Royal Astronomical Society, vol. 509, no. 2, pp. 1690-1702.
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ABSTRACT We present results from a search for the H i 21-cm line in absorption towards 16 bright radio sources with the six-antenna commissioning array of the Australian Square Kilometre Array Pathfinder. Our targets were selected from the 2-Jy sample, a flux-limited survey of the southern radio sky with extensive multiwavelength follow-up. Two sources were detected in H i absorption including a new detection towards the bright Fanaroff–Riley Type II radio galaxy PKS 0409−75 at a redshift of $z$ = 0.674. The H i absorption line is blueshifted by ∼3300 km s−1 compared to the optical redshift of the host galaxy of PKS 0409−75 at $z$ = 0.693. Deep optical imaging and spectroscopic follow-up with the GMOS instrument on the Gemini-South telescope reveal that the H i absorption is associated with a galaxy in front of the southern radio lobe with a stellar mass of 3.2–6.8 × 1011 M⊙, a star formation rate of ∼1.24 M⊙ yr−1, and an estimated H i column density of 2.16 × 1021 cm−2, assuming a spin temperature of Tspin = 500 K and source covering factor of Cf = 0.3. Using polarization measurements of PKS 0409−75 from the literature, we estimate the magnetic field of the absorbing galaxy to be ∼14.5 $\mu$G, consistent with field strengths observed in nearby spiral galaxies but larger than expected for an elliptical galaxy. Results from this pilot study can inform future surveys as new wide-field telescopes allow us to search for 21-cm H i absorption towards all bright radio sources as opposed to smaller targeted samples.

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.
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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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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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AbstractCorals 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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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 of bacter...

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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Background

Results

Conclusion

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.

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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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 (Basel, Switzerland), 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.

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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The 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.

McDonagh, AM, Tkacheva, A, Sun, B, Zhang, J & Wang, G 2021, 'Nitronyl nitroxide-based redox mediators for Li-O2 batteries', The Journal of Physical Chemistry C: Energy Conversion and Storage, Optical and Electronic Devices, Interfaces, Nanomaterials, and Hard Matter, 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.

McDonald, A, Murray, B, Krix, D & Murray, M 2021, 'Complex soil contamination severely impacts seed-sown crop viability in Australia', Australasian Journal of Crop Science, vol. 15, no. 4, pp. 531-537.
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Food security is a critical issue for many global communities. Heavy metal contaminationin soilspresenta majorand ongoingecologicalriskassociated with human activitieswhich may impactthe viability and safety ofseed-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 vegetablecropspecies to copper, zinc, andleadcontaminationat levels likely to be foundin contaminated regions inAustralia. We compared the germination attributes of days to first germination, germination period, and total proportion of seeds germinated underconcentrationlimitsof heavy metals detectedat degraded sites andcurrentAustralianNational Environment Protection Measure thresholds for domestic soils (i.e., copper 6,000 mgkg-1, zinc 4,700 mgkg-1, lead 300 mgkg-1). Thecombined 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-contaminatedconditions. Seed viability was significantly decreasedin mulberry (M.alba var.tatarica, M. nigra, and M. rubra) andlettuce(L. sativa),with loweredseed germination in all metalscomparedtocarrot(D. carota),radish(R. sativus), tomato(S. lycopersicum) andcommon bean(P. vulgaris). These results indicate heavy metal contamination is a notable risk to seed-sown crop species, with multi-metal contaminationeventslikely to be severely damagingto 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. 1-20.
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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

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.', J Food Biochem, 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. 0, no. 0, 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.

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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At 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.', Anal Bioanal Chem, 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.

Messer, LF, Brown, MV, Van, RPD, 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. 1-32.
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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 Pseudomonas stutzeri, and Cluster 3 sulfate-reducing deltaproteobacteria. Diazotroph community composition was significantly influenced by salinity and SiO4 concentrations, reflecting the transition from UCYN-A-dominated assemblages in the continental shelf waters, to Cluster 3-dominated assemblages in the hypersaline waters of the inverse estuary. Diverse, transitional diazotrophic communities, comprised of a mixture of ...

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.

Mitchell, A, Booth, DJ & Nagelkerken, I 2021, 'Ocean warming and acidification degrade shoaling performance and lateralization of novel tropical-temperate fish shoals.', Glob Chang Biol, vol. 28, no. 4, pp. 1388-1401.
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Gregarious behaviours are common in animals and provide various benefits such as food acquisition and protection against predators. Many gregarious tropical species are shifting poleward under current ocean warming, creating novel species and social interactions with local temperate taxa. However, how the dynamics of these novel shoals might be altered by future ocean warming and acidification remains untested. Here we evaluate how novel species interactions, ocean acidification and warming affect shoaling dynamics, motor lateralization and boldness of range-extending tropical and co-shoaling temperate fishes under controlled laboratory conditions. Fishes were exposed to 1 of 12 treatments (combinations of three temperature levels, two pCO2  levels and two shoal type levels: mixed species or temperate only) for 38 days. Lateralization (a measure of asymmetric expression of cognitive function in group coordination and predator escape) of tropical and temperate species was right-side biased under present-day conditions, but side bias significantly diminished in tropical and temperate fishes under ocean acidification. Ocean acidification also decreased shoal cohesion irrespective of shoaling type, with mixed-species shoals showing significantly lower cohesion than temperate-only shoals irrespective of climate stressors. Tropical fish became bolder under ocean acidification (after 4 weeks), and temperate fish became bolder with increasing temperature, while ocean acidification dampened temperate fish boldness. Our findings highlight the direct effect of climate stressors on fish behaviour and the interplay with the indirect effects of novel species interactions. Because strong shoal cohesion and lateralization are key determinants of species fitness, their degradation under ocean warming and acidification could adversely affect species performance in novel assemblages in a future ocean, and might slow down tropical species range extensions.

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, including novel RNA viruses, and paves the way for a greater understanding of the complex relationships among the constituents of the pulmonary infectome.

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 Rep, 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.

Mizerek, TL, Madin, JS, Benzoni, F, Huang, D, Luiz, OJ, Mera, H, Schmidt-Roach, S, Smith, SDA, Sommer, B & Baird, AH 2021, 'No evidence for tropicalization of coral assemblages in a subtropical climate change hot spot', Coral Reefs, vol. 40, no. 5, pp. 1451-1461.
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Climate change is causing the distribution and abundance of many organisms to change. In particular, organisms typical of the tropics are increasing in abundance in many subtropical regions, a process known as tropicalization. Here, we examine changes in coral abundance and assemblage structure in the Solitary Islands Marine Park (SIMP), over a 23-year period between 1990 and 2013–14. Total coral cover decreased at all six islands sampled with a concomitant decline in total coral cover at the regional scale (i.e. between sampling occasions). When coral taxa were classified as either cosmopolitan or subtropical, cosmopolitan corals decreased in cover at the regional scale. In contrast, subtropical coral cover did not change at the regional scale because large increases in cover at some islands, such as North Solitary Island, were matched by decreases at other islands. Of 16 common coral taxa examined at the regional level, one declined and two increased in cover with no change in the remaining 13 taxa. In particular, there was no increase in the abundance of coral taxa typically associated with tropical reefs. Similarly, multivariate analyses of coral assemblage structure using these 16 common taxa indicated changes in two of the six island assemblages but, again, provided no evidence for tropicalization. Modelling suggested very low probabilities of larval dispersal from the southern Great Barrier Reef to the SIMP suggesting that limited connectivity with tropical coral populations is one possible cause of the lack of tropicalization in the coral assemblages. We therefore conclude that, despite significant increases in mean sea surface temperature over the last few decades, there has been no tropicalization of the coral fauna in the SIMP. Furthermore, the small proportional reduction in total coral cover, despite the occasional incidence of coral bleaching, coral disease outbreaks and a number of large storms, suggest that the reefs of the SIMP were in ...

Mohamed, A, 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, '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 the widesp...

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 conclusio...

Montgomery, E, Newton, PJ, Chang, S, Peng, W, Jha, SR, Wilhelm, K, Macdonald, PS & Malouf, M 2021, 'Frailty Measures in Patients Listed for Lung Transplantation.', Transplantation, vol. Publish Ahead of Print, no. 5, pp. 1084-1092.
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Morris, S, Wright, K, Malyla, V, Britton, WJ, Hansbro, PM, Cholan, PM & 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, RD, Alsadat, RM, Razavi, BS, Kashaninejad, N, Jin, D & Ebrahimi, WM 2021, 'A Comprehensive Review on Intracellular Delivery.', Advanced materials (Deerfield Beach, Fla.), vol. 33, no. 13, pp. e2005363-2005363.
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Intracellular 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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Murphy, T, Kaplan, DL, Stewart, AJ, O'Brien, A, Lenc, E, Pintaldi, S, Pritchard, J, Dobie, D, Fox, A, Leung, JK, An, T, Bell, ME, Broderick, JW, Chatterjee, S, Dai, S, D'Antonio, D, Doyle, G, Gaensler, BM, Heald, G, Horesh, A, Jones, ML, McConnell, D, Moss, VA, Raja, W, Ramsay, G, Ryder, S, Sadler, EM, Sivakoff, GR, Wang, Y, Wang, Z, Wheatland, MS, Whiting, M, Allison, JR, Anderson, CS, Ball, L, Bannister, K, Bock, DCJ, Bolton, R, Bunton, JD, Chekkala, R, Chippendale, AP, Cooray, FR, Gupta, N, Hayman, DB, Jeganathan, K, Koribalski, B, Lee-Waddell, K, Mahony, EK, Marvil, J, McClure-Griffiths, NM, Mirtschin, P, Ng, A, Pearce, S, Phillips, C & Voronkov, MA 2021, 'The ASKAP Variables and Slow Transients (VAST) Pilot Survey', Publications of the Astronomical Society of Australia, vol. 38.
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The Variables and Slow Transients Survey (VAST) on the Australian Square Kilometre Array Pathfinder (ASKAP) is designed to detect highly variable and transient radio sources on timescales from 5 s to ~5 yr. In this paper, we present the survey description, observation strategy and initial results from the VAST Phase I Pilot Survey. This pilot survey consists of ~162 h of observations conducted at a central frequency of 888 MHz between 2019 August and 2020 August, with a typical rms sensitivity of 0.24 mJy beam-1 and angular resolution of 12 -20 arcseconds. There are 113 fields, each of which was observed for 12 min integration time, with between 5 and 13 repeats, with cadences between 1 day and 8 months. The total area of the pilot survey footprint is 5 131 square degrees, covering six distinct regions of the sky. An initial search of two of these regions, totalling 1 646 square degrees, revealed 28 highly variable and/or transient sources. Seven of these are known pulsars, including the millisecond pulsar J2039-5617. Another seven are stars, four of which have no previously reported radio detection (SCR J0533-4257, LEHPM 2-783, UCAC3 89-412162 and 2MASS J22414436-6119311). Of the remaining 14 sources, two are active galactic nuclei, six are associated with galaxies and the other six have nomulti-wavelength counterparts and are yet to be identified.

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, Triglia, ET, 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, NHLBI, LC & Human, CALBN 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.

Naidu, V, Shah, B, Kamath, KS, Chien, A, Nagy, S, Pokhrel, A, Molloy, M, Hassan, KA & Paulsen, IT 2021, 'Identification of a Novel Ciprofloxacin Tolerance Gene, aciT , Which Contributes to Filamentation in Acinetobacter baumannii', Antimicrobial Agents and Chemotherapy, vol. 65, no. 6.
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Fluoroquinolones are one of the most prescribed broad-spectrum antibiotics. However, their effectiveness is being compromised by high rates of resistance in clinically important organisms, including Acinetobacter baumannii .

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 Microbiol, vol. 21, no. 1, p. 255.
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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 increased. Furthermore, only the RSCV showed increased c-di-GMP, while wild type and SCV were no different from the parental strain. CONCLUSIONS: This suggests that while starvation can induce dispersal from the biofilm, it also results in strong selection for mutants that overproduce c-di-GMP and that fail to disperse in response to the dispersal cue, starvation.

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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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 cholera pathogen, in which non-O1 non-O139 variant strains overproducing AI-2 presumably contribute in resuscitation of the latent pathogen, leading to seasonal cholera epidemics. Importance. Toxigenic Vibrio cholerae which causes seasonal epidemics of cholera persists in aquatic reservoirs in endemic areas. The bacteria mostly exist in a dormant state during inter-epidemic periods, but periodically resuscitate to ...

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, 'COL4A3 expression 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 of ZNF263 silencing, using small interfering RNA, on the COL4A3 expression were studied using qPCR.ResultsCOL4A3 expression was significantly reduced in bronchial biopsies compared to healthy controls, whereas DNA methylation levels at cg11797365 were increased. COL4A3 expression 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 cg11797365 in vitro were increased upon consecutive rhinovirus infections.ConclusionOur data indicate an epigenetic modification as a contributing factor for the loss of COL4A3 expression 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.', The 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, 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, HP, Fu, Q, Abu, HJM, Ibrahim, I, Mofijur, M, Labeeuw, L, Pernice, M, Ralph, PJ & Nghiem, LD 2021, 'Synthesis and evaluation of cationic polyacrylamide and polyacrylate flocculants for harvesting freshwater and marine microalgae', Chemical Engineering Journal, vol. 433, pp. 133623-133623.
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This study addresses the challenge of microalgae harvesting through the development of flocculants. Two positively charged cationic polymers including poly[2 (acryloyloxy)ethyl]trimethylammonium chloride (PAETAC) and poly(3 acrylamidopropyl)trimethylammonium chloride (PAmPTAC) were synthesized using the UV-induced radical polymerization, for harvesting both freshwater and marine microalgae. The results show that the synthesized polymers have excellent flocculation performance for both freshwater green microalgae (Chlorella vulgaris) and marine red microalgae (Porphyridium purpureum). PAETAC outperformed PAmPTAC for both Chlorella vulgaris and Porphyridium purpureum microalgae. The optimal PAETAC doses for Chlorella vulgaris and Porphyridium purpureum microalgae were 50 and 4.8 mg/g of dry biomass while the optimal PAmPTAC doses were 252 and 35 mg/g of dry biomass respectively. Additionally, the floc formation with the PAETAC was more stable than PAmPTAC, which supported the dewatering step via sieving. The superior performance can be attributed to the higher molecular weight of the PAETAC polymer when compared to the PAmPTAC polymer. In comparison to commercially available polydiallyldimethylammonium chloride (PolyDADMAC), the newly synthesised PAETAC and PAmPTAC polymers demonstrated superior flocculation efficiency at a lower dose. The findings of this study established a platform technology for designing and synthesising cationic flocculants for use in microalgae harvesting.

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. 021103-021103.
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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 (Amsterdam, Netherlands), vol. 541, pp. Not-Available.
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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, 'Noise and pulse dynamics in backward stimulated Brillouin scattering.', Optics express, vol. 29, no. 3, pp. 3132-3146.
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We theoretically and numerically study the effects of thermal noise on pulses in backwards stimulated Brillouin scattering (SBS). Using a combination of stochastic calculus and numerical methods, we derive a theoretical model that can be used to quantitatively predict noise measurements. We study how the optical pulse configuration, including the input powers of the pump and Stokes fields, pulse durations and interaction time, affects the noise in the output Stokes field. We investigate the effects on the noise of the optical loss and waveguide length, and we find that the signal-to-noise ratio can be significantly improved, or reduced, for specific combinations of waveguide properties and pulse parameters.

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: Optical Physics, vol. 38, no. 8, pp. 2343-2352.
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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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Diamond 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.

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.
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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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O'Farrell, HE, Brown, R, Brown, Z, Milijevic, B, Ristovski, ZD, Bowman, RV, Fong, KM, Vaughan, A & Yang, IA 2021, 'E-cigarettes induce toxicity comparable to tobacco cigarettes in airway epithelium from patients with COPD.', Toxicol In Vitro, vol. 75, pp. 105204-105204.
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BACKGROUND: The health effects of e-cigarettes in patients with pre-existing lung disease are unknown. The aim of this study was to investigate whether aerosols from a fourth-generation e-cigarette produces similar in-vitro cytotoxic, DNA damage and inflammatory effects on bronchial epithelial cells (BECs) from patients with COPD, as cigarette smoke. METHODS: BECs from patients with COPD who underwent surgery for lung cancer and comparator (immortalised 16HBE) cells were grown at air liquid interface (ALI). BECs were exposed to aerosols from a JUUL® e-cigarette (Virginia Tobacco and Menthol pods at 5% nicotine strength) or reference 3R4F cigarette for 30 min at ALI. Cell cytotoxicity, DNA damage and inflammation were measured. RESULTS: In response to the Virginia Tobacco and Menthol flavoured e-cigarette aerosols, COPD BECs showed comparable LDH release (cell cytotoxicity, p = 0.59, p = 0.67 respectively), DNA damage (p = 0.41, p = 0.51) and inflammation (IL-8, p = 0.20, p = 0.89 and IL-6, p = 0.24, p = 0.93), to cigarette smoke. 16HBE cells also showed comparable cellular responses to cigarette smoke. CONCLUSION: In airway cells from patients with COPD, aerosols from a fourth-generation e-cigarette were associated with similar toxicity to cigarette smoke. These results have potential implications for the safety of e-cigarette use in patients with lung disease.

Olander, A, Lawson, CA, Possell, M, Raina, JB, 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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Oliver, T, Sánchez-Baracaldo, P, Larkum, AW, Rutherford, AW & Cardona, T 2021, 'Time-resolved comparative molecular evolution of oxygenic photosynthesis', Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol. 1862, no. 6, p. 2020.02.28.969766.
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AbstractOxygenic photosynthesis starts with the oxidation of water to O2, a light-driven reaction catalysed by photosystem II. Cyanobacteria are the only prokaryotes capable of water oxidation and therefore, it is assumed that relative to the origin of life and bioenergetics, the origin of oxygenic photosynthesis is a late innovation. However, when exactly water oxidation originated remains an unanswered question. Here we use relaxed molecular clocks to compare one of the two ancestral core duplications that are unique to water-oxidizing photosystem II, that leading to CP43 and CP47, with some of the oldest well-described events in the history of life. Namely, the duplication leading to the Alpha and Beta subunits of the catalytic head of ATP synthase, and the divergence of archaeal and bacterial RNA polymerases and ribosomes. We also compare it with more recent events such as the duplication of cyanobacteria-specific FtsH metalloprotease subunits, of CP43 variants used in a variety of photoacclimation responses, and the speciation events leading to Margulisbacteria, Sericytochromatia, Vampirovibrionia, and other clades containing anoxygenic phototrophs. We demonstrate that the ancestral core duplication of photosystem II exhibits patterns in the rates of protein evolution through geological time that are nearly identical to those of the ATP synthase, RNA polymerase, or the ribosome. Furthermore, we use ancestral sequence reconstruction in combination with comparative structural biology of photosystem subunits, to provide additional evidence supporting the premise that water oxidation had originated before the ancestral core duplications. Our work suggests that photosynthetic water oxidation originated closer to the origin of life and bioenergetics than can be documented based on species trees alone.

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: the ACS journal of surfaces and colloids, 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.

O'Rourke, MB, Sahni, S, Samra, J, Mittal, A & Molloy, MP 2021, 'Data independent acquisition of plasma biomarkers of response to neoadjuvant chemotherapy in pancreatic ductal adenocarcinoma', Journal of Proteomics, vol. 231, pp. 103998-103998.
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Pacheco, AG, Holt, SA & He, L 2021, 'Uranyl-Binding Proteins on Silica Nanoparticles for Repeatable Capture of Uranyl Ions', ACS Applied Nano Material, 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.', Antioxid Redox Signal, 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. 1-9.
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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. vaigiensis displayed 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. vaigiensis showed no preference for larger mixed‐species shoals over smaller single‐species shoals. These outcomes are discussed within the context of climate change‐driven redistribution of A. vaigiensis in 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. 1-16.
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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. 1-19.
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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, JS, 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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Plasma 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.

Papanicolaou, M, He, P, Rutting, S, Ammit, A, Xenaki, D, van, RD & 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.', The Journal of experimental biology, vol. 224, no. 12, p. jeb.239269.
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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, Nicolini, G & et al. 2021, 'Author Correction: The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data', Scientific Data, vol. 8, no. 1.
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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, 'Author Correction: Triple SILAC identified progestin-independent and dependent PRA and PRB interacting partners in breast cancer', Scientific Data, vol. 8, no. 1.
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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.
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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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Tumours are abnormal growths of cells that reproduce by redirecting essential nutrients and resources from surrounding tissue. Changes to cell metabolism that trigger the growth of tumours are reflected in subtle differences between the chemical composition of healthy and malignant cells. We used LA-ICP-MS imaging to investigate whether these chemical differences can be used to spatially identify tumours and support detection of primary colorectal tumours in anatomical pathology. First, we generated quantitative LA-ICP-MS images of three colorectal surgical resections with case-matched normal intestinal wall tissue and used this data in a Monte Carlo optimisation experiment to develop an algorithm that can classify pixels as tumour positive or negative. Blinded testing and interrogation of LA-ICP-MS images with micrographs of haematoxylin and eosin stained and Ki67 immunolabelled sections revealed Monte Carlo optimisation accurately identified primary tumour cells, as well as returning false positive pixels in areas of high cell proliferation. We analysed an additional 11 surgical resections of primary colorectal tumours and re-developed our image processing method to include a random forest regression machine learning model to correctly identify heterogenous tumours and exclude false positive pixels in images of non-malignant tissue. Our final model used over 1.6 billion calculations to correctly discern healthy cells from various types and stages of invasive colorectal tumours. The imaging mass spectrometry and data analysis methods described, developed in partnership with clinical cancer researchers, have the potential to further support cancer detection as part of a comprehensive digital pathology approach to cancer care through validation of a new chemical biomarker of tumour cells.

Paull, NJ, Krix, D, Irga, PJ & Torpy, FR 2021, 'Green wall plant tolerance to ambient urban air pollution', Urban Forestry and Urban Greening, vol. 63, pp. 1-11.
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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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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.', Microb Genom, 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 time. These findings have general applicability to outbreak detection of bacterial pathogens.

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 and Translational Immunology, vol. 10, no. 6, pp. 1-12.
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Objectives: Non-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. Methods: The 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. Results: Six 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%. Conclusions: A 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.

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: an interdisciplinary journal, vol. 252, pp. 1-18.
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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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Coral 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 coral Acropora millepora exposed 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 two key proteins directly involved in bilateral nutrient exchange as po...

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, OP, Kim, YJ, 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. 1-12.
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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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Pinkerton, JW, Kim, RY, Brown, AC, Rae, BE, Donovan, C, Mayall, JR, Carroll, OR, Khadem, AM, Scott, HA, Berthon, BS, Baines, KJ, Starkey, MR, Kermani, NZ, Guo, Y-K, Robertson, AAB, O'Neill, LAJ, Adcock, IM, Cooper, MA, Gibson, PG, Wood, LG, Hansbro, PM & Horvat, JC 2021, 'Relationship between type 2 cytokine and inflammasome responses in obesity-associated asthma.', J Allergy Clin Immunol, vol. 149, no. 4, pp. 1270-1280.
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BACKGROUND: Obesity is a risk factor for asthma, and obese asthmatic individuals are more likely to have severe, steroid-insensitive disease. How obesity affects the pathogenesis and severity of asthma is poorly understood. Roles for increased inflammasome-mediated neutrophilic responses, type 2 immunity, and eosinophilic inflammation have been described. OBJECTIVE: We investigated how obesity affects the pathogenesis and severity of asthma and identified effective therapies for obesity-associated disease. METHODS: We assessed associations between body mass index and inflammasome responses with type 2 (T2) immune responses in the sputum of 25 subjects with asthma. Functional roles for NLR family, pyrin domain-containing (NLRP) 3 inflammasome and T2 cytokine responses in driving key features of disease were examined in experimental high-fat diet-induced obesity and asthma. RESULTS: Body mass index and inflammasome responses positively correlated with increased IL-5 and IL-13 expression as well as C-C chemokine receptor type 3 expression in the sputum of subjects with asthma. High-fat diet-induced obesity resulted in steroid-insensitive airway hyperresponsiveness in both the presence and absence of experimental asthma. High-fat diet-induced obesity was also associated with increased NLRP3 inflammasome responses and eosinophilic inflammation in airway tissue, but not lumen, in experimental asthma. Inhibition of NLRP3 inflammasome responses reduced steroid-insensitive airway hyperresponsiveness but had no effect on IL-5 or IL-13 responses in experimental asthma. Depletion of IL-5 and IL-13 reduced obesity-induced NLRP3 inflammasome responses and steroid-insensitive airway hyperresponsiveness in experimental asthma. CONCLUSION: We found a relationship between T2 cytokine and NLRP3 inflammasome responses in obesity-associated asthma, highlighting the potential utility of T2 cytokine-targeted biologics and inflammasome inhibitors.

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. 2972-2975.
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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.

Plucinski, MM & Barratt, JLN 2021, 'Nonparametric Binary Classification to Distinguish Closely Related versus Unrelated Plasmodium falciparum Parasites', The American Journal of Tropical Medicine and Hygiene, vol. 104, no. 5, pp. 1830-1835.
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ABSTRACTAssessing genetic relatedness of Plasmodium falciparum genotypes is a key component of antimalarial efficacy trials. Previous methods have focused on determining a priori definitions of the level of genetic similarity sufficient to classify two infections as sharing the same strain. However, factors such as mixed-strain infections, allelic suppression, imprecise typing methods, and heterozygosity complicate comparisons of apicomplexan genotypes. Here, we introduce a novel method for nonparametric statistical testing of relatedness for P. falciparum parasites. First, the background distribution of genetic distance between unrelated strains is computed. Second, a threshold genetic distance is computed from this empiric distribution of distances to demarcate genetic distances that are unlikely to have arisen by chance. Third, the genetic distance between paired samples is computed, and paired samples with genetic distances below the threshold are classified as related. The method is designed to work with any arbitrary genetic distance definition. We validated this procedure using two independent approaches to calculating genetic distance. We assessed the concordance of the novel nonparametric classification with a gold-standard Bayesian approach for 175 pairs of recurrent P. falciparum episodes from previously published malaria efficacy trials with microsatellite data from five studies in Guinea and Angola. The novel nonparametric approach was 98% sensitive and 84–89% specific in correctly identifying related genotypes compared with a gold-standard Bayesian algorithm. The approach provides a unified and systematic method to statistically assess relatedness of P. falciparum parasites using arbitrary genetic distance methodologies.

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.
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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 facilitate its suc...

Polonchuk, L, Surija, L, Lee, MH, Sharma, P, Liu, CMC, Richter, F, Ben-Sefer, E, Alsadat, RM, Mahmodi, SSH, Al, SW, 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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Currentin vivoandin vitromodels fail to accurately recapitulate the human heart microenvironment for biomedical applications. This study explores the use of cardiac spheroids (CSs) to biofabricate advancedin vitromodels 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 termin vitrotesting. 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 (Basel), 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.

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 cou