Publications

Choi, AH, Cazalbou, S & Ben-Nissan, B 2015, 'Nanobiomaterial Coatings in Dentistry' in Frontiers of Oral Biology, S. Karger AG, pp. 49-61.
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During the last decade, there has been a major increase in the interest of nanostructured materials in advanced technologies for biomedical and dental clinical applications. Nanostructured materials are associated with a variety of applications within the dental and biomedical field, for example nanoparticles in drug delivery systems and nanostructured scaffolds in tissue engineering. More importantly, nanotechnology has also been linked with the modification of surface properties of synthetic implants in an attempt to improve their bioactivity, reliability and protection from the release of harmful or unnecessary metal ions. This is achieved through the use of nanocoatings and nanocomposite coatings. These new-generation coatings based on inorganic materials and biological materials such as proteins and peptides are currently investigated and applied. This chapter aims to give an overview of the recent advances in nanocoatings and their composites being investigated or used in dentistry.

Cranfield, C, Carne, S, Martinac, B & Cornell, B 2015, 'The Assembly and Use of Tethered Bilayer Lipid Membranes (tBLMs)' in Methods in Molecular Biology, Springer New York, pp. 45-53.
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© Springer Science+Business Media New York 2015. Because they are firmly held in place, tethered bilayer lipid membranes (tBLMs) are considerably more robust than supported lipid bilayers such as black lipid membranes (BLMs) (Cornell et al. Nature 387(6633): 580–583, 1997). Here we describe the procedures required to assemble and test tethered lipid bilayers that can incorporate various lipid species, peptides, and ion channel proteins.

Fowler, AM & Booth, DJ 2015, 'Fish Habitat Provided by Saipan’s WWII Submerged Heritage' in McKinnon, JF & Carrell, TL (eds), SpringerBriefs in Archaeology, Springer International Publishing, Cham, pp. 117-134.
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Gale, PA 2015, 'Anion Receptors Based on Organic Frameworks: Recent Advances' in Structure and Bonding, Springer International Publishing, pp. 19-34.
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Gu, H, Schutt, A, Stuckey, PJ, Wallace, MG & Chu, G 2015, 'Exact and Heuristic Methods for the Resource-Constrained Net Present Value Problem' in Schwindt, C & Zimmermann, J (eds), Handbook on Project Management and Scheduling Vol.1, Springer International Publishing, Switzerland, pp. 299-318.
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Huete, A, Ponce-Campos, G, Zhang, Y, Restrepo-Coupe, N, Ma, X & Moran, MS 2015, 'Land Resources Monitoring, Modeling, and Mapping with Remote Sensing' in Thenkabail, PDPS (ed), Land Resources Monitoring, Modeling, and Mapping with Remote Sensing, CRC Press, Boca Raton, pp. 3-22.
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© 2016 by Taylor and Francis Group, LLC. Vegetation productivity is defined as the process by which plants use sunlight to produce organic matter from carbon dioxide through photosynthesis. Gross primary productivity (GPP), or photosynthesis, is the rate of carbon fixation or total plant organic matter produced per unit of time and over a defined area, whereas the amount of carbon fixed by plants and accumulated as biomass is known as terrestrial net primary production (Cramer et al. 1999; Zhao and Running 2010). Productivity forms the basis of terrestrial biosphere functioning and carbon, energy, and water budgets. Accurate estimates of plant productivity across space and time are thus necessary for quantifying carbon balances at regional to global scales (Lieth 1975; Schimel 1998). Vegetation productivity is generally limited by the availability of spatially and temporally varying plant resources (e.g., nutrients, light, water, and temperature) (Field et al. 1995; Churkina and Running 1998; Nemani et al. 2003) (Figure 1.1). Improved knowledge of the main drivers and resource constraints of plant productivity is thus needed for predictable assessments of climate change.

Kohli, GS, Farrell, H & Murray, SA 2015, '9. Gambierdiscus, the cause of ciguatera fish poisoning: an increased human health threat influenced by climate change' in Climate Change and Marine and Freshwater Toxins, DE GRUYTER, pp. 273-312.
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Kohli, GS, Farrell, H & Murray, SA 2015, 'Gambierdiscus, the cause of ciguatera fish poisoning: a review of progress in ecology and toxicology' in Luis Botana, Natalia.Vilarino (ed), Climate change and marine and freshwater toxins, Walter de Gruyter, Germany, pp. 273-312.

Kohli, GS, Farrell, H & Murray, SA 2015, 'Gambierdiscus, the cause of ciguatera fish poisoning: an increased human health threat influenced by climate change' in Climate Change and Marine and Freshwater Toxins, pp. 273-312.
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Liu, H, Sun, B & Wang, G 2015, 'Advances in Electrochemical Energy Materials and Technologies' in Electrochemical Energy Storage and Conversion, CRC Press, USA, pp. 33-53.
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Greenhouse gas emissions from consumption of fossil fuels by traditional vehicles are major causes of global warming and worldwide climate change. Rechargeable batteries are widely considered as the promising power source for the next generation of electric vehicles in order to relieve our reliance on fossil fuels. The lithium ion battery is well recognized as the best choice among all different electrochemical power sources, such as fuel cells, solar cells, lead-acid, Nickel-Cadmium and Nickel metal hydride batteries. The research and development (R&D) on the lithium ion batteries has progressed rapidly since it was first commercialized in the 1990s. Rechargeable lithium ion batteries have revolutionized portable electronic devices and have become the dominant power source for mobile phones, laptop computers and digital cameras because of their high energy density.[1,2] However, the charge/discharge process in lithium ion batteries at high current rates can cause a high level of polarization for bulk materials and degrade the electrochemical properties of the batteries. The development of electric vehicles or hybrid electric vehicles demands high power batteries, which can operate under high current conditions. In following sections, we will briefly introduce advances in materials and technologies for lithium ion batteries and lithium oxygen batteries.

McGuffey, EJ, Morris, JS, Manyam, GC, Carroll, RJ & Baladandayuthapani, V 2015, 'Bayesian Models for Flexible Integrative Analysis of Multi-Platform Genomics Data' in Integrating Omics Data, Cambridge University Press, UK, pp. 221-241.
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© Cambridge University Press 2015. We present hierarchical Bayesian models to integrate an arbitrary number of genomic data platforms incorporating known biological relationships between platforms, with the goal of identifying biomarkers significantly related to a clinical phenotype. Our integrative approach offers increased power and lower false discovery rates, and our model structure allows us to not only identify which gene(s) is (are) significantly related to the outcome, but also to understand which upstream platform(s) is (are) modulating the effect(s). We present both a linear and a more flexible non-linear formulation of our model, with the latter allowing for detection of non-linear dependencies between the platform-specific features. We illustrate our method using both formulations on a multi-platform brain tumor dataset. We identify several important genes related to cancer progression, along with the corresponding mechanistic information, and discuss and compare the results obtained from the two formulations.

Miura, T, Obata, K, Azuma, JT, Huete, A & Yoshioka, H 2015, 'Remotely Sensed Data Characterization, Classification, and Accuracies' in Thenkabail, PD (ed), Remotely Sensed Data Characterization, Classification, and Accuracies, CRC Press, pp. 155-174.
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© 2016 Taylor and Francis Group, LLC. NIR Near-infrared NOAA National Oceanic and Atmospheric Administration NPP National Polar-orbiting Partnership OLI Operational Land Imager PAC Partial atmosphere correction RMSD Root mean square diference SAVI Soil-Adjusted Vegetation Index SeaWiFS Sea-Viewing Wide Field-of-View Sensor SGLI Second-generation Global Imager SPOT Système Pour l'Observation de la Terre sRMPD Systematic square root of mean product diference TM Yematic Mapper TOA Top of the atmosphere TOC Top of canopy uRMPD Unsystematic square root of mean product diference VGT VEGETATION VIIRS Visible Infrared Imaging Radiometer Suite Ye Enhanced Vegetation Index (EVI), an index developed for the National Aeronautics and Space Administration (NASA) Earth Observing System (EOS) Moderate Resolution Imaging Spectroradiometer (MODIS) mission (Huete et al., 2002), has been shown useful across a wide range of terrestrial vegetation studies. xese include climate-vegetation interactions (Saleska

Murray, S, John, U & Kremp, A 2015, '4. Alexandrium spp.: genetic and ecological factors influencing saxitoxin production and proliferation' in Botana, LM, Louzao, MC & Vilarino, N (eds), Climate Change and Marine and Freshwater Toxins, DE GRUYTER, Germany, pp. 125-154.
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Post, DF, Bryant, RB, Batchily, AK, Huete, AR, Levine, SJ, Mays, MD & Escadafal, R 2015, 'Correlations between field and laboratory measurements of soil color' in Soil Color, pp. 35-49.
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We prepared sets of <2 mm soil samples, distributed them to soil scientists, and asked them to determine the dry and moist Munsell color of each soil. We observed that soil scientists agreed on the same color chip for a single color component (hue, value, or chroma) 71% of the time, and there was an average of 52% agreement for all three color components. The standard deviation (SD) varied from 0.45 (value-moist) to 0.68 (chroma-moist) with an average SD of 0.57. Regression equations were computed that compared the mean soil color with the nearest color chip noted by an individual soil scientist, and the coefficient of simple determination (r 2) ranged from 0.49 (chroma-moist) to 0.79 (value-moist and dry). When “in-between” colors were estimated the r 2 improved and ranged from 0.70 (chroma-moist) to 0.95 (value-moist). A detailed evaluation was made of data from a commercial tristimulus colorimeter, and results were compared to colors described by soil scientists. The r 2 ranged from 0.88 (chroma-moist) to 0.96 (value-dry); however the slopes and intercepts were different. Commercial colorimeters have great potential as tools for measuring soil colors, but field colors by soil scientists are not identical to instrumental data. They differ because the sensor, light source, and angle of light refraction are different for each color measurement method. The inherent complexity of color identification by humans vs. instrumental measurements is also a contributing factor.

Powell, DA, Liu, M & Lapine, M 2015, 'Coupled Electromagnetic and Elastic Dynamics in Metamaterials' in Shadrivov, IV, Lapine, M & Kivshar, YS (eds), Springer Series in Materials Science, Springer International Publishing, Germany, pp. 59-87.
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Metamaterials are well established in the field of electromagnetism, where they have demonstrated a wide variety of exotic material properties. More recently, mechanical metamaterials have also been shown to be quite promising in achieving exotic properties for acoustic waves. Here we discuss an emerging class of metamaterials with both electromagnetic and elastic properties, which are coupled to each other, giving rise to a new range of metamaterial properties. In particular, this can yield a very strong nonlinear response, including bistable states and self-oscillations. We present several structures which exhibit these properties, and experimentally demonstrate their feasibility.

Ralph, PJ, Hill, R, Doblin, MA & Davy, SK 2015, 'Theory and Application of Pulse Amplitude Modulated Chlorophyll Fluorometry in Coral Health Assessment' in Woodley, CM, Downs, CA, Bruckner, AW, Porter, JW & Galloway, SB (eds), Diseases of Coral, Wiley, Hoboken, New Jersey, pp. 506-523.
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© 2016 John Wiley & Sons, Inc. Scleractinian corals exist in symbiosis with dinoflagellate alga (genus Symbiodinium), which provides access to nutrients by the host but also makes it makes the holobiont vulnerable to photosynthetic stress, providing an opportunity for rapid health assessment using chlorophyll a (chl-a) fluorescence techniques. Common photosynthetic stressors of corals are high irradiance, ultraviolet light, temperature extremes, chemical pollution and low salinity, which are further compounded by other major anthropogenic pressures on coral reefs. Coral Symbiodinium cells contain chlorophyll (chl) a, c2 and a range of accessory pigments. The chl-a within the pigment complex absorbs light maximally in the blue (peak at 440 nm) and red (peak at 678 nm) regions of the spectrum and re-emits light energy in the form of fluorescence, maximally in the red bandwidth (630 to 770 m with a peak at 680 nm). In vivo chl-a has a variable fluorescence yield that is dependent upon the wavelength of excitation irradiance and varies over time as a result of the complex interaction of the photosynthetic pathways (Kautsky effect). When a chloroplast captures a photon of energy, the chl a molecule is excited from its ground state to an excited state. There are three competing and complementary energy dissipation processes for that excited molecule: (i) driving photosynthesis via the electron transport chain leading to carbon fixation, (ii) heat dissipation, or (iii) returning to the ground state and re-emitting some of the energy as fluorescence. This is why chl a fluorescence can be used as a proxy for photochemistry (and energy dissipation). During periods of high incident irradiance, if the amount of absorbed light exceeds the maximum rate of electron transport, then the excess energy must be dissipated, or photodamage can occur. Pulse-amplitude modulated (PAM) fluorometry provides a versatile technique for monitoring and assessing zooxanthellae health. It measure...

Rodgers, KJ, Samardzic, K & Main, BJ 2015, 'Toxic Nonprotein Amino Acids' in Gopalakrishnakone, P, Carlini, CR & Ligabue-Braun, R (eds), Plant Toxins, Springer Netherlands, Netherlands, pp. 1-20.
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The 20 DNA-coded protein amino acids play central roles in the metabolism of most organisms. As well as being the building blocks for proteins, they play essential roles in a diverse range of metabolic pathways. They are estimated to be around 1000 molecules in nature, which share the same basic structure as these organic amino acids consisting of an α-carbon attached to a carboxyl group, an amino group, a hydrogen atom, and a unique side-chain group. Many “nonprotein” amino acids (NPAAs) are plant secondary metabolites. In this chapter, the authors discuss plant NPAAs that have a similar chemical structure, size, shape, and charge to protein amino acids and can be mistakenly used in protein synthesis, interfere in biochemical pathways, overstimulate receptors, or chelate metal ions. Most often this results in some level of toxicity to the target organism and can confer some advantage to the plant. Toxic NPAAs might have evolved as defense chemicals that can be released into the soil to inhibit the growth of other plants or agents that can limit insect herbivory. The effects of NPAAs on human health are not well understood. Consumption of a number of plants that contain NPAAs has been shown to have acutely toxic effects in humans. The key questions that remain unanswered are to what extent can NPAAs enter the food chain and what are the effects of a chronic low-level exposure to toxic plant NPAAs?

Ting, SRS, Min, EH, Cortie, MB, Nguyen, HT & Hutvagner, G 2015, 'Frontiers in Nanomedicine' in Bondì, M, Botto, C & Amore, E (eds), Frontiers in Nanomedicine, BENTHAM SCIENCE PUBLISHERS, UAE, pp. 222-255.
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The development of therapeutic nucleic acids has led to new strategies for treating various diseases. Non-viral, synthetic nano-vectors in gene therapy have attracted increasing attention due to their low immunogenicity and low toxicity compared to viral counterparts. Due to the molecular structure of nucleic acids, they are very prone to degradation in pH sensitive biological environments. Therefore, synthetic nano-vehicles for therapeutic delivery, known as ‘nano-vectors’, need to be cleverly designed and engineered to protect and deliver appropriate therapeutic nucleic acids to the targeted sites for action. In this chapter, a brief overview of various types of therapeutic nucleic acids is first provided, followed by analysis of the synthetic nanomaterials under development as delivery systems to carry nucleic acids. The nucleic acid-encapsulated nano-vectors discussed here open a window for a new generation of nanomedicine.

Ton-That, C & Phillips, MR 2015, '14 Cathodoluminescence microanalysis of ZnO nanowires' in Semiconductor Nanowires, pp. 393-407.
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Ton-That, C & Phillips, MR 2015, 'Cathodoluminescence microanalysis of ZnO nanowires' in Arbiol, J & Xiong, Q (eds), Semiconductor Nanowires, Elsevier, Cambridge, England, pp. 393-407.
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© 2015 Elsevier Ltd. All rights reserved. Cathodoluminescence (CL) is an enabling quantitative technique for the characterisation of luminescent materials. In this chapter, following a brief review of the basic principles and recent advances in CL imaging and spectroscopy, a number of examples are chosen to demonstrate the utility of CL for the microcharacterisation of semiconductor nanowires, with a focus on ZnO material. Various analytical methods such as monochromatic CL imaging, depth-resolved analysis, and excitation density-resolved analysis are presented, which can provide information on the local optical and electronic properties of nanowires at the nanometre spatial resolution.

Torpy, FR, Irga, PJ & Burchett, MD 2015, 'Reducing Indoor Air Pollutants Through Biotechnology' in Torgal, FP, Labrincha, JA, Diamanti, MV, Yu, C-P & Lee, HK (eds), Biotechnologies and Biomimetics for Civil Engineering, Springer International Publishing, Switzerland, pp. 181-210.
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© Springer International Publishing Switzerland 2015. Indoor environmental quality is a growing concern, as populations become more urbanised and people spend a greater proportion of their lives indoors. Volatile organic compounds outgassing from synthetic materials and carbon dioxide from human respiration have been major indoor air quality concerns. The growing use of energy-efficient recirculating ventilation solutions has led to greater accumulation of these pollutants indoors. A range of physiochemical methods have been developed to remove contaminants from indoor air, but all methods have high maintenance costs and none reduce CO2, which some biological systems can achieve effectively with the additional benefit of the self-sustaining capacity of biological material. Bacteria are the major organisms involved in bioremediation of VOCs, although green plants may help sustain the bacterial community and add the capacity for CO2 reduction to a system. The main problems faced by indoor air bioremediation systems is the extremely low concentrations of VOCs present indoors and the possibility of microbial release. Simple, passive biofiltration with potted green plants may be the simplest and most effective system for indoor air cleaning, but further research into substrate types, ventilation, and the microbiology of biodegradation processes is required to reveal their ultimate potential. Purely microbial systems have potential for the bioamelioration of high concentrations of toxic gases, but not without significant maintenance costs. Despite many years of study and substantial market demand, a proven formula for indoor air bioremediation for all applications is yet to be developed.

Wallman, JF 2015, 'Forensic Entomology' in Tomberlin, JK & Benbow, ME (eds), Forensic Entomology: International Dimensions and Frontiers, CRC Press, pp. 3-6.
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© 2015 by Taylor & Francis Group, LLC. This rst chapter of the book acts as an introduction to Chapters 2 through 6, which concern the history and activities of workers in forensic entomology in Asia, Australia, and New Zealand. While these regions cover a part of the world that is exceptionally varied both ecologically and culturally, there are also certain underlying evolutionary afnities that unite them. I highlight here the main themes that have been dealt with in these chapters. China, the topic of Chapter 2, is notable in that it can be considered the “birthplace” of forensic entomology, given that the earliest known documentation of ies (Diptera) being used to solve crimes comes from the Far East (Giles 1924). It is therefore entirely appropriate that China be the rst country in this book to have its achievements in forensic entomology addressed.

Wallman, JF & Archer, MS 2015, 'Australia and New Zealand' in Forensic Entomology: International Dimensions and Frontiers, pp. 53-72.
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The rst known Australian or New Zealand case featuring forensic entomology occurred in 1923 (Morgan 2012). Insect evidence recovered from a corpse found in a river suggested that infestation had occurred at a forested site before the body was immersed. However, the analysis appears to have been made by the pathologist and police rather than an entomologist. There are two other early New South Wales records of minimum postmortem interval (mPMI) estimates from 1960 (Clarke 1962) and 1978 (Miller 1991). Regular use of forensic entomology increased from the 1980s onward, and reference to Australian and New Zealand casework can be found in O’Flynn (1980), Smeeton et al. (1984), Crosby et al. (1985), Morris (1993), Levot (2003), Archer and Ranson (2005), Archer et al. (2005, 2006), and Porter (2012). Acceptance of forensic entomology in Australia was also further increased by its inclusion in the Expert Evidence series, which summarizes elds of accepted expertise for the legal community (Morris and Dadour 2011). Today, there are usually between 10 and 15 practitioners, researchers, and students working in Australia and New Zealand at any one time.

Adlard, PA, Parncutt, J, Lal, V, James, S, Hare, D, Doble, P, Finkelstein, DI & Bush, AI 2015, 'Metal chaperones prevent zinc-mediated cognitive decline', NEUROBIOLOGY OF DISEASE, vol. 81, pp. 196-202.
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Aguilar, JLC, Gentle, AR, Smith, GB & Chen, D 2015, 'A method to measure total atmospheric long-wave down-welling radiation using a low cost infrared thermometer tilted to the vertical', ENERGY, vol. 81, pp. 233-244.
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© 2014 Elsevier Ltd. Atmospheric long-wave down-welling radiation is a fundamental element of climate change and of input to thermal simulation. Measuring long-wave radiation is needed to calculate locally total energy flows to the earth's surface and night cooling rates in urban precincts. It is an important parameter for the weather files used by energy building simulation software to calculate the thermal performance of buildings and their energy efficiency. Currently, atmospheric down-welling radiation is usually measured by a pyrgeometer, for radiation beyond 3μm. This is expensive and bulky. A simple methodology for measurement and calculation, with good accuracy, of average atmospheric long-wave down-welling radiation using a tilted, low-cost infrared thermometer is described. Tilt setting, comparison to data gathered by the pyrgeometer, and comparison of simulation studies with both data sets is described. A link of the magnitude of divergence between instant data pairs and radiant intensity is demonstrated and shown to depend on asymmetry in cloud density.

Ajani, PA 2015, 'Photo Credit, corrected after print 16 April 2015. Editorial 'Ocean wanderers' the image did not show marine phytoplankton.', Nature Climate Change, vol. 5, pp. 1-1.

Akbarzadeh, K, Wallman, JF, Sulakova, H & Szpila, K 2015, 'Species identification of Middle Eastern blowflies (Diptera: Calliphoridae) of forensic importance', Parasitology Research, vol. 114, no. 4, pp. 1463-1472.
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Akhondi, E, Wu, B, Sun, S, Marxer, B, Lim, W, Gu, J, Liu, L, Burkhardt, M, McDougald, D, Pronk, W & Fane, AG 2015, 'Gravity-driven membrane filtration as pretreatment for seawater reverse osmosis: Linking biofouling layer morphology with flux stabilization', Water Research, vol. 70, pp. 158-173.
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© 2014 Elsevier Ltd. In this study gravity-driven membrane (GDM) ultrafiltration is investigated for the pretreatment of seawater before reverse osmosis (RO). The impacts of temperature (21±1 and 29±1°C) and hydrostatic pressure (40 and 100mbar) on dynamic flux development and biofouling layer structure were studied. The data suggested pore constriction fouling was predominant at the early stage of filtration, during which the hydrostatic pressure and temperature had negligible effects on permeate flux. With extended filtration time, cake layer fouling played a major role, during which higher hydrostatic pressure and temperature improved permeate flux. The permeate flux stabilized in a range of 3.6L/m2h (21±1°C, 40mbar) to 7.3L/m2h (29±1°C, 100mbar) after slight fluctuations and remained constant for the duration of the experiments (almost 3 months). An increase in biofouling layer thickness and a variable biofouling layer structure were observed over time by optical coherence tomography and confocal laser scanning microscopy. The presence of eukaryotic organisms in the biofouling layer was observed by light microscopy and the microbial community structure of the biofouling layer was analyzed by sequences of 16S rRNA genes. The magnitude of permeate flux was associated with the combined effect of the biofouling layer thickness and structure. Changes in the biofouling layer structure were attributed to (1) the movement and predation behaviour of the eukaryotic organisms which increased the heterogeneous nature of the biofouling layer; (2) the bacterial debris generated by eukaryotic predation activity which reduced porosity; (3) significant shifts of the dominant bacterial species over time that may have influenced the biofouling layer structure. As expected, most of the particles and colloids in the feed seawater were removed by the GDM process, which led to a lower RO fouling potential. However, the dissolved organic carbon in the permeate was not be r...

Al Khamici, H, Brown, LJ, Hossain, KR, Hudson, AL, Sinclair-Burton, AA, Ng, JPM, Daniel, EL, Hare, JE, Cornell, BA, Curmi, PMG, Davey, MW & Valenzuela, SM 2015, 'Members of the Chloride Intracellular Ion Channel Protein Family Demonstrate Glutaredoxin-Like Enzymatic Activity', PLOS ONE, vol. 10, no. 1.
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© 2015 Al Khamici et al. The Chloride Intracellular Ion Channel (CLIC) family consists of six evolutionarily conserved proteins in humans. Members of this family are unusual, existing as both monomeric soluble proteins and as integral membrane proteins where they function as chloride selective ion channels, however no function has previously been assigned to their soluble form. Structural studies have shown that in the soluble form, CLIC proteins adopt a glutathione S-transferase (GST) fold, however, they have an active site with a conserved glutaredoxin monothiol motif, similar to the omega class GSTs. We demonstrate that CLIC proteins have glutaredoxin-like glutathione-dependent oxidoreductase enzymatic activity. CLICs 1, 2 and 4 demonstrate typical glutaredoxin-like activity using 2-hydroxyethyl disulfide as a substrate. Mutagenesis experiments identify cysteine 24 as the catalytic cysteine residue in CLIC1, which is consistent with its structure. CLIC1 was shown to reduce sodium selenite and dehydroascorbate in a glutathione-dependent manner. Previous electrophysiological studies have shown that the drugs IAA-94 and A9C specifically block CLIC channel activity. These same compounds inhibit CLIC1 oxidoreductase activity. This work for the first time assigns a functional activity to the soluble form of the CLIC proteins. Our results demonstrate that the soluble form of the CLIC proteins has an enzymatic activity that is distinct from the channel activity of their integral membrane form. This CLIC enzymatic activity may be important for protecting the intracellular environment against oxidation. It is also likely that this enzymatic activity regulates the CLIC ion channel function.

Alvarado, R, O'Brien, B, Tanaka, A, Dalton, JP & Donnelly, S 2015, 'A parasitic helminth-derived peptide that targets the macrophage lysosome is a novel therapeutic option for autoimmune disease', IMMUNOBIOLOGY, vol. 220, no. 2, pp. 262-269.
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© 2014. Parasitic worms (helminths) reside in their mammalian hosts for many years. This is attributable, in part, to their ability to skew the host's immune system away from pro-inflammatory responses and towards anti-inflammatory or regulatory responses. This immune modulatory ability ensures helminth longevity within the host, while simultaneously minimises tissue destruction for the host. The molecules that the parasite releases clearly exert potent immune-modulatory actions, which could be exploited clinically, for example in the prophylactic and therapeutic treatment of pro-inflammatory and autoimmune diseases. We have identified a novel family of immune-modulatory proteins, termed helminth defence molecules (HDMs), which are secreted by several medically important helminth parasites. These HDMs share biochemical and structural characteristics with mammalian cathelicidin-like host defence peptides (HDPs), which are significant components of the innate immune system. Like their mammalian counterparts, parasite HDMs block the activation of macrophages via toll like receptor (TLR) 4 signalling, however HDMs are significantly less cytotoxic than HDPs. HDMs can traverse the cell membrane of macrophages and enter the endolysosomal system where they reduce the acidification of lysosomal compartments by inhibiting vacuolar (v)-ATPase activity. In doing this, HDMs can modulate critical cellular functions, such as cytokine secretion and antigen processing/presentation. Here, we review the role of macrophages, specifically their lysosomal mediated activities, in the initiation and perpetuation of pro-inflammatory immune responses. We also discuss the potential of helminth defence molecules (HDMs) as therapeutics to counteract the pro-inflammatory responses underlying autoimmune disease. Given the current lack of effective, non-cytotoxic treatment options to limit the progression of autoimmune pathologies, HDMs open novel treatment avenues.

Anantachaisilp, S, Smith, SM, Ton-That, C, Pornsuwan, S, Moon, AR, Nenstiel, C, Hoffmann, A & Phillips, MR 2015, 'Nature of red luminescence in oxygen treated hydrothermally grown zinc oxide nanorods', JOURNAL OF LUMINESCENCE, vol. 168, pp. 20-25.
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© 2015 Published by Elsevier B.V. A strong broad red luminescence (RL) peak centered at 1.69 eV (FWHM=0.57 eV) at 15 K [1.78 eV (FWHM=0.69 eV) at 300 K] is formed in ZnO nanorods hydrothermally grown at low temperature following thermal annealing at 650 °C for 30 min in an O2 gas environment. The optical properties of this peak were comprehensively studied using a range of characterization techniques, including photoluminescence and cathodoluminescence spectroscopy, X-ray absorption near edge spectroscopy and electron paramagnetic resonance spectroscopy. With decreasing temperature the RL peak position red shifted and its FWHM became narrower in accordance with the configuration coordinate model. Using these results, the RL has been assigned to highly lattice coupled VZn-related acceptor-like centers. No correlation was found between the observed red luminescence and nitrogen impurities.

ANSARI, WM, NAVEED, AK, ISMAIL, M & REHMAN, SF 2015, 'Role Of Interleukin-6 (-174 G/C) Gene Promoter Polymorphism And Il-6 Levels In Risk Prediction Of Coronary Artery Disease In Young Pakistani Subjects', International Journal of Advances in Science, Engineering and Technology (IJASEAT), vol. 3, no. 4, Spl. Iss-3 ( Oct, 2015 ), pp. 83-86.
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IL-6 is a pleiotropic cytokine which actively participates in the immune-inflammatory process underlying the pathogenesis of CAD.The most widely studied of these is the -174 G/C variant in the IL-6 gene promoter region. there is still paucity of studies reporting the effect of the IL-6 gene promoter SNP -174 G/C (Rs1800795) on the serum IL-6 levels and the risk prediction of CAD in Premature coronary artery disease patients of Pakistan. Hence, we sought to assess the role of the IL-6 gene promoter SNP -174 G/C(Rs1800795) and IL-6 serum levels in the diagnosis and risk prediction of PCAD patients.

Antonosyan, DA, Solntsev, AS & Sukhorukov, AA 2015, 'Parity-time anti-symmetric parametric amplifier', Optics Letters, vol. 40, no. 20, pp. 4575-4578.
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We describe the process of parametric amplification in a directional coupler of quadratically nonlinear and lossy waveguides, which belongs to a class of optical systems with spatial parity-time (PT) symmetry in the linear regime. We identify a distinct spectral PT anti-symmetry associated with optical parametric interaction, and show that pumpcontrolled symmetry breaking can facilitate spectrally selective mode amplification in analogy with PT lasers. We also establish a connection between the breaking of spectral and spatial mode symmetries, revealing the potential to implement unconventional regimes of spatial light switching through ultrafast control of PT breaking by pump pulses.

Ao, Z, Jiang, Q, Li, S, Liu, H, Peeters, FM, Li, S & Wang, G 2015, 'Enhancement of the Stability of Fluorine Atoms on Defective Graphene and at Graphene/Fluorographene Interface', ACS APPLIED MATERIALS & INTERFACES, vol. 7, no. 35, pp. 19659-19665.
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Fluorinated graphene is one of the most important derivatives of graphene and has been found to have great potential in optoelectronic and photonic nanodevices. However, the stability of F atoms on fluorinated graphene under different conditions, which is essential to maintain the desired properties of fluorinated graphene, is still unclear. In this work, we investigate the diffusion of F atoms on pristine graphene, graphene with defects, and at graphene/fluorographene interfaces by using density functional theory calculations. We find that an isolated F atom diffuses easily on graphene, but those F atoms can be localized by inducing vacancies or absorbates in graphene and by creating graphene/fluorographene interfaces, which would strengthen the binding energy of F atoms on graphene and increase the diffusion energy barrier of F atoms remarkably.

Apgaua, DMG, Ishida, FY, Tng, DYP, Laidlaw, MJ, Santos, RM, Rumman, R, Eamus, D, Holtum, JAM & Laurance, SGW 2015, 'Functional Traits and Water Transport Strategies in Lowland Tropical Rainforest Trees', PLOS ONE, vol. 10, no. 6.
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Applebaum, D & Dooley, A 2015, 'A generalised Gangolli–Lévy–Khintchine formula for infinitely divisible measures and Lévy processes on semi-simple Lie groups and symmetric spaces', Annales de l'Institut Henri Poincaré, Probabilités et Statistiques, vol. 51, no. 2, pp. 599-619.
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Aramesh, M, Shimoni, O, Fox, K, Karle, TJ, Lohrmann, A, Ostrikov, K, Prawer, S & Cervenka, J 2015, 'Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids', Nanoscale, vol. 7, no. 14, pp. 5998-6006.
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Single-molecule-detection, selectivity, broad-range detection and biocompatibility are achieved using nanoporous diamond-like carbon coated oxide membranes.

Aramesh, M, Shimoni, O, Ostrikov, K, Prawer, S & Cervenka, J 2015, 'Surface charge effects in protein adsorption on nanodiamonds', Nanoscale, vol. 7, no. 13, pp. 5726-5736.
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An electrostatic model is developed to qualitatively explain the protein adsorption based on charge-induced pH modifications near the charged nanoparticles/surfaces.

Archer, NS, Nassif, NT & O'Brien, BA 2015, 'Genetic variants of SLC11A1 are associated with both autoimmune and infectious diseases: systematic review and meta-analysis', Genes & Immunity, vol. 16, no. 4, pp. 275-283.
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© 2015 Macmillan Publishers Limited All rights reserved. A systematic review and meta-analyses were undertaken to investigate the association of SLC11A1 genetic variants with disease occurrence. Literature searching indentified 109 publications to include in the meta-analyses assessing the association of 11 SLC11A1 variants with autoimmune and infectious disease. The (GT) n promoter alleles 2 and 3 (rs534448891), which alter SLC11A1 expression, were significantly associated with tuberculosis (OR=1.47 (1.30-1.66), OR=0.76 (0.65-0.89), respectively) and infectious disease (OR=1.25 (1.10-1.42), OR=0.83 (0.74-0.93), respectively). However, although no association was observed with autoimmune disease, a modest significant association was observed with type 1 diabetes (allele 2 OR=0.94 (0.89-0.98)). On the basis of a stronger association of (GT) n allele 2 with tuberculosis, compared with the protective effect of allele 3, we hypothesise that allele 2 is likely the disease-causing variant influencing disease susceptibility. Significant associations were observed between the 469+14G/C polymorphism (rs3731865) and autoimmune disease (OR=1.30 (1.04-1.64)) and rheumatoid arthritis (OR=1.60 (1.20-2.13)) and between the -237C/T polymorphism (rs7573065) and inflammatory bowel disease (OR=0.60 (0.43-0.84)). Further, significant associations were identified between the 469+14G/C, 1730G/A and 1729+55del4 polymorphisms (rs3731865, rs17235409 and rs17235416, respectively) and both infectious disease per se and tuberculosis. These findings show a clear association between variants in the SLC11A1 locus and autoimmune and infectious disease susceptibility.

Arora, M & Hare, DJ 2015, 'Tooth lead levels as an estimate of lead body burden in rats following pre- and neonatal exposure', RSC Advances, vol. 5, no. 82, pp. 67308-67314.
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Accurate assessment of early life lead exposure requires an accessible and reliable biomarker.

Arotsker, L, Kramarsky-Winter, E, Ben-Dov, E, Siboni, N & Kushmaro, A 2015, 'Changes in the bacterial community associated with black band disease in a Red Sea coral, Favia sp., in relation to disease phases', DISEASES OF AQUATIC ORGANISMS, vol. 116, no. 1, pp. 47-58.
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Changes of the black band disease (BBD)-associated microbial consortium on the surface of a Favia sp. coral colony were assessed in relation to the different disease phases. A number of highly active bacterial groups changed in numbers as the BBD disease signs changed. These included Gamma- and Epsilonproteobacteria, Bacteroidetes and Firmicutes groups. One cyanobacterium strain, BGP10_4ST (FJ210722), was constantly present in the disease interface and adjacent tissues of the affected corals, regardless of disease phase. The dynamics of the operational taxonomic units (OTUs) of this BBD-specific strain provide a marker regarding the disease phase. The disease's active phase is characterized by a wide dark band progressing along the tissue-skeleton interface and by numerous bacterial OTUs. Cyanobacterial OTUs decreased in numbers as the disease signs waned, perhaps opening a niche for additional microorganisms. Even when black band signs disappeared there was a consistent though low abundance of the BBD-specific cyanobacteria (BGP10_4ST), and the microbial community of the disease-skeleton interface remained surprisingly similar to the original band community. These results provide an indication that the persistence of even low numbers of this BBD-specific cyanobacterium in coral tissues during the non-active (or subclinical) state could facilitate reinitiation of BBD signs during the following summer. This may indicate that this bacterium is major constituent of the disease and that its persistence and ability to infiltrate the coral tissues may act to facilitate the assembly of the other BBD-specific groups of bacteria.

Asatryan, AA 2015, 'Summation of a Schlomilch type series', PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, vol. 471, no. 2183.
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Assaad, HI, Hou, Y, Zhou, L, Carroll, RJ & Wu, G 2015, 'Rapid publication-ready MS-Word tables for two-way ANOVA', SpringerPlus, vol. 4, no. 1.
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© 2015, Assaad et al.; licensee Springer. Background: Statistical tables are an essential component of scientific papers and reports in biomedical and agricultural sciences. Measurements in these tables are summarized as mean ± SEM for each treatment group. Results from pairwise-comparison tests are often included using letter displays, in which treatment means that are not significantly different, are followed by a common letter. However, the traditional manual processes for computation and presentation of statistically significant outcomes in MS Word tables using a letter-based algorithm are tedious and prone to errors.Results: Using the R package ‘Shiny’, we present a web-based program freely available online, at https://houssein-assaad.shinyapps.io/TwoWayANOVA/. No download is required. The program is capable of rapidly generating publication-ready tables containing two-way analysis of variance (ANOVA) results. Additionally, the software can perform multiple comparisons of means using the Duncan, Student-Newman-Keuls, Tukey Kramer, Westfall, and Fisher’s least significant difference (LSD) tests. If the LSD test is selected, multiple methods (e.g., Bonferroni and Holm) are available for adjusting p-values. Significance statements resulting from all pairwise comparisons are included in the table using the popular letter display algorithm. With the application of our software, the procedures of ANOVA can be completed within seconds using a web-browser, preferably Mozilla Firefox or Google Chrome, and a few mouse clicks. To our awareness, none of the currently available commercial (e.g., Stata, SPSS and SAS) or open-source software (e.g., R and Python) can perform such a rapid task without advanced knowledge of the corresponding programming language.Conclusions: The new and user-friendly program described in this paper should help scientists perform statistical analysis and rapidly generate publication-ready MS-Word tables for two-way ANOVA. Our softwar...

Augustinus, D, Gahan, ME & McNevin, D 2015, 'Development of a forensic identity SNP panel for Indonesia', International Journal of Legal Medicine, vol. 129, no. 4, pp. 681-691.
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Ayton, S, Lei, P, Hare, DJ, Duce, JA, George, JL, Adlard, PA, McLean, C, Rogers, JT, Cherny, RA, Finkelstein, DI & Bush, AI 2015, 'Parkinson's Disease Iron Deposition Caused by Nitric Oxide-Induced Loss of beta-Amyloid Precursor Protein', JOURNAL OF NEUROSCIENCE, vol. 35, no. 8, pp. 3591-3597.
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© 2015 the authors. Elevation of both neuronal iron and nitric oxide (NO) in the substantia nigra are associated with Parkinson’s disease (PD) pathogenesis. We reported previously that the Alzheimer-associated β-amyloid precursor protein (APP) facilitates neuronal iron export. Here we report markedly decreased APP expression in dopaminergic neurons of human PD nigra and that APP−/−mice develop iron-dependent nigral cell loss. Conversely, APP-overexpressing mice are protected in the MPTP PD model. NO suppresses APP translation in mouse MPTP models, explaining how elevated NO causes iron-dependent neurodegeneration in PD.

Bachmann, NL, Sullivan, MJ, Jelocnik, M, Myers, GSA, Timms, P & Polkinghorne, A 2015, 'Culture-Independent Genome Sequencing of Clinical Samples Reveals an Unexpected Heterogeneity of Infections by Chlamydia pecorum', Journal of Clinical Microbiology, vol. 53, no. 5, pp. 1573-1581.
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ABSTRACT Chlamydia pecorum is an important global pathogen of livestock, and it is also a significant threat to the long-term survival of Australia's koala populations. This study employed a culture-independent DNA capture approach to sequence C. pecorum genomes directly from clinical swab samples collected from koalas with chlamydial disease as well as from sheep with arthritis and conjunctivitis. Investigations into single-nucleotide polymorphisms within each of the swab samples revealed that a portion of the reads in each sample belonged to separate C. pecorum strains, suggesting that all of the clinical samples analyzed contained mixed populations of genetically distinct C. pecorum isolates. This observation was independent of the anatomical site sampled and the host species. Using the genomes of strains identified in each of these samples, whole-genome phylogenetic analysis revealed that a clade containing a bovine and a koala isolate is distinct from other clades comprised of livestock or koala C. pecorum strains. Providing additional evidence to support exposure of koalas to Australian livestock strains, two minor strains assembled from the koala swab samples clustered with livestock strains rather than koala strains. Culture-independent probe-based genome capture and sequencing of clinical samples provides the strongest evidence yet to suggest that naturally occurring chlamydial infections are comprised of multiple genetically distinct strai...

Baechler, S, Morelato, M, Ribaux, O, Beavis, A, Tahtouh, M, Kirkbride, KP, Esseiva, P, Margot, P & Roux, C 2015, 'Forensic intelligence framework. Part II: Study of the main generic building blocks and challenges through the examples of illicit drugs and false identity documents monitoring', FORENSIC SCIENCE INTERNATIONAL, vol. 250, pp. 44-52.
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© 2015. The development of forensic intelligence relies on the expression of suitable models that better represent the contribution of forensic intelligence in relation to the criminal justice system, policing and security. Such models assist in comparing and evaluating methods and new technologies, provide transparency and foster the development of new applications. Interestingly, strong similarities between two separate projects focusing on specific forensic science areas were recently observed. These observations have led to the induction of a general model (Part I) that could guide the use of any forensic science case data in an intelligence perspective. The present article builds upon this general approach by focusing on decisional and organisational issues. The article investigates the comparison process and evaluation system that lay at the heart of the forensic intelligence framework, advocating scientific decision criteria and a structured but flexible and dynamic architecture. These building blocks are crucial and clearly lay within the expertise of forensic scientists. However, it is only part of the problem. Forensic intelligence includes other blocks with their respective interactions, decision points and tensions (e.g. regarding how to guide detection and how to integrate forensic information with other information). Formalising these blocks identifies many questions and potential answers. Addressing these questions is essential for the progress of the discipline. Such a process requires clarifying the role and place of the forensic scientist within the whole process and their relationship to other stakeholders.

Baillet, AC, Rehaume, LM, Benham, H, O'Meara, CP, Armitage, CW, Ruscher, R, Brizard, G, Harvie, MCG, Velasco, J, Hansbro, PM, Forrester, JV, Degli‐Esposti, MA, Beagley, KW & Thomas, R 2015, 'High Chlamydia Burden Promotes Tumor Necrosis Factor–Dependent Reactive Arthritis in SKG Mice', Arthritis & Rheumatology, vol. 67, no. 6, pp. 1535-1547.
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ObjectiveChlamydia trachomatis is a sexually transmitted obligate intracellular pathogen that causes inflammatory reactive arthritis, spondylitis, psoriasiform dermatitis, and conjunctivitis in some individuals after genital infection. The immunologic basis for this inflammatory response in susceptible hosts is poorly understood. As ZAP‐70W163C–mutant BALB/c (SKG) mice are susceptible to spondylo‐arthritis after systemic exposure to microbial β‐glucan, we undertook the present study to compare responses to infection with Chlamydia muridarum in SKG mice and BALB/c mice.MethodsAfter genital or respiratory infection with C muridarum, conjunctivitis and arthritis were assessed clinically, and eye, skin, and joint specimens were analyzed histologically. Chlamydial major outer membrane protein antigen–specific responses were assessed in splenocytes. Treg cells were depleted from FoxP3‐DTR BALB/c or SKG mice, and chlamydial DNA was quantified by polymerase chain reaction.ResultsFive weeks after vaginal infection with live C muridarum, arthritis, spondylitis, and psoriasiform dermatitis developed in female SKG mice, but not in BALB/c mice. Inflammatory bowel disease did not occur in mice of either strain. The severity of inflammatory disease was correlated with C muridarum inoculum size and vaginal burden postinoculation. Treatment with combination antibiotics starting 1 day postinoculation prevented disease. Chlamydial antigen was present in macrophages and spread from the infection site to lymphoid organs and peripheral tissue. In response to chlamydial antigen, production of interferon‐γ and interleukin‐17 was impaired in T cells from SKG ...

Baldeaux, JF, Fung, MC, Ignatieva, K & Platen, E 2015, 'A Hybrid Model for Pricing and Hedging of Long Dated Bonds', UNSW Business School Research Paper, vol. 22, no. 2015, pp. 366-398.
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Long-dated fixed income securities play an important role in asset-liability management, in life insurance and in annuity businesses. This paper applies the benchmark approach, where the growth optimal portfolio (GOP) is employed as numéraire together with the real-world probability measure for pricing and hedging of long-dated bonds. It employs a time-dependent constant elasticity of variance model for the discounted GOP and takes stochastic interest rate risk into account. This results in a hybrid framework that models the stochastic dynamics of the GOP and the short rate simultaneously. We estimate and compare a variety of continuous-time models for short-term interest rates using non-parametric kernel-based estimation. The hybrid models remain highly tractable and fit reasonably well the observed dynamics of proxies of the GOP and interest rates. Our results involve closed-form expressions for bond prices and hedge ratios. Across all models under consideration we find that the hybrid model with the 3/2 dynamics for the interest rate provides the best fit to the data with respect to lowest prices and least expensive hedges.

Banik, G, Stark, D, Rashid, H & Ellis, J 2015, 'Recent Advances in Molecular Biology of Parasitic Viruses', Infectious Disorders - Drug Targets, vol. 14, no. 3, pp. 155-167.
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The numerous protozoa that can inhabit the human gastro-intestinal tract are known, yet little is understood of the viruses which infect these protozoa. The discovery, morphologic details, purification methods of virus-like particles, genome and proteome of the parasitic viruses, Entamoeba histolytica, Giardia lamblia, Trichomonas vaginalis, and the Eimeria sp. are described in this review. The protozoan viruses share many common features: most of them are RNA or double-stranded RNA viruses, ranging between 5 and 8 kilobases, and are spherical or icosahedral in shape with an average diameter of 30-40 nm. These viruses may influence the function and pathogenicity of the protozoa which they infect, and may be important to investigate from a clinical perspective. The viruses may be used as specific genetic transfection vectors for the parasites and may represent a research tool. This review provides an overview on recent advances in the field of protozoan viruses.

Barkhagen, M, Blomvall, J & Platen, E 2015, 'Recovering the Real-World Density and Liquidity Premia From Option Data', Quantitative Finance, vol. 16, no. 7, pp. 1147-1164.
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In this paper we develop a methodology for simultaneous recovery of the real-world probability density and liquidity premia from observed S&P 500 index option prices. Assuming the existence of a num´eraire portfolio for the US equity market, fair prices of derivatives under the benchmark approach can be obtained directly under the real-world measure. Under this modeling framework there exists a direct link between observed call option prices on the index and the real-world density for the underlying index. We use a novel method for estimation of option implied volatility surfaces of high quality, which enables the subsequent analysis. We show that the real-world density that we recover is consistent with the observed realized dynamics of the underlying index. This admits the identification of liquidity premia embedded in option price data. We identify and estimate two separate liquidity premia embedded in S&P 500 index options that are consistent with previous findings in the literature.

Barnes, MK, Tilstone, GH, Smyth, TJ, Widdicombe, CE, Gloël, J, Robinson, C, Kaiser, J & Suggett, DJ 2015, 'Drivers and effects of Karenia mikimotoi blooms in the western English Channel', Progress in Oceanography, vol. 137, no. B, pp. 456-469.
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© 2015 Published by Elsevier Ltd. Naturally occurring red tides and harmful algal blooms (HABs) are of increasing importance in the coastal environment and can have dramatic effects on coastal benthic and epipelagic communities worldwide. Such blooms are often unpredictable, irregular or of short duration, and thus determining the underlying driving factors is problematic. The dinoflagellate Karenia mikimotoi is an HAB, commonly found in the western English Channel and thought to be responsible for occasional mass finfish and benthic mortalities. We analysed a 19-year coastal time series of phytoplankton biomass to examine the seasonality and interannual variability of K. mikimotoi in the western English Channel and determine both the primary environmental drivers of these blooms as well as the effects on phytoplankton productivity and oxygen conditions. We observed high variability in timing and magnitude of K. mikimotoi blooms, with abundances reaching 1000cellsmL-1 at 10m depth, inducing up to a 12-fold increase in the phytoplankton carbon content of the water column. No long-term trends in the timing or magnitude of K. mikimotoi abundance were evident from the data. Key driving factors were identified as persistent summertime rainfall and the resultant input of low-salinity high-nutrient river water. The largest bloom in 2009 was associated with highest annual primary production and led to considerable oxygen depletion at depth, most likely as a result of enhanced biological breakdown of bloom material; however, this oxygen depletion may not affect zooplankton. Our data suggests that K. mikimotoi blooms are not only a key and consistent feature of western English Channel productivity, but importantly can potentially be predicted from knowledge of rainfall or river discharge.

Barnes, MK, Tilstone, GH, Suggett, DJ, Widdicombe, CE, Bruun, J, Martinez-Vicente, V & Smyth, TJ 2015, 'Temporal variability in total, micro- and nano-phytoplankton primary production at a coastal site in the Western English Channel', Progress in Oceanography, vol. 137, no. B, pp. 470-483.
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© 2015 Published by Elsevier Ltd. Primary productivity and subsequent carbon cycling in the coastal zone have a significant impact on the global carbon budget. It is currently unclear how anthropogenic activity could alter these budgets but long term coastal time series of hydrological, biogeochemical and biological measurements represent a key means to better understand past drivers, and hence to predicting future seasonal and inter-annual variability in carbon fixation in coastal ecosystems. An 8-year time series of primary production from 2003 to 2010, estimated using a recently developed absorption-based algorithm, was used to determine the nature and extent of change in primary production at a coastal station (L4) in the Western English Channel (WEC). Analysis of the seasonal and inter-annual variability in production demonstrated that on average, nano- and pico-phytoplankton account for 48% of the total carbon fixation and micro-phytoplankton for 52%. A recent decline in the primary production of nano- and pico-phytoplankton from 2005 to 2010 was observed, corresponding with a decrease in winter nutrient concentrations and a decrease in the biomass of Phaeocystis sp. Micro-phytoplankton primary production (PPM) remained relatively constant over the time series and was enhanced in summer during periods of high precipitation. Increases in sea surface temperature, and decreases in wind speeds and salinity were associated with later spring maxima in PPM. Together these trends indicate that predicted increases in temperature and decrease in wind speeds in future would drive later spring production whilst predicted increases in precipitation would also continue these blooms throughout the summer at this site.

Barnes, RJ, Low, JH, Bandi, RR, Tay, M, Chua, F, Aung, T, Fane, AG, Kjelleberg, S & Rice, SA 2015, 'Nitric Oxide Treatment for the Control of Reverse Osmosis Membrane Biofouling', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 81, no. 7, pp. 2515-2524.
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Barratt, JLN, Cao, M, Stark, DJ & Ellis, JT 2015, 'The Transcriptome Sequence of Dientamoeba fragilis Offers New Biological Insights on its Metabolism, Kinome, Degradome and Potential Mechanisms of Pathogenicity', PROTIST, vol. 166, no. 4, pp. 389-408.
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Barraud, N, Kjelleberg, S & Rice, SA 2015, 'Dispersal from Microbial Biofilms', Microbiology Spectrum, vol. 3, no. 6.
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ABSTRACT One common feature of biofilm development is the active dispersal of cells from the mature biofilm, which completes the biofilm life cycle and allows for the subsequent colonization of new habitats. Dispersal is likely to be critical for species survival and appears to be a precisely regulated process that involves a complex network of genes and signal transduction systems. Sophisticated molecular mechanisms control the transition of sessile biofilm cells into dispersal cells and their coordinated detachment and release in the bulk liquid. Dispersal cells appear to be specialized and exhibit a unique phenotype different from biofilm or planktonic bacteria. Further, the dispersal population is characterized by a high level of heterogeneity, reminiscent of, but distinct from, that in the biofilm, which could potentially allow for improved colonization under various environmental conditions. Here we review recent advances in characterizing the molecular mechanisms that regulate biofilm dispersal events and the impact of dispersal in a broader ecological context. Several strategies that exploit the mechanisms controlling biofilm dispersal to develop as applications for biofilm control are also presented.

Barraza, V, Restrepo-Coupe, N, Huete, A, Grings, F & Van Gorsel, E 2015, 'Passive microwave and optical index approaches for estimating surface conductance and evapotranspiration in forest ecosystems', AGRICULTURAL AND FOREST METEOROLOGY, vol. 213, pp. 126-137.
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Bathgate, EJ, Maynard-Casely, HE, Caprarelli, G, Xiao, L, Stuart, B, Smith, KT & Pogson, R 2015, 'Raman, FTIR and XRD study of Icelandic tephra minerals: implications for Mars', JOURNAL OF RAMAN SPECTROSCOPY, vol. 46, no. 10, pp. 846-855.
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Beggs, PJ, Katelaris, CH, Medek, D, Johnston, FH, Burton, PK, Campbell, B, Jaggard, AK, Vicendese, D, Bowman, DMJS, Godwin, I, Huete, AR, Erbas, B, Green, BJ, Newnham, RM, Newbigin, E, Haberle, SG & Davies, JM 2015, 'Differences in grass pollen allergen exposure across Australia', AUSTRALIAN AND NEW ZEALAND JOURNAL OF PUBLIC HEALTH, vol. 39, no. 1, pp. 51-55.
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© 2015 The Authors © 2015 Public Health Association of Australia. Objective: Allergic rhinitis and allergic asthma are important chronic diseases posing serious public health issues in Australia with associated medical, economic, and societal burdens. Pollen are significant sources of clinically relevant outdoor aeroallergens, recognised as both a major trigger for, and cause of, allergic respiratory diseases. This study aimed to provide a national, and indeed international, perspective on the state of Australian pollen data using a large representative sample. Methods: Atmospheric grass pollen concentration is examined over a number of years within the period 1995 to 2013 for Brisbane, Canberra, Darwin, Hobart, Melbourne, and Sydney, including determination of the 'clinical' grass pollen season and grass pollen peak. Results: The results of this study describe, for the first time, a striking spatial and temporal variability in grass pollen seasons in Australia, with important implications for clinicians and public health professionals, and the Australian grass pollen-allergic community. Conclusions: These results demonstrate that static pollen calendars are of limited utility and in some cases misleading. This study also highlights significant deficiencies and limitations in the existing Australian pollen monitoring and data. Implications: Establishment of an Australian national pollen monitoring network would help facilitate advances in the clinical and public health management of the millions of Australians with asthma and allergic rhinitis.

Behrendt, L, Brejnrod, A, Schliep, M, Sorensen, SJ, Larkum, AWD & Kuhl, M 2015, 'Chlorophyll f-driven photosynthesis in a cavernous cyanobacterium', ISME JOURNAL, vol. 9, no. 9, pp. 2108-2111.
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Bennett, R, Yakkundi, A, McKeen, HD, McClements, L, McKeogh, TJ, McCrudden, CM, Arthur, K, Robson, T & McCarthy, HO 2015, 'RALA-Mediated Delivery of FKBPL Nucleic Acid Therapeutics', Nanomedicine, vol. 10, no. 19, pp. 2989-3001.
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Aims: RALA is a novel 30 mer bioinspired amphipathic peptide that is showing promise for gene delivery. Here, we used RALA to deliver the FK506-binding protein like – FKBPL gene (pFKBPL) – a novel member of the immunophilin protein family. FKBPL is a secreted protein, with overexpression shown to inhibit angiogenesis, tumor growth and stemness, through a variety of intra- and extracellular signaling mechanisms. We also elucidated proangiogenic activity and stemness after utilizing RALA to deliver siRNA (siFKBPL). Materials & methods: The RALA/pFKBPL and RALA/siFKBPL nanoparticles were characterized in terms of size, charge, stability and toxicity. Overexpression and knockdown of FKBPL was assessed in vitro and in vivo. Results: RALA delivered both pFKBPL and siFKBPL with less cytotoxicity than commercially available counterparts. In vivo, RALA/pFKBPL delivery retarded tumor growth, and prolonged survival with an associated decrease in angiogenesis, while RALA/siFKBPL had no effect on tumor growth rate or survival, but resulted in an increase in angiogenesis and stemness. Conclusion: RALA is an effective delivery system for both FKBPL DNA and RNAi and highlights an alternative therapeutic approach to harnessing FKBPL's antiangiogenic and antistemness activity.

Berhane, AM, Choi, S, Kato, H, Makino, T, Mizuochi, N, Yamasaki, S & Aharonovich, I 2015, 'Electrical excitation of silicon-vacancy centers in single crystal diamond', Applied Physics Letters, vol. 106, no. 17, pp. 171102-171102.
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Electrically driven emission from negatively charged silicon-vacancy (SiV)− centers in single crystal diamond is demonstrated. The SiV centers were generated using ion implantation into an i region of a p-i-n single crystal diamond diode. Both electroluminescence and the photoluminescence signals exhibit the typical emission that is attributed to the (SiV)− centers. Under forward and reversed biased PL measurements, no signal from the neutral (SiV)0 defect could be observed. The realization of electrically driven (SiV)− emission is promising for scalable nanophotonics devices employing color centers in single crystal diamond.

Beringer, J, Hutley, LB, Abramson, D, Arndt, SK, Briggs, P, Bristow, M, Canadell, JG, Cernusak, LA, Eamus, D, Edwards, AC, Evans, BJ, Fest, B, Goergen, K, Grover, SP, Hacker, J, Haverd, V, Kanniah, K, Livesley, SJ, Lynch, A, Maier, S, Moore, C, Raupach, M, Russell-Smith, J, Scheiter, S, Tapper, NJ & Uotila, P 2015, 'Fire in Australian savannas: from leaf to landscape', GLOBAL CHANGE BIOLOGY, vol. 21, no. 1, pp. 62-81.
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Savanna ecosystems comprise 22% of the global terrestrial surface and 25% of Australia (almost 1.9 million km2) and provide significant ecosystem services through carbon and water cycles and the maintenance of biodiversity. The current structure, composition and distribution of Australian savannas have coevolved with fire, yet remain driven by the dynamic constraints of their bioclimatic niche. Fire in Australian savannas influences both the biophysical and biogeochemical processes at multiple scales from leaf to landscape. Here, we present the latest emission estimates from Australian savanna biomass burning and their contribution to global greenhouse gas budgets. We then review our understanding of the impacts of fire on ecosystem function and local surface water and heat balances, which in turn influence regional climate. We show how savanna fires are coupled to the global climate through the carbon cycle and fire regimes. We present new research that climate change is likely to alter the structure and function of savannas through shifts in moisture availability and increases in atmospheric carbon dioxide, in turn altering fire regimes with further feedbacks to climate. We explore opportunities to reduce net greenhouse gas emissions from savanna ecosystems through changes in savanna fire management.

Bi, J, Knyazikhin, Y, Choi, S, Park, T, Barichivich, J, Ciais, P, Fu, R, Ganguly, S, Hall, F, Hilker, T, Huete, A, Jones, M, Kimball, J, Lyapustin, AI, Mottus, M, Nemani, RR, Piao, S, Poulter, B, Saleska, SR, Saatchi, SS, Xu, L, Zhou, L & Myneni, RB 2015, 'Sunlight mediated seasonality in canopy structure and photosynthetic activity of Amazonian rainforests', ENVIRONMENTAL RESEARCH LETTERS, vol. 10, no. 6.
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Bids, RC, Rust, LT, Nizio, KD, Rai, T, Stuart, BH & Forbes, SL 2015, 'Investigating the sensitivity of cadaver-detection dogs to decomposition fluid', Journal of Forensic Identification, vol. 65, no. 6, pp. 985-997.
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Cadaver-detection dogs are regularly used by police and emergency services to locate human remains. Because of ethical restrictions, the dogs are not trained using cadavers, but instead, on pseudo-scents or human tissues, such as blood, bone, and decomposition fluid. However, the accuracy of these training aids as substitutes for human remains is unknown. The aim of this study was to investigate the dogs' sensitivity to human decomposition fluid as a training aid and to determine whether their sensitivity increased with exposure.

Bishop, DP, Hare, DJ, de Grazia, A, Fryer, F & Doble, PA 2015, 'Speciation and quantification of organotin compounds in sediment and drinking water by isotope dilution liquid chromatography-inductively coupled plasma-mass spectrometry', ANALYTICAL METHODS, vol. 7, no. 12, pp. 5012-5018.
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Bishop, DP, Hare, DJ, Fryer, F, Taudte, RV, Cardoso, BR, Cole, N & Doble, PA 2015, 'Determination of selenium in serum in the presence of gadolinium with ICP-QQQ-MS', The Analyst, vol. 140, no. 8, pp. 2842-2846.
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Triple–quadrupole ICP-MS using O₂mass-shift technology is superior for removing gadolinium interference on selenium in serum.

Biswas, NN, Kutty, SK, Barraud, N, Iskander, GM, Griffith, R, Rice, SA, Willcox, M, Black, DS & Kumar, N 2015, 'Indole-based novel small molecules for the modulation of bacterial signalling pathways', Organic & Biomolecular Chemistry, vol. 13, no. 3, pp. 925-937.
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Indole basedN-acylatedl-homoserine lactone (AHL) mimics were developed as quorum sensing (QS) inhibitors for Gram-negative bacteriaPseudomonas aeruginosaand can be used as novel antimicrobial agents.

Bogema, DR, Deutscher, AT, Fell, S, Collins, D, Eamens, GJ & Jenkins, C 2015, 'Development and Validation of a Quantitative PCR Assay Using Multiplexed Hydrolysis Probes for Detection and Quantification of Theileria orientalis Isolates and Differentiation of Clinically Relevant Subtypes', JOURNAL OF CLINICAL MICROBIOLOGY, vol. 53, no. 3, pp. 941-950.
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Copyright © 2015, American Society for Microbiology. All Rights Reserved. Theileria orientalis is an emerging pathogen of cattle in Asia, Australia, and New Zealand. This organism is a vector-borne hemoprotozoan that causes clinical disease characterized by anemia, abortion, and death, as well as persistent subclinical infections. Molecular methods of diagnosis are preferred due to their sensitivity and utility in differentiating between pathogenic and apathogenic genotypes. Conventional PCR (cPCR) assays for T. orientalis detection and typing are laborious and do not provide an estimate of parasite load. Current real-time PCR assays cannot differentiate between clinically relevant and benign genotypes or are only semiquantitative without a defined clinical threshold. Here, we developed and validated a hydrolysis probe quantitative PCR (qPCR) assay which universally detects and quantifies T. orientalis and identifies the clinically associated Ikeda and Chitose genotypes (UIC assay). Comparison of the UIC assay results with previously validated universal and genotype-specific cPCR results demonstrated that qPCR detects and differentiates T. orientalis with high sensitivity and specificiy. Comparison of quantitative results based on percent parasitemia, determined via blood film analysis and packed cell volume (PCV) revealed significant positive and negative correlations, respectively. One-way analysis of variance (ANOVA) indicated that blood samples from animals with clinical signs of disease contained statistically higher concentrations of T. orientalis DNA than animals with subclinical infections. We propose clinical thresholds to assist in classifying high-, moderate-, and low-level infections and describe how parasite load and the presence of the Ikeda and Chitose genotypes relate to disease.

Bogema, DR, Fell, SA, O'Rourke, BA, Collins, D, Eamens, GJ & Jenkins, C 2015, 'Development and validation of an inexpensive and efficient method for the extraction of Theileria orientalis DNA from blood', VETERINARY PARASITOLOGY, vol. 212, no. 3-4, pp. 379-381.
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Booth, DJ, Gribben, P & Parkinson, K 2015, 'Impact of cigarette butt leachate on tidepool snails', Marine Pollution Bulletin, vol. 95, no. 1, pp. 362-364.
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© 2015 Elsevier Ltd. In urban areas, cigarette butts are the most common discarded refuse articles. In marine intertidal zones, they often fall into tidepools. We tested how common intertidal molluscs were affected by butt leachate in a laboratory experiment, where snails were exposed to various leachate concentrations. Mortality was very high, with all species showing 100% mortality at the full leachate concentration (5 butts per litre and 2. h soak time) after 8. days. However, Austrocochlea porcata showed higher mortality than the other 2 species at lower concentrations (10%, 25%) which may affect the relative abundance of the 3 snails under different concentrations of leachate pollution. Also, sublethal effects of leachate on snail activity were observed, with greater activity of Nerita atramentosa than the other 2 species at higher concentrations, suggesting it is more resilient than the other 2 species. While human health concerns predominate with respect to smoking, we show strong lethal and sublethal (via behavioural modifications) impacts of discarded butts on intertidal organisms, with even closely-related taxa responding differently.

Bordin, DCM, Monedeiro, FFDSS, Campos, EGD, Alves, MNR, Bueno, LHP & Martinis, BSD 2015, 'Técnicas de preparo de amostras biológicas com interesse forense', Scientia Chromatographica, vol. 7, no. 2, pp. 125-143.
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Bradfield, LA, Dezfouli, A, van Holstein, M, Chieng, B & Balleine, BW 2015, 'Medial Orbitofrontal Cortex Mediates Outcome Retrieval in Partially Observable Task Situations', Neuron, vol. 88, no. 6, pp. 1268-1280.
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Choice between actions often requires the ability to retrieve action consequences in circumstances where they are only partially observable. This capacity has recently been argued to depend on orbitofrontal cortex; however, no direct evidence for this hypothesis has been reported. Here, we examined whether activity in the medial orbitofrontal cortex (mOFC) underlies this critical determinant of decision-making in rats. First, we simulated predictions from this hypothesis for various tests of goal-directed action by removing the assumption that rats could retrieve partially observable outcomes and then tested those predictions experimentally using manipulations of the mOFC. The results closely followed predictions; consistent deficits only emerged when action consequences had to be retrieved. Finally, we put action selection based on observable and unobservable outcomes into conflict and found that whereas intact rats selected actions based on the value of retrieved outcomes, mOFC rats relied solely on the value of observable outcomes.

Bray, K, Previdi, R, Gibson, BC, Shimoni, O & Aharonovich, I 2015, 'Enhanced photoluminescence from single nitrogen-vacancy defects in nanodiamonds coated with phenol-ionic complexes', Nanoscale, vol. 7, no. 11, pp. 4869-4874.
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© The Royal Society of Chemistry 2015. Fluorescent nanodiamonds are attracting major attention in the field of bio-sensing and bio-labeling. In this work we demonstrate a robust approach to achieve an encapsulation of individual nanodiamonds with phenol-ionic complexes that enhance the photoluminescence from single nitrogen vacancy (NV) centers. We show that single NV centres in the coated nanodiamonds also exhibit shorter lifetimes, opening another channel for high resolution sensing. We propose that the nanodiamond encapsulation reduces the non-radiative decay pathways of the NV color centers. Our results provide a versatile and assessable way to enhance photoluminescence from nanodiamond defects that can be used in a variety of sensing and imaging applications.

Brayley-Morris, H, Sorrell, A, Revoir, AP, Meakin, GE, Court, DS & Morgan, RM 2015, 'Persistence of DNA from laundered semen stains: Implications for child sex trafficking cases', Forensic Science International: Genetics, vol. 19, pp. 165-171.
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Brodersen, KE, Nielsen, DA, Ralph, PJ & Kuhl, M 2015, 'Oxic microshield and local pH enhancement protects Zostera muelleri from sediment derived hydrogen sulphide', NEW PHYTOLOGIST, vol. 205, no. 3, pp. 1264-1276.
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© 2014 New Phytologist Trust. Seagrass is constantly challenged with transporting sufficient O2 from above- to belowground tissue via aerenchyma in order to maintain aerobic metabolism and provide protection against phytotoxins. Electrochemical microsensors were used in combination with a custom-made experimental chamber to analyse the belowground biogeochemical microenvironment of Zostera muelleri under changing environmental conditions. Measurements revealed high radial O2 release of up to 500 nmol O2 cm-2 h-1 from the base of the leaf sheath, maintaining a c. 300-μm-wide plant-mediated oxic microzone and thus protecting the vital meristematic regions of the rhizome from reduced phytotoxic metabolites such as hydrogen sulphide (H2S). H2S intrusion was prevented through passive diffusion of O2 to belowground tissue from leaf photosynthesis in light, as well as from the surrounding water column into the flow-exposed plant parts during darkness. Under water column hypoxia, high belowground H2S concentrations at the tissue surface correlated with the inability to sustain the protecting oxic microshield around the meristematic regions of the rhizome. We also found increased pH levels in the immediate rhizosphere of Z. muelleri, which may contribute to further detoxification of H2S through shifts in the chemical speciation of sulphide. Zostera muelleri can modify the geochemical conditions in its immediate rhizosphere, thereby reducing its exposure to H2S.

Broich, M, Huete, A, Paget, M, Ma, X, Tulbure, M, Coupe, NR, Evans, B, Beringer, J, Devadas, R, Davies, K & Held, A 2015, 'A spatially explicit land surface phenology data product for science, monitoring and natural resources management applications', ENVIRONMENTAL MODELLING & SOFTWARE, vol. 64, pp. 191-204.
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© 2014 Elsevier Ltd. Land surface phenology (LSP) characterizes episodes of greening and browning of the vegetated land surface from remote sensing imagery. LSP is of interest for quantification and monitoring of crop yield, wildfire fuel accumulation, vegetation condition, ecosystem response and resilience to climate variability and change. Deriving LSP represents an effort for end users and existing global products may not accommodate conditions in Australia, a country with a dry climate and high rainfall variability. To fill this information gap we developed the Australian LSP Product in contribution to AusCover/Terrestrial Ecosystem Research Network (TERN).We describe the product's algorithm and information content consisting of metrics that characterize LSP greening and browning episodes of the vegetated land surface. Our product allows tracking LSP metrics over time and thereby quantifying inter- and intraannual variability across Australia. We demonstrate the metrics' response to ENSO-driven climate variability. Lastly, we discuss known limitations of the current product and future development plans.

Brown, JJ 2015, 'Future Models for Population Census: Can We Have an Administrative Based Census without a Population Register?', Statistics of Ukraine, vol. 2015, no. 3, pp. 45-50.

Bruno, A, de Lange, G, Asaad, S, van der Enden, KL, Langford, NK & DiCarlo, L 2015, 'Reducing intrinsic loss in superconducting resonators by surface treatment and deep etching of silicon substrates', Applied Physics Letters, vol. 106, no. 18, pp. 182601-182601.
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We present microwave-frequency NbTiN resonators on silicon, systematically achieving internal quality factors above 1 M in the quantum regime. We use two techniques to reduce losses associated with two-level systems: an additional substrate surface treatment prior to NbTiN deposition to optimize the metal-substrate interface and deep reactive-ion etching of the substrate to displace the substrate-vacuum interfaces away from high electric fields. The temperature and power dependence of resonator behavior indicate that two-level systems still contribute significantly to energy dissipation, suggesting that more interface optimization could further improve performance.

Buividas, R, Aharonovich, I, Seniutinas, G, Wang, XW, Rapp, L, Rode, AV, Taniguchi, T & Juodkazis, S 2015, 'Photoluminescence from voids created by femtosecond-laser pulses inside cubic-BN', OPTICS LETTERS, vol. 40, no. 24, pp. 5711-5713.
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Busschaert, N, Caltagirone, C, Van Rossom, W & Gale, PA 2015, 'Applications of Supramolecular Anion Recognition', Chemical Reviews, vol. 115, no. 15, pp. 8038-8155.
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Cabrera-Guzmán, E, Crossland, MR, Pearson, D, Webb, JK & Shine, R 2015, 'Predation on invasive cane toads (Rhinella marina) by native Australian rodents', Journal of Pest Science, vol. 88, no. 1, pp. 143-153.
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© 2014, Springer-Verlag Berlin Heidelberg. The success of an invasive species can be reduced by biotic resistance from the native fauna. For example, an invader that is eaten by native predators is less likely to thrive than one that is invulnerable. The ability of invasive cane toads (Rhinella marina) to spread through Australia has been attributed to the toad’s potent defensive chemicals that can be fatal if ingested by native snakes, lizards, marsupials and crocodiles. However, several taxa of native insects and birds are resistant to cane toad toxins. If native rodents are also capable of eating toads (as suggested by anecdotal reports), these large, abundant and voracious predators might reduce toad numbers. Our field observations and laboratory trials confirm that native rodents (Melomys burtoni, Rattus colletti and Rattus tunneyi) readily kill and consume cane toads (especially small toads), and are not overtly affected by toad toxins. Captive rodents did not decrease their consumption of toads over successive trials, and ate toads even when alternative food types were available. In combination with anecdotal reports, our data suggest that rodents (both native and invasive) are predators of cane toads in Australia. Despite concerns about the decline of rodents following the invasion of toads, our data suggest that the species we studied are not threatened by toads as toxic prey, and no specific conservation actions are required to ensure their persistence.

Cai, H, An, X, Wen, S, Li, J, Zhang, G, Shi, X & Shen, M 2015, 'Facile Synthesis of Gd(OH)₃‐Doped Fe₃O₄ Nanoparticles for Dual‐Mode T₁‐ and T₂‐Weighted Magnetic Resonance Imaging Applications', Particle & Particle Systems Characterization, vol. 32, no. 10, pp. 934-943.
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The facile hydrothermal synthesis of polyethyleneimine (PEI)‐coated iron oxide (Fe3O4) nanoparticles (NPs) doped with Gd(OH)3 (Fe3O4‐Gd(OH)3‐PEI NPs) for dual mode T1‐ and T2‐weighted magnetic resonance (MR) imaging applications is reported. In this approach, Fe3O4‐Gd(OH)3‐PEI NPs are synthesized via a hydrothermal method in the presence of branched PEI and Gd(III) ions. The PEI coating onto the particle surfaces enables further modification of poly(ethylene glycol) (PEG) in order to render the particles with good water dispersibility and improved biocompatibility. The formed Fe3O4‐Gd(OH)3‐PEI‐PEG NPs have a Gd/Fe molar ratio of 0.25:1 and a mean particle size of 14.4 nm and display a relatively high r2 (151.37 × 10−3m−1 s−1) and r1 (5.63 × 10−3m−1 s−1) relaxivity, affording their uses as a unique contrast agent for T1‐ and T2‐weighted MR imaging of rat livers after mesenteric vein injection of the particles and the mouse liver after intravenous injection of the particles, respectively. The developed Fe3O4‐Gd(OH)3‐PEI‐PEG NPs may hold great promise to be used as a contrast agent for dual mode T1‐ and T2‐weighted self‐confirmation MR imaging of different biological systems.

Cai, H, Li, K, Li, J, Wen, S, Chen, Q, Shen, M, Zheng, L, Zhang, G & Shi, X 2015, 'Dendrimer-Assisted Formation of Fe₃O₄/Au Nanocomposite Particles for Targeted Dual Mode CT/MR Imaging of Tumors', Small, vol. 11, no. 35, pp. 4584-4593.
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Cai, M, Wei, T, Zhou, B, Tian, Y, Zhou, J, Xu, S & Zhang, J 2015, 'Analysis of energy transfer process based emission spectra of erbium doped germanate glasses for mid-infrared laser materials', Journal of Alloys and Compounds, vol. 626, pp. 165-172.
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Er3+ activated germanate glass with good thermal stability was prepared. Bonding parameters have been calculated and the nature of ionic bonding of the germanate glass has been determined. Mid-infrared fluorescence was observed and corresponding radiative properties were investigated. For Er3+:4I11/2→4I13/2 transition, high spontaneous radiative transition probability (30.09 s−1), large emission cross section ((14.84 ± 0.10) × 10−21 cm2) and superior gain performance were obtained from the prepared glass. Besides, energy transfer processes concerning the 2.7 μm emission were also discussed in detail. According to simplified rate equation and Dexter’s theory, energy transfer microscopic parameters were computed to elucidate observed 2.7 μm emissions. Results demonstrate that the prepared germanate glass possessing excellent spectroscopic properties might be an attractive candidate for mid-infrared laser or amplifier.

Cai, M, Zhou, B, Wang, F, Tian, Y, Zhou, J, Xu, S & Zhang, J 2015, 'Highly efficient mid-infrared 2 μm emission in Ho^3+/Yb^3+-codoped germanate glass', Optical Materials Express, vol. 5, no. 6, pp. 1431-1431.
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This work reports the mid-infrared emission properties around 2 μm in Ho3+/Yb3+ codoped germanate glasses. The glass not only possesses good chemical durability and good thermal stability but also has high mid-infrared transmittance around 2 μm (90%). In addition, the glass possesses considerably low OH− content (20.45 ppm) and large spontaneous transition probability (103.38 s−1) corresponding to the Ho3+:5I7→5I8 transition. Moreover, the measured lifetime of Ho3+:5I7 level is as high as 7.68 ms, and the quantum efficiency at 2 μm can reach 79.4%. The energy transfer processes of Yb3+:2F5/2 level and Ho3+:5I6 level were quantitatively analyzed according to the rate equation. Results indicate that the prepared germanate glass is a promising candidate for 2 μm mid-infrared laser materials applications.

Cai, M, Zhou, B, Wang, F, Tian, Y, Zhou, J, Xu, S & Zhang, J 2015, 'Mid-infrared emission and quantitative analysis of energy transfer processes in Er3+ doped oxyfluogermanate glasses', Journal of Applied Physics, vol. 117, no. 24, pp. 243106-243106.
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Oxyfluogermanate glasses with good thermal stability were prepared by melt-quenching method. The investigation of 2.7 μm fluorescence spectra and energy transfer mechanism was performed pumped by an 808 nm laser diode. The 2.7 μm radiative transition probability and emission cross section are 32.62 s−1 and 12.88 × 10−21 cm2, respectively. The energy transfer parameters between 4I11/2 and 4I13/2 levels were calculated by Inokuti-Hirayama and Yokota-Tanimoto's model to further elucidate 2.7 μm fluorescent behaviors. It is found that the energy transfer mechanism among Er3+ is mainly dominated by dipole-dipole interactions. Results indicate that the prepared oxyfluogermanate glass is a promising candidate for mid-infrared laser applications.

Cai, M, Zhou, B, Wang, F, Wei, T, Tian, Y, Zhou, J, Xu, S & Zhang, J 2015, 'R2O3 (R = La, Y) modified erbium activated germanate glasses for mid-infrared 2.7 μm laser materials', Scientific Reports, vol. 5, no. 1, pp. 1-11.
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AbstractEr3+ activated germanate glasses modified by La2O3 and Y2O3 with good thermal stability were prepared. 2.7 μm fluorescence was observed and corresponding radiative properties were investigated. A detailed discussion of J–O parameters has been carried out based on absorption spectra and Judd–Ofelt theory. The peak emission cross sections of La2O3 and Y2O3 modified germanate glass are (14.3 ± 0.10) × 10−21 cm2 and (15.4 ± 0.10) × 10−21 cm2, respectively. Non-radiative relaxation rate constants and energy transfer coefficients of 4I11/2 and 4I13/2 levels have been obtained and discussed to understand the 2.7 μm fluorescence behavior. Moreover, the energy transfer processes of 4I11/2 and 4I13/2 level were quantitatively analyzed according to Dexter’s theory and Inokuti–Hirayama model. The theoretical calculations are in good agreement with the observed 2.7 μm fluorescence phenomena. Results demonstrate that the Y2O3 modified germanate glass, which possesses more excellent spectroscopic properties than La2O3 modified germanate glass, might be an attractive candidate for mid-infrared laser.

Camp, EF, Krause, S-L, Santos, LMF, Naumann, MS, Kikuchi, RKP, Smith, DJ, Wild, C & Suggett, DJ 2015, 'The “Flexi-Chamber”: A Novel Cost-Effective In Situ Respirometry Chamber for Coral Physiological Measurements', PLOS ONE, vol. 10, no. 10, pp. e0138800-e0138800.
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© 2015 Camp et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Coral reefs are threatened worldwide, with environmental stressors increasingly affecting the ability of reef-building corals to sustain growth from calcification (G), photosynthesis (P) and respiration (R). These processes support the foundation of coral reefs by directly influencing biogeochemical nutrient cycles and complex ecological interactions and therefore represent key knowledge required for effective reef management. However, metabolic rates are not trivial to quantify and typically rely on the use of cumbersome in situ respirometry chambers and/or the need to remove material and examine ex situ, thereby fundamentally limiting the scale, resolution and possibly the accuracy of the rate data. Here we describe a novel low-cost in situ respirometry bag that mitigates many constraints of traditional glass and plexi-glass incubation chambers. We subsequently demonstrate the effectiveness of our novel 'Flexi-Chamber' approach via two case studies: 1) the Flexi-Chamber provides values of P, R and G for the reef-building coral Siderastrea cf. stellata collected from reefs close to Salvador, Brazil, which were statistically similar to values collected from a traditional glass respirometry vessel; and 2) wide-scale application of obtaining P, R and G rates for different species across different habitats to obtain inter- and intra-species differences. Our novel cost-effective design allows us to increase sampling scale of metabolic rate measurements in situ without the need for destructive sampling and thus significantly expands on existing research potential, not only for corals as we have demonstrated here, but also other important benthic groups.

Campbell, LT, Padula, MP, Harry, E & Carter, DA 2015, 'You are what you secrete: extracellular proteins and virulence in Cryptococcus', Microbiology Australia, vol. 36, no. 2, pp. 93-93.
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Fungal organisms secrete a wide range of biomolecules, including degradative enzymes that are essential for nutrition, toxins, effectors and secondary compounds that modulate interactions with host animals and plants, and a variety of signaling and stress-related proteins1 . As these are likely to be key determinants of virulence and may also be useful diagnostic and therapeutic targets, we investigated the secretome of different strains of the fungal pathogen Cryptococcus. Virulent strains secreted predominantly hydrolytic and proteolytic enzymes, while the least virulent strain secreted a range of additional non-degradative proteins including many that lacked secretion signals, some that appear to be ‘moonlighting’, and a number that are known to be allergenic. It appears that in Cryptococcus, the secretome may influence virulence both through the presence of harmful enzymes and through the absence of proteins that alert the host defence mechanisms.

Campbell, LT, Simonin, AR, Chen, C, Ferdous, J, Padula, MP, Harry, E, Hofer, M, Campbell, IL & Carter, DA 2015, 'Cryptococcus Strains with Different Pathogenic Potentials Have Diverse Protein Secretomes', Eukaryotic Cell, vol. 14, no. 6, pp. 554-563.
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ABSTRACT Secreted proteins are the frontline between the host and pathogen. In mammalian hosts, secreted proteins enable invasive infection and can modulate the host immune response. Cryptococcosis, caused by pathogenic Cryptococcus species, begins when inhaled infectious propagules establish to produce pulmonary infection, which, if not resolved, can disseminate to the central nervous system to cause meningoencephalitis. Strains of Cryptococcus species differ in their capacity to cause disease, and the mechanisms underlying this are not well understood. To investigate the role of secreted proteins in disease, we determined the secretome for three genome strains of Cryptococcus species, including a hypovirulent and a hypervirulent strain of C. gattii and a virulent strain of C. neoformans . Sixty-seven unique proteins were identified, with different numbers and types of proteins secreted by each strain. The secretomes of the virulent strains were largely limited to proteolytic and hydrolytic enzymes, while the hypovirulent strain had a diverse secretome, including non-conventionally secreted canonical cytosolic and immunogenic proteins that have been implicated in virulence. The hypovirulent strain cannot establish pulmonary infection in a mouse model, but strains of this genotype have caused human meningitis. To directly test brain infection, we used intracranial inoculation and found that the hypovirulent strain was substantially more ...

Cao, X, Tao, L, Wen, S, Hou, W & Shi, X 2015, 'Hyaluronic acid-modified multiwalled carbon nanotubes for targeted delivery of doxorubicin into cancer cells', Carbohydrate Research, vol. 405, pp. 70-77.
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Cardoso, BR, Roberts, BR, Bush, AI & Hare, DJ 2015, 'Selenium, selenoproteins and neurodegenerative diseases', Metallomics, vol. 7, no. 8, pp. 1213-1228.
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AbstractIt is unsurprising that our understanding of the role of selenium in neurological function is somewhat immature, considering its relatively recent discovery as an essential element to human health. Selenocysteine, the 21st amino acid, is the defining feature of the 25 selenoprotein-encoding genes so far discovered within the human genome. The low abundance of these proteins in the brain belies the integral role they play in normal neurological function, from well-characterised antioxidant activity in the periphery to poorly understood mechanisms that modulate mitochondrial function and response to brain pathology. Selenium has been identified as playing a role in several neurodegenerative disorders, including Alzheimer's and Parkinson's disease, though its function as a ‘cause or effect’ of disease process remains unclear. This review discusses selenium metabolism in detail, specifically with regard to the role it plays within the central nervous system, and examines the most current literature investigating how selenium may be involved in chronic diseases of the central nervous system.

Care, A, Bergquist, PL & Sunna, A 2015, 'Solid-binding peptides: smart tools for nanobiotechnology', Trends in Biotechnology, vol. 33, no. 5, pp. 259-268.
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Carney, RL, Mitrovic, SM, Jeffries, T, Westhorpe, D, Curlevski, N & Seymour, JR 2015, 'River bacterioplankton community responses to a high inflow event', Aquatic Microbial Ecology, vol. 75, no. 3, pp. 187-205.
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© Inter-Research 2015. Microbes drive chemical cycling and productivity within river ecosystems, but their influence may shift when intense allochthonous inputs accompany high freshwater inflow (flood) events. Investigating how floods influence microbial processes is fundamentally important for our understanding of river ecology, but is generally overlooked. We analysed bacterioplankton community composition (BCC) and abundance over 4 mo following an enormous flood event in the Hunter River, Australia, that resulted in a major fish kill. Concentrations of dissolved organic carbon (DOC) and inorganic nutrients (N and P) were up to 3 times higher during the flood event compared to prior and subsequent months. Bacterial cell abundances were up to 10 times higher at impacted sites during the flood event. Using Automated Ribosomal Intergenic Spacer Analysis we found significant shifts in BCC between the flood impacted month and subsequent months (p < 0.05). Distance linear modelling indicated that DOC and dissolved N and P correlated most strongly with BCC patterns during the high inflow, whereas community dynamics correlated most strongly with nitrogen oxides and ammonium during the river's recovery phase. 16S rRNA amplicon pyrosequencing revealed that common soil-associated and facultative anaerobic genera of Proteobacteria were most dominant during the flood period, suggesting that a proportion of the bacterial community observed during this event were potentially inactive soil microbes transported into the river via terrestrial runoff. During the recovery period, Cyanobacteria and freshwater- associated genera of Actinobacteria and Proteobacteria became dominant in 16S rRNA pyrosequencing profiles. These observations indicate that allochthonous nutrients delivered via floods can significantly stimulate bacterial growth, underpinning substrate-controlled succession of bacterial communities and ultimately shaping the ecology within river ecosystems.

Carroll, L, Pattison, DI, Fu, S, Schiesser, CH, Davies, MJ & Hawkins, CL 2015, 'Reactivity of selenium-containing compounds with myeloperoxidase-derived chlorinating oxidants: Second-order rate constants and implications for biological damage', FREE RADICAL BIOLOGY AND MEDICINE, vol. 84, pp. 279-288.
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© 2015 Elsevier Inc. All rights reserved. Hypochlorous acid (HOCl) and N-chloramines are produced by myeloperoxidase (MPO) as part of the immune response to destroy invading pathogens. However, MPO also plays a detrimental role in inflammatory pathologies, including atherosclerosis, as inappropriate production of oxidants, including HOCl and N-chloramines, causes damage to host tissue. Low molecular mass thiol compounds, including glutathione (GSH) and methionine (Met), have demonstrated efficacy in scavenging MPO-derived oxidants, which prevents oxidative damage in vitro and ex vivo. Selenium species typically have greater reactivity toward oxidants compared to the analogous sulfur compounds, and are known to be efficient scavengers of HOCl and other hypohalous acids produced by MPO. In this study, we examined the efficacy of a number of sulfur and selenium compounds to scavenge a range of biologically relevant N-chloramines and oxidants produced by both isolated MPO and activated neutrophils and characterized the resulting selenium-derived oxidation products in each case. A dose-dependent decrease in the concentration of each N-chloramine was observed on addition of the sulfur compounds (cysteine, methionine) and selenium compounds (selenomethionine, methylselenocysteine, 1,4-anhydro-4-seleno-L-talitol, 1,5-anhydro-5-selenogulitol) studied. In general, selenomethionine was the most reactive with N-chloramines (k2 0.8-3.4×10³ M^-1 s^-1) with 1,5-anhydro-5-selenogulitol and 1,4-anhydro-4-seleno-L-talitol (k2 1.1-6.8×10² M^-1 s^-1) showing lower reactivity. This resulted in the formation of the respective selenoxides as the primary oxidation products. The selenium compounds demonstrated greater ability to remove protein N-chloramines compared to the analogous sulfur compounds. These reactions may have implications for preventing cellular damage in vivo, particularly under...

Carter, DR, Murray, J, Cheung, BB, Gamble, L, Koach, J, Tsang, J, Sutton, S, Kalla, H, Syed, S, Gifford, AJ, Issaeva, N, Biktasova, A, Atmadibrata, B, Sun, Y, Sokolowski, N, Ling, D, Kim, PY, Webber, H, Clark, A, Ruhle, M, Liu, B, Oberthuer, A, Fischer, M, Byrne, J, Saletta, F, Thwe, LM, Purmal, A, Haderski, G, Burkhart, C, Speleman, F, De Preter, K, Beckers, A, Ziegler, DS, Liu, T, Gurova, KV, Gudkov, AV, Norris, MD, Haber, M & Marshall, GM 2015, 'Therapeutic targeting of the MYC signal by inhibition of histone chaperone FACT in neuroblastoma', Science Translational Medicine, vol. 7, no. 312.
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Histone chaperone FACT acts in a positive feedback loop with MYCN and is a therapeutic target in neuroblastoma.

Castorina, A & Marzagalli, R 2015, 'The seeming paradox of adenosine receptors as targets for the treatment of Alzheimer′s disease: agonists or antagonists?', Neural Regeneration Research, vol. 10, no. 2, pp. 205-205.
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Castorina, A, Szychlinska, M, Marzagalli, R & Musumeci, G 2015, 'Mesenchymal stem cells-based therapy as a potential treatment in neurodegenerative disorders: is the escape from senescence an answer?', Neural Regeneration Research, vol. 10, no. 6, pp. 850-850.
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Castorina, A, Waschek, JA, Marzagalli, R, Cardile, V & Drago, F 2015, 'PACAP Interacts with PAC1 Receptors to Induce Tissue Plasminogen Activator (tPA) Expression and Activity in Schwann Cell-Like Cultures', PLOS ONE, vol. 10, no. 2, pp. e0117799-e0117799.
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Cawsey, T, Duflou, J, Weickert, CS & Gorrie, CA 2015, 'Nestin-Positive Ependymal Cells Are Increased in the Human Spinal Cord after Traumatic Central Nervous System Injury', Journal of Neurotrauma, vol. 32, no. 18, pp. 1393-1402.
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© 2015, Mary Ann Liebert, Inc. Endogenous neural progenitor cell niches have been identified in adult mammalian brain and spinal cord. Few studies have examined human spinal cord tissue for a neural progenitor cell response in disease or after injury. Here, we have compared cervical spinal cord sections from 14 individuals who died as a result of nontraumatic causes (controls) with 27 who died from injury with evidence of trauma to the central nervous system. Nestin immunoreactivity was used as a marker of neural progenitor cell response. There were significant increases in the percentage of ependymal cells that were nestin positive between controls and trauma cases. When sections from lumbar and thoracic spinal cord were available, nestin positivity was seen at all three spinal levels, suggesting that nestin reactivity is not simply a localized reaction to injury. There was a positive correlation between the percentage of ependymal cells that were nestin positive and post-injury survival time but not for age, postmortem delay, or glial fibrillary acidic protein (GFAP) immunoreactivity. No double-labelled nestin and GFAP cells were identified in the ependymal, subependymal, or parenchymal regions of the spinal cord. We need to further characterize this subset of ependymal cells to determine their role after injury, whether they are a population of neural progenitor cells with the potential for proliferation, migration, and differentiation for spinal cord repair, or whether they have other roles more in line with hypothalamic tanycytes, which they closely resemble.

Červený, J, Sinetova, M, Zavřel, T & Los, D 2015, 'Mechanisms of High Temperature Resistance of Synechocystis sp. PCC 6803: An Impact of Histidine Kinase 34', Life, vol. 5, no. 1, pp. 676-699.
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Synechocystis sp. PCC 6803 is a widely used model cyanobacterium for studying responses and acclimation to different abiotic stresses. Changes in transcriptome, proteome, lipidome, and photosynthesis in response to short term heat stress are well studied in this organism, and histidine kinase 34 (Hik34) is shown to play an important role in mediating such response. Corresponding data on long term responses, however, are fragmentary and vary depending on parameters of experiments and methods of data collection, and thus are hard to compare. In order to elucidate how the early stress responses help cells to sustain long-term heat stress, as well as the role of Hik34 in prolonged acclimation, we examined the resistance to long-term heat stress of wild-type and ΔHik34 mutant of Synechocystis. In this work, we were able to precisely control the long term experimental conditions by cultivating Synechocystis in automated photobioreactors, measuring selected physiological parameters within a time range of minutes. In addition, morphological and ultrastructural changes in cells were analyzed and western blotting of individual proteins was used to study the heat stress-affected protein expression. We have shown that the majority of wild type cell population was able to recover after 24 h of cultivation at 44 °C. In contrast, while ΔHik34 mutant cells were resistant to heat stress within its first hours, they could not recover after 24 h long high temperature treatment. We demonstrated that the early induction of HspA expression and maintenance of high amount of other HSPs throughout the heat incubation is critical for successful adaptation to long-term stress. In addition, it appears that histidine kinase Hik34 is an essential component for the long term high temperature resistance.

Chacko, A, Beagley, KW, Timms, P & Huston, WM 2015, 'Human Chlamydia pneumoniae isolates demonstrate ability to recover infectivity following penicillin treatment whereas animal isolates do not', FEMS Microbiology Letters, vol. 362, no. 6, pp. 1-7.
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© FEMS 2015. All rights reserved. Chlamydia pneumoniae strains have recently been demonstrated to have substantially different capacities to enter and recover from IFN-γ-induced persistence, depending on whether they are from human or animal host sources. Here, we examined the ability of two human and two animal strains to enter and be rescued from penicillin-induced persistence. The ability to form inclusions after the addition of penicillin was much reduced in the two animal isolates (koala LPCoLN, bandicoot B21) compared to the two human isolates (respiratory AR39 and heart A03). The penicillin treatment resulted in a dose-dependent loss of infectious progeny for all isolates, with the human strains failing to produce infectious progeny at lower doses of penicillin than the animal strains. The most remarkable finding however was the contrasting ability of the isolates to recover infectious progeny production after rescue by removal of the penicillin (at 72 h) and continued culture. The animal isolates both showed virtually no recovery from the penicillin treatment conditions. In contrast, the human isolates showed a significant ability to recovery infectivity, with the heart isolate (A03) showing the most marked recovery. Combined, these data further support the hypothesis that the ability to establish and recover from persistence appears to be enhanced in human C. pneumoniae strains compared to animal strains.

Chaiyadet, S, Smout, M, Johnson, M, Whitchurch, C, Turnbull, L, Kaewkes, S, Sotillo, J, Loukas, A & Sripa, B 2015, 'Excretory/secretory products of the carcinogenic liver fluke are endocytosed by human cholangiocytes and drive cell proliferation and IL6 production', International Journal for Parasitology, vol. 45, no. 12, pp. 773-781.
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© 2015 Australian Society for Parasitology Inc. Liver fluke infection caused by Opisthorchis viverrini remains a major public health problem in many parts of Asia including Thailand, Lao PDR, Vietnam and Cambodia, where there is a strikingly high incidence of cholangiocarcinoma (CCA - hepatic cancer of the bile duct epithelium). Among other factors, uptake of O. viverrini excretory/secretory products (OvES) by biliary epithelial cells has been postulated to be responsible for chronic inflammation and proliferation of cholangiocytes, but the mechanisms by which cells internalise O. viverrini excretory/secretory products are still unknown. Herein we incubated normal human cholangiocytes (H69), human cholangiocarcinoma cells (KKU-100, KKU-M156) and human colon cancer (Caco-2) cells with O. viverrini excretory/secretory products and analysed the effects of different endocytic inhibitors to address the mechanism of cellular uptake of ES proteins. Opisthorchis viverrini excretory/secretory products was internalised preferentially by liver cell lines, and most efficiently/rapidly by H69 cells. There was no evidence for trafficking of ES proteins to cholangiocyte organelles, and most of the fluorescence was detected in the cytoplasm. Pretreatment with clathrin inhibitors significantly reduced the uptake of O. viverrini excretory/secretory products, particularly by H69 cells. Opisthorchis viverrini excretory/secretory products induced proliferation of liver cells (H69 and CCA lines) but not intestinal (Caco-2) cells, and proliferation was blocked using inhibitors of the classical endocytic pathways (clathrin and caveolae). Opisthorchis viverrini excretory/secretory products drove IL6 secretion by H69 cells but not Caco-2 cells, and cytokine secretion was significantly reduced by endocytosis inhibitors. This the first known study to address the endocytosis of helminth ES proteins by host epithelial cells and sheds light on the pathways by which this parasite caus...

Chaiyadet, S, Sotillo, J, Smout, M, Cantacessi, C, Jones, MK, Johnson, MS, Turnbull, L, Whitchurch, CB, Potriquet, J, Laohaviroj, M, Mulvenna, J, Brindley, PJ, Bethony, JM, Laha, T, Sripa, B & Loukas, A 2015, 'Carcinogenic Liver Fluke Secretes Extracellular Vesicles That Promote Cholangiocytes to Adopt a Tumorigenic Phenotype', Journal of Infectious Diseases, vol. 212, no. 10, pp. 1636-1645.
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© The Author 2015. Background. Throughout Asia, there is an unprecedented link between cholangiocarcinoma and infection with the liver fluke Opisthorchis viverrini. Multiple processes, including chronic inflammation and secretion of parasite proteins into the biliary epithelium, drive infection toward cancer. Until now, the mechanism and effects of parasite protein entry into cholangiocytes was unknown. Methods. Various microscopy techniques were used to identify O. viverrini extracellular vesicles (EVs) and their internalization by human cholangiocytes. Using mass spectrometry we characterized the EV proteome and associated changes in cholangiocytes after EV uptake, and we detected EV proteins in bile of infected hamsters and humans. Cholangiocyte proliferation and interleukin 6 (IL-6) secretion was measured to assess the impact of EV internalization. Results. EVs were identified in fluke culture medium and bile specimens from infected hosts. EVs internalized by cholangiocytes drove cell proliferation and IL-6 secretion and induced changes in protein expression associated with endocytosis, wound repair, and cancer. Antibodies to an O. viverrini tetraspanin blocked EV uptake and IL-6 secretion by cholangiocytes. Conclusions. This is the first time that EVs from a multicellular pathogen have been identified in host tissues. Our findings imply a role for O. viverrini EVs in pathogenesis and highlight an approach to vaccine development for this infectious cancer.

Chan, D, Barratt, J, Roberts, T, Lee, R, Shea, M, Marriott, D, Harkness, J, Malik, R, Jones, M, Aghazadeh, M, Ellis, J & Stark, D 2015, 'The Prevalence of Angiostrongylus cantonensis/mackerrasae Complex in Molluscs from the Sydney Region', PLOS ONE, vol. 10, no. 5.
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© 2015 Chan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Angiostrongylus cantonensis and Angiostrongylus mackerrasae are metastrongyloid nematodes that infect various rat species. Terrestrial and aquatic molluscs are intermediate hosts of these worms while humans and dogs are accidental hosts. Angiostrongylus cantonensis is the major cause of angiostrongyliasis, a disease characterised by eosinophilic meningitis. Although both A. cantonensis and A. mackerrasae are found in Australia, A. cantonensis appears to account for most infections in humans and animals. Due to the occurrence of several severe clinical cases in Sydney and Brisbane, the need for epidemiological studies on angiostrongyliasis in this region has become apparent. In the present study, a conventional PCR and a TaqMan assay were compared for their ability to amplify Angiostrongylus DNA from DNA extracted from molluscs. The TaqMan assay was more sensitive, capable of detecting the DNA equivalent to one hundredth of a nematode larva. Therefore, the TaqMan assay was used to screen molluscs (n=500) of 14 species collected from the Sydney region. Angiostrongylus DNA was detected in 2 of the 14 mollusc species; Cornu aspersum [14/ 312 (4.5%)], and Bradybaenia similaris [1/10 (10%)], which are non-native terrestrial snails commonly found in urban habitats. The prevalence of Angiostrongylus spp. was 3.0% ±0.8% (CI 95%). Additionally, experimentally infected Austropeplea lessoni snails shed A. cantonensis larvae in their mucus, implicating mucus as a source of infection. This is the first Australian study to survey molluscs using real-time PCR and confirms that the garden snail, C. aspersum, is a common intermediate host for Angiostrongylus spp. in Sydney.

Chan, JGY, Tyne, AS, Pang, A, McLachlan, AJ, Perera, V, Chan, JCY, Britton, WJ, Chan, HK, Duke, CC, Young, PM & Traini, D 2015, 'Murine pharmacokinetics of rifapentine delivered as an inhalable dry powder', International Journal of Antimicrobial Agents, vol. 45, no. 3, pp. 319-323.
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Chan, JY, Zhang, K, Zhang, C, Tian, H & Liu, S 2015, 'Novel tungsten stabilizing SrCo1−W O3− membranes for oxygen production', Ceramics International, vol. 41, no. 10, pp. 14935-14940.
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Chan, L & Platen, E 2015, 'Pricing Volatility Derivatives Under the Modified Constant Elasticity of Variance Model', OPERATIONS RESEARCH LETTERS, vol. 43, no. 4, pp. 419-422.
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This paper studies volatility derivatives such as variance and volatility swaps, options on variance in the modified constant elasticity of variance model using the benchmark approach. The analytical expressions of pricing formulas for variance swaps are presented. In addition, the numerical solutions for variance swaps, volatility swaps and options on variance are demonstrated.

Chan, Y, Millard, AD, Wheatley, PJ, Holmes, AB, Mohr, R, Whitworth, AL, Mann, NH, Larkum, AWD, Hess, WR, Scanlan, DJ & Clokie, MRJ 2015, 'Genomic and proteomic characterization of two novel siphovirus infecting the sedentary facultative epibiont cyanobacterium Acaryochloris marina', Environmental Microbiology, vol. 17, no. 11, pp. 4239-4252.
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SummaryAcaryochloris marina is a symbiotic species of cyanobacteria that is capable of utilizing far‐red light. We report the characterization of the phages A‐HIS1 and A‐HIS2, capable of infecting Acaryochloris. Morphological characterization of these phages places them in the family Siphoviridae. However, molecular characterization reveals that they do not show genetic similarity with any known siphoviruses. While the phages do show synteny between each other, the nucleotide identity between the phages is low at 45–67%, suggesting they diverged from each other some time ago. The greatest number of genes shared with another phage (a myovirus infecting marine Synechococcus) was four. Unlike most other cyanophages and in common with the Siphoviridae infecting Synechococcus, no photosynthesis‐related genes were found in the genome. CRISPR (clustered regularly interspaced short palindromic repeats) spacers from the host

Chan, YL, Saad, S, Simar, D, Oliver, B, McGrath, K, van Reyk, D, Bertrand, PP, Gorrie, C, Pollock, C & Chen, H 2015, 'Short term exendin-4 treatment reduces markers of metabolic disorders in female offspring of obese rat dams', INTERNATIONAL JOURNAL OF DEVELOPMENTAL NEUROSCIENCE, vol. 46, pp. 67-75.
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© 2015 Elsevier Ltd. Objectives: Maternal obesity imposes significant health risks in the offspring including diabetes and dyslipidemia. We previously showed that the hypoglycaemic agent exendin-4 (Ex-4) administered from weaning can reverse the maternal impact of 'transmitted disorders' in such offspring. However daily injection for six-weeks was required and the beneficial effect may lapse upon drug withdrawal. This study aimed to investigate whether short term Ex-4 treatment during suckling period in a rodent model can reverse transmitted metabolic disorders due to maternal obesity. Methods: Maternal obesity was induced in female Sprague Dawley rats by high-fat diet feeding for 6 weeks, throughout gestation and lactation. Female offspring were treated with Ex-4 (5. μg/kg/day) between postnatal day (P) 4 and 14. Female offspring were harvested at weaning (P20). Lipid and glucose metabolic markers were measured in the liver and fat. Appetite regulators were measured in the plasma and hypothalamus. Results: Maternal obesity significantly increased body weight, fat mass, and liver weight in the offspring. There was an associated inhibition of peroxisomal proliferator activated receptor gamma coactivator 1α (PGC1α), increased fatty acid synthase (FASN) expression in the liver, and reduced adipocyte triglyceride lipase (ATGL) expression. It also increased the plasma gut hormone ghrelin and reduced glucagon-like peptide-1. Ex-4 treatment partially reversed the maternal impact on adiposity and impaired lipid metabolism in the offspring, with increased liver PGC1α and inhibition of FASN mRNA expression. Ex-4 treatment also increased the expression of a novel fat depletion gene a2-zinc-glycoprotein 1 in the fat tissue. Conclusion: Short term Ex-4 treatment during the suckling period significantly improved the metabolic profile in the offspring from the obese mothers at weaning. Long-term studies are needed to follow such offspring to adulthood to examine the s...

Chejara, DR, Kondaveeti, S & Siddhanta, AK 2015, 'Facile synthesis of new sodium alginate–anthracene based photosensitizers', Polymer Bulletin, vol. 72, no. 1, pp. 35-48.
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Chen, P, Jia, H, Zhong, Z, Han, J, Guo, Q, Zhou, J, Liu, X & Qiu, J 2015, 'Magnetic field modulated upconversion luminescence in NaYF₄:Yb,Er nanoparticles', Journal of Materials Chemistry C, vol. 3, no. 34, pp. 8794-8798.
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Magnetic field enhanced the upconversion luminescence for the enhanced energy transfer from Yb³⁺ to Er³⁺ in NaYF₄ nanoparticles.

Chen, P, Song, M, Wu, E, Wu, B, Zhou, J, Zeng, H, Liu, X & Qiu, J 2015, 'Polarization modulated upconversion luminescence: single particle vs. few-particle aggregates', Nanoscale, vol. 7, no. 15, pp. 6462-6466.
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Luminescence from crystals is often anisotropic and it leads to the polarization behavior of luminescence from single crystalline particles, as exemplified here with the upconversion luminescence from a single NaYF4 nanodisk. Nanodisk aggregates exhibit polarization dependent luminescence with different polarization degrees, which depends on the orientation and distribution of nanoparticles.

Chen, Q, Wang, H, Liu, H, Wen, S, Peng, C, Shen, M, Zhang, G & Shi, X 2015, 'Multifunctional Dendrimer-Entrapped Gold Nanoparticles Modified with RGD Peptide for Targeted Computed Tomography/Magnetic Resonance Dual-Modal Imaging of Tumors', Analytical Chemistry, vol. 87, no. 7, pp. 3949-3956.
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Chen, S, Sun, B, Xie, X, Mondal, AK, Huang, X & Wang, G 2015, 'Multi-chambered micro/mesoporous carbon nanocubes as new polysulfides reserviors for lithium-sulfur batteries with long cycle life', NANO ENERGY, vol. 16, pp. 268-280.
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© 2015 Elsevier Ltd. Achieving rechargeable batteries with high-energy density, long cycle life and excellent rate capability is of significant importance for a vast energy-consuming society. Lithium sulfur (Li-S) batteries, attracting extensive attentions, are regarded as one of the most promising energy storage system. However, Li-S batteries are facing big challenges, owing to the fast capacity degradation, low Coulombic efficiency and poor rate capabilities. By adopting a dual confinement strategy, we successfully synthesized homogenous poly(3,4-ethylenedioxythiophene) (PEDOT) coated multi-chambered micro/mesoporous carbon nanocube encapsulated sulfur (P@CNC-S) composites. Sulfur is impregnated in individual interconnected multi-chambered micro/mesoporous carbon nanocubes, which act as the physical confinement and multilayered reservoirs for soluble lithium polysulfides. The PEDOT conductive polymer provides chemical bondings to soluble lithium polysulfides. When applied as cathodes in Li-S batteries, the P@CNC-S composites exhibited superior performances, including high specific capacities, long cycle life and outstanding high rate capabilities. Ex-situ TEM analysis confirmed the successful confinement of the dissolution of lithium polysulfides and volume expansion of the discharged product (Li2S), which could contribute to the high Coulombic efficiency and excellent cyclabilities.

Chen, S, Zhao, Y, Sun, B, Ao, Z, Xie, X, Wei, Y & Wang, G 2015, 'Microwave-assisted Synthesis of Mesoporous Co3O4 Nanoflakes for Applications in Lithium Ion Batteries and Oxygen Evolution Reactions', ACS APPLIED MATERIALS & INTERFACES, vol. 7, no. 5, pp. 3306-3313.
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© 2015 American Chemical Society. Mesoporous Co3O4 nanoflakes with an interconnected architecture were successfully synthesized using a microwave-assisted hydrothermal and low-temperature conversion method, which exhibited excellent electrochemical performances as anode materials in lithium ion batteries and as catalysts in the oxygen evolution reaction (OER). Field-emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM) observations showed the unique interconnected and mesoporous structure. When employed as anode materials for lithium ion batteries, mesoporous Co3O4 nanoflakes delivered a high specific capacity of 883 mAh/g at 0.1C current rate and stable cycling performances even at higher current rates. Post-mortem analysis of ex situ FESEM images revealed that the mesoporous and interconnected structure had been well maintained after long-term cycling. The mesoporous Co3O4 nanoflakes also showed both OER active properties and good catalytic stability. This could be attributed to both the stability of unique mesoporous structure and highly reactive facets.

Chen, Y, Zeng, D, Cortie, MB, Dowd, A, Guo, H, Wang, J & Peng, D 2015, 'Seed‐Induced Growth of Flower‐Like Au–Ni–ZnO Metal–Semiconductor Hybrid Nanocrystals for Photocatalytic Applications', Small, vol. 11, no. 12, pp. 1460-1469.
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The combination of metal and semiconductor components in nanoscale to form a hybrid nanocrystal provides an important approach for achieving advanced functional materials with special optical, magnetic and photocatalytic functionalities. Here, a facile solution method is reported for the synthesis of Au–Ni–ZnO metal–semiconductor hybrid nanocrystals with a flower‐like morphology and multifunctional properties. This synthetic strategy uses noble and magnetic metal Au@Ni nanocrystal seeds formed in situ to induce the heteroepitaxial growth of semiconducting ZnO nanopyramids onto the surface of metal cores. Evidence of epitaxial growth of ZnO{0001} facets on Ni {111} facets is observed on the heterojunction, even though there is a large lattice mismatch between the semiconducting and magnetic components. Adjustment of the amount of Au and Ni precursors can control the size and composition of the metal core, and consequently modify the surface plasmon resonance (SPR) and magnetic properties. Room‐temperature superparamagnetic properties can be achieved by tuning the size of Ni core. The as‐prepared Au–Ni–ZnO nanocrystals are strongly photocatalytic and can be separated and re‐cycled by virtue of their magnetic properties. The simultaneous combination of plasmonic, semiconducting and magnetic components within a single hybrid nanocrystal furnishes it multifunctionalities that may find wide potential applications.

CHENG, Y, YANG, Z, LIAO, J, QIU, J, SONG, Z & YANG, Y 2015, 'Color tunable upconversion emission in CeO2:Yb,Er three-dimensional ordered macroporous materials', Journal of Rare Earths, vol. 33, no. 6, pp. 599-603.
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Chen-Yu Hsu, A, Starkey, MR, Hanish, I, Parsons, K, Haw, TJ, Howland, LJ, Barr, I, Mahony, JB, Foster, PS, Knight, DA, Wark, PA & Hansbro, PM 2015, 'Targeting PI3K-p110α Suppresses Influenza Virus Infection in Chronic Obstructive Pulmonary Disease', American Journal of Respiratory and Critical Care Medicine, vol. 191, no. 9, pp. 1012-1023.
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Rationale

Chronic obstructive pulmonary disease (COPD) and influenza virus infections are major global health issues. Patients with COPD are more susceptible to infection, which exacerbates their condition and increases morbidity and mortality. The mechanisms of increased susceptibility remain poorly understood, and current preventions and treatments have substantial limitations.

Objectives

To characterize the mechanisms of increased susceptibility to influenza virus infection in COPD and the potential for therapeutic targeting.

Methods

We used a combination of primary bronchial epithelial cells (pBECs) from COPD and healthy control subjects, a mouse model of cigarette smoke-induced experimental COPD, and influenza infection. The role of the phosphoinositide-3-kinase (PI3K) pathway was characterized using molecular methods, and its potential for targeting assessed using inhibitors.

Measurements and main results

COPD pBECs were susceptible to increased viral entry and replication. Infected mice with experimental COPD also had more severe infection (increased viral titer and pulmonary inflammation, and compromised lung function). These processes were associated with impaired antiviral immunity, reduced retinoic acid-inducible gene-I, and IFN/cytokine and chemokine responses. Increased PI3K-p110α levels and activity in COPD pBECs and/or mice were responsible for increased infection and reduced antiviral responses. Global PI3K, specific therapeutic p110α inhibitors, or exogenous IFN-β restored protective antiviral responses, suppressed infection, and improved lung function.

Conclusions

The increased susceptibility of individuals with COPD to influenza likely results from impaired antiviral responses, which are mediated by increased PI3K-p110α activity. This pathway may be targeted therapeutically in COPD, or in healthy individuals, during seasonal or pandemic outbreaks to prevent and/or treat influenza.

Chew, SC, Kundukad, B, Seviour, T, van der Maarel, JRC, Yang, L, Rice, SA, Doyle, P & Kjelleberg, S 2015, 'Erratum for “Dynamic Remodeling of Microbial Biofilms by Functionally Distinct Exopolysaccharides”', mBio, vol. 6, no. 3, p. e00688.
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Chew, SC, Rice, SA, Kjelleberg, S & Yang, L 2015, '<em>In Situ</em> Mapping of the Mechanical Properties of Biofilms by Particle-tracking Microrheology', Journal of Visualized Experiments, no. 106.
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Cho, HR, Lee, Y, Doble, P, Bishop, D, Hare, D, Kim, Y-J, Kim, KG, Jung, HS, Park, KS, Choi, SH & Moon, WK 2015, 'Magnetic resonance imaging of the pancreas in streptozotocin-induced diabetic rats: Gadofluorine P and Gd-DOTA', WORLD JOURNAL OF GASTROENTEROLOGY, vol. 21, no. 19, pp. 5831-5842.
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Choi, AH & Ben-Nissan, B 2015, 'Calcium Phosphate Nanocoatings and Nanocomposites, Part I: Recent Developments and Advancements in Tissue Engineering and Bioimaging', Nanomedicine, vol. 10, no. 14, pp. 2249-2261.
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A number of materials have been applied as implant coatings and as tissue regeneration materials. Calcium phosphate holds a special consideration, due to its chemical similarity to human bone and, most importantly, its dissolution characteristics, which allow for bone growth and regeneration. The applications of molecular and nanoscale-based biological materials have been and will continue to play an ever increasing role in enhancing and improving the osseointegration of dental and orthopedic implants. More recently, extensive research efforts have been focused on the development and applications of fluorescent nanoparticles and nanocoatings for in vivo imaging and diagnostics as well as devising methods of adding luminescent or fluorescent capabilities to enhance the in vivo functionality of calcium phosphate-based biomedical materials.

Choi, AH, Conway, RC, Taraschi, V & Ben‐Nissan, B 2015, 'Biomechanics and functional distortion of the human mandible', Journal of Investigative and Clinical Dentistry, vol. 6, no. 4, pp. 241-251.
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AbstractThe reaction to the use of finite element analysis (FEA) in the study of the human body has been particularly enthusiastic. Of equal and challenging complexity is the investigation of load/stress distribution and morphological distortion of the human mandible under functional loads. Furthermore, the mandible also impacts directly on body function and esthetics, playing a vital role, such as mastication and speech. The application of FEA to the biomechanical investigation of the oral systems, such as human teeth and mandibular bone remodeling, began in the early 1970s. The clinical significance of jaw deformation is unknown. The primary concern is that deformation might result in an ill‐fitting superstructure or the creation of harmful strains in the patient–implant complex. Although mandibular implant treatment has a high success rate, the possibility of failure caused by these dimensional changes and the related micromotion cannot be ignored.

Choi, S & Aharonovich, I 2015, 'Zinc Oxide Nanophotonics', Nanophotonics, vol. 4, no. 4, pp. 437-458.
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Abstract The emerging field of nanophotonics initiated a dedicated study of single photon sources and optical resonators in new class of materials. One such material is zinc oxide (ZnO) that has been long considered only for classical light-emitting applications. However, it recently showed promise for quantum photonics technologies. In this review, we highlight the recent advances in studying single emitters in ZnO, engineering of optical cavities and practical nanophotonics devices including nanolasers and electrically triggered devices. We finalize with an outlook at this promising area, as well as provide perspectives and open questions in solid state nanophotonics employing ZnO.

Choi, S, Berhane, AM, Gentle, A, Ton-That, C, Phillips, MR & Aharonovich, I 2015, 'Electroluminescence from Localized Defects in Zinc Oxide: Toward Electrically Driven Single Photon Sources at Room Temperature', ACS APPLIED MATERIALS & INTERFACES, vol. 7, no. 10, pp. 5619-5623.
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© 2015 American Chemical Society. Single photon sources are required for a wide range of applications in quantum information science, quantum cryptography, and quantum communications. However, the majority of room temperature emitters to date are only excited optically, which limits their proper integration into scalable devices. In this work, we overcome this limitation and present room temperature electrically driven light emission from localized defects in zinc oxide (ZnO) nanoparticles and thin films. The devices emit in the red spectral range and show excellent rectifying behavior. The emission is stable over an extensive period of time, providing an important prerequisite for practical devices. Our results open possibilities for building new ZnO-based quantum integrated devices that incorporate solid-state single photon sources for quantum information technologies. (Graph Presented).

Choi, S, Phillips, MR, Aharonovich, I, Pornsuwan, S, Cowie, BCC & Ton-That, C 2015, 'Photophysics of Point Defects in ZnO Nanoparticles', ADVANCED OPTICAL MATERIALS, vol. 3, no. 6, pp. 821-827.
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© 2015 WILEY-VCH Verlag GmbH & Co. Zinc oxide (ZnO) nanoparticles have recently been identified as a promising candidate for advanced nanophotonics applications and quantum technologies. This work reports the formation of luminescent point defects and describes their photophysical properties. In particular, it is shown using correlative photoluminescence, cathodoluminescence, electron paramagnetic resonance (EPR), and X-ray absorption near-edge spectroscopy that green luminescence at 2.48 eV and an EPR line at g = 2.00 belong to a surface oxygen vacancy (Vo,s⁺) center, while a second green emission at 2.28 eV is associated with zinc vacancy (VZn) centers. It is established that radiative point defects can be excited in the visible that exhibits nanosecond lifetimes using both above bandgap and sub-bandgap 405 and 532 nm excitation. This work provides important knowledge towards employment of point defects in ZnO in nanophotonics technologies.

Chou, J, Hao, J, Hatoyama, H, Ben-Nissan, B, Milthorpe, B & Otsuka, M 2015, 'Effect of biomimetic zinc-containing tricalcium phosphate (Zn-TCP) on the growth and osteogenic differentiation of mesenchymal stem cells', Journal of Tissue Engineering and Regenerative Medicine, vol. 9, no. 7, pp. 852-858.
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© 2014 John Wiley & Sons, Ltd. Several studies have shown the effectiveness of zinc-tricalcium phosphate (Zn-TCP) for bone tissue engineering. In this study, marine calcareous foraminifera possessing uniform pore size distribution were hydrothermally converted to Zn-TCP. The ability of a scaffold to combine effectively with mesenchymal stem cells (MSCs) is a key tissue-engineering aim. In order to demonstrate the osteogenic ability of MSCs with Zn-TCP, the scaffolds were cultured in an osteogenic induction medium to elicit an osteoblastic response. The physicochemical properties of Zn-TCP were characterized by XRD, FT-IR and ICP-MS. MSCs were aspirated from rat femurs and cultured for 3 days before indirectly placing four samples into each respective well. After culture for 7, 10 and 14 days, osteoblastic differentiation was evaluated using alizarin red S stain, measurement of alkaline phosphatase (ALP) levels, cell numbers and cell viability. XRD and FT-IR patterns both showed the replacement of CO32- with PO43-. Chemical analysis showed zinc incorporation of 5 mol%. Significant increases in cell numbers were observed at 10 and 14 days in the Zn-TCP group, while maintaining high levels of cell viability (> 90%). ALP activity in the Zn-TCP group was statistically higher at 10 days. Alizarin red S staining also showed significantly higher levels of calcium mineralization in Zn-TCP compared with the control groups. This study showed that MSCs in the presence of biomimetically derived Zn-TCP can accelerate their differentiation to osteoblasts and could potentially be useful as a scaffold for bone tissue engineering.

Chowdhury, PR, Charles, IG & Djordjevic, SP 2015, 'A Role for Tn6029 in the Evolution of the Complex Antibiotic Resistance Gene Loci in Genomic Island 3 in Enteroaggregative Hemorrhagic Escherichia coli O104:H4', PLOS ONE, vol. 10, no. 2, pp. e0115781-e0115781.
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© 2015 Chowdhury et al. In enteroaggregative hemorrhagic Escherichia coli (EAHEC) O104 the complex antibiotic resistance gene loci (CRL) found in the region of divergence 1 (RD1) within E. coli genomic island 3 (GI3) contains blaTEM-1, strAB, sul2, tet(A)A, and dfrA7 genes encoding resistance to ampicillin, streptomycin, sulfamethoxazole, tetracycline and trimethoprim respectively. The precise arrangement of antibiotic resistance genes and the role of mobile elements that drove the evolutionary events and created the CRL have not been investigated. We used a combination of bioinformatics and iterative BLASTn searches to determine the micro-evolutionary events that likely led to the formation of the CRL in GI3 using the closed genome sequences of EAHEC O104:H4 strains 2011C-3493 and 2009EL-2050 and high quality draft genomes of EAHEC E. coli O104:H4 isolates from sporadic cases not associated with the initial outbreak. Our analyses indicate that the CRL in GI3 evolved from a progenitor structure that contained an In2-derived class 1 integron in a Tn21/Tn1721 hybrid backbone. Within the hybrid backbone, a Tn6029-family transposon, identified here as Tn6029C abuts the sul1 gene in the 3′-Conserved Segment (-CS) of a class 1 integron generating a unique molecular signature that has only previously been observed in pASL01a, a small plasmid found in commensal E. coli in West Africa. From this common progenitor, independent IS26-mediated events created two novel transposons identified here as Tn6029D and Tn6222 in 2011C-3493 and 2009EL-2050 respectively. Analysis of RD1 within GI3 reveals IS26 has played a crucial role in the assembly of regions within the CRL.

Chung, L, Phillips, L, Lin, MZ, Moore, K, Marsh, DJ, Boyle, FM & Baxter, RC 2015, 'A novel truncated form of S100P predicts disease-free survival in patients with lymph node positive breast cancer', Cancer Letters, vol. 368, no. 1, pp. 64-70.
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Ciobanu, L, Diekert, V & Elder, M 2015, 'Solution sets for equations over free groups are EDT0L languages', International Journal of Algebra and Computation, vol. 26, no. 5, pp. 843-886.
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We show that, given an equation over a finitely generated free group, the setof all solutions in reduced words forms an effectively constructible EDT0Llanguage. In particular, the set of all solutions in reduced words is anindexed language in the sense of Aho. The language characterization we give, aswell as further questions about the existence or finiteness of solutions,follow from our explicit construction of a finite directed graph which encodesall the solutions. Our result incorporates the recently invented recompressiontechnique of Je\.z, and a new way to integrate solutions of linear Diophantineequations into the process. As a byproduct of our techniques, we improve the complexity from quadraticnondeterministic space in previous works to $\mathsf{NSPACE}(n\log n)$ here.

Cleverly, J, Thibault, JR, Teet, SB, Tashjian, P, Hipps, LE, Dahm, CN & Eamus, D 2015, 'Flooding Regime Impacts on Radiation, Evapotranspiration, and Latent Energy Fluxes over Groundwater-Dependent Riparian Cottonwood and Saltcedar Forests', ADVANCES IN METEOROLOGY, vol. 2015, pp. 1-14.
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Radiation and energy balances are key drivers of ecosystem water and carbon cycling. This study reports on ten years of eddy covariance measurements over groundwater-dependent ecosystems (GDEs) in New Mexico, USA, to compare the role of drought and flooding on radiation,water, and energy budgets of forests differing in species composition (native cottonwood versus nonnative saltcedar) and flooding regime. After net radiation (700–800Wm−2), latent heat flux was the largest energy flux, with annual values of evapotranspiration exceeding annual precipitation by 250–600%. Evaporative cooling dominated the energy fluxes of both forest types, although cottonwood generatedmuch lower daily values of sensible heat flux (<−5MJm−2 d−1). Drought caused a reduction in evaporative cooling, especially in the saltcedar sites where evapotranspiration was also reduced, but without a substantial decline in depth-to-groundwater. Our findings have broad implications on water security and the management of native and nonnative vegetation within semiarid southwestern North America. Specifically, consideration of the energy budgets of GDEs as they respond to fluctuations in climatic conditions can inform the management options for reducing evapotranspiration and maintaining instream flow, which is legally mandated as part of interstate and international water resources agreements.

Clifton, LA, Holt, SA, Hughes, AV, Daulton, EL, Arunmanee, W, Heinrich, F, Khalid, S, Jefferies, D, Charlton, TR, Webster, JRP, Kinane, CJ & Lakey, JH 2015, 'An Accurate In Vitro Model of the E. coli Envelope', Angewandte Chemie International Edition, vol. 54, no. 41, pp. 11952-11955.
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AbstractGram‐negative bacteria are an increasingly serious source of antibiotic‐resistant infections, partly owing to their characteristic protective envelope. This complex, 20 nm thick barrier includes a highly impermeable, asymmetric bilayer outer membrane (OM), which plays a pivotal role in resisting antibacterial chemotherapy. Nevertheless, the OM molecular structure and its dynamics are poorly understood because the structure is difficult to recreate or study in vitro. The successful formation and characterization of a fully asymmetric model envelope using Langmuir–Blodgett and Langmuir–Schaefer methods is now reported. Neutron reflectivity and isotopic labeling confirmed the expected structure and asymmetry and showed that experiments with antibacterial proteins reproduced published in vivo behavior. By closely recreating natural OM behavior, this model provides a much needed robust system for antibiotic development.

Clifton, LA, Holt, SA, Hughes, AV, Daulton, EL, Arunmanee, W, Heinrich, F, Khalid, S, Jefferies, D, Charlton, TR, Webster, JRP, Kinane, CJ & Lakey, JH 2015, 'An Accurate In Vitro Model of the E. coli Envelope', Angewandte Chemie, vol. 127, no. 41, pp. 12120-12123.
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AbstractGram‐negative bacteria are an increasingly serious source of antibiotic‐resistant infections, partly owing to their characteristic protective envelope. This complex, 20 nm thick barrier includes a highly impermeable, asymmetric bilayer outer membrane (OM), which plays a pivotal role in resisting antibacterial chemotherapy. Nevertheless, the OM molecular structure and its dynamics are poorly understood because the structure is difficult to recreate or study in vitro. The successful formation and characterization of a fully asymmetric model envelope using Langmuir–Blodgett and Langmuir–Schaefer methods is now reported. Neutron reflectivity and isotopic labeling confirmed the expected structure and asymmetry and showed that experiments with antibacterial proteins reproduced published in vivo behavior. By closely recreating natural OM behavior, this model provides a much needed robust system for antibiotic development.

Clifton, LA, Skoda, MWA, Le Brun, AP, Ciesielski, F, Kuzmenko, I, Holt, SA & Lakey, JH 2015, 'Effect of Divalent Cation Removal on the Structure of Gram-Negative Bacterial Outer Membrane Models', Langmuir, vol. 31, no. 1, pp. 404-412.
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Coil, DA, Alexiev, A, Wallis, C, O’Flynn, C, Deusch, O, Davis, I, Horsfall, A, Kirkwood, N, Jospin, G, Eisen, JA, Harris, S & Darling, AE 2015, 'Draft Genome Sequences of 26 Porphyromonas Strains Isolated from the Canine Oral Microbiome', Genome Announcements, vol. 3, no. 2.
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ABSTRACT We present the draft genome sequences for 26 strains of Porphyromonas ( P. canoris , P. gulae , P. cangingavalis , P. macacae , and 7 unidentified) and an unidentified member of the Porphyromonadaceae family. All of these strains were isolated from the canine oral cavity, from dogs with and without early periodontal disease.

Cole, AJ, Clifton-Bligh, R & Marsh, DJ 2015, 'Histone H2B monoubiquitination: roles to play in human malignancy', Endocrine-Related Cancer, vol. 22, no. 1, pp. T19-T33.
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Ubiquitination has traditionally been viewed in the context of polyubiquitination that is essential for marking proteins for degradation via the proteasome. Recent discoveries have shed light on key cellular roles for monoubiquitination, including as a post-translational modification (PTM) of histones such as histone H2B. Monoubiquitination plays a significant role as one of the largest histone PTMs, alongside smaller, better-studied modifications such as methylation, acetylation and phosphorylation. Monoubiquitination of histone H2B at lysine 120 (H2Bub1) has been shown to have key roles in transcription, the DNA damage response and stem cell differentiation. The H2Bub1 enzymatic cascade involves E3 RING finger ubiquitin ligases, with the main E3 generally accepted to be the RNF20–RNF40 complex, and deubiquitinases including ubiquitin-specific protease 7 (USP7), USP22 and USP44. H2Bub1 has been shown to physically disrupt chromatin strands, fostering a more open chromatin structure accessible to transcription factors and DNA repair proteins. It also acts as a recruiting signal, actively attracting proteins with roles in transcription and DNA damage. H2Bub1 also appears to play central roles in histone cross-talk, influencing methylation events on histone H3, including H3K4 and H3K79. Most significantly, global levels of H2Bub1 are low to absent in advanced cancers including breast, colorectal, lung and parathyroid, marking H2Bub1 and the enzymes that regulate it as key molecules of interest as possible new therapeutic targets for the treatment of cancer. This review offers an overview of current knowledge regarding H2Bub1 and highlights links between dysregulation of H2Bub1-associated enzymes, stem cells and malignancy.

Cooray, MCD, Liu, Y, Langford, SJ, Bond, AM & Zhang, J 2015, 'One pot synthesis of poly(5-hydroxyl-1,4-naphthoquinone) stabilized gold nanoparticles using the monomer as the reducing agent for nonenzymatic electrochemical detection of glucose', Analytica Chimica Acta, vol. 856, pp. 27-34.
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Craddock, M 2015, 'Fourier type transforms on Lie symmetry groups', Journal of Mathematical Physics, vol. 56, no. 9, pp. 091501-091501.
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In this paper, we construct operators on a Lie symmetry group which may be regarded as Fourier transforms. Essentially, we integrate solutions generated by Lie symmetries against suitable test functions. We show that this idea leads to a powerful method for solving Cauchy problems for parabolic and hyperbolic equations in two and higher dimensions. We also discuss applications to the elliptic case.

Cramb, SM, Baade, PD, White, NM, Ryan, LM & Mengersen, KL 2015, 'Inferring lung cancer risk factor patterns through joint Bayesian spatio-temporal analysis', CANCER EPIDEMIOLOGY, vol. 39, no. 3, pp. 430-439.
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© 2015 Elsevier Ltd. Background: Preventing risk factor exposure is vital to reduce the high burden from lung cancer. The leading risk factor for developing lung cancer is tobacco smoking. In Australia, despite apparent success in reducing smoking prevalence, there is limited information on small area patterns and small area temporal trends. We sought to estimate spatio-temporal patterns for lung cancer risk factors using routinely collected population-based cancer data. Methods: The analysis used a Bayesian shared component spatio-temporal model, with male and female lung cancer included separately. The shared component reflected lung cancer risk factors, and was modelled over 477 statistical local areas (SLAs) and 15 years in Queensland, Australia. Analyses were also run adjusting for area-level socioeconomic disadvantage, Indigenous population composition, or remoteness. Results: Strong spatial patterns were observed in the underlying risk factor estimates for both males (median Relative Risk (RR) across SLAs compared to the Queensland average ranged from 0.48 to 2.00) and females (median RR range across SLAs 0.53-1.80), with high risks observed in many remote areas. Strong temporal trends were also observed. Males showed a decrease in the underlying risk across time, while females showed an increase followed by a decrease in the final 2 years. These patterns were largely consistent across each SLA. The high underlying risk estimates observed among disadvantaged, remote and indigenous areas decreased after adjustment, particularly among females. Conclusion: The modelled underlying risks appeared to reflect previous smoking prevalence, with a lag period of around 30 years, consistent with the time taken to develop lung cancer. The consistent temporal trends in lung cancer risk factors across small areas support the hypothesis that past interventions have been equally effective across the state. However, this also means that spatial inequalities have r...

Cranfield, CG, Bettler, T & Cornell, B 2015, 'Nanoscale Ion Sequestration To Determine the Polarity Selectivity of Ion Conductance in Carriers and Channels', LANGMUIR, vol. 31, no. 1, pp. 292-298.
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© 2014 American Chemical Society. The nanoscale spacing between a tethered lipid bilayer membrane (tBLM) and its supporting gold electrode can be utilized to determine the polarity selectivity of the conduction of ion channels and ion carriers embedded in a membrane. The technique relies upon a bias voltage sequestering or eliminating ions, of a particular polarity, into or out of the aqueous electrolyte region between the gold electrode and the tethered membrane. A demonstration is given, using ac swept frequency impedance spectrometry, of the bias polarity dependence of the ionophore conductance of gramicidin A, a cationic selective channel, and valinomycin, a potassium ion selective carrier. We further use pulsed amperometry to show that the intrinsic voltage dependence of the ion conduction is actually selective of the polarity of the transported ion and not simply of the direction of the ionic current flow.

Cremona, T, Mella, VSA, Webb, JK & Crowther, MS 2015, 'Do individual differences in behavior influence wild rodents more than predation risk?', Journal of Mammalogy, vol. 96, no. 6, pp. 1337-1343.
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© 2015 American Society of Mammalogists. Prey can enhance their survival by eliciting an appropriate response to predators. Theoretically, prey should distinguish odors of predators and nonpredators. The manifestation of defensive antipredator behaviors has been extensively researched in domestic species (i.e., the relationship between laboratory-bred rats and domestic cats). However, little is known about the expression of these behaviors in wild rodents. Studies have so far focused on quantitative assessments of cost-benefit trade-offs or giving-up densities. We examined the expression of finescale defensive behaviors in Arnhem rock rats (Zyzomys maini) in response to fecal cues from 2 predators (the northern quoll [Dasyurus hallucatus] and the dingo [Canis dingo]), a nonpredator (the short-eared rock-wallaby [Petrogale brachyotis]), and a control (water). We adapted a predator-odor avoidance apparatus that has been widely used for domestic rodent studies to film the behavior of wild rock rats in a captive environment. Rock rats did not alter their behavior in the presence of odors of nonpredators, predators, or controls. In the current study, individual rock rats behaved in a consistent manner across time, and we identified 3 individually consistent behaviors which may suggest the existence of personality traits in this species. We suggest that these individual differences may influence wild rock rat behavior more than predation risk. These differences should therefore be taken into consideration when investigating behavioral responses to predators in wild populations.

Crispino, F, Rossy, Q, Ribaux, O & Roux, C 2015, 'Education and training in forensic intelligence: a new challenge', AUSTRALIAN JOURNAL OF FORENSIC SCIENCES, vol. 47, no. 1, pp. 49-60.
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From recent calls for positioning forensic scientists within the criminal justice system, but also policing and intelligence missions, this paper emphasises the need for the development of educational and training programmes in the area of forensic intelligence. It is argued that an imbalance exists between perceived and actual understanding of forensic intelligence by police and forensic science managers, and that this imbalance can only be overcome through education. The challenge forforensic intelligence education and training is therefore to devise programmes that increase forensic intelligence awareness, firstly for managers to help prevent poor decisions on how to develop information processing. Two recent European courses are presented as examples of education offerings, along with lessons learned and suggested paths forward. It is concluded that the new focus on forensic intelligence could restore a pro-active approach to forensic science, better quantify its efficiency and let it get more involved in investigative and managerial decisions. A new educational challenge is opened to forensic science university programmes around theworld: to refocus criminal trace analysis on a more holistic security problem solving approach.

Cullen, J, Bahm, A, Lobo, CJ, Ford, MJ & Toth, M 2015, 'Localized Probing of Gas Molecule Adsorption Energies and Desorption Attempt Frequencies', The Journal of Physical Chemistry C, vol. 119, no. 28, pp. 15948-15953.
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© 2015 American Chemical Society. Gas-mediated electron beam induced etching (EBIE) and deposition (EBID) can be used to measure activation energies that are interpreted as the adsorption energies of surface-adsorbed precursor molecules. However, the measured quantities often disagree with adsorption energies measured by conventional analysis techniques such as thermally programmed desorption and have anomalous dependencies on parameters such as the electron beam current used to perform EBID. Here, we use the theory of EBIE and EBID rate kinetics to explain this behavior and identify conditions under which the activation energies and the associated pre-exponential factors correspond to gas molecule adsorption energies and desorption attempt frequencies, respectively. Under these conditions, EBIE and EBID can be used as robust, nanoscale techniques for the analysis of adsorbates.

Cullen, J, Lobo, CJ, Ford, MJ & Toth, M 2015, 'Electron-Beam-Induced Deposition as a Technique for Analysis of Precursor Molecule Diffusion Barriers and Prefactors', ACS Applied Materials & Interfaces, vol. 7, no. 38, pp. 21408-21415.
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© 2015 American Chemical Society. Electron-beam-induced deposition (EBID) is a direct-write chemical vapor deposition technique in which an electron beam is used for precursor dissociation. Here we show that Arrhenius analysis of the deposition rates of nanostructures grown by EBID can be used to deduce the diffusion energies and corresponding preexponential factors of EBID precursor molecules. We explain the limitations of this approach, define growth conditions needed to minimize errors, and explain why the errors increase systematically as EBID parameters diverge from ideal growth conditions. Under suitable deposition conditions, EBID can be used as a localized technique for analysis of adsorption barriers and prefactors.

D Ainsworth, T, Krause, L, Bridge, T, Torda, G, Raina, J-B, Zakrzewski, M, Gates, RD, Padilla-Gamiño, JL, Spalding, HL, Smith, C, Woolsey, ES, Bourne, DG, Bongaerts, P, Hoegh-Guldberg, O & Leggat, W 2015, 'The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts', The ISME Journal, vol. 9, no. 10, pp. 2261-2274.
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Abstract Despite being one of the simplest metazoans, corals harbor some of the most highly diverse and abundant microbial communities. Differentiating core, symbiotic bacteria from this diverse host-associated consortium is essential for characterizing the functional contributions of bacteria but has not been possible yet. Here we characterize the coral core microbiome and demonstrate clear phylogenetic and functional divisions between the micro-scale, niche habitats within the coral host. In doing so, we discover seven distinct bacterial phylotypes that are universal to the core microbiome of coral species, separated by thousands of kilometres of oceans. The two most abundant phylotypes are co-localized specifically with the corals’ endosymbiotic algae and symbiont-containing host cells. These bacterial symbioses likely facilitate the success of the dinoflagellate endosymbiosis with corals in diverse environmental regimes.

Danastas, K, Combes, V, Lindsay, LA, Grau, GER, Thompson, MB & Murphy, CR 2015, 'VEGF111: new insights in tissue invasion', Frontiers in Physiology, vol. 6.
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Daniel, R, Santos, C, Phillips, C, Fondevila, M, van Oorschot, RAH, Carracedo, A, Lareu, MV & McNevin, D 2015, 'A SNaPshot of next generation sequencing for forensic SNP analysis', FORENSIC SCIENCE INTERNATIONAL-GENETICS, vol. 14, pp. 50-60.
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Forensic phenotyping can provide useful intelligence regarding the biogeographical ancestry (BGA) and externally visible characteristics (EVCs) of the donor of an evidentiary sample. Currently, single nucleotide polymorphism (SNP) based inference of BGA and EVCs is performed most commonly using SNaPshot(®), a single base extension (SBE) assay. However, a single SNaPshot multiplex PCR is limited to 30-40 SNPs. Next generation sequencing (NGS) offers the potential to genotype hundreds to thousands of SNPs from multiple samples in a single experimental run. The PCR multiplexes from five SNaPshot assays (SNPforID 52plex, SNPforID 34plex, Eurasiaplex, IrisPlex and an unpublished BGA assay) were applied to three different DNA template amounts (0.1, 0.2 and 0.3 ng) in three samples (9947A and 007 control DNAs and a male donor). The pooled PCR amplicons containing 136 unique SNPs were sequenced using Life Technologies' Ion Torrent™ PGM system. Approximately 72 Mb of sequence was generated from two 10 Mb Ion 314™ v1 chips. Accurate genotypes were readily obtained from all three template amounts. Of a total of 408 genotypes, 395 (97%) were fully concordant with SNaPshot across all three template amounts. Of those genotypes discordant with SNaPshot, six Ion Torrent sequences (1.5%) were fully concordant with Sanger sequencing across the three template amounts. Seven SNPs (1.7%) were either discordant between template amounts or discordant with Sanger sequencing. Sequence coverage observed in the negative control, and, allele coverage variation for heterozygous genotypes highlights the need to establish a threshold for background levels of sequence output and heterozygous balance. This preliminary study of the Ion Torrent PGM system has demonstrated considerable potential for use in forensic DNA analyses as a low to medium throughput NGS platform using established SNaPshot assays.

Davies, JM, Beggs, PJ, Medek, DE, Newnham, RM, Erbas, B, Thibaudon, M, Katelaris, CH, Haberle, SG, Newbigin, EJ & Huete, AR 2015, 'Trans-disciplinary research in synthesis of grass pollen aerobiology and its importance for respiratory health in Australasia', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 534, pp. 85-96.
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© 2015 Published by Elsevier B.V. Grass pollen is a major trigger for allergic rhinitis and asthma, yet little is known about the timing and levels of human exposure to airborne grass pollen across Australasian urban environments. The relationships between environmental aeroallergen exposure and allergic respiratory disease bridge the fields of ecology, aerobiology, geospatial science and public health. The Australian Aerobiology Working Group comprised of experts in botany, palynology, biogeography, climate change science, plant genetics, biostatistics, ecology, pollen allergy, public and environmental health, and medicine, was established to systematically source, collate and analyse atmospheric pollen concentration data from 11 Australian and six New Zealand sites. Following two week-long workshops, post-workshop evaluations were conducted to reflect upon the utility of this analysis and synthesis approach to address complex multidisciplinary questions. This Working Group described i) a biogeographically dependent variation in airborne pollen diversity, ii) a latitudinal gradient in the timing, duration and number of peaks of the grass pollen season, and iii) the emergence of new methodologies based on trans-disciplinary synthesis of aerobiology and remote sensing data. Challenges included resolving methodological variations between pollen monitoring sites and temporal variations in pollen datasets. Other challenges included 'marrying' ecosystem and health sciences and reconciling divergent expert opinion. The Australian Aerobiology Working Group facilitated knowledge transfer between diverse scientific disciplines, mentored students and early career scientists, and provided an uninterrupted collaborative opportunity to focus on a unifying problem globally. The Working Group provided a platform to optimise the value of large existing ecological datasets that have importance for human respiratory health and ecosystems research. Compilation of current ...

Davies, KM, Hare, DJ, Bohic, S, James, SA, Billings, JL, Finkelstein, DI, Doble, PA & Double, KL 2015, 'Comparative Study of Metal Quantification in Neurological Tissue Using Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry Imaging and X-ray Fluorescence Microscopy', Analytical Chemistry, vol. 87, no. 13, pp. 6639-6645.
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© 2015 American Chemical Society. Redox-active metals in the brain mediate numerous biochemical processes and are also implicated in a number of neurodegenerative diseases. A number of different approaches are available for quantitatively measuring the spatial distribution of biometals at an image resolution approaching the subcellular level. Measured biometal levels obtained using laser ablation-inductively coupled plasma mass spectrometry (LA-ICPMS; spatial resolution 15 μm × 15 μm) were within the range of those obtained using X-ray fluorescence microscopy (XFM; spatial resolution 2 μm × 7 μm) and regional changes in metal concentration across discrete brain regions were replicated to the same degree. Both techniques are well suited to profiling changes in regional biometal distribution between healthy and diseased brain tissues, but absolute quantitation of metal levels varied significantly between methods, depending on the metal of interest. Where all possible variables affect metal levels, independent of a treatment/phenotype are controlled, either method is suitable for examining differences between experimental groups, though, as with any method for imaging post mortem brain tissue, care should be taken when interpreting the total metal levels with regard to physiological concentrations. (Figure Presented).

Davoodi, A, Maddahfar, M & Ramezani, M 2015, 'Application of mercaptoacetic acid as a capping agent, solvent, and precursor to fabricate In2S3 nanostructures', Journal of Industrial and Engineering Chemistry, vol. 22, pp. 368-372.
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de la Hunty, M, Moret, S, Chadwick, S, Lennard, C, Spindler, X & Roux, C 2015, 'Understanding physical developer (PD): Part I - Is PD targeting lipids?', FORENSIC SCIENCE INTERNATIONAL, vol. 257, pp. 481-487.
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© 2015 Elsevier Ireland Ltd. Physical developer (PD) is a fingermark development technique that involves the selective reduction of silver onto fingermark residue. PD can develop marks on porous substrates even if they have been wet, leading to the logical, long held belief that the reagent targets the water insoluble constituents in the fingermark residue. The present research has tested this hypothesis as part of a broader study that aims to identify the targets of physical developer. Spot tests of some fatty acids, cholesterol and squalene, treated with PD, showed that only cholesterol produced significant silver deposition. PD is known to be particularly effective on aged marks, however cholesterol degrades over time. These observations indicate that PD reactivity with fingermarks cannot solely be due to the presence of cholesterol.Fingermarks were deposited on paper and washed with various organic solvents before being treated with PD. PD effectiveness was intermittent on both solvent washed and unwashed sides of both natural and groomed marks; however, it was seen to effectively develop groomed samples that had been exposed to common lipid extraction solvents, shown to have removed the lipids by visualisation using the lipid stain Nile red. PD effectiveness was most affected by exposure of samples to solvents that could dissolve water soluble components, showing that the removal of these constituents (by either water, or other solvents) decreases the amount of silver deposited on the fingermark residue by the working solution.Close observation of PD developed samples showed variation in silver deposition uniformity when comparing a developed ridge to a pore site located on that ridge. Some samples showed an absence of silver, and other showed an increase of silver at pore locations. This indicates that the material excreted by the pores on the finger has an effect on silver deposition, suggesting that PD may be specifically targeting eccrine const...

de la Hunty, M, Moret, S, Chadwick, S, Lennard, C, Spindler, X & Roux, C 2015, 'Understanding Physical Developer (PD): Part II - Is PD targeting eccrine constituents?', FORENSIC SCIENCE INTERNATIONAL, vol. 257, pp. 488-495.
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© 2015 Elsevier Ireland Ltd. Physical developer (PD) is a fingermark development technique that deposits silver onto fingermark ridges. It is the only technique currently in routine operational use that gives results on porous substrates that have been wet. There is a reasonable understanding of the working solution chemistry, but the chemical constituent(s) contained in fingermark residue that are specifically targeted by PD are largely unknown. A better understanding of the PD technique will permit a more informed selection of alternative or complementary detection methods, and greater usage in operational laboratories. Recent research by our group has shown that PD does not selectively target the lipids present in the residue.This research investigated the hypothesis that PD targets the eccrine constituents in fingermark residue. This was tested by comparison of PD and indanedione-zinc (Ind-Zn) treated natural fingermarks that had been deposited successively, and marks that had been deposited with a ten second interval in between depositions. Such an interval allows for the regeneration of secretions from the pores located on the ridges of the fingers. On fingermark depletions with no time interval between depositions, PD and Ind-Zn treated depletions successively (and comparatively) decreased in development intensity as the amount of residue diminished. Short time intervals in between successive depletions resulted in additional secretions from the pores intermittently occurring, the increased development of which was visualised by treatment with both PD and Ind-Zn. The changes in development intensity were seen with both techniques on the same split depletions in a series, comparably and proportionately. These results indicate that the components targeted by PD are contained in the material excreted by the friction ridge pores through its mirrored development with Ind-Zn.Repetition of the experiments on marks that only contained eccrine material sh...

De Silva, KSB, Gentle, A, Arnold, M, Keast, VJ & Cortie, MB 2015, 'Dielectric function and its predicted effect on localized plasmon resonances of equiatomic Au-Cu', JOURNAL OF PHYSICS D-APPLIED PHYSICS, vol. 48, no. 21.
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© 2015 IOP Publishing Ltd. Equiatomic (Au,Cu) solid solution orders below 658 K to form a tetragonal AuCu (I) phase with significant changes in physical properties and the crystal structure. The effect of ordering on the dielectric function of the material is controversial however, with inconsistent results reported in the literature. Since the nature of any localized surface plasmon resonance (LSPR) in the nanostructures is very sensitive to the dielectric function, this uncertainty hinders the use of AuCu in plasmonic devices or structures. Therefore, we re-examine the question using a combination of measurements and computations. We find that no significant change in the dielectric function occurs when this material becomes ordered, at least over the range of photon energies relevant to LSPRs. The likely properties of LSPRs in plasmonic devices made of AuCu are analyzed. Use of the alloy offers some advantages over pure Cu, however pure Au would still be the superior option in most situations.

Deeudom, M, Huston, W & Moir, JWB 2015, 'Lipid-modified azurin of Neisseria meningitidis is a copper protein localized on the outer membrane surface and not regulated by FNR', Antonie van Leeuwenhoek, vol. 107, no. 4, pp. 1107-1116.
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Deplazes, E, Begg, SL, van Wonderen, JH, Campbell, R, Kobe, B, Paton, JC, MacMillan, F, McDevitt, CA & O'Mara, ML 2015, 'Characterizing the conformational dynamics of metal-free PsaA using molecular dynamics simulations and electron paramagnetic resonance spectroscopy', Biophysical Chemistry, vol. 207, pp. 51-60.
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Dhouib, R, Pg Othman, DSM, Essilfie, A-T, Hansbro, PM, Hanson, JO, McEwan, AG & Kappler, U 2015, 'Maturation of molybdoenzymes and its influence on the pathogenesis of non-typeable Haemophilus influenzae', Frontiers in Microbiology, vol. 6, no. NOV.
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© 2015 Dhouib, Pg Othman, Essilfie, Hansbro, Hanson, McEwan and Kappler. Mononuclear molybdenum enzymes of the dimethylsulfoxide (DMSO) reductase family occur exclusively in prokaryotes, and a loss of some these enzymes has been linked to a loss of bacterial virulence in several cases. The MobA protein catalyzes the final step in the synthesis of the molybdenum guanine dinucleotide (MGD) cofactor that is exclusive to enzymes of the DMSO reductase family. MobA has been proposed as a potential target for control of virulence since its inhibition would affect the activities of all molybdoenzymes dependent upon MGD. Here, we have studied the phenotype of a mobA mutant of the host-adapted human pathogen Haemophilus influenzae. H. influenzae causes and contributes to a variety of acute and chronic diseases of the respiratory tract, and several enzymes of the DMSO reductase family are conserved and highly expressed in this bacterium. The mobA mutation caused a significant decrease in the activities of all Mo-enzymes present, and also resulted in a small defect in anaerobic growth. However, we did not detect a defect in in vitro biofilm formation nor in invasion and adherence to human epithelial cells in tissue culture compared to the wild-type. In a murine in vivo model, the mobA mutant showed only a mild attenuation compared to the wild-type. In summary, our data show that MobA is essential for the activities of molybdenum enzymes, but does not appear to affect the fitness of H. influenzae. These results suggest that MobA is unlikely to be a useful target for antimicrobials, at least for the purpose of treating H. influenzae infections.

Di Giacomo, S, Brito, BP, Perez, AM, Bucafusco, D, Pega, J, Rodríguez, L, Borca, MV & Pérez-Filgueira, M 2015, 'Heterogeneity in the Antibody Response to Foot-and-Mouth Disease Primo-vaccinated Calves', Transboundary and Emerging Diseases, vol. 62, no. 3, pp. 280-287.
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Donovan, C, Bailey, SR, Tran, J, Haitsma, G, Ibrahim, ZA, Foster, SR, Tang, MLK, Royce, SG & Bourke, JE 2015, 'Rosiglitazone elicits in vitro relaxation in airways and precision cut lung slices from a mouse model of chronic allergic airways disease', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 309, no. 10, pp. L1219-L1228.
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Rosiglitazone (RGZ), a peroxisome proliferator-activated receptor-γ (PPARγ) ligand, is a novel dilator of small airways in mouse precision cut lung slices (PCLS). In this study, relaxation to RGZ and β-adrenoceptor agonists were compared in trachea from naïve mice and guinea pigs and trachea and PCLS from a mouse model of chronic allergic airways disease (AAD). Airways were precontracted with methacholine before addition of PPARγ ligands [RGZ, ciglitazone (CGZ), or 15-deoxy-Δ12,14-prostaglandin J2 (15-deoxy-PGJ2)] or β-adrenoceptor agonists (isoprenaline and salbutamol). The effects of T0070907 and GW9662 (PPARγ antagonists) or epithelial removal on relaxation were assessed. Changes in force of trachea and lumen area in PCLS were measured using preparations from saline-challenged mice and mice sensitized ( days 0 and 14) and challenged with ovalbumin (3 times/wk, 6 wk). RGZ and CGZ elicited complete relaxation with greater efficacy than β-adrenoceptor agonists in mouse airways but not guinea pig trachea, while 15-deoxy-PGJ2 did not mediate bronchodilation. Relaxation to RGZ was not prevented by T0070907 or GW9662 or by epithelial removal. RGZ-induced relaxation was preserved in the trachea and increased in PCLS after ovalbumin-challenge. Although RGZ was less potent than β-adrenoceptor agonists, its effects were additive with salbutamol and isoprenaline and only RGZ maintained potency and full efficacy in maximally contracted airways or after allergen challenge. Acute PPARγ-independent, epithelial-independent airway relaxation to RGZ is resistant to functional antagonism and maintained in both trachea and PCLS from a model of chronic AAD. These novel efficacious actions of RGZ support its therapeutic potential in asthma when responsiveness to β-adrenoceptor agonists is limited.

Donovan, C, Royce, SG, Vlahos, R & Bourke, JE 2015, 'Lipopolysaccharide Does Not Alter Small Airway Reactivity in Mouse Lung Slices', PLOS ONE, vol. 10, no. 3, pp. e0122069-e0122069.
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© 2015 Donovan et al. The bacterial endotoxin, lipopolysaccharide (LPS) has been associated with occupational airway diseases with asthma-like symptoms and in acute exacerbations of COPD. The direct and indirect effects of LPS on small airway reactivity have not been fully elucidated. We tested the hypothesis that both in vitro and in vivo LPS treatment would increase contraction and impair relaxation of mouse small airways. Lung slices were prepared from naï ve Balb/C mice and cultured in the absence or presence of LPS (10 μg/ml) for up to 48 h for measurement of TNFα levels in conditioned media. Alternatively, mice were challenged with PBS or LPS in vivo once a day for 4 days for preparation of lung slices or for harvest of lungs for Q-PCR analysis of gene expression of pro-inflammatory cytokines and receptors involved in airway contraction. Reactivity of small airways to contractile agonists, methacholine and serotonin, and bronchodilator agents, salbutamol, isoprenaline and rosiglitazone, were assessed using phase-contrast microscopy. In vitro LPS treatment of slices increased TNFα release 6-fold but did not alter contraction or relaxation to any agonists tested. In vivo LPS treatment increased lung gene expression of TNFα, IL-1β and ryanodine receptor isoform 2 more than 5-fold. However there were no changes in reactivity in lung slices from these mice, even when also incubated with LPS ex vivo. Despite evidence of LPS-induced inflammation, neither airway hyperresponsiveness or impaired dilator reactivity were evident. The increase in ryanodine receptor isoform 2, known to regulate calcium signaling in vascular smooth muscle, warrants investigation. Since LPS failed to elicit changes in small airway reactivity in mouse lung slices following in vitro or in vivo treatment, alternative approaches are required to define the potential contribution of this endotoxin to altered small airway reactivity in human lung diseases.

Donovan, C, Seow, HJ, Royce, SG, Bourke, JE & Vlahos, R 2015, 'Alteration of Airway Reactivity and Reduction of Ryanodine Receptor Expression by Cigarette Smoke in Mice', American Journal of Respiratory Cell and Molecular Biology, vol. 53, no. 4, pp. 471-478.
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Copyright © 2015 by the American Thoracic SocietyGrant: This work was supported by grants 1041575 and 1027112 from the National Health and Medical Research Council of Australia. Small airways are a major site of airflow limitation in chronic obstructive pulmonary disease (COPD). Despite the detrimental effects of long-term smoking in COPD, the effects of acute cigarette smoke (CS) exposure on small airway reactivity have not been fully elucidated. Balb/C mice were exposed to room air (sham) or CS for 4 days to cause airway inflammation. Changes in small airway lumen area in response to contractile agents were measured in lung slices in situ using phase-contrast microscopy. Separate slices were pharmacologically maintained at constant intracellular Ca2+ using caffeine/ryanodine before contractile measurements. Gene and protein analysis of contractile signaling pathways were performed on separate lungs. Monophasic contraction to serotonin became biphasic after CS exposure, whereas contraction to methacholine was unaltered. This altered pattern of contraction was normalized by caffeine/ryanodine. Expression of contractile agonist-specific receptors was unaltered; however, all isoforms of the ryanodine receptor were down-regulated. This is the first study to show that acute CS exposure selectively alters small airway contraction to serotonin and down-regulates ryanodine receptors involved in maintaining Ca2+ oscillations in airway smooth muscle. Understanding the contribution of ryanodine receptors to altered airway reactivity may inform the development of novel treatment strategies for COPD.

Dontschuk, N, Stacey, A, Tadich, A, Rietwyk, KJ, Schenk, A, Edmonds, MT, Shimoni, O, Pakes, CI, Prawer, S & Cervenka, J 2015, 'A graphene field-effect transistor as a molecule-specific probe of DNA nucleobases', Nature Communications, vol. 6, no. 1.
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© 2015 Macmillan Publishers Limited. All rights reserved. Fast and reliable DNA sequencing is a long-standing target in biomedical research. Recent advances in graphene-based electrical sensors have demonstrated their unprecedented sensitivity to adsorbed molecules, which holds great promise for label-free DNA sequencing technology. To date, the proposed sequencing approaches rely on the ability of graphene electric devices to probe molecular-specific interactions with a graphene surface. Here we experimentally demonstrate the use of graphene field-effect transistors (GFETs) as probes of the presence of a layer of individual DNA nucleobases adsorbed on the graphene surface. We show that GFETs are able to measure distinct coverage-dependent conductance signatures upon adsorption of the four different DNA nucleobases; a result that can be attributed to the formation of an interface dipole field. Comparison between experimental GFET results and synchrotron-based material analysis allowed prediction of the ultimate device sensitivity, and assessment of the feasibility of single nucleobase sensing with graphene.

Duan, X, Ao, Z, Sun, H, Zhou, L, Wang, G & Wang, S 2015, 'Insights into N-doping in single-walled carbon nanotubes for enhanced activation of superoxides: a mechanistic study', Chemical Communications, vol. 51, no. 83, pp. 15249-15252.
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Nitrogen-doped SWCNTs with enhanced carbocatalysis were investigated in the activation of superoxides by advanced oxidation and theoretical calculations.

Dubern, J, Cigana, C, De Simone, M, Lazenby, J, Juhas, M, Schwager, S, Bianconi, I, Döring, G, Eberl, L, Williams, P, Bragonzi, A & Cámara, M 2015, 'Integrated whole‐genome screening for Pseudomonas aeruginosa virulence genes using multiple disease models reveals that pathogenicity is host specific', Environmental Microbiology, vol. 17, no. 11, pp. 4379-4393.
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SummaryPseudomonas aeruginosa is a multi‐host opportunistic pathogen causing a wide range of diseases because of the armoury of virulence factors it produces, and it is difficult to eradicate because of its intrinsic resistance to antibiotics. Using an integrated whole‐genome approach, we searched for P. aeruginosa virulence genes with multi‐host relevance. We constructed a random library of 57 360 Tn5 mutants in P. aeruginosa PAO1‐L and screened it in vitro for those showing pleiotropic effects in virulence phenotypes (reduced swarming, exo‐protease and pyocyanin production). A set of these pleiotropic mutants were assayed for reduced toxicity in Drosophila melanogaster, Caenorhabditis elegans, human cell lines and mice. Surprisingly, the screening revealed that the virulence of the majority of P. aeruginosa mutants varied between disease models, suggesting that virulence is dependent on the disease model used and hence the host environment. Genomic analysis revealed that these virulence‐related genes encoded proteins from almos...

Duggin, IG, Aylett, CHS, Walsh, JC, Michie, KA, Wang, Q, Turnbull, L, Dawson, EM, Harry, EJ, Whitchurch, CB, Amos, LA & Loewe, J 2015, 'CetZ tubulin-like proteins control archaeal cell shape', NATURE, vol. 519, no. 7543, pp. 362-+.
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© 2015 Macmillan Publishers Limited. All rights reserved. Tubulin is a major component of the eukaryotic cytoskeleton, controlling cell shape, structure and dynamics, whereas its bacterial homologue FtsZ establishes the cytokinetic ring that constricts during cell division. How such different roles of tubulin and FtsZ evolved is unknown. Studying Archaea may provide clues as these organisms share characteristics with Eukarya and Bacteria. Here we report the structure and function of proteins from a distinct family related to tubulin and FtsZ, named CetZ, which co-exists with FtsZ in many archaea. CetZ X-ray crystal structures showed the FtsZ/tubulin superfamily fold, and one crystal form contained sheets of protofilaments, suggesting a structural role. However, inactivation of CetZ proteins in Haloferax volcanii did not affect cell division. Instead, CetZ1 was required for differentiation of the irregular plate-shaped cells into a rod-shaped cell type that was essential for normal swimming motility. CetZ1 formed dynamic cytoskeletal structures in vivo, relating to its capacity to remodel the cell envelope and direct rod formation. CetZ2 was also implicated in H. volcanii cell shape control. Our findings expand the known roles of the FtsZ/tubulin superfamily to include archaeal cell shape dynamics, suggesting that a cytoskeletal role might predate eukaryotic cell evolution, and they support the premise that a major function of the microbial rod shape is to facilitate swimming.

Duncan, C, Perret, L, Palomba, S, Lapine, M, Kuhlmey, BT & de Sterke, CM 2015, 'New avenues for phase matching in nonlinear hyperbolic metamaterials', SCIENTIFIC REPORTS, vol. 5.
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Dunitz, MI, Lang, JM, Jospin, G, Darling, AE, Eisen, JA & Coil, DA 2015, 'Swabs to genomes: a comprehensive workflow', PeerJ, vol. 3, pp. e960-e960.
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Dunlop, RA, Main, BJ & Rodgers, KJ 2015, 'The deleterious effects of non-protein amino acids from desert plants on human and animal health', JOURNAL OF ARID ENVIRONMENTS, vol. 112, pp. 152-158.
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Since plants lack the ability to remove themselves from sites of predation, they have evolved alternative defences to keep predators at bay. Mechanical defences include camouflage, the addition of thorns and spikes as well as growing in locations not easily accessed by herbivores. Chemical defences include the synthesis of compounds that are toxic to predatory species and can also inhibit or retard the growth of other plant species in a process termed allelopathy. Amongst these chemicals is a reservoir of non-protein amino acids that mediate toxicity. These non-protein amino acids can be charged by tRNA synthetases and subsequently mis-incorporated into nascent polypeptides, resulting in aberrant, dysfunctional proteins that can be toxic to predators. Some species such as the bruchid beetle Bruchus rufimanus (Chrysomelidae), which feeds on the jack bean Canavalia ensiformis (Fabaceae) plant, have evolved advanced tRNA synthetases that are able to discriminate between protein and non-protein amino acids, thus remain unaffected. Other species including livestock and humans that do not possess such selectivity are susceptible to plant toxins. In this brief review we discuss the mechanisms of action and consequences of exposure to plant-derived non-protein amino acids with a focus on those derived from plants from arid environments.

Eamus, D, Zolfaghar, S, Villalobos-Vega, R, Cleverly, J & Huete, A 2015, 'Groundwater-dependent ecosystems: recent insights from satellite and field-based studies', HYDROLOGY AND EARTH SYSTEM SCIENCES, vol. 19, no. 10, pp. 4229-4256.
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© 2015 Author(s). Groundwater-dependent ecosystems (GDEs) are at risk globally due to unsustainable levels of groundwater extraction, especially in arid and semi-arid regions. In this review, we examine recent developments in the ecohydrology of GDEs with a focus on three knowledge gaps: (1) how do we locate GDEs, (2) how much water is transpired from shallow aquifers by GDEs and (3) what are the responses of GDEs to excessive groundwater extraction? The answers to these questions will determine water allocations that are required to sustain functioning of GDEs and to guide regulations on groundwater extraction to avoid negative impacts on GDEs. We discuss three methods for identifying GDEs: (1) techniques relying on remotely sensed information; (2) fluctuations in depth-to-groundwater that are associated with diurnal variations in transpiration; and (3) stable isotope analysis of water sources in the transpiration stream. We then discuss several methods for estimating rates of GW use, including direct measurement using sapflux or eddy covariance technologies, estimation of a climate wetness index within a Budyko framework, spatial distribution of evapotranspiration (ET) using remote sensing, groundwater modelling and stable isotopes. Remote sensing methods often rely on direct measurements to calibrate the relationship between vegetation indices and ET. ET from GDEs is also determined using hydrologic models of varying complexity, from the White method to fully coupled, variable saturation models. Combinations of methods are typically employed to obtain clearer insight into the components of groundwater discharge in GDEs, such as the proportional importance of transpiration versus evaporation (e.g. using stable isotopes) or from groundwater versus rainwater sources. Groundwater extraction can have severe consequences for the structure and function of GDEs. In the most extreme cases, phreatophytes experience crown dieback and death following groundwater...

Eamus, D, Zolfaghar, S, Villalobos-Vega, R, Cleverly, J & Huete, A 2015, 'Groundwater-dependent ecosystems: recent insights, new techniques and an ecosystem-scale threshold response', Hydrology and Earth System Sciences Discussions, vol. 12, no. 5, pp. 4677-4754.
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Abstract. Groundwater-dependent ecosystems (GDEs) are at risk globally due to unsustainable levels of groundwater extraction, especially in arid and semi-arid regions. In this review, we examine recent developments in the ecohydrology of GDEs with a focus on three knowledge gaps: (1) how do we locate GDEs, (2) how much water is transpired from shallow aquifers by GDEs; and (3) what are the responses of GDEs to excessive groundwater extraction? The answers to these questions will determine water allocations that are required to sustain functioning of GDEs and to guide regulations on groundwater extraction to avoid negative impacts on GDEs. We discuss three methods for identifying GDEs: (1) fluctuations in depth-to-groundwater that are associated with diurnal variations in transpiration, (2) stable isotope analysis of water sources in the transpiration stream; and (3) remote sensing methods. We then discuss several methods for estimating rates of GW use, including direct measurement using sapflux or eddy covariance technologies, estimation of a climate wetness index within a Budyko framework, spatial distribution of ET using remote sensing, groundwater modelling and stable isotopes. Remote sensing methods often rely on direct measurements to calibrate the relationship between vegetation indices and ET. ET from GDEs is also determined using hydrologic models of varying complexity, from the 'White method' to fully coupled, variable saturation models. Combinations of methods are typically employed to obtain clearer insight into the components of groundwater discharge in GDEs, such as the proportional importance of transpiration vs. evaporation (e.g., using stable isotopes) or from groundwater vs. rainwater sources. Groundwater extraction can have severe consequences on structure and function of GDEs. In the most extreme cases, phreatophytes experience crown dieback and death following groundwater drawdown. We provide a brief review of two case stu...

Edwards, SJ, Valkenier, H, Busschaert, N, Gale, PA & Davis, AP 2015, 'High‐Affinity Anion Binding by Steroidal Squaramide Receptors', Angewandte Chemie International Edition, vol. 54, no. 15, pp. 4592-4596.
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AbstractExceptionally powerful anion receptors have been constructed by placing squaramide groups in axial positions on a steroidal framework. The steroid preorganizes the squaramide NH groups such that they can act cooperatively on a bound anion, while maintaining solubility in nonpolar media. The acidic NH groups confer higher affinities than previously‐used ureas or thioureas. Binding constants exceeding 1014 M−1 have been measured for tetraethylammonium salts in chloroform by employing a variation of Cram’s extraction procedure. The receptors have also been studied as transmembrane anion carriers in unilamellar vesicles. Unusually their activities do not correlate with anion affinities, thus suggesting an upper limit for binding strength in the design of anion carriers.

Elder, M & Taback, J 2015, 'Thompson's group F is 1-counter graph automatic', Groups. Complexity. Cryptology, vol. 8, pp. 21-33.
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It is not known whether Thompson's group F is automatic. With the recentextensions of the notion of an automatic group to graph automatic byKharlampovich, Khoussainov and Miasnikov and then to C-graph automatic by theauthors, a compelling question is whether F is graph automatic or C-graphautomatic for an appropriate language class C. The extended definitions allowthe use of a symbol alphabet for the normal form language, replacing thedependence on generating set. In this paper we construct a 1-counter graphautomatic structure for F based on the standard infinite normal form for groupelements.

Erken, M, Lutz, C & McDougald, D 2015, 'Interactions ofVibriospp. with Zooplankton', Microbiology Spectrum, vol. 3, no. 3, pp. 1-15.
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ABSTRACTMembers of the genusVibrioare known to interact with phyto- and zooplankton in aquatic environments. These interactions have been proven to protect the bacterium from various environmental stresses, serve as a nutrient source, facilitate exchange of DNA, and to serve as vectors of disease transmission. This review highlights the impact ofVibrio-zooplankton interactions at the ecosystem scale and the importance of studies focusing on a wide range ofVibrio-zooplankton interactions. The current knowledge on chitin utilization (i.e., chemotaxis, attachment, and degradation) and the role of these factors in attachment to nonchitinous zooplankton is also presented.

Essilfie, A-T, Horvat, J, Kim, R, Mayall, J, Pinkerton, J, Beckett, E, Starkey, M, Simpson, J, Foster, P, Gibson, P & Hansbro, P 2015, 'Macrolide therapy suppresses key features of experimental steroid-sensitive and steroid-insensitive asthma (HYP2P.342)', The Journal of Immunology, vol. 194, no. 1_Supplement, pp. 53.23-53.23.
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Abstract Background Steroid-insensitive endotypes of asthma are an important clinical problem requiring effective treatments. They are associated with non-eosinophilic inflammatory responses and bacterial infections. Macrolide therapy is effective in steroid-insensitive endotypes, such as non-eosinophilic asthma, however the mechanisms of how they work is unknown. Objectives To determine the efficacy of macrolide and non-macrolide antibiotic treatments in infection-induced, severe, steroid-insensitive allergic airways disease (SSIAAD). Methods Mouse models of Chlamydia and Haemophilus lung infection-induced SSIAAD were used to investigate the effects of clarithromycin and amoxicillin treatment on immune responses and AHR in steroid-sensitive AAD and SSIAAD compared to dexamethasone treatment. Results Amoxicillin and clarithromycin had similar anti-microbial effects on infection. Amoxicillin did not suppress either form of AAD, but restored steroid sensitivity in SSIAAD by reducing infection. In contrast, clarithromycin alone widely suppressed inflammation and AHR in both steroid-sensitive and SSIAAD. This occurred through reductions in both Th2 responses that drive steroid-sensitive, eosinophilic AAD, and TNF-α and IL-17 responses that induce neutrophilic SSIAAD. Conclusions Macrolides have broad anti-inflammatory effects that are independent of their anti-microbial effects. The specific responses suppressed are dependent upon the responses that dominate during disease

Essilfie, A-T, Horvat, JC, Kim, RY, Mayall, JR, Pinkerton, JW, Beckett, EL, Starkey, MR, Simpson, JL, Foster, PS, Gibson, PG & Hansbro, PM 2015, 'Macrolide therapy suppresses key features of experimental steroid-sensitive and steroid-insensitive asthma', Thorax, vol. 70, no. 5, pp. 458-467.
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Background

Steroid-insensitive endotypes of asthma are an important clinical problem and effective therapies are required. They are associated with bacterial infection and non-eosinophilic inflammatory responses in the asthmatic lung. Macrolide therapy is effective in steroid-insensitive endotypes, such as non-eosinophilic asthma. However, whether the effects of macrolides are due to antimicrobial or anti-inflammatory mechanisms is not known.

Objective

To determine and assess the efficacy of macrolide (ie, clarithromycin) and non-macrolide (ie, amoxicillin) antibiotic treatments in experimental models of infection-induced, severe, steroid-insensitive neutrophilic allergic airways disease (SSIAAD), compared with steroid-sensitive AAD and to delineate the antimicrobial and anti-inflammatory effects of macrolide therapy.

Methods

We developed and used novel mouse models of Chlamydia and Haemophilus lung infection-induced SSIAAD. We used these models to investigate the effects of clarithromycin and amoxicillin treatment on immune responses and airways hyper-responsiveness (AHR) in Ova-induced, T helper lymphocyte (Th) 2 -associated steroid-sensitive AAD and infection-induced Th1/Th17-associated SSIAAD compared with dexamethasone treatment.

Results

Clarithromycin and amoxicillin had similar antimicrobial effects on infection. Amoxicillin did attenuate some features, but did not broadly suppress either form of AAD. It did restore steroid sensitivity in SSIAAD by reducing infection. In contrast, clarithromycin alone widely suppressed inflammation and AHR in both steroid-sensitive AAD and SSIAAD. This occurred through reductions in Th2 responses that drive steroid-sensitive eosinophilic AAD and tumour necrosis factor α and interleukin 17 responses that induce SSIAAD.

Conclusions

Macrolides have broad anti-inflammatory effects in AAD that are likely independent of their antimicrobial effects. The specific responses that are sup...

Everett, JD & Doblin, MA 2015, 'Characterising primary productivity measurements across a dynamic western boundary current region', DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS, vol. 100, pp. 105-116.
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© 2015 Elsevier Ltd. Determining the magnitude of primary production (PP) in a changing ocean is a major research challenge. Thousands of estimates of marine PP exist globally, but there remain significant gaps in data availability, particularly in the Southern Hemisphere. In situ PP estimates are generally single-point measurements and therefore we rely on satellite models of PP in order to scale up over time and space. To reduce the uncertainty around the model output, these models need to be assessed against in situ measurements before use. This study examined the vertically-integrated productivity in four water-masses associated with the East Australian Current (EAC), the major western boundary current (WBC) of the South Pacific. We calculated vertically integrated PP from shipboard ¹⁴C PP estimates and then compared them to estimates from four commonly used satellite models (ESQRT, VGPM, VGPM-Eppley, VGPM-Kameda) to assess their utility for this region. Vertical profiles of the water-column show each water-mass had distinct temperature-salinity signatures. The depth of the fluorescence-maximum (fmax) increased from onshore (river plume) to offshore (EAC) as light penetration increased. Depth integrated PP was highest in river plumes (792±181mgCm^-2d^-1) followed by the EAC (534±116mgCm^-2d^-1), continental shelf (140±47mgCm^-2d^-1) and cyclonic eddy waters (121±4mgCm^-2d^-1). Surface carbon assimilation efficiency was greatest in the EAC (301±145mgC (mgChl-a)^-1d^-1) compared to other water masses. All satellite primary production models tested underestimated EAC PP and overestimated continental shelf PP. The ESQRT model had the highest skill and lowest bias of the tested models, providing the best first-order estimates of PP on the continental shelf, including at a coastal time-series station, Port Hacking, which showed conside...

Exton, DA, McGenity, TJ, Steinke, M, Smith, DJ & Suggett, DJ 2015, 'Uncovering the volatile nature of tropical coastal marine ecosystems in a changing world', Global Change Biology, vol. 21, no. 4, pp. 1383-1394.
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AbstractBiogenic volatile organic compounds (BVOCs), in particular dimethyl sulphide (DMS) and isoprene, have fundamental ecological, physiological and climatic roles. Our current understanding of these roles is almost exclusively established from terrestrial or oceanic environments but signifies a potentially major, but largely unknown, role forBVOCs in tropical coastal marine ecosystems. The tropical coast is a transition zone between the land and ocean, characterized by highly productive and biodiverse coral reefs, seagrass beds and mangroves, which house primary producers that are amongst the greatest emitters ofBVOCs on the planet. Here, we synthesize our existing understanding ofBVOCemissions to produce a novel conceptual framework of the tropical marine coast as a continuum fromDMS‐dominated reef producers to isoprene‐dominated mangroves. We use existing and previously unpublished data to consider how current environmental conditions shapeBVOCproduction across the tropical coastal continuum, and in turn howBVOCs can regulate environmental stress tolerance or species interactions via infochemical networks. We use this as a framework to discuss how existing predictions of future tropical coastalBVOCemissions, and the roles they play, are effectively restricted to present day ‘baseline’ trends ofBVOCproductio...

Fair, KM & Ford, MJ 2015, 'Phase transitions and optical properties of the semiconducting and metallic phases of single-layer MoS₂', Nanotechnology, vol. 26, no. 43, pp. 435705-435705.
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We report density functional theory calculations for single layer MoS2 in its 2H, semiconducting and 1T metallic phases in order to understand the relative stability of these two phases and transition between them in the presence of adsorbed lithium atoms and under compressive strain. We have determined the diffusion barriers between the two phases and demonstrate how the presence of Li adatoms or strain can significantly reduce these barriers. We show that the 2H and 1T structures have the same energy under 15% biaxial, compressive strain. This is the same strain value posited by Lin et al (2014 Nat. Nanotechnology 9 391–396) for their intermediate α phase. Calculations of the 1T and 2H permittivity and electron energy loss spectrum are also performed and characterized.

Fang, J, Levchenko, I, Yan, W, Aharonovich, I, Aramesh, M, Prawer, S & Ostrikov, KK 2015, 'Plasmonic Metamaterial Sensor with Ultra‐High Sensitivity in the Visible Spectral Range', Advanced Optical Materials, vol. 3, no. 6, pp. 750-755.
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A metamaterial-based plasmonic sensor composed of thin metal and polymer layers deposited on top of a highly ordered porous alumina exhibits a sensitivity of more than 4800 nm per refractive index unit in the visible spectral range. The device is robust, cheap, has a large functional area of about 2 cm2, and the overall transmission is tunable by varying the film thickness.

Fang, J, Levchenko, I, Yan, W, Aharonovich, I, Aramesh, M, Prawer, S & Ostrikov, KK 2015, 'Sensors: Plasmonic Metamaterial Sensor with Ultra‐High Sensitivity in the Visible Spectral Range (Advanced Optical Materials 6/2015)', Advanced Optical Materials, vol. 3, no. 6, pp. 716-716.
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Farrell, H, Seebacher, F, O'Connor, W, Zammit, A, Harwood, DT & Murray, S 2015, 'Warm temperature acclimation impacts metabolism of paralytic shellfish toxins from Alexandrium minutum in commercial oysters', GLOBAL CHANGE BIOLOGY, vol. 21, no. 9, pp. 3402-3413.
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© 2015 John Wiley & Sons Ltd. Species of Alexandrium produce potent neurotoxins termed paralytic shellfish toxins and are expanding their ranges worldwide, concurrent with increases in sea surface temperature. The metabolism of molluscs is temperature dependent, and increases in ocean temperature may influence both the abundance and distribution of Alexandrium and the dynamics of toxin uptake and depuration in shellfish. Here, we conducted a large-scale study of the effect of temperature on the uptake and depuration of paralytic shellfish toxins in three commercial oysters (Saccostrea glomerata and diploid and triploid Crassostrea gigas, n = 252 per species/ploidy level). Oysters were acclimated to two constant temperatures, reflecting current and predicted climate scenarios (22 and 27 °C), and fed a diet including the paralytic shellfish toxin-producing species Alexandrium minutum. While the oysters fed on A. minutum in similar quantities, concentrations of the toxin analogue GTX1,4 were significantly lower in warm-acclimated S. glomerata and diploid C. gigas after 12 days. Following exposure to A. minutum, toxicity of triploid C. gigas was not affected by temperature. Generally, detoxification rates were reduced in warm-acclimated oysters. The routine metabolism of the oysters was not affected by the toxins, but a significant effect was found at a cellular level in diploid C. gigas. The increasing incidences of Alexandrium blooms worldwide are a challenge for shellfish food safety regulation. Our findings indicate that rising ocean temperatures may reduce paralytic shellfish toxin accumulation in two of the three oyster types; however, they may persist for longer periods in oyster tissue.

FERGUSSON, K & PLATEN, E 2015, 'APPLICATION OF MAXIMUM LIKELIHOOD ESTIMATION TO STOCHASTIC SHORT RATE MODELS', Annals of Financial Economics, vol. 10, no. 02, pp. 1-26.
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The application of maximum likelihood estimation is not well studied for stochastic short rate models because of the cumbersome detail of this approach. We investigate the applicability of maximum likelihood estimation to stochastic short rate models. We restrict our consideration to three important short rate models, namely the Vasicek, Cox–Ingersoll–Ross (CIR) and 3/2 short rate models, each having a closed-form formula for the transition density function. The parameters of the three interest rate models are fitted to US cash rates and are found to be consistent with market assessments.

Fisher, C, Botten, LC, Poulton, CG, McPhedran, RC & De Sterke, CM 2015, 'Efficient end-fire coupling of surface plasmons in a metal waveguide', Journal of the Optical Society of America B: Optical Physics, vol. 32, no. 3, pp. 412-425.
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We present a semi-analytical study exploring the end-fire coupling of an incident beam into a surface plasmon mode propagating on a metal-dielectric interface. An energy-conserving projection method is used to solve for the resultant reflected and transmitted fields for a given incident beam, thereby determining the efficiency of the surface plasmon coupling. The coupling efficiency is found to be periodic with waveguide width due to the presence of a coupled, transversely propagating surface plasmon. Optimization of the incident beam parameters, such as beam width, position, and wavelength, leads to numerically observed maximum efficiencies of approximately 80% when the beam width roughly matches the width of the surface plasmon.

Fletcher, G, Arnold, MD, Pedersen, T, Keast, VJ & Cortie, MB 2015, 'Multipolar and dark-mode plasmon resonances on drilled silver nano-triangles', OPTICS EXPRESS, vol. 23, no. 14, pp. 18002-18013.
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© 2015 Optical Society of America. Dark-mode plasmon resonances can be excited by positioning a suitable nano-antenna above a nanostructure to couple a planar incident wave-front into a virtual point source. We explore this phenomenon using a prototypical nanostructure consisting of a silver nanotriangle into which a hole has been drilled and a rod-like nano-antenna of variable aspect ratio. Using numerical simulations, we establish the behavior of the basic drilled nanotriangle under plane wave illumination and electron beam irradiation to provide a baseline, and then add the nano-antenna to investigate the stimulation of additional dark-mode plasmon resonances. The introduction of a suitably tuned nano-antenna provides a new and general means of exciting dark-mode resonances using plane wave light. The resulting system exhibits a very rich variety of radiant and sub-radiant resonance modes.

Fletcher, S, Sibbritt, D, Stark, D, Harkness, J, Rawlinson, W, Andresen, D, Van Hal, S, Merif, J & Ellis, J 2015, 'Descriptive epidemiology of infectious gastrointestinal illnesses in Sydney, Australia, 2007–2010', Western Pacific Surveillance and Response Journal, vol. 6, no. 4, pp. 7-16.
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OBJECTIVE: There is a lack of information about the prevalence of gastrointestinal illnesses in Australia. Current disease surveillance systems capture only a few pathogens. The aim of this study is to describe the epidemiology of infectious gastrointestinal illnesses in Sydney, Australia.METHODS: A retrospective cross-sectional study of patients with gastrointestinal symptoms who visited tertiary public hospitals in Sydney was conducted between 2007 and 2010. Patients with diarrhoea or loose stools with an enteric pathogen detected were identified. Demographic, clinical and potential risk factor data were collected from their medical records. Measures of association, descriptive and inferential statistics were analysed.RESULTS: In total, 1722 patients were included in this study. Campylobacter (22.0%) and Clostridium difficile (19.2%) were the most frequently detected pathogens. Stratified analysis showed that rotavirus (22.4%), norovirus (20.7%) and adenovirus (18.1%) mainly affected children under 5 years; older children (5-12 years) were frequently infected with Campylobacter spp. (29.8%) and non-typhoid Salmonella spp. (24.4%); infections with C. difficile increased with age.Campylobacter and non-typhoid Salmonella spp. showed increased incidence in summer months (December to February), while rotavirus infections peaked in the cooler months (June to November).DISCUSSION: This study revealed that gastrointestinal illness remains a major public health issue in Sydney. Improvement of current disease surveillance and prevention and control measures are required. This study emphasizes the importance of laboratory diagnosis of enteric infections and the need for better clinical data collection to improve management of disease risk factors in the community.

Fogarty, S, Stojanovska, L, Harris, D, Zaslawski, C, Mathai, ML & McAinch, AJ 2015, 'A randomised cross-over pilot study investigating the use of acupuncture to promote weight loss and mental health in overweight and obese individuals participating in a weight loss program', EATING AND WEIGHT DISORDERS-STUDIES ON ANOREXIA BULIMIA AND OBESITY, vol. 20, no. 3, pp. 379-387.
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Fotheringham, I, Meakin, G, Punekar, Y, Riley, J, Cockle, S & Singh, S 2015, 'Comparison of laboratory- and field-based exercise tests for COPD: a systematic review', International Journal of Chronic Obstructive Pulmonary Disease, vol. 10, pp. 625-625.
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Exercise tests are often used to evaluate the functional status of patients with COPD. However, to the best of our knowledge, a comprehensive systematic comparison of these tests has not been performed. We systematically reviewed studies reporting the repeatability and/or reproducibility of these tests, and studies comparing their sensitivity to therapeutic intervention. A systematic review identified primary manuscripts in English reporting relevant data on the following exercise tests: 6-minute walk test (6MWT) and 12-minute walk test, incremental and endurance shuttle walk tests (ISWT and ESWT, respectively), incremental and endurance cycle ergometer tests, and incremental and endurance treadmill tests. We identified 71 relevant studies. Good repeatability (for the 6MWT and ESWT) and reproducibility (for the 6MWT, 12-minute walk test, ISWT, ESWT, and incremental cycle ergometer test) were reported by most studies assessing these tests, providing patients were familiarized with them beforehand. The 6MWT, ISWT, and particularly the ESWT were reported to be sensitive to therapeutic intervention. Protocol variations (eg, track layout or supplemental oxygen use) affected performance significantly in several studies. This review shows that while the validity of several tests has been established, for others further study is required. Future work will assess the link between these tests, physiological mechanisms, and patient-reported measures.

Fourment, M & Holmes, EC 2015, 'Avian influenza virus exhibits distinct evolutionary dynamics in wild birds and poultry', BMC Evolutionary Biology, vol. 15, no. 1.
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Fowler, AM, Macreadie, PI & Booth, DJ 2015, 'Renewables-to-reefs: Participatory multicriteria decision analysis is required to optimize wind farm decommissioning', MARINE POLLUTION BULLETIN, vol. 98, no. 1-2, pp. 368-371.
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Fowler, AM, Macreadie, PI, Bishop, DP & Booth, DJ 2015, 'Using otolith microchemistry and shape to assess the habitat value of oil structures for reef fish', MARINE ENVIRONMENTAL RESEARCH, vol. 106, no. 1, pp. 103-113.
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© 2015 Elsevier Ltd. Over 7500 oil and gas structures (e.g. oil platforms) are installed in offshore waters worldwide and many will require decommissioning within the next two decades. The decision to remove such structures or turn them into reefs (i.e. 'rigs-to-reefs') hinges on the habitat value they provide, yet this can rarely be determined because the residency of mobile species is difficult to establish. Here, we test a novel solution to this problem for reef fishes; the use of otolith (earstone) properties to identify oil structures of residence. We compare the otolith microchemistry and otolith shape of a site-attached coral reef fish (. Pseudanthias rubrizonatus) among four oil structures (depth 82-135m, separated by 9.7-84.2km) on Australia's North West Shelf to determine if populations developed distinct otolith properties during their residency. Microchemical signatures obtained from the otolith edge using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) differed among oil structures, driven by elements Sr, Ba and Mn, and to a lesser extent Mg and Fe. A combination of microchemical data from the otolith edge and elliptical Fourier (shape) descriptors allowed allocation of individuals to their 'home' structure with moderate accuracy (overall allocation accuracy: 63.3%, range: 45.5-78.1%), despite lower allocation accuracies for each otolith property in isolation (microchemistry: 47.5%, otolith shape: 45%). Site-specific microchemical signatures were also stable enough through time to distinguish populations during 3 separate time periods, suggesting that residence histories could be recreated by targeting previous growth zones in the otolith. Our results indicate that reef fish can develop unique otolith properties during their residency on oil structures which may be useful for assessing the habitat value of individual structures. The approach outlined here may also be useful for determining the residency of reef fish ...

Freedman, LS, Midthune, D, Carroll, RJ, Commins, JM, Arab, L, Baer, DJ, Moler, JE, Moshfegh, AJ, Neuhouser, ML, Prentice, RL, Rhodes, D, Spiegelman, D, Subar, AF, Tinker, LF, Willett, W & Kipnis, V 2015, 'Application of a New Statistical Model for Measurement Error to the Evaluation of Dietary Self-report Instruments', Epidemiology, vol. 26, no. 6, pp. 925-933.
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Copyright © 2015 Wolters Kluwer Health, Inc. All rights reserved. Most statistical methods that adjust analyses for dietary measurement error treat an individual's usual intake as a fixed quantity. However, usual intake, if defined as average intake over a few months, varies over time. We describe a model that accounts for such variation and for the proximity of biomarker measurements to self-reports within the framework of a meta-analysis, and apply it to the analysis of data on energy, protein, potassium, and sodium from a set of five large validation studies of dietary self-report instruments using recovery biomarkers as reference instruments. We show that this time-varying usual intake model fits the data better than the fixed usual intake assumption. Using this model, we estimated attenuation factors and correlations with true longer-term usual intake for single and multiple 24-hour dietary recalls (24HRs) and food frequency questionnaires (FFQs) and compared them with those obtained under the 'fixed' method. Compared with the fixed method, the estimates using the time-varying model showed slightly larger values of the attenuation factor and correlation coefficient for FFQs and smaller values for 24HRs. In some cases, the difference between the fixed method estimate and the new estimate for multiple 24HRs was substantial. With the new method, while four 24HRs had higher estimated correlations with truth than a single FFQ for absolute intakes of protein, potassium, and sodium, for densities the correlations were approximately equal. Accounting for the time element in dietary validation is potentially important, and points toward the need for longer-term validation studies.

Freedman, LS, Midthune, D, Dodd, KW, Carroll, RJ & Kipnis, V 2015, 'A statistical model for measurement error that incorporates variation over time in the target measure, with application to nutritional epidemiology', Statistics in Medicine, vol. 34, no. 27, pp. 3590-3605.
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Most statistical methods that adjust analyses for measurement error assume that the target exposure T is a fixed quantity for each individual. However, in many applications, the value of T for an individual varies with time. We develop a model that accounts for such variation, describing the model within the framework of a meta‐analysis of validation studies of dietary self‐report instruments, where the reference instruments are biomarkers. We demonstrate that in this application, the estimates of the attenuation factor and correlation with true intake, key parameters quantifying the accuracy of the self‐report instrument, are sometimes substantially modified under the time‐varying exposure model compared with estimates obtained under a traditional fixed‐exposure model. We conclude that accounting for the time element in measurement error problems is potentially important. Copyright © 2015 John Wiley & Sons, Ltd.

Fristedt, R, Herdean, A, Blaby-Haas, CE, Mamedov, F, Merchant, SS, Last, RL & Lundin, B 2015, 'PHOTOSYSTEM II PROTEIN33, a Protein Conserved in the Plastid Lineage, Is Associated with the Chloroplast Thylakoid Membrane and Provides Stability to Photosystem II Supercomplexes in Arabidopsis', Plant Physiology, vol. 167, no. 2, pp. 481-492.
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Frommlet, JC, Sousa, ML, Alves, A, Vieira, SI, Suggett, DJ & Serôdio, J 2015, 'Coral symbiotic algae calcify ex hospite in partnership with bacteria', Proceedings of the National Academy of Sciences, vol. 112, no. 19, pp. 6158-6163.
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Significance The dinoflagellate genus Symbiodinium is best known for harboring important endosymbiotic algae of marine invertebrates, notably reef-building corals. However, these dinoflagellates also live freely within coral reef waters and sediments and provide an important environmental pool for the colonization of new coral recruits. Although Symbiodinium facilitate coral calcification indirectly when in hospite , we show that they also can calcify in partnership with bacteria when free living. This discovery offers entirely new perspectives on fundamental questions regarding the life cycle and ecology of these dinoflagellates and could help explain how changes in ocean chemistry created a selective pressure that ultimately led Symbiodinium to establish an endosymbiotic life style. To our knowledge, our findings document the first identified dinoflagellate–bacterial calcifying community.

Fronzi, M, Kimizuka, H & Ogata, S 2015, 'Atomistic investigation of vacancy assisted diffusion mechanism in Mg ternary (Mg–RE–M) alloys', Computational Materials Science, vol. 98, pp. 76-82.
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Fu, F, Wen, S, Zhu, J & Shi, X 2015, 'Encapsulation of doxorubicin within lactobionic acid-modified multifunctional poly(amidoamine) dendrimers for targeted therapy of liver cancer cells', Journal of Controlled Release, vol. 213, pp. e31-e32.
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Fung, J, Singh, G & Zinder, Y 2015, 'Capacity planning in supply chains of mineral resources', INFORMATION SCIENCES, vol. 316, pp. 397-418.
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The paper addresses the existing gap in the literature on the optimisation in capacity planning for mineral supply chains. The presented optimisation procedure aims at minimising the cost of infrastructure expansion for any given scenario of future demand. The optimisation procedure is designed as a matheuristic - a hybridisation of mixed integer linear programming (MILP), and a simulated annealing based scheduler. The optimisation procedure is iterative in nature and has the following distinctive features. Each iteration starts with generating a MILP model and finding a minimal cost infrastructure expansion for this model. Then, the scheduler analyses the MILP solution by constructing a schedule. In constructing this schedule, the scheduler reduces its search space using the MILP solution. The scheduler identifies bottlenecks in the infrastructure, which are used for generating a new MILP model at the next iteration. The MILP and the scheduler use different levels of data aggregation and their interaction mechanism is designed as a solution process of a bi-criteria optimisation problem. The computational experiments on data, originating from the world's largest coal exporter, shows the ability of the developed matheuristic to solve industrial-scaled instances of the problem.

Gahan, ME, Thomas, R, Rossi, R, Nelson, M, Roffey, P, Richardson, MM & McNevin, D 2015, 'Background frequency of Bacillus species at the Canberra Airport: A 12 month study', Forensic Science International, vol. 257, pp. 142-148.
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Gao, Y, Yu, R-C, Murray, SA, Chen, J-H, Kang, Z-J, Zhang, Q-C, Kong, F-Z & Zhou, M-J 2015, 'High Specificity of a Quantitative PCR Assay Targeting a Saxitoxin Gene for Monitoring Toxic Algae Associated with Paralytic Shellfish Toxins in the Yellow Sea', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 81, no. 20, pp. 6973-6981.
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Gardner, SG, Nielsen, DA, Petrou, K, Larkum, AWD & Ralph, PJ 2015, 'Characterisation of coral explants: a model organism for cnidarian-dinoflagellate studies', CORAL REEFS, vol. 34, no. 1, pp. 133-142.
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Ge, Q, Chen, L, Jaffar, J, Argraves, WS, Twal, WO, Hansbro, P, Black, JL, Burgess, JK & Oliver, B 2015, 'Fibulin1C peptide induces cell attachment and extracellular matrix deposition in lung fibroblasts', Scientific Reports, vol. 5, no. 1.
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AbstractFibulin-1 is an extracellular matrix (ECM) protein, levels of which are elevated in serum and lung tissue from patients with idiopathic pulmonary fibrosis compared to healthy volunteers. Inhibition of fibulin-1C, one of four fibulin-1 isoforms, reduced proliferation and wound healing in human airway smooth muscle (ASM) cells. This study identified the bioactive region/s of fibulin-1C which promotes fibrosis. Seven fibulin-1C peptides were synthesized and used to pre-coat tissue culture plates before lung derived ASM cells and fibroblasts from patients with pulmonary fibrosis (PF), chronic obstructive pulmonary disease (COPD) or neither disease (Control) were plated. Peptide effects on in vitro measures of fibrosis: cell attachment, proliferation and viability and ECM deposition, were examined. Among these peptides, peptide 1C1 (FBLN1C1) enhanced ASM cell and fibroblast attachment. FBLN1C1 increased mitochondrial activity and proliferation in fibroblasts. In addition, FBLN1C1 stimulated fibulin1 deposition in PF and COPD fibroblasts and augmented fibronectin and perlecan deposition in all three groups. Peptides FBLN1C2 to FBLN1C7 had no activity. The active fibulin-1C peptide identified in this study describes a useful tool for future studies. Ongoing investigation of the role of fibulin-1 may reveal the mechanisms underlying the pathphysiology of chronic lung diseases.

Ge, Q, Zeng, Q, Tjin, G, Lau, E, Black, JL, Oliver, BGG & Burgess, JK 2015, 'Differential deposition of fibronectin by asthmatic bronchial epithelial cells', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 309, no. 10, pp. L1093-L1102.
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Altered ECM protein deposition is a feature in asthmatic airways. Fibronectin (Fn), an ECM protein produced by human bronchial epithelial cells (HBECs), is increased in asthmatic airways. This study investigated the regulation of Fn production in asthmatic or nonasthmatic HBECs and whether Fn modulated HBEC proliferation and inflammatory mediator secretion. The signaling pathways underlying transforming growth factor (TGF)-β1-regulated Fn production were examined using specific inhibitors for ERK, JNK, p38 MAPK, phosphatidylinositol 3 kinase, and activin-like kinase 5 (ALK5). Asthmatic HBECs deposited higher levels of Fn in the ECM than nonasthmatic cells under basal conditions, whereas cells from the two groups had similar levels of Fn mRNA and soluble Fn. TGF-β1 increased mRNA levels and ECM and soluble forms of Fn but decreased cell proliferation in both cells. The rate of increase in Fn mRNA was higher in nonasthmatic cells. However, the excessive amounts of ECM Fn deposited by asthmatic cells after TGF-β1 stimulation persisted compared with nonasthmatic cells. Inhibition of ALK5 completely prevented TGF-β1-induced Fn deposition. Importantly, ECM Fn increased HBEC proliferation and IL-6 release, decreased PGE2 secretion, but had no effect on VEGF release. Soluble Fn had no effect on cell proliferation and inflammatory mediator release. Asthmatic HBECs are intrinsically primed to produce more ECM Fn, which when deposited into the ECM, is capable of driving remodeling and inflammation. The increased airway Fn may be one of the key driving factors in the persistence of asthma and represents a novel, therapeutic target.

Gentle, AR & Smith, GB 2015, 'A Subambient Open Roof Surface under the Mid-Summer Sun', ADVANCED SCIENCE, vol. 2, no. 9.
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Gentle, AR, Yambem, SD, Smith, GB, Burn, PL & Meredith, P 2015, 'Optimized multilayer indium-free electrodes for organic photovoltaics', PHYSICA STATUS SOLIDI A-APPLICATIONS AND MATERIALS SCIENCE, vol. 212, no. 2, pp. 348-355.
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© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Flexible multilayer electrodes that combine high transparency, high conductivity, and efficient charge extraction have been deposited, characterised and used as the anode in organic solar cells. The anode consists of an AZO/Ag/AZO stack plus a very thin oxide interlayer whose ionization potential is fine-tuned by manipulating its gap state density to optimise charge transfer with the bulk heterojunction active layer consisting of poly(n-3- hexylthiophene-2,5-diyl) and phenyl-C61-butyric acid methyl ester (P3HT:BC61BM). The deposition method for the stack was compatible with the low temperatures required for polymer substrates. Optimisation of the electrode stack was achieved by modelling the optical and electrical properties of the device and a power conversion efficiency of 2.9% under AM1.5 illumination compared to 3.0% with an ITO-only anode and 3.5% for an ITO:PEDOT electrode. Dark I-V reverse bias characteristics indicate very low densities of occupied buffer states close to the HOMO level of the hole conductor, despite observed ionization potential being high enough. Their elimination should raise efficiency to that with ITO:PEDOT.

George, MJ, Marjanovic, L & Williams, DBG 2015, 'Picogram-level quantification of some growth hormones in bovine urine using mixed-solvent bubble-in-drop single drop micro-extraction', Talanta, vol. 144, pp. 445-450.
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George, MJ, Marjanovic, L & Williams, DBG 2015, 'Solvent-Assisted Headspace Sampling Using Solid Phase Microextraction for the Analysis of Phenols in Water', Analytical Chemistry, vol. 87, no. 19, pp. 9559-9562.
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Gerace, D, Martiniello-Wilks, R, O'Brien, BA & Simpson, AM 2015, 'The use of beta-cell transcription factors in engineering artificial beta cells from non-pancreatic tissue', GENE THERAPY, vol. 22, no. 1, pp. 1-8.
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Type 1 diabetes results from the autoimmune destruction of the insulin-producing pancreatic beta (β) cells. Patients with type 1 diabetes control their blood glucose levels using several daily injections of exogenous insulin; however, this does not eliminate the long-term complications of hyperglycaemia. Currently, the only clinically viable treatments for type 1 diabetes are whole pancreas and islet transplantation. As a result, there is an urgent need to develop alternative therapies. Recently, cell and gene therapy have shown promise as a potential cure for type 1 diabetes through the genetic engineering of 'artificial' β cells to regulate blood glucose levels without adverse side effects and the need for immunosuppression. This review compares putative target cells and the use of pancreatic transcription factors for gene modification, with the ultimate goal of engineering a glucose-responsive 'artificial' β cell that mimics the function of pancreatic β cells, while avoiding autoimmune destruction.

Girod, A, Xiao, L, Reedy, B, Roux, C & Weyermann, C 2015, 'Fingermark initial composition and aging using Fourier transform infrared microscopy (mu-FTIR)', FORENSIC SCIENCE INTERNATIONAL, vol. 254, pp. 185-196.
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Giunta, S, Castorina, A, Marzagalli, R, Szychlinska, M, Pichler, K, Mobasheri, A & Musumeci, G 2015, 'Ameliorative Effects of PACAP against Cartilage Degeneration. Morphological, Immunohistochemical and Biochemical Evidence from in Vivo and in Vitro Models of Rat Osteoarthritis', International Journal of Molecular Sciences, vol. 16, no. 3, pp. 5922-5944.
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Osteoarthritis (OA); the most common form of degenerative joint disease, is associated with variations in pro-inflammatory growth factor levels, inflammation and hypocellularity resulting from chondrocyte apoptosis. Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide endowed with a range of trophic effects in several cell types; including chondrocytes. However; its role in OA has not been studied. To address this issue, we investigated whether PACAP expression is affected in OA cartilage obtained from experimentally-induced OA rat models, and then studied the effects of PACAP in isolated chondrocytes exposed to IL-1β in vitro to mimic the inflammatory milieu of OA cartilage. OA induction was established by histomorphometric and histochemical analyses. Changes in PACAP distribution in cartilage, or its concentration in synovial fluid (SF), were assessed by immunohistochemistry and ELISA. Results showed that PACAP abundance in cartilage tissue and SF was high in healthy controls. OA induction decreased PACAP levels both in affected cartilage and SF. In vitro, PACAP prevented IL-1β-induced chondrocyte apoptosis, as determined by MTT assay; Hoechst staining and western blots of apoptotic-related proteins. These changes were also accompanied by decreased i-NOS and COX-2 levels, suggesting an anti-inflammatory effect. Altogether, these findings support a potential role for PACAP as a chondroprotective agent for the treatment of OA.

Glastras, SJ, Wong, MG, Chen, H, Zhang, J, Zaky, A, Pollock, CA & Saad, S 2015, 'FXR expression is associated with dysregulated glucose and lipid levels in the offspring kidney induced by maternal obesity', Nutrition & Metabolism, vol. 12, no. 1.
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© 2015 Glastras et al. Background: Maternal obesity is associated with dysregulation of glucose and lipid metabolism with consequent exposure of the fetus to an abnormal metabolic milieu. It is recognized that maternal obesity predisposes offspring to chronic kidney disease (CKD). We aimed to determine whether the nuclear Farnesoid X receptor (FXR), known to play a role in maintaining homeostasis of glucose and lipid metabolism, is involved in renal injury in offspring of obese mothers. Methods: Maternal obesity was established in a rat model by feeding dams with high-fat diet prior to and during pregnancy and lactation. The offspring's kidneys were examined at postnatal Day 1and Day 20. Human kidney 2 (HK2) cells were exposed to high glucose with or without the FXR agonist GW4064 or when FXR mRNA was silenced. Results: Glucose intolerance in the offspring of obese mothers was evident at weaning, with associated downregulation of renal FXR expression and upregulation of monocyte chemoattractant protein-1 (MCP-1) and transforming growth factor-β1 (TGF-β1). HK2 cells exposed to high glucose had reduced FXR expression and increased MCP-1, TGF-β1, fibronectin and collagen IV expression, which was reversed in the presence of GW4064. FXR-silenced HK2 cells had amplified pro-inflammatory and pro-fibrotic markers under high glucose conditions. Conclusions: Maternal obesity influences renal expression of pro-inflammatory and fibrotic factors that predispose the offspring to CKD. This was associated with the downregulation of the renal FXR expression suggesting a potential protective role for FXR.

Gloag, ES, Turnbull, L & Whitchurch, CB 2015, 'Bacterial Stigmergy: An Organising Principle of Multicellular Collective Behaviours of Bacteria', Scientifica, vol. 2015, pp. 1-8.
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The self-organisation of collective behaviours often manifests as dramatic patterns of emergent large-scale order. This is true for relatively “simple” entities such as microbial communities and robot “swarms,” through to more complex self-organised systems such as those displayed by social insects, migrating herds, and many human activities. The principle of stigmergy describes those self-organised phenomena that emerge as a consequence of indirect communication between individuals of the group through the generation of persistent cues in the environment. Interestingly, despite numerous examples of multicellular behaviours of bacteria, the principle of stigmergy has yet to become an accepted theoretical framework that describes how bacterial collectives self-organise. Here we review some examples of multicellular bacterial behaviours in the context of stigmergy with the aim of bringing this powerful and elegant self-organisation principle to the attention of the microbial research community.

Goh, W-K, Gardner, CR, Chandra Sekhar, KVG, Biswas, NN, Nizalapur, S, Rice, SA, Willcox, M, Black, DS & Kumar, N 2015, 'Synthesis, quorum sensing inhibition and docking studies of 1,5-dihydropyrrol-2-ones', Bioorganic & Medicinal Chemistry, vol. 23, no. 23, pp. 7366-7377.
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Golicz, AA, Schliep, M, Lee, HT, Larkum, AWD, Dolferus, R, Batley, J, Chan, C-KK, Sablok, G, Ralph, PJ & Edwards, D 2015, 'Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network', JOURNAL OF EXPERIMENTAL BOTANY, vol. 66, no. 5, pp. 1489-1498.
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Gonçalves, LFFF, Silva, CJR, Kanodarwala, FK, Stride, JA & Pereira, MR 2015, 'Effect of acid or alkaline catalyst and of different capping agents on the optical properties of CdS nanoparticles incorporated within a diureasil hybrid matrix', Optical Materials, vol. 49, pp. 171-181.
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Goodswen, SJ, Barratt, JLN, Kennedy, PJ & Ellis, JT 2015, 'Improving the gene structure annotation of the apicomplexan parasite Neospora caninum fulfils a vital requirement towards an in silico-derived vaccine', INTERNATIONAL JOURNAL FOR PARASITOLOGY, vol. 45, no. 5, pp. 305-318.
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© 2015 Australian Society for Parasitology Inc. Neospora caninum is an apicomplexan parasite which can cause abortion in cattle, instigating major economic burden. Vaccination has been proposed as the most cost-effective control measure to alleviate this burden. Consequently the overriding aspiration for N. caninum research is the identification and subsequent evaluation of vaccine candidates in animal models. To save time, cost and effort, it is now feasible to use an in silico approach for vaccine candidate prediction. Precise protein sequences, derived from the correct open reading frame, are paramount and arguably the most important factor determining the success or failure of this approach. The challenge is that publicly available N. caninum sequences are mostly derived from gene predictions. Annotated inaccuracies can lead to erroneously predicted vaccine candidates by bioinformatics programs. This study evaluates the current N. caninum annotation for potential inaccuracies. Comparisons with annotation from a closely related pathogen, Toxoplasma gondii, are also made to distinguish patterns of inconsistency. More importantly, a mRNA sequencing (RNA-Seq) experiment is used to validate the annotation. Potential discrepancies originating from a questionable start codon context and exon boundaries were identified in 1943 protein coding sequences. We conclude, where experimental data were available, that the majority of N. caninum gene sequences were reliably predicted. Nevertheless, almost 28% of genes were identified as questionable. Given the limitations of RNA-Seq, the intention of this study was not to replace the existing annotation but to support or oppose particular aspects of it. Ideally, many studies aimed at improving the annotation are required to build a consensus. We believe this study, in providing a new resource on gene structure and annotation, is a worthy contributor to this endeavour.

Grant, DS, Bazaka, K, Siegele, R, Holt, SA & Jacob, MV 2015, 'Ion irradiation as a tool for modifying the surface and optical properties of plasma polymerised thin films', Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, vol. 360, pp. 54-59.
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Greaves, IK, Gonzalez-Bayon, R, Wang, L, Zhu, A, Liu, P-C, Groszmann, M, Peacock, WJ & Dennis, ES 2015, 'Epigenetic Changes in Hybrids', PLANT PHYSIOLOGY, vol. 168, no. 4, pp. 1197-1205.
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Gregory, KB, Carroll, RJ, Baladandayuthapani, V & Lahiri, SN 2015, 'A Two-Sample Test for Equality of Means in High Dimension', Journal of the American Statistical Association, vol. 110, no. 510, pp. 837-849.
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© 2015 American Statistical Association. We develop a test statistic for testing the equality of two population mean vectors in the “large-p-small-n” setting. Such a test must surmount the rank-deficiency of the sample covariance matrix, which breaks down the classic Hotelling T2 test. The proposed procedure, called the generalized component test, avoids full estimation of the covariance matrix by assuming that the p components admit a logical ordering such that the dependence between components is related to their displacement. The test is shown to be competitive with other recently developed methods under ARMA and long-range dependence structures and to achieve superior power for heavy-tailed data. The test does not assume equality of covariance matrices between the two populations, is robust to heteroscedasticity in the component variances, and requires very little computation time, which allows its use in settings with very large p. An analysis of mitochondrial calcium concentration in mouse cardiac muscles over time and of copy number variations in a glioblastoma multiforme dataset from The Cancer Genome Atlas are carried out to illustrate the test. Supplementary materials for this article are available online.

Griebel, A, Bennett, LT, Culvenor, DS, Newnham, GJ & Arndt, SK 2015, 'Reliability and limitations of a novel terrestrial laser scanner for daily monitoring of forest canopy dynamics', Remote Sensing of Environment, vol. 166, pp. 205-213.
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Leaf area index (LAI) or plant area index (PAI) are commonly used to represent canopy structure and dynamics, but daily estimation of these variables using traditional ground-based methods is impractical and prone to multiple errors during data acquisition and processing. Existing terrestrial laser scanners can provide accurate representation of forest canopy structure, but the sensors are expensive, data processing is complex, and measurements are typically confined to a single event, which severely limits their utility in the interpretation of canopy trends indicated by remotely sensed data. We tested a novel, low-cost terrestrial laser scanner for its capacity to provide reliable and successive assessments of canopy PAI in an evergreen eucalypt forest. Daily scans comprised of 920 range measurements were made by three scanners at one forest site over a two-year period, providing mostly consecutive estimates of PAI, and of vertical structure profiles (as Plant Area Volume Density, PAVD). Data filtering, involving objective statistical methods to identify outliers, indicated that scan quality was adversely affected by moist weather and moderate wind speeds (>4ms−1), suggesting limited utility in some forest environments. Data cleaning (associated with sensor malfunctions) plus filtering removed 32 to 49% of scans, leaving on average 57% of data over the two-year period. Nonetheless, we found strong agreement between lidar-derived PAI estimates, and those from monthly hemispherical images (±0.1 PAI); with both methods indicating mostly stable PAI over multiple seasons. The PAVD profiles from the laser scanner indicated that leaf flush in the upper canopy concomitantly balanced leaf loss from the middle canopy in summer, which was consistent with measured summer peaks in litter fall. This clearly illustrated the advantages of three-dimensional lidar data over traditional two-dimensional PAI estimates in monitoring tree phenology, and in interpreting changes in can...

Griekspoor, P, Hansbro, PM, Waldenström, J & Olsen, B 2015, 'Campylobacter jejuni sequence types show remarkable spatial and temporal stability in Blackbirds', Infection Ecology & Epidemiology, vol. 5, no. 1, pp. 28383-28383.
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BACKGROUND: The zoonotic bacterium Campylobacter jejuni has a broad host range but is especially associated with birds, both domestic and wild. Earlier studies have indicated thrushes of the genus Turdus in Europe to be frequently colonized with C. jejuni, and predominately with host-associated specific genotypes. The European Blackbird Turdus merula has a large distribution in Europe, including some oceanic islands, and was also introduced to Australia by European immigrants in the 1850s. METHODS: The host specificity and temporal stability of European Blackbird C. jejuni was investigated with multilocus sequence typing in a set of isolates collected from Sweden, Australia, and The Azores. RESULTS: Remarkably, we found that the Swedish, Australian, and Azorean isolates were genetically highly similar, despite extensive spatial and temporal isolation. This indicates adaptation, exquisite specificity, and stability in time for European Blackbirds, which is in sharp contrast with the high levels of recombination and mutation found in poultry-related C. jejuni genotypes. CONCLUSION: The maintenance of host-specific signals in spatially and temporally separated C. jejuni populations suggests the existence of strong purifying selection for this bacterium in European Blackbirds.

Griffin, CT, Mitrovic, SM, Danaher, M & Furey, A 2015, 'Development of a fast isocratic LC-MS/MS method for the high-throughput analysis of pyrrolizidine alkaloids in Australian honey', Food Additives & Contaminants: Part A, vol. 32, no. 2, pp. 214-228.
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Grillo, VL, Arzey, KE, Hansbro, PM, Hurt, AC, Warner, S, Bergfeld, J, Burgess, GW, Cookson, B, Dickason, CJ, Ferenczi, M, Hollingsworth, T, Hoque, MDA, Jackson, RB, Klaassen, M, Kirkland, PD, Kung, NY, Lisovski, S, O'Dea, MA, O'Riley, K, Roshier, D, Skerratt, LF, Tracey, JP, Wang, X, Woods, R & Post, L 2015, 'Avian influenza in Australia: a summary of 5 years of wild bird surveillance', Australian Veterinary Journal, vol. 93, no. 11, pp. 387-393.
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BackgroundAvian influenza viruses (AIVs) are found worldwide in numerous bird species, causing significant disease in gallinaceous poultry and occasionally other species. Surveillance of wild bird reservoirs provides an opportunity to add to the understanding of the epidemiology of AIVs.MethodsThis study examined key findings from the National Avian Influenza Wild Bird Surveillance Program over a 5‐year period (July 2007–June 2012), the main source of information on AIVs circulating in Australia.ResultsThe overall proportion of birds that tested positive for influenza A via PCR was 1.9 ± 0.1%, with evidence of widespread exposure of Australian wild birds to most low pathogenic avian influenza (LPAI) subtypes (H1–13, H16). LPAI H5 subtypes were found to be dominant and widespread during this 5‐year period.ConclusionGiven Australia's isolation, both geographically and ecologically, it is important for Australia not to assume that the epidemiology of AIV from other geographic regions applies here. Despite all previous highly pathogenic avian influenza outbreaks in Australian poultry being attributed to H7 subtypes, widespread detection of H5 subtypes in wild birds may represent an ongoing risk to the Australian poultry industry.

Groen, L, Coupland, M, Langtry, T, Memar, J, Moore, BJ & Stanley, J 2015, 'The Mathematics Problem and Mastery Learning for First-Year, Undergraduate STEM Students', International Journal of Learning, Teaching and Educational Research, vol. 11, no. 1, pp. 141-160.
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In the 2014 academic year Mastery Learning was implemented in four first-year mathematics subjects in an effort to address a lack of preparedness and poor outcomes of increasing numbers of undergraduate students in science, engineering and mathematics programs. This followed partial success in the use of diagnostic testing and pre-teaching, active learning, and a greater emphasis on problem solving in context - under-prepared students were still more likely to fail the pre-teaching subject and to struggle with subsequent mathematics subjects. Also, failure rates overall were higher than benchmarks required. This paper describes the learning design used, and the outcomes achieved, with implementing Mastery Learning – the positive: improved academic success, time management, and attitudes towards learning and Mathematics, an increased sense of independence, confidence and retention of content, and reduced stress and anxiety; and the negative: students having a sense of being taught how to pass a test rather than having a deeper understanding of the content. It will be seen that this negative is a consequence of a small but important difference in implementation.

Groen, L, Coupland, M, Memar, J & Langtry, T 2015, 'Mastery learning to address the assumed mathematics knowledge gap, encourage learning and reflection, and future-proof academic performance', International Journal of Innovation in Science and Mathematics Education, vol. 23, no. 4, pp. 64-78.
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UTS Science, Engineering and Mathematics students who have studied General Mathematics at high school are far more likely to fail their first undergraduate mathematics subject compared to their counterparts who meet the non-compulsory Assumed Knowledge of 2 unit Mathematics. This problem has been growing in recent years as an increasing number of students seek to improve their tertiary entrance score by taking the no-calculus General Mathematics at the Higher School Certificate. This problem is not unique to the University of Technology, Sydney-mathematical under-preparedness is a problem world-wide, with a decade, or more, long history. For some years, UTS has used diagnostic testing and pre-teaching to assist under-prepared students. Unfortunately, students who studied General Mathematics are also more likely to fail the pre-teaching subject. This suggested something more was required. Mastery Learning was chosen as a potential solution. Results to date have been promising with improvements in academic success for under-prepared students. Students have also reported increased satisfaction, confidence and retention of content. However, some students felt all Mastery Learning taught them was how to pass the Mastery Tests. Differences in student experience appear to be due to differences in how Mastery Learning was implemented.

Groszmann, M, Gonzalez-Bayon, R, Lyons, RL, Greaves, IK, Kazan, K, Peacock, WJ & Dennis, ES 2015, 'Hormone-regulated defense and stress response networks contribute to heterosis in Arabidopsis F1 hybrids', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 112, no. 46, pp. E6397-E6406.
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Gurgis, FMS, Yeung, YT, Tang, MXM, Heng, B, Buckland, M, Ammit, AJ, Haapasalo, J, Haapasalo, H, Guillemin, GJ, Grewal, T & Munoz, L 2015, 'The p38-MK2-HuR pathway potentiates EGFRvIII–IL-1β-driven IL-6 secretion in glioblastoma cells', Oncogene, vol. 34, no. 22, pp. 2934-2942.
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Haass, NK, Nassif, N & McGowan, EM 2015, 'Switching the Sphingolipid Rheostat in the Treatment of Diabetes and Cancer Comorbidity from a Problem to an Advantage', BioMed Research International, vol. 2015, pp. 1-9.
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Cancer and diabetes are among the most common diseases in western societies. Epidemiological studies have shown that diabetic patients have a significantly higher risk of developing a number of different types of cancers and that individuals with comorbidity (cancer and diabetes/prediabetes) have a poorer prognosis relative to nondiabetic cancer patients. The increasing frequency of comorbidity of cancer and diabetes mellitus, mainly type 2 diabetes, has driven the development of therapeutic interventions that target both disease states. There is strong evidence to suggest that balancing the sphingolipid rheostat, ceramide—sphingosine—sphingosine-1-phosphate (S1P) is crucial in the prevention of diabetes and cancer and sphingosine kinase/S1P modulators are currently under development for the treatment of cancer and diabetes. This paper will highlight some of the complexities inherent in the use of the emerging sphingosine kinase/S1P modulators in the treatment of comorbidity of diabetes and cancer.

Haghi, M, Hittinger, M, Zeng, Q, Olivert, B, Traini, D, Young, PM, Huwer, H, Schneider-Daum, N & Lehr, C-M 2015, 'Mono- and Cocultures of Bronchial and Alveolar Epithelial Cells Respond Differently to Proinflammatory Stimuli and Their Modulation by Salbutamol and Budesonide', MOLECULAR PHARMACEUTICS, vol. 12, no. 8, pp. 2625-2632.
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© 2015 American Chemical Society. The aim of this study was to investigate the changes in transport and effectiveness of salbutamol sulfate (SAL) and budesonide (BD) following stimulation with transforming growth factor-β (TGF-β) in mono- and coculture models of bronchial and alveolar epithelium. Primary bronchial and alveolar epithelial cells, grown at air interface on filters, either as monocultures or in coculture with airway smooth muscle cells or alveolar macrophages, respectively, were stimulated with TGF-β. The biological response was modulated by depositing aerosolized SAL and BD on bronchial and alveolar models, respectively. Barrier integrity, permeability to fluorescein-Na, transport of the deposited drug, and the pharmacological response to SAL (cAMP and IL-8 levels) or BD (IL-6 and -8 levels) were measured. While stimulation with TGF-β did not have any significant effect on the transepithelial electrical resistance and permeability to fluorescein-Na in mono- and coculture models, transport of SAL and BD were affected in cultures from some of the patients (6 out of 12 for bronchial and 2 out of 4 for alveolar cells). The bronchial coculture showed a better responsiveness to SAL in terms of cAMP release than the monoculture. In contrast, the difference between alveolar mono- and cocultures to TGF-β mediated interleukin release and its modulation by BD was less pronounced. Our data point to intrinsic differences in the transport of, and responsiveness to, SAL and BD when epithelial cell cultures originate from different patients. Moreover, if the biological responses (e.g., IL-8, cAMP) involve communication between different cell types, coculture models are more relevant to measure such effects than monocultures.

Haghi, M, Traini, D, Wood, LG, Oliver, B, Young, PM & Chrzanowski, W 2015, 'A 'soft spot' for drug transport: modulation of cell stiffness using fatty acids and its impact on drug transport in lung model', JOURNAL OF MATERIALS CHEMISTRY B, vol. 3, no. 13, pp. 2583-2589.
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© The Royal Society of Chemistry 2015. The impact of a polyunsaturated fatty acid, arachidonic acid (AA), on membrane fluidity of epithelial cells and subsequent modulation of the drug transport was investigated. Membrane fluidity was assessed using molecular force microscopy. Calu-3 human bronchial epithelial cells were cultured on Transwell® inserts and the cell stiffness was assessed in the absence of fatty acids or in the presence of 30 μM AA. The morphology of the epithelial cells was distinctly different when AA was present, with the cell monolayer becoming more uniform. Furthermore the cell stiffness and variation in stiffness was lower in the presence of AA. In the fat-free medium, the median cell stiffness was 9.1 kPa which dropped to 2.1 kPa following exposure to AA. To further study this, transport of a common β2-agonist, salbutamol sulphate (SS) was measured in the presence of AA and in a fat free medium. The transport of SS was significantly higher when AA was present (0.61 ± 0.09 μg versus 0.11 ± 0.003 μg with and without AA respectively). It was evidenced that AA play a vital role in cell membrane fluidity and drug transport. This finding highlights the significance of the dietary fatty acids in transport and consequentially effectiveness of medications used to treat pulmonary diseases such as asthma. This journal is

Haines, AM, Tobe, SS, Kobus, H & Linacre, A 2015, 'Duration of in situ fluorescent signals within hairs follicles', Forensic Science International: Genetics Supplement Series, vol. 5, pp. e175-e176.
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Haines, AM, Tobe, SS, Kobus, H & Linacre, A 2015, 'Finding DNA: Using fluorescent in situ detection', Forensic Science International: Genetics Supplement Series, vol. 5, pp. e501-e502.
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Haines, AM, Tobe, SS, Kobus, H & Linacre, A 2015, 'Successful direct STR amplification of hair follicles after nuclear staining', Forensic Science International: Genetics Supplement Series, vol. 5, pp. e65-e66.
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Haines, AM, Tobe, SS, Kobus, HJ & Linacre, A 2015, 'Effect of nucleic acid binding dyes on DNA extraction, amplification, and STR typing', ELECTROPHORESIS, vol. 36, no. 20, pp. 2561-2568.
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We report on the effects of six dyes used in the detection of DNA on the process of DNA extraction, amplification, and detection of STR loci. While dyes can be used to detect the presence of DNA, their use is restricted if they adversely affect subsequent DNA typing processes. Diamond™ Nucleic Acid Dye, GelGreen™, GelRed™, RedSafe™, SYBR® Green I, and EvaGreen™ were evaluated in this study. The percentage of dye removed during the extraction process was determined to be: 70.3% for SYBR® Green I; 99.6% for RedSafe™; 99.4% for EvaGreen™; 52.7% for Diamond™ Dye; 50.6% for GelRed™, and; could not be determined for GelGreen™. It was then assumed that the amount of dye in the fluorescent quantification assay had no effect on the DNA signal. The presence of all six dyes was then reviewed for their effect on DNA extraction. The t‐test showed no significant difference between the dyes and the control. These extracts were then STR profiled and all dyes and control produced full DNA profiles. STR loci in the presence of GelGreenTM at 1X concentration showed increased amplification products in comparison to the control samples. Full STR profiles were detected in the presence of EvaGreen™ (1X), although with reduced amplification products. RedSafe™ (1X), Diamond™ Dye (1X), and SYBR® Green I (1X) all exhibited varying degrees of locus drop‐out with GelRed™ generating no loci at all. We provide recommendations for the best dye to visualize the presence of DNA profile as a biological stain and its subsequent amplification and detection.

Haines, AM, Tobe, SS, Kobus, HJ & Linacre, A 2015, 'Properties of nucleic acid staining dyes used in gel electrophoresis', ELECTROPHORESIS, vol. 36, no. 6, pp. 941-944.
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Nucleic acid staining dyes are used for detecting nucleic acids in electrophoresis gels. Historically, the most common dye used for gel staining is ethidium bromide, however due to its toxicity and mutagenicity other dyes that are safer to the user and the environment are preferred. This Short Communication details the properties of dyes now available and their sensitivity for detection of DNA and their ability to permeate the cell membrane. It was found that GelRed™ was the most sensitive and safest dye to use with UV light excitation, and both GelGreen™ and Diamond™ Nucleic Acid Dye were sensitive and the safer dyes using blue light excitation.

Hamidian, M, Hawkey, J, Holt, KE & Hall, RM 2015, 'Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1', Genome Announcements, vol. 3, no. 6.
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ABSTRACT Multiply antibiotic-resistant Acinetobacter baumannii isolate D36 was recovered in Australia in 2008 and belongs to a distinct lineage of global clone 1 (GC1). Here, we present the complete 4.13 Mbp genome sequence (chromosome plus 4 plasmids), generated via long read sequencing (PacBio).

Hamidian, M, Holt, KE & Hall, RM 2015, 'Genomic resistance island AGI1 carrying a complex class 1 integron in a multiply antibiotic-resistant ST25Acinetobacter baumanniiisolate', Journal of Antimicrobial Chemotherapy, vol. 70, no. 9, pp. 2519-2523.
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Hamidian, M, Holt, KE & Hall, RM 2015, 'The complete sequence of Salmonella genomic island SGI1-K', Journal of Antimicrobial Chemotherapy, vol. 70, no. 1, pp. 305-306.
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Hamidian, M, Holt, KE & Hall, RM 2015, 'The complete sequence of Salmonella genomic island SGI2', Journal of Antimicrobial Chemotherapy, vol. 70, no. 2, pp. 617-619.
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Hammer, JF, Emery, D, Bogema, DR & Jenkins, C 2015, 'Detection of Theileria orientalis genotypes in Haemaphysalis longicornis ticks from southern Australia', Parasites & Vectors, vol. 8, no. 1.
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© 2015 Hammer et al.; licensee BioMed Central. Background: Theileria are blood-borne intracellular protozoal parasites belonging to the phylum Apicomplexa. Previously considered a benign parasite in Australia, outbreaks of clinical disease resulting from Theileria orientalis genotypes have been reported in Australia since 2006. Since this time, outbreaks have become widespread in south-eastern Australia, resulting in significant adverse impacts on local dairy and beef industries. This paper provides the first investigation into the possible biological and mechanical vectors involved in the rapid spread of the parasite. Methods: To identify possible vectors for disease, ticks, biting flies and mosquitoes were collected within active outbreak regions of Gippsland, Victoria. Ticks were collected from cattle and wildlife, and mosquitoes and biting flies were collected in traps in close proximity to outbreak herds. Ticks were identified via DNA barcoding of the mitochondrial cytochrome oxidase I gene. Barcoded ticks were pooled according to species or phylogenetic group and tested for the presence of T. orientalis and the genotypes Ikeda, Chitose and Buffeli using real-time PCR. Results: DNA barcoding and phylogenetic analysis identified ticks from the following species: Haemaphysalis longicornis, Ixodes holocyclus, Ixodes cornuatus, Ixodes hirsti, and Bothriocroton concolor. Additional Haemaphysalis, Ixodes and Bothriocroton spp. were also identified. Of the ticks investigated, only H. longicornis ticks from cattle carried theilerial DNA, with the genotypes Ikeda, Chitose and Buffeli represented. Mosquitoes collected in close proximity to outbreak herds included; Aedes camptorhynchus, Aedes notoscriptus, Coquillettidia linealis, Culex australicus, and Culex molestus. Low levels of T. orientalis Buffeli genotype were detected in some mosquitoes. The haematophagous flies tested negative. Conclusions: This is the first demonstration of a potential vector for T...

Hansen, CS, Blanksby, SJ, Chalyavi, N, Bieske, EJ, Reimers, JR & Trevitt, AJ 2015, 'Ultraviolet photodissociation action spectroscopy of the N-pyridinium cation', The Journal of Chemical Physics, vol. 142, no. 1, pp. 014301-014301.
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The S1←S0 electronic transition of the N-pyridinium ion (C5H5NH+) is investigated using ultraviolet photodissociation (PD) spectroscopy of the bare ion and also the N2-tagged complex. Gas-phase N-pyridinium ions photodissociate by the loss of molecular hydrogen (H2) in the photon energy range 37 000–45 000 cm−1 with structurally diagnostic ion-molecule reactions identifying the 2-pyridinylium ion as the exclusive co-product. The photodissociation action spectra reveal vibronic details that, with the aid of electronic structure calculations, support the proposal that dissociation occurs through an intramolecular rearrangement on the ground electronic state following internal conversion. Quantum chemical calculations are used to analyze the measured spectra. Most of the vibronic features are attributed to progressions of totally symmetric ring deformation modes and out-of-plane modes active in the isomerization of the planar excited state towards the non-planar excited state global minimum.

Hare, DJ, Arora, M, Jenkins, NL, Finkelstein, DI, Doble, PA & Bush, AI 2015, 'Is early-life iron exposure critical in neurodegeneration?', NATURE REVIEWS NEUROLOGY, vol. 11, no. 9, pp. 536-544.
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© 2015 Macmillan Publishers Limited. The effects of iron deficiency are well documented, but relatively little is known about the long-term implications of iron overload during development. High levels of redox-active iron in the brain have been associated with neurodegenerative disorders, most notably Parkinson disease, yet a gradual increase in brain iron seems to be a feature of normal ageing. Increased brain iron levels might result from intake of infant formula that is excessively fortified with iron, thereby altering the trajectory of brain iron uptake and amplifying the risk of iron-associated neurodegeneration in later life. In this Perspectives article, we discuss the potential long-term implications of excessive iron intake in early life, propose the analysis of iron deposits in teeth as a method for retrospective determination of iron exposure during critical developmental windows, and call for evidence-based optimization of the chemical composition of infant dietary supplements.

Hare, DJ, Doecke, JD, Faux, NG, Rembach, A, Volitakis, I, Fowler, CJ, Grimm, R, Doble, PA, Cherny, RA, Masters, CL, Bush, AI & Roberts, BR 2015, 'Decreased Plasma Iron in Alzheimer's Disease Is Due to Transferrin Desatu ration', ACS CHEMICAL NEUROSCIENCE, vol. 6, no. 3, pp. 398-402.
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© 2015 American Chemical Society. Plasma iron levels are decreased in Alzheimer's disease (AD) and associated with an idiopathic anemia. We examined iron-binding plasma proteins from AD patients and healthy controls from the Australian Imaging, Biomarkers and Lifestyle (AIBL) Flagship Study of Ageing using size exclusion chromatography-inductively coupled plasma-mass spectrometry. Peak area corresponding to transferrin (Tf) saturation was directly compared to routine pathological testing. We found a significant decrease in transferrin-associated iron in AD that was missed by routine pathological tests of transferrin saturation, and that was able to discriminate between AD and controls. The AD cases showed no significant difference in transferrin concentration, only a decrease in total transferrin-bound iron. These findings support that a previously identified decrease in plasma iron levels in AD patients within the AIBL study is attributable to decreased loading of iron into transferrin, and that this subtle but discriminatory change is not observed through routine pathological testing.

Hare, DJ, New, EJ, de Jonge, MD & McColl, G 2015, 'Imaging metals in biology: balancing sensitivity, selectivity and spatial resolution', Chemical Society Reviews, vol. 44, no. 17, pp. 5941-5958.
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A Tutorial Review to aid in designing the most comprehensive metal imaging experiments for biological samples.

Hare, NJ, Chan, B, Chan, E, Kaufman, KL, Britton, WJ & Saunders, BM 2015, 'Microparticles released from Mycobacterium tuberculosis‐infected human macrophages contain increased levels of the type I interferon inducible proteins including ISG15', PROTEOMICS, vol. 15, no. 17, pp. 3020-3029.
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Microparticles (MPs) are small membranous particles (100–1000 nm) released under normal steady‐state conditions and are thought to provide a communication network between host cells. Previous studies demonstrated that Mycobacterium tuberculosis (M. tb) infection of macrophages increased the release of MPs, and these MPs induced a proinflammatory response from uninfected macrophages in vitro and in vivo following their transfer into uninfected mice. To determine how M. tb infection modulates the protein composition of the MPs, and if this contributes to their proinflammatory properties, we compared the proteomes of MPs derived from M. tb‐infected (TBinf‐MP) and uninfected human THP‐1 monocytic cells. MP proteins were analyzed by GeLC‐MS/MS with spectral counting revealing 68 proteins with statistically significant differential abundances. The 42 proteins increased in abundance in TBinf‐MPs included proteins associated with immune function (7), lysosomal/endosomal maturation (4), vesicular formation (12), nucleosome proteins (4), and antigen processing (9). Prominent among these were the type I interferon inducible proteins, ISG15, IFIT1, IFIT2, and IFIT3. Exposure of uninfected THP‐1 cells to TBinf‐MPs induced increased gene expression of isg15, ifit1, ifit2, and ifit3 and the release of proinflammatory cytokines. These proteins may regulate the proinflammatory potential of the MPs and provide candidate biomarkers for M. tb infection.

Hassler, CS, Norman, L, Nichols, CAM, Clementson, LA, Robinson, C, Schoemann, V, Watson, RJ & Doblin, MA 2015, 'Iron associated with exopolymeric substances is highly bioavailable to oceanic phytoplankton', MARINE CHEMISTRY, vol. 173, pp. 136-147.
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© 2014 Elsevier B.V. Growth limitation of marine algae due to lack of iron occurs in up to 40% of the global ocean. Despite important advances on the impact of organic compounds on iron biogeochemistry, their roles in controlling iron availability to prokaryotic and eukaryotic phytoplankton remain unclear. Whether algal and bacterial exopolymeric substances (EPS) include organic ligands which may help iron-limited phytoplankton growth remains an unknown. If so, then EPS could relieve phytoplankton iron limitation with implications for the biological carbon pump and hence the regulation of atmospheric CO2. Here we compared the biological impact of algal, bacterial and in situ EPS with model compounds, a siderophore and two saccharides on biological parameters including, iron bioavailability, phytoplankton growth, photo-physiology and community structure. Laboratory and field experiments demonstrated that EPS produced by marine microorganisms are efficient in sustaining biological iron uptake as well as algal growth, and can affect natural phytoplankton community structure. Our data suggest that natural phytoplankton growth enhancement in the presence of EPS was not solely due to highly bioavailable iron forms, but also because EPS contains other micronutrients. Stronger ligands were detected following iron-siderophore enrichments (log KFe'L=12.0) and weaker ligands were measured in the presence of EPS (log KFe'L=10.4-11.0). The trend of the conditional stability constants of organic ligands did not seem to be affected as a result of biological activity and photo-chemistry during our four day incubations. The shift in the phytoplankton community observed during our field experiments was not uniformly observed between different sites rendering it difficult to extrapolate which functional group(s) would benefit the most from iron bound to EPS.

Hatoum, D & McGowan, EM 2015, 'Recent Advances in the Use of Metformin: Can Treating Diabetes Prevent Breast Cancer?', BioMed Research International, vol. 2015, pp. 1-13.
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There is substantial epidemiological evidence pointing to an increased incidence of breast cancer and morbidity in obese, prediabetic, and diabetic patients.In vitrostudies strongly support metformin, a diabetic medication, in breast cancer therapy. Although metformin has been heralded as an exciting new breast cancer treatment, the principal consideration is whether metformin can be used as a generic treatment for all breast cancer types. Importantly, will metformin be useful as an inexpensive therapy for patients with comorbidity of diabetes and breast cancer? In general, meta-analyses of clinical trial data from retrospective studies in which metformin treatment has been used for patients with diabetes and breast cancer have a positive trend; nevertheless, the supporting clinical data outcomes remain inconclusive. The heterogeneity of breast cancer, confounded by comorbidity of disease in the elderly population, makes it difficult to determine the actual benefits of metformin therapy. Despite the questionable evidence available from observational clinical studies and meta-analyses, randomized phases I–III clinical trials are ongoing to test the efficacy of metformin for breast cancer. This special issue review will focus on recent research, highlightingin vitroresearch and retrospective observational clinical studies and current clinical trials on metformin action in breast cancer.

Hawkey, J, Hamidian, M, Wick, RR, Edwards, DJ, Billman-Jacobe, H, Hall, RM & Holt, KE 2015, 'ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data', BMC Genomics, vol. 16, no. 1.
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Heather, E, Shimmon, R & McDonagh, AM 2015, 'Organic impurity profiling of 3,4-methylenedioxymethamphetamine (MDMA) synthesised from catechol', FORENSIC SCIENCE INTERNATIONAL, vol. 248, pp. 140-147.
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© 2015. This work examines the organic impurity profile of 3,4-methylenedioxymethamphetamine (MDMA) that has been synthesised from catechol (1,2-dihydroxybenzene), a common chemical reagent available in industrial quantities. The synthesis of MDMA from catechol proceeded via the common MDMA precursor safrole. Methylenation of catechol yielded 1,3-benzodioxole, which was brominated and then reacted with magnesium allyl bromide to form safrole. Eight organic impurities were identified in the synthetic safrole. Safrole was then converted to 3,4-methylenedioxyphenyl-2-propanone (MDP2P) using two synthetic methods: Wacker oxidation (Route 1) and an isomerisation/peracid oxidation/acid dehydration method (Route 2). MDMA was then synthesised by reductive amination of MDP2P. Thirteen organic impurities were identified in MDMA synthesised via Route 1 and eleven organic impurities were identified in MDMA synthesised via Route 2.Overall, organic impurities in MDMA prepared from catechol indicated that synthetic safrole was used in the synthesis. The impurities also indicated which of the two synthetic routes was utilised.

Henschke, N, Everett, JD, Suthers, KM, Smith, JA, Hunt, BPV, Doblin, MA & Taylor, MD 2015, 'Zooplankton trophic niches respond to different water types of the western Tasman Sea: A stable isotope analysis', DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS, vol. 104, pp. 1-8.
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Herbert, C, Sebesfi, M, Zeng, Q, Oliver, BG, Foster, PS & Kumar, RK 2015, 'Using multiple online databases to help identify microRNAs regulating the airway epithelial cell response to a virus‐like stimulus', Respirology, vol. 20, no. 8, pp. 1206-1212.
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AbstractBackground and objectiveExacerbations of allergic asthma are often triggered by respiratory viral infections. We have previously shown that in a T‐helper type 2 (Th2)‐biased cytokine environment, mouse and human airway epithelial cells (AEC) exhibit increased expression of pro‐inflammatory and anti‐viral genes in response to synthetic double‐stranded ribonucleic acid (dsRNA), a virus‐like stimulus. This implies coordinated regulation of gene expression, suggesting possible involvement of microRNA. To investigate this, we developed a novel approach to identifying candidate microRNA using online databases, then confirmed their expression by quantitative real‐time polymerase chain reaction (qRT‐PCR).MethodsUsing a list of genes of interest, defined on the basis of the previous study as being up‐regulated in a Th2 environment, we searched mouse and human microRNA databases for possible regulatory microRNA, and selected 10 candidates that were conserved across species or predicted by more than one human database. Expression of these microRNA was tested by The FASEB Journal, vol. 29, no. S1.
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Elevated serum cholesterol is a major contributor to cardiovascular disease (CVD) risk, which is responsible for 1 in every 3 deaths in the United States. High density lipoprotein (HDL) and low density lipoprotein (LDL) can be further characterized into density subfractions that demonstrate greater efficacy in predicting atherogenesis and ultimately CVD risk. Condensed tannins, such as those present in sumac sorghum, have been shown to improve vascular mechanics and reduce systemic markers of inflammation. Therefore, the goal of this experiment was to determine if this sorghum‐based source of condensed tannins would alter lipoprotein density distributions in a manner consistent with reduced CVD risk. Overweight humans (n=23) were assigned to either a low dose (50 g) or high dose (100 g) of sumac sorghum puff cereal daily in a randomized crossover design. Plasma samples were obtained at 0, 4, 7 and 11 wk and isopycnic ultracentrifugation was used to quantify density distributions of fluorescently stained lipoproteins as area under the curve (AUC). Consumption of sorghum cereal increased AUC of larger and less dense LDL2 (p=0.0214) and LDL3 (p=0.0035) and decreased the small dense LDL5 (p=0.0016) subfraction; both changes are associated with reduced CVD risk. These data suggest that consumption of this ancient grain containing elevated polyphenol levels can beneficially alter lipoprotein fractions, which may correspond to a decreased CVD risk profile. Funded by USCP HVM01‐14.

Higginbotham, HF, Maniam, S, Langford, SJ & Bell, TDM 2015, 'New brightly coloured, water soluble, core-substituted naphthalene diimides for biophysical applications', Dyes and Pigments, vol. 112, pp. 290-297.
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Hill, R, Bellgrove, A, Macreadie, PI, Petrou, K, Beardall, J, Steven, A & Ralph, PJ 2015, 'Can macroalgae contribute to blue carbon? An Australian perspective', LIMNOLOGY AND OCEANOGRAPHY, vol. 60, no. 5, pp. 1689-1706.
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Hirota, JA, Gold, MJ, Hiebert, PR, Parkinson, LG, Wee, T, Smith, D, Hansbro, PM, Carlsten, C, VanEeden, S, Sin, DD, McNagny, KM & Knight, DA 2015, 'The Nucleotide-Binding Domain, Leucine-Rich Repeat Protein 3 Inflammasome/IL-1 Receptor I Axis Mediates Innate, but Not Adaptive, Immune Responses after Exposure to Particulate Matter under 10 μm', American Journal of Respiratory Cell and Molecular Biology, vol. 52, no. 1, pp. 96-105.
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Exposure to particulate matter (PM), a major component of air pollution, contributes to increased morbidity and mortality worldwide. Inhaled PM induces innate immune responses by airway epithelial cells that may lead to the exacerbation or de novo development of airway disease. We have previously shown that 10-μm PM (PM10) activates the nucleotide-binding domain, leucine-rich repeat protein (NLRP) 3 inflammasome in human airway epithelial cells. Our objective was to determine the innate and adaptive immune responses mediated by the airway epithelium NLRP3 inflammasome in response to PM10 exposure. Using in vitro cultures of human airway epithelial cells and in vivo studies with wild-type and Nlrp3(-/-) mice, we investigated the downstream consequences of PM10-induced NLPR3 inflammasome activation on cytokine production, cellular inflammation, dendritic cell activation, and PM10-facilitated allergic sensitization. PM10 activates an NLRP3 inflammasome/IL-1 receptor I (IL-1RI) axis in airway epithelial cells, resulting in IL-1β, CC chemokine ligand-20, and granulocyte/macrophage colony-stimulating factor production, which is associated with dendritic cell activation and lung neutrophilia. Despite these profound innate immune responses in the airway epithelium, the NLRP3 inflammasome/IL-1RI axis is dispensable for PM10-facilitated allergic sensitization. We demonstrate the importance of the lung NLRP3 inflammasome in mediating PM10 exposure-associated innate, but not adaptive, immune responses. Our study highlights a mechanism by which PM10 exposure can contribute to the exacerbation of airway disease, but not PM10-facilitated allergic sensitization.

Hitchcock, JN & Mitrovic, SM 2015, 'After the flood: changing dissolved organic carbon bioavailability and bacterial growth following inflows to estuaries', Biogeochemistry, vol. 124, no. 1-3, pp. 219-233.
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Hitchcock, JN & Mitrovic, SM 2015, 'Highs and lows: The effect of differently sized freshwater inflows on estuarine carbon, nitrogen, phosphorus, bacteria and chlorophyll a dynamics', Estuarine, Coastal and Shelf Science, vol. 156, pp. 71-82.
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Freshwater inflows play a key role in the delivery of organic carbon to estuaries. However, our understanding of the dynamics between discharge and carbon globally is limited. In this study we performed a 30-month monitoring study on the Bega and Clyde River estuaries, Australia, to understand the influence that discharge had on carbon, nitrogen, phosphorus, bacteria and chlorophyll a dynamics. We hypothesised that 1) discharge would be the most important factor influencing carbon and nutrient concentrations, though during low flows chlorophyll a would also be positively related to carbon, 2) bacteria would be related to dissolved organic carbon (DOC), and chlorophyll a to temperature, nitrogen and phosphorus, and 3) that concentrations of carbon, nitrogen, phosphorus, bacterial biomass and chlorophyll a would be significantly different between large 'flood flows', smaller 'fresh flows' and base flow conditions. We found that discharge was always the most important factor influencing carbon and nutrient concentrations, and that primary production appeared to have little influence on the variation in DOC concentration even during base flow conditions. We suggest this relationship is likely due to highly episodic discharge that occurred during the study period. Bacteria were related to DOC in the lower estuary sites, but phosphorus in the upper estuary. We suggest this is likely due to the input of bioavailable carbon in the upper estuary leading bacteria to be P limited, which changes downstream to carbon limitation as DOC becomes more refractory. Chlorophyll a was positively related to temperature but not nutrients, which we suggest may be due to competition with bacteria for phosphorus in the upper estuary. Carbon, nitrogen and phosphorus concentrations were different under flood, fresh and base flow conditions, though these differences sometimes varied between estuary locations for different resources. Overall, the results demonstrate that discharge plays an im...

Hjelm, A, Söderström, B, Vikström, D, Jong, WSP, Luirink, J & de Gier, J-W 2015, 'Autotransporter-Based Antigen Display in Bacterial Ghosts', Applied and Environmental Microbiology, vol. 81, no. 2, pp. 726-735.
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ABSTRACT Bacterial ghosts are empty cell envelopes of Gram-negative bacteria that can be used as vehicles for antigen delivery. Ghosts are generated by releasing the bacterial cytoplasmic contents through a channel in the cell envelope that is created by the controlled production of the bacteriophage ϕX174 lysis protein E. While ghosts possess all the immunostimulatory surface properties of the original host strain, they do not pose any of the infectious threats associated with live vaccines. Recently, we have engineered the Escherichia coli autotransporter hemoglobin protease (Hbp) into a platform for the efficient surface display of heterologous proteins in Gram-negative bacteria, HbpD. Using the Mycobacterium tuberculosis vaccine target ESAT6 (early secreted antigenic target of 6 kDa), we have explored the application of HbpD to decorate E. coli and Salmonella ghosts with antigens. The use of different promoter systems enabled the concerted production of HbpD-ESAT6 and lysis protein E. Ghost formation was monitored by determining lysis efficiency based on CFU, the localization of a set of cellular markers, fluorescence microscopy, flow cytometry, and electron microscopy. Hbp-mediated surface display of ESAT6 was monitored using a combination of a protease accessibility assay, fluorescence microscopy, flow cytometry and (immuno-)electron microscopy. Here, we show that the concerted production of HbpD and lysis protein E in E. coli and...

Hocking, JS, Kong, FYS, Timms, P, Huston, WM & Tabrizi, SN 2015, 'Treatment of rectal chlamydia infection may be more complicated than we originally thought', Journal of Antimicrobial Chemotherapy, vol. 70, no. 4, pp. 961-964.
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Abstract Rectal chlamydia diagnoses have been increasing among MSM and may also rise among women as anal sex rates increase among heterosexuals. However, there is growing concern about treatment for rectal chlamydia with treatment failures of up to 22% being reported. This article addresses factors that may be contributing to treatment failure for rectal chlamydia, including the pharmacokinetic properties of azithromycin and doxycycline in rectal tissue, the ability of chlamydia to transform into a persistent state that is less responsive to antimicrobial therapy, the impact of the rectal microbiome on chlamydia, heterotypic resistance, failure to detect cases of lymphogranuloma venereum and the performance of screening tests. If we are to reduce the burden of genital chlamydia, treatment for rectal chlamydia must be efficacious. This highlights the need for randomized controlled trial evidence comparing azithromycin with doxycycline for the treatment of rectal chlamydia.

Hoeksema, BW & Matthews, JL 2015, 'Partial bleaching in an assemblage of small apozooxanthellate corals of the genera Heteropsammia and Heterocyathus', Coral Reefs, vol. 34, no. 4, pp. 1227-1227.
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Holt, KE, Hamidian, M, Kenyon, JJ, Wynn, MT, Hawkey, J, Pickard, D & Hall, RM 2015, 'Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1', Genome Announcements, vol. 3, no. 2.
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ABSTRACT Acinetobacter baumannii isolate A1 was recovered in the United Kingdom in 1982 and belongs to global clone 1 (GC1). Here, we present its complete 3.91-Mbp genome sequence, generated via a combination of short-read sequencing (Illumina), long-read sequencing (PacBio), and manual finishing.

Hong, Y, Burford, MA, Ralph, PJ & Doblin, MA 2015, 'Subtropical zooplankton assemblage promotes the harmful cyanobacterium Cylindrospermopsis raciborskii in a mesocosm experiment', JOURNAL OF PLANKTON RESEARCH, vol. 37, no. 1, pp. 90-101.
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Hosseinpour-Mashkani, SM, Maddahfar, M, Sadeghinia, A & Ramezani, M 2015, 'PbSe@PbSO4 nanoparticles: sonochemical synthesis and characterization and its photocatalytic degradation of methylene blue', Journal of Materials Science: Materials in Electronics, vol. 26, no. 5, pp. 3352-3356.
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Hou, W, Wen, S, Guo, R, Wang, S & Shi, X 2015, 'Partially Acetylated Dendrimer-Entrapped Gold Nanoparticles with Reduced Cytotoxicity for Gene Delivery Applications', Journal of Nanoscience and Nanotechnology, vol. 15, no. 6, pp. 4094-4105.
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Hu, P, Thinschmidt, JS, Caballero, S, Adamson, S, Cole, L, Chan-Ling, T & Grant, MB 2015, 'Loss of survival factors and activation of inflammatory cascades in brain sympathetic centers in type 1 diabetic mice', American Journal of Physiology-Endocrinology and Metabolism, vol. 308, no. 8, pp. E688-E698.
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Neuroinflammation and neurodegeneration have been observed in the brain in type 1 diabetes (T1D). However, little is known about the mediators of these effects. In T1D mice with 12- and 35-wk duration of diabetes we examined two mechanisms of neurodegeneration, loss of the neuroprotective factors insulin-like growth factor I (IGF-I) and IGF-binding protein-3 (IGFBP-3) and changes in indoleamine 2,3-dioxygenase (IDO) expression in the brain, and compared the response to age-matched controls. Furthermore, levels of matrix metalloproteinase-2 (MMP-2), nucleoside triphosphate diphosphohydrolase-1 (CD39), and ionized calcium-binding adaptor molecule 1 (Iba-1) were utilized to assess inflammatory changes in astrocytes, microglia, and blood vessels. In the diabetic hypothalamus (HYPO), we observed 20% reduction in neuronal soma diameter ( P < 0.05) and reduced neuronal expression of IGFBP-3 (−32%, P < 0.05) and IGF-I (−15%, P < 0.05) compared with controls at 35 wk. In diabetic HYPO, MMP-2 expression was increased in astrocytes (46%, P < 0.01), and IDO+cell density rose by (62%, P < 0.05). CD39 expression dropped by 30% ( P < 0.05) in microglia and blood vessels. With 10 wk of systemic treatment using minocycline, an anti-inflammatory agent that crosses the blood-brain barrier, MMP-2, IDO, and CD39 levels normalized ( P < 0.05). Our results suggest that increased IDO and early loss of CD39+protective cells lead to activation of inflammation in sympathetic centers of the CNS. As a downstream effect, the loss of the neuronal survival factors IGFBP-3 and IGF-I and the neurotoxic products of the kynurenine pathway contribute to the loss of neuronal density observed in the HYPO in T1D.

Hunt, PR, Friesen, MC, Sama, S, Ryan, L & Milton, D 2015, 'Log-Linear Modeling of Agreement among Expert Exposure Assessors', ANNALS OF OCCUPATIONAL HYGIENE, vol. 59, no. 6, pp. 764-774.
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Hutchinson, AT, Jones, DR & Raison, RL 2015, 'Preclinical and clinical development of an anti-kappa free light chain mAb for multiple myeloma', Molecular Immunology, vol. 67, no. 2, pp. 89-94.
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Irga, PJ, Burchett, MD & Torpy, FR 2015, 'Does urban forestry have a quantitative effect on ambient air quality in an urban environment?', ATMOSPHERIC ENVIRONMENT, vol. 120, pp. 173-181.
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© 2015. Increasing urban greenspace has been proposed as a means of reducing airborne pollutant concentrations; however limited studies provide experimental data, as opposed to model estimates, of its ability to do so. The current project examined whether higher concentrations of urban forestry might be associated with quantifiable effects on ambient air pollutant levels, whilst accounting for the predominant source of localized spatial variations in pollutant concentrations, namely vehicular traffic. Monthly air samples for one year were taken from eleven sites in central Sydney, Australia. The sample sites exhibited a range of different traffic density, population usage, and greenspace/urban forest density conditions. Carbon dioxide (CO2), carbon monoxide (CO), total volatile organic compounds (TVOCs), nitric oxide (NO), nitrogen dioxide (NO2), sulfur dioxide (SO2), total suspended particulate matter (TSP), suspended particles <10 μm in diameter (PM10) and particulate matter <2.5 μm (PM2.5), were recorded, using portable devices. It was found that air samples taken from sites with less greenspace frequently had high concentrations of all fractions of aerosolized particulates than other sites, whilst sites with high proximal greenspace had lower particulates, even when vehicular traffic was taken into account. No observable trends in concentrations of NO, TVOC and SO2 were observed, as recorded levels were generally very low across all sampled areas. The findings indicate, first, that within the urban areas of a city, localized differences in air pollutant loads occur. Secondly, we conclude that urban areas with proportionally higher concentrations of urban forestry may experience better air quality with regards to reduced ambient particulate matter; however conclusions about other air pollutants are yet to be elucidated.

Ismael, FO, Proudfoot, JM, Brown, BE, van Reyk, DM, Croft, KD, Davies, MJ & Hawkins, CL 2015, 'Comparative reactivity of the myeloperoxidase-derived oxidants HOCl and HOSCN with low-density lipoprotein (LDL): Implications for foam cell formation in atherosclerosis', ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, vol. 573, pp. 40-51.
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Jackson, F, Bunford, J, Maynard, P & Roux, C 2015, 'Surveys of vehicle colour frequency and the transfer of vehicle paints to stationary objects in Sydney, Australia', Forensic Science International, vol. 248, pp. 124-128.
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Jaggard, AK, Smith, N, Torpy, FR & Munro, U 2015, 'Rules of the roost: characteristics of nocturnal communal roosts of rainbow lorikeets (Trichoglossus haematodus, Psittacidae) in an urban environment', URBAN ECOSYSTEMS, vol. 18, no. 2, pp. 489-502.
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© 2014, Springer Science+Business Media New York. Rainbow lorikeets (Trichoglossus haematodus) have successfully adapted to urban environments and are today abundant in many Australian cities. Here they often form noisy communal roosts and may damage infrastructure. While extensive studies on problem birds (mainly passeriforms) and their roosts have been conducted in other parts of the world, no detailed studies exist in Australia, where non-passeriform birds (e.g. parrots) can cause problems. This study investigates the roosting preferences of rainbow lorikeets in Sydney (Australia) and establishes the site characteristics that typify these roosts. Lorikeets preferred three exotic tree species, namely the plane tree (Platanus spp. including Platanus x hybrida), Canary Island palm (Phoenix canariensis) and Norfolk Island pine (Araucaria heterophylla). They were also common in brush boxes (Lophostemon confertus), a tree native to Queensland, Australia. Rainbow lorikeets commonly roosted in tall trees with thick trunks and medium density foliage and the trees next to their roost trees were of the same species. Roosting trees were often in areas of high anthropogenic disturbance and close to streetlights.

James, SA, Roberts, BR, Hare, DJ, de Jonge, MD, Birchall, IE, Jenkins, NL, Cherny, RA, Bush, AI & McColl, G 2015, 'Direct in vivo imaging of ferrous iron dyshomeostasis in ageing Caenorhabditis elegans', CHEMICAL SCIENCE, vol. 6, no. 5, pp. 2952-2962.
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Jarocki, VM, Padula, MP & Djordjevic, S 2015, 'Mycoplasmal surface-associated aminopeptidases are multifunctional moonlighting proteins', Inflammation and Cell Signaling, vol. 2, no. 3, pp. 1-4.
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Many bacterial pathogens require adhesion to the mucosal epithelium to establish colonisation and employ numerous strategies to then avoid clearance by the host immune system. One such strategy involves expressing plasminogen receptors on the cell surface. Recently we showed that Mycoplasma hyopneumoniae is adept at capturing porcine plasminogen onto cell surface adhesins. This interaction promotes the conversion of bound plasminogen to plasmin where it plays an important role in regulating lung inflammation. Cell surface plasmin triggers a proteolytic cascade that is thought to promote dissemination of the pathogen from the initial site of colonisation. M. hyopneumoniae is a genome-reduced pathogen that has lost the genes required to synthesise amino acids and is thus reliant on the host for amino acids for growth. We have shown M. hyopneumoniae expresses a glutamyl-aminopeptidase (MHJ_0125) and a leucyl-aminopeptidase (MHJ_0461) on the extracellular surface of the cell membrane and both are perceived as playing a key role in the generation of a pool of free amino acids for growth during pathogenesis. MHJ_0461 displays a catalytic preference for leucine, phenylalanine, and methionine, whilst MHJ_0125 demonstrates a preference for glutamic acid and alanine. In addition to their catalytic functions as aminopeptidases, both enzymes bind porcine plasminogen, promoting its conversion to plasmin by tPA, and display an affinity for highly sulphated glycosaminoglycans. MHJ_0461 was also shown to bind extracellular DNA. These studies highlight the multifunctional properties of surface proteins in M. hyopneumoniae and the increasing pool of evidence that moonlighting proteins play important roles during microbial pathogenesis.

Jarocki, VM, Santos, J, Tacchi, JL, Raymond, BBA, Deutscher, AT, Jenkins, C, Padula, MP & Djordjevic, SP 2015, 'MHJ_0461 is a multifunctional leucine aminopeptidase on the surface of Mycoplasma hyopneumoniae', Open Biology, vol. 5, no. 1, pp. 140175-140175.
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Aminopeptidases are part of the arsenal of virulence factors produced by bacterial pathogens that inactivate host immune peptides. Mycoplasma hyopneumoniae is a genome-reduced pathogen of swine that lacks the genetic repertoire to synthesize amino acids and relies on the host for availability of amino acids for growth. M. hyopneumoniae recruits plasmin(ogen) onto its cell surface via the P97 and P102 adhesins and the glutamyl aminopeptidase MHJ_0125. Plasmin plays an important role in regulating the inflammatory response in the lungs of pigs infected with M. hyopneumoniae . We show that recombinant MHJ_0461 (rMHJ_0461) functions as a leucine aminopeptidase (LAP) with broad substrate specificity for leucine, alanine, phenylalanine, methionine and arginine and that MHJ_0461 resides on the surface of M. hyopneumoniae . rMHJ_0461 also binds heparin, plasminogen and foreign DNA. Plasminogen bound to rMHJ_0461 was readily converted to plasmin in the presence of tPA. Computational modelling identified putative DNA and heparin-binding motifs on solvent-exposed sites around a large pore on the LAP hexamer. We conclude that MHJ_0461 is a LAP that moonlights as a multifunctional adhesin on the cell surface of M. hyopneumoniae .

Jarocki, VM, Tacchi, JL & Djordjevic, SP 2015, 'Non‐proteolytic functions of microbial proteases increase pathological complexity', PROTEOMICS, vol. 15, no. 5-6, pp. 1075-1088.
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Proteases are enzymes that catalyse hydrolysis of peptide bonds thereby controlling the shape, size, function, composition, turnover and degradation of other proteins. In microbes, proteases are often identified as important virulence factors and as such have been targets for novel drug design. It is emerging that some proteases possess additional non‐proteolytic functions that play important roles in host epithelia adhesion, tissue invasion and in modulating immune responses. These additional “moonlighting” functions have the potential to obfuscate data interpretation and have implications for therapeutic design. Moonlighting enzymes comprise a subcategory of multifunctional proteins that possess at least two distinct biological functions on a single polypeptide chain. Presently, identifying moonlighting proteins relies heavily on serendipitous empirical data with clues arising from proteins lacking signal peptides that are localised to the cell surface. Here, we describe examples of microbial proteases with additional non‐proteolytic functions, including streptococcal pyrogenic exotoxin B, PepO and C5a peptidases, mycoplasmal aminopeptidases, mycobacterial chaperones and viral papain‐like proteases. We explore how these non‐proteolytic functions contribute to host cell adhesion, modulate the coagulation pathway, assist in non‐covalent folding of proteins, participate in cell signalling, and increase substrate repertoire. We conclude by describing how proteomics has aided in moonlighting protein discovery, focusing attention on potential moonlighters in microbial exoproteomes.

Jelocnik, M, Bachmann, NL, Kaltenboeck, B, Waugh, C, Woolford, L, Speight, KN, Gillett, A, Higgins, DP, Flanagan, C, Myers, GSA, Timms, P & Polkinghorne, A 2015, 'Genetic diversity in the plasticity zone and the presence of the chlamydial plasmid differentiates Chlamydia pecorum strains from pigs, sheep, cattle, and koalas', BMC Genomics, vol. 16, no. 1.
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Jenkins, C, Micallef, M, Alex, SM, Collins, D, Djordjevicb, SP & Bogema, DR 2015, 'Temporal dynamics and subpopulation analysis of Theileria orientalis genotypes in cattle', INFECTION GENETICS AND EVOLUTION, vol. 32, pp. 199-207.
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© 2015 Elsevier B.V. In Australia, outbreaks of clinical theileriosis caused by Theileria orientalis have been largely associated with the Ikeda genotype which can occur as a sole infection, or more commonly, as a mixture of genotypes. The most prevalent genotype, Chitose, frequently co-occurs with type Ikeda, however the role of this genotype in clinical disease has not been clearly established. Furthermore, the dynamics of individual genotypes in field infection of cattle have not been examined. In this study we developed quantitative PCR (qPCR) and genotyping methods to examine the role of the Chitose genotype in clinical disease and to investigate the temporal dynamics of T. orientalis Ikeda, Chitose and Buffeli genotypes in naïve animals introduced to a T. orientalis-endemic area. Analysis of the major piroplasm surface protein (MPSP) genes of Chitose isolates revealed the presence of two distinct phylogenetic clusters, Chitose A and Chitose B. A genotyping assay aimed at determining Chitose A/B allele frequency revealed that the Chitose A phylogenetic cluster is strongly associated with clinical disease but nearly always co-occurs with the Ikeda genotype. qPCR revealed that the Chitose genotype (particularly Chitose A), undergoes temporal switching in conjunction with the Ikeda genotype and contributes substantially to the overall parasite burden. The benign Buffeli genotype can also undergo temporal switching but levels of this genotype appear to remain low relative to the Ikeda and Chitose types. Interplay between vector and host immunological factors is presumed to be critical to the population dynamics observed in this study. Genotypic switching likely contributes to the persistence of T. orientalis in the host.

Jha, SR, Ha, KSK, Hickman, LD, Hannu, M, Davidson, PM, Macdonald, PS & Newton, PJ 2015, 'Frailty in advanced heart failure: a systematic review', HEART FAILURE REVIEWS, vol. 20, no. 5, pp. 553-560.
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© 2015, Springer Science+Business Media New York. Frailty is a common geriatric syndrome of increased vulnerability to adverse events. The prevalence of frailty among chronic heart failure (CHF) is high and confers a greater risk of adverse events including falls, hospitalisation and mortality. There have been few studies assessing frailty in CHF. A review of the key databases was conducted from 2004 to 2014 including the key search terms ‘frail elderly’ and ‘heart failure’. The following electronic databases were searched: Medline, Cumulative Index for Nursing and Allied Health and Academic Search Complete, with reference lists being manually searched. Articles were included if frailty was assessed using a valid measuring tool in a population with a confirmed diagnosis of CHF. The search yielded a total of 393 articles with 8 articles being selected for review. The prevalence of frailty among those with CHF was high, ranging from 18 to 54 %. The frailty phenotype and geriatric assessments tools were the most common frailty measures utilised; high rates of co-morbidity, hospitalisation and mortality were identified. Frailty is common in CHF and is associated with adverse outcomes.

Jia, H, Ping, C, Xu, C, Zhou, J, Sang, X, Wang, J, Liu, C, Liu, X & Qiu, J 2015, 'Fabrication of the (Y₂O₃:Yb–Er)/Bi₂S₃ composite film for near-infrared photoresponse', Journal of Materials Chemistry A, vol. 3, no. 11, pp. 5917-5922.
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Y₂O₃:Yb-Er/Bi₂S₃ composite films with photoactive current generation under NIR light excitation were fabricated by electro-deposition and a simple successive ionic layer adsorption and reaction (SILAR) method.

Johnston, EL, Mayer-Pinto, M, Hutchings, PA, Marzinelli, EM, Ahyong, ST, Birch, G, Booth, DJ, Creese, RG, Doblin, MA, Figueira, W, Gribben, PE, Pritchard, T, Roughan, M, Steinberg, PD & Hedge, LH 2015, 'Sydney Harbour: what we do and do not know about a highly diverse estuary', MARINE AND FRESHWATER RESEARCH, vol. 66, no. 12, pp. 1073-1087.
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© 2015 CSIRO. Sydney Harbour is a global hotspot for marine and estuarine diversity. Despite its social, economic and biological value, the available knowledge has not previously been reviewed or synthesised. We systematically reviewed the published literature and consulted experts to establish our current understanding of the Harbour's natural systems, identify knowledge gaps, and compare Sydney Harbour to other major estuaries worldwide. Of the 110 studies in our review, 81 focussed on ecology or biology, six on the chemistry, 10 on geology and 11 on oceanography. Subtidal rocky reef habitats were the most studied, with a focus on habitat forming macroalgae. In total 586 fish species have been recorded from the Harbour, which is high relative to other major estuaries worldwide. There has been a lack of process studies, and an almost complete absence of substantial time series that constrains our capacity to identify trends, environmental thresholds or major drivers of biotic interactions. We also highlight a lack of knowledge on the ecological functioning of Sydney Harbour, including studies on microbial communities. A sound understanding of the complexity, connectivity and dynamics underlying ecosystem functioning will allow further advances in management for the Harbour and for similarly modified estuaries around the world.

Jones, A, Pravadali-Cekic, S, Dennis, GR & Shalliker, RA 2015, 'Post column derivatisation analyses review. Is post-column derivatisation incompatible with modern HPLC columns?', Analytica Chimica Acta, vol. 889, pp. 58-70.
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Jones, EM, Doblin, MA, Matear, R & King, E 2015, 'Assessing and evaluating the ocean-colour footprint of a regional observing system', JOURNAL OF MARINE SYSTEMS, vol. 143, pp. 49-61.
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Jones, PM & George, AM 2015, 'The Nucleotide-Free State of the Multidrug Resistance ABC Transporter LmrA: Sulfhydryl Cross-Linking Supports a Constant Contact, Head-to-Tail Configuration of the Nucleotide-Binding Domains', PLOS ONE, vol. 10, no. 6, pp. e0131505-e0131505.
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Jones, SD, Wallman, JF & Byrne, PG 2015, 'Do male secondary sexual characters correlate with testis size and sperm length in the small hairy maggot blowfly?', Zoology, vol. 118, no. 6, pp. 439-445.
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Kabakova, I, Marpaung, D, Poulton, C & Eggleton, B 2015, 'Harnessing On-Chip SBS', Optics and Photonics News, vol. 26, no. 2, pp. 34-34.
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Stimulated Brillouin scattering—a familiar nonlinear effect in macroscopic systems such as fiber optics—is finding new applications in communication, quantum manipulation and microwave filtering in an era of integrated photonics

Kabir, ER & Morshed, N 2015, 'Different approaches in the treatment of obstructive pulmonary diseases', European Journal of Pharmacology, vol. 764, pp. 306-317.
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Kadam, SA, Martin, K, Haav, K, Toom, L, Mayeux, C, Pung, A, Gale, PA, Hiscock, JR, Brooks, SJ, Kirby, IL, Busschaert, N & Leito, I 2015, 'Towards the Discrimination of Carboxylates by Hydrogen‐Bond Donor Anion Receptors', Chemistry – A European Journal, vol. 21, no. 13, pp. 5145-5160.
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AbstractThe binding constants (log Kass) of small synthetic receptor molecules based on indolocarbazole, carbazole, indole, urea and some others, as well as their combinations were measured for small carboxylate anions of different basicity, hydrophilicity and steric demands, that is, trimethylacetate, acetate, benzoate and lactate, in 0.5 % H2O/[D6]DMSO by using the relative NMR‐based measurement method. As a result, four separate binding affinity scales (ladders) including thirty‐eight receptors were obtained with the scales anchored to indolocarbazole. The results indicate that the binding strength is largely, but not fully, determined by the strength of the primary hydrogen‐bonding interaction. The latter in turn is largely determined by the basicity of the anion. The higher is the basicity of the anion the stronger in general is the binding, leading to the approximate order of increasing binding strength, lactate<benzoate<acetate≤trimethylacetate, which holds with all investigated receptors. Nevertheless, there are a number of occasions when the binding order changes with changing of the carboxylate anion, sometimes quite substantially. Principal component analysis (PCA) reveals that this is primarily connected to preferential binding of trimethylacetate, supposedly caused by an additional hydrophobic/solvophobic interaction. These findings enable making better predictions, which receptor framework or cavity is best suited for carboxylate anions in receptor design.

Kan, CWS, Howell, VM, Hahn, MA & Marsh, DJ 2015, 'Genomic alterations as mediators of miRNA dysregulation in ovarian cancer', Genes, Chromosomes and Cancer, vol. 54, no. 1, pp. 1-19.
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Ovarian cancer is the fifth most common cause of cancer death in women worldwide. Serous epithelial ovarian cancer (SEOC) is the most common and aggressive histological subtype. Widespread genomic alterations go hand‐in‐hand with aberrant DNA damage signaling and are a hallmark of high‐grade SEOC. MicroRNAs (miRNAs) are a class of small noncoding RNA molecules that are nonrandomly distributed in the genome. They are frequently located in chromosomal regions susceptible to copy number variation (CNV) associated with malignancy that can influence their expression. Widespread changes in miRNA expression have been reported in multiple cancer types including ovarian cancer. This review examines CNV and single nucleotide polymorphisms, two common types of genomic alterations that occur in ovarian cancer, in the context of their influence on the expression of miRNA and the ability of miRNA to bind to and regulate their target genes. This includes genes encoding proteins involved in DNA repair and the maintenance of genomic stability. Improved understanding of mechanisms of miRNA dysregulation and the role of miRNA in ovarian cancer will provide further insight into the pathogenesis and treatment of this disease. © 2014 Wiley Periodicals, Inc.

Kanodarwala, FK, Wang, F, Reece, PJ & Stride, JA 2015, 'Phase transformations in CdSe quantum dots induced by reaction time', Materials Letters, vol. 141, pp. 67-69.
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© 2014 Published by Elsevier B.V. This paper reports the synthesis of high-quality TOP/TOPO capped CdSe nanocrystals using a simple colloidal method. The effects of varying the reaction time on the size and crystallinity of the synthesized CdSe quantum dots were studied in detail. Powder X-ray diffraction (PXRD) analysis showed a dependence of the crystallite phases as a function of reaction time, from cubic zinc-blende to hexagonal wurtzite and back again to the cubic phase. PXRD data was found to be consistent with high resolution transmission electron microscopy (HRTEM) images of the particles, whilst optical spectroscopy demonstrated the quantum dot nature of the particles. The reaction time-dependent phase behavior is best accounted for by rapid growth along the {111} crystallite facets, after which the facial facets then 'catch-up', resulting once again in cubic symmetry.

Karlsson, PM, Herdean, A, Adolfsson, L, Beebo, A, Nziengui, H, Irigoyen, S, Ünnep, R, Zsiros, O, Nagy, G, Garab, G, Aronsson, H, Versaw, WK & Spetea, C 2015, 'The Arabidopsis thylakoid transporter PHT4;1 influences phosphate availability for ATP synthesis and plant growth', The Plant Journal, vol. 84, no. 1, pp. 99-110.
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SummaryThe Arabidopsis phosphate transporter PHT4;1 was previously localized to the chloroplast thylakoid membrane. Here we investigated the physiological consequences of the absence of PHT4;1 for photosynthesis and plant growth. In standard growth conditions, two independent Arabidopsis knockout mutant lines displayed significantly reduced leaf size and biomass but normal phosphorus content. When mutants were grown in high‐phosphate conditions, the leaf phosphorus levels increased and the growth phenotype was suppressed. Photosynthetic measurements indicated that in the absence of PHT4;1 stromal phosphate was reduced to levels that limited ATP synthase activity. This resulted in reduced CO2 fixation and accumulation of soluble sugars, limiting plant growth. The mutants also displayed faster induction of non‐photochemical quenching than the wild type, in line with the increased contribution of ΔpH to the proton‐motive force across thylakoids. Small‐angle neutron scattering showed a smaller lamellar repeat distance, whereas circular dichroism spectroscopy indicated a perturbed long‐range order of photosystem II (PSII) complexes in the mutant thylakoids. The absence of PHT4;1 did not alter the PSII repair cycle, as indicated by wild‐type levels of phosphorylation of PSII proteins, inactivation ...

Karnaushenko, D, Ibarlucea, B, Lee, S, Lin, G, Baraban, L, Pregl, S, Melzer, M, Makarov, D, Weber, WM, Mikolajick, T, Schmidt, OG & Cuniberti, G 2015, 'Flexible Electronics: Light Weight and Flexible High‐Performance Diagnostic Platform (Adv. Healthcare Mater. 10/2015)', Advanced Healthcare Materials, vol. 4, no. 10, pp. 1419-1419.
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Karnaushenko, D, Ibarlucea, B, Lee, S, Lin, G, Baraban, L, Pregl, S, Melzer, M, Makarov, D, Weber, WM, Mikolajick, T, Schmidt, OG & Cuniberti, G 2015, 'Light Weight and Flexible High‐Performance Diagnostic Platform', Advanced Healthcare Materials, vol. 4, no. 10, pp. 1517-1525.
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A flexible diagnostic platform is realized and its performance is demonstrated for early detection of avian influenza virus (AIV) subtype H1N1 DNA sequences. The key component of the platform is high‐performance biosensors based on high output currents and low power dissipation Si nanowire field effect transistors (SiNW‐FETs) fabricated on flexible 100 μm thick polyimide foils. The devices on a polymeric support are about ten times lighter compared to their rigid counterparts on Si wafers and can be prepared on large areas. While the latter potentially allows reducing the fabrication costs per device, the former makes them cost efficient for high‐volume delivery to medical institutions in, e.g., developing countries. The flexible devices withstand bending down to a 7.5 mm radius and do not degrade in performance even after 1000 consecutive bending cycles. In addition to these remarkable mechanical properties, on the analytic side, the diagnostic platform allows fast detection of specific DNA sequences of AIV subtype H1N1 with a limit of detection of 40 × 10−12 m within 30 min suggesting its suitability for early stage disease diagnosis.

Katz, A, McDonagh, A, Tijing, L & Shon, HK 2015, 'Fouling and Inactivation of Titanium Dioxide-Based Photocatalytic Systems', Critical Reviews in Environmental Science and Technology, vol. 45, no. 17, pp. 1880-1915.
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Titanium dioxide is an effective photocatalyst for the breakdown of many environmental contaminants. The complex mixtures that can occur in water matrices can significantly affect the breakdown of the contaminants in water by titanium dioxide (TiO2). The authors discuss a wide variety of foulants and inhibitors of photocatalytic TiO2 systems and review different methods that can be effective for their fouling prevention. Approaches to regenerate a fouled or contaminated TiO2 catalysts are explored and the effect of substrates on immobilized titanium dioxide is also reviewed.

Kearney, M, Burden, K & Rai, T 2015, 'Investigating teachers' adoption of signature mobile pedagogies', COMPUTERS & EDUCATION, vol. 80, pp. 48-57.
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© 2014 Elsevier Ltd. All rights reserved. This study investigated how teachers are using distinctive pedagogical features of mobile learning: collaboration, personalisation and authenticity. The researchers developed and validated a survey instrument based on these three established constructs (Kearney, Schuck, Burden, & Aubusson, 2012) and used it to interrogate current mobile learning practices in school and university education. This paper focuses on data from school teachers (n = 107). Findings indicated that teachers' perceptions of authenticity were high but aspects of online collaboration, networking and student agency were rated surprisingly lower than expected, given the rhetoric about enhanced connection and flexible learning opportunities afforded by mobile technologies. Device ownership was identified as one factor influencing adoption of these mobile pedagogies. Implications for effective use of handheld devices in teaching are addressed.

Keast, VJ, Ewald, J, De Silva, KSB, Cortie, MB, Monnier, B, Cuskelly, D & Kisi, EH 2015, 'Optical properties and electronic structure of the Cu-Zn brasses', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 647, pp. 129-135.
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© 2015 Elsevier B.V. The color of Cu-Zn brasses range from the red of copper through bright yellow to grey-silver as the Zn content increases. Here we examine the mechanism by which these color changes occur. The optical properties of this set of alloys has been calculated using density functional theory (DFT) and compared to experimental spectroscopy measurements. The optical response of the low Zn content α-brasses is shown to have a distinctly different origin to that in the higher content β′, γ and ε-brasses. The response of β′-brass is unique in that it is strongly influenced by an overdamped plasmon excitation and this alloy will also have a strong surface plasmon response.

Keast, VJ, Wallace, JW, Wrightson, CJ, Tai, M, Gentle, A, Arnold, MD & Cortie, MB 2015, 'The effect of vacancies on the optical properties of AuAl2', JOURNAL OF PHYSICS-CONDENSED MATTER, vol. 27, no. 50.
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© 2015 IOP Publishing Ltd. AuAl2 is an intermetallic compound with a vivid purple colour attributable to a bulk plasmon energy in the visible part of the spectrum. However, the colour of as-deposited thin films is not as strong and only develops upon annealing. Density functional theory calculations of the dielectric function are presented for a variety of vacancy types and concentrations. The results support the view that the effect of annealing on colour is correlated with a reduction in concentration of Al vacancies. The effect of vacancies on the optical properties can be understood as arising from the complex interplay between interband transitions around the Fermi level and the plasmon energy.

Kennan, RM, Lovitt, CJ, Han, X, Parker, D, Turnbull, L, Whitchurch, CB & Rood, JI 2015, 'A two-component regulatory system modulates twitching motility in Dichelobacter nodosus', Veterinary Microbiology, vol. 179, no. 1-2, pp. 34-41.
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© 2015 Elsevier B.V. All rights reserved. Dichelobacter nodosus is the essential causative agent of footrot in sheep and type IV fimbriae-mediated twitching motility has been shownto be essential for virulence.Wehave identified a two-component signal transduction system (TwmSR) that shows similarity to chemosensory systems from other bacteria. Insertional inactivation of the gene encoding the response regulator, TwmR, led to a twitching motility defect, with the mutant having a reduced rate of twitching motility when compared to the wild-type and a mutant complemented with the wild-type twmR gene. The reduced rate of twitching motility was not a consequence of a reduced growth rate or decreased production of surface located fimbriae, but video microscopy indicated that it appeared to result from an overall loss of twitching directionality. These results suggest that a chemotactic response to environmental factors may play an important role in the D. nodosus-mediated disease process.

Khachadorian, S, Gillen, R, Choi, S, Ton-That, C, Kliem, A, Maultzsch, J, Phillips, MR & Hoffmann, A 2015, 'Effects of annealing on optical and structural properties of zinc oxide nanocrystals', PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS, vol. 252, no. 11, pp. 2620-2625.
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& Co. KGaA, Weinheim. The optical and vibrational properties of zinc oxide nanocrystals (ZnO NCs), grown by chemical precipitation method, were investigated following thermal annealing treatments in oxygen, argon, and zinc vapors at temperatures up to 900{ring operator}C. Raman scattering and photoluminescence techniques were utilized to show the effect of temperature annealing in various environments on optical and structural properties of ZnO NCs, referring them to the reduction and increase of certain intrinsic defect concentrations. The experimental results are complemented by density functional theory calculations for understanding the correlation between Raman modes induced with different annealing procedures and certain intrinsic point defects. © 2015 WILEY-VCH Verlag GmbH

Kim, CHJ, Mitchell, JB, Bursill, CA, Sowers, AL, Thetford, A, Cook, JA, van Reyk, DM & Davies, MJ 2015, 'The nitroxide radical TEMPOL prevents obesity, hyperlipidaemia, elevation of inflammatory cytokines, and modulates atherosclerotic plaque composition in apoE(-/-) mice', ATHEROSCLEROSIS, vol. 240, no. 1, pp. 234-241.
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© 2015 Elsevier Ireland Ltd. The nitroxide compound TEMPOL (4-hydroxy-2,2,6,6-tetramethylpiperidine-N-oxyl radical) has been shown to prevent obesity-induced changes in adipokines in cell and animal systems. In this study we investigated whether supplementation with TEMPOL inhibits inflammation and atherosclerosis in apoE-/- mice fed a high fat diet (HFD). Methods: ApoE-/- mice were fed for 12 weeks on standard chow diet or a high-fat diet. Half the mice were supplemented with 10mg/g TEMPOL in their food. Plasma samples were analysed for triglycerides, cholesterol, low- and high-density lipoprotein cholesterol, inflammatory cytokines and markers (interleukin-6, IL-6; monocyte-chemotactic protein, MCP-1; myeloperoxidase, MPO; serum amyloid A, SAA; adiponectin; leptin). Plaques in the aortic sinus were analysed for area, and content of collagen, lipid, macrophages and smooth muscle cells. Results: High fat feeding resulted in marked increases in body mass and plasma lipid levels. Dietary TEMPOL decreased both parameters. In the high-fat-fed mice significant elevations in plasma lipid levels and the inflammatory markers IL-6, MCP-1, MPO, SAA were detected, along with an increase in leptin and a decrease in adiponectin. TEMPOL supplementation reversed these effects. When compared to HFD-fed mice, TEMPOL supplementation increased plaque collagen content, decreased lipid content and increased macrophage numbers. Conclusions: These data indicate that in a well-established model of obesity-associated hyperlipidaemia and atherosclerosis, TEMPOL had a significant impact on body mass, atherosclerosis, hyperlipidaemia and inflammation. TEMPOL may therefore be of value in suppressing obesity, metabolic disorders and increasing atherosclerotic plaque stability.

Kim, RY, Pinkerton, JW, Gibson, PG, Cooper, MA, Horvat, JC & Hansbro, PM 2015, 'Inflammasomes in COPD and neutrophilic asthma', Thorax, vol. 70, no. 12, pp. 1199-1201.
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Kim, SY, Naskar, D, Kundu, SC, Bishop, DP, Doble, PA, Boddy, AV, Chan, H-K, Wall, IB & Chrzanowski, W 2015, 'Formulation of Biologically-Inspired Silk-Based Drug Carriers for Pulmonary Delivery Targeted for Lung Cancer', Scientific Reports, vol. 5, no. 1.
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AbstractThe benefits of using silk fibroin, a major protein in silk, are widely established in many biomedical applications including tissue regeneration, bioactive coating and in vitro tissue models. The properties of silk such as biocompatibility and controlled degradation are utilized in this study to formulate for the first time as carriers for pulmonary drug delivery. Silk fibroin particles are spray dried or spray-freeze-dried to enable the delivery to the airways via dry powder inhalers. The addition of excipients such as mannitol is optimized for both the stabilization of protein during the spray-freezing process as well as for efficient dispersion using an in vitro aerosolisation impactor. Cisplatin is incorporated into the silk-based formulations with or without cross-linking, which show different release profiles. The particles show high aerosolisation performance through the measurement of in vitro lung deposition, which is at the level of commercially available dry powder inhalers. The silk-based particles are shown to be cytocompatible with A549 human lung epithelial cell line. The cytotoxicity of cisplatin is demonstrated to be enhanced when delivered using the cross-linked silk-based particles. These novel inhalable silk-based drug carriers have the potential to be used as anti-cancer drug delivery systems targeted for the lungs.

King, DJM, Middleburgh, SC, Liu, ACY, Tahini, HA, Lumpkin, GR & Cortie, MB 2015, 'Formation and structure of V–Zr amorphous alloy thin films', Acta Materialia, vol. 83, pp. 269-275.
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© 2014 Published by Elsevier Ltd. on behalf of Acta Materialia Inc. All rights reserved. Although the equilibrium phase diagram predicts that alloys in the central part of the V-Zr system should consist of V2Zr Laves phase with partial segregation of one element, it is known that under non-equilibrium conditions these materials can form amorphous structures. Here we examine the structures and stabilities of thin film V-Zr alloys deposited at room temperature by magnetron sputtering. The films were characterized by X-ray diffraction, transmission electron microscopy and computational methods. Atomic-scale modelling was used to investigate the enthalpies of formation of the various competing structures. The calculations confirmed that an amorphous solid solution would be significantly more stable than a random body-centred solid solution of the elements, in agreement with the experimental results. In addition, the modelling effort provided insight into the probable atomic configurations of the amorphous structures allowing predictions of the average distance to the first and second nearest neighbours in the system.

King, DM, Middleburgh, SC, Edwards, L, Lumpkin, GR & Cortie, M 2015, 'Predicting the Crystal Structure and Phase Transitions in High-Entropy Alloys', JOM, vol. 67, no. 10, pp. 2375-2380.
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King, PT, Sharma, R, O’Sullivan, K, Selemidis, S, Lim, S, Radhakrishna, N, Lo, C, Prasad, J, Callaghan, J, McLaughlin, P, Farmer, M, Steinfort, D, Jennings, B, Ngui, J, Broughton, BRS, Thomas, B, Essilfie, A-T, Hickey, M, Holmes, PW, Hansbro, P, Bardin, PG & Holdsworth, SR 2015, 'Nontypeable Haemophilus influenzae Induces Sustained Lung Oxidative Stress and Protease Expression', PLOS ONE, vol. 10, no. 3, pp. e0120371-e0120371.
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© 2015 King et al. Nontypeable Haemophilus influenzae (NTHi) is a prevalent bacterium found in a variety of chronic respiratory diseases. The role of this bacterium in the pathogenesis of lung inflammation is not well defined. In this study we examined the effect of NTHi on two important lung inflammatory processes 1), oxidative stress and 2), protease expression. Bronchoalveolar macrophages were obtained from 121 human subjects, blood neutrophils from 15 subjects, and human-lung fibroblast and epithelial cell lines from 16 subjects. Cells were stimulated with NTHi to measure the effect on reactive oxygen species (ROS) production and extracellular trap formation. We also measured the production of the oxidant, 3-nitrotyrosine (3-NT) in the lungs of mice infected with this bacterium. NTHi induced widespread production of 3-NT in mouse lungs. This bacterium induced significantly increased ROS production in human fibroblasts, epithelial cells, macrophages and neutrophils; with the highest levels in the phagocytic cells. In human macrophages NTHi caused a sustained, extracellular production of ROS that increased over time. The production of ROS was associated with the formation of macrophage extracellular trap-like structures which co-expressed the protease metalloproteinase-12. The formation of the macrophage extracellular trap-like structures was markedly inhibited by the addition of DNase. In this study we have demonstrated that NTHi induces lung oxidative stress with macrophage extracellular trap formation and associated protease expression. DNase inhibited the formation of extracellular traps.

King, S, Massicot, J & McDonagh, A 2015, 'A Straightforward Route to Tetrachloroauric Acid from Gold Metal and Molecular Chlorine for Nanoparticle Synthesis', Metals, vol. 5, no. 3, pp. 1454-1461.
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Aqueous solutions of tetrachloroauric acid of high purity and stability were synthesised using the known reaction of gold metal with chlorine gas. The straightforward procedure developed here allows the resulting solution to be used directly for gold nanoparticle synthesis. The procedure involves bubbling chlorine gas through pure water containing a pellet of gold. The reaction is quantitative and progressed at a satisfactory rate at 50 °C. The gold(III) chloride solutions produced by this method show no evidence of returning to metallic gold over at least twelve months. This procedure also provides a straightforward method to determine the concentration of the resulting solution using the initial mass of gold and volume of water.

Kobayashi, R & Reimers, JR 2015, 'Free energies for the coordination of ligands to the magnesium of chlorophyll-a in solvents', Molecular Physics, vol. 113, no. 13-14, pp. 1648-1654.
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© 2015 Taylor & Francis. The coordination of bases to chlorophyll magnesium modifies spectroscopic properties in solution as well as in situ in reaction centres. We evaluate the free energies of complexation of one or two pyridine, 1-propanol, diethyl ether or water solvent molecules at 298 and 150 K to rationalise observed phenomena. Various a priori dispersion-corrected density functional theory calculations are performed as well as second-order Møller-Plesset calculations, focusing on the effects of dispersion modifying the intermolecular interactions, of dispersion modifying solvation energies, of entropy, and of basis-set superposition error. A process of particular interest is magnesium complexation in ether at low temperature that is often exploited to assign the Q-band visible absorption spectrum of chlorophyll. Recently, we demonstrated that trace water interferes with this process, but the nature of the resulting complex could not be uniquely determined; here, it is identified as ether.Chlorophyll-a.H2O, consistent with interpretations based on our authoritative 2013 assignment.

Koedsin, W & Huete, A 2015, 'Mapping Rubber Tree Stand Age using Pléiades Satellite Imagery: A Case Study in Talang District, Phuket, Thailand', Engineering Journal, vol. 19, no. 4, pp. 45-56.
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The rubber stand age information is an important variable for determining the distribution of carbon pools and fluxes in rubber plantation ecosystems as well as for production management. This study demonstrates the capability of high spatial resolution satellite imagery as Pléiades Satellite Imagery with the help of feature selection (i.e., Sequential Forward Floating Selection) to improve the accuracy of rubber stand age mapping at a part of Thalang district, Phuket, Thailand. The 238 sample plots were used to classification and accuracy assessment. This study found that the Pléiades imagery with the help of Sequential Forward Floating Selection can successfully classify rubber stands age between less than 7 years, 7-15 years and more than 15 years, respectively. The total testing accuracy was improved from 94.07% to 94.92% and 96.61% after applying the Principal Component and the Sequential Forward Floating Selection algorithms, respectively. Since the methodology proposed in this study can accurately classify 3 classes of rubber stand age, it is anticipated that this methodology can be used as a guideline for rubber tree stand age mapping in other study areas.

Kohli, GS, John, U, Figueroa, RI, Rhodes, LL, Harwood, DT, Groth, M, Bolch, CJS & Murray, SA 2015, 'Polyketide synthesis genes associated with toxin production in two species of Gambierdiscus (Dinophyceae)', BMC GENOMICS, vol. 16, no. 1.
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© 2015 Kohli et al.; licensee BioMed Central. Background: Marine microbial protists, in particular, dinoflagellates, produce polyketide toxins with ecosystem-wide and human health impacts. Species of Gambierdiscus produce the polyether ladder compounds ciguatoxins and maitotoxins, which can lead to ciguatera fish poisoning, a serious human illness associated with reef fish consumption. Genes associated with the biosynthesis of polyether ladder compounds are yet to be elucidated, however, stable isotope feeding studies of such compounds consistently support their polyketide origin indicating that polyketide synthases are involved in their biosynthesis. Results: Here, we report the toxicity, genome size, gene content and transcriptome of Gambierdiscus australes and G. belizeanus. G. australes produced maitotoxin-1 and maitotoxin-3, while G. belizeanus produced maitotoxin-3, for which cell extracts were toxic to mice by IP injection (LD50 = 3.8 mg kg-1). The gene catalogues comprised 83,353 and 84,870 unique contigs, with genome sizes of 32.5 ± 3.7 Gbp and 35 ± 0.88 Gbp, respectively, and are amongst the most comprehensive yet reported from a dinoflagellate. We found three hundred and six genes involved in polyketide biosynthesis, including one hundred and ninty-two ketoacyl synthase transcripts, which formed five unique phylogenetic clusters. Conclusions: Two clusters were unique to these maitotoxin-producing dinoflagellate species, suggesting that they may be associated with maitotoxin biosynthesis. This work represents a significant step forward in our understanding of the genetic basis of polyketide production in dinoflagellates, in particular, species responsible for ciguatera fish poisoning.

Kondaveeti, S, Chudasama, NA, Chaudhary, JP, Meena, R & Siddhanta, AK 2015, 'Functional modification of agarose: Synthesis of nanosize half-esters of succinic, phthalic and maleic acids', Indian Journal of Chemistry - Section A Inorganic, Physical, Theoretical and Analytical Chemistry, vol. 54A, no. 6, pp. 734-743.
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A facile synthetic method for preparing new half-esters of agarose (Ag) with succinic (SA), phthalic (PA) and maleic (MA) acids has been described. The half-esters (Ag-SA, Ag-PA and Ag-MA) wherein the acid moieties are attached to the backbone of the agarose are characterized. Dynamic light scattering measurements show that nano-sized polymeric vesicles (32-124 nm) are formed in aqueous solution. A series of Ag-SA, Ag-PA and Ag-MA derivatives have been prepared with degrees of substitution ranging from 0.36 to 0.89 using varying molar ratios of Ag/SA, Ag/PA and Ag/MA (1:1-1:5). The highest degrees of substitution are found to be 0.89, 0.69 and 0.39 for Ag-SA (1:4), Ag-PA (1:3) and Ag-MA (1:2) respectively. The aqueous solution of sodium salts of these esters exhibit enhanced electrical conductivity (ca. 17.5 mS/cm at 40 °C) as compared to those of the parent half-esters (ca. 0.3 mS/cm at 40 °C). These new agarose based nanosized materials may have potential applications in electrochemical devices, sensors and as drug carriers.

Kondaveeti, S, Chudasama, NA, Chaudhary, JP, Meena, R & Siddhanta, AK 2015, 'Functional modification of agarose: Synthesis of nanosize half-esters of succinic, phthalic and maleic acids', INDIAN JOURNAL OF CHEMISTRY SECTION A-INORGANIC BIO-INORGANIC PHYSICAL THEORETICAL & ANALYTICAL CHEMISTRY, vol. 54, no. 6, pp. 734-743.

Kong, FYS, Tabrizi, SN, Fairley, CK, Vodstrcil, LA, Huston, WM, Chen, M, Bradshaw, C & Hocking, JS 2015, 'The efficacy of azithromycin and doxycycline for the treatment of rectal chlamydia infection: a systematic review and meta-analysis', Journal of Antimicrobial Chemotherapy, vol. 70, no. 5, pp. 1290-1297.
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Abstract Background There are increasing concerns about treatment failure following treatment for rectal chlamydia with 1 g of azithromycin. A systematic review and meta-analysis was conducted to investigate the efficacy of 1 g of azithromycin as a single dose or 100 mg of doxycycline twice daily for 7 days for the treatment of rectal chlamydia. Methods Medline, Embase, PubMed, Cochrane Controlled Trials Register, Australia New Zealand Clinical Trial Register and ClinicalTrials.gov were searched to the end of April 2014. Studies using 1 g of azithromycin or 7 days of doxycycline for the treatment of rectal chlamydia were eligible. Gender, diagnostic test, serovar, symptomatic status, other sexually transmitted infections, follow-up time, attrition and microbial cure were extracted. Meta-analysis was used to calculate pooled (i) azithromycin and doxycycline efficacy and (ii) efficacy difference. Results All eight included studies were observational. The random-effects pooled efficacy for azithromycin (based on eight studies) was 82.9% (95% CI 76.0%–89.8%; I2 = 71.0%; P &lt; 0.01) and for doxycycline (based on five studies) was 99.6% (95% CI 98.6%–100%; I2 = 0%; P = 0.571), resulting in a random-effects pooled efficacy difference (based on five studies) of 19.9% (95% CI 11.4%–28.3%; I2 = 48.5%; P = 0.101) in favour of doxycycline. Conclusions The efficacy of single-dose azithromycin may be considerably lower than 1 week of doxycycline for treating ...

Kretschmer, K, Sun, B, Su, D, Zhao, Y & Wang, G 2015, 'Scalable Preparation of LiFePO4/C Nanocomposites with sp(2)-Coordinated Carbon Coating as High-Performance Cathode Materials for Lithium-Ion Batteries', CHEMELECTROCHEM, vol. 2, no. 12, pp. 2096-2103.
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© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. We hereby report carbon-coated LiFePO4 cathode materials prepared by industrial ball milling and a solid-state reaction with Li2CO3, NH4H2PO4, and FeC2O4⋅2H2O as starting materials. Soluble starch as the primary carbon source was investigated for its capability of generating a highly graphitic carbon coating, whilst sufficiently controlling the crystal growth of LiFePO4. XRD analysis, Raman spectroscopy, and electrochemical testing revealed the significant impact of the amount of starch added to the pre-sintered precursor on phase purity, carbon quality, and electrochemical performance of the final LiFePO4/C composite. The optimum soluble starch content to achieve a highly sp2-coordinated carbon coating is 10wt%, which enabled our LiFePO4/C composite to achieve competitive reversible capacities as well as improved rate performance.

Kumar, M, Pandya-Kumar, N, Dam, A, Haor, H, Mayzlish-Gati, E, Belausov, E, Wininger, S, Abu-Abied, M, McErlean, CSP, Bromhead, LJ, Prandi, C, Kapulnik, Y & Koltai, H 2015, 'Arabidopsis response to low-phosphate conditions includes active changes in actin filaments and PIN2 polarization and is dependent on strigolactone signalling', Journal of Experimental Botany, vol. 66, no. 5, pp. 1499-1510.
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© The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. Strigolactones (SLs) are plant hormones that regulate the plant response to phosphate (Pi) growth conditions. At least part of SL-signalling execution in roots involves MAX2-dependent effects on PIN2 polar localization in the plasma membrane (PM) and actin bundling and dynamics. We examined PIN2 expression, PIN2 PM localization, endosome trafficking, and actin bundling under low-Pi conditions: a MAX2-dependent reduction in PIN2 trafficking and polarization in the PM, reduced endosome trafficking, and increased actin-filament bundling were detected in root cells. The intracellular protein trafficking that is related to PIN proteins but unassociated with AUX1 PM localization was selectively inhibited. Exogenous supplementation of the synthetic SL GR24 to a SL-deficient mutant (max4) led to depletion of PIN2 from the PM under low-Pi conditions. Accordingly, roots of mutants in MAX2, MAX4, PIN2, TIR3, and ACTIN2 showed a reduced low-Pi response compared with the wild type, which could be restored by auxin (for all mutants) or GR24 (for all mutants except max2-1). Changes in PIN2 polarity, actin bundling, and vesicle trafficking may be involved in the response to low Pi in roots, dependent on SL/MAX2 signalling.

Kumar, M, Pandya-Kumar, N, Kapulnik, Y & Koltai, H 2015, 'Strigolactone signaling in root development and phosphate starvation', Plant Signaling & Behavior, vol. 10, no. 7, pp. e1045174-e1045174.
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Strigolactones (SLs), have recently been recognized as phytohormone involve in orchestrating shoot and root architecture. In, roots SLs positively regulate root hair length and density, suppress lateral root formation and promote primary root meristem cell number. The biosynthesis and exudation of SLs increases under low phosphate level to regulate root responses. This hormonal response suggests an adaptation strategy of plant to optimize growth and development under nutrient limitations. However, little is known on signal-transduction pathways associated with SL activities. In this review, we outline the current knowledge on SL biology by describing their role in the regulation of root development. Also, we discuss the recent findings on the non-cell autonomous signaling of SLs, that involve PIN polarization, vesicle trafficking, changes in actin architecture and dynamic in response to phosphate starvation.

Kumar, M, Reddy, CRK & Ralph, PJ 2015, 'Polyamines in morphogenesis and development: a promising research area in seaweeds', Frontiers in Plant Science, vol. 6, no. FEB, pp. 27-27.
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Kutty, SK, Barraud, N, Ho, KKK, Iskander, GM, Griffith, R, Rice, SA, Bhadbhade, M, Willcox, MDP, Black, DS & Kumar, N 2015, 'Hybrids of acylated homoserine lactone and nitric oxide donors as inhibitors of quorum sensing and virulence factors in Pseudomonas aeruginosa', Organic & Biomolecular Chemistry, vol. 13, no. 38, pp. 9850-9861.
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This paper discusses conversion of agonist acylated homoserine lactones (AHL) to antagonist AHLs with dual properties of quorum sensing inhibition and nitric oxide release.

Kuzhiumparambil, U, Watanabe, S & Fu, S 2015, 'Oxidation of testosterone by permanganate and its implication in sports drug testing', NEW JOURNAL OF CHEMISTRY, vol. 39, no. 3, pp. 1597-1602.
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© The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2015. Manipulations of urine samples by urine substitution, urine dilution, and urine adulteration with highly oxidative chemicals to escape detection in doping control analysis have been reported in the past. Adulteration of urine with oxidising chemicals such as potassium permanganate, cerium ammonium nitrate, pyridinium chlorochromate etc. can lead to considerable changes in the endogenous steroidal profile parameters and thus mask the abnormality in the steroidal profile following steroid abuse. In this study we have identified the formation of two stable oxidation products upon reaction of potassium permanganate with testosterone, an important endogenous urinary steroid. Isolation and characterisation of these oxidation products were performed using chromatography and spectroscopy and the products were elucidated as 4α,5α-dihydroxytestosterone and 4β,5β-dihydroxytestosterone. Formation of these two molecules in human urine after adulteration with potassium permanganate has been demonstrated by liquid chromatography-mass spectrometry (LC-MS) analysis. The products 4α,5α-dihydroxytestosterone and 4β,5β-dihydroxytestosterone have not been previously reported in urine and hence have the potential to be included in the routine drug testing program for monitoring possible testosterone abuse and permanganate adulteration of urine.

Lafleur, JE & Rice, SA 2015, 'Induction of resistance to S. aureus in an environmental marine biofilm grown in Sydney Harbor, NSW, Australia', World Journal of Microbiology and Biotechnology, vol. 31, no. 2, pp. 353-358.
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Lai, S, Yang, Z, Wu, H, Liao, J, Qiu, J, Song, Z, Yang, Y & Zhou, D 2015, 'Effect of Zr⁴⁺ ions doping on ultraviolet long afterglowproperty in CdSiO3: Bi³⁺ phosphor powder', Optoelectronics and Advanced Materials, Rapid Communications, vol. 9, no. 1-2, pp. 48-52.
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The CdSiO3: Bi3+, Zr4+ phosphor powder with ultraviolet long afterglow emission was synthesized by high temperature solid state reaction and influence of Zr4+ ions on the ultravioletlong afterglow luminescence properties wasinvestigated. The Zr4+ ions as co-dopants enhance greatly the long afterglow emission intensity and durationof CdSiO3: Bi3+ phosphor powders and theenhancement mechanismarediscussed in this paper. The ultraviolet region long afterglow phosphor powdermay find many technologically important applications in disinfectingandphoto-catalysis as the ultraviolet light source.

Lajus, D, Yurtseva, A, Birch, G & Booth, DJ 2015, 'Fluctuating asymmetry as a pollution monitor: The Australian estuarine smooth toadfish Tetractenos glaber (Teleostei: Tetraodontidae)', Marine Pollution Bulletin, vol. 101, no. 2, pp. 758-767.
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© 2015 Elsevier Ltd. The relationship between pollution level in estuarine sediment and fluctuating asymmetry (FA) of resident smooth toadfish Tetractenos glaber was evaluated. A total of 188 fish from Sydney and Hawkesbury River estuaries (5 locations from each) were analysed for 28 bilateral skull bone characters. Sediment pollution was quantified based on analysis of heavy metals (Cd, Cr, Cu, Ni, Pb and Zn) and organochlorine pesticides (DDT, DDD, DDE, chlordane, dieldrin, lindane). Sediment toxicity was characterized using the mean quotient approach (MERMQ) and ranged from low to moderate level for heavy metals and from low to severe for organochlorides. The mean shape and directional asymmetry of fish bones differed among locations, suggesting a response to local environments. FA was positively correlated with organochlorine pesticides across locations, but not with heavy metals. These results suggest that fish FA could be a useful estimator of stress caused by organic toxicity based on the MERMQ approach.

Lao, W, Tan, Y, Jin, X, Xiao, L, Kim, JJY & Qu, X 2015, 'Comparison of Cytotoxicity and the Anti-Adipogenic Effect of Green Tea Polyphenols with Epigallocatechin-3-Gallate in 3T3-L1 Preadipocytes', The American Journal of Chinese Medicine, vol. 43, no. 06, pp. 1177-1190.
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Recent studies have demonstrated the effects of green tea polyphenols (GTP) and epigallocatechin-3-gallate (EGCG) on obesity. However, high doses of EGCG have also exhibited cytotoxicity. The aim of this study was to compare total GTP with purified EGCG on cytotoxicity, and to investigate the effects and the molecular mechanism of total GTP and EGCG on adipogenesis. Cytotoxicity was determined by cell viability assay. For the adipogenesis study, 3T3-L1 preadipocytes were incubated with three doses of GTP (1, 10, and 100 μg/ml) and the effect of EGCG (6.8 μg/ml) was compared with 10 μg/ml GTP containing 68% EGCG. Oil Red O staining and triglyceride content assay were carried out 10 days after differentiation and treatment. Adipogenic regulators CCAAT element binding protein α (C/EBPα), peroxisome proliferator-activated receptor gamma (PPARγ) and sterol regulatory element-binding protein-1c (SREBP-1c) were determined by qRT-PCR and immunoblotting. GTP at 1000 μg/ml and EGCG (68 and 680 μg/ml) significantly affected cell viability. Purified EGCG had greater cytotoxicity than corresponding doses of GTP. About 10 μg/ml of GTP showed stronger reduction in triglyceride accumulation than EGCG treatment. Transcriptional factors of C/EBPα, SREBP-1c and PPARγ were markedly decreased in both GTP and EGCG-treated cells and GTP exhibited stronger inhibitory effects on C/EBPα and PPARγ protein expression than EGCG (p < 0.05). In conclusion, total GTP exerted greater inhibitory effects than purified EGCG on adipogenesis through down-regulating the adipogenic factor C/EBPα, SREBP-1c and PPARγ expression. These findings support that a polyphenol mixture is safer and more effective than EGCG alone for preventing obesity and obesity-related chronic diseases.

Latham, SL, Tiberti, N, Gokoolparsadh, N, Holdaway, K, Olivier Couraud, P, Grau, GER & Combes, V 2015, 'Immuno-analysis of microparticles: probing at the limits of detection', Scientific Reports, vol. 5, no. 1.
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AbstractMicroparticle (MP) research is clouded by debate regarding the accuracy and validity of flow cytometry (FCM) as an analytical methodology, as it is influenced by many variables including the pre-analytical conditions, instruments physical capabilities and detection parameters. This study utilises a simplistic in vitro system for generating MP and through comparative analysis with immuno-electron microscopy (Immuno-EM) assesses the strengths and limitations of probe selection and high-sensitivity FCM. Of the markers examined, MP were most specifically labelled with phosphatidylserine ligands, annexin V and lactadherin, although only ~60% MP are PS positive. Whilst these two ligands detect comparable absolute MP numbers, they interact with the same population in distinct manners; annexin V binding is enhanced on TNF induced MP. CD105 and CD54 expression were, as expected, consistent and enhanced following TNF activation respectively. Their labelling however accounted for as few as 30–40% of MP. The greatest discrepancies between FCM and I-EM were observed in the population solely labelled for the surface antigen. These findings demonstrate that despite significant improvements in resolution, high-sensitivity FCM remains limited in detecting small-size MP expressing low antigen levels. This study highlights factors to consider when selecting endothelial MP probes, as well as interpreting and representing data.

Lawandi, J, Tao, C, Ren, B, Williams, P, Ling, D, Swan, MA, Nassif, NT, Torpy, FR, O'Brien, BA & Simpson, AM 2015, 'Reversal of diabetes following transplantation of an insulin-secreting human liver cell line: Melligen cells', Molecular Therapy - Methods & Clinical Development, vol. 2, pp. 15011-15011.
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© 2015 American Society of Gene & Cell Therapy As an alternative to the transplantation of islets, a human liver cell line has been genetically engineered to reverse type 1 diabetes (TID). The initial liver cell line (Huh7ins) commenced secretion of insulin in response to a glucose concentration of 2.5 mmol/l. After transfection of the Huh7ins cells with human islet glucokinase, the resultant Melligen cells secreted insulin in response to glucose within the physiological range; commencing at 4.25 mmol/l. Melligen cells exhibited increased glucokinase enzymatic activity in response to physiological glucose concentrations, as compared with Huh7ins cells. When transplanted into diabetic immunoincompetent mice, Melligen cells restored normoglycemia. Quantitative real-time polymerase chain reaction (qRT-PCR) revealed that both cell lines expressed a range of β-cell transcription factors and pancreatic hormones. Exposure of Melligen and Huh7ins cells to proinflammatory cytokines (TNF-α, IL-1β, and IFN-γ) affected neither their viability nor their ability to secrete insulin to glucose. Gene expression (microarray and qRT-PCR) analyses indicated the survival of Melligen cells in the presence of known β-cell cytotoxins was associated with the expression of NF-κB and antiapoptotic genes (such as BIRC3). This study describes the successful generation of an artificial β-cell line, which, if encapsulated to avoid allograft rejection, may offer a clinically applicable cure for T1D.

Le Brun, AP, Soliakov, A, Shah, DSH, Holt, SA, McGill, A & Lakey, JH 2015, 'Engineered self-assembling monolayers for label free detection of influenza nucleoprotein', Biomedical Microdevices, vol. 17, no. 3.
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Le, V-M, Wang, J-J, Yuan, M, Nguyen, T-L, Yin, G-F, Zheng, Y-H, Shi, W-B, Lang, M-D, Xu, L-M & Liu, J-W 2015, 'An investigation of antitumor efficiency of novel sustained and targeted 5-fluorouracil nanoparticles', European Journal of Medicinal Chemistry, vol. 92, pp. 882-889.
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© 2015 Published by Elsevier Masson SAS. Traditional chemotherapeutic drugs remain the major treatment for advanced colorectal cancer. However, due to the lack of tumor specificity these drug also destroy healthy tissue and organs, which has been the main reason for treatment failure and mortality. Folate-based drug delivery systems for improving nanoparticle endocytosis have been used to address these problems. Here, folic acid (FA) conjugated mPEG-b-P(CABCL-co-ACL) diblock copolymers were synthesized and characterized by TEM and NMR. Drug loaded nanoparticles were prepared using dialysis method and was obtained with a mean diameter of 45.2 nm with sustained in vitro release profile. In vitro cytotoxicity assay indicated that the cytotoxicity of folate modified nanoparticles were significantly increased compared to free drug and non-folate nanoparticles. In addition, results of hemolytic and histopathologic study suggested that the non-loaded nanoparticle (NL/NP) was non-toxic and biocompatible at the testing concentration. Moreover, in vivo results showed that FA/5-FU/NP effectively inhibited growth of HCT-8 cell-based xenograft tumors in BALB/c mice and revealed stronger antitumor efficacy than other treated groups. Thus, both in vitro and in vivo results exhibited that the folate conjugated mPEG-b-P(CABCL-co-ACL) copolymers have great potential to be used as sustainable and specific colon cancer targeting delivery system for anticancer agents.

Lee, H-H, Paudel, KR & Kim, D-W 2015, 'Terminalia chebulaFructus Inhibits Migration and Proliferation of Vascular Smooth Muscle Cells and Production of Inflammatory Mediators in RAW 264.7', Evidence-Based Complementary and Alternative Medicine, vol. 2015, pp. 1-10.
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Pathogenesis of atherosclerosis and neointima formation after angioplasty involves vascular smooth muscle cells (VSMCs) migration and proliferation followed by inflammatory responses mediated by recruited macrophages in the neointima.Terminalia chebulais widely used traditional medicine in Asia for its beneficial effects against cancer, diabetes, and bacterial infection. The study was designed to determine whetherTerminalia chebulafructus water extract (TFW) suppresses VSMC migration and proliferation and inflammatory mediators production in macrophage (RAW 264.7). Our results showed that TFW possessed strong antioxidative effects in 1,1-diphenyl-2-picryl hydrazyl (DPPH) scavenging and lipid peroxidation assays. In addition, TFW reduced nitric oxide (NO) production, inducible nitric oxide synthase (iNOS), and cyclooxygenase-2 (COX-2) expression in RAW 264.7 cells. Also, TFW inhibited platelet-derived growth factor (PDGF-BB) induced VSMC migration as determined by wound healing and Boyden chamber assays. The antimigratory effect of TFW was due to its inhibitory effect on metalloproteinase-9 (MMP-9) expression, focal adhesion kinase (FAK) activation, and Rho-family of small GTPases (Cdc42 and RhoA) expression in VSMCs. Furthermore, TFW suppressed PDGF-BB induced VSMC proliferation by downregulation of mitogen activated protein kinases (MAPKs) signaling molecules. These results suggest that TFW could be a beneficial resource in the prevention of atherosclerosis.

Lee, S, Kim, J-E, Hong, S-H, Lee, A-Y, Park, E-J, Seo, HW, Chae, C, Doble, P, Bishop, D & Cho, M-H 2015, 'High Inorganic Phosphate Intake Promotes Tumorigenesis at Early Stages in a Mouse Model of Lung Cancer', PLOS ONE, vol. 10, no. 8, pp. e0135582-e0135582.
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Lees, JG, Gorgani, NN, Ammit, AJ, McCluskey, A, Robinson, PJ & O'Neill, GM 2015, 'Role of dynamin in elongated cell migration in a 3D matrix', Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol. 1853, no. 3, pp. 611-618.
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Leggio, GM, Torrisi, SA, Castorina, A, Platania, CBM, Impellizzeri, AAR, Fidilio, A, Caraci, F, Bucolo, C, Drago, F & Salomone, S 2015, 'Dopamine D3 receptor-dependent changes in alpha6 GABAA subunit expression in striatum modulate anxiety-like behaviour: Responsiveness and tolerance to diazepam', European Neuropsychopharmacology, vol. 25, no. 9, pp. 1427-1436.
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Lei, L, Zhou, J, Zhang, J & Xu, S 2015, 'The use of zinc ions to control the size of Yb/Er:KMnF₃ nanocrystals with single band emission', CrystEngComm, vol. 17, no. 44, pp. 8457-8462.
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A novel method to modify the size of Yb/Er:KMnF₃ NCs by introducing Zn²⁺ in the initial solution is presented, and the results can provide direct evidence for the size-dependent upconversion luminescence.

Lélé, MI, Leslie, LM & Lamb, PJ 2015, 'Analysis of Low-Level Atmospheric Moisture Transport Associated with the West African Monsoon', Journal of Climate, vol. 28, no. 11, pp. 4414-4430.
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Abstract The major objective of this study is to re-evaluate the ocean–land transport of moisture for rainfall in West Africa using 1979–2008 NCEP–NCAR reanalysis data. The vertically integrated atmospheric water vapor flux for the surface–850 hPa is calculated to account for total low-level moisture flux contribution to rainfall over West Africa. Analysis of mean monthly total vapor fluxes shows a progressive penetration of the flux into West Africa from the south and west. During spring (April–June), the northward flux forms a “moisture river” transporting moisture current into the Gulf of Guinea coast. In the peak monsoon season (July–September), the southerly transport weakens, but westerly transport is enhanced and extends to 20°N owing to the strengthening West African jet off the west coast. Mean seasonal values of total water vapor flux components across boundaries indicate that the zonal component is the largest contributor to mean moisture transport into the Sahel, while the meridional transport contributes the most over the Guinea coast. For the wet years of the Sahel rainy season (July–September), active anomalies are displaced farther north compared to the long-term average. This includes the latitude of the intertropical front (ITF), the extent of moisture flux, and the zone of strong moisture flux convergence, with an enhanced westerly flow. For the dry Sahel years, the opposite patterns are observed. Statistically significant positive correlations between the zonal moisture fluxes and Sudan–Sahel rainfall totals are most pronounced when the zonal fluxes lead by 1–4 pentads. However, although weak, they still are statistically significant at lags 3 and 4 for meridional moisture fluxes.

Letnic, M, Webb, JK, Jessop, TS & Dempster, T 2015, 'Restricting access to invasion hubs enables sustained control of an invasive vertebrate', Journal of Applied Ecology, vol. 52, no. 2, pp. 341-347.
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SummaryBiological invasions often occur through expansion of satellite populations that become established at ‘invasion hubs’. Invasion hubs can result from random dispersal events, but frequently arise when invading individuals actively choose habitats using cues that signify high‐quality environments where the fitness consequences are positive. Theoretical studies suggest that targeted control at invasion hubs can effectively suppress the populations and impacts of invaders.In arid Australia, small dams that provide water for livestock function as invasion hubs by providing an invasive vertebrate, the cane toad Rhinella marina, with refuge from extreme aridity during the annual dry season. Toads are attracted to dams and use them as stepping stone habitats from which they disperse during rainy periods. Here, we ask whether sustained control of this invasive vertebrate can be achieved by converting invasion hubs into ecological traps. We did this by manipulating invasion hub habitats to induce a mismatch between toads' habitat preference and the fitness consequences of their habitat choice to cause high mortality.We constructed fences to exclude toads from dams and maintained these fences for 1 year. This period encompassed periods of dry and wet seasonal climatic conditions. Our manipulation did not alter the attractive cues for invading toads which died en masse while attempting to settle at fenced dams that prevented toads from reaching water. Toad populations at the fenced dams were suppressed by 1–2 orders of magnitude compared to unfenced controls and procedural controls. Toad populations remained su...

Leykam, D, Solntsev, AS, Sukhorukov, AA & Desyatnikov, AS 2015, 'Lattice topology and spontaneous parametric down-conversion in quadratic nonlinear waveguide arrays', Physical Review A, vol. 92, no. 3.
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Li, D, Wen, S & Shi, X 2015, 'Dendrimer‐entrapped metal colloids as imaging agents', WIREs Nanomedicine and Nanobiotechnology, vol. 7, no. 5, pp. 678-690.
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This review reports the recent advances in dendrimer‐entrapped metal colloids as contrast agents for biomedical imaging applications. The versatile dendrimer scaffolds with 3‐dimensional spherical shape, highly branched internal cavity, tunable surface conjugation chemistry, and excellent biocompatibility and nonimmunogenicity afford their uses as templates to create multifunctional dendrimer‐entrapped metal colloids for mono‐ or multi‐ mode molecular imaging applications. In particular, multifunctional dendrimer‐entrapped gold nanoparticles with different surface modifications have been used for fluorescence imaging, targeted tumor computed tomography (CT) imaging, enhanced blood pool CT imaging, dual mode CT/MR imaging, and tumor theranostics (combined CT imaging and chemotherapy) will be introduced and discussed in detail. WIREs Nanomed Nanobiotechnol 2015, 7:678–690. doi: 10.1002/wnan.1331This article is categorized under:Diagnostic Tools > Diagnostic NanodevicesDiagnostic Tools > In Vivo Nanodiagnostics and ImagingNanotechnology Approaches to Biology > Nanoscale Systems in Biology

Li, H, Kozey Keadle, S, Staudenmayer, J, Assaad, H, Huang, JZ & Carroll, RJ 2015, 'Methods to assess an exercise intervention trial based on 3-level functional data', Biostatistics, vol. 16, no. 4, pp. 754-771.
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Li, J, Yang, Z, Shao, B, Liao, J, Lai, S, Qiu, J, Song, Z & Yang, Y 2015, 'Ag Nanoparticles‐Enhanced Photoluminescence in LaPO₄: Eu Three‐Dimensional Ordered Macroporous Films', Journal of the American Ceramic Society, vol. 98, no. 5, pp. 1562-1566.
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The three‐dimensional ordered macroporous (3DOM) LaPO4:Eu3+ films and Ag nanoparticles (NPs) were prepared via a template‐assisted process and sodium citrate reduction method, respectively. Composite systems consisting of 3DOM LaPO4:Eu3+ films and Ag NPs were obtained by adding the Ag NPs into voids of 3DOM LaPO4:Eu3+ films. The influence of Ag NPs on photoluminescence of 3DOM LaPO4:Eu3+ was investigated. The results show that photoluminescence properties of 3DOM LaPO4:Eu3+ films were enhanced after addition of Ag NPs, which was attributed to the local surface plasmons resonance effect of Ag NPs.

Li, K, Su, D, Liu, H & Wang, G 2015, 'Antimony-Carbon-Graphene Fibrous Composite as Freestanding Anode Materials for Sodium-ion Batteries', ELECTROCHIMICA ACTA, vol. 177, pp. 304-309.
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© 2015 Elsevier Ltd. Antimony-carbon-graphene fibrous composites were prepared by the electrospinning/spray process as freestanding anodes for sodium-ion batteries. Antimony nanoparticles distribute in conductive carbonized polymer fibers and graphene flakes. The unique structure prevents the aggregation of the antimony nanoparticles and buffers the mechanical stress from volume change of antimony during repeated alloying/de-alloying process. The composites demonstrated an excellent electrochemical performance as anode material for sodium-ion batteries, with a reversible capacity of 274 mAh/g after 100 charge-discharge cycles at a current density of 100 mA/g.

Lian, H, Liang, H & Carroll, RJ 2015, 'Variance Function Partially Linear Single-Index Models', Journal of the Royal Statistical Society Series B: Statistical Methodology, vol. 77, no. 1, pp. 171-194.
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SummaryWe consider heteroscedastic regression models where the mean function is a partially linear single-index model and the variance function depends on a generalized partially linear single-index model. We do not insist that the variance function depends only on the mean function, as happens in the classical generalized partially linear single-index model. We develop efficient and practical estimation methods for the variance function and for the mean function. Asymptotic theory for the parametric and non-parametric parts of the model is developed. Simulations illustrate the results. An empirical example involving ozone levels is used to illustrate the results further and is shown to be a case where the variance function does not depend on the mean function.

Liao, J, Yang, Z, Sun, J, Lai, S, Shao, B, Li, J, Qiu, J, Song, Z & Yang, Y 2015, 'Preparation and Upconversion Emission Modification of Crystalline Colloidal Arrays and Rare Earth Fluoride Microcrystal Composites', Scientific Reports, vol. 5, no. 1.
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In this paper, highly ordered crystalline colloidal arrays containing rare earth fluoride microcrystals were fabricated. The upconversion emission property of rare earth fluoride microcrystals in crystalline colloidal arrays was studied and modified. A significant suppression and enhancement of the upconversion emission from the rare earth fluorides can be observed in the regions of the photonic band gap and its band edge, respectively. The suppression or enhancement factor was shown to be related to the ordered degree of the crystalline colloidal arrays and is critical in the preparation of upconversion displays and low-threshold lasers.

Liggins, L, Booth, DJ, Figueira, WF, Treml, EA, Tonk, L, Ridgway, T, Harris, DA & Riginos, C 2015, 'Latitude‐wide genetic patterns reveal historical effects and contrasting patterns of turnover and nestedness at the range peripheries of a tropical marine fish', Ecography, vol. 38, no. 12, pp. 1212-1224.
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Few studies have examined core–periphery genetic patterns in tropical marine taxa. The core–periphery hypothesis (CPH) predicts that core populations will have higher genetic diversity and lower genetic differentiation than peripheral populations as a consequence of greater population sizes and population connectivity in the core. However, the applicability of the CPH to many tropical marine taxa may be confounded by their complex population histories and/or high (asymmetric) population connectivity. In this study we investigated genetic patterns (based on mtDNA) across the latitudinal range of the neon damselfish Pomacentrus coelestis (36°N, Japan – 37°S, east Australia). We suggest a novel hypothetical framework for core–periphery genetic patterns and extend typical analyses to include genealogical analyses, partitioned β‐diversity measures (total βSOR, turnover βSIM, and nestedness‐resultant βSNE), and analyses of nestedness. We found that the existence of two divergent lineages of the neon damselfish led levels of genetic diversity to deviate from CPH expectations. When focusing on the widespread lineage (Pacific clade) nucleotide diversity was higher in the core, supporting the CPH. However, genetic patterns differed toward the northern and southern peripheries of the Pacific clade. The turnover of haplotypes (pairwise‐βsim) increased over distance in the north, indicative of historical colonization with little contemporary migration. In contrast, although turnover was still dominant in the south (βSIM), there was no relationship to distance (pairwise‐βsim), suggesting the influence of more contemporary processes. Moreover, the haplotype compositions of populations in the south were nested according to latitude, indicating immigration from lower latitudes toward the southern periphery. By e...

Lim, DCE & Cheng, NCL 2015, 'The effect of TJ‐38 on peripheral blood flow in women with peripheral coldness', Focus on Alternative and Complementary Therapies, vol. 20, no. 3-4, pp. 155-156.
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Lin, G, Fomin, VM, Makarov, D & Schmidt, OG 2015, 'Supervised discriminant analysis for droplet micro-magnetofluidics', Microfluidics and Nanofluidics, vol. 19, no. 2, pp. 457-464.
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Lin, G, Makarov, D & Schmidt, O 2015, 'Strong Ferromagnetically-Coupled Spin Valve Sensor Devices for Droplet Magnetofluidics', Sensors, vol. 15, no. 6, pp. 12526-12538.
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We report a magnetofluidic device with integrated strong ferromagnetically-coupled and hysteresis-free spin valve sensors for dynamic monitoring of ferrofluid droplets in microfluidics. The strong ferromagnetic coupling between the free layer and the pinned layer of spin valve sensors is achieved by reducing the spacer thickness, while the hysteresis of the free layer is eliminated by the interplay between shape anisotropy and the strength of coupling. The increased ferromagnetic coupling field up to the remarkable 70 Oe, which is five-times larger than conventional solutions, brings key advantages for dynamic sensing, e.g., a larger biasing field giving rise to larger detection signals, facilitating the operation of devices without saturation of the sensors. Studies on the fundamental effects of an external magnetic field on the evolution of the shape of droplets, as enabled by the non-visual monitoring capability of the device, provides crucial information for future development of a magnetofluidic device for multiplexed assays.

Lin, G, Makarov, D, Medina-Sánchez, M, Guix, M, Baraban, L, Cuniberti, G & Schmidt, OG 2015, 'Magnetofluidic platform for multidimensional magnetic and optical barcoding of droplets', Lab on a Chip, vol. 15, no. 1, pp. 216-224.
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A magnetofluidic platform with integrated GMR sensors is demonstrated for on-demand facile generation and high-throughput real-time decoding of droplet barcodes.

Lin, Y-S, Medlyn, BE, Duursma, RA, Prentice, IC, Wang, H, Baig, S, Eamus, D, Resco de Dios, V, Mitchell, P, Ellsworth, DS, Op de Beeck, M, Wallin, G, Uddling, J, Tarvainen, L, Linderson, M-L, Cernusak, LA, Nippert, JB, Ocheltree, T, Tissue, DT, Martin-St Paul, NK, Rogers, A, Warren, JM, De Angelis, P, Hikosaka, K, Han, Q, Onoda, Y, Gimeno, TE, Barton, CVM, Bennie, J, Bonal, D, Bosc, A, Loew, M, Macinins-Ng, C, Rey, A, Rowland, L, Setterfield, SA, Tausz-Posch, S, Zaragoza-Castells, J, Broadmeadow, MSJ, Drake, JE, Freeman, M, Ghannoum, O, Hutley, LB, Kelly, JW, Kikuzawa, K, Kolari, P, Koyama, K, Limousin, J-M, Meir, P, Lola da Costa, AC, Mikkelsen, TN, Salinas, N, Sun, W & Wingate, L 2015, 'Optimal stomatal behaviour around the world', NATURE CLIMATE CHANGE, vol. 5, no. 5, pp. 459-464.
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© 2015 Macmillan Publishers Limited. All rights reserved. Stomatal conductance (g s) is a key land-surface attribute as it links transpiration, the dominant component of global land evapotranspiration, and photosynthesis, the driving force of the global carbon cycle. Despite the pivotal role of g s in predictions of global water and carbon cycle changes, a global-scale database and an associated globally applicable model of g s that allow predictions of stomatal behaviour are lacking. Here, we present a database of globally distributed g s obtained in the field for a wide range of plant functional types (PFTs) and biomes. We find that stomatal behaviour differs among PFTs according to their marginal carbon cost of water use, as predicted by the theory underpinning the optimal stomatal model and the leaf and wood economics spectrum. We also demonstrate a global relationship with climate. These findings provide a robust theoretical framework for understanding and predicting the behaviour of g s across biomes and across PFTs that can be applied to regional, continental and global-scale modelling of ecosystem productivity, energy balance and ecohydrological processes in a future changing climate.

Liu, H, Li, W, Shen, D, Zhao, D & Wang, G 2015, 'Graphitic Carbon Conformal Coating of Mesoporous TiO2 Hollow Spheres for High-Performance Lithium Ion Battery Anodes', JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 137, no. 40, pp. 13161-13166.
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Liu, H, Zheng, Y, Wang, G & Qiao, SZ 2015, 'A Three-Component Nanocomposite with Synergistic Reactivity for Oxygen Reduction Reaction in Alkaline Solution', ADVANCED ENERGY MATERIALS, vol. 5, no. 3.
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Liu, L, Chen, Y, Lv, H, Wang, G, Hu, X & Wang, C 2015, 'Construction of a non-enzymatic glucose sensor based on copper nanoparticles/poly(o-phenylenediamine) nanocomposites', Journal of Solid State Electrochemistry, vol. 19, no. 3, pp. 731-738.
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© 2014, Springer-Verlag Berlin Heidelberg. An electrochemical non-enzymatic glucose sensor was fabricated by electrodeposition of copper nanoparticles (CuNPs) onto a poly(o-phenylenediamine) (PoPD) film-modified glassy carbon electrode (CuNPs/PoPD/GCE). We had studied some factors such as the pH value of supporting electrolyte, the amount of PoPD and applied potentials and optimize the experiment conditions. Under the optimum conditions, the as-obtained sensor for glucose sensing had achieved a wide linear range, low detection limit, and fast response time. The current response of the as-obtained sensor towards electrochemical oxidation of glucose was linear with the concentration of glucose in the range of 5.0 μM to 1.6 mM (R = 0.998) in the solution of 0.1 M NaOH at the applied potential of 0.5 V. The detection limit is 0.25 μM and the fast response achieves within 1 s. The sensor exhibits good sensitivity, selectivity, and reproducibility. The proposed non-enzymatic glucose was successfully employed to determine glucose in blood samples.

Liu, L, Lv, H, Teng, Z, Wang, C & Wang, G 2015, 'Glucose Sensors Based on Core@Shell Magnetic Nanomaterials and Their Application in Diabetes Management: A Review', Current Pharmaceutical Design, vol. 21, no. 37, pp. 5359-5368.
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© 2015 Bentham Science Publishers. This review presents a comprehensive attempt to conclude and discuss various glucose biosensors based on core@shell magnetic nanomaterials. Owing to good biocompatibility and stability, the core@shell magnetic nanomaterials have found widespread applications in many fields and draw extensive attention. Most magnetic nanoparticles possess an intrinsic enzyme mimetic activity like natural peroxidases, which invests magnetic nanomaterials with great potential in the construction of glucose sensors. We summarize the synthesis of core@shell magnetic nanomaterials, fundamental theory of glucose sensor and the advances in glucose sensors based on core@shell magnetic nanomaterials. The aim of the review is to provide an overview of the exploitation of the core@shell magnetic nanomaterials for glucose sensors construction.

Liu, L, Xu, D, Hu, Y, Liu, S, Wei, H, Zheng, J, Wang, G, Hu, X & Wang, C 2015, 'Construction of an impedimetric immunosensor for label-free detecting carbofuran residual in agricultural and environmental samples', Food Control, vol. 53, pp. 72-80.
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Liu, M & Darling, A 2015, 'Metagenomic Chromosome Conformation Capture (3C): techniques, applications, and challenges', F1000Research, vol. 4, pp. 1377-1377.
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We review currently available technologies for deconvoluting metagenomic data into individual genomes that represent populations, strains, or genotypes present in the community. An evaluation of chromosome conformation capture (3C) and related techniques in the context of metagenomics is presented, using mock microbial communities as a reference. We provide the first independent reproduction of the metagenomic 3C technique described last year, propose some simple improvements to that protocol, and compare the quality of the data with that provided by the more complex Hi-C protocol.

Liu, M, Lu, J, Mueller, P, Turnbull, L, Burke, CM, Schlothauer, RC, Carter, DA, Whitchurch, CB & Harry, EJ 2015, 'Antibiotic-specific differences in the response of Staphylococcus aureus to treatment with antimicrobiala combined with manuka honey', Frontiers in Microbiology, vol. 5, pp. 1-9.
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Skin infections caused by antibiotic resistant Staphylococcus aureus are a significant health problem worldwide; often associated with high treatment cost and mortality rate. Complex natural products like New Zealand (NZ) manuka honey have been revisited and studied extensively as an alternative to antibiotics due to their potent broad-spectrum antimicrobial activity, and the inability to isolate honey-resistant S. aureus. Previous studies showing synergistic effects between manuka-type honeys and antibiotics have been demonstrated against the growth of one methicillin-resistant S. aureus (MRSA) strain. We have previously demonstrated strong synergistic activity between NZ manuka-type honey and rifampicin against growth and biofilm formation of multiple S. arueus strains. Here, we have expanded our investigation using multiple S. aureus strains and four different antibiotics commonly used to treat S. aureus-related skin infections: rifampicin, oxacillin, gentamicin, and clindamycin. Using checkerboard microdilution and agar diffusion assays with S. aureus strains including clinical isolates and MRSA we demonstrate that manuka-type honey combined with these four antibiotics frequently produces a synergistic effect. In some cases when synergism was not observed, there was a significant enhancement in antibiotic susceptibility. Some strains that were highly resistant to an antibiotic when present alone become sensitive to clinically achievable concentrations when combined with honey. However, not all of the S. aureus strains tested responded in the same way to these combinational treatments. Our findings support the use of NZ manuka-type honeys in clinical treatment against S. aureus-related infections and extend their potential use as an antibiotic adjuvant in combinational therapy. Our data also suggest that manuka-type honeys may not work as antibiotic adjuvants for all strains of S. aureus, and this may help determine the mechanistic processes behind honey synergy.

Liu, T, Yu, Y, Deng, X, Ng, CK, Cao, B, Wang, J, Rice, SA, Kjelleberg, S & Song, H 2015, 'Enhanced Shewanella biofilm promotes bioelectricity generation', Biotechnology and Bioengineering, vol. 112, no. 10, pp. 2051-2059.
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ABSTRACTElectroactive biofilms play essential roles in determining the power output of microbial fuel cells (MFCs). To engineer the electroacitve biofilm formation of Shewanella oneidensis MR‐1, a model exoelectrogen, we herein heterologously overexpressed a c‐di‐GMP biosynthesis gene ydeH in S. oneidensis MR‐1, constructing a mutant strain in which the expression of ydeH is under the control of IPTG‐inducible promoter, and a strain in which ydeH is under the control of a constitutive promoter. Such engineered Shewanella strains had significantly enhanced biofilm formation and bioelectricity generation. The MFCs inoculated with these engineered strains accomplished a maximum power density of 167.6 ± 3.6 mW/m2, which was ∼ 2.8 times of that achieved by the wild‐type MR‐1 (61.0 ± 1.9 mW/m2). In addition, the engineered strains in the bioelectrochemical system at poised potential of 0.2 V vs. saturated calomel electrode (SCE) generated a stable current density of 1100 mA/m2, ∼ 3.4 times of that by wild‐type MR‐1 (320 mA/m2). Biotechnol. Bioeng. 2015;112: 2051–2059. © 2015 Wiley Periodicals, Inc.

Loo, C-Y, Lee, W-H, Young, PM, Cavaliere, R, Whitchurch, CB & Rohanizadeh, R 2015, 'Implications and emerging control strategies for ventilator-associated infections', EXPERT REVIEW OF ANTI-INFECTIVE THERAPY, vol. 13, no. 3, pp. 379-393.
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© 2015 Informa UK, Ltd Ventilator-associated pneumonia (VAP) remains a major burden to the healthcare system and intubated patients in intensive care units. In fact, VAP is responsible for at least 50% of prescribed antibiotics to patients who need mechanical ventilation. One of the factors contributing to VAP pathogenesis is believed to be rapid colonization of biofilm-forming pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus on the surface of inserted endotracheal tubes. These biofilms serve as a protective environment for bacterial colonies and provide enhanced resistance towards many antibiotics. This review presents and discusses an overview of current strategies to inhibit the colonization and formation of biofilm on endotracheal tubes, including antibiotic treatment, surface modification and antimicrobial agent incorporation onto endotracheal tube materials.

Lu, J, Chen, Y, Liu, D, Ren, W, Lu, Y, Shi, Y, Piper, J, Paulsen, I & Jin, D 2015, 'One-Step Protein Conjugation to Upconversion Nanoparticles', Analytical Chemistry, vol. 87, no. 20, pp. 10406-10413.
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The emerging upconversion nanoparticles offer a fascinating library of ultrasensitive luminescent probes for a range of biotechnology applications from biomarker discovery to single molecule tracking, early disease diagnosis, deep tissue imaging, and drug delivery and therapies. The effective bioconjugation of inorganic nanoparticles to the molecule-specific proteins, free of agglomeration, nonspecific binding, or biomolecule deactivation, is crucial for molecular recognition of target molecules or cells. The current available protocols require multiple steps which can lead to low probe stability, specificity, and reproducibility. Here we report a simple and rapid protein bioconjugation method based on a one-step ligand exchange using the DNAs as the linker. Our method benefits from the robust DNA–protein conjugates as well as from multiple ions binding capability. Protein can be preconjugated via an amino group at the 3′ end of a synthetic DNA molecule, so that the 5′ end phosphoric acid group and multiple phosphate oxygen atoms in the phosphodiester bonds are exposed to replace the oleic acid ligands on the surface of upconversion nanoparticles due to their stronger chelating capability to lanthanides. We demonstrated that our method can efficiently pull out the upconversion nanoparticles from organic solvent into an aqueous phase. The upconversion nanoparticles then become hydrophilic, stable, and specific biomolecules recognition. This allows us to successfully functionalize the upconversion nanoparticles with horseradish peroxidise (HRP) for catalytic colorimetric assay and for streptavidin (SA)–biotin immunoassays.

Luo, J, Zhang, J, Barnes, RJ, Tan, X, McDougald, D, Fane, AG, Zhuang, G, Kjelleberg, S, Cohen, Y & Rice, SA 2015, 'The application of nitric oxide to control biofouling of membrane bioreactors', Microbial Biotechnology, vol. 8, no. 3, pp. 549-560.
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SummaryA novel strategy to control membrane bioreactor (MBR) biofouling using the nitric oxide (NO) donor compound PROLI NONOate was examined. When the biofilm was pre‐established on membranes at transmembrane pressure (TMP) of 88–90 kPa, backwashing of the membrane module with 80 μM PROLI NONOate for 45 min once daily for 37 days reduced the fouling resistance (Rf) by 56%. Similarly, a daily, 1 h exposure of the membrane to 80 μM PROLI NONOate from the commencement of MBR operation for 85 days resulted in reduction of the TMP and Rf by 32.3% and 28.2%. The microbial community in the control MBR was observed to change from days 71 to 85, which correlates with the rapid TMP increase. Interestingly, NO‐treated biofilms at 85 days had a higher similarity with the control biofilms at 71 days relative to the control biofilms at 85 days, indicating that the NO treatment delayed the development of biofilm bacterial community. Despite this difference, sequence analysis indica...

Luo, J, Zhang, J, Tan, X, McDougald, D, Zhuang, G, Fane, AG, Kjelleberg, S, Cohen, Y & Rice, SA 2015, 'Characterization of the archaeal community fouling a membrane bioreactor', Journal of Environmental Sciences, vol. 29, pp. 115-123.
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Biofilm formation, one of the primary causes of biofouling, results in reduced membrane flux or increased transmembrane pressure and thus represents a major impediment to the wider implementation of membrane bioreactor (MBR) technologies for water purification. Most studies have focused on the role of bacteria in membrane fouling as they are the most dominant and best studied organisms present in the MBR. In contrast, there is limited information on the role of the archaeal community in biofilm formation in MBRs. This study investigated the composition of the archaeal community during the process of biofouling in an MBR. The archaeal community was observed to have lower richness and diversity in the biofilm than the sludge during the establishment of biofilms at low transmembrane pressure (TMP). Clustering of the communities based on the Bray-Curtis similarity matrix indicated that a subset of the sludge archaeal community formed the initial biofilms. The archaeal community in the biofilm was mainly composed of Thermoprotei, Thermoplasmata, Thermococci, Methanopyri, Methanomicrobia and Halobacteria. Among them, the Thermoprotei and Thermoplasmata were present at higher relative proportions in the biofilms than they were in the sludge. Additionally, the Thermoprotei, Thermoplasmata and Thermococci were the dominant organisms detected in the initial biofilms at low TMP, while as the TMP increased, the Methanopyri, Methanomicrobia, Aciduliprofundum and Halobacteria were present at higher abundances in the biofilms at high TMP.

Luong, S, Kuzhiumparambil, U & Fu, S 2015, 'Elucidation of markers for monitoring morphine and its analogs in urine adulterated with pyridinium chlorochromate', BIOANALYSIS, vol. 7, no. 18, pp. 2283-2295.
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Currently, procedures that identify the drugs 'destroyed' in adulterated urine specimens are very limited. This study aimed to determine the effect of pyridinium chlorochromate (PCC) on routine opiate assays and identify reaction products formed. Results/methodology: Opiate-positive urines adulterated with PCC (20 and 100 mM) were analyzed using CEDIA(®) immunoassay and GC-MS. Urine and water samples spiked with 6-monoacetylmorphine, morphine and its glucuronides (10 µg/ml) and PCC (0.02-100 mM) were monitored with LC-MS, and the products characterized.PCC significantly decreased the abundance of morphine, codeine and IS. Adulterated water and urine samples containing 6-monoacetylmorphine, morphine and morphine-3-glucuronide yielded morphinone-3-glucuronide, 7,14-dihydroxy-6-monoacetylmorphine, 7,8-diketo-6-monoacetylmorphine and 7,8-diketo-morphine (tentative assignment). Reaction pathways may be different in the two matrices.

Lutz, A, Raina, J-B, Motti, CA, Miller, DJ & van Oppen, MJH 2015, 'Host Coenzyme Q Redox State Is an Early Biomarker of Thermal Stress in the Coral Acropora millepora', PLOS ONE, vol. 10, no. 10, pp. e0139290-e0139290.
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Bleaching episodes caused by increasing seawater temperatures may induce mass coral mortality and are regarded as one of the biggest threats to coral reef ecosystems worldwide. The current consensus is that this phenomenon results from enhanced production of harmful reactive oxygen species (ROS) that disrupt the symbiosis between corals and their endosymbiotic dinoflagellates, Symbiodinium. Here, the responses of two important antioxidant defence components, the host coenzyme Q (CoQ) and symbiont plastoquinone (PQ) pools, are investigated for the first time in colonies of the scleractinian coral, Acropora millepora, during experimentally-induced bleaching under ecologically relevant conditions. Liquid chromatography-mass spectrometry (LC-MS) was used to quantify the states of these two pools, together with physiological parameters assessing the general state of the symbiosis (including photosystem II photochemical efficiency, chlorophyll concentration and Symbiodinium cell densities). The results show that the responses of the two antioxidant systems occur on different timescales: (i) the redox state of the Symbiodinium PQ pool remained stable until twelve days into the experiment, after which there was an abrupt oxidative shift; (ii) by contrast, an oxidative shift of approximately 10% had occurred in the host CoQ pool after 6 days of thermal stress, prior to significant changes in any other physiological parameter measured. Host CoQ pool oxidation is thus an early biomarker of thermal stress in corals, and this antioxidant pool is likely to play a key role in quenching thermally-induced ROS in the coral-algal symbiosis. This study adds to a growing body of work that indicates host cellular responses may precede the bleaching process and symbiont dysfunction.

Lutz, C, Martin Tay, QX, Sun, S & McDougald, D 2015, 'Draft Genome Sequence of Shewanella sp. Strain CP20', Genome Announcements, vol. 3, no. 2.
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ABSTRACT Shewanella sp. CP20 is a marine bacterium that survives ingestion by Tetrahymena pyriformis and is expelled from the protozoan within membrane-bound vacuoles, where the bacterial cells show long-term survival. Here, we report the draft genome sequence of Shewanella sp. CP20 and discuss the potential mechanisms facilitating intraprotozoan survival.

Ly, D & Oliver, B 2015, 'Do We Really Need to Keep Redesigning &#946;₂-agonists for the Management of Asthma?', Current Drug Delivery, vol. 12, no. 1, pp. 9-15.
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© 2015 Bentham Science Publishers. There is an enormous drive to refine therapeutic designs and delivery systems, but in this review we ask if this is always the right direction? We choose to play devil's advocate, and argue that refining drug design is not always needed, and what is actually needed is a greater understanding of the biology of the disease. Here we focus on asthma and the β2-agonist group of bronchodilators as an example of how a class of therapeutic has been developed and continues to be developmentally refined. In this review, we define viralinduced exacerbations as the greatest cause of lung attacks and the most crucial time β2-agonist therapy is needed. We explore the reasons why β2-agonist therapy fails in patients with rhinovirus-induced exacerbations, and explain why further “engineered” β2-agonist therapies are likely to continue to fail in this subset of asthmatic population. We justify our perspective by returning to the biology that underlies the cause of disease and highlight the need for “more research” into alternative therapies for this population of asthmatic patients.

Ma, X, Huete, A, Moran, S, Ponce-Campos, G & Eamus, D 2015, 'Abrupt shifts in phenology and vegetation productivity under climate extremes', JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, vol. 120, no. 10, pp. 2036-2052.
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©2015. American Geophysical Union. All Rights Reserved. Amplification of the hydrologic cycle as a consequence of global warming is predicted to increase climate variability and the frequency and severity of droughts. Recent large-scale drought and flooding over numerous continents provide unique opportunities to understand ecosystem responses to climatic extremes. In this study, we investigated the impacts of the early 21st century extreme hydroclimatic variations in southeastern Australia on phenology and vegetation productivity using Moderate Resolution Imaging Spectroradiometer Enhanced Vegetation Index and Standardized Precipitation-Evapotranspiration Index. Results revealed dramatic impacts of drought and wet extremes on vegetation dynamics, with abrupt between year changes in phenology. Drought resulted in widespread reductions or collapse in the normal patterns of seasonality such that in many cases there was no detectable phenological cycle during drought years. Across the full range of biomes examined, we found semiarid ecosystems to exhibit the largest sensitivity to hydroclimatic variations, exceeding that of arid and humid ecosystems. This result demonstrated the vulnerability of semiarid ecosystems to climatic extremes and potential loss of ecosystem resilience with future mega-drought events. A skewed distribution of hydroclimatic sensitivity with aridity is of global biogeochemical significance because it suggests that current drying trends in semiarid regions will reduce hydroclimatic sensitivity and suppress the large carbon sink that has been reported during recent wet periods (e.g., 2011 La Niña).

Macha, IJ, Cazalbou, S, Ben-Nissan, B, Harvey, KL & Milthorpe, B 2015, 'Marine Structure Derived Calcium Phosphate-Polymer Biocomposites for Local Antibiotic Delivery', MARINE DRUGS, vol. 13, no. 1, pp. 666-680.
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© 2015 by the authors. Hydrothermally converted coralline hydroxyapatite (HAp) particles loaded with medically active substances were used to develop polylactic acid (PLA) thin film composites for slow drug delivery systems. The effects of HAp particles within PLA matrix on the gentamicin (GM) release and release kinetics were studied. The gentamicin release kinetics seemed to follow Power law Korsmeyer Peppas model with mainly diffusional process with a number of different drug transport mechanisms. Statistical analysis shows very significant difference on the release of gentamicin between GM containing PLA (PLAGM) and GM containing HAp microspheres within PLA matrix (PLAHApGM) devices, which PLAHApGM displays lower release rates. The use of HAp particles improved drug stabilization and higher drug encapsulation efficiency of the carrier. HAp is also the source of Ca2+ for the regeneration and repair of diseased bone tissue. The release profiles, exhibited a steady state release rate with significant antimicrobial activity against Staphylococcus aureus (S. aureus) (SH1000) even at high concentration of bacteria. The devices also indicated significant ability to control the growth of bacterial even after four weeks of drug release. Clinical release profiles can be easily tuned from drug-HAp physicochemical interactions and degradation kinetics of polymer matrix. The developed systems could be applied to prevent microbial adhesion to medical implant surfaces and to treat infections mainly caused by S. aureus in surgery.

Macha, IJ, Ozyegin, LS, Oktar, FN & Ben-Nissan, B 2015, 'Conversion of Ostrich Eggshells (Struthio camelus) to Calcium Phosphates', Journal of the Australian Ceramic Society, vol. 51, no. 1, pp. 125-133.
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© Copyright 2015, The Australian Ceramic Society. The exceptional progress made in orthopaedic and dental applications have increased the demand of calcium phosphate bioceramics due to their chemical similarities to the inorganic component of hard tissues. Low cost production of calcium phosphate bioceramics could be achieved by using pure natural biogenic materials by relatively simple methods. In this study calcium phosphate powders were produced from ostrich (Struthio camelus) eggshell powder at a moderate temperature of 80°C by relatively simple process of low temperature heating by hot plate (HP) and hot platting while agitation with ultrasonication (HPUS) hence introducing mechanical activation. The product structure and compositions were studied with FTIR, SEM, DTA/TCA, XRD and ICP techniques. The results showed that calcium deficient hydroxyapatite and dicalcium phosphate were obtained from HP and HPUS methods. Poorly crystalline calcium deficient hydroxyapatite was converted into whilockite after calcining at 800°C. The results suggest that this low cost and relatively simple method is efficient to easily produce calcium phosphate powders from adequately feed controlled farms to obtain pure uncontaminated eggshells for a range of biomedical applications.

Macreadie, PI, Trevathan-Tackett, SM, Skilbeck, CG, Sanderman, J, Curlevski, N, Jacobsen, G & Seymour, JR 2015, 'Losses and recovery of organic carbon from a seagrass ecosystem following disturbance', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 282, no. 1817.
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Maddahfar, M, Ramezani, M, Sadeghi, M & Sobhani-Nasab, A 2015, 'NiAl2O4 nanoparticles: synthesis and characterization through modify sol–gel method and its photocatalyst application', Journal of Materials Science: Materials in Electronics, vol. 26, no. 10, pp. 7745-7750.
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Mahmood, A, Xia, W, Mahmood, N, Wang, Q & Zou, R 2015, 'Hierarchical Heteroaggregation of Binary Metal-Organic Gels with Tunable Porosity and Mixed Valence Metal Sites for Removal of Dyes in Water', Scientific Reports, vol. 5, no. 1.
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AbstractHierarchical heteronuclear metal-organic gels (MOGs) based on iron (Fe) and aluminium (Al) metal-organic framework (MOF) backbones bridged by tri-carboxylate ligands have firstly been synthesized by simple solvothermal method. Monometallic MOGs based on Fe or Al give homogenous monoliths, which have been tuned by introduction of heterogeneity in the system (mismatched growth). The developed gels demonstrate that surface areas, pore volumes and pore sizes can be readily tuned by optimizing heterogeneity. The work also elaborates effect of heterogeneity on size of MOG particles which increase substantially with increasing heterogeneity as well as obtaining mixed valence sites in the gels. High surface areas (1861 m2/g) and pore volumes (9.737 cc/g) were obtained for heterogeneous gels (0.5Fe-0.5Al). The large uptakes of dye molecules (290 mg/g rhodamine B and 265 mg/g methyl orange) with fast sorption kinetics in both neutral and acidic mediums show good stability and accessibility of MOG channels (micro and meso-/macropores), further demonstrating their potential applications in catalysis and sorption of large molecules.

Mahmood, N, Tahir, M, Mahmood, A, Yang, W, Gu, X, Cao, C, Zhang, Y & Hou, Y 2015, 'Role of anions on structure and pseudocapacitive performance of metal double hydroxides decorated with nitrogen-doped graphene', Science China Materials, vol. 58, no. 2, pp. 114-125.
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Mahmood, N, Tahir, M, Mahmood, A, Zhu, J, Cao, C & Hou, Y 2015, 'Chlorine-doped carbonated cobalt hydroxide for supercapacitors with enormously high pseudocapacitive performance and energy density', Nano Energy, vol. 11, pp. 267-276.
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Mai-Prochnow, A, Hui, JGK, Kjelleberg, S, Rakonjac, J, McDougald, D & Rice, SA 2015, '‘Big things in small packages: the genetics of filamentous phage and effects on fitness of their host’', FEMS Microbiology Reviews, vol. 39, no. 4, pp. 465-487.
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© FEMS 2015. This review synthesizes recent and past observations on filamentous phages and describes how these phages contribute to host phentoypes. For example, the CTXφ phage of Vibrio cholerae encodes the cholera toxin genes, responsible for causing the epidemic disease, cholera. The CTXφ phage can transduce non-toxigenic strains, converting them into toxigenic strains, contributing to the emergence of new pathogenic strains. Other effects of filamentous phage include horizontal gene transfer, biofilm development, motility, metal resistance and the formation of host morphotypic variants, important for the biofilm stress resistance. These phages infect a wide range of Gram-negative bacteria, including deep-sea, pressure-adapted bacteria. Many filamentous phages integrate into the host genome as prophage. In some cases, filamentous phages encode their own integrase genes to facilitate this process, while others rely on host-encoded genes. These differences are mediated by different sets of 'core' and 'accessory' genes, with the latter group accounting for some of the mechanisms that alter the host behaviours in unique ways. It is increasingly clear that despite their relatively small genomes, these phages exert signficant influence on their hosts and ultimately alter the fitness and other behaviours of their hosts.

Malik, A, Lenzen, M, Ralph, PJ & Tamburic, B 2015, 'Hybrid life-cycle assessment of algal biofuel production', BIORESOURCE TECHNOLOGY, vol. 184, pp. 436-443.
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© 2014 Elsevier Ltd. The objective of this work is to establish whether algal bio-crude production is environmentally, economically and socially sustainable. To this end, an economic multi-regional input-output model of Australia was complemented with engineering process data on algal bio-crude production. This model was used to undertake hybrid life-cycle assessment for measuring the direct, as well as indirect impacts of producing bio-crude. Overall, the supply chain of bio-crude is more sustainable than that of conventional crude oil. The results indicate that producing 1. million tonnes of bio-crude will generate almost 13,000 new jobs and 4. billion dollars' worth of economic stimulus. Furthermore, bio-crude production will offer carbon sequestration opportunities as the production process is net carbon-negative.

Maniam, S, Cox, RP, Langford, SJ & Bell, TDM 2015, 'Unexpected Photoluminescence of Fluorinated Naphthalene Diimides', Chemistry – A European Journal, vol. 21, no. 10, pp. 4133-4140.
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AbstractTwo new amino core‐substituted naphthalene diimides (cNDIs) bearing fluorinated side chains have been synthesised. Steady‐state and time‐resolved fluorescence spectroscopy reveals unprecedented optical properties for the cNDIs with high quantum yields of ∼0.8 and fluorescence lifetimes of ∼13 ns in a range of solvents. These properties are apparent at the level of single molecules, where the compounds also show exceptional photostability under pulsed‐laser excitation. Photon emission is remarkably consistent with very few long timescale (millisecond or longer) interruptions with molecules regularly undergoing >107 cycles of excitation and emission. Intermittencies owing to triplet‐state formation occur on a sub‐millisecond timescale with a low yield of 1–2 %, indicating that the presence of the fluorine atoms does not lead to a significant triplet yield through the heavy‐atom effect. These properties make the compounds excellent candidates for single‐molecule labelling applications.

Marsh, DJ 2015, 'Networks regulating ubiquitin and ubiquitin-like proteins promise new therapeutic targets', Endocrine-Related Cancer, vol. 22, no. 1, pp. E1-E3.
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Marsh, DJ, Foster, K & Scott, CD 2015, 'Match that PhD', Nature, vol. 523, no. 7559, pp. 247-247.
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Marsh, JW, Wee, BA, Tyndall, JDA, Lott, WB, Bastidas, RJ, Caldwell, HD, Valdivia, RH, Kari, L & Huston, WM 2015, 'A Chlamydia trachomatis strain with a chemically generated amino acid substitution (P370L) in the cthtrA gene shows reduced elementary body production', BMC Microbiology, vol. 15, no. 1, pp. 1-13.
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Martens, IBG, Cardoso, BR, Hare, DJ, Niedzwiecki, MM, Lajolo, FM, Martens, A & Cozzolino, SMF 2015, 'Selenium status in preschool children receiving a Brazil nut–enriched diet', Nutrition, vol. 31, no. 11-12, pp. 1339-1343.
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© 2015 Elsevier Inc. Objective: The Brazilian Amazon region has selenium (Se)-rich soil, which is associated with higher Se levels in populations fed locally grown produce. Brazil nuts are a major source of dietary Se and are included with meals offered to children enrolled in public preschool in Macapá. The aim of this study was to examine Se intake and status of these children. Methods: The Macapá group consisted of 41 children from a public preschool who received 15 to 30 g of Brazil nuts 3 d/wk. The control group included 88 children from the nearby city of Belém who did not receive Brazil nut-enriched meals. In both groups, school meals comprised ≥90% of the children's total food consumption. Selenium was assessed using hydride generation quartz tube atomic absorption spectroscopy in plasma, erythrocytes, nails, hair and urine. Dietary intakes (macronutrients and Se) were evaluated using the duplicate-portion method. Results: Both groups received inadequate intakes of energy and macronutrients. Selenium intake was excessive in both groups (155.30 and 44.40 μg/d, in Macapá and Belém, respectively). Intake was potentially toxic in Macapá on days when Brazil nuts were added to meals. Although biomarkers of Se exposure exceeded reference levels in the Macapá group, no clinical symptoms of Se overload (selenosis) were observed. Conclusions: The inclusion of Brazil nuts in school meals provided to children with already high dietary Se intakes increased Se levels and may result in an increased risk for toxicity. As selenosis is associated with some chronic diseases, we recommend continued monitoring of Se intake and status in this population.

Martí, I, Burguete, MI, Gale, PA & Luis, SV 2015, 'Acyclic Pseudopeptidic Hosts as Molecular Receptors and Transporters for Anions', European Journal of Organic Chemistry, vol. 2015, no. 23, pp. 5150-5158.
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AbstractThe synthesis and characterization of different pseudopeptidic hosts derived from open chain systems with C2 and C3 symmetry has been achieved. These receptors are based on structures containing phenylalanine amino acid residues and amine, amide, urea and thiourea groups as the structural elements providing their capability to interact with anions. The transport of chloride and organic anions of biological relevance (L‐lactate, L‐maleate and L‐aspartate) through lipid bilayer membranes has been studied for these receptors. The chloride‐binding properties of the selected hosts have been studied in solution by NMR titrations. In addition, in order to rationalize the results, lipophilicity studies have been carried out. It has been observed that transport activity is affected by the nature of the aliphatic central spacer and the side chains, the most active receptors being 9b, derived from a tripodal precursor with the shortest aliphatic side chain and 3c, derived from a bis(amino amide) but having the longest spacer. These hosts are more selective for the anion chloride than for the studied organic anions.

Martin, AA, Bahm, A, Bishop, J, Aharonovich, I & Toth, M 2015, 'Dynamic Pattern Formation in Electron-Beam-Induced Etching', Physical Review Letters, vol. 115, no. 25.
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© 2015 American Physical Society. We report highly ordered topographic patterns that form on the surface of diamond, span multiple length scales, and have a symmetry controlled by the precursor gas species used in electron-beam-induced etching (EBIE). The pattern formation dynamics reveals an etch rate anisotropy and an electron energy transfer pathway that is overlooked by existing EBIE models. We, therefore, modify established theory such that it explains our results and remains universally applicable to EBIE. The patterns can be exploited in controlled wetting, optical structuring, and other emerging applications that require nano- and microscale surface texturing of a wide band-gap material.

Martin, AA, McCredie, G & Toth, M 2015, 'Electron beam induced etching of carbon', Applied Physics Letters, vol. 107, no. 4, pp. 041603-041603.
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Nanopatterning of graphene and diamond by low energy (≤30 keV) electrons has previously been attributed to mechanisms that include atomic displacements caused by knock-on, electron beam heating, sputtering by ionized gas molecules, and chemical etching driven by a number of gases that include N2. Here, we show that a number of these mechanisms are insignificant, and the nanopatterning process can instead be explained by etching caused by electron induced dissociation of residual H2O molecules. Our results have significant practical implications for gas-mediated electron beam nanopatterning techniques and help elucidate the underlying mechanisms.

Martin, AA, Randolph, S, Botman, A, Toth, M & Aharonovich, I 2015, 'Maskless milling of diamond by a focused oxygen ion beam', SCIENTIFIC REPORTS, vol. 5.
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Recent advances in focused ion beam technology have enabled high-resolution, maskless nanofabrication using light ions. Studies with light ions to date have, however, focused on milling of materials where sub-surface ion beam damage does not inhibit device performance. Here we report on maskless milling of single crystal diamond using a focused beam of oxygen ions. Material quality is assessed by Raman and luminescence analysis, and reveals that the damage layer generated by oxygen ions can be removed by non-intrusive post-processing methods such as localised electron beam induced chemical etching.

Marzagalli, R, Scuderi, S, Drago, F, Waschek, JA & Castorina, A 2015, 'Emerging Role of PACAP as a New Potential Therapeutic Target in Major Diabetes Complications', International Journal of Endocrinology, vol. 2015, pp. 1-11.
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Enduring diabetes increases the probability of developing secondary damage to numerous systems, and these complications represent a cause of morbidity and mortality. Establishing the causes of diabetes remains the key step to eradicate the disease, but prevention as well as finding therapies to ameliorate some of the major diabetic complications is an equally important step to increase life expectancy and quality for the millions of individuals already affected by the disease or who are likely to develop it before cures become routinely available. In this review, we will firstly summarize some of the major complications of diabetes, including endothelial and pancreatic islets dysfunction, retinopathy, and nephropathy, and then discuss the emerging roles exerted by the neuropeptide pituitary adenylate cyclase activating polypeptide (PACAP) to counteract these ranges of pathologies that are precipitated by the prolonged hyperglycemic state. Finally, we will describe the main signalling routes activated by the peptide and propose possible future directions to focus on developing more effective peptide-based therapies to treat the major complications associated with longstanding diabetes.

Mateer, SW, Maltby, S, Marks, E, Foster, PS, Horvat, JC, Hansbro, PM & Keely, S 2015, 'Potential mechanisms regulating pulmonary pathology in inflammatory bowel disease', Journal of Leukocyte Biology, vol. 98, no. 5, pp. 727-737.
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AbstractInflammatory bowel disease is associated with a number of comorbidities that arise at extraintestinal sites, including the lung. Pulmonary manifestations reported in inflammatory bowel disease include bronchiectasis, chronic bronchitis and importantly, a range of subclinical respiratory abnormalities that are often overlooked in routine clinical evaluation. Whereas evidence for the pulmonary manifestations of Inflammatory bowel disease is increasing, little is known about the immunologic and physiologic mechanisms regulating cross-talk between the gut and lung during disease. This review examines reported lung involvement in Inflammatory bowel disease and discusses the possible immune pathways that underlie pulmonary pathologies. These mechanisms include dysfunctional immune-cell homing, systemic inflammation, and microbial dysbiosis; all of which may contribute to Inflammatory bowel disease-induced pulmonary inflammation. These mechanisms are discussed in the context of our current knowledge of the shared mucosal immune system and the immunology of Inflammatory bowel disease.

Matthews, JL, Sproles, AE, Oakley, CA, Grossman, AR, Weis, VM & Davy, SK 2015, 'Menthol-induced bleaching rapidly and effectively provides experimental aposymbiotic sea anemones (Aiptasiasp.) for symbiosis investigations', Journal of Experimental Biology, vol. 219, no. Pt 3, pp. 306-310.
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Experimental manipulation of the symbiosis between cnidarians and photosynthetic dinoflagellates (Symbiodinium spp.) is critical to advance understanding of the cellular mechanisms involved in host–symbiont interactions, and overall coral reef ecology. The anemone Aiptasia sp. is a model for the cnidarian-dinoflagellate symbiosis, and notably it can be rendered aposymbiotic (i.e. dinoflagellate-free) and re-infected with a range of Symbiodinium types. Various methods exist for generating aposymbiotic hosts, however they can be hugely time-consuming and not wholly effective. Here, we optimise a method using menthol for production of aposymbiotic Aiptasia. The menthol treatment produced aposymbiotic hosts within just four weeks (97–100% symbiont loss), which was maintained long after treatment when anemones were held under a standard light/dark cycle. The ability of Aiptasia to form a stable symbiosis appeared unaffected by menthol exposure, as demonstrated by successful symbiosis re-establishment when experimentally re-infected. Furthermore, there was no significant impact on photosynthetic or respiratory performance of re-infected anemones.

Mayer-Pinto, M, Johnston, EL, Hutchings, PA, Marzinelli, EM, Ahyong, ST, Birch, G, Booth, DJ, Creese, RG, Doblin, MA, Figueira, W, Gribben, PE, Pritchard, T, Roughan, M, Steinberg, PD & Hedge, LH 2015, 'Sydney Harbour: a review of anthropogenic impacts on the biodiversity and ecosystem function of one of the world's largest natural harbours', MARINE AND FRESHWATER RESEARCH, vol. 66, no. 12, pp. 1088-1105.
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© 2015 CSIRO. Sydney Harbour is a hotspot for diversity. However, as with estuaries worldwide, its diversity and functioning faces increasing threats from urbanisation. This is the first synthesis of threats and impacts in Sydney Harbour. In total 200 studies were reviewed: 109 focussed on contamination, 58 on habitat modification, 11 addressed non-indigenous species (NIS) and eight investigated fisheries. Metal concentrations in sediments and seaweeds are among the highest recorded worldwide and organic contamination can also be high. Contamination is associated with increased abundances of opportunistic species, and changes in benthic community structure. The Harbour is also heavily invaded, but invaders' ecological and economic impacts are poorly quantified. Communities within Sydney Harbour are significantly affected by extensive physical modification, with artificial structures supporting more NIS and lower diversity than their natural equivalents. We know little about the effects of fishing on the Harbour's ecology, and although ocean warming along Sydney is among the fastest in the world, we know little about how the ecosystem will respond to warming. The interactive and cumulative effects of stressors on ecosystem functioning and services in the Harbour are largely unknown. Sustainable management of this iconic natural system requires that knowledge gaps are addressed and translated into coherent environmental plans.

McCauley, JI, Meyer, BJ, Winberg, PC, Ranson, M & Skropeta, D 2015, 'Selecting Australian marine macroalgae based on the fatty acid composition and anti-inflammatory activity', Journal of Applied Phycology, vol. 27, no. 5, pp. 2111-2121.
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McClements, L, Annett, S, Yakkundi, A & Robson, T 2015, 'The Role of Peptidyl Prolyl Isomerases in Aging and Vascular Diseases', Current Molecular Pharmacology, vol. 9, no. 2, pp. 165-179.
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McGrath, KCY, Li, X-H, McRobb, LS & Heather, AK 2015, 'Inhibitory Effect of a French Maritime Pine Bark Extract-Based Nutritional Supplement on TNF-α-Induced Inflammation and Oxidative Stress in Human Coronary Artery Endothelial Cells', Evidence-Based Complementary and Alternative Medicine, vol. 2015, pp. 1-7.
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Oxidative stress and inflammation, leading to endothelial dysfunction, contribute to the pathogenesis of atherosclerosis. The popularity of natural product supplements has increased in recent years, especially those with purported anti-inflammatory and/or antioxidant effects. The efficacy and mechanism of many of these products are not yet well understood. In this study, we tested the antioxidant and anti-inflammatory effects of a supplement, HIPER Health Supplement (HIPER), on cytokine-induced inflammation and oxidative stress in human coronary artery endothelial cells (HCAECs). HIPER is a mixture of French maritime pine bark extract (PBE), honey, aloe vera, and papaya extract. Treatment for 24 hours with HIPER reduced TNF-α-induced reactive oxygen species (ROS) generation that was associated with decreased NADPH oxidase 4 and increased superoxide dismutase-1 expression. HIPER inhibited TNF-αinduced monocyte adhesion to HCAECs that was in keeping with decreased expression of vascular cell adhesion molecule-1 and intercellular cell adhesion molecule-1 and decreased nuclear factor-kappa B (NF-κB) activation. Further investigation of mechanism showed HIPER reduced TNF-αinduced IκBαand p38 and MEK1/2 MAP kinases phosphorylation. Our findings show that HIPER has potent inhibitory effects on HCAECs inflammatory and oxidative stress responses that may protect against endothelial dysfunction that underlies early atherosclerotic lesion formation.

McIntosh, L, Whitelaw, C, Rekas, A, Holt, SA & van der Walle, CF 2015, 'Interrogating protonated/deuterated fibronectin fragment layers adsorbed to titania by neutron reflectivity and their concomitant control over cell adhesion', Journal of The Royal Society Interface, vol. 12, no. 107, pp. 20150164-20150164.
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The fibronectin fragment, 9th–10th-type III domains (FIII9–10), mediates cell attachment and spreading and is commonly investigated as a bioadhesive interface for implant materials such as titania (TiO 2 ). How the extent of the cell attachment–spreading response is related to the nature of the adsorbed protein layer is largely unknown. Here, the layer thickness and surface fraction of two FIII9–10 mutants (both protonated and deuterated) adsorbed to TiO 2 were determined over concentrations used in cell adhesion assays. Unexpectedly, the isotopic forms had different adsorption behaviours. At solution concentrations of 10 mg l −1 , the surface fraction of the less conformationally stable mutant (FIII9′10) was 42% for the deuterated form and 19% for the protonated form (fitted to the same monolayer thickness). Similarly, the surface fraction of the more stable mutant (FIII9′10–H2P) was 34% and 18% for the deuterated and protonated forms, respectively. All proteins showed a transition from monolayer to bilayer between 30 and 100 mg l −1 , with the protein longitudinal orientation moving away from the plane of the TiO 2 surface at high concentrations. Baby hamster kidney cells adherent to TiO 2 surfaces coated with the proteins (100 mg l −1 ) showed a strong spreading response, irrespective of protein conformational stability. After surface washing, FIII9′10 and FIII9′10–H2P bilayer surface fractions were 30/25% and 42/39% for the lower/upper layers, respectively, implying that the cell spreading response requires only a partial protein surface fraction. Thus, we can use neutron reflectivity to inform the coating process for g...

McKemmish, LK, McKenzie, RH, Hush, NS & Reimers, JR 2015, 'Electron–vibration entanglement in the Born–Oppenheimer description of chemical reactions and spectroscopy', Physical Chemistry Chemical Physics, vol. 17, no. 38, pp. 24666-24682.
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Entanglement in the diabatic basis produces useful quantum information whilst that in the adiabatic basis tells how good is the Born–Oppenheimer approximation.

McNevin, D, Edson, J, Robertson, J & Austin, JJ 2015, 'Reduced reaction volumes and increased Taq DNA polymerase concentration improve STR profiling outcomes from a real-world low template DNA source: telogen hairs', Forensic Science, Medicine, and Pathology, vol. 11, no. 3, pp. 326-338.
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PURPOSE: The primary method for analysis of low template DNA (LTDNA) is known as the low copy number (LCN) method involving an increased number of PCR cycles (typically 34). In common with other LTDNA methods, LCN profiles are characterized by allelic imbalance, drop in, and drop out that require complicated interpretation rules. They often require replicate PCR reactions to generate a 'consensus' profile in a specialized facility. An ideal method for analysis of LTDNA should enhance profiling outcomes without elevated error rates and be performed using standard facilities, with minimum additional cost. METHODS: In this study, we present a comparison of four method variations for the amplification of STRs from LTDNA with a widely used, commercially available kit (AmpFℓSTR(®) Profiler Plus(®)): the standard method, the standard method with a post-PCR clean up, the LCN method, and a reduced reaction volume with increased Taq DNA polymerase concentration. RESULTS: Using telogen hairs-a common source of LTDNA-and matched reference DNA, the LCN method produced the highest number of concordant and non-concordant (i.e., dropped-in) alleles. In comparison, the reduced reaction volume with increased Taq polymerase yielded more full and concordant DNA profiles (all alleles combined) and less off-ladder alleles from a broad range of input DNA. In addition, this method resulted in less non-concordant alleles than LCN and no more than for standard PCR, which suggests that it may be preferred over increased PCR cycles for LTDNA analysis, either with or without consensus profiling and statistical modelling. CONCLUSIONS: Overall, this study highlights the importance and benefit of optimizing PCR conditions and developing improved laboratory methods to amplify and analyze LTDNA.

McPhee, JJ, Freewater, P, Gladstone, W, Platell, ME & Schreider, MJ 2015, 'Glassfish switch feeding from thalassinid larvae to crab zoeae after tidal inundation of saltmarsh', MARINE AND FRESHWATER RESEARCH, vol. 66, no. 11, pp. 1037-1044.
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Meakin, GE, Butcher, EV, van Oorschot, RAH & Morgan, RM 2015, 'The deposition and persistence of indirectly-transferred DNA on regularly-used knives', Forensic Science International: Genetics Supplement Series, vol. 5, pp. e498-e500.
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© 2015 Elsevier Ireland Ltd Considerations concerning how DNA recovered from a crime scene was deposited are of increasing significance to forensic casework. While the possibility of indirect DNA transfer is well established, research into such transfer is limited and focused mainly on the handling of DNA-free items. This study investigated whether secondarily-transferred DNA can be detected on regularly-used items, and if so, for how long might it persist. Volunteers each used a set of knives regularly over a period of two days, after which, each of these ‘regular users’ shook hands with another person (‘handshaker’) and then immediately, without touching anything else, repeatedly stabbed one of their own regularly-used knives into foam for 60 s. DNA was recovered from the knife handles using mini-tapes approximately one hour, one day, and one week after the stabbings. In three of the four pairings of volunteers, complete and partial DNA profiles matching those of the regular user and handshaker respectively, at ratios of ∼10:1, were recovered from the knives within one hour. Alleles attributed to the handshaker were still detected after one week, but were significantly reduced in number and peak height for two of the three pairings. Unknown alleles were also recovered from the knives, suggesting other indirect DNA transfer events. These included repeated detection of alleles attributed to the DNA profile of a volunteer's partner. For the fourth pairing, only complete single-source DNA profiles matching the regular user's profile were recovered. This study demonstrates that, on regularly-used items, secondarily-transferred DNA can be detected and can persist for at least a week; this has implications for forensic reconstructions.

Melzer, M, Karnaushenko, D, Lin, G, Baunack, S, Makarov, D & Schmidt, OG 2015, 'Direct Transfer of Magnetic Sensor Devices to Elastomeric Supports for Stretchable Electronics', Advanced Materials, vol. 27, no. 8, pp. 1333-1338.
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Melzer, M, Karnaushenko, D, Lin, G, Baunack, S, Makarov, D & Schmidt, OG 2015, 'Stretchable Electronics: Direct Transfer of Magnetic Sensor Devices to Elastomeric Supports for Stretchable Electronics (Adv. Mater. 8/2015)', Advanced Materials, vol. 27, no. 8, pp. 1306-1306.
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Menictas, M & Wand, MP 2015, 'Variational Inference for Heteroscedastic Semiparametric Regression', Australian & New Zealand Journal of Statistics, vol. 57, no. 1, pp. 119-138.
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SummaryWe develop fast mean field variational methodology for Bayesian heteroscedastic semiparametric regression, in which both the mean and variance are smooth, but otherwise arbitrary, functions of the predictors. Our resulting algorithms are purely algebraic, devoid of numerical integration and Monte Carlo sampling. The locality property of mean field variational Bayes implies that the methodology also applies to larger models possessing variance function components. Simulation studies indicate good to excellent accuracy, and considerable time savings compared with Markov chain Monte Carlo. We also provide some illustrations from applications.

Menon, S, Timms, P, Allan, JA, Alexander, K, Rombauts, L, Horner, P, Keltz, M, Hocking, J & Huston, WM 2015, 'Human and Pathogen Factors Associated with Chlamydia trachomatis-Related Infertility in Women', CLINICAL MICROBIOLOGY REVIEWS, vol. 28, no. 4, pp. 969-985.
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Merklein, M, Kabakova, IV, Büttner, TFS, Choi, D-Y, Luther-Davies, B, Madden, SJ & Eggleton, BJ 2015, 'Enhancing and inhibiting stimulated Brillouin scattering in photonic integrated circuits', Nature Communications, vol. 6, no. 1.
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AbstractOn-chip nonlinear optics is a thriving research field, which creates transformative opportunities for manipulating classical or quantum signals in small-footprint integrated devices. Since the length scales are short, nonlinear interactions need to be enhanced by exploiting materials with large nonlinearity in combination with high-Q resonators or slow-light structures. This, however, often results in simultaneous enhancement of competing nonlinear processes, which limit the efficiency and can cause signal distortion. Here, we exploit the frequency dependence of the optical density-of-states near the edge of a photonic bandgap to selectively enhance or inhibit nonlinear interactions on a chip. We demonstrate this concept for one of the strongest nonlinear effects, stimulated Brillouin scattering using a narrow-band one-dimensional photonic bandgap structure: a Bragg grating. The stimulated Brillouin scattering enhancement enables the generation of a 15-line Brillouin frequency comb. In the inhibition case, we achieve stimulated Brillouin scattering free operation at a power level twice the threshold.

Messer, LF, Doubell, M, Jeffries, TC, Brown, MV & Seymour, JR 2015, 'Prokaryotic and diazotrophic population dynamics within a large oligotrophic inverse estuary', Aquatic Microbial Ecology, vol. 74, no. 1, pp. 1-15.
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Moheimani, F, Roth, H, Cross, J, Reid, A, Shaheen, F, Warner, S, Hackett, T, Hirota, J, Utokaparch, S, Kicic, A, Hansbro, P, Hallstrand, T, Kahn, M, Stick, S & Knight, D 2015, 'SUPPRESSION OF beta-CATENIN/CBP SIGNALING INHIBITS EPITHELIAL-MESENCHYMAL TRANSITION AND MIGRATION OF HUMAN AIRWAY EPITHELIUM', RESPIROLOGY, vol. 20, pp. 97-97.

Moheimani, F, Roth, HM, Cross, J, Reid, AT, Shaheen, F, Warner, SM, Hirota, JA, Kicic, A, Hallstrand, TS, Kahn, M, Stick, SM, Hansbro, PM, Hackett, T-L & Knight, DA 2015, 'Disruption of beta-catenin/CBP signaling inhibits human airway epithelial-mesenchymal transition and repair', INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, vol. 68, pp. 59-69.
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The epithelium of asthmatics is characterized by reduced expression of E-cadherin and increased expression of the basal cell markers ck-5 and p63 that is indicative of a relatively undifferentiated repairing epithelium. This phenotype correlates with increased proliferation, compromised wound healing and an enhanced capacity to undergo epithelial-mesenchymal transition (EMT). The transcription factor β-catenin plays a vital role in epithelial cell differentiation and regeneration, depending on the co-factor recruited. Transcriptional programs driven by the β-catenin/CBP axis are critical for maintaining an undifferentiated and proliferative state, whereas the β-catenin/p300 axis is associated with cell differentiation. We hypothesized that disrupting the β-catenin/CBP signaling axis would promote epithelial differentiation and inhibit EMT. We treated monolayer cultures of human airway epithelial cells with TGFβ1 in the presence or absence of the selective small molecule ICG-001 to inhibit β-catenin/CBP signaling. We used western blots to assess expression of an EMT signature, CBP, p300, β-catenin, fibronectin and ITGβ1 and scratch wound assays to assess epithelial cell migration. Snai-1 and -2 expressions were determined using q-PCR. Exposure to TGFβ1 induced EMT, characterized by reduced E-cadherin expression with increased expression of α-smooth muscle actin and EDA-fibronectin. Either co-treatment or therapeutic administration of ICG-001 completely inhibited TGFβ1-induced EMT. ICG-001 also reduced the expression of ck-5 and -19 independent of TGFβ1. Exposure to ICG-001 significantly inhibited epithelial cell proliferation and migration, coincident with a down regulation of ITGβ1 and fibronectin expression. These data support our hypothesis that modulating the β-catenin/CBP signaling axis plays a key role in epithelial plasticity and function.

Molina-Hernandez, V, Mulcahy, G, Perez, J, Martinez-Moreno, A, Donnelly, S, O'Neill, SM, Dalton, JP & Cwiklinski, K 2015, 'Fasciola hepatica vaccine: We may not be there yet but we're on the right road', VETERINARY PARASITOLOGY, vol. 208, no. 1-2, pp. 101-111.
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© 2015 The Authors. Major advances have been made in identifying potential vaccine molecules for the control of fasciolosis in livestock but we have yet to reach the level of efficacy required for commercialisation. The pathogenesis of fasciolosis is associated with liver damage that is inflicted by migrating and feeding immature flukes as well as host inflammatory immune responses to parasite-secreted molecules and tissue damage alarm signals. Immune suppression/modulation by the parasites prevents the development of protective immune responses as evidenced by the lack of immunity observed in naturally and experimentally infected animals. In our opinion, future efforts need to focus on understanding how parasites invade and penetrate the tissues of their hosts and how they potentiate and control the ensuing immune responses, particularly in the first days of infection. Emerging 'omics' data employed in an unbiased approach are helping us understand liver fluke biology and, in parallel with new immunological data, to identify molecules that are essential to parasite development and accessible to vaccine-induced immune responses.

Mondal, AK, Chen, S, Su, D, Kretschmer, K, Liu, H & Wang, G 2015, 'Microwave synthesis of alpha-Fe2O3 nanoparticles and their lithium storage properties: A comparative study', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 648, pp. 732-739.
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© 2015 Elsevier B.V. All rights reserved. This work introduces a simple microwave method for the preparation of α-Fe2O3 nanoparticles with two different sizes. Both the materials were characterized by X-ray powder diffraction, scanning electron microscopy, transmission electron microscopy and Brunauer-Emmett-Teller methods. The lithium storage properties were evaluated and compared in terms of their reversible capacity, rate capability and cycling performance. Interestingly, the electrode made of large particles (200-300 nm) show the reversible capacity of 1012 mA h g-1, better rate capability and excellent cycling stability than those of the small particles (20-30 nm). The poor electrochemical performances of small particles can be ascribed to their agglomeration during repeated charging and discharge process. The agglomeration of small particles may substantially decrease the surface area, which results in the lack of sufficient electro active sites for electrochemical reaction.

Mondal, AK, Su, D, Chen, S, Kretschmer, K, Xie, X, Ahn, H-J & Wang, G 2015, 'A Microwave Synthesis of Mesoporous NiCo2O4 Nanosheets as Electrode Materials for Lithium-Ion Batteries and Supercapacitors', CHEMPHYSCHEM, vol. 16, no. 1, pp. 169-175.
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© 2015 Wiley-VCH Verlag GmbH & Co. KGaA , Weinheim. A facile microwave method was employed to synthesize NiCo2O4 nanosheets as electrode materials for lithium-ion batteries and supercapacitors. The structure and morphology of the materials were characterized by X-ray diffraction, fieldemission scanning electron microscopy, transmission electron microscopy and Brunauer-Emmett-Teller methods. Owing to the porous nanosheet structure, the NiCo2O4 electrodes exhibited a high reversible capacity of 891 mAhg-1 at a current density of 100 mAg-1, good rate capability and stable cycling performance. When used as electrode materials for supercapacitors, NiCo2O4 nanosheets demonstrated a specific capacitance of 400 Fg-1 at a current density of 20 Ag-1 and superior cycling stability over 5000 cycles. The excellent electrochemical performance could be ascribed to the thin porous structure of the nanosheets, which provides a high specific surface area to increase the electrode-electrolyte contact area and facilitate rapid ion transport.

Mondal, AK, Su, D, Chen, S, Ung, A, Kim, H & Wang, G 2015, 'Mesoporous MnCo₂O₄ with a Flake‐Like Structure as Advanced Electrode Materials for Lithium‐Ion Batteries and Supercapacitors', Chemistry – A European Journal, vol. 21, no. 4, pp. 1526-1532.
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AbstractA mesoporous flake‐like manganese‐cobalt composite oxide (MnCo2O4) is synthesized successfully through the hydrothermal method. The crystalline phase and morphology of the materials are characterized by X‐ray diffraction, field‐emission scanning electron microscopy, transmission electron microscopy, and Brunauer–Emmett–Teller methods. The flake‐like MnCo2O4 is evaluated as the anode material for lithium‐ion batteries. Owing to its mesoporous nature, it exhibits a high reversible capacity of 1066 mA h g−1, good rate capability, and superior cycling stability. As an electrode material for supercapacitors, the flake‐like MnCo2O4 also demonstrates a high supercapacitance of 1487 F g−1 at a current density of 1 A g−1, and an exceptional cycling performance over 2000 charge/discharge cycles.

Morelato, M, Beavis, A, Tahtouh, M, Ribaux, O, Kirkbride, KP & Roux, C 2015, 'The use of methylamphetamine chemical profiling in an intelligence-led perspective and the observation of inhomogeneity within seizures', FORENSIC SCIENCE INTERNATIONAL, vol. 246, pp. 55-64.
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© 2014 Elsevier Ireland Ltd. This study focuses on methylamphetamine (MA) seizures made by the Australian Federal Police (AFP) to investigate the use of chemical profiling in an intelligence perspective. Correlation coefficients were used to obtain a similarity degree between a population of linked samples and a population of unlinked samples. Although it was demonstrated that a general framework can be followed for the use of any forensic case data in an intelligence-led perspective, threshold values have to be re-evaluated for each type of illicit drug investigated. Unlike the results obtained in a previous study on 3,4-methylenedioxymethylamphetamine (MDMA) seizures, chemical profiles of MA samples coming from the same seizure showed relative inhomogeneity, limiting their ability to link seizures. Different hypotheses were investigated to obtain a better understanding of this inhomogeneity although no trend was observed. These findings raise an interesting discussion in regards to the homogeneity and representativeness of illicit drug seizures (for intelligence purposes). Further, it also provides some grounds to discuss the initial hypotheses and assumptions that most forensic science studies are based on.

Moret, S, Spindler, X, Lennard, C & Roux, C 2015, 'Microscopic examination of fingermark residues: Opportunities for fundamental studies', FORENSIC SCIENCE INTERNATIONAL, vol. 255, pp. 28-37.
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© 2015 Elsevier Ireland Ltd. Despite significant ongoing research, a substantial proportion of latent fingermarks remain undetected in casework. Therefore, to improve existing detection techniques and to allow the development of new approaches, it is important to gain a better understanding of detection mechanisms rather than solely focusing on method formulations. As a starting point, it is crucial to gain a deeper understanding of the fingermark residue itself. Even if the chemical composition is reasonably well understood, little research has been reported on the physical aspects related to the deposition of fingermarks and their interactions with the environment and underlying substrates.This study aimed at exploring various techniques that can be used for the non-destructive visualisation of fingermarks before applying detection techniques. Both light and electron microscopy were investigated. Phase contrast imaging and environmental scanning electron microscopy, coupled with energy-dispersive X-ray spectrometry, proved to be essential tools for the study of latent fingermark deposits. These methods can be used to gather fundamental information that will add to our body of knowledge in this field.

Mowat, EJ, Webb, JK & Crowther, MS 2015, 'Fire‐mediated niche‐separation between two sympatric small mammal species', Austral Ecology, vol. 40, no. 1, pp. 50-59.
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AbstractFire is a key ecological process influencing the population dynamics of small mammals. Whilst shifting competitive advantage amongst small mammal species following a single fire event is well‐documented, there has been little investigation of the potential influence of fire frequency on small mammal interspecific interactions. In this study, we investigated the effect of fire frequency on the abundance of two small dasyurid mammals, Antechinus stuartii and A. flavipes, which occur sympatrically in some parts of their range. The two antechinus species are known to have different habitat preferences, so it is possible that fire regimes may promote their coexistence in areas of sympatry by altering vegetation structure. To investigate this possibility, we estimated the abundance of both species using replicate sites which differed in the number of times burnt (1–4) during the last four decades, but with identical time‐since‐fire. Proportionally, we captured greater numbers of A. stuartii in less frequently burnt sites and greater numbers of A. flavipes in more‐frequently burnt sites. Hence, fire may mediate niche‐separation between these two species. To clarify further this pattern of response to fire frequency, we investigated which structural habitat variables differed between fire frequencies, and compared antechinus abundances with structural vegetation characteristics. We found a trend for lower ground cover density under higher fire frequencies. This offe...

Mowe, MAD, Mitrovic, SM, Lim, RP, Furey, A & Yeo, DCJ 2015, 'Tropical cyanobacterial blooms: a review of prevalence, problem taxa, toxins and influencing environmental factors', Journal of Limnology, vol. 73, no. AoP, pp. 205-224.
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© 2015, Page Press Publications. All rights reserved. Toxic cyanobacterial blooms are a major issue in freshwater systems in many countries. The potentially toxic species and their ecological causes are likely to be different in tropical zones from those in temperate water bodies; however, studies on tropical toxic cyanobacterial blooms are sporadic and currently there is no global synthesis. In this review, we examined published information on tropical cyanobacterial bloom occurrence and toxin production to investigate patterns in their growth and distribution. Microcystis was the most frequently occurring bloom genus throughout tropical Asia, Africa and Central America, while Cylindrospermopsis and Anabaena blooms occurred in various locations in tropical Australia, America and Africa. Microcystis blooms were more prevalent during the wet season while Cylindrospermopsis blooms were more prevalent during the dry period. Microcystin was the most encountered toxin throughout the tropics. A meta-analysis of tropical cyanobacterial blooms showed that Microcystis blooms were more associated with higher total nitrogen concentrations, while Cylindrospermopsis blooms were more associated with higher maximum temperatures. Meta-analysis also showed a positive linear relationship between levels of microcystin and N:P (nitrate:phosphate) ratio. Tropical African Microcystis blooms were found to have the lowest microcystin levels in relation to biomass and N:P (nitrate:phosphate) compared to tropical Asian, Australian and American blooms. There was also no significant correlation between microcystin concentration and cell concentration for tropical African blooms as opposed to tropical Asian and American blooms. Our review illustrates that some cyanobacteria and toxins are more prevalent in tropical areas. While some tropical countries have considerable information regarding toxic blooms, others have few or no reported studies.

Mowe, MAD, Porojan, C, Abbas, F, Mitrovic, SM, Lim, RP, Furey, A & Yeo, DCJ 2015, 'Rising temperatures may increase growth rates and microcystin production in tropical Microcystis species', Harmful Algae, vol. 50, pp. 88-98.
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Mreich, E, Chen, X, Zaky, A, Pollock, CA & Saad, S 2015, 'The role of Krüppel‐like factor 4 in transforming growth factor‐β–induced inflammatory and fibrotic responses in human proximal tubule cells', Clinical and Experimental Pharmacology and Physiology, vol. 42, no. 6, pp. 680-686.
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SummaryKrüppel‐like factor 4 (KLF4) is known to mitigate inflammation in several cell types. Using human proximal tubule cells, the present study aimed to investigate the role of KLF4 in regulating transforming growth factor (TGF)‐β1 induced inflammatory and fibrotic responses. Human kidney proximal tubular cells were exposed to high glucose, or TGF‐β1 and KLF4 expressions were determined. Cells were then transfected with empty vector or KLF4 and exposed to 2‐ng/mL TGF‐β1 for up to 72 h. Inflammatory proteins (macrophage migration inhibitory factor and monocyte chemoattractant protein‐1) and pro‐fibrotic proteins (fibronectin and collagen IV) were measured after 72 h by enzyme‐linked immunosorbent assay and western blot, respectively. To determine the relevance to in vivo models of chronic kidney disease, KLF4 protein expression in streptozotocin‐induced diabetic mice was determined. Krüppel‐like factor 4 messenger RNA (mRNA) levels were significantly reduced in high glucose‐treated human kidney proximal tubular cells. High glucose increased TGF...

Müller, S & Mitrovic, SM 2015, 'Phytoplankton co-limitation by nitrogen and phosphorus in a shallow reservoir: progressing from the phosphorus limitation paradigm', Hydrobiologia, vol. 744, no. 1, pp. 255-269.
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Phosphorus (P) limitation has been regarded as the rule in freshwater systems and the basis for phytoplankton growth management. We hypothesised that P would be the limiting nutrient for phytoplankton growth in Grahamstown Dam, a shallow, mesotrophic reservoir, across different seasons and on different experimental time scales. Seven fully factorial microcosm assays with additions of nitrogen (N) and P were conducted in situ during different seasons. The influence of longer experimental duration was examined in two 18-day mesocosm assays. Additions of N and P in combination evoked significantly higher phytoplankton biomass and biovolumes of individual algal genera compared with controls and other treatments in both types of experiment. There were some significant responses to P additions in the microcosm assays in winter. Some genera first responded to combined P and N addition and then to P only addition during the mesocoms assays. Our results show that P was not the limiting nutrient across all seasons but that phytoplankton was mostly co-limited by N and P. A longer experimental time scale did not change this outcome at the biomass level. This implies that input of N as well as of P should be considered in the management of phytoplankton growth.

Munoz, L, Kavanagh, ME, Phoa, AF, Heng, B, Dzamko, N, Chen, EJ, Doddareddy, MR, Guillemin, GJ & Kassiou, M 2015, 'Optimisation of LRRK2 inhibitors and assessment of functional efficacy in cell-based models of neuroinflammation', European Journal of Medicinal Chemistry, vol. 95, pp. 29-34.
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LRRK2IN1 is a highly potent inhibitor of leucine-rich repeat kinase 2 (LRRK2, IC50 = 7.9 nM), an established target for treatment of Parkinson's disease. Two LRRK2IN1 analogues 1 and 2 were synthesised which retained LRRK2 inhibitory activity (1: IC50 = 72 nM; 2: IC50 = 51 nM), were predicted to have improved bioavailability and were efficacious in cell-based models of neuroinflammation. Analogue 1 inhibited IL-6 secretion from LPS-stimulated primary human microglia with EC50 = 4.26 μM. In order to further optimize the molecular properties of LRRK2IN1, a library of truncated analogues was designed based on docking studies. Despite lacking LRRK2 inhibitory activity, these compounds show antineuroinflammatory efficacy at micromolar concentration. The compounds developed were valuable tools in establishing a cell-based assay for assessing anti-neuroinflammatory efficacy of LRRK2 inhibitors. Herein, we present data that IL-1β stimulated U87 glioma cell line is a reliable model for neuroinflammation, as data obtained in this model were consistent with results obtained using primary human microglia and astrocytes.

Murray, M, Hraiki, A, Bebawy, M, Pazderka, C & Rawling, T 2015, 'Anti-tumor activities of lipids and lipid analogues and their development as potential anticancer drugs', PHARMACOLOGY & THERAPEUTICS, vol. 150, pp. 109-128.
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Murray, SA, Diwan, R, Orr, RJS, Kohli, GS & John, U 2015, 'Gene duplication, loss and selection in the evolution of saxitoxin biosynthesis in alveolates', MOLECULAR PHYLOGENETICS AND EVOLUTION, vol. 92, pp. 165-180.
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© 2015 Elsevier Inc. A group of marine dinoflagellates (Alveolata, Eukaryota), consisting of ~10 species of the genus Alexandrium, Gymnodinium catenatum and Pyrodinium bahamense, produce the toxin saxitoxin and its analogues (STX), which can accumulate in shellfish, leading to ecosystem and human health impacts. The genes, sxt, putatively involved in STX biosynthesis, have recently been identified, however, the evolution of these genes within dinoflagellates is not clear. There are two reasons for this: uncertainty over the phylogeny of dinoflagellates; and that the sxt genes of many species of Alexandrium and other dinoflagellate genera are not known. Here, we determined the phylogeny of STX-producing and other dinoflagellates based on a concatenated eight-gene alignment. We determined the presence, diversity and phylogeny of sxtA, domains A1 and A4 and sxtG in 52 strains of Alexandrium, and a further 43 species of dinoflagellates and thirteen other alveolates. We confirmed the presence and high sequence conservation of sxtA, domain A4, in 40 strains (35 Alexandrium, 1 Pyrodinium, 4 Gymnodinium) of 8 species of STX-producing dinoflagellates, and absence from non-producing species. We found three paralogs of sxtA, domain A1, and a widespread distribution of sxtA1 in non-STX producing dinoflagellates, indicating duplication events in the evolution of this gene. One paralog, clade 2, of sxtA1 may be particularly related to STX biosynthesis. Similarly, sxtG appears to be generally restricted to STX-producing species, while three amidinotransferase gene paralogs were found in dinoflagellates. We investigated the role of positive (diversifying) selection following duplication in sxtA1 and sxtG, and found negative selection in clades of sxtG and sxtA1, clade 2, suggesting they were functionally constrained. Significant episodic diversifying selection was found in some strains in clade 3 of sxtA1, a clade that may not be involved in STX biosynthesis, indicatin...

Murray, SA, Kohli, GS, Farrell, H, Spiers, ZB, Place, AR, Dorantes-Aranda, JJ & Ruszczyk, J 2015, 'A fish kill associated with a bloom of Amphidinium carterae in a coastal lagoon in Sydney, Australia', HARMFUL ALGAE, vol. 49, pp. 19-28.
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© 2015 Elsevier B.V. We report on a dense bloom (~1.80×105cellsmL-1) of the marine dinoflagellate species Amphidinium carterae (Genotype 2) in a shallow, small intermittently open coastal lagoon in south eastern Australia. This bloom co-occurred with the deaths of >300 individuals of three different species of fish. The opening of the lagoon to the ocean, as well as localized high nutrient levels, preceded the observations of very high cell numbers. A. carterae is usually benthic and sediment-dwelling, but temporarily became abundant throughout the water column in this shallow (<2m) sandy habitat. Histopathological results showed that the Anguilla reinhardtii individuals examined had damage to epithelial and gill epithelial cells. An analysis of the bloom water indicated the presence of a compound with a retention time and UV spectra similar to Luteophanol A, a compound known from a strain of Amphidinium. Assays with a fish gill cell line were conducted using a purified compound from cells concentrated from the bloom, and was found to cause a loss of 87% in cell viability in 6h. The fish deaths were likely due to the low dissolved oxygen levels in the water and/or the presence of Luteophanol A-like compounds released during the bloom.

Mustapic, M, De Silva, KSB, Aboutalebi, SH, Barua, S, Xu, X, Wang, J, Hossain, MS, Horvat, J & Dou, SX 2015, 'Improvements in the Dispersion of Nanosilver in a MgB2 Matrix through a Graphene Oxide Net', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 119, no. 19, pp. 10631-10640.
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© 2015 American Chemical Society. The effects of graphene oxide (GO) addition on the dispersion of nanosilver (Ag) in an MgB2 matrix were studied using bulk samples prepared through a diffusion process. The influence of the dispersion of Ag and Ag/GO particles on the critical current density (Jc) of MgB2 was also investigated. GO has emerged as an excellent dopant which can significantly improve both the low- and high-field performance of MgB2 due to its capability to improve intergrain connectivity (GO) and inter- and intragrain pinning (GO and AgMg). The addition of nanosize Ag particles also results in an improvement of vortex pinning, and at the same time, it offers the advantage of preventing the loss of Mg during the sintering process. It is found that the dispersion of nanosilver in the presence of GO results in significant improvements in the critical current density in MgB2, particularly at high magnetic fields, due to improved intergrain connectivity and flux pinning. The use of the GO net as a platform for doping MgB2 in our case with Ag yielded a 10-fold-better critical current density (Jc) than standard Ag doping at 9 T and 5 K. Even without sophisticated processes, we obtained a Jc result of 104 A/cm2 at 9 T and 5 K, which is one of the best ever achieved.

Musumeci, G, Magro, G, Cardile, V, Coco, M, Marzagalli, R, Castrogiovanni, P, Imbesi, R, Graziano, ACE, Barone, F, Di Rosa, M, Castorina, S & Castorina, A 2015, 'Characterization of matrix metalloproteinase-2 and -9, ADAM-10 and N-cadherin expression in human glioblastoma multiforme', Cell and Tissue Research, vol. 362, no. 1, pp. 45-60.
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Najafpour, MM, Ghobadi, MZ, Larkum, AW, Shen, J-R & Allakhverdiev, SI 2015, 'The biological water-oxidizing complex at the nano–bio interface', Trends in Plant Science, vol. 20, no. 9, pp. 559-568.
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Nelson, L, McKeen, HD, Marshall, A, Mulrane, L, Starczynski, J, Storr, SJ, Lanigan, F, Byrne, C, Arthur, K, Hegarty, S, Ali, AA, Furlong, F, McCarthy, HO, Ellis, IO, Green, AR, Rakha, E, Young, L, Kunkler, I, Thomas, J, Jack, W, Cameron, D, Jirström, K, Yakkundi, A, McClements, L, Martin, SG, Gallagher, WM, Dunn, J, Bartlett, J, O’Connor, D & Robson, T 2015, 'FKBPL: a marker of good prognosis in breast cancer', Oncotarget, vol. 6, no. 14, pp. 12209-12223.
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FK506-binding protein-like (FKBPL) has established roles as an anti-tumor protein, with a therapeutic peptide based on this protein, ALM201, shortly entering phase I/II clinical trials. Here, we evaluated FKBPL's prognostic ability in primary breast cancer tissue, represented on tissue microarrays (TMA) from 3277 women recruited into five independent retrospective studies, using immunohistochemistry (IHC). In a meta-analysis, FKBPL levels were a significant predictor of BCSS; low FKBPL levels indicated poorer breast cancer specific survival (BCSS) (hazard ratio (HR) = 1.30, 95% confidence interval (CI) 1.14-1.49, p < 0.001). The prognostic impact of FKBPL remained significant after adjusting for other known prognostic factors (HR = 1.25, 95% CI 1.07-1.45, p = 0.004). For the sub-groups of 2365 estrogen receptor (ER) positive patients and 1649 tamoxifen treated patients, FKBPL was significantly associated with BCSS (HR = 1.34, 95% CI 1.13-1.58, p < 0.001, and HR = 1.25, 95% CI 1.04-1.49, p = 0.02, respectively). A univariate analysis revealed that FKBPL was also a significant predictor of relapse free interval (RFI) within the ER positive patient group, but it was only borderline significant within the smaller tamoxifen treated patient group (HR = 1.32 95% CI 1.05-1.65, p = 0.02 and HR = 1.23 95% CI 0.99-1.54, p = 0.06, respectively). The data suggests a role for FKBPL as a prognostic factor for BCSS, with the potential to be routinely evaluated within the clinic.

Neuendorf, E, Gajer, P, Bowlin, AK, Marques, PX, Ma, B, Yang, H, Fu, L, Humphrys, MS, Forney, LJ, Myers, GSA, Bavoil, PM, Rank, RG & Ravel, J 2015, 'Chlamydia caviae infection alters abundance but not composition of the guinea pig vaginal microbiota', Pathogens and Disease, vol. 73, no. 4, pp. 1-12.
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In humans, the vaginal microbiota is thought to be the first line of defense again pathogens including Chlamydia trachomatis. The guinea pig has been extensively used as a model to study chlamydial infection because it shares anatomical and physiological similarities with humans, such as a squamous vaginal epithelium as well as some of the long-term outcomes caused by chlamydial infection. In this study, we aimed to evaluate the guinea pig-C. caviae model of genital infection as a surrogate for studying the role of the vaginal microbiota in the early steps of C. trachomatis infection in humans. We used culture-independent molecular methods to characterize the relative and absolute abundance of bacterial phylotypes in the guinea pig vaginal microbiota in animals non-infected, mock-infected or infected by C. caviae. We showed that the guinea pig and human vaginal microbiotas are of different bacterial composition and abundance. Chlamydia caviae infection had a profound effect on the absolute abundance of bacterial phylotypes but not on the composition of the guinea pig vaginal microbiota. Our findings compromise the validity of the guinea pig-C. caviae model to study the role of the vaginal microbiota during the early steps of sexually transmitted infection.

Nezafat, N, Sadraeian, M, Rahbar, MR, Khoshnoud, MJ, Mohkam, M, Gholami, A, Banihashemi, M & Ghasemi, Y 2015, 'Production of a novel multi-epitope peptide vaccine for cancer immunotherapy in TC-1 tumor-bearing mice', Biologicals, vol. 43, no. 1, pp. 11-17.
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Ng, HY, Oliver, BGG, Burgess, JK, Krymskaya, VP, Black, JL & Moir, LM 2015, 'Doxycycline reduces the migration of tuberous sclerosis complex‐2 null cells ‐ effects on RhoA‐GTPase and focal adhesion kinase', Journal of Cellular and Molecular Medicine, vol. 19, no. 11, pp. 2633-2646.
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AbstractLymphangioleiomyomatosis (LAM) is associated with dysfunction of the tuberous sclerosis complex (TSC) leading to enhanced cell proliferation and migration. This study aims to examine whether doxycycline, a tetracycline antibiotic, can inhibit the enhanced migration of TSC2‐deficient cells, identify signalling pathways through which doxycycline works and to assess the effectiveness of combining doxycycline with rapamycin (mammalian target of rapamycin complex 1 inhibitor) in controlling cell migration, proliferation and wound closure. TSC2‐positive and TSC2‐negative mouse embryonic fibroblasts (MEF), 323‐TSC2‐positive and 323‐TSC2‐null MEF and Eker rat uterine leiomyoma (ELT3) cells were treated with doxycycline or rapamycin alone, or in combination. Migration, wound closure and proliferation were assessed using a transwell migration assay, time‐lapse microscopy and manual cell counts respectively. RhoA‐GTPase activity, phosphorylation of p70S6 kinase (p70S6K) and focal adhesion kinase (FAK) in TSC2

Nguyen, D, Nguyen, T-K, Rice, SA & Boyer, C 2015, 'CO-Releasing Polymers Exert Antimicrobial Activity', Biomacromolecules, vol. 16, no. 9, pp. 2776-2786.
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Nguyen, LT, Stangenberg, S, Chen, H, Al-Odat, I, Chan, YL, Gosnell, ME, Anwer, AG, Goldys, EM, Pollock, CA & Saad, S 2015, 'l-Carnitine reverses maternal cigarette smoke exposure-induced renal oxidative stress and mitochondrial dysfunction in mouse offspring', American Journal of Physiology-Renal Physiology, vol. 308, no. 7, pp. F689-F696.
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Maternal smoking is associated with metabolic disorders, renal underdevelopment, and a predisposition to chronic kidney disease in offspring, yet the underlying mechanisms are unclear. By exposing female Balb/c mice to cigarette smoke for 6 wk premating and during gestation and lactation, we showed that maternal smoke exposure induced glucose intolerance, renal underdevelopment, inflammation, and albuminuria in male offspring. This was associated with increased renal oxidative stress and mitochondrial dysfunction at birth and in adulthood. Importantly, we demonstrated that dietary supplementation of l-carnitine, an amino acid shown to increase antioxidant defenses and mitochondrial function in numerous diseases, in smoke-exposed mothers during pregnancy and lactation significantly reversed the detrimental maternal impacts on kidney pathology in these male offspring. It increased SOD2 and glutathione peroxidase 1, reduced ROS accumulation, and normalized levels of mitochondrial preprotein translocases of the outer membrane, and oxidative phosphorylation complexes I–V in the kidneys of mouse progeny after intrauterine cigarette smoke exposure. These findings support the hypothesis that oxidative stress and mitochondrial dysfunction are closely linked to the adverse effects of maternal smoking on male offspring renal pathology. The results of our study suggest that l-carnitine administration in cigarette smoke-exposed mothers mitigates these deleterious renal consequences.

Nielsen, DA, Pernice, M, Schliep, M, Sablok, G, Jeffries, TC, Kuehl, M, Wangpraseurt, D, Ralph, PJ & Larkum, AWD 2015, 'Microenvironment and phylogenetic diversity of Prochloron inhabiting the surface of crustose didemnid ascidians', ENVIRONMENTAL MICROBIOLOGY, vol. 17, no. 10, pp. 4121-4132.
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Nolan, LM, Cavaliere, R, Turnbull, L & Whitchurch, CB 2015, 'Extracellular ATP inhibits twitching motility-mediated biofilm expansion by Pseudomonas aeruginosa', BMC MICROBIOLOGY, vol. 15, pp. 1-12.
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Pseudomonas aeruginosa is an opportunistic pathogen that exploits damaged epithelia to cause infection. Type IV pili (tfp) are polarly located filamentous structures which are the major adhesins for attachment of P. aeruginosa to epithelial cells. The extension and retraction of tfp powers a mode of surface translocation termed twitching motility that is involved in biofilm development and also mediates the active expansion of biofilms across surfaces. Extracellular adenosine triphosphate (eATP) is a key "danger" signalling molecule that is released by damaged epithelial cells to alert the immune system to the potential presence of pathogens. As P. aeruginosa has a propensity for infecting damaged epithelial tissues we have explored the influence of eATP on tfp biogenesis and twitching motility-mediated biofilm expansion by P. aeruginosa.In this study we have found that eATP inhibits P. aeruginosa twitching motility-mediated expansion of interstitial biofilms at levels that are not inhibitory to growth. We have determined that eATP does not inhibit expression of the tfp major subunit, PilA, but reduces the levels of surface assembled tfp. We have also determined that the active twitching zone of expanding P. aeruginosa interstitial biofilms contain large quantities of eATP which may serve as a signalling molecule to co-ordinate cell movements in the expanding biofilm. The inhibition of twitching motility-mediated interstitial biofilm expansion requires eATP hydrolysis and does not appear to be mediated by the Chp chemosensory system.Endogenous eATP produced by P. aeruginosa serves as a signalling molecule to co-ordinate complex multicellular behaviours of this pathogen. Given the propensity for P. aeruginosa to infect damaged epithelial tissues, our observations suggest that eATP released by damaged cells may provide a cue to reduce twitching motility of P. aeruginosa in order to establish infection at the site of damage. Furthermore, eATP produced by P. aerugino...

Nolan, LM, Cavaliere, R, Turnbull, L & Whitchurch, CB 2015, 'Extracellular ATP inhibits twitching motility-mediated biofilm expansion by Pseudomonas aeruginosa', BMC Microbiology, vol. 15, no. 1, p. 392.
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BACKGROUND: Pseudomonas aeruginosa is an opportunistic pathogen that exploits damaged epithelia to cause infection. Type IV pili (tfp) are polarly located filamentous structures which are the major adhesins for attachment of P. aeruginosa to epithelial cells. The extension and retraction of tfp powers a mode of surface translocation termed twitching motility that is involved in biofilm development and also mediates the active expansion of biofilms across surfaces. Extracellular adenosine triphosphate (eATP) is a key "danger" signalling molecule that is released by damaged epithelial cells to alert the immune system to the potential presence of pathogens. As P. aeruginosa has a propensity for infecting damaged epithelial tissues we have explored the influence of eATP on tfp biogenesis and twitching motility-mediated biofilm expansion by P. aeruginosa. RESULTS: In this study we have found that eATP inhibits P. aeruginosa twitching motility-mediated expansion of interstitial biofilms at levels that are not inhibitory to growth. We have determined that eATP does not inhibit expression of the tfp major subunit, PilA, but reduces the levels of surface assembled tfp. We have also determined that the active twitching zone of expanding P. aeruginosa interstitial biofilms contain large quantities of eATP which may serve as a signalling molecule to co-ordinate cell movements in the expanding biofilm. The inhibition of twitching motility-mediated interstitial biofilm expansion requires eATP hydrolysis and does not appear to be mediated by the Chp chemosensory system. CONCLUSIONS: Endogenous eATP produced by P. aeruginosa serves as a signalling molecule to co-ordinate complex multicellular behaviours of this pathogen. Given the propensity for P. aeruginosa to infect damaged epithelial tissues, our observations suggest that eATP released by damaged cells may provide a cue to reduce twitching motility of P. aeruginosa in order to establish infection at the site of damage. Furth...

O’Flynn, C, Deusch, O, Darling, AE, Eisen, JA, Wallis, C, Davis, IJ & Harris, SJ 2015, 'Comparative Genomics of the GenusPorphyromonasIdentifies Adaptations for Heme Synthesis within the Prevalent Canine Oral SpeciesPorphyromonas cangingivalis', Genome Biology and Evolution, vol. 7, no. 12, pp. 3397-3413.
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Ollivier, QR, Bramwell, NA, Hammill, E, Foster-Thorpe, C & Booth, DJ 2015, 'Are the effects of adjacent habitat type on seagrass gastropod communities being masked by previous focus on habitat dyads?', AUSTRALIAN JOURNAL OF ZOOLOGY, vol. 63, no. 5, pp. 357-363.
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© 2015 CSIRO. Variation in abundance and diversity of organisms along habitat edges has long been a key research focus in both terrestrial and marine ecosystems. Previous investigations into edge effects in seagrass ecosystems have predominantly focussed on the seagrass-sandy substrate boundary. However, little is known about what role other habitats (e.g. rocky algal reefs) may play in faunal assemblage patterns. This study investigated the strength to which habitat type influenced gastropod assemblages within seagrass (Posidonia australis) beds, bordered by both sandy substrate and rocky algal reef. We found that benthic invertebrate community composition significantly changed with distance from rocky algal reef, but not with distance from sandy substrate. Proximity to rocky reef had a stronger effect on community composition than other local drivers examined (seagrass biomass and sand particle size). We hypothesise that gastropod affinity for rocky algal reef may be a result of both species-specific habitat preference, and lower predation pressure along adjacent rocky algal reef habitats. This study provides evidence that heterogeneous habitats within close proximity to seagrass beds may exert previously overlooked effects on the distribution of gastropod assemblages, highlighting the need for the inclusion of adjacent habitat type in experimental design for gastropod assemblage distribution studies.

Ong, VA, Lawrence, A, Timms, P, Vodstrcil, LA, Tabrizi, SN, Beagley, KW, Allan, JA, Hocking, JS & Huston, WM 2015, 'In vitro susceptibility of recent Chlamydia trachomatis clinical isolates to the CtHtrA inhibitor JO146', MICROBES AND INFECTION, vol. 17, no. 11-12, pp. 738-744.
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© 2015 Institut Pasteur. The present study aimed to establish if a previously identified Chlamydia trachomatis HtrA (CtHtrA) inhibitor, JO146, is effective against currently circulating clinical isolates to validate if CtHtrA is a clinically relevant target for future therapeutic development. Inhibition of CtHtrA during the middle of the chlamydial replicative cycle until the completion of the cycle resulted in loss of infectious progeny for six unique clinical isolates representing different serovars. This supports the potential for CtHtrA to be a clinically relevant target for development of new therapeutics and suggests the importance of further investigation of JO146 as a lead compound.

O'Rourke, MB, Djordjevic, SP & Padula, MP 2015, 'A non-instrument-based method for the analysis of formalin-fixed paraffin-embedded human spinal cord via matrix-assisted laser desorption/ionisation imaging mass spectrometry', RAPID COMMUNICATIONS IN MASS SPECTROMETRY, vol. 29, no. 19, pp. 1836-1840.
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Copyright © 2015 John Wiley & Sons, Ltd. Rationale This paper, in conjunction with a work published earlier this year by O'Rourke et al., aims to provide a comprehensive set of protocols for the analysis of formalin-fixed paraffin-embedded (FFPE) tissue via matrix-assisted laser desorption/ionisation imaging mass spectrometry (MALDI IMS) in a low-cost and highly repeatable and robust way, thereby allowing other research teams to begin their own IMS-centered avenues of research. Methods Samples of FFPE tissue were sectioned at 5 μm, water float mounted to specially prepared ITO glass slides and then dilipidated in a graded alcohol series. Tissue sections were then antigen retrieved under pressure in 20 mmol Tris-HCl (pH 8.8), coated with trypsin and digested O/N at 37°C. Samples were then sublimated with matrix to a final coverage of 0.2 mg/cm², recrystallised at 37 C with 50:50 acetonitrile (ACN)/0.1% trifluoroacetic acid (TFA) for 1 h and analysed with a MALDI TOF/TOF mass spectrometer. Results Serial sections were imaged, revealing little to no variation with regards to image quality and corresponding spectra. We have also attempted to describe the processes that govern the various aspects of this protocol with respect to each step necessary to ensure reproducibility. Conclusions We are confident that this protocol in conjunction with the work published earlier by O'Rourke et al. provides the basis for a repeatable and robust protocol for the analysis of tissues from various sources via MALDI-IMS. The descriptions of key steps within allows for easy adoption of the protocol while allowing for desired modifications to be performed with minimal yet intuitive adjustment.

O'Rourke, MB, Raymond, BBA, Djordjevic, SP & Padula, MP 2015, 'A versatile cost-effective method for the analysis of fresh frozen tissue sections via matrix-assisted laser desorption/ionisation imaging mass spectrometry', RAPID COMMUNICATIONS IN MASS SPECTROMETRY, vol. 29, no. 7, pp. 637-644.
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© 2015 John Wiley & Sons, Ltd. Rationale There are currently multiple methods available for the preparation of fresh frozen tissue samples for analysis via matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) imaging mass spectrometry (IMS). Although these methods report excellent results, many are expensive automated approaches. With no published attempt to standardise less expensive manual processes, our work aims to provide a robust and repeatable method of sample preparation for MALDI-TOF-IMS that is applicable to a variety of tissue types, well explained, simple and cost effective. Methods Fresh frozen tissue was sectioned at 12 μm and mounted onto liquid nitrocellulose coated slides, washed in a graded alcohol series and then mounted into a modified sublimation apparatus. Matrix is deposited onto the slide to achieve a desired coating of 0.2 mg/cm². Once coated, the slide is mounted into a custom-built vapor chamber and recrystallised with 50% acetonitrile (ACN), 0.1% trifluoroacetic acid (TFA) for 1 h at 37C. The slide is then analysed using MALDI-IMS. Results We have successfully implemented this method for a host of tissue samples, including brain, liver, kidney and heart, with no variation in relative spectra or processing method required. When the protocol is followed correctly, sublimations and recrystallisations are highly predictable with limited variation between samples and a very low failure rate. Additional apparatuses can be easily constructed by following the included instructions, that perform as per specifications with no variation. Conclusions We believe that we have described a complete protocol for MALDI-IMS that is easy to use and highly reproducible. The lack of expensive commercially available equipment makes this process very cheap with a relatively low initial outlay and our hope is that more laboratories will begin IMS-based avenues of research based on the work we have performed.

Otsuka, Y, Takeuchi, M, Otsuka, M, Ben-Nissan, B, Grossin, D & Tanaka, H 2015, 'Effect of carbon dioxide on self-setting apatite cement formation from tetracalcium phosphate and dicalcium phosphate dihydrate; ATR-IR and chemoinformatics analysis', Colloid and Polymer Science, vol. 293, no. 10, pp. 2781-2788.
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Ouyang, R, Yan, J, Jensen, PS, Ascic, E, Gan, S, Tanner, D, Mao, B, Niu, L, Zhang, J, Tang, C, Hush, NS, Reimers, JR & Ulstrup, J 2015, 'Intermixed Adatom and Surface-Bound Adsorbates in Regular Self-Assembled Monolayers of Racemic 2-Butanethiol on Au(111)', CHEMPHYSCHEM, vol. 16, no. 5, pp. 928-932.
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In situ scanning tunneling microscopy combined with density functional theory molecular dynamics simulations reveal a complex structure for the self-assembled monolayer (SAM) of racemic 2-butanethiol on Au(111) in aqueous solution. Six adsorbate molecules occupy a (10×√3)R30 cell organized as two RSAuSR adatom-bound motifs plus two RS species bound directly to face-centered-cubic and hexagonally close-packed sites. This is the first time that these competing head-group arrangements have been observed in the same ordered SAM. Such unusual packing is favored as it facilitates SAMs with anomalously high coverage (30 %), much larger than that for enantiomerically resolved 2-butanethiol or secondary-branched butanethiol (25 %) and near that for linear-chain 1-butanethiol (33 %).

Pacheco, JM, Smoliga, GR, O’Donnell, V, Brito, BP, Stenfeldt, C, Rodriguez, LL & Arzt, J 2015, 'Persistent Foot-and-Mouth Disease Virus Infection in the Nasopharynx of Cattle; Tissue-Specific Distribution and Local Cytokine Expression', PLOS ONE, vol. 10, no. 5, pp. e0125698-e0125698.
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Palanca-Tan, R, Garces, LPDM, Purisima, ANC & Zaratan, ACL 2015, 'Tourism and crime: Evidence from the Philippines', Southeast Asian Studies, vol. 4, no. 3, pp. 565-580.
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Using panel data gathered from 16 regions of the Philippines for the period 2009–11, this paper investigates the relationship between tourism and crime. The findings of the study show that the relation between tourism and crime may largely depend on the characteristics of visitors and the types of crime. For all types of crime and their aggregate, no significant correlation between the crime rate (defined as the number of crime cases divided by population) and total tourist arrivals is found. However, a statistically significant positive relation is found between foreign tourism and robbery and theft cases as well as between overseas Filipino tourism and robbery. On the other hand, domestic tourism is not significantly correlated with any of the four types of crimes. These results, together with a strong evidence of the negative relationship between crime and the crime clearance efficiency, present much opportunity for policy intervention in order to minimize the crime externality of the country’s tourism-led development strategy.

Pan, G, Zhang, YC, Reyk, DV, Rayner, B & Hawkins, C 2015, 'Hypothiocyanous Acid (HOSCN) Promotes Increases in Cytokine/chemokine Production Through the Activation of MAP Kinase Pathways in Macrophages: A Pathway to Lesion Development in Atherosclerosis', Free Radical Biology and Medicine, vol. 87, pp. S51-S52.
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Pandrala, M, Sundaraneedi, MK, Ammit, AJ, Woodward, CE, Wallace, L, Keene, FR & Collins, JG 2015, 'Differential Anticancer Activities of the Geometric Isomers of Dinuclear Iridium(III) Complexes', European Journal of Inorganic Chemistry, vol. 2015, no. 34, pp. 5694-5701.
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AbstractThe anticancer activities of dinuclear iridium(III) complexes [{Ir(tpy)Cl}2{μ‐bbn}]4+ {Cl‐Irbbn; tpy = 2,2′:6′,2″‐terpyridine, bbn = bis[4(4′‐methyl‐2,2′‐bipyridyl)]‐1,n‐alkane (n = 7, 12 and 16)} against MCF‐7 and MDA‐MB‐231 breast cancer cell lines have been determined. The activities of the Cl‐Irbbn complexes increased with increasing chain length, the Cl‐Irbb16 complex showing the best anticancer properties. However, while Cl‐Irbb16 was active against the metastatic MDA‐MB‐231 cells (3 μM), it was relatively inactive against the nonmetastatic MCF‐7 line (29 μM). The three geometric isomers of Cl‐Irbb16 were isolated and characterised by NMR spectroscopy and mass spectrometry, and their anticancer activities, lipophilicities (log P) and DNA‐binding abilities were examined. The trans,trans (t,t) isomer (IC50 = 2 μM against MDA‐MB‐231) showed considerably greater anticancer activity than the cis,trans (c,t) and cis,cis (c,c) isomers (8 and 31 μM, respectively). From log P measurements, the t,t isomer of Cl‐Irbb16 (log P = –0.62) was found to be slightly more lipophilic than the other geometric isomers (–0.95...

Park, J-W, Kim, C, Ryu, H-S, Cho, G-B, Cho, K-K, Kim, K-W, Ahn, J-H, Wang, G, Ahn, J-P & Ahn, H-J 2015, 'Effect of sulfur content in a sulfur-activated carbon composite on the electrochemical properties of a lithium/sulfur battery', Materials Research Bulletin, vol. 69, pp. 24-28.
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The content of sulfur in sulfur/activated carbon composite is controlled from 32.37wt.% to 55.33wt.% by a one-step solution-based process. When the sulfur content is limited to 41.21wt.%, it can be loaded into the pores of an activated carbon matrix in a highly dispersed state. On the contrary, when the sulfur content is 55.33wt.%, crystalline sulfur can be detected on the surface of the activated carbon matrix. The best electrochemical performance can be obtained for a sulfur electrode with the lowest sulfur content. The sulfur/activated carbon composite with 32.37wt.% sulfur afforded the highest first discharge capacity of 1360mAhg-1 at 1C rate and a large reversible capacity of 702mAhg-1 at 10C (16.75A/g).

Parkes, SL, Bradfield, LA & Balleine, BW 2015, 'Interaction of Insular Cortex and Ventral Striatum Mediates the Effect of Incentive Memory on Choice Between Goal-Directed Actions', The Journal of Neuroscience, vol. 35, no. 16, pp. 6464-6471.
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The anterior insular cortex (IC) and the nucleus accumbens (NAc) core have been separately implicated in the selection and performance of actions based on the incentive value of the instrumental outcome. Here, we examined the role of connections between the IC and the NAc core in the performance of goal-directed actions. Rats were trained on two actions for distinct outcomes, after which one of the two outcomes was devalued by specific satiety immediately before a choice extinction test. We first confirmed the projection from the IC to the NAc core and then disconnected these structures via asymmetrical excitotoxic lesions before training. Contralateral, but not ipsilateral, disconnection of the IC and NAc core disrupted outcome devaluation. We hypothesized that communication between the IC and NAc core is necessary for the retrieval of incentive value at test. To test this, we infused the GABAAagonist muscimol into the IC and the μ-opioid receptor antagonist CTAP into the contralateral NAc before the choice extinction test. As expected, inactivation of the IC in one hemisphere and blocking μ-opioid receptors in the contralateral NAc core abolished outcome-selective devaluation. These results suggest that the IC and NAc core form part of a circuit mediating the retrieval of outcome values and the subsequent choice between goal-directed actions based on those values.

Pasin, D, Bidny, S & Fu, S 2015, 'Analysis of New Designer Drugs in Post-Mortem Blood Using High-Resolution Mass Spectrometry', JOURNAL OF ANALYTICAL TOXICOLOGY, vol. 39, no. 3, pp. 163-171.
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Patel, BS, Co, WS, Donat, C, Wang, M, Che, W, Prabhala, P, Schuster, F, Schulz, V, Martin, JL & Ammit, AJ 2015, 'Repression of breast cancer cell growth by proteasome inhibitorsin vitro: impact of mitogen-activated protein kinase phosphatase 1', Cancer Biology & Therapy, vol. 16, no. 5, pp. 780-789.
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Patel, BS, Prabhala, P, Oliver, BG & Ammit, AJ 2015, 'Inhibitors of Phosphodiesterase 4, but Not Phosphodiesterase 3, Increase β₂-Agonist–Induced Expression of Antiinflammatory Mitogen-Activated Protein Kinase Phosphatase 1 in Airway Smooth Muscle Cells', American Journal of Respiratory Cell and Molecular Biology, vol. 52, no. 5, pp. 634-640.
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Copyright © 2015 by the American Thoracic Society. β2-agonists are principally used in asthma to provide bronchodilation; however, they also have antiinflammatory properties, due, in part, to their ability to up-regulate mitogenactivated protein kinase phosphatase (MKP) 1 in a cAMP-dependent manner. Phosphodiesterases (PDEs) are attractive targets for potentiating the antiinflammatory response. There are 11 subfamilies of PDE enzymes; among these, inhibition of PDE3 and PDE4 are the main targets for airway smooth muscle (ASM). PDE enzymes are important intracellular regulators that catalyze the breakdown of cyclic adenosine monophosphate (cAMP) and/or 3',5'-cyclic guanosine monophosphate to their inactive forms. Given that MKP-1 is cAMP dependent, and inhibition of PDE acts to increase β2-agonist-induced cAMP, it is possible that the presence of PDE inhibitors may enhance β2-adrenoceptor-mediated responses. We address this herein by comparing the ability of a panel of inhibitors against PDE3 (cilostamide, cilostazol, milrinone) or PDE4 (cilomilast, piclamilast, rolipram) to increase cAMP, MKP-1 mRNA expression, and protein up-regulation in ASM cells induced in response to the β2-agonist formoterol. Our data show that inhibitors of PDE4, but not PDE3, increase β2-agonist-induced cAMP and induce MKP-1 mRNA expression and protein up-regulation. When cAMP was increased, there was a concomitant increase in MKP-1 levels and significant inhibition of TNF-α-induced CXCL8 (IL-8). This result was consistent with all PDE4 inhibitors examined but not for the PDE3 inhibitors. These findings reinforce cAMP-dependent control of MKP-1 expression, and suggest that PDE4 is the predominant PDE isoform responsible for formoterolinduced cAMP breakdown in ASM cells. Our study is the first to demonstrate that PDE4 inhibitors augment antiinflammatory effects of β2-agonists via increased MKP-1 expression in ASM cells.

Patra, RW, Chapman, JC, Lim, RP, Gehrke, PC & Sunderam, RM 2015, 'Interactions between water temperature and contaminant toxicity to freshwater fish', Environmental Toxicology and Chemistry, vol. 34, no. 8, pp. 1809-1817.
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AbstractWarming of freshwaters as a result of climate change is expected to have complex interactions with the toxicity of contaminants to aquatic organisms. The present study evaluated the effects of temperature on the acute toxicity of endosulfan, chlorpyrifos, and phenol to 3 warm water species of fish—silver perch, rainbowfish, and western carp gudgeon—and 1 cold water species, rainbow trout. Endosulfan was more toxic to silver perch at 30 °C and 35 °C than at 15 °C, 20 °C and 25 °C during short exposures of 24 h, but at 96 h, temperature had no effect on toxicity. Toxicity to rainbow trout increased with increasing temperature, whereas warm water species exhibited maximum toxicity at around 30 °C, decreasing again toward 35 °C. Chlorpyrifos became more toxic to all species with increasing temperature. Phenol toxicity to all species decreased at low to intermediate temperatures; but as temperatures increased further toward the upper thermal limit, phenol became more toxic. Increasing toxicity in the upper thermal range of cold water species may contribute to upstream range contraction in rivers with high toxicant loads. In contrast, warm water species may not exhibit a range shift within rivers as a result of interactions between temperature and toxicity. Catchment management to offset global warming at local scales may present opportunities to mitigate increased toxicity of contaminants to fish. Environ Toxicol Chem 2015;34:1809–1817. © 2015 SETAC

Paudel, KR & Panth, N 2015, 'Phytochemical Profile and Biological Activity ofNelumbo nucifera', Evidence-Based Complementary and Alternative Medicine, vol. 2015, pp. 1-16.
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Nelumbo nuciferaGaertn. (Nymphaeaceae) is a potential aquatic crop grown and consumed throughout Asia. All parts ofN. nuciferahave been used for various medicinal purposes in various systems of medicine including folk medicines, Ayurveda, Chinese traditional medicine, and oriental medicine. Many chemical constituents have been isolated till the date. However, the bioactive constituents of lotus are mainly alkaloids and flavonoids. Traditionally, the whole plant of lotus was used as astringent, emollient, and diuretic. It was used in the treatment of diarrhea, tissue inflammation, and homeostasis. The rhizome extract was used as antidiabetic and anti-inflammatory properties due to the presence of asteroidal triterpenoid. Leaves were used as an effective drug for hematemesis, epistaxis, hemoptysis, hematuria, and metrorrhagia. Flowers were used to treat diarrhea, cholera, fever, and hyperdipsia. In traditional medicine practice, seeds are used in the treatment of tissue inflammation, cancer and skin diseases, leprosy, and poison antidote. Embryo of lotus seeds is used in traditional Chinese medicine as Lian Zi Xin, which primarily helps to overcome nervous disorders, insomnia, and cardiovascular diseases (hypertension and arrhythmia). Nutritional value of lotus is as important as pharmaceutical value. These days’ different parts of lotus have been consumed as functional foods. Thus, lotus can be regarded as a potential nutraceutical source.

Paul, B, Hare, DJ, Bishop, DP, Paton, C, Nguyen, VT, Cole, N, Niedwiecki, MM, Andreozzi, E, Vais, A, Billings, JL, Bray, L, Bush, AI, McColl, G, Roberts, BR, Adlard, PA, Finkelstein, DI, Hellstrom, J, Hergt, JM, Woodhead, JD & Doble, PA 2015, 'Visualising mouse neuroanatomy and function by metal distribution using laser ablation-inductively coupled plasma-mass spectrometry imaging', Chemical Science, vol. 6, no. 10, pp. 5383-5393.
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Studying the neuroanatomy of the mouse brain using imaging mass spectrometry and chemometric analysis.

Periasamy, S, Nair, HAS, Lee, KWK, Ong, J, Goh, JQJ, Kjelleberg, S & Rice, SA 2015, 'Pseudomonas aeruginosa PAO1 exopolysaccharides are important for mixed species biofilm community development and stress tolerance', Frontiers in Microbiology, vol. 6.
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Pernice, M, Dunn, SR, Tonk, L, Dove, S, Domart‐Coulon, I, Hoppe, P, Schintlmeister, A, Wagner, M & Meibom, A 2015, 'A nanoscale secondary ion mass spectrometry study of dinoflagellate functional diversity in reef‐building corals', Environmental Microbiology, vol. 17, no. 10, pp. 3570-3580.
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SummaryNutritional interactions between corals and symbiotic dinoflagellate algae lie at the heart of the structural foundation of coral reefs. Whilst the genetic diversity of Symbiodinium has attracted particular interest because of its contribution to the sensitivity of corals to environmental changes and bleaching (i.e. disruption of coral–dinoflagellate symbiosis), very little is known about the in hospite metabolic capabilities of different Symbiodinium types. Using a combination of stable isotopic labelling and nanoscale secondary ion mass spectrometry (NanoSIMS), we investigated the ability of the intact symbiosis between the reef‐building coral Isopora palifera, and Symbiodinium C or D types, to assimilate dissolved inorganic carbon (via photosynthesis) and nitrogen (as ammonium). Our results indicate that Symbiodinium types from two clades naturally associated with I. palifera possess different metabolic capabilities. The S

Perrault, KA, Rai, T, Stuart, BH & Forbes, SL 2015, 'Seasonal comparison of carrion volatiles in decomposition soil using comprehensive two-dimensional gas chromatography – time of flight mass spectrometry', Analytical Methods, vol. 7, no. 2, pp. 690-698.
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This study examines the effects of extrinsic variables (weather, soil characteristics, etc.) on the variation in volatiles produced during carrion decomposition during Australian summer and winter seasons.

Perrault, KA, Stefanuto, P-H, Stuart, BH, Rai, T, Focant, J-F & Forbes, SL 2015, 'Detection of decomposition volatile organic compounds in soil following removal of remains from a surface deposition site', Forensic Science, Medicine, and Pathology, vol. 11, no. 3, pp. 376-387.
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© 2015, Springer Science+Business Media New York. Purpose: Cadaver-detection dogs use volatile organic compounds (VOCs) to search for human remains including those deposited on or beneath soil. Soil can act as a sink for VOCs, causing loading of decomposition VOCs in the soil following soft tissue decomposition. The objective of this study was to chemically profile decomposition VOCs from surface decomposition sites after remains were removed from their primary location. Methods: Pig carcasses were used as human analogues and were deposited on a soil surface to decompose for 3 months. The remains were then removed from each site and VOCs were collected from the soil for 7 months thereafter and analyzed by comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (GC×GC–TOFMS). Results: Decomposition VOCs diminished within 6 weeks and hydrocarbons were the most persistent compound class. Decomposition VOCs could still be detected in the soil after 7 months using Principal Component Analysis. Conclusions: This study demonstrated that the decomposition VOC profile, while detectable by GC×GC–TOFMS in the soil, was considerably reduced and altered in composition upon removal of remains. Chemical reference data is provided by this study for future investigations of canine alert behavior in scenarios involving scattered or scavenged remains.

Perrault, KA, Stefanuto, P-H, Stuart, BH, Rai, T, Focant, J-F & Forbes, SL 2015, 'Reducing variation in decomposition odour profiling using comprehensive two-dimensional gas chromatography', Journal of Separation Science, vol. 38, no. 1, pp. 73-80.
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© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Challenges in decomposition odour profiling have led to variation in the documented odour profile by different research groups worldwide. Background subtraction and use of controls are important considerations given the variation introduced by decomposition studies conducted in different geographical environments. The collection of volatile organic compounds (VOCs) from soil beneath decomposing remains is challenging due to the high levels of inherent soil VOCs, further confounded by the use of highly sensitive instrumentation. This study presents a method that provides suitable chromatographic resolution for profiling decomposition odour in soil by comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry using appropriate controls and field blanks. Logarithmic transformation and t-testing of compounds permitted the generation of a compound list of decomposition VOCs in soil. Principal component analysis demonstrated the improved discrimination between experimental and control soil, verifying the value of the data handling method. Data handling procedures have not been well documented in this field and standardisation would thereby reduce misidentification of VOCs present in the surrounding environment as decomposition byproducts. Uniformity of data handling and instrumental procedures will reduce analytical variation, increasing confidence in the future when investigating the effect of taphonomic variables on the decomposition VOC profile.

Perrault, KA, Stefanuto, P-H, Stuart, BH, Rai, T, Focant, J-F & Forbes, SL 2015, 'Reducing variation in decomposition odour profiling using comprehensive two-dimensional gas chromatography', Journal of Separation Science, vol. 38, no. 1, pp. NA-NA.
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Perry, Y, Murrihy, RC, Varlow, M, Dedousis‐Wallace, A, Ellis, DM, Langdon, R & Kidman, AD 2015, 'The development and implementation of a pilot CBT for early psychosis service: achievements and challenges', Early Intervention in Psychiatry, vol. 9, no. 3, pp. 252-259.
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AbstractAimCognitive behaviour therapy (CBT) is a clinically indicated treatment for first‐episode psychosis. Despite this, CBT for early psychosis is not routinely available as part of standard mental health services in Australia. The aim of this pilot project was to develop a CBT for early psychosis service to be provided as an adjunct to existing community mental health services. This study examined the feasibility of this service model, delivered in a real‐world setting. A secondary aim was to explore the effectiveness of this service, as measured by clinical and functional outcomes.MethodsParticipants living in northern Sydney, Australia, and who had recently experienced a first episode of psychosis, were offered up to 20 sessions of individual CBT. Service feasibility was measured via attrition rates, therapy attendance and referrer feedback. Measures of psychosis, depression, anxiety and psychosocial functioning, were assessed pretreatment, after six and 12 sessions, and at 3 months post‐treatment.ResultsNineteen clients attended treatment to completion. Survey feedback from referrers affirmed the positive impact of the service on clients' recovery. Additionally, clients showed improvements in symptoms of psychosis over the first three time points. Psychosocial functioning also shifted from the moderately to mildly impaired range ...

Plank, MW, Maltby, S, Tay, HL, Stewart, J, Eyers, F, Hansbro, PM & Foster, PS 2015, 'MicroRNA Expression Is Altered in an Ovalbumin-Induced Asthma Model and Targeting miR-155 with Antagomirs Reveals Cellular Specificity', PLOS ONE, vol. 10, no. 12, pp. e0144810-e0144810.
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©2015 Plank et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source arecredited. MicroRNAs are post-transcriptional regulators of gene expression that are differentially regulated during development and in inflammatory diseases. A role for miRNAs in allergic asthma is emerging and further investigation is required to determine whether they may serve as potential therapeutic targets. We profiled miRNA expression in murine lungs from an ovalbumin-induced allergic airways disease model, and compared expression to animals receiving dexamethasone treatment and non-allergic controls. Our analysis identified 29 miRNAs that were significantly altered during allergic inflammation. Target prediction analysis revealed novel genes with altered expression in allergic airways disease and suggests synergistic miRNA regulation of target mRNAs. To assess the impacts of one induced miRNA on pathology, we targeted miR-155-5p using a specific antagomir. Antagomir administration successfully reduced miR-155-5p expression with high specificity, but failed to alter the disease phenotype. Interestingly, further investigation revealed that antagomir delivery has variable efficacy across different immune cell types, effectively targeting myeloid cell populations, but exhibiting poor uptake in lymphocytes. Our findings demonstrate that antagomir-based targeting of miRNA function in the lung is highly specific, but highlights cell-specificity as a key limitation to be considered for antagomir-based strategies as therapeutics.

Platen, E & Tappe, S 2015, 'Real-World Forward Rate Dynamics With Affine Realizations', STOCHASTIC ANALYSIS AND APPLICATIONS, vol. 33, no. 4, pp. 573-608.
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Prabhala, P & Ammit, AJ 2015, 'Tristetraprolin and Its Role in Regulation of Airway Inflammation', Molecular Pharmacology, vol. 87, no. 4, pp. 629-638.
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Prabhala, P, Bunge, K, Rahman, MM, Ge, Q, Clark, AR & Ammit, AJ 2015, 'Temporal regulation of cytokine mRNA expression by tristetraprolin: dynamic control by p38 MAPK and MKP-1', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 308, no. 9, pp. L973-L980.
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Cytokines drive many inflammatory diseases, including asthma. Understanding the molecular mechanisms responsible for cytokine secretion will allow us to develop novel strategies to repress inflammation in the future. Harnessing the power of endogenous anti-inflammatory proteins is one such strategy. In this study, we investigate the p38 MAPK-mediated regulatory interaction of two anti-inflammatory proteins, mitogen-activated protein kinase phosphatase 1 (MKP-1) and tristetraprolin (TTP), in the context of asthmatic inflammation. Using primary cultures of airway smooth muscle cells in vitro, we explored the temporal regulation of IL-6 cytokine mRNA expression upon stimulation with TNF-α. Intriguingly, the temporal profile of mRNA expression was biphasic. This was not due to COX-2-derived prostanoid upregulation, increased expression of NLRP3 inflammasome components, or upregulation of the cognate receptor for TNF-α-TNFR1. Rather, the biphasic nature of TNF-α-induced IL-6 mRNA expression was regulated temporally by the RNA-destabilizing molecule, TTP. Importantly, TTP function is controlled by p38 MAPK, and our study reveals that its expression in airway smooth muscle cells is p38 MAPK-dependent and its anti-inflammatory activity is also controlled by p38 MAPK-mediated phosphorylation. MKP-1 is a MAPK deactivator; thus, by controlling p38 MAPK phosphorylation status in a temporally distinct manner, MKP-1 ensures that TTP is expressed and made functional at precisely the correct time to repress cytokine expression. Together, p38 MAPK, MKP-1, and TTP may form a regulatory network that exerts significant control on cytokine secretion in proasthmatic inflammation through precise temporal signaling.

Pravadali-Cekic, S, Jones, A, Kazarian, AA, Paull, B, Soliven, A, Ritchie, H, Camenzuli, M, Dennis, GR & Andrew Shalliker, R 2015, 'Using reaction flow chromatography for the analysis of amino acid: Derivatisation with fluorescamine reagent', Microchemical Journal, vol. 121, pp. 141-149.
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Pravadali-Cekic, S, Kocic, D, Conlan, X & Shalliker, RA 2015, 'Multiplexed Detection: Fast Comprehensive Sample Analysis of Tobacco Leaf Extracts Using HPLC with AFT Columns', Journal of Liquid Chromatography & Related Technologies, vol. 38, no. 19, pp. 1753-1758.
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Pulpitel, T, Pernice, M, Simpson, S & Ponton, F 2015, 'Tissue-Specific Immune Gene Expression in the Migratory Locust, Locusta Migratoria', Insects, vol. 6, no. 2, pp. 368-380.
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The ability of hosts to respond to infection involves several complex immune recognition pathways. Broadly conserved pathogen-associated molecular patterns (PAMPs) allow individuals to target a range of invading microbes. Recently, studies on insect innate immunity have found evidence that a single pathogen can activate different immune pathways across species. In this study, expression changes in immune genes encoding peptidoglycan-recognition protein SA (PGRP-SA), gram-negative binding protein 1 (GNBP1) and prophenoloxidase (ProPO) were investigated in Locusta migratoria, following an immune challenge using injected lipopolysaccharide (LPS) solution from Escherichia coli. Since immune activation might also be tissue-specific, gene expression levels were followed across a range of tissue types. For PGRP-SA, expression increased in response to LPS within all seven of the tissue-types assayed and differed significantly between tissues. Expression of GNBP1 similarly varied across tissue types, yet showed no clear expression difference between LPS-injected and uninfected locusts. Increases in ProPO expression in response to LPS, however, could only be detected in the gut sections. This study has revealed tissue-specific immune response to add a new level of complexity to insect immune studies. In addition to variation in recognition pathways identified in previous works, tissue-specificity should be carefully considered in similar works.

Qi, X, Luo, R, Carroll, RJ & Zhao, H 2015, 'Sparse Regression by Projection and Sparse Discriminant Analysis', Journal of Computational and Graphical Statistics, vol. 24, no. 2, pp. 416-438.
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© 2015, © American Statistical Association, Institute of Mathematical Statistics, and Interface Foundation of North America. Recent years have seen active developments of various penalized regression methods, such as LASSO and elastic net, to analyze high-dimensional data. In these approaches, the direction and length of the regression coefficients are determined simultaneously. Due to the introduction of penalties, the length of the estimates can be far from being optimal for accurate predictions. We introduce a new framework, regression by projection, and its sparse version to analyze high-dimensional data. The unique nature of this framework is that the directions of the regression coefficients are inferred first, and the lengths and the tuning parameters are determined by a cross-validation procedure to achieve the largest prediction accuracy. We provide a theoretical result for simultaneous model selection consistency and parameter estimation consistency of our method in high dimension. This new framework is then generalized such that it can be applied to principal components analysis, partial least squares, and canonical correlation analysis. We also adapt this framework for discriminant analysis. Compared with the existing methods, where there is relatively little control of the dependency among the sparse components, our method can control the relationships among the components. We present efficient algorithms and related theory for solving the sparse regression by projection problem. Based on extensive simulations and real data analysis, we demonstrate that our method achieves good predictive performance and variable selection in the regression setting, and the ability to control relationships between the sparse components leads to more accurate classification. In supplementary materials available online, the details of the algorithms and theoretical proofs, and R codes for all simulation studies are provided.

Quiroz, M, Tran, M-N, Villani, M & Kohn, R 2015, 'Speeding Up MCMC by Delayed Acceptance and Data Subsampling', Journal of Computational and Graphical Statistics, vol. 27, no. 1, pp. 12-22.
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The complexity of the Metropolis-Hastings (MH) algorithm arises from therequirement of a likelihood evaluation for the full data set in each iteration.Payne and Mallick (2015) propose to speed up the algorithm by a delayedacceptance approach where the acceptance decision proceeds in two stages. Inthe first stage, an estimate of the likelihood based on a random subsampledetermines if it is likely that the draw will be accepted and, if so, thesecond stage uses the full data likelihood to decide upon final acceptance.Evaluating the full data likelihood is thus avoided for draws that are unlikelyto be accepted. We propose a more precise likelihood estimator whichincorporates auxiliary information about the full data likelihood while onlyoperating on a sparse set of the data. We prove that the resulting delayedacceptance MH is more efficient compared to that of Payne and Mallick (2015).The caveat of this approach is that the full data set needs to be evaluated inthe second stage. We therefore propose to substitute this evaluation by anestimate and construct a state-dependent approximation thereof to use in thefirst stage. This results in an algorithm that (i) can use a smaller subsamplem by leveraging on recent advances in Pseudo-Marginal MH (PMMH) and (ii) isprovably within $O(m^{-2})$ of the true posterior.

Rahman, MA, Hogan, B, Duncan, E, Doyle, C, Rahman, MM, Nguyen, TV, Lim, RP, Maher, W, Naidu, R, Krassoi, R, Vigneswaran, S & Hassler, C 2015, 'Ecotoxicological Effects of an Arsenic Remediation Method on Three Freshwater Organisms—Lemna disperma, Chlorella sp. CE-35 and Ceriodaphnia cf. dubia', Water, Air, & Soil Pollution, vol. 226, no. 12, pp. 1-10.
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© 2015 Springer International Publishing Switzerland. Chemical methods have been used for the remediation of arsenic (As)-contaminated water; however, ecological consequences of these methods have not been properly addressed. The present study evaluated the effects of the Fe-oxide-coated sand (IOCS) remediation method on As toxicity to freshwater organisms (Lemna disperma, Chlorella sp. CE-35, and Ceriodaphnia cf. dubia). The As removal efficiency by IOCS decreased substantially with time. The IOCS remediation method was less effective at suppressing the toxicity of AsV than AsIII to L. disperma but was highly effective in reducing both the AsIII and AsV toxicity to C. cf. dubia. The growth of Chlorella sp. was significantly higher (p < 0.05) in remediated and pre-remediated water than in controls (non-As-contaminated filtered Colo River water) for AsIII, while the opposite was observed for AsV, indicating that AsV is more toxic than AsIII to this microalga. Although the IOCS can efficiently remove As from contaminated water, residual As and other constituents (e.g. Fe, nitrate) in the remediated water had a significant effect on freshwater organisms.

Rahman, MM, Rumzhum, NN, Morris, JC, Clark, AR, Verrills, NM & Ammit, AJ 2015, 'Basal protein phosphatase 2A activity restrains cytokine expression: role for MAPKs and tristetraprolin', Scientific Reports, vol. 5, no. 1, pp. 1-16.
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AbstractPP2A is a master controller of multiple inflammatory signaling pathways. It is a target in asthma; however the molecular mechanisms by which PP2A controls inflammation warrant further investigation. In A549 lung epithelial cells in vitro we show that inhibition of basal PP2A activity by okadaic acid (OA) releases restraint on MAPKs and thereby increases MAPK-mediated pro-asthmatic cytokines, including IL-6 and IL-8. Notably, PP2A inhibition also impacts on the anti-inflammatory protein – tristetraprolin (TTP), a destabilizing RNA binding protein regulated at multiple levels by p38 MAPK. Although PP2A inhibition increases TTP mRNA expression, resultant TTP protein builds up in the hyperphosphorylated inactive form. Thus, when PP2A activity is repressed, pro-inflammatory cytokines increase and anti-inflammatory proteins are rendered inactive. Importantly, these effects can be reversed by the PP2A activators FTY720 and AAL(s), or more specifically by overexpression of the PP2A catalytic subunit (PP2A-C). Moreover, PP2A plays an important role in cytokine expression in cells stimulated with TNFα; as inhibition of PP2A with OA or PP2A-C siRNA results in significant increases in cytokine production. Collectively, these data reveal the molecular mechanisms of PP2A regulation and highlight the potential of boosting the power of endogenous phosphatases as novel anti-inflammatory strategies to combat asthmatic inflammation.

Rajoka, MI, Idrees, S, Ashfaq, UA, Ehsan, B & Haq, A 2015, 'Determination of Substrate Specificities Against ��-Glucosidase A (BglA) from Thermotoga maritime: A Molecular Docking Approach', Journal of Microbiology and Biotechnology, vol. 25, no. 1, pp. 44-49.
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Raven, JA & Ralph, PJ 2015, 'Enhanced biofuel production using optimality, pathway modification and waste minimization', JOURNAL OF APPLIED PHYCOLOGY, vol. 27, no. 1, pp. 1-31.
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In response to their environment, algae in the wild may use an approximation to optimality of resource allocation in cellular structures, photosynthetic pigments, enzymes, transporters in membranes and RNAs and in their genetic material. However, under controlled conditions, when algae are grown for biofuel (lipid) production for example, some of these processes can be altered to increase the efficiency of photosynthesis and therefore, lipid yield. This suggests that there is scope for selecting mutations and for genetic engineering at various levels in the photosynthetic apparatus with the aim of increasing efficiency of photon use and the rate of transformation of resources per unit biomass to improve biofuel yields. More specifically, the wavelength range covered by photosynthetic pigments and photochemical reaction centres could be increased, the number of protons transported from the thylakoid lumen to the stroma per unit ATP synthesised by the ATP synthetase could be decreased, the fluctuating light effect could be utilised and photosynthetic pathways changed, e.g. replacing part or all of the current machinery for autotrophic fixation of inorganic carbon. There are also possibilities for decreasing carbon loss by decreasing `wasteful aspects of dark respiration and of dissolved organic carbon loss. Provided that the environmental fluctuations to which algal growth conditions are constrained, there are possibilities for decreasing the resource costs of protection from ROS, and by down-regulating photoprotective mechanisms, as well as limiting the capacity to repair processes related to photoinhibition. Decreased protein turnover is also a potential energetic saving. These interventions apply to individual processes; however, this may not be immediately incorporated into the optimal allocation of resources by the alga, and further intervention using a system biology approach may be required.

Raymond, BBA & Djordjevic, S 2015, 'Exploitation of plasmin(ogen) by bacterial pathogens of veterinary significance', Veterinary Microbiology, vol. 178, no. 1-2, pp. 1-13.
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© 2015 Elsevier B.V. The plasminogen (Plg) system plays an important homeostatic role in the degradation of fibrin clots, extracellular matrices and tissue barriers important for cellular migration, as well as the promotion of neurotransmitter release. Plg circulates in plasma at physiologically high concentrations (150-200μgml^-1) as an inactive proenzyme. Proteins enriched in lysine and other positively charged residues (histidine and arginine) as well as glycosaminoglycans and gangliosides bind Plg. The binding interaction initiates a structural adjustment to the bound Plg that facilitates cleavage by proteases (plasminogen activators tPA and uPA) that activate Plg to the active serine protease plasmin. Both pathogenic and commensal bacteria capture Plg onto their cell surface and promote its conversion to plasmin. Many microbial Plg-binding proteins have been described underpinning the importance this process plays in how bacteria interact with their hosts. Bacteria exploit the proteolytic capabilities of plasmin by (i) targeting the mammalian fibrinolytic system and degrading fibrin clots, (ii) remodeling the extracellular matrix and generating bioactive cleavage fragments of the ECM that influence signaling pathways, (iii) activating matrix metalloproteinases that assist in the destruction of tissue barriers and promote microbial metastasis and (iv) destroying immune effector molecules. There has been little focus on the exploitation of the fibrinolytic system by veterinary pathogens. Here we describe several pathogens of veterinary significance that possess adhesins that bind plasmin(ogen) onto their cell surface and promote its activation to plasmin. Cumulative data suggests that these attributes provide pathogenic and commensal bacteria with a means to colonize and persist within the host environment.

Raymond, BBA, Jenkins, C, Seymour, LM, Tacchi, JL, Widjaja, M, Jarocki, VM, Deutscher, AT, Turnbull, L, Whitchurch, CB, Padula, MP & Djordjevic, SP 2015, 'Proteolytic processing of the cilium adhesin MHJ_0194 (P123(J)) in Mycoplasma hyopneumoniae generates a functionally diverse array of cleavage fragments that bind multiple host molecules', CELLULAR MICROBIOLOGY, vol. 17, no. 3, pp. 425-444.
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© 2014 John Wiley & Sons Ltd. Summary: Mycoplasma hyopneumoniae, the aetiological agent of porcine enzootic pneumonia, regulates the presentation of proteins on its cell surface via endoproteolysis, including those of the cilial adhesin P123 (MHJ_0194). These proteolytic cleavage events create functional adhesins that bind to proteoglycans and glycoproteins on the surface of ciliated and non-ciliated epithelial cells and to the circulatory host molecule plasminogen. Two dominant cleavage events of the P123 preprotein have been previously characterized; however, immunoblotting studies suggest that more complex processing events occur. These extensive processing events are characterized here. The functional significance of the P97 cleavage fragments is also poorly understood. Affinity chromatography using heparin, fibronectin and plasminogen as bait and peptide arrays were used to expand our knowledge of the adhesive capabilities of P123 cleavage fragments and characterize a novel binding motif in the C-terminus of P123. Further, we use immunohistochemistry to examine in vivo, the biological significance of interactions between M.hyopneumoniae and fibronectin and show that M.hyopneumoniae induces fibronectin deposition at the site of infection on the ciliated epithelium. Our data supports the hypothesis that M. hyopneumoniae possesses the molecular machinery to influence key molecular communication pathways in host cells.

Rees, JD, Webb, JK, Crowther, MS & Letnic, M 2015, 'Carrion subsidies provided by fishermen increase predation of beach‐nesting bird nests by facultative scavengers', Animal Conservation, vol. 18, no. 1, pp. 44-49.
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AbstractMany predators are also scavengers that feed on carrion and human refuse. Therefore, the availability of carrion can elevate the abundance or activity of facultative scavengers, amplifying predation pressure on prey. On Australian beaches, fishermen often discard fish carcasses that could attract facultative scavengers, both native, such as Australian ravens Corvus coronoides, and invasive, such as European red foxes Vulpes vulpes, and result in elevated rates of predation on wildlife. We tested whether the presence of fish carcasses increased the risk of depredation for nearby nests of beach‐nesting birds by deploying artificial nests in 12 subsidized and 12 control patches, spaced 1 km apart, on a beach. We placed a fish carcass in each subsidized patch, but not at control patches. In each patch, we placed two artificial nests, which resembled red‐capped plover Charadrius ruficapillus nests, 80 m apart and 40 m from carcasses at subsidized patches. Nest predators were identified from tracks and predator activity near subsidized and control nests was measured by counting tracks crossing a straight transect (220 m). The activity of a native predator, the Australian raven, was 17 times higher near (<80 m) nests with fish carcasses than nests without carcasses. After 72 h, 96% of nests near carcasses were depredated compared with 30% of nests without carcasses. Ravens were identified as t...

Rees, JD, Webb, JK, Crowther, MS & Letnic, M 2015, 'Ravens are a key threat to beach-nesting birds', Australian Field Ornithology, vol. 32, no. 2, pp. 100-107.
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Depredation of nests by native and introduced predators is contributing to the decline of beach-nesting shorebirds in many parts of Australia. Determining the relative importance of these predators is crucial for designing and implementing appropriate management strategies for shorebird conservation. We deployed and monitored 82 artificial Red-capped Plover Charadrius ruficapillus nests, on six beaches within a 140-km stretch of the New South Wales Lower North Coast, to identify the main predators of beach-nesting shorebird nests and their relative importance. After 18 days, 53 (63%) artificial nests were depredated. Australian Ravens Corvus coronoides and Forest Ravens C. tasmanicus were the chief nest-predators, and were responsible for depredating 40 (49%) nests collectively. Comparatively few nests were depredated by European Red Foxes Vulpes vulpes, which depredated 8 (10%) nests. The rate of depredation (nests depredated/2 days) by ravens was greater than the rate of depredation by foxes (P < 0.05). Other predators preyed upon 5 (5%) nests.

Reid, CJ, Chowdhury, PR & Djordjevic, SP 2015, 'Tn6026 and Tn6029 are found in complex resistance regions mobilised by diverse plasmids and chromosomal islands in multiple antibiotic resistant Enterobacteriaceae', Plasmid, vol. 80, pp. 127-137.
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Transposons flanked by direct copies of IS26 are important contributors to the evolution of multiple antibiotic resistance. Tn6029 and Tn6026 are examples of composite transposons that have become widely disseminated on small and large plasmids with different incompatibility markers in pathogenic and commensal Escherichia coli and various serovars of Salmonella enterica. Some of the plasmids that harbour these transposons also carry combinations of virulence genes. Recently, Tn6029 and Tn6026 and derivatives thereof have been found on chromosomal islands in both established and recently emerged pathogens. While Tn6029 and Tn6026 carry genes encoding resistance to older generation antibiotics, they also provide a scaffold for the introduction of genes encoding resistance to a wide variety of clinically relevant antibiotics that are mobilised by IS26. As a consequence, Tn6029 and Tn6026 or variants are likely to increasingly feature in complex resistance regions in multiple antibiotic resistant Enterobacteriaceae that threaten the health of humans and food production animals.

Reimers, JR 2015, 'The Importance of Motions that Accompany Those Occurring Along the Reaction Coordinate', Australian Journal of Chemistry, vol. 68, no. 8, pp. 1202-1202.
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The reaction coordinate is a well known quantity used to define the motions critical to chemical reactions, but many other motions always accompany it. These other motions are typically ignored but this is not always possible. Sometimes it is not even clear as to which motions comprise the reaction coordinate: spectral measurements that one may assume are dominated by the reaction coordinate could instead be dominated by the accompanying modes. Examples of different scenarios are considered. The assignment of the visible absorption spectrum of chlorophyll-a was debated for 50 years, with profound consequences for the understanding of how light energy is transported and harvested in natural and artificial solar-energy devices. We recently introduced a new, comprehensive, assignment, the centrepiece of which was determination of the reaction coordinate for an unrecognized photochemical process. The notion that spectroscopy and reactivity are so closely connected comes directly from Hush’s adiabatic theory of electron-transfer reactions. Its basic ideas are reviewed, similarities to traditional chemical theories drawn, key analytical results described, and the importance of the accompanying modes stressed. Also highlighted are recent advances that allow this theory to be applied to general transformations including isomerization processes, hybridization, aromaticity, hydrogen bonding, and understanding why the properties of first-row molecules such as NH3 (bond angle 108°) are so different to those of PH3–BiH3 (bond angles 90–93°). Historically, the question of what is the reaction coordinate and what is just an accompanying motion has not commonly been at the forefront of attention. In our new approach in which all chemical processes are described using the same core theory, this question becomes thrust forward as always being the most important qualitative feature to determine.

Reimers, JR, McKemmish, LK, McKenzie, RH & Hush, NS 2015, 'A unified diabatic description for electron transfer reactions, isomerization reactions, proton transfer reactions, and aromaticity', Physical Chemistry Chemical Physics, vol. 17, no. 38, pp. 24598-24617.
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A way is found for describing general chemical reactions using diabatic multi-state and “twin-state” models. (Image adapted with permission from https://www.flickr.com/photos/cybaea/64638988/).

Reimers, JR, McKemmish, LK, McKenzie, RH & Hush, NS 2015, 'Bond angle variations in XH₃[X = N, P, As, Sb, Bi]: the critical role of Rydberg orbitals exposed using a diabatic state model', Physical Chemistry Chemical Physics, vol. 17, no. 38, pp. 24618-24640.
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The origins of the observed bond angles in XH₃and XH₃⁺are explained using high-level calculations and a simple diabatic model.

Reimers, JR, McKemmish, LK, McKenzie, RH & Hush, NS 2015, 'Non-adiabatic effects in thermochemistry, spectroscopy and kinetics: the general importance of all three Born–Oppenheimer breakdown corrections', Physical Chemistry Chemical Physics, vol. 17, no. 38, pp. 24641-24665.
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Analytical and numerical solutions describing Born–Oppenheimer breakdown in a simple, widely applicable, model depict shortcomings in modern computational methods.

Reimers, JR, Panduwinata, D, Visser, J, Chin, Y, Tang, C, Goerigk, L, Ford, MJ, Sintic, M, Sum, T-J, Coenen, MJJ, Hendriksen, BLM, Elemans, JAAW, Hush, NS & Crossley, MJ 2015, 'A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers', Proceedings of the National Academy of Sciences, vol. 112, no. 45, pp. E6101-E6110.
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Significance First-principles free energy calculations, characterizing polymorphism of self-assembled monolayers (SAMs) of porphyrin molecules formed from solution onto graphite, are performed using efficient methods previously applied only to small-molecule reactivity. SAM structures are typically optimized in the absence of solvent using density functional theory embodying explicit dispersion corrections. Added then are dispersion-dominated implicit solvation energies and SAM formation entropies derived from both molecular and phonon vibration frequencies. Scanning tunneling microscopy (STM) images are measured, and polymorph formation free energies are approximated. Close parallels between experiment and theory support the hypothesis that the first seconds of SAM formation are under thermodynamic control, despite formed SAMs being kinetically trapped. Polymorphism is associated with large opposing changes to entropy and substrate−molecule and solvent−molecule interaction energies.

Ren, D & Leslie, LM 2015, 'Changes in Tropical Cyclone Activity over Northwest Western Australia in the Past 50 Years and a View of the Future 50 Years', Earth Interactions, vol. 19, no. 15, pp. 1-24.
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Abstract In the first half of this research, this study examines the trend in tropical cyclone (TC) activity over the economically important northwest Western Australia (NWA) TC basin (equator–40°S, 80°–140°E) based on statistical analyses of the International Best Track Archive for Climate Stewardship (IBTrACS) and large-scale environmental variables, which are known to be closely linked to the formation and longevity of TCs, from NCEP–NCAR reanalyses. In the second half, changes in TC activity from climate model projections for 2000–60 are compared for (i) no scenario change (CNTRL) and (ii) the moderate IPCC Special Report on Emission Scenarios (SRES) A1B scenario (EGHG). The aims are to (i) determine differences in mean annual TC frequency and intensity trends, (ii) test for differences between genesis and decay positions of CNTRL and EGHG projections using a nonparametric permutation test, and (iii) use kernel density estimation (KDE) for a cluster analysis of CNTRL and EGHG genesis and decay positions and generate their probability distribution functions. The main findings are there is little difference in the mean TC number over the period, but there is a difference in mean intensity; CNTRL and EGHG projections differ in mean genesis and decay positions in both latitude and longitude; and the KDE reveals just one cluster in both CNTRL and EGHG mean genesis and decay positions. The EGHG KDE is possibly disjoint, with a wider longitudinal spread. The results can be explained in terms of physical, meteorological, and sea surface temperature (SST) conditions, which provide natural limits to the spread of the genesis and decay points.

Ren, J, Liu, Q, Ellis, J & Li, J 2015, 'Positive-unlabeled learning for the prediction of conformational B-cell epitopes', BMC BIOINFORMATICS, vol. 16, no. 18.
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© 2015 Ren et al. Background: The incomplete ground truth of training data of B-cell epitopes is a demanding issue in computational epitope prediction. The challenge is that only a small fraction of the surface residues of an antigen are confirmed as antigenic residues (positive training data); the remaining residues are unlabeled. As some of these uncertain residues can possibly be grouped to form novel but currently unknown epitopes, it is misguided to unanimously classify all the unlabeled residues as negative training data following the traditional supervised learning scheme. Results: We propose a positive-unlabeled learning algorithm to address this problem. The key idea is to distinguish between epitope-likely residues and reliable negative residues in unlabeled data. The method has two steps: (1) identify reliable negative residues using a weighted SVM with a high recall; and (2) construct a classification model on the positive residues and the reliable negative residues. Complex-based 10-fold cross-validation was conducted to show that this method outperforms those commonly used predictors DiscoTope 2.0, ElliPro and SEPPA 2.0 in every aspect. We conducted four case studies, in which the approach was tested on antigens of West Nile virus, dihydrofolate reductase, beta-lactamase, and two Ebola antigens whose epitopes are currently unknown. All the results were assessed on a newly-established data set of antigen structures not bound by antibodies, instead of on antibody-bound antigen structures. These bound structures may contain unfair binding information such as bound-state B-factors and protrusion index which could exaggerate the epitope prediction performance. Source codes are available on request.

Restrepo-Coupe, N, Huete, A, Davies, K, Cleverly, J, Beringer, J, Eamus, D, van Gorsel, E, Hutley, LB & Meyer, WS 2015, 'Supplementary material to &quot;MODIS vegetation products as proxies of photosynthetic potential: a look across meteorological and biologic driven ecosystem productivity&quot;'.
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Ribaux, O, Crispino, F & Roux, C 2015, 'Forensic intelligence: deregulation or return to the roots of forensic science?', AUSTRALIAN JOURNAL OF FORENSIC SCIENCES, vol. 47, no. 1, pp. 61-71.
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This paper presents an overview of forensic intelligence through historical, operational and academic considerations. While forensic intelligence is thriving through new traceability of human activities, theoretical developments in policing and innovative technologies, it should mainly be seen as an opportunity for forensic science to contribute to making policing more` scientific in the broad sense. This paper supports the development of a modern framework to holistically use the information conveyed by forensic case data to inform policing processes, support decision-making and ensure transparency. It is argued that the scientific information, the trace, has to be privileged, rather than rejected from current debates, despite the potential fears prompted by the misinterpretation of the term `intelligence. Ulti- mately, forensic intelligence enables the emergence of a modern conception of forensic science.

Richman, MB & Leslie, LM 2015, 'Uniqueness and Causes of the California Drought', Procedia Computer Science, vol. 61, pp. 428-435.
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Richman, MB, Leslie, LM, Trafalis, TB & Mansouri, H 2015, 'Data selection using support vector regression', Advances in Atmospheric Sciences, vol. 32, no. 3, pp. 277-286.
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Ritchie, LE, Sturino, JM, Carroll, RJ, Rooney, LW, Azcarate-Peril, MA & Turner, ND 2015, 'Polyphenol-rich sorghum brans alter colon microbiota and impact species diversity and species richness after multiple bouts of dextran sodium sulfate-induced colitis', FEMS Microbiology Ecology, vol. 91, no. 3.
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Roberts, BR, Hare, DJ, McLean, CA, Conquest, A, Lind, M, Li, Q-X, Bush, AI, Masters, CL, Morganti-Kossmann, M-C & Frugier, T 2015, 'Traumatic brain injury induces elevation of Co in the human brain', METALLOMICS, vol. 7, no. 1, pp. 124-128.
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Roberts, T, Barratt, J, Sandaradura, I, Lee, R, Harkness, J, Marriott, D, Ellis, J & Stark, D 2015, 'Molecular Epidemiology of Imported Cases of Leishmaniasis in Australia from 2008 to 2014', PLOS ONE, vol. 10, no. 3.
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© 2015 Roberts et al. Leishmaniasis is a vector borne disease caused by protozoa of the genus Leishmania. Human leishmaniasis is not endemic in Australia though imported cases are regularly encountered. This study aimed to provide an update on the molecular epidemiology of imported leishmaniasis in Australia. Of a total of 206 biopsies and bone marrow specimens submitted to St Vincent's Hospital Sydney for leishmaniasis diagnosis by PCR, 55 were found to be positive for Leishmania DNA. All PCR products were subjected to restriction fragment length polymorphism analysis for identification of the causative species. Five Leishmania species/species complexes were identified with Leishmania tropica being the most common (30/55). Travel or prior residence in a Leishmania endemic region was the most common route of acquisition with ∼47% of patients having lived in or travelled to Afghanistan. Cutaneous leishmaniasis was the most common manifestation (94%) with only 3 cases of visceral leishmaniasis and no cases of mucocutaneous leishmaniasis encountered. This report indicates that imported leishmaniasis is becoming increasingly common in Australia due to an increase in global travel and immigration. As such, Australian clinicians must be made aware of this trend and consider leishmaniasis in patients with suspicious symptoms and a history of travel in endemic areas. This study also discusses the recent identification of a unique Leishmania species found in native kangaroos and a potential vector host which could create the opportunity for the establishment of a local transmission cycle within humans.

Roberts, T, Bush, S, Ellis, J, Harkness, J & Stark, D 2015, 'In Vitro Antimicrobial Susceptibility Patterns of Blastocystis', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, vol. 59, no. 8, pp. 4417-4423.
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Copyright © 2015, American Society for Microbiology. All Rights Reserved. Blastocystis is the most common human enteric protist with controversial clinical significance. Metronidazole is considered a first-line treatment for Blastocystis infection; however, there has been increasing evidence for the lack of efficacy of this treatment. Treatment failure has been reported in several clinical cases, and recent in vitro studies have suggested the occurrence of metronidazole-resistant strains. In this study, we tested 12 Blastocystis isolates from 4 common Blastocystis subtypes (ST1, ST3, ST4, and ST8) against 12 commonly used antimicrobials (metronidazole, paromomycin, ornidazole, albendazole, ivermectin, trimethoprim-sulfamethoxazole [TMP-SMX], furazolidone, nitazoxanide, secnidazole, fluconazole, nystatin, and itraconazole) at 10 different concentrations in vitro. It was found that each subtype showed little sensitivity to the commonly used metronidazole, paromomycin, and triple therapy (furazolidone, nitazoxanide, and secnidazole). This study highlights the efficacy of other potential drug treatments, including trimethoprim-sulfamethoxazole and ivermectin, and suggests that current treatment regimens be revised.

Roseblade, A, Luk, F, Ung, A & Bebawy, M 2015, 'Targeting Microparticle Biogenesis: A Novel Approach to the Circumvention of Cancer Multidrug Resistance', CURRENT CANCER DRUG TARGETS, vol. 15, no. 3, pp. 205-214.
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© 2015 Bentham Science Publishers. Microparticles (MPs) are released from most eukaryotic cells after the vesiculation of the plasma membrane and serve as vectors of long and short-range signaling. MPs derived from multidrug resistant (MDR) cancer cells carry molecular components of the donor cell such as nucleic acids and proteins, and can alter the activity of drug-sensitive recipient cells through the transfer of their cargo. Given the substantial role of MPs in the acquisition and dissemination of MDR, we propose that the inhibition of MP release provides a novel therapeutic approach. This study characterises the effect of a panel of molecules known to act on MP-biosynthetic pathways. We demonstrate a differential effect by these molecules on MP inhibition that appear dependent on the release of intracellular calcium stores following activation with the calcium ionophore A23187. Calpain inhibitor, PD-150606; a selective inhibitor of Rho-associated, coiled-coil containing protein kinase (ROCK), Y-27632; and the vitamin B5 derivative pantethine, inhibited MP release only upon prior activation with A23187. Calpain inhibitor II showed significant inhibition in the absence of cell activation, whereas the vitamin B5 derivatives cystamine dihydrochloride and cysteamine hydrochloride showed no effect on MP inhibition under either condition. In contrast the classical pharmacological inhibitor of MDR, the calcium channel blocker Verapamil, showed an increase in MP formation on resting cells. These results suggest a potential role for calcium in the mechanism of action for PD-150606, Y-27632 and pantethine. These molecules, together with calpain inhibitor II have shown promise as modulators of MP release and warrant consideration as potential candidates for the development of an alternative therapeutic strategy for the prevention of MP-mediated MDR in cancer.

ROSER, DJ, VAN DEN AKKER, B, BOASE, S, HAAS, CN, ASHBOLT, NJ & RICE, SA 2015, 'Dose–response algorithms for water-bornePseudomonas aeruginosafolliculitis', Epidemiology and Infection, vol. 143, no. 7, pp. 1524-1537.
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SUMMARYWe developed two dose–response algorithms forP. aeruginosapool folliculitis using bacterial and lesion density estimates, associated with undetectable, significant, and almost certain folliculitis. Literature data were fitted to Furumoto & Mickey's equations, developed for plant epidermis-invading pathogens:Nl = Aln(1 + BC) (log-linear model);Pinf = 1−e(−rcC)(exponential model), whereAandBare 2.51644 × 107lesions/m2and 2.28011 × 10−11 c.f.u./mlP. aeruginosa, respectively;C = pathogen density (c.f.u./ml),Nl = folliculitis lesions/m2,Pinf = probability of infection, andrC = 4·3 × 10−7 c.f.u./mlP. aeruginosa. Outbreak data indicates these algorithms apply to exposure durations of 41 ± 25 min. Typical water quality benchmarks (≈10−2 c.f.u./ml) appear conservative but still useful as the literature indicated repeated detection likely implies unstable control barriers and bacterial bloom potential. In future, culture-based outbreak testing should be supplemented with quantitative polymerase chain reaction and organic carbon assays, and quantification of folliculitis aetiology to better understandP. aeruginosa

Roulis, E, Bachmann, N, Humphrys, M, Myers, G, Huston, W, Polkinghorne, A & Timms, P 2015, 'Phylogenetic analysis of human Chlamydia pneumoniae strains reveals a distinct Australian indigenous clade that predates European exploration of the continent', BMC Genomics, vol. 16, no. 1, pp. 1-15.
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© 2015 Roulis et al. Background: The obligate intracellular bacterium Chlamydia pneumoniae is a common respiratory pathogen, which has been found in a range of hosts including humans, marsupials and amphibians. Whole genome comparisons of human C. pneumoniae have previously highlighted a highly conserved nucleotide sequence, with minor but key polymorphisms and additional coding capacity when human and animal strains are compared. Results: In this study, we sequenced three Australian human C. pneumoniae strains, two of which were isolated from patients in remote indigenous communities, and compared them to all available C. pneumoniae genomes. Our study demonstrated a phylogenetically distinct human C. pneumoniae clade containing the two indigenous Australian strains, with estimates that the most recent common ancestor of these strains predates the arrival of European settlers to Australia. We describe several polymorphisms characteristic to these strains, some of which are similar in sequence to animal C. pneumoniae strains, as well as evidence to suggest that several recombination events have shaped these distinct strains. Conclusions: Our study reveals a greater sequence diversity amongst both human and animal C. pneumoniae strains, and suggests that a wider range of strains may be circulating in the human population than current sampling indicates.

Roulis, E, Bachmann, NL, Myers, GSA, Huston, W, Summersgill, J, Hudson, A, Dreses-Werringloer, U, Polkinghorne, A & Timms, P 2015, 'Comparative genomic analysis of human Chlamydia pneumoniae isolates from respiratory, brain and cardiac tissues', Genomics, vol. 106, no. 6, pp. 373-383.
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© 2015 Elsevier Inc. Chlamydia pneumoniae is an obligate intracellular bacterium implicated in a wide range of human diseases including atherosclerosis and Alzheimer's disease. Efforts to understand the relationships between C. pneumoniae detected in these diseases have been hindered by the availability of sequence data for non-respiratory strains. In this study, we sequenced the whole genomes for C. pneumoniae isolates from atherosclerosis and Alzheimer's disease, and compared these to previously published C. pneumoniae genomes. Phylogenetic analyses of these new C. pneumoniae strains indicate two sub-groups within human C. pneumoniae, and suggest that both recombination and mutation events have driven the evolution of human C. pneumoniae. Further fine-detailed analyses of these new C. pneumoniae sequences show several genetically variable loci. This suggests that similar strains of C. pneumoniae are found in the brain, lungs and cardiovascular system and that only minor genetic differences may contribute to the adaptation of particular strains in human disease.

Roux, C, Talbot-Wright, B, Robertson, J, Crispino, F & Ribaux, O 2015, 'The end of the (forensic science) world as we know it? The example of trace evidence', PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 370, no. 1674.
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© 2015 The Author(s) Published by the Royal Society. All rights reserved. The dominant conception of forensic science as a patchwork of disciplines primarily assisting the criminal justice system (i.e. forensics) is in crisis or at least shows a series of anomalies and serious limitations. In recent years, symptoms of the crisis have been discussed in a number of reports by various commentators, without a doubt epitomized by the 2009 report by the US National Academies of Sciences (NAS 2009 Strengthening forensic science in the United States: a path forward). Although needed, but viewed as the solution to these drawbacks, the almost generalized adoption of stricter business models in forensic science casework compounded with ever- increasing normative and compliance processes not only place additional pressures on a discipline that already appears in difficulty, but also induce more fragmentation of the different forensic science tasks, a tenet many times denounced by the same NAS report and other similar reviews. One may ask whether these issues are not simply the result of an unfit paradigm. If this is the case, the current problems faced by forensic science may indicate future significant changes for the discipline. To facilitate broader discussion this presentation focuses on trace evidence, an area that is seminal to forensic science both for epistemological and historical reasons. There is, however, little doubt that this area is currently under siege worldwide. Current and future challenges faced by trace evidence are discussed along with some possible answers. The current situation ultimately presents some significant opportunities to re-invent not only trace evidence but also forensic science. Ultimately, a distinctive, more robust and more reliable science may emerge through rethinking the forensics paradigm built on specialisms, revisiting fundamental forensic science principles and adapting them to the twenty-first century.

Ryan, L 2015, 'A Conversation with Nan Laird', STATISTICAL SCIENCE, vol. 30, no. 4, pp. 582-596.
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Ryan, TM, Roberts, BR, McColl, G, Hare, DJ, Doble, PA, Li, Q-X, Lind, M, Roberts, AM, Mertens, HDT, Kirby, N, Pham, CLL, Hinds, MG, Adlard, PA, Barnham, KJ, Curtain, CC & Masters, CL 2015, 'Stabilization of Nontoxic Aβ-Oligomers: Insights into the Mechanism of Action of Hydroxyquinolines in Alzheimer's Disease', The Journal of Neuroscience, vol. 35, no. 7, pp. 2871-2884.
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The extracellular accumulation of amyloid β (Aβ) peptides is characteristic of Alzheimer's disease (AD). However, formation of diffusible, oligomeric forms of Aβ, both on and off pathways to amyloid fibrils, is thought to include neurotoxic species responsible for synaptic loss and neurodegeneration, rather than polymeric amyloid aggregates. The 8-hydroxyquinolines (8-HQ) clioquinol (CQ) and PBT2 were developed for their ability to inhibit metal-mediated generation of reactive oxygen species from Aβ:Cu complexes and have both undergone preclinical and Phase II clinical development for the treatment of AD. Their respective modes of action are not fully understood and may include both inhibition of Aβ fibrillar polymerization and direct depolymerization of existing Aβ fibrils. In the present study, we find that CQ and PBT2 can interact directly with Aβ and affect its propensity to aggregate. Using a combination of biophysical techniques, we demonstrate that, in the presence of these 8-HQs and in the absence of metal ions, Aβ associates with two 8-HQ molecules and forms a dimer. Furthermore, 8-HQ bind Aβ with an affinity of 1–10 μmand suppress the formation of large (>30 kDa) oligomers. The stabilized low molecular weight species are nontoxic. Treatment with 8-HQs also reduces the levels ofin vivosoluble oligomers in aCaenorhabditis elegansmodel of Aβ toxicity. We propose that 8-HQs possess an additional mechanism of action that neutralizes neurotoxic Aβ oligomer formation through stabilization of small (dimeric) nontoxic Aβ conformers.

Sablok, G, Raju, GVP, Mudunuri, SB, Prabha, R, Singh, DP, Baev, V, Yahubyan, G, Ralph, PJ & La Porta, N 2015, 'ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection', DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.
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Sablok, G, Srivastva, AK, Suprasanna, P, Baev, V & Ralph, PJ 2015, 'isomiRs: Increasing Evidences of isomiRs Complexity in Plant Stress Functional Biology', FRONTIERS IN PLANT SCIENCE, vol. 6, pp. 949-949.
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Saez, NJ, Deplazes, E, Cristofori‐Armstrong, B, Chassagnon, IR, Lin, X, Mobli, M, Mark, AE, Rash, LD & King, GF 2015, 'Molecular dynamics and functional studies define a hot spot of crystal contacts essential for PcTx1 inhibition of acid‐sensing ion channel 1a', British Journal of Pharmacology, vol. 172, no. 20, pp. 4985-4995.
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Background and PurposeThe spider‐venom peptide PcTx1 is the most potent and selective inhibitor of acid‐sensing ion channel (ASIC) 1a. It has centrally acting analgesic activity and is neuroprotective in rodent models of ischaemic stroke. Understanding the molecular details of the PcTx1 : ASIC1a interaction should facilitate development of therapeutically useful ASIC1a modulators. Previously, we showed that several key pharmacophore residues of PcTx1 reside in a dynamic β‐hairpin loop; conclusions confirmed by recent crystal structures of the complex formed between PcTx1 and chicken ASIC1 (cASIC1). Numerous peptide : channel contacts were observed in these crystal structures, but it remains unclear which of these are functionally important.Experimental ApproachWe combined molecular dynamics (MD) simulations of the PcTx1 : cASIC1 complex with mutagenesis of PcTx1 and rat ASIC1a.Key ResultsCrystal structures of the PcTx1 : cASIC1 complex indicated that 15 PcTx1 residues form a total of 57 pairwise intermolecular contacts (<5 Å) with 32 channel residues. MD simulations, however, suggested that about half of these interactions do not persist in solution. Mutation to alanine of only eight of 15 PcTx1 contact residues substantially altered ASIC1a inhibition by PcTx1. Our data reveal that many of the peptide–channel interactions observed in the PcTx1 : cASIC1 crystal structures are not important for PcTx1 inhibition of rat ASIC1a.Conclusions and ImplicationsWe identified the atomic interactions that are critical for PcTx1 inhibition of ASIC1a. Our data highlight the value of combining structural information, MD and functional experiments to obtain detailed insight into the molecular basis of protein : protein interactions.

Safarchi, A, Octavia, S, Luu, LDW, Tay, CY, Sintchenko, V, Wood, N, Marshall, H, McIntyre, P & Lan, R 2015, 'Pertactin negative Bordetella pertussis demonstrates higher fitness under vaccine selection pressure in a mixed infection model', Vaccine, vol. 33, no. 46, pp. 6277-6281.
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Şahin, YM, Gündüz, O, Bulut, B, Özyeğin, LS, Gökçe, H, Ağaoğulları, D, Chou, J, Kayalı, ES, Ben-Nissan, B & Oktar, FN 2015, 'Nano-Bioceramic Synthesis from Tropical Sea Snail Shells (Tiger Cowrie - Cypraea Tigris) with Simple Chemical Treatment', Acta Physica Polonica A, vol. 127, no. 4, pp. 1055-1058.
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Sam, I-C, Su, YCF, Chan, YF, Nor'E, SS, Hassan, A, Jafar, FL, Joseph, U, Halpin, RA, Ghedin, E, Hooi, PS, Fourment, M, Hassan, H, AbuBakar, S, Wentworth, DE & Smith, GJD 2015, 'Evolution of Influenza B Virus in Kuala Lumpur, Malaysia, between 1995 and 2008', Journal of Virology, vol. 89, no. 18, pp. 9689-9692.
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ABSTRACT Influenza B virus causes significant disease but remains understudied in tropical regions. We sequenced 72 influenza B viruses collected in Kuala Lumpur, Malaysia, from 1995 to 2008. The predominant circulating lineage (Victoria or Yamagata) changed every 1 to 3 years, and these shifts were associated with increased incidence of influenza B. We also found poor lineage matches with recommended influenza virus vaccine strains. While most influenza B virus lineages in Malaysia were short-lived, one circulated for 3 to 4 years.

Satija, S, Bansal, P, Dureja, H & Garg, M 2015, 'Microwave Assisted Extraction of Tinospora cordifolia and Optimization through Central Composite Design', Journal of Biological Sciences, vol. 15, no. 3, pp. 106-115.
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© 2015 Asian Network for Scientific Information. Present study was conducted to develop a new optimized Microwave- Assisted Extraction (MAE) method for Tinospora cordifolia in order to improve the efficiency and yield of chief bioactive compounds. Stems of the Tinospora cordifolia were subjected for extraction using MAE technique using three variable factors (extraction time, irradiation power and solvent concentration) optimized through central composite design. Berberine which was used, as marker was estimated in prepared extract by High Performance Thin Layer Chromatography (HPTLC) and compared with extracts prepared by conventional techniques like maceration and soxhlation. The results revealed that MAE of Tinospora cordifolia at 60% irradiation power, 80% ethanol concentration and at 3 min extraction time produced highest extract yield (91.3% better yield than maceration and 25.7% than soxhlation) as well as berberine content (492.8% better than maceration and 59.6% than soxhlation) as compared to extracts prepared with conventional techniques. Efficiency of the MAE method was considerably better than the conventional procedures, especially in terms of shortening extraction time (3 min as compared to 3 h for soxhlation and 7 days fort maceration), reduction of solvent used and energy consumption. The optimized microwave extraction method can provide a valuable extraction alternative of Tinospora cordifolia stem at industrial scale.

Schliep, M, Pernice, M, Sinutok, S, Bryant, CV, York, PH, Rasheed, MA & Ralph, PJ 2015, 'Evaluation of Reference Genes for RT-qPCR Studies in the Seagrass Zostera muelleri Exposed to Light Limitation', SCIENTIFIC REPORTS, vol. 5.
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Segele, Z, Leslie, L & Tarhule, A 2015, 'Sensitivity of Horn of Africa Rainfall to Regional Sea Surface Temperature Forcing', Climate, vol. 3, no. 2, pp. 365-390.
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The Abdus Salam International Center for Theoretical Physics (ICTP) version 4.4 Regional Climate Model (RegCM4) is used to investigate the rainfall response to cooler/warmer sea surface temperature anomaly (SSTA) forcing in the Indian and Atlantic Oceans. The effect of SSTA forcing in a specific ocean basin is identified by ensemble, averaging 10 individual simulations in which a constant or linearly zonally varying SSTA is prescribed in individual basins while specifying the 1971–2000 monthly varying climatological sea surface temperature (SST) across the remaining model domain. The nonlinear rainfall response to SSTA amplitude also is investigated by separately specifying +1K, +2K, and +4K SSTA forcing in the Atlantic and Indian Oceans. The simulation results show that warm SSTs over the entire Indian Ocean produce drier conditions across the larger Blue Nile catchment, whereas warming ≥ +2K generates large positive rainfall anomalies exceeding 10 mm·day−1 over drought prone regions of Northeastern Ethiopia. However, the June–September rainy season tends to be wetter (drier) when the SST warming (cooling) is limited to either the Northern or Southern Indian Ocean. Wet rainy seasons generally are characterized by deepening of the monsoon trough, east of 40°E, intensification of the Mascarene high, strengthening of the Somali low level jet and the tropical easterly jet, enhanced zonal and meridional vertically integrated moisture fluxes, and steeply vertically decreasing moist static energy. The opposite conditions hold for dry monsoon seasons.

Segele, ZT, Richman, MB, Leslie, LM & Lamb, PJ 2015, 'Seasonal-to-Interannual Variability of Ethiopia/Horn of Africa Monsoon. Part II: Statistical Multimodel Ensemble Rainfall Predictions', Journal of Climate, vol. 28, no. 9, pp. 3511-3536.
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AbstractAn ensemble-based multiple linear regression technique is developed to assess the predictability of regional and national June–September (JJAS) anomalies and local monthly rainfall totals for Ethiopia. The ensemble prediction approach captures potential predictive signals in regional circulations and global sea surface temperatures (SSTs) two to three months in advance of the monsoon season. Sets of 20 potential predictors are selected from visual assessments of correlation maps that relate rainfall with regional and global predictors. Individual predictors in each set are utilized to initialize specific forward stepwise regression models to develop ensembles of equal number of statistical model estimates, which allow quantifying prediction uncertainties related to individual predictors and models. Prediction skill improvement is achieved through error minimization afforded by the ensemble.For retroactive validation (RV), the ensemble predictions reproduce well the observed all-Ethiopian JJAS rainfall variability two months in advance. The ensemble mean prediction outperforms climatology, with mean square error reduction (SSClim) of 62%. The skill of the prediction remains high for leave-one-out cross validation (LOOCV), with the observed–predicted correlation r (SSClim) being +0.81 (65%) for 1970–2002. For tercile predictions (below, near, and above normal), the ranked probability skill score is 0.45, indicating improvement compared to climatological forecasts. Similarly high prediction skill is found for local prediction of monthly rainfall total at Addis Ababa (r = +0.72) and Combolcha (r = +0.68), and for regional prediction of JJAS standardized rainfall anomalies for northeastern Ethiopia (r = +0.80). Compared to the previous generation of rainfall forecasts, the ensemble predictions developed in this paper show substantial value to benefit society.

Seidel, D, Hicks, K, Taddeo, S, Azcarate‐Peril, M, Carroll, R & Turner, N 2015, 'Dried Plums Modify Colon Microbiota Composition And Spatial Distribution, And Protect Against Chemically‐Induced Carcinogenesis', The FASEB Journal, vol. 29, no. S1.
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Differences in microbial populations in the proximal and distal colon may impact apparent site‐specific differences in pathology. Diet is known to alter metabolism and composition of colon microbiota, which has major implications for disease prevention and treatment. The hypothesis tested by this experiment was that consumption of dried plums would promote retention of beneficial microbiota and patterns of microbial metabolism throughout the colon, and that by doing so would reduce colon cancer incidence. Male Sprague‐Dawley rats were provided either a control (CD, n=25) or plum diet (PD, 5% of calories, n=26) 3 wk before being given two injections of AOM (15 mg/kg BW) or saline, and sacrificed 8 wk later. Tissues were resected and fecal contents isolated separately from the proximal and distal colon. Irrespective of treatment, the PD increased Bacteroidetes (p<0.0001) and reduced Firmicutes (p<0.0001) in the distal colon without affecting their proximal proportions, compared to the CD, which suppressed Bacteroidetes and increased Firmicutes in the distal colon. Additionally, rats consuming PD had significantly reduced numbers of aberrant crypts (p=0.0025), aberrant crypt foci (p=0.0060), and high multiplicity aberrant crypt foci (p=0.0008) compared to CD rats. These data support our hypothesis that dried plums protect against colon cancer, and this may be due in part to their ability to establish putatively beneficial colon microbiota compositions in the distal colon. Supported by California Dried Plum Board PN 12‐20.

Seo, DH, Yick, S, Pineda, S, Su, D, Wang, G, Han, ZJ & Ostrikov, KK 2015, 'Single-Step, Plasma-Enabled Reforming of Natural Precursors into Vertical Graphene Electrodes with High Areal Capacitance', ACS Sustainable Chemistry & Engineering, vol. 3, no. 3, pp. 544-551.
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© 2015 American Chemical Society. Graphene nanostructures possess excellent physical properties such as high surface area, good mechanical stability, and good electric conductivity, which make them attractive as electrodes for high-performance energy storage devices. However, graphene-based nanomaterials have yet to be materialized into commercial energy storage devices, mainly due to the high cost in fabrication processes and the difficulty in achieving high mass loading. In particular, the high mass loading of active materials on the electrode represents an important step toward the translation of excellent electrochemical activity seen in the microscopic regime into the practical applications. Here, supercapacitor electrodes made of vertical graphene nanosheets (VGNS) are fabricated from a range of commercially available cheese precursors via green, low-temperature, plasma-based reforming processes. Taking advantage of the fast solidification of cheese molecules and plasma-matter interactions, the produced VGNS exhibit a high mass loading of 3.2 mg/cm2 and a high areal capacitance of 0.46 F/cm2. These results demonstrate a single-step, scalable, environmentally benign, and cost-effective approach for the transformation of natural precursors into high-quality graphene structures, which could be promising for a variety of advanced electronic and energy applications.

Seo, DH, Yick, S, Su, D, Wang, G, Han, ZJ & Ostrikov, KK 2015, 'Sustainable process for all-carbon electrodes: Horticultural doping of natural-resource-derived nano-carbons for high-performance supercapacitors', Carbon, vol. 91, pp. 386-394.
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© 2015 Elsevier Ltd. All rights reserved. We demonstrate a novel chemical synthesis and functional doping process of vertical graphene nanosheets and other nano-carbons using natural precursors. The all-carbon electrodes are synthesized via the plasma reformation of natural fats and functionalized by microwave-assisted doping using leaf extracts from a variety of horticultural plants such as bok choy, chrysanthemum, and spinach. The resulting nanostructures possess a high loading of electrochemically active dopants and a desirable morphology for energy storage. This combination enables the electrodes to exhibit excellent supercapacitor performance.

Seoudi, RS, Dowd, A, Del Borgo, M, Kulkarni, K, Perlmutter, P, Aguilar, M-I & Mechler, A 2015, 'Amino acid sequence controls the self-assembled superstructure morphology of N-acetylated tri-β³-peptides', Pure and Applied Chemistry, vol. 87, no. 9-10, pp. 1021-1028.
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Abstract Peptides based on unnatural β3-amino acids offer a versatile platform for the design of self-assembling nanostructures due to the folding stability of the 14-helix and the high symmetry of the side chains inherent in this geometry. We have previously described that N-terminal acetylation (Ac-) forms a supramolecular self-assembly motif that allows β3-peptides to assemble head-to-tail into a helical nanorod which then further bundles into hierarchical superstructures. Here we investigate the effect of the topography of the 14-helical nanorod on lateral self-assembly. Specifically, we report on the variations in the superstructure of three isomeric peptides comprising the same three β3-amino acid residues: β3-leucine (L), β3-isoleucine (I) β3-alanine (A) to give peptides Ac-β3[LIA], Ac-β3[IAL] and Ac-β3[ALI]. AFM imaging shows markedly different superstructures for the three peptides. Well defined synchrotron far-infrared spectra reveal uniform geometries with a high degree of similarity between the isomeric peptides in the amide modes of the 400–650 wavenumber range. Far-IR also confirms that the C-terminal carboxyl group is free in the assemblies, thus it is solvated in the dispersant. Hence, the differences in the superstructures formed by the fibers are defined primarily by van der Waals energy minimization between the varied cross sectional morphologies of the core nanorods.

Sergeyev, A, Geiss, R, Solntsev, AS, Sukhorukov, AA, Schrempel, F, Pertsch, T & Grange, R 2015, 'Enhancing Guided Second-Harmonic Light in Lithium Niobate Nanowires', ACS Photonics, vol. 2, no. 6, pp. 687-691.
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We experimentally demonstrate practical approaches to enhance second-harmonic (SH) generation in individual lithium niobate nanowires (NWs) with a sub-micrometer cross-section and length up to tens of micrometers. We establish that parametric interactions of guided modes propagating along the NW determine the SH output power, which can be therefore controlled by the NW length. We show that the SH power is increased by about 84 times at wavelengths corresponding to modal phase-matching. Importantly, at non-phase-matched wavelengths the SH power can be improved by a factor of up to 9.3 by adjusting the NW length with a focused ion beam. We also characterize SH emission directionality, which can be further tailored for applications in integrated optical circuits and nonlinear microscopy.

Seviour, T, Doyle, LE, Lauw, SJL, Hinks, J, Rice, SA, Nesatyy, VJ, Webster, RD, Kjelleberg, S & Marsili, E 2015, 'Voltammetric profiling of redox-active metabolites expressed by Pseudomonas aeruginosa for diagnostic purposes', Chemical Communications, vol. 51, no. 18, pp. 3789-3792.
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Voltammetric analysis ofPseudomonas aeruginosagrowth cultures unveils the interplay between PQS and phenazines under a potential bias.

Seviour, T, Weerachanchai, P, Hinks, J, Roizman, D, Rice, SA, Bai, L, Lee, J-M & Kjelleberg, S 2015, 'Solvent optimization for bacterial extracellular matrices: a solution for the insoluble', RSC Advances, vol. 5, no. 10, pp. 7469-7478.
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Ionic liquids enable solvent optimization for different biofilms through solubility parameter concept.

Shahcheraghi, N, Dowd, A, Arnold, MD & Cortie, MB 2015, 'Plasmon resonances on opto-capacitive nanostructures', SPIE Proceedings, vol. 9668, pp. 96685C-96685C.
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Silver is considered as one of the most desirable materials for plasmonic devices due to it having low loss, low epsilon2, across the visible spectrum. In addition, silver nanotriangles can self-assemble into complex structures that can include tip-totip or base-to-base arrangements. While the optical properties of tip-to-tip dimers of nanotriangles have been quite intensively studied, the geometric inverse, the base-to-base configuration, has received much less attention. Here we report the results of a computational study of the optical response of this latter configuration. Calculations were performed using the discrete dipole approximation. The effect of gap size and substrate are considered. The results indicate that the base-to-base configuration can sustain a strong coupled dipole and various multimode resonances. The pairing of the parallel triangle edges produces a strongly capacitive configuration and very intense electric fields over an extended volume of space. Therefore, the base-to-base configuration could be suitable for a range of plasmonic applications that require a strong and uniform concentration of electric field. Examples include refractometeric sensing or metal-enhanced fluorescence.

Shahid, M, McDonagh, A, Kim, JH & Shon, HK 2015, 'Magnetised titanium dioxide (TiO2) for water purification: preparation, characterisation and application', Desalination and Water Treatment, vol. 54, no. 4-5, pp. 979-1002.
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The study of titanium dioxide (TiO2) as a photocatalyst for water purification has attracted significant attention over the past four decades. However, the separation of photocatalyst from water suspension may be difficult, costly and jeopardise the use of this water treatment technology. Recently, the development and production of magnetised TiO2 have been achieved to offer a solution for the photocatalyst separation problem. This paper discusses the preparation techniques, characterisation and the applications of magnetised TiO2. Many researchers have studied magnetised TiO2 photocatalysts but the lack of articles discussing the water purification processes is still slowing any advance in this field. Here, the progress of the scientific research on preparation techniques to coat magnetic particles by materials such as organic polymers, silica, magnesia, and alumina are reviewed to compare and discuss recent findings. The doping of photoactive TiO2 photocatalyst into the magnetic-coated particles is also emphasised. In addition, the characterisation of magnetised TiO2 in terms of physicochemical properties and operating conditions produced by each technique are critically reviewed. Moreover, examples of applications of TiO2 and magnetised TiO2 photocatalyst in water purification are summarised. In general, the effectiveness of organic removal by magnetised TiO2 is still lower compared to single phase TiO2. The future prospect of this field is deliberated to develop a novel, economic and efficient magnetised TiO2 photocatalyst, which has high organic removal properties.

Shahid, M, Saliby, IE, Tijing, LD, McDonagh, A, Park, SM, Lee, KY, Shon, HK & Kim, J-H 2015, 'Synthesis and Characterisation of Silica-Modified Titania for Photocatalytic Decolouration of Crystal Violet', Journal of Nanoscience and Nanotechnology, vol. 15, no. 7, pp. 5326-5329.
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In the past few years, silica-modified titania has drawn increasing attention due to their special properties making them ideal candidates for a wide range of applications. In this study, we report a novel method for the synthesis of silica-modified titania by a sol–gel method using sodium silicate solution (1 M). The hydrolysis and condensation reactions of titanium dioxide (TiO2, Degussa Aeroxide® P25) in sodium silicate solution proceeded with citric acid (3 M) as a catalyst. The orbital shaking method was followed for the removal of sodium salt formed during the sol–gel process. Solvent exchange was carried out using methanol and hexane. Finally, chemical modification of the gel was conducted using trimethylchlorosilane followed by ambient pressure drying. The obtained silica-modified titania was characterised for nanostructural analysis using scanning electron microscopy and transmission electron microscopy. The nitrogen adsorption–desorption measurements were employed to investigate the BET surface area, pore structure and pore volume of specimens. Thermal gravimetric analysis showed exothermic peaks at temperature range of 90–190 °C representing the oxidation of organic groups from –Si–R network. The silica-modified titania showed high photocatalytic activity and an easy recovery using crystal violet as model water pollutant.

Shanafield, M, Cook, PG, Gutierrez-Jurado, HA, Faux, R, Cleverly, J & Eamus, D 2015, 'Field comparison of methods for estimating groundwater discharge by evaporation and evapotranspiration in an arid-zone playa', JOURNAL OF HYDROLOGY, vol. 527, pp. 1073-1083.
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SHAO, BO, YANG, Z, LI, JUN, LIAO, J, LAI, S, QIU, J, SONG, Z, YANG, Y & ZHOU, D 2015, 'PHOTONIC CRYSTAL SURFACE ENHANCED UPCONVERSION EMISSION OF YF₃:Yb³⁺, Er³⁺ NANOPARTICLES', Surface Review and Letters, vol. 22, no. 01, pp. 1550010-1550010.
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The opal photonic crystals made of polystyrene microspheres with 155, 230, 270 or 410 nm in diameter were used to enhance upconversion (UC) emission of YF 3: Yb 3+, Er 3+ nanoparticles, respectively. The red or green UC emission of YF 3: Yb 3+, Er 3+ nanoparticles can be selectively enhanced when the red or green UC emission wavelength overlapped with the photonic bandgaps of opals, which is attributed to Bragg reflection of photonic bandgap. In addition, when the 980 nm excitation light wavelength was in the region of the photonic bandgap, red and green UC emissions of YF 3: Yb 3+, Er 3+ nanoparticles were enhanced due to the enhancement of excitation field.

Sharpe, LJ, Rao, G, Jones, PM, Glancey, E, Aleidi, SM, George, AM, Brown, AJ & Gelissen, IC 2015, 'Cholesterol sensing by the ABCG1 lipid transporter: Requirement of a CRAC motif in the final transmembrane domain', Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, vol. 1851, no. 7, pp. 956-964.
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© 2015 Elsevier B.V. All rights reserved. Abstract The ATP-binding cassette (ABC) transporter, ABCG1, is a lipid exporter involved in removal of cholesterol from cells that has been investigated for its role in foam cells formation and atherosclerosis. The mechanism by which ABC lipid transporters bind and recognise their substrates is currently unknown. In this study, we identify a critical region in the final transmembrane domain of ABCG1, which is essential for its export function and stabilisation by cholesterol, a post-translational regulatory mechanism that we have recently identified as dependent on protein ubiquitination. This transmembrane region contains several Cholesterol Recognition/interaction Amino acid Consensus (CRAC) motifs, and its inverse CARC motifs. Mutational analyses identify one CRAC motif in particular with Y667 at its core, that is especially important for transport activity to HDL as well as stability of the protein in the presence of cholesterol. In addition, we present a model of how cholesterol docks to this CRAC motif in an energetically favourable manner. This study identifies for the first time how ABCG1 can interact with cholesterol via a functional CRAC domain, which provides the first insight into the substrate-transporter interaction of an ABC lipid exporter.

Shen, W-X, Au, PCK, Shi, B-J, Smith, NA, Dennis, ES, Guo, H-S, Zhou, C-Y & Wane, M-B 2015, 'Satellite RNAs interfere with the function of viral RNA silencing suppressors', FRONTIERS IN PLANT SCIENCE, vol. 6.
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Shiozawa-West, N, Dunlop, RA & Rodgers, KJ 2015, 'Using an in vitro model to study oxidised protein accumulation in ageing fibroblasts', BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, vol. 1850, no. 11, pp. 2177-2184.
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© 2015 Elsevier B.V. All rights reserved. Background The accumulation of oxidised proteins in ageing cells and tissues results from an increase in oxidant damage coupled with impaired degradation of the damaged proteins. Heat Shock Proteins (HSP) and other chaperones are required to recognise damaged proteins and transport them to the lysosomal and proteasomal degradation pathways. How these systems fail in ageing cells is not clear. Methods We monitor oxidised protein accumulation, the activity of the proteasome and lysosomal proteases, and HSP levels in MRC-5 fibroblasts throughout their mitotic lifespan. We then use a novel in vitro cell culture model to experimentally generate oxidised proteins in young and old MRC-5 fibroblasts and compare their rates of degradation and changes in the key pathways involved in oxidised protein removal. Results We show that the activity of the proteasome and some lysosomal enzymes decreases with ageing in MRC-5 cells as do levels of HSP70 but this is not associated with an accumulation of oxidised proteins which only occurs as cells closely approach post-mitotic senescence. Old cells are unable to degrade experimentally generated oxidised proteins as efficiently as young cells. Exposure to mild heat stress however increases the efficiency of oxidised protein degradation by young cells and increases levels of HSP70. Conclusions Our results highlight the importance of the HSP/chaperone system in oxidised protein metabolism, particularly in ageing cells. General significance These data might have implications for the development of therapies for pathologies associated with protein accumulation and suggest that the HSP/chaperone system would be an important target.

Siboni, N, Abrego, D, Evenhuis, C, Logan, M & Motti, CA 2015, 'Adaptation to local thermal regimes by crustose coralline algae does not affect rates of recruitment in coral larvae', CORAL REEFS, vol. 34, no. 4, pp. 1243-1253.
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Crustose coralline algae (CCA) are well known for their ability to induce settlement in coral larvae. While their wide distribution spans reefs that differ substantially in temperature regimes, the extent of local adaptation to these regimes and the impact they have on CCA inductive ability are unknown. CCA Porolithon onkodes from Heron (southern) and Lizard (northern) islands on Australia’s Great Barrier Reef (separated by 1181 km) were experimentally exposed to acute or prolonged thermal stress events and their thermal tolerance and recruitment capacity determined. A sudden onset bleaching model was developed to determine the health status of CCA based on the rate of change in the CCA live surface area (LSA). The interaction between location and temperature was significant (F (2,119) = 6.74, p = 0.0017), indicating that thermally driven local adaptation had occurred. The southern population remained healthy after prolonged exposure to 28 °C and exhibited growth compared to the northern population (p = 0.022), with its optimum temperature determined to be slightly below 28 °C. As expected, at the higher temperatures (30 and 32 °C) the Lizard Island population performed better that those from Heron Island, with an optimum temperature of 30 °C. Lizard Island CCA displayed the lowest bleaching rates at 30 °C, while levels consistently increased with temperature in their southern counterparts. The ability of those CCA deemed thermally tolerant (based on LSA) to induce Acropora millepora larval settlement was then assessed. While spatial differences influenced the health and bleaching levels of P. onkodes during prolonged and acute thermal exposure, thermally tolerant fragments, regardless of location, induced similar rates of coral larval settlement. This confirmed that recent thermal history does not influence the ability of CCA to induce settlement of A. millepora larvae.

Silsbe, GM, Oxborough, K, Suggett, DJ, Forster, RM, Ihnken, S, Komárek, O, Lawrenz, E, Prášil, O, Röttgers, R, Šicner, M, Simis, SGH, Van Dijk, MA & Kromkamp, JC 2015, 'Toward autonomous measurements of photosynthetic electron transport rates: An evaluation of active fluorescence‐based measurements of photochemistry', Limnology and Oceanography: Methods, vol. 13, no. 3, pp. 138-155.
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AbstractThis study presents a methods evaluation and intercalibration of active fluorescence‐based measurements of the quantum yield () and absorption coefficient () of photosystem II (PSII) photochemistry. Measurements of , , and irradiance (E) can be scaled to derive photosynthetic electron transport rates (), the process that fuels phytoplankton carbon fixation and growth. Bio‐optical estimates of and were evaluated using 10 phytoplankton cultures across different pigment groups with varying bio‐optical absorption characteristics on six different fast‐repetition rate fluorometers that span two different manufacturers and four differe...

Simpson, A, Gerace, D & Martiniello-Wilks, R 2015, 'Diabetes reversal via gene transfer: building on successes in animal models', Research and Reports in Endocrine Disorders, vol. 5, pp. 15-15.
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Type 1 diabetes (T1D) is caused by the autoimmune destruction of the insulin-producing pancreatic β-cells. People with T1D manage their hyperglycemia using daily insulin injections; however, this does not prevent the development of long-term diabetic complications such as retinopathy, nephropathy, neuropathy, and various macrovascular disorders. Currently, the only 'cure' for T1D is pancreas transplantation or islet-cell transplantation; however, this is hampered by the limited number of donors and the requirement for life-long immunosuppression. As a result, the need for alternative therapies is vital. One of the strategies employed to correct T1D is the use of gene transfer to generate the production of an “artificial” β-cell that is capable of secreting insulin in response to fluctuating glucose concentrations that normally occurs in people without T1D. The treatment of many diseases using cell and gene therapy is generating significant attention in the T1D research community; however, for a cell therapy to enter clinical trials, success and safety must first be shown in an appropriate animal model. Animal models have been used in diabetes research for over a century, have improved our understanding of the pathophysiology of diabetes, and have led to the discovery of useful drugs for the treatment of the disease. Currently, the nonobese diabetic mouse is the animal model of choice for the study of T1D as it most closely reflects disease development in humans. The aim of this review is to evaluate the success of cell and gene therapy to reverse T1D in animal models for future clinical application.

Singanayagam, A, Glanville, N, Walton, RP, Aniscenko, J, Pearson, RM, Pinkerton, JW, Horvat, JC, Hansbro, PM, Bartlett, NW & Johnston, SL 2015, 'A short-term mouse model that reproduces the immunopathological features of rhinovirus-induced exacerbation of COPD', Clinical Science, vol. 129, no. 3, pp. 245-258.
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Viral exacerbations of chronic obstructive pulmonary disease (COPD), commonly caused by rhinovirus (RV) infections, are poorly controlled by current therapies. This is due to a lack of understanding of the underlying immunopathological mechanisms. Human studies have identified a number of key immune responses that are associated with RV-induced exacerbations including neutrophilic inflammation, expression of inflammatory cytokines and deficiencies in innate anti-viral interferon. Animal models of COPD exacerbation are required to determine the contribution of these responses to disease pathogenesis. We aimed to develop a short-term mouse model that reproduced the hallmark features of RV-induced exacerbation of COPD. Evaluation of complex protocols involving multiple dose elastase and lipopolysaccharide (LPS) administration combined with RV1B infection showed suppression rather than enhancement of inflammatory parameters compared with control mice infected with RV1B alone. Therefore, these approaches did not accurately model the enhanced inflammation associated with RV infection in patients with COPD compared with healthy subjects. In contrast, a single elastase treatment followed by RV infection led to heightened airway neutrophilic and lymphocytic inflammation, increased expression of tumour necrosis factor (TNF)-α, C-X-C motif chemokine 10 (CXCL10)/IP-10 (interferon γ-induced protein 10) and CCL5 [chemokine (C-C motif) ligand 5]/RANTES (regulated on activation, normal T-cell expressed and secreted), mucus hypersecretion and preliminary evidence for increased airway hyper-responsiveness compared with mice treated with elastase or RV infection alone. In summary, we have developed a new mouse model of RV-induced COPD exacerbation that mimics many of the inflammatory features of human disease. This model, in conjunction with human models of disease, will provide an essential tool for studying disease mechanisms and allow testing of novel therapies...

Small, AG, Thwe, LM, Byrne, JA, Lau, L, Chan, A, Craig, ME, Cowell, CT & Garnett, SP 2015, 'Neuroblastoma, Body Mass Index, and Survival', Medicine, vol. 94, no. 14, pp. e713-e713.
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Smallie, T, Ross, EA, Ammit, AJ, Cunliffe, HE, Tang, T, Rosner, DR, Ridley, ML, Buckley, CD, Saklatvala, J, Dean, JL & Clark, AR 2015, 'Dual-Specificity Phosphatase 1 and Tristetraprolin Cooperate To Regulate Macrophage Responses to Lipopolysaccharide', The Journal of Immunology, vol. 195, no. 1, pp. 277-288.
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Abstract Dual-specificity phosphatase (DUSP) 1 dephosphorylates and inactivates members of the MAPK superfamily, in particular, JNKs, p38α, and p38β MAPKs. It functions as an essential negative regulator of innate immune responses, hence disruption of the Dusp1 gene renders mice extremely sensitive to a wide variety of experimental inflammatory challenges. The principal mechanisms behind the overexpression of inflammatory mediators by Dusp1−/− cells are not known. In this study, we use a genetic approach to identify an important mechanism of action of DUSP1, involving the modulation of the activity of the mRNA-destabilizing protein tristetraprolin. This mechanism is key to the control of essential early mediators of inflammation, TNF, CXCL1, and CXCL2, as well as the anti-inflammatory cytokine IL-10. The same mechanism also contributes to the regulation of a large number of transcripts induced by treatment of macrophages with LPS. These findings demonstrate that modulation of the phosphorylation status of tristetraprolin is an important physiological mechanism by which innate immune responses can be controlled.

Smirnova, DA & Solntsev, AS 2015, 'Cascaded third-harmonic generation in hybrid graphene-semiconductor waveguides', Physical Review B, vol. 92, no. 15.
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Smith, MJA, Kuhlmey, BT, de Sterke, CM, Wolff, C, Lapine, M & Poulton, CG 2015, 'Electrostriction enhancement in metamaterials', Physical Review B, vol. 91, no. 21.
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© 2015 American Physical Society. We demonstrate a controllable enhancement in the electrostrictive properties of a medium using dilute composite artificial materials. Analytical expressions for the composite electrostriction are derived and used to show that enhancement, tunability, and suppression can be achieved through a careful choice of constituent materials. Numerical examples with Ag, As2S3, Si, and SiO2 demonstrate that even in a nonresonant regime, artificial materials can bring more than a threefold enhancement in the electrostriction.

Smout, MJ, Sotillo, J, Laha, T, Papatpremsiri, A, Rinaldi, G, Pimenta, RN, Chan, LY, Johnson, MS, Turnbull, L, Whitchurch, CB, Giacomin, PR, Moran, CS, Golledge, J, Daly, N, Sripa, B, Mulvenna, JP, Brindley, PJ & Loukas, A 2015, 'Carcinogenic Parasite Secretes Growth Factor That Accelerates Wound Healing and Potentially Promotes Neoplasia', PLoS Pathogens, vol. 11, no. 10.
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© 2015 Smout et al. Infection with the human liver fluke Opisthorchis viverrini induces cancer of the bile ducts, cholangiocarcinoma (CCA). Injury from feeding activities of this parasite within the human biliary tree causes extensive lesions, wounds that undergo protracted cycles of healing, and re-injury over years of chronic infection. We show that O. viverrini secreted proteins accelerated wound resolution in human cholangiocytes, an outcome that was compromised following silencing of expression of the fluke-derived gene encoding the granulin-like growth factor, Ov-GRN-1. Recombinant Ov-GRN-1 induced angiogenesis and accelerated mouse wound healing. Ov-GRN-1 was internalized by human cholangiocytes and induced gene and protein expression changes associated with wound healing and cancer pathways. Given the notable but seemingly paradoxical properties of liver fluke granulin in promoting not only wound healing but also a carcinogenic microenvironment, Ov-GRN-1 likely holds marked potential as a therapeutic wound-healing agent and as a vaccine against an infection-induced cancer of major public health significance in the developing world.

Soleymani, S, Ireland, T & McNevin, D 2015, 'Toning Japanese tissue papers: An international survey of paper conservation practitioners', AICCM Bulletin, vol. 36, no. 2, pp. 116-123.
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This paper presents the findings of an international online survey designed to understand more about accepted practice in paper conservation around the world. Japanese tissue papers have long been used for repairing old documents; however, their colour needs to be visually adjusted to be in keeping with the tonality of the document being repaired. Despite substantial literature on the dyeing of textiles, few studies have been conducted on the effects of toning materials on Japanese mending papers used for paper conservation purposes. The findings of this study suggest that paper conservators generally rely on personal experience, the information passed on from their colleagues and Japanese paper suppliers, and that they tend to feel confident about their choices, despite the fact that there has been little research on the long-term effects of toning materials on Japanese papers. We suggest that further research into the realities of practice and how different conservation and toning techniques have evolved in specific local, cultural and historical circumstances is a fruitful field for further research.

Solntsev, AS & Sukhorukov, AA 2015, 'Modulated coupled nanowires for ultrashort pulses', Optics Letters, vol. 40, no. 17, pp. 4078-4078.
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Solntsev, AS, Kitaeva, GK, Naumova, II & Penin, AN 2015, 'Characterization of aperiodic domain structure in lithium niobate by spontaneous parametric down-conversion spectroscopy', Laser Physics Letters, vol. 12, no. 9, pp. 095702-095702.
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Solntsev, AS, Setzpfandt, F, Clark, AS, Wu, CW, Collins, MJ, Xiong, C, Schreiber, A, Katzschmann, F, Eilenberger, F, Schiek, R, Sohler, W, Mitchell, A, Silberhorn, C, Eggleton, BJ, Pertsch, T, Sukhorukov, AA, Neshev, DN & Kivshar, YS 2015, 'Quantum Walks of Photons on a Nonlinear Chip', Asia Pacific Physics Newsletter, vol. 04, no. 01, pp. 56-56.
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Quantum entanglement underpins the realization of quantum simulators and computers, which can be used for unbreakable cryptography and powerful computational algorithms. Entangled photons are an ideal medium for creating and manipulating quantum states due to the low noise and ease of transmission. A qubit encoded into a photon can be easily sent between different photonic elements along an optical fiber, in analogy with the transmission of classical bits along electrical wires. Furthermore, logic operations can be performed on entangled photons by exploiting the nonlinearity inherent to quantum measurements [1]. The practical implementation of complex applications requires the minimization of coupling losses, as well as stable quantum interference. Low losses and interferometric stability allow strong entanglement between output photons. One of the biggest milestones in achieving these requirements is the integration of photon sources together with optical circuits on the same photonic chip.

Song, B, Ye, Z, Yang, Y, Ma, H, Zheng, X, Jin, D & Yuan, J 2015, 'Background-free in-vivo Imaging of Vitamin C using Time-gateable Responsive Probe', Scientific Reports, vol. 5, no. 1, pp. 1-10.
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AbstractSensitive optical imaging of active biomolecules in the living organism requires both a molecular probe specifically responsive to the target and a high-contrast approach to remove the background interference from autofluorescence and light scatterings. Here, a responsive probe for ascorbic acid (vitamin C) has been developed by conjugating two nitroxide radicals with a long-lived luminescent europium complex. The nitroxide radical withholds the probe on its “off” state (barely luminescent), until the presence of vitamin C will switch on the probe by forming its hydroxylamine derivative. The probe showed a linear response to vitamin C concentration with a detection limit of 9.1 nM, two orders of magnitude lower than that achieved using electrochemical methods. Time-gated luminescence microscopy (TGLM) method has further enabled real-time, specific and background-free monitoring of cellular uptake or endogenous production of vitamin C and mapping of vitamin C in living Daphnia magna. This work suggests a rational design of lanthanide complexes for background-free small animal imaging of biologically functional molecules.

Sozo, F, Horvat, JC, Essilfie, A-T, O’Reilly, M, Hansbro, PM & Harding, R 2015, 'Altered lung function at mid-adulthood in mice following neonatal exposure to hyperoxia', Respiratory Physiology & Neurobiology, vol. 218, pp. 21-27.
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Infants born very preterm are usually exposed to high oxygen concentrations but this may impair lung function in survivors in later life. However, the precise changes involved are poorly understood. We determined how neonatal hyperoxia alters lung function at mid-adulthood in mice. Neonatal C57BL/6J mice inhaled 65% oxygen (HE group) from birth for 7 days. They then breathed room air until 11 months of age (P11mo); these mice experienced growth restriction. Controls breathed only room air. To exclude the effects of growth restriction, a group of dams was rotated between hyperoxia and normoxia during the exposure period (HE+DR group). Lung function was measured at P11mo. HE mice had increased inspiratory capacity, work of breathing and tissue damping. HE+DR mice had further increases in inspiratory capacity and work of breathing, and reduced FEV100/FVC. Total lung capacity was increased in HE+DR males. HE males had elevated responses to methacholine. Neonatal hyperoxia alters lung function at mid-adulthood, especially in males.

Spindler, X, Shimmon, R, Roux, C & Lennard, C 2015, 'Visualising substrate-fingermark interactions: Solid-state NMR spectroscopy of amino acid reagent development on cellulose substrates', FORENSIC SCIENCE INTERNATIONAL, vol. 250, pp. 8-16.
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© 2015 Elsevier Ireland Ltd. Most spectroscopic studies of the reaction products formed by ninhydrin, 1,2-indanedione-zinc (Ind-Zn) and 1,8-diazafluoren-9-one (DFO) when reacted with amino acids or latent fingermarks on paper substrates are focused on visible absorption or luminescence spectroscopy. In addition, structural elucidation studies are typically limited to solution-based mass spectrometry or liquid nuclear magnetic resonance (NMR) spectroscopy, which does not provide an accurate representation of the fingermark development process on common paper substrates. The research presented in this article demonstrates that solid-state carbon-13 magic angle spinning NMR (13C-MAS-NMR) is a technique that can not only be utilised for structural studies of fingermark enhancement reagents, but is a promising technique for characterising the effect of paper chemistry on fingermark deposition and enhancement. The latter opens up a research area that has been under-explored to date but has the potential to improve our understanding of how fingermark secretions and enhancement reagents interact with paper substrates.

Staicu, A-M, Lahiri, SN & Carroll, RJ 2015, 'Significance tests for functional data with complex dependence structure', Journal of Statistical Planning and Inference, vol. 156, pp. 1-13.
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© 2014 Elsevier B.V. We propose an L2-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

Stangenberg, S, Nguyen, LT, Chen, H, Al-Odat, I, Killingsworth, MC, Gosnell, ME, Anwer, AG, Goldys, EM, Pollock, CA & Saad, S 2015, 'Oxidative stress, mitochondrial perturbations and fetal programming of renal disease induced by maternal smoking', The International Journal of Biochemistry & Cell Biology, vol. 64, pp. 81-90.
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© 2015 Elsevier Ltd. An adverse in-utero environment is increasingly recognized to predispose to chronic disease in adulthood. Maternal smoking remains the most common modifiable adverse in-utero exposure leading to low birth weight, which is strongly associated with chronic kidney disease (CKD) in later life. In order to investigate underlying mechanisms for such susceptibility, female Balb/c mice were sham or cigarette smoke-exposed (SE) for 6 weeks before mating, throughout gestation and lactation. Offspring kidneys were examined for oxidative stress, expression of mitochondrial proteins, mitochondrial structure as well as renal functional parameters on postnatal day 1, day 20 (weaning) and week 13 (adult age). From birth throughout adulthood, SE offspring had increased renal levels of mitochondrial-derived reactive oxygen species (ROS), which left a footprint on DNA with increased 8-hydroxydeoxyguanosin (8-OHdG) in kidney tubular cells. Mitochondrial structural abnormalities were seen in SE kidneys at day 1 and week 13 along with a reduction in oxidative phosphorylation (OXPHOS) proteins and activity of mitochondrial antioxidant Manganese superoxide dismutase (MnSOD). Smoke exposure also resulted in increased mitochondrial DNA copy number (day 1-week 13) and lysosome density (day 1 and week 13). The appearance of mitochondrial defects preceded the onset of albuminuria at week 13. Thus, mitochondrial damage caused by maternal smoking may play an important role in development of CKD at adult life.

Stefanuto, P-H, Perrault, KA, Lloyd, RM, Stuart, B, Rai, T, Forbes, SL & Focant, J-F 2015, 'Exploring new dimensions in cadaveric decomposition odour analysis', Analytical Methods, vol. 7, no. 6, pp. 2287-2294.
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This study demonstrates the first documented use of comprehensive two-dimensional gas chromatography – high-resolution time-of-flight mass spectrometry (GC×GC-HRTOFMS) for volatile organic compound analysis in the forensic sciences.

Stojanovska, N, De Grazia, A, Tahtouh, M, Shimmon, R & Reedy, B 2015, 'Refining Fingermark Development using Diacetylene Copolymers on Difficult Surfaces', JOURNAL OF FORENSIC SCIENCES, vol. 60, no. 3, pp. 619-626.
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Stojanovska, N, Tahtouh, M, Kelly, T, Beavis, A & Fu, S 2015, 'Qualitative analysis of seized cocaine samples using desorption electrospray ionization- mass spectrometry (DESI-MS)', DRUG TESTING AND ANALYSIS, vol. 7, no. 5, pp. 393-400.
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Desorption electrospray ionization - mass spectrometry (DESI-MS) is a useful technique for the qualitative analysis of compounds found in seized drug material. In this study, DESI-MS was utilized in the screening analysis of illicit cocaine samples. The technique was also applied to the geographical origin determination of these samples. The limit of detection was determined to be 24.3μg (or 3.47μg/mm2) and the analysis time was less than 1minute per sample. The intra-day and inter-day precision for the detection of cocaine was 11 % and 42 %, respectively; therefore the quantitative data provided by DESI-MS was limited in its use for accurate determination of cocaine concentration in a sample. Using the quadrupole time-of-flight (QTOF) mass spectrometer, the presence of cocaine and impurities detected were confirmed by accurate tandem MS data. The qualitative chemical profiles obtained using DESI-MS were compared to two popular analysis techniques, GC-MS and LC-MS. The effects of a range of adulterants including caffeine, procaine, levamisole, lignocaine, paracetamol, and atropine on the detectability of cocaine were also investigated. It was found that the addition of these adulterants in a cocaine sample did not prevent the detection of the analyte itself (there was slight enhancement in some samples), which was useful in drug detection. The detection of truxillines in the seized samples by DESI-MS aided in the preliminary determination of geographical origin, i.e.,Bolivian, Peruvian or Colombian leaf origin. The application of DESI-MS to the qualitative analysis and screening of seized cocaine samples demonstrates the potential and applicability of the technique to the fast chemical profiling of illicit samples. © 2014 John Wiley & Sons, Ltd.

Streubel, R, Han, L, Im, M-Y, Kronast, F, Rößler, UK, Radu, F, Abrudan, R, Lin, G, Schmidt, OG, Fischer, P & Makarov, D 2015, 'Manipulating Topological States by Imprinting Non-Collinear Spin Textures', Scientific Reports, vol. 5, no. 1.
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AbstractTopological magnetic states, such as chiral skyrmions, are of great scientific interest and show huge potential for novel spintronics applications, provided their topological charges can be fully controlled. So far skyrmionic textures have been observed in noncentrosymmetric crystalline materials with low symmetry and at low temperatures. We propose theoretically and demonstrate experimentally the design of spin textures with topological charge densities that can be tailored at ambient temperatures. Tuning the interlayer coupling in vertically stacked nanopatterned magnetic heterostructures, such as a model system of a Co/Pd multilayer coupled to Permalloy, the in-plane non-collinear spin texture of one layer can be imprinted into the out-of-plane magnetised material. We observe distinct spin textures, e.g. vortices, magnetic swirls with tunable opening angle, donut states and skyrmion core configurations. We show that applying a small magnetic field, a reliable switching between topologically distinct textures can be achieved at remanence.

Sturmberg, BCP, Dossou, KB, Botten, LC, McPhedran, RC & de Sterke, CM 2015, 'Fano resonances of dielectric gratings: symmetries and broadband filtering', Optics Express, vol. 23, no. 24, pp. A1672-A1672.
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© 2015 Optical Society of America. The guided mode resonances (GMRs) of diffraction gratings surrounded by low index materials can be designed to produce broadband regions of near perfect reflection and near perfect transmission. These have many applications, including in optical isolators, in hybrid lasers cavities and in photovoltaics. The excitation of rapid GMRs occurs in a background of slowly varying Fabry-Perot oscillation, which produces Fano resonances.We demonstrate the critical role of the polarity of adjacent Fano resonances in the formation of the broadband features. We design gratings for photovoltaic applications that operate at wavelengths where material absorption must be considered and where light is incident at non-normal angles.

Su, D, Dou, S & Wang, G 2015, 'Anatase TiO₂: Better Anode Material Than Amorphous and Rutile Phases of TiO₂ for Na-Ion Batteries', Chemistry of Materials, vol. 27, no. 17, pp. 6022-6029.
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Su, D, Dou, S & Wang, G 2015, 'Bismuth: A new anode for the Na-ion battery', Nano Energy, vol. 12, pp. 88-95.
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© 2015. Bismuth nanoparticles wrapped by graphene have been synthesized. Refined X-ray diffraction, scanning electron microscopy, and transmission electron microscopy analyses have revealed the phase, crystal structure, and morphology of the Bi@graphene nanocomposite. When applied as anode in Na-ion batteries, Bi@graphene nanocomposite exhibited a high reversible sodium storage capacity of about 561mAhg-1 within the 2.0-0.01V voltage range and 358mAhg-1 within the 0.9-0.3V voltage range. Ex-situ X-ray diffraction measurements were used to study the reaction mechanism with Na. It was found that bismuth does not follow the alloying mechanism with Na, and surprisingly, an intercalation process has been evidenced. The as-prepared Bi@graphene nanocomposite also demonstrated excellent high rate performance. This superior electrochemical performance could be ascribed to the unique layered crystal structure of Bi, which has large interlayer spacing along the c-axis (d(003)=3.95Å) to accommodate the Na ions. Furthermore, the three-dimensional architecture of the Bi@graphene nanocomposite also contributes to better conductivity and stability of the electrodes. Via density function theory calculations, it was found that the Bi could provide facile sites for Na ion diffusion and accommodation, based on the intercalation mechanism instead of the alloying process.

Su, D, Dou, S & Wang, G 2015, 'Gold nanocrystals with variable index facets as highly effective cathode catalysts for lithium–oxygen batteries', NPG Asia Materials, vol. 7, no. 1, pp. e155-e155.
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© 2015 Nature Publishing Group All rights reserved. Cathode catalysts are the key factor in improving the electrochemical performance of lithium-oxygen (Li-O2) batteries via their promotion of the oxygen reduction and oxygen evolution reactions (ORR and OER). Generally, the catalytic performance of nanocrystals (NCs) toward ORR and OER depends on both composition and shape. Herein, we report the synthesis of polyhedral Au NCs enclosed by a variety of index facets: cubic gold (Au) NCs enclosed by {100} facets; truncated octahedral Au NCs enclosed by {100} and {110} facets; and trisoctahedral (TOH) Au NCs enclosed by 24 high-index {441} facets, as effective cathode catalysts for Li-O2 batteries. All Au NCs can significantly reduce the charge potential and have high reversible capacities. In particular, TOH Au NC catalysts demonstrated the lowest charge-discharge overpotential and the highest capacity of ∼ 20 298 mA h g^-1. The correlation between the different Au NC crystal planes and their electrochemical catalytic performances was revealed: high-index facets exhibit much higher catalytic activity than the low-index planes, as the high-index planes have a high surface energy because of their large density of atomic steps, ledges and kinks, which can provide a high density of reactive sites for catalytic reactions.

Su, D, Dou, S & Wang, G 2015, 'Hierarchical Vanadium Pentoxide Spheres as High‐Performance Anode Materials for Sodium‐Ion Batteries', ChemSusChem, vol. 8, no. 17, pp. 2877-2882.
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AbstractWe report the synthesis of hierarchical vanadium pentoxide (V2O5) spheres as anode materials for sodium‐ion batteries (Na‐ion batteries). Through field emission scanning electron microscopy, X‐ray diffraction, and transmission electron microscopy characterizations, it was found that the as‐prepared V2O5 spheres are composed of primary nanoparticles with pores between them. The as‐prepared hierarchical V2O5 spheres achieved a discharge capacity of 271 mA h g−1 at a current density of 40 mA g−1, and 177 mA h g−1 discharge capacity after 100 cycles. Even at high current densities, V2O5 spheres still delivered high capacity and superior cyclability (179 and 140 mA h g−1 discharge capacities at 640 and 1280 mA g−1 current densities, respectively). The promising electrochemical performances of V2O5 spheres should be ascribed to the unique architecture of hierarchical spheres and the predominant exposed (110) facets, which provides open interlayers for facile sodium ion intercalation. Each nanoparticle contains predominantly exposed (110) crystal planes. The ex situ FESEM analysis revealed that the pores formed by the primary nanocrystals effectively buffer volume changes in the electrode during cycling, contributing to the excellent cycling performance.

Su, D, Dou, S & Wang, G 2015, 'Ultrathin MoS₂ Nanosheets as Anode Materials for Sodium‐Ion Batteries with Superior Performance', Advanced Energy Materials, vol. 5, no. 6, pp. 1401205-1401205.
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Few‐layer MoS2 nanosheets are successfully synthesized using a simple and scalable ultrasonic exfoliation technique. The thicknesses of the MoS2 nanosheets ares about 10 nm as measured by scanning electron microscopy (SEM) and atomic force microscopy (AFM). The unique nanosheet architecture renders the high‐rate transportation of sodium ions due to the short diffusion paths provided by ultrathin thickness and the large interlayer space within the MoS2 crystal structure (d(002) = 6.38 Å). When applied as anode materials in sodium‐ion batteries, MoS2 nanosheets exhibit a high, reversible sodium storage capacity and excellent cyclability. The MoS2 nanosheets also demonstrate good electrochemical performance at high current densities.

Su, D, Zhang, J, Dou, S & Wang, G 2015, 'Polypyrrole hollow nanospheres: stable cathode materials for sodium-ion batteries', Chemical Communications, vol. 51, no. 89, pp. 16092-16095.
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Hollow polypyrrole nanospheres demonstrated high current rate capacity and superior stable rate capability for Na-ion batteries.

Su, DW, Dou, SX & Wang, GX 2015, 'Hierarchical Ru nanospheres as highly effective cathode catalysts for Li-O-2 batteries', JOURNAL OF MATERIALS CHEMISTRY A, vol. 3, no. 36, pp. 18384-18388.
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© The Royal Society of Chemistry. Carbon-free, hierarchical Ru nanospheres are reported as an effective cathode catalyst for Li-O2 batteries. The hierarchical Ru nanospheres were synthesized by a simple one-step hydrothermal method. As evaluated by electrochemical measurements, it was found that the carbon-free hierarchical Ru nanosphere cathode can significantly reduce discharge and charge overpotential (∼0.3 V with the capacity limited to 1000 mA h g-1) with a high discharge capacity of 3445 mA h g-1 at a current density of 200 mA g-1 (ORR). This superior oxygen evolution reaction (OER) and oxygen reduction reaction catalytic performance can be maintained over long time cycling at different current densities. Ex situ scanning electron microscopy, X-ray diffraction, and Raman measurements reveal that leaf-shaped Li2O2 is the only reaction product during the discharge process, and the hierarchical Ru nanospheres can effectively decompose the Li2O2 discharge product, facilitate the OER, and promote a high round-trip efficiency. Therefore, the carbon-free hierarchical Ru nanospheres are a promising cathode catalyst for rechargeable Li-O2 batteries with low charge overpotential, long cycle life, and high specific capacity.

Su, J, Garvey, CJ, Holt, S, Tabor, RF, Winther-Jensen, B, Batchelor, W & Garnier, G 2015, 'Adsorption of cationic polyacrylamide at the cellulose–liquid interface: A neutron reflectometry study', Journal of Colloid and Interface Science, vol. 448, pp. 88-99.
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Suann, M, Bogema, DR, Chen, Y, Mansfield, S, Barchia, IM & Herron, GA 2015, 'A TaqMan qPCR method for detecting kdr resistance in Aphis gossypii demonstrates improved sensitivity compared to conventional PCR-RFLP', JOURNAL OF PEST SCIENCE, vol. 88, no. 4, pp. 785-791.
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© 2015, Springer-Verlag Berlin Heidelberg. Cotton aphid, Aphis gossypii Glover, has emerged as a prominent pest in Australian cotton production, and monitoring pesticide resistance including pyrethroids in field populations is crucial for its sustainable management. We examined the distribution of kdr resistance in 35 field-collected A. gossypii populations and used TaqMan qPCR assays with pooled samples. The study demonstrated proof of concept that pooled insect qPCR methodology provided effective detection with better sensitivity than individual PCR–RFLP genotyping techniques for the kdr resistance allele. The practical outcome is that routine resistance monitoring can examine more sites while increasing the likelihood of detecting incipient resistance at those sites. More importantly, the method is adaptable to any genetically caused resistance and so not limited to A. gossypii or even insect control. It cannot be overstressed that the ability to detected resistance at very low frequencies is critical to all sustainable resistance management. Early detection of resistance provides critical time for the modification of chemical use prior to potential insecticide control failure.

Suggett, DJ, Goyen, S, Evenhuis, C, Szabo, M, Pettay, DT, Warner, ME & Ralph, PJ 2015, 'Functional diversity of photobiological traits within the genus Symbiodinium appears to be governed by the interaction of cell size with cladal designation', NEW PHYTOLOGIST, vol. 208, no. 2, pp. 370-381.
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© 2015 New Phytologist Trust. Dinoflagellates of the genus Symbiodinium express broad diversity in both genetic identity (phylogeny) and photosynthetic function to presumably optimize ecological success across extreme light environments; however, whether differences in the primary photobiological characteristics that govern photosynthetic optimization are ultimately a function of phylogeny is entirely unresolved. We applied a novel fast repetition rate fluorometry approach to screen genetically distinct Symbiodinium types (n=18) spanning five clades (A-D, F) for potential phylogenetic trends in factors modulating light absorption (effective cross-section, reaction center content) and utilization (photochemical vs dynamic nonphotochemical quenching; [1 - C] vs [1 - Q]) by photosystem II (PSII). The variability of PSII light absorption was independent of phylogenetic designation, but closely correlated with cell size across types, whereas PSII light utilization intriguingly followed one of three characteristic patterns: (1) similar reliance on [1 - C] and [1 - Q] or (2) preferential reliance on [1 - C] (mostly A, B types) vs (3) preferential reliance on [1 - Q] (mostly C, D, F types), and thus generally consistent with cladal designation. Our functional trait-based approach shows, for the first time, how Symbiodinium photosynthetic function is governed by the interplay between phylogenetically dependent and independent traits, and is potentially a means to reconcile complex biogeographic patterns of Symbiodinium phylogenetic diversity in nature.

Sule, N, Rice, SA, Gray, SK & Scherer, NF 2015, 'An electrodynamics-Langevin dynamics (ED-LD) approach to simulate metal nanoparticle interactions and motion', Optics Express, vol. 23, no. 23, pp. 29978-29978.
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Sun, B, Chen, S, Liu, H & Wang, G 2015, 'Mesoporous Carbon Nanocube Architecture for High-Performance Lithium-Oxygen Batteries', ADVANCED FUNCTIONAL MATERIALS, vol. 25, no. 28, pp. 4436-4444.
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© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. One of the major challenges to develop high-performance lithium-oxygen (Li-O2) battery is to find effective cathode catalysts and design porous architecture for the promotion of both oxygen reduction reactions and oxygen evolution reactions. Herein, the synthesis of mesoporous carbon nanocubes as a new cathode nanoarchitecture for Li-O2 batteries is reported. The oxygen electrodes made of mesoporous carbon nanocubes contain numerously hierarchical mesopores and macropores, which can facilitate oxygen diffusion and electrolyte impregnation throughout the electrode, and provide sufficient spaces to accommodate insoluble discharge products. When they are applied as cathode catalysts, the Li-O2 cells deliver discharge capacities of 26 100 mA h g^-1 at 200 mA g^-1, which is much higher than that of commercial carbon black catalysts. Furthermore, the mesoporous nanocube architecture can also serve as a conductive host structure for other highly efficient catalysts. For instance, the Ru functionalized mesoporous carbon nanocubes show excellent catalytic activities toward oxygen evolution reactions. Li-O2 batteries with Ru functionalized mesoporous carbon nanocube catalysts demonstrate a high charge/discharge electrical energy efficiency of 86.2% at 200 mA g^-1 under voltage limitation and a good cycling performance up to 120 cycles at 400 mA g^-1 with the curtaining capacity of 1000 mA h g^-1. Mesoporous carbon nanocubes (MCCs) are synthesized by a chemical vapor deposition method. Oxygen electrode made of MCCs contains a hierarchical porous structure, which can facilitate oxygen diffusion, electrolyte impregnation, and accommodation of discharge products during the charge and discharge processes.

Sun, S, Tay, QXM, Kjelleberg, S, Rice, SA & McDougald, D 2015, 'Quorum sensing-regulated chitin metabolism provides grazing resistance to Vibrio cholerae biofilms', The ISME Journal, vol. 9, no. 8, pp. 1812-1820.
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Abstract Association of Vibrio cholerae with chitinous surfaces of zooplankton is important for its persistence in marine environments, as it provides accessibility to nutrients and resistance to stresses. Predation by heterotrophic protists has a major impact on the survival of V. cholerae. V. cholerae forms biofilms as its main defensive strategy, and quorum sensing (QS) additionally regulates the production of antiprotozoal factors. The role of chitin and QS regulation in V. cholerae grazing resistance was investigated by exposing V. cholerae wild-type (WT) and QS mutant biofilms grown on chitin flakes to the bacteriotrophic, surface-feeding flagellate Rhynchomonas nasuta. V. cholerae formed more biofilm biomass on chitin flakes compared with nonchitinous surfaces. The growth of R. nasuta was inhibited by WT biofilms grown on chitin flakes, whereas the inhibition was attenuated in QS mutant biofilms. The chitin-dependent toxicity was also observed when the V. cholerae biofilms were developed under continuous flow or grown on a natural chitin source, the exoskeleton of Artemia. In addition, the antiprotozoal activity and ammonium concentration of V. cholerae biofilm supernatants were quantified. The ammonium levels (3.5 mm) detected in the supernatants of V. cholerae WT biofilms grown on chitin flakes were estimated to reduce the number of R. nasuta by &gt;80% in add-back experiments, and the supernatant of QS mutant biofilms was less toxic owing to a decrease in ammonium production. Transcriptomic analysis revealed that the majority of genes involved in chitin metabolism and chemotaxis were significantly downregulated in QS mutant biofilms when grown on chitin compared with the WT biofilms.

Sun, X, Luo, X, Zhao, C, Chung Ng, RW, Lim, CED, Zhang, B & Liu, T 2015, 'The association between fine particulate matter exposure during pregnancy and preterm birth: a meta-analysis', BMC Pregnancy and Childbirth, vol. 15, no. 1.
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© 2015 Sun et al. Background: Although several previous studies have assessed the association of fine particulate matter (PM2.5) exposure during pregnancy with preterm birth, the results have been inconsistent and remain controversial. This meta-analysis aims to quantitatively summarize the association between maternal PM2.5 exposure and preterm birth and to further explore the sources of heterogeneity in findings on this association. Methods: We searched for all studies published before December 2014 on the association between PM2.5 exposure during pregnancy and preterm birth in the MEDLINE, PUBMED and Embase databases as well as the China Biological Medicine and Wanfang databases. A pooled OR for preterm birth in association with each 10μg/m3 increase in PM2.5 exposure was calculated by a random-effects model (for studies with significant heterogeneity) or a fixed-effects model (for studies without significant heterogeneity). Results: A total of 18 studies were included in this analysis. The pooled OR for PM2.5 exposure (per 10μg/m3 increment) during the entire pregnancy on preterm birth was 1.13 (95 % CI = 1.03-1.24) in 13 studies with a significant heterogeneity (Q = 80.51, p < 0.001). The pooled ORs of PM2.5 exposure in the first, second and third trimester were 1.08 (95 % CI = 0.92-1.26), 1.09 (95 % CI = 0.82-1.44) and 1.08 (95 % CI = 0.99-1.17), respectively. The corresponding meta-estimates of PM2.5 effects in studies assessing PM2.5 exposure at individual, semi-individual and regional level were 1.11 (95 % CI = 0.89-1.37), 1.14 (95 % CI = 0.97-1.35) and 1.07 (95 % CI = 0.94-1.23). In addition, significant meta-estimates of PM2.5 exposures were found in retrospective studies (OR = 1.10, 95 % CI = 1.01-1.21), prospective studies (OR = 1.42, 95 % CI = 1.08-1.85), and studies conducted in the USA (OR = 1.16, 95 % CI = 1.05-1.29). Conclusions: Maternal PM2.5 exposure during pregnancy may increase the risk of preterm birth,but significant heterogeneity was fou...

Supansomboon, S, Dowd, A, Gentle, A, van der Lingen, E & Cortie, MB 2015, 'Thin films of PtAl2 and AuAl2 by solid-state reactive synthesis', Thin Solid Films, vol. 589, pp. 805-812.
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© 2015 Elsevier B.V. The intermetallic compounds AuAl < inf > 2 < /inf > and PtAl < inf > 2 < /inf > are colored purple and yellow respectively. In the past they have been prepared by bulk melting techniques or by co-deposition in a magnetron sputterer. Here, however, we investigate films of AuAl < inf > 2 < /inf > , PtAl < inf > 2 < /inf > and (Au,Pt)Al < inf > 2 < /inf > prepared by sequential physical vapor deposition of the elements, followed by in situ solid-state reaction. The microstructure, dielectric functions, optical properties and thermal stability of the resulting films are characterized and compared to those prepared by bulk melting or co-deposition. The (Au,Pt)Al < inf > 2 < /inf > films show a color gamut that stretches from purple to brassy yellow depending on composition and microstructure. High temperature synchrotron X-ray diffraction experiments show that the (Au,Pt)Al < inf > 2 < /inf > phase is metastable, decomposing when heated above 420 °C. In contrast, the pure AuAl < inf > 2 < /inf > or PtAl < inf > 2 < /inf > phases are stable to about 580 °C before they oxidize or decompose. The alternative possibility of producing the purple-to-yellow color gamut by depositing optical stacks of very thin films of AuAl < inf > 2 < /inf > and PtAl < inf > 2 < /inf > is also assessed. Either scheme will provide a range of colors lying between those of the binary compound endpoints. Calculations predict that deposition of AuAl < inf > 2 < /inf > onto PtAl < inf > 2 < /inf > will produce more intense colors than vice versa, an unexpected finding that is worth further investigation.

Tahir, M, Mahmood, N, Zhu, J, Mahmood, A, Butt, FK, Rizwan, S, Aslam, I, Tanveer, M, Idrees, F, Shakir, I, Cao, C & Hou, Y 2015, 'One Dimensional Graphitic Carbon Nitrides as Effective Metal-Free Oxygen Reduction Catalysts', Scientific Reports, vol. 5, no. 1.
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AbstractTo explore the effect of morphology on catalytic properties of graphitic carbon nitride (GCN), we have studied oxygen reduction reaction (ORR) performance of two different morphologies of GCN in alkaline media. Among both, tubular GCN react with dissolved oxygen in the ORR with an onset potential close to commercial Pt/C. Furthermore, the higher stability and excellent methanol tolerance of tubular GCN compared to Pt/C emphasizes its suitability for fuel cells.

Tai, MC, Gentle, A, de Silva, KSB, Arnold, MD, van der Lingen, E & Cortie, MB 2015, 'Thermal Stability of Nanoporous Raney Gold Catalyst', METALS, vol. 5, no. 3, pp. 1197-1211.
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Tamburic, B, Evenhuis, CR, Suggett, DJ, Larkum, AWD, Raven, JA & Ralph, PJ 2015, 'Gas Transfer Controls Carbon Limitation During Biomass Production by Marine Microalgae', CHEMSUSCHEM, vol. 8, no. 16, pp. 2727-2736.
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© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. This study presents the first in-depth analysis of CO2 limitation on the biomass productivity of the biofuel candidate marine microalga Nannochloropsis oculata. Net photosynthesis decreased by 60 from 125 to 50 μmolO2L^-1h^-1 over a 12 h light cycle as a direct result of carbon limitation. Continuous dissolved O2 and pH measurements were used to develop a detailed diurnal mechanism for the interaction between photosynthesis, gas exchange and carbonate chemistry in the photo-bioreactor. Gas exchange determined the degree of carbon limitation experienced by the algae. Carbon limitation was confirmed by delivering more CO2, which increased net photosynthesis back to its steady-state maximum. This study highlights the importance of maintaining replete carbon concentrations in photo-bioreactors and other culturing facilities, either by constant pH operation or preferably by designing a feedback loop based on the dissolved O2 concentration. Just grow it: We present the first in-depth analysis of CO2 limitation on biomass productivity of the marine microalga Nannochloropsis oculata. Net photosynthesis decreases by 60 over a 12 h light cycle as a direct result of carbon limitation. Continuous dissolved O2 and pH measurements are used to develop a detailed diurnal mechanism for the interaction between photosynthesis, gas exchange and carbonate chemistry in the photo-bioreactor.

Tan, CH, Koh, KS, Xie, C, Zhang, J, Tan, XH, Lee, GP, Zhou, Y, Ng, WJ, Rice, SA & Kjelleberg, S 2015, 'Community quorum sensing signalling and quenching: microbial granular biofilm assembly', npj Biofilms and Microbiomes, vol. 1, no. 1.
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Abstract Background: Recent reports exploring the role of gradients of quorum sensing (QS) signals in functional activated sludge have raised the question of whether shared systems of signalling synthesis and degradation, or quorum quenching (QQ), across the community inform of the means by which QS biology regulate floccular and granular biofilm assembly. Aims: In this study, we aimed to explore the species origin and interactive role of QS and QQ activities in such highly diverse microbial biofilm communities. Methods: Here, such aims were addressed systematically by a comprehensive multi-pronged RNA-sequencing, microbiological and analytical chemistry experimental approach, using two related but independently evolved floccular and granular sludge communities. Results: Our data revealed a distinct difference between the QS and QQ potentials of the two communities, with different species largely displaying either QS or QQ functions. The floccular sludge community showed a high rate of QQ activity, and this rate was dependent on the acyl chain length demonstrating specificity of degradation. When the floccular biomass was transformed into the granular sludge, the QQ activity of the community was reduced by 30%. N-acyl homoserine lactones with four to eight carbons on the acyl chain accumulated at the granular stage, and their concentrations were at least threefold higher than those of the floccular stage. These findings corroborated meta-community analysis where a major shift in the dominant species from ...

Tan, Y, Jin, XL, Lao, W, Kim, J, Xiao, L & Qu, X 2015, 'Antiresistin RNA Oligonucleotide Ameliorates Diet-Induced Nonalcoholic Fatty Liver Disease in Mice through Attenuating Proinflammatory Cytokines', BioMed Research International, vol. 2015, pp. 1-13.
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The aim of this study was to determine whether inhibition of resistin by a synthetic antiresistin RNA (oligonucleotide) oligo ameliorates metabolic and histological abnormalities in nonalcoholic fatty liver disease (NAFLD) induced by high-fat diet (HFD) in mice. The antiresistin RNA oligo and a scrambled control oligo (25 mg/kg of body weight) were i.p. injected to HFD mice. Serum metabolic parameters and hepatic enzymes were measured after 4-week treatment. The treatment significantly reduced epididymal fat and attenuated the elevated serum resistin, cholesterol, triglycerides, glucose, and insulin with an improved glucose tolerance test. Antiresistin RNA oligo also normalized serum AST and ALT levels with improved pathohistology of NAFLD. Immunoblotting and qRT-PCR revealed that decreased protein and mRNA expression of resistin in fat and liver tissues of the treated mice were associated with reduction of adipose TNF-αand IL-6 expression and secretion into circulation. mRNA and protein expression of hepatic phosphoenolpyruvate carboxykinase (PEPCK) and sterol regulatory element-binding protein-1c (SREBP-1c) were also significantly decreased in the treated mice. Our results suggest that resistin may exacerbate NAFLD in metabolic syndrome through upregulating inflammatory cytokines and hepatic PEPCK and SREBP-1c. Antiresistin RNA oligo ameliorated metabolic abnormalities and histopathology of NAFLD through attenuating proinflammatory cytokines.

Tang, FSM, Foxley, GJ, Gibson, PG, Burgess, JK, Baines, KJ & Oliver, BG 2015, 'Altered Innate Immune Responses in Neutrophils from Patients with Well‐ and Suboptimally Controlled Asthma', Mediators of Inflammation, vol. 2015, no. 1, pp. 1-11.
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Background. Respiratory infections are a major cause of asthma exacerbations where neutrophilic inflammation dominates and is associated with steroid refractory asthma. Structural airway cells in asthma differ from nonasthmatics; however it is unknown if neutrophils differ. We investigated neutrophil immune responses in patients who have good (AGood) and suboptimal (ASubopt) asthma symptom control. Methods. Peripheral blood neutrophils from AGood (ACQ < 0.75, n = 11), ASubopt (ACQ > 0.75, n = 7), and healthy controls (HC) (n = 9) were stimulated with bacterial (LPS (1 μg/mL), fMLF (100 nM)), and viral (imiquimod (3 μg/mL), R848 (1.5 μg/mL), and poly I:C (10 μg/mL)) surrogates or live rhinovirus (RV) 16 (MOI1). Cell‐free supernatant was collected after 1 h for neutrophil elastase (NE) and matrix metalloproteinase‐ (MMP‐) 9 measurements or after 24 h for CXCL8 release. Results. Constitutive NE was enhanced in AGood neutrophils compared to HC. fMLF stimulated neutrophils from ASubopt but not AGood produced 50% of HC levels. fMLF induced MMP‐9 was impaired in ASubopt and AGood compared to HC. fMLF stimulated CXCL8 but not MMP‐9 was positively correlated with FEV1 and FEV1/FVC. ASubopt and AGood responded similarly to other stimuli. Conclusions. Circulating neutrophils are different in asthma; however, this is likely to be related to airflow limitation rather than asthma control.

Taudte, RV, Roux, C, Bishop, D, Blanes, L, Doble, P & Beavis, A 2015, 'Development of a UHPLC method for the detection of organic gunshot residues using artificial neural networks', Analytical Methods, vol. 7, no. 18, pp. 7447-7454.
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A UHPLC method was developed for a broad range of OGSR compounds using ANNs and evaluated using simulated case samples.

Tay, H, Kaiko, G, Mattes, J, Hansbro, P & Foster, P 2015, 'The role of miR-328 in respiratory diseases (INM3P.410)', The Journal of Immunology, vol. 194, no. 1_Supplement, pp. 127.15-127.15.
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Abstract Introduction: MicroRNAs (miRNAs) are small non-coding RNA that can bind to multiple target mRNA to repress protein production. Deregulation of miRNAs have been linked with pathogenesis of multiple human diseases. In immune cells, miRNAs regulate cell development, differentiation and production of inflammatory mediators. Aim: To investigate the roles of miRNAs in regulating immune cell function and its role in respiratory diseases. Methods: Lung miRNAs that were differentially expressed following non-typeable Haemophilus Influenzae (NTHi) challenge were identified by microarray. miRNA inhibitors (antagomirs) were used to investigate the role of miRNA in regulating bacterial clearance in in mouse models of immunosuppresion and emphysema. Results: Upon NTHi infection, 15 miRNAs were up-regulated while 49 were down-regulated by &gt; 2.5 fold in lungs. In vitro, miR-328 knockdown reduced bacterial load and increased phagocytosis by macrophages and neutrophils. Transferred of macrophages or neutrophils (deficient in miR-328) to naïve recipient mice enhanced clearance of the bacteria in vivo. Similarly, inhibition of miR-328 by antagomirs promote NTHi clearance in mouse models of immunosuppresion and emphysema. Conclusion: : Our study identify a novel role for miR-328 in the regulation of phagocytosis and provide proof of principle that miRNA pathways can be targeted in the lung and offer a potential new anti-microbial approach for the treatment of respiratory infection.

Tay, HL, Kaiko, GE, Plank, M, Li, J, Maltby, S, Essilfie, A-T, Jarnicki, A, Yang, M, Mattes, J, Hansbro, PM & Foster, PS 2015, 'Antagonism of miR-328 Increases the Antimicrobial Function of Macrophages and Neutrophils and Rapid Clearance of Non-typeable Haemophilus Influenzae (NTHi) from Infected Lung', PLOS Pathogens, vol. 11, no. 4, pp. e1004549-e1004549.
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© 2015 Tay et al. Pathogenic bacterial infections of the lung are life threatening and underpin chronic lung diseases. Current treatments are often ineffective potentially due to increasing antibiotic resistance and impairment of innate immunity by disease processes and steroid therapy. Manipulation miRNA directly regulating anti-microbial machinery of the innate immune system may boost host defence responses. Here we demonstrate that miR-328 is a key element of the host response to pulmonary infection with non-typeable haemophilus influenzae and pharmacological inhibition in mouse and human macrophages augments phagocytosis, the production of reactive oxygen species, and microbicidal activity. Moreover, inhibition of miR-328 in respiratory models of infection, steroid-induced immunosuppression, and smoke-induced emphysema enhances bacterial clearance. Thus, miRNA pathways can be targeted in the lung to enhance host defence against a clinically relevant microbial infection and offer a potential new anti-microbial approach for the treatment of respiratory diseases.

Tay, HL, Kaiko, GE, Plank, M, Li, J, Maltby, S, Essilfie, A-T, Jarnicki, A, Yang, M, Mattes, J, Hansbro, PM & Foster, PS 2015, 'Correction: Antagonism of miR-328 Increases the Antimicrobial Function of Macrophages and Neutrophils and Rapid Clearance of Non-typeable Haemophilus Influenzae (NTHi) from Infected Lung', PLOS Pathogens, vol. 11, no. 6, pp. e1004956-e1004956.
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Tebben, J, Motti, CA, Siboni, N, Tapiolas, DM, Negri, AP, Schupp, PJ, Kitamura, M, Hatta, M, Steinberg, PD & Harder, T 2015, 'Chemical mediation of coral larval settlement by crustose coralline algae', SCIENTIFIC REPORTS, vol. 5.
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Thompson, PA, Bonham, P, Thomson, P, Rochester, W, Doblin, MA, Waite, AM, Richardson, A & Rousseaux, CS 2015, 'Climate variability drives plankton community composition changes: the 2010-2011 El Nino to La Nina transition around Australia', JOURNAL OF PLANKTON RESEARCH, vol. 37, no. 5, pp. 966-984.
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Thomson, ACG, York, PH, Smith, TM, Sherman, CDH, Booth, DJ, Keough, MJ, Ross, DJ & Macreadie, PI 2015, 'Seagrass Viviparous Propagules as a Potential Long-Distance Dispersal Mechanism', ESTUARIES AND COASTS, vol. 38, no. 3, pp. 927-940.
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© 2014, Coastal and Estuarine Research Federation. Resilience of seagrass meadows relies on the ability of seagrass to successfully recolonise denuded areas or disperse to new areas. While seed germination and rhizome extension have been explored as modes of recovery and expansion, the contribution of seagrass viviparous propagules to meadow population dynamics has received little attention. Here, we investigated the potential of seagrass viviparous propagules to act as dispersal vectors. We performed a series of density surveys, and in situ and mesocosm-based experiments in Port Phillip Bay, VIC, Australia, using Zostera nigricaulis, a species known to produce viviparous propagules. Production of viviparous propagules was higher at sites with high wind and current exposure, compared to more sheltered environments. A number of propagules remained buoyant and healthy for more than 85 days, suggesting the capacity for relatively long-distance dispersal. Transplanted propagules were found to have improved survivorship within seagrass habitats compared to bare sediment over the short term (4 weeks); however, all propagules suffered longer-term (<100 days) mortality in field experiments. Conditions outside of meadows, including sediment scouring, reduced the likelihood of successful colonisation in bare sediment. Furthermore, sediment characteristics within meadows, such as a smaller grain size and high organic content, positively influenced propagule establishment. This research provides preliminary evidence that propagules have the potential to act as an important long-distance dispersal vector, a process that has previously gone unrecognised. Even though successful establishment of propagules may be rare, viviparous propagules show great potential for seagrass populations given they are facing global decline.

Tian, C, Pei, H, Hu, W, Hao, D, Doblin, MA, Ren, Y, Wei, J & Feng, Y 2015, 'Variation of phytoplankton functional groups modulated by hydraulic controls in Hongze Lake, China', ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH, vol. 22, no. 22, pp. 18163-18175.
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Titchener, JG, Solntsev, AS & Sukhorukov, AA 2015, 'Generation of photons with all-optically-reconfigurable entanglement in integrated nonlinear waveguides', Physical Review A, vol. 92, no. 3.
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Togashi, HF, Prentice, IC, Evans, BJ, Forrester, DI, Drake, P, Feikema, P, Brooksbank, K, Eamus, D & Taylor, D 2015, 'Morphological and moisture availability controls of the leaf area-to-sapwood area ratio: analysis of measurements on Australian trees', ECOLOGY AND EVOLUTION, vol. 5, no. 6, pp. 1263-1270.
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© 2015 Published by John Wiley & Sons Ltd. The leaf area-to-sapwood area ratio (LA:SA) is a key plant trait that links photosynthesis to transpiration. The pipe model theory states that the sapwood cross-sectional area of a stem or branch at any point should scale isometrically with the area of leaves distal to that point. Optimization theory further suggests that LA:SA should decrease toward drier climates. Although acclimation of LA:SA to climate has been reported within species, much less is known about the scaling of this trait with climate among species. We compiled LA:SA measurements from 184 species of Australian evergreen angiosperm trees. The pipe model was broadly confirmed, based on measurements on branches and trunks of trees from one to 27 years old. Despite considerable scatter in LA:SA among species, quantile regression showed strong (0.2 < R1 < 0.65) positive relationships between two climatic moisture indices and the lowermost (5%) and uppermost (5-15%) quantiles of log LA:SA, suggesting that moisture availability constrains the envelope of minimum and maximum values of LA:SA typical for any given climate. Interspecific differences in plant hydraulic conductivity are probably responsible for the large scatter of values in the mid-quantile range and may be an important determinant of tree morphology. We compiled LA:SA measurements from 183 species of Australian evergreen angiosperm trees. The pipe model was broadly confirmed. LA:SA quantile regression showed positive relationships between two climatic moisture indices and the lowermost and uppermost quantiles.

Tolosa, JM, Parsons, KS, Hansbro, PM, Smith, R & Wark, PAB 2015, 'The Placental Protein Syncytin-1 Impairs Antiviral Responses and Exaggerates Inflammatory Responses to Influenza', PLOS ONE, vol. 10, no. 4, pp. e0118629-e0118629.
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© 2015 Tolosa et al. Background Pregnancy increases susceptibility to influenza. The placenta releases an immunosuppressive endogenous retroviral protein syncytin-1.We hypothesised that exposure of peripheral monocytes (PBMCs) to syncytin-1 would impair responses to H1N1pdm09 influenza. Methods and Findings Recombinant syncytin-1 was produced. PBMCs from non-pregnant women (n=10) were exposed to H1N1pdm09 in the presence and absence of syncytin-1 and compared to responses of PBMCs from pregnant women (n=12). PBMCs were characterised using flow cytometry, release of interferon (IFN)-α, IFN-λ, IFN-γ, IL-10, IL-2, IL-6 and IL-1β were measured by cytometric bead array or ELISA. Exposure of PBMCs to H1N1pdm09 resulted in the release of IFN-α, (14,787 pg/mL, 95% CI 7311-22,264 pg/mL) IFN-λ (1486 pg/mL, 95% CI 756-2216 pg/mL) and IFN-γ (852 pg/mL, 95% CI 193-1511 pg/mL) after 48 hours. This was significantly impaired in pregnant women (IFN-α; p<0.0001 and IFN-λ; p<0.001). Furthermore, in the presence of syncytin-1, PBMCs demonstrated marked reductions in IFN-α and IFN-λ, while enhanced release of IL-10 as well as IL-6 and IL-1β. Conclusions Our data indicates that a placental derived protein, syncytin-1 may be responsible for the heightened vulnerability of pregnant women to influenza.

Tonkin, RS, Mao, Y, O’Carroll, SJ, Nicholson, LFB, Green, CR, Gorrie, CA & Moalem-Taylor, G 2015, 'Gap junction proteins and their role in spinal cord injury', Frontiers in Molecular Neuroscience, vol. 7, no. JAN, pp. 1-9.
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© 2015 Tonkin, Mao, O'Carroll, Nicholson, Green, Gorrie and Moalem-Taylor. Gap junctions are specialized intercellular communication channels that are formed by two hexameric connexin hemichannels, one provided by each of the two adjacent cells. Gap junctions and hemichannels play an important role in regulating cellular metabolism, signaling, and functions in both normal and pathological conditions. Following spinal cord injury (SCI), there is damage and disturbance to the neuronal elements of the spinal cord including severing of axon tracts and rapid cell death. The initial mechanical disruption is followed by multiple secondary cascades that cause further tissue loss and dysfunction. Recent studies have implicated connexin proteins as playing a critical role in the secondary phase of SCI by propagating death signals through extensive glial networks. In this review, we bring together past and current studies to outline the distribution, changes and roles of various connexins found in neurons and glial cells, before and in response to SCI. We discuss the contribution of pathologically activated connexin proteins, in particular connexin 43, to functional recovery and neuropathic pain, as well as providing an update on potential connexin specific pharmacological agents to treat SCI.

Ton-That, C, Zhu, L, Lockrey, MN, Phillips, MR, Cowie, BCC, Tadich, A, Thomsen, L, Khachadorian, S, Schlichting, S, Jankowski, N & Hoffmann, A 2015, 'Molecular nitrogen acceptors in ZnO nanowires induced by nitrogen plasma annealing', PHYSICAL REVIEW B, vol. 92, no. 2.
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©2015 American Physical Society. X-ray absorption near-edge spectroscopy, photoluminescence, cathodoluminescence, and Raman spectroscopy have been used to investigate the chemical states of nitrogen dopants in ZnO nanowires. It is found that nitrogen exists in multiple states: NO,NZn, and loosely bound N2 molecule. The results establish a direct link between a donor-acceptor pair emission at 3.232 eV and the concentration of loosely bound N2. This work confirms that N2 at Zn site is a potential candidate for producing a shallow acceptor state in N-doped ZnO as theoretically predicted by Lambrecht and Boonchun [Phys. Rev. B 87, 195207 (2013)10.1103/PhysRevB.87.195207]. Additionally, shallow acceptor states arising from NO complexes have been ruled out in this paper.

Toth, M, Lobo, C, Friedli, V, Szkudlarek, A & Utke, I 2015, 'Continuum models of focused electron beam induced processing', Beilstein Journal of Nanotechnology, vol. 6, no. 1, pp. 1518-1540.
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Focused electron beam induced processing (FEBIP) is a suite of direct-write, high resolution techniques that enable fabrication and editing of nanostructured materials inside scanning electron microscopes and other focused electron beam (FEB) systems. Here we detail continuum techniques that are used to model FEBIP, and release software that can be used to simulate a wide range of processes reported in the FEBIP literature. These include: (i) etching and deposition performed using precursors that interact with a surface through physisorption and activated chemisorption, (ii) gas mixtures used to perform simultaneous focused electron beam induced etching and deposition (FEBIE and FEBID), and (iii) etch processes that proceed through multiple reaction pathways and generate a number of reaction products at the substrate surface. We also review and release software for Monte Carlo modeling of the precursor gas flux which is needed as an input parameter for continuum FEBIP models.

Touchard, A, Koh, JMS, Aili, SR, Dejean, A, Nicholson, GM, Orivel, J & Escoubas, P 2015, 'The complexity and structural diversity of ant venom peptidomes is revealed by mass spectrometry profiling', RAPID COMMUNICATIONS IN MASS SPECTROMETRY, vol. 29, no. 5, pp. 385-396.
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Tout, J, Jeffries, TC, Petrou, K, Tyson, GW, Webster, NS, Garren, M, Stocker, R, Ralph, PJ & Seymour, JR 2015, 'Chemotaxis by natural populations of coral reef bacteria', ISME JOURNAL, vol. 9, no. 8, pp. 1764-1777.
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© 2015 International Society for Microbial Ecology. All rights reserved. Corals experience intimate associations with distinct populations of marine microorganisms, but the microbial behaviours underpinning these relationships are poorly understood. There is evidence that chemotaxis is pivotal to the infection process of corals by pathogenic bacteria, but this evidence is limited to experiments using cultured isolates under laboratory conditions. We measured the chemotactic capabilities of natural populations of coral-associated bacteria towards chemicals released by corals and their symbionts, including amino acids, carbohydrates, ammonium and dimethylsulfoniopropionate (DMSP). Laboratory experiments, using a modified capillary assay, and in situ measurements, using a novel microfabricated in situ chemotaxis assay, were employed to quantify the chemotactic responses of natural microbial assemblages on the Great Barrier Reef. Both approaches showed that bacteria associated with the surface of the coral species Pocillopora damicornis and Acropora aspera exhibited significant levels of chemotaxis, particularly towards DMSP and amino acids, and that these levels of chemotaxis were significantly higher than that of bacteria inhabiting nearby, non-coral-associated waters. This pattern was supported by a significantly higher abundance of chemotaxis and motility genes in metagenomes within coral-associated water types. The phylogenetic composition of the coral-associated chemotactic microorganisms, determined using 16S rRNA amplicon pyrosequencing, differed from the community in the seawater surrounding the coral and comprised known coral associates, including potentially pathogenic Vibrio species. These findings indicate that motility and chemotaxis are prevalent phenotypes among coral-associated bacteria, and we propose that chemotaxis has an important role in the establishment and maintenance of specific coral-microbe associations, which may ultimately infl...

Tout, J, Siboni, N, Messer, LF, Garren, M, Stocker, R, Webster, NS, Ralph, PJ & Seymour, JR 2015, 'Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicomis', FRONTIERS IN MICROBIOLOGY, vol. 6, pp. 432-432.
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Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2-3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2-3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems.

Tout, J, Siboni, N, Messer, LF, Garren, M, Stocker, R, Webster, NS, Ralph, PJ & Seymour, JR 2015, 'Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis', Frontiers in Microbiology, vol. 6, pp. 1-12.
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Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2–3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2–3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems.

Tovey, ER, Stelzer-Braid, S, Toelle, BG, Oliver, BG, Reddel, HK, Willenborg, CM, Belessis, Y, Garden, FL, Jaffe, A, Strachan, R, Eyles, D, Rawlinson, WD & Marks, GB 2015, 'Rhinoviruses significantly affect day-to-day respiratory symptoms of children with asthma', Journal of Allergy and Clinical Immunology, vol. 135, no. 3, pp. 663-669.e12.
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© 2014 American Academy of Allergy, Asthma & Immunology. Background Viruses are frequently associated with acute exacerbations of asthma, but the extent to which they contribute to the level of day-to-day symptom control is less clear.Objective We sought to explore the relationship between viral infections, host and environmental factors, and respiratory symptoms in children.Methods Sixty-seven asthmatic children collected samples twice weekly for an average of 10 weeks. These included nasal wash fluid and exhaled breath for PCR-based detection of viral RNA, lung function measurements, and records of medication use and asthma and respiratory symptoms in the previous 3 days. Atopy, mite allergen exposure, and vitamin D levels were also measured. Mixed-model regression analyses were performed.Results Human rhinoviruses (hRVs) were detected in 25.5% of 1232 nasal samples and 11.5% of breath samples. Non-hRV viruses were detected in less than 3% of samples. hRV in nasal samples was associated with asthma symptoms (cough and phlegm: odds ratio = 2.0; 95% CI = 1.4-2.86, P =.0001; wheeze and chest tightness: odds ratio = 2.34, 95% CI = 1.55-3.52, P <.0001) and with cold symptoms, as reported concurrently with sampling and 3 to 4 days later. No differences were found between the 3 hRV genotypes (hRV-A, hRV-B, and hRV-C) in symptom risk. A history of inhaled corticosteroid use, but not atopic status, mite allergen exposure, or vitamin D levels, modified the association between viruses and asthma symptoms.Conclusion The detection of nasal hRV was associated with a significantly increased risk of day-to-day asthma symptoms in children. Host, virus genotype, and environmental factors each had only a small or no effect on the relationship of viral infections to asthma symptoms.

Tran, TT, Bray, K, Ford, MJ, Toth, M & Aharonovich, I 2015, 'Quantum Emission From Hexagonal Boron Nitride Monolayers', 2016 Conference on Lasers and Electro-Optics, CLEO 2016, vol. 11, no. 1, pp. 37-41.
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Atomically thin van der Waals crystals have recently enabled new scientificand technological breakthroughs across a variety of disciplines in materialsscience, nanophotonics and physics. However, non-classical photon emission fromthese materials has not been achieved to date. Here we report room temperaturequantum emission from hexagonal boron nitride nanoflakes. The single photonemitter exhibits a combination of superb quantum optical properties at roomtemperature that include the highest brightness reported in the visible part ofthe spectrum, narrow line width, absolute photo-stability, a short excitedstate lifetime and a high quantum efficiency. Density functional theorymodeling suggests that the emitter is the antisite nitrogen vacancy defect thatis present in single and multi-layer hexagonal boron nitride. Our resultsconstitute the unprecedented potential of van der Waals crystals fornanophotonics, optoelectronics and quantum information processing.

Tran, TT, Fang, J, Zhang, H, Rath, P, Bray, K, Sandstrom, R, Shimoni, O, Toth, M & Aharonovich, I 2015, 'Facile Self-Assembly of Quantum Plasmonic Circuit Components', Adv. Mater., vol. 27, no. 27, pp. 4048-4053.
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Efficient coupling between solid state quantum emitters and plasmonicwaveguides is important for the realization of integrated circuits for quantuminformation, communication and sensing. However, realization of plasmoniccircuits is still scarce, particularly due to challenges associated withaccurate positioning of quantum emitters near plasmonic resonators. Currentpathways for the construction of plasmonic circuits involve cumbersome andcostly methods such as scanning atomic force microscopy or mechanicalmanipulation, where individual elements are physically relocated using thescanning tip. Here, we introduce a simple, fast and cost effective chemicalself-assembly method for the attachment of two primary components of apractical plasmonic circuit: a single photon emitter and a waveguide. Ourmethod enables coupling of nanodiamonds with a single quantum emitter (thenitrogen-vacancy (NV) center) onto the terminal of a silver nanowire, by simplyvarying the concentration of ascorbic acid (AA) in a reaction solution. The AAconcentration is used to control the extent of agglomeration, and can beoptimised so as to cause preferential, selective activation of the tips of thenanowires. The nanowire-nanodiamond structures show efficient plasmoniccoupling of fluorescence emission from single NV centers into surface plasmonpolariton (SPP) modes, evidenced by a more than two-fold reduction influorescence lifetime and an increase in fluorescence intensity.

Tran, VS, Ngo, HH, Guo, W, Zhang, J, Liang, S, Ton-That, C & Zhang, X 2015, 'Typical low cost biosorbents for adsorptive removal of specific organic pollutants from water', BIORESOURCE TECHNOLOGY, vol. 182, pp. 353-363.
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Specific organic pollutants (SOPs) such as phenolic compounds, PAHs, organic pesticides, and organic herbicides cause health and environmental problems due to their excessive toxic properties and poor biodegradability. Low-cost biosorbents are considered as a promising alternative for conventional adsorbents to remove SOPs from water. These materials have several advantages such as high sorption capacities, good modifiability and recoverability, insensitivity to toxic substances, simple operation in the treatment processes. However, previous reports on various types of biosorbents for removing SOPs are still moderately fragmented. Hence, this paper provides a comprehensive review on using typical low-cost biosorbents obtained from lignocellulose and chitin/chitosan for SOPs adsorption. Especially, their characteristics, biosorption mechanism together with utilization for eliminating SOPs are presented and discussed. The paper also gives a critical view regarding future applications of low-cost biosorbents in SOPs-contaminated water treatment.

Traut-Johnstone, T, Kanyanda, S, Kriel, FH, Viljoen, T, Kotze, PDR, van Zyl, WE, Coates, J, Rees, DJG, Meyer, M, Hewer, R & Williams, DBG 2015, 'Heteroditopic P,N ligands in gold(I) complexes: Synthesis, structure and cytotoxicity', Journal of Inorganic Biochemistry, vol. 145, pp. 108-120.
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Trevathan-Tackett, SM, Kelleway, J, Macreadie, PI, Beardall, J, Ralph, P & Bellgrove, A 2015, 'Comparison of marine macrophytes for their contributions to blue carbon sequestration', ECOLOGY, vol. 96, no. 11, pp. 3043-3057.
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Tristram, CJ, Ingham, B, Williams, DBG & Hinkley, SFR 2015, 'Determination of glass transitions in novel cellulose polymers by synchrotron wide-angle X-ray scattering', Materials Today Communications, vol. 2, pp. e49-e54.
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© 2014 Elsevier Ltd. Synchrotron wide angle X-ray scattering (WAXS) was used to measure the glass-transition temperature (Tg) values for various cellulosic materials including a novel cellulose ester. WAXS patterns were obtained of films cast on silicon nitride windows. Two strong scattering peaks were observed that correlated with the intramolecular repeating anhydroglucose unit (d=10.6-14.3Å) and an intermolecular packing spacing (d=4.4-4.5Å). Real-time measurements were made during temperature cycling over a range of 80-160°C at 5°C/min. Significant shifts in position, width and area for the peak assigned to the intermolecular arrangement of the pseudo-linear cellulose mixed-ester chains were correlated with temperature. The calculated Tg mid-points correlated well with Tg values determined by differential scanning calorimetry (DSC). This application of temperature-dependent WAXS measurements shows promise for Tg determination in samples where shallow second-order transitions are observed by DSC and where other techniques are not applicable.

Tristram, CJ, Mason, JM, Williams, DBG & Hinkley, SFR 2015, 'Cover Picture: Doubly Renewable Cellulose Polymer for Water‐Based Coatings (ChemSusChem 1/2015)', ChemSusChem, vol. 8, no. 1, pp. 1-1.
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Tristram, CJ, Mason, JM, Williams, DBG & Hinkley, SFR 2015, 'Doubly Renewable Cellulose Polymer for Water‐Based Coatings', ChemSusChem, vol. 8, no. 1, pp. 3-3.
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AbstractInvited for this month′s cover is the Industrial Formulations group at the Ferrier Research Institute, Victoria University of Wellington. The image depicts plant matter being converted into a novel cellulose ester and, in turn, into a paint formulation suitable for architectural coatings. The Full Paper itself is available at 10.1002/cssc.201402590

Ueland, M, Nizio, KD, Forbes, SL & Stuart, BH 2015, 'The interactive effect of the degradation of cotton clothing and decomposition fluid production associated with decaying remains', Forensic Science International, vol. 255, pp. 56-63.
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Abstract Textiles are a commonly encountered source of evidence in forensic cases. In the past, most research has been focused on how textiles affect the decomposition process while little attention has been paid to how the decomposition products interact with the textiles. While some studies have shown that the presence of remains will have an effect on the degradation of clothing associated with a decaying body, very little work has been carried out on the specific mechanisms that prevent or delay textile degradation when in contact with decomposing remains. In order to investigate the effect of decomposition fluid on textile degradation, three clothed domestic pig (Sus scrofa domesticus) carcasses were placed on a soil surface, textile specimens were collected over a period of a year and were then analysed using ATR-FTIR spectroscopy and GC-MS. Multivariate statistical analysis was used to analyse the data. Cotton specimens not associated with remains degraded markedly, whereas the samples exposed to decomposition fluids remained relatively intact over the same time frame. An investigation of the decomposition by-products found that the protein-related bands remained stable and unchanged throughout the experiment. Lipid components, on the other hand, demonstrated a significant change; this was confirmed with the use of both ATR-FTIR spectroscopy and GC-MS. Through an advanced statistical approach, information about the decomposition by-products and their characteristics was obtained. There is potential that the lipid profile in a textile specimen could be a valuable tool used in the examination of clothing located at a crime scene.

Ujvari, B, Casewell, NR, Sunagar, K, Arbuckle, K, Wüster, W, Lo, N, O’Meally, D, Beckmann, C, King, GF, Deplazes, E & Madsen, T 2015, 'Widespread convergence in toxin resistance by predictable molecular evolution', Proceedings of the National Academy of Sciences, vol. 112, no. 38, pp. 11911-11916.
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SignificanceConvergence has strong bearing on the fundamental debate about whether evolution is stochastic and unpredictable or subject to constraints. Here we show that, in certain circumstances, evolution can be highly predictable. We demonstrate that several lineages of insects, amphibians, reptiles, and mammals have utilized the same molecular solution, via the process of convergence, to evolve resistance to toxic cardiac glycosides produced defensively by plants and bufonid toads. The repeatability of this process across the animal kingdom demonstrates that evolution can be constrained to proceed along highly predictable pathways at molecular and functional levels. Our study has important implications for conservation biology by providing a predictive framework for assessing the vulnerability of native fauna to the introduction of invasive toxic toads.

Umsumarng, S, Pitchakarn, P, Sastraruji, K, Yodkeeree, S, Ung, AT, Pyne, SG & Limtrakul, P 2015, 'Reversal of Human Multi‐Drug Resistance Leukaemic Cells by Stemofoline Derivatives via Inhibition of P‐Glycoprotein Function', Basic & Clinical Pharmacology & Toxicology, vol. 116, no. 5, pp. 390-397.
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AbstractOur previous study reported multi‐drug resistance (MDR) reversing properties of synthetic stemofoline derivatives (STFD), OH‐A1, NH‐B6 and NH‐D6 on P‐glycoprotein (P‐gp) overexpressing leukaemic cells (K562/Adr); however, the mechanism was unclear. In this study, we further investigated whether the STFD reverse MDR through either the inhibition of P‐gp function or expression in K562/Adr cells, or both. The P‐gp functional studies showed that the STFD increased the accumulation of calcein‐AM, rhodamine 123 and [14C]‐doxorubicin in K562/Adr cells, while the effects have not been seen in their parental sensitive cancer cell line (K562). Further, the STFD did not alter the P‐gp expression as determined by Western blotting. This study concludes that the STFD reverse MDR via the inhibition of P‐gp function. The efficacy of the STFD to inhibit P‐gp function followed the order: NH‐B6 >  OH‐A1 >  NH‐D6. These compounds cou...

Valery Combes, AC 2015, 'MicroRNAs and Malaria – A Dynamic Interaction Still Incompletely Understood', Journal of Neuroinfectious Diseases, vol. 06, no. 01, pp. 165-176.
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Malaria is a mosquito-borne infectious disease caused by parasitic protozoa of the genus Plasmodium. It remains a major problem affecting humans today, especially children. However, the pathogenesis of malaria, especially severe malaria, remains incompletely understood, hindering our ability to treat this disease. Of recent interest is the role that small, non-coding RNAs play in the progression, pathogenesis of, and resistance to, malaria. Independent studies have now revealed the presence of microRNA (miRNA) in the malaria parasite, vector, and host, though these studies are relatively few. Here, we review these studies, focusing on the roles specific miRNA have in the disease, and how they may be harnessed for therapeutic purposes.

Vanders, RL, Murphy, VE, Gibson, PG, Hansbro, PM & Wark, PAB 2015, 'CD8 T cells and dendritic cells: key players in the attenuated maternal immune response to influenza infection', Journal of Reproductive Immunology, vol. 107, pp. 1-9.
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Pregnancy provides a unique challenge for maternal immunity, requiring the ability to tolerate the presence of a semi-allogeneic foetus, and yet still being capable of inducing an immune response against invading pathogens. To achieve this, numerous changes must occur in the activity and function of maternal immune cells throughout the course of pregnancy. Respiratory viruses take advantage of these changes, altering the sensitive balance of maternal immunity, leaving the mother with increased susceptibility to viral infections and increased disease severity. Influenza virus is one of the most common respiratory virus infections during pregnancy, leading to an increased risk of ICU hospitalisations, pneumonia, acute respiratory distress syndrome and even death. Whilst much research has been performed to understand the changes that must take place in maternal immunity during pregnancy, considerable work is still needed to fully comprehend this tremendous feat. To date, few studies have focused on the alterations that occur in maternal immunity during respiratory virus infections. This review highlights the role of dendritic cells (DCs) and CD8 T cells during pregnancy, and the changes that occur in these antiviral cells following influenza virus infections.

Vijaykrishna, D, Holmes, EC, Joseph, U, Fourment, M, Su, YCF, Halpin, R, Lee, RTC, Deng, Y-M, Gunalan, V, Lin, X, Stockwell, TB, Fedorova, NB, Zhou, B, Spirason, N, Kühnert, D, Bošková, V, Stadler, T, Costa, A-M, Dwyer, DE, Huang, QS, Jennings, LC, Rawlinson, W, Sullivan, SG, Hurt, AC, Maurer-Stroh, S, Wentworth, DE, Smith, GJD & Barr, IG 2015, 'The contrasting phylodynamics of human influenza B viruses', eLife, vol. 4, no. 4.
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A complex interplay of viral, host, and ecological factors shapes the spatio-temporal incidence and evolution of human influenza viruses. Although considerable attention has been paid to influenza A viruses, a lack of equivalent data means that an integrated evolutionary and epidemiological framework has until now not been available for influenza B viruses, despite their significant disease burden. Through the analysis of over 900 full genomes from an epidemiological collection of more than 26,000 strains from Australia and New Zealand, we reveal fundamental differences in the phylodynamics of the two co-circulating lineages of influenza B virus (Victoria and Yamagata), showing that their individual dynamics are determined by a complex relationship between virus transmission, age of infection, and receptor binding preference. In sum, this work identifies new factors that are important determinants of influenza B evolution and epidemiology.

Visconti, AJ, Santos, G-M, Lemos, NP, Burke, C & Coffin, PO 2015, 'Opioid Overdose Deaths in the City and County of San Francisco: Prevalence, Distribution, and Disparities', Journal of Urban Health, vol. 92, no. 4, pp. 758-772.
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Vodstrcil, LA, McIver, R, Huston, WM, Tabrizi, SN, Timms, P & Hocking, JS 2015, 'The Epidemiology of Chlamydia trachomatis Organism Load During Genital Infection: A Systematic Review', Journal of Infectious Diseases, vol. 211, no. 10, pp. 1628-1645.
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© 2014 The Author. Background. The role of organism load in Chlamydia trachomatis infection is not well understood. We conducted a systematic review to investigate the epidemiology of C. trachomatis organism load in human genital chlamydia infection. Methods. Embase, PubMed, and Medline databases were searched for literature published through August 2014. English-language publications that quantified load in humans were eligible. Participant characteristics and laboratory data were extracted. Results. A total of 737 records were identified, and 29 publications involving 40 883 participants were included. In women, load was highest for cervical swabs and lowest for urine specimens. In men, load was highest for rectal swabs and similar for urethral swabs and urine specimens. Evidence of any association between load and age, serovar, risk of transmission, hormone levels, and concurrent sexually transmitted infections was inconsistent. Eight of 9 culture-based studies found an association between load and signs and symptoms, in contrast with only 3 of 8 nucleic acid amplification test (NAAT)-based studies (P =. 03). Conclusion. Chlamydia organism load varies by specimen type and site of sampling, and viable chlamydia organism load may be a more important indicator of severity of infection than total load measured by NAAT.

Voyer, M, Gladstone, W & Goodall, H 2015, 'Obtaining a social licence for MPAs - influences on social acceptability', MARINE POLICY, vol. 51, pp. 260-266.
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The biological success of Marine Protected Areas (MPAs) depends to a large extent on their social acceptability, sometimes referred to as a social licence. Local resistance has slowed international progress towards a global network of MPAs. The causes of local resistance and limited social acceptability are poorly known, which constrains the development of new planning paradigms that could address these issues. Two case studies in New South Wales, Australia determined the factors that influenced community attitudes towards MPAs. The Port Stephens-Great Lakes Marine Park (PSGLMP) and Batemans Marine Park (BMP) underwent virtually identical and concurrent planning processes, however resistance to the BMP was more intense and sustained. Differences in the demographics, history, local media coverage and social impacts of each marine park contributed to these different community responses. The BMP demonstrated the 'perfect storm' of opposition triggers - a community struggling in the transition away from a primary production economy, a highly politicised media dominated by powerful elites with ideological objections to the park, and social impacts sufficiently profound to motivate local citizens to support an active campaign against the park. These impacts included loss of access, identity and increased competition for resources. This research points to the importance of developing a deeper understanding of the social, cultural and political landscape of the communities in which MPAs are proposed and a rethink of planning processes to better incorporate community objectives and knowledge.

Voyer, M, Gollan, N, Barclay, K & Gladstone, W 2015, ''It's part of me', understanding the values, images and principles of coastal users and their influence on the social acceptability of MPAs', MARINE POLICY, vol. 52, pp. 93-102.
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© 2014 Elsevier Ltd. Improving the social acceptability or 'social licence' of Marine Protected Areas (MPAs) is a key challenge facing countries all around the world. As the world moves slowly towards the establishment of a global network of MPAs, it is increasingly apparent that a greater understanding of social responses to MPAs is required, given they are often met with resistance from local communities. A series of in-depth, semi structured interviews were conducted across coastal users in New South Wales, Australia, including surfers, recreational fishers, professional fishers, spearfishers, walkers, divers, snorkellers, kayakers and other community members. The research identified the values, images and principles at work amongst coastal users to determine the dominant 'cultural models' within the community and how these models influenced attitudes towards MPAs. This research indicates that traditional consultation models may not be sufficient to address the full spectrum of community needs, and in fact suggests the need to re-conceive the make -up of 'the community' itself. In the context of MPA planning 'the community' is not an amalgamation of a range of homogenous stakeholder groups but instead a diverse and complex mix of identities and value systems which are not confined to particular interest groups. Incorporating consideration of the diverse range of values, images and principles found within and across stakeholder groups will require new and innovative approaches to participation and management.

Vyssotski, M, Bloor, SJ, Lagutin, K, Wong, H & Williams, DBG 2015, 'Efficient Separation and Analysis of Triacylglycerols: Quantitation of β-Palmitate (OPO) in Oils and Infant Formulas', Journal of Agricultural and Food Chemistry, vol. 63, no. 26, pp. 5985-5992.
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Walczewska-Szewc, K, Deplazes, E & Corry, B 2015, 'Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins', Journal of Chemical Theory and Computation, vol. 11, no. 7, pp. 3455-3465.
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Walsh, JC, Angstmann, CN, Duggin, IG & Curmi, PMG 2015, 'Molecular Interactions of the Min Protein System Reproduce Spatiotemporal Patterning in Growing and Dividing Escherichia coli Cells', PLOS ONE, vol. 10, no. 5.
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Walsh, MS, Hope, E, Isaia, L, Righarts, A, Niupulusu, T, Temese, SVA, Iosefa-Siitia, L, Auvaa, L, Tapelu, SA, Motu, MF, Edwards, C, Wernick, M, Huston, WM, Suaalii-Sauni, T & Hill, PC 2015, 'Prevalence of Chlamydia trachomatis infection in Samoan women aged 18 to 29 and assessment of possible risk factors: a community-based study', Transactions of the Royal Society of Tropical Medicine and Hygiene, vol. 109, no. 4, pp. 245-251.
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Wang, L, Greaves, IK, Groszmann, M, Wu, LM, Dennis, ES & Peacock, WJ 2015, 'Hybrid mimics and hybrid vigor in Arabidopsis', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 112, no. 35, pp. E4959-E4967.
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F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor that form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants that have a F1-like phenotype, we have by recurrent selection produced pure breeding F5/F6 lines, hybrid mimics, in which the characteristics of the F1 hybrid are stabilized. These hybrid mimic lines, like the F1 hybrid, have larger leaves than the parent plant, and the leaves have increased photosynthetic cell numbers, and in some lines, increased size of cells, suggesting an increased supply of photosynthate. A comparison of the differentially expressed genes in the F1 hybrid with those of eight hybrid mimic lines identified metabolic pathways altered in both; these pathways include down-regulation of defense response pathways and altered abiotic response pathways. F6 hybrid mimic lines are mostly homozygous at each locus in the genome and yet retain the large F1-like phenotype. Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent. We consider this altered expression to be a consequence of transregulation of genes from one parent by genes from the other parent. Transregulation could also arise from epigenetic modifications in the F1. The pure breeding hybrid mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture.

Wang, Q, Zou, R, Xia, W, Ma, J, Qiu, B, Mahmood, A, Zhao, R, Yang, Y, Xia, D & Xu, Q 2015, 'Facile Synthesis of Ultrasmall CoS₂Nanoparticles within Thin N-Doped Porous Carbon Shell for High Performance Lithium-Ion Batteries', Small, vol. 11, no. 21, pp. 2511-2517.
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Wang, Q, Zou, R, Xia, W, Ma, J, Qiu, B, Mahmood, A, Zhao, R, Yang, Y, Xia, D & Xu, Q 2015, 'Lithium Ion Batteries: Facile Synthesis of Ultrasmall CoS₂Nanoparticles within Thin N-Doped Porous Carbon Shell for High Performance Lithium-Ion Batteries (Small 21/2015)', Small, vol. 11, no. 21, pp. 2510-2510.
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Wang, Y, Wang, S & Carroll, RJ 2015, 'The direct integral method for confidence intervals for the ratio of two location parameters', Biometrics, vol. 71, no. 3, pp. 704-713.
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SummaryIn a relative risk analysis of colorectal caner on nutrition intake scores across genders, we show that, surprisingly, when comparing the relative risks for men and women based on the index of a weighted sum of various nutrition scores, the problem reduces to forming a confidence interval for the ratio of two (asymptotically) normal random variables. The latter is an old problem, with a substantial literature. However, our simulation results suggest that existing methods often either give inaccurate coverage probabilities or have a positive probability to produce confidence intervals with infinite length. Motivated by such a problem, we develop a new methodology which we call the Direct Integral Method for Ratios (DIMER), which, unlike the other methods, is based directly on the distribution of the ratio. In simulations, we compare this method to many others. These simulations show that, generally, DIMER more closely achieves the nominal confidence level, and in those cases that the other methods achieve the nominal levels, DIMER has comparable confidence interval lengths. The methodology is then applied to a real data set, and with follow up simulations.

Webb, JK, Scott, ML, Whiting, MJ & Shine, R 2015, 'Territoriality in a snake', Behavioral Ecology and Sociobiology, vol. 69, no. 10, pp. 1657-1661.
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© 2015, Springer-Verlag Berlin Heidelberg. Territorial behaviour, whereby dominant animals gain priority access to critical resources, is widespread in some animal lineages, but rare in others. Theory suggests that territoriality will evolve only when animals can economically defend sites that contain critical resources (typically mates, sometimes food). In striking contrast to their close relatives the lizards, male defence of territories for access to mates has not been reported in snakes. In south-eastern Australia, receptive female small-eyed snakes thermoregulate under “hot rocks”, concentrating mating opportunities and thus, potentially allowing males to enhance their fitness by defending these rocks from rivals. We videotaped staged contests between resident and intruder males and analysed data on cohabitation patterns from a long-term (21 years) mark-recapture study. In staged contests, males actively defended hot rocks from intruder males; and thus, larger males actively displaced their smaller rivals. In the wild, larger males were found under rocks with more or larger females. These results suggest that the thermally driven concentration of female small-eyed snakes has rendered hot rocks economically defensible, and thus favoured the evolution of territoriality in a snake.

Westhorpe, DP, Mitrovic, SM, Growns, IO, Hadwen, WL & Rees, GN 2015, 'Disruption in water quality patterns along the river continuum by a large bottom release dam', AUSTRALASIAN JOURNAL OF ENVIRONMENTAL MANAGEMENT, vol. 22, no. 4, pp. 400-416.
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Wichitaksorn, N, Wang, JJJ, Choy, STB & Gerlach, R 2015, 'Analyzing return asymmetry and quantiles through stochastic volatility models using asymmetric Laplace error via uniform scale mixtures', Applied Stochastic Models in Business and Industry, vol. 31, no. 5, pp. 584-608.
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This paper proposes a new approach to analyze stock return asymmetry and quantiles. We also present a new scale mixture of uniform (SMU) representation for the asymmetric Laplace distribution (ALD). The use of the SMU for a probability distribution is a data augmentation technique that simplifies the Gibbs sampler of the Bayesian Markov chain Monte Carlo algorithms. We consider a stochastic volatility (SV) model with an ALD error distribution. With the SMU representation, the full conditional distribution for some parameters is shown to have closed form. It is also known that the ALD can be used to obtain the coefficients of quantile regression models. This paper also considers a quantile SV model by fixing the skew parameter of the ALD at specific quantile level. Simulation study shows that the proposed methodology works well in both SV and quantile SV models using Bayesian approach. In the empirical study, we analyze index returns of the stock markets in Australia, Japan, Hong Kong, Thailand, and the UK and study the effect of S&P 500 on these returns. The results show the significant return asymmetry in some markets and the influence by S&P 500 in all markets at all quantile levels. Copyright © 2014 John Wiley & Sons, Ltd.

Widjaja, M, Berry, I, Pont, E, Padula, M & Djordjevic, S 2015, 'P40 and P90 from Mpn142 are Targets of Multiple Processing Events on the Surface of Mycoplasma pneumoniae', Proteomes, vol. 3, no. 4, pp. 512-537.
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Mycoplasma pneumoniae is a significant cause of community acquired pneumonia globally. Despite having a genome less than 1 Mb in size, M. pneumoniae presents a structurally sophisticated attachment organelle that (i) provides cell polarity, (ii) directs adherence to receptors presented on respiratory epithelium, and (iii) plays a major role in cell motility. The major adhesins, P1 (Mpn141) and P30 (Mpn453), are localised to the tip of the attachment organelle by the surface accessible cleavage fragments P90 and P40 derived from Mpn142. Two events play a defining role in the formation of P90 and P40; removal of a leader peptide at position 26 (23SLA↓NTY28) during secretion to the cell surface and cleavage at amino acid 455 (452GPL↓RAG457) generating P40 and P90. Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) analysis of tryptic peptides generated by digesting size-fractionated cell lysates of M. pneumoniae identified 15 cleavage fragments of Mpn142 ranging in mass from 9–84 kDa. Further evidence for the existence of cleavage fragments of Mpn142 was generated by mapping tryptic peptides to proteins recovered from size fractionated eluents from affinity columns loaded with heparin, fibronectin, fetuin, actin, plasminogen and A549 surface proteins as bait. To define the sites of cleavage in Mpn142, neo-N-termini in cell lysates of M. pneumoniae were dimethyl-labelled and characterised by LC-MS/MS. Our data suggests that Mpn142 is cleaved to generate adhesins that are auxiliary to P1 and P30.

Wilkinson, AD, Collier, CJ, Flores, F, Mercurio, P, O'Brien, J, Ralph, PJ & Negri, AP 2015, 'A Miniature Bioassay for Testing the Acute Phytotoxicity of Photosystem II Herbicides on Seagrass', PLOS ONE, vol. 10, no. 2.
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Wilkinson, AM, Johnson, CE, Walker, H, Colgan, V, Arnet, H & Rai, T 2015, 'Evaluating the Liverpool Care Pathway for care of the terminally ill in rural Australia', Supportive Care in Cancer, vol. 23, no. 11, pp. 3173-3181.
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© 2015, Springer-Verlag Berlin Heidelberg. Purpose: This study evaluates a pilot implementation of the Liverpool Care Pathway (LCP), a clinical tool used to guide the care of dying patients in the last days of life, on the end-of-life care for dying patients in three regions in rural Australia. Methods: The LCP was implemented at 13 participating sites: nine hospitals (general wards), one community-based palliative care service, and three in-hospital palliative care units. To evaluate the implementation of the LCP, 415 eligible patient records were examined: 223 pre-implementation and 192 post-implementation (116 on the LCP and 76 receiving usual care). The primary analysis compared all patients pre-implementation of the LCP versus all patients post-implementation. Results: Increases were found post-implementation for communication with other health professionals and with patients or family (pre-69 %, post-87 %; p ≤ 0.000), use of palliative medications (pre-87 %, post-98 %; p ≤ 0.000) and frequency of symptom assessments (pre-66 %, post-82 %; p ≤ 0.000). Fewer blood and radiological investigations were conducted and venous access devices used in the post-implementation groups than in the pre-implementation period. Conclusions: This study suggests that when rigorously implemented, the LCP improves important components of end-of-life care for dying patients and their families.

Williams, DBG, Mason, JM, Tristram, CJ & Hinkley, SFR 2015, 'Cellulose as a Source of Water Dispersible Renewable Film-Forming Materials', Macromolecules, vol. 48, no. 23, pp. 8497-8508.
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Wolff, C, Gutsche, P, Steel, MJ, Eggleton, BJ & Poulton, CG 2015, 'Impact of nonlinear loss on stimulated Brillouin scattering', Journal of the Optical Society of America B, vol. 32, no. 9, pp. 1968-1968.
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Wolff, C, Gutsche, P, Steel, MJ, Eggleton, BJ & Poulton, CG 2015, 'Power limits and a figure of merit for stimulated Brillouin scattering in the presence of third and fifth order loss', Optics Express, vol. 23, no. 20, pp. 26628-26628.
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© 2015 Optical Society of America. We derive a set of design guidelines and a figure of merit to aid the engineering process of on-chip waveguides for strong Stimulated Brillouin Scattering (SBS). To this end, we examine the impact of several types of loss on the total amplification of the Stokes wave that can be achieved via SBS. We account for linear loss and nonlinear loss of third order (two-photon absorption, 2PA) and fifth order, most notably 2PA-induced free carrier absorption (FCA). From this, we derive an upper bound for the output power of continuous-wave Brillouin-lasers and show that the optimal operating conditions and maximal realisable Stokes amplification of any given waveguide structure are determined by a dimensionless parameter F involving the SBS-gain and all loss parameters. We provide simple expressions for optimal pump power, waveguide length and realisable amplification and demonstrate their utility in two example systems. Notably, we find that 2PA-induced FCA is a serious limitation to SBS in silicon and germanium for wavelengths shorter than 2200nm and 3600nm, respectively. In contrast, three-photon absorption is of no practical significance.

Wolff, C, Steel, MJ, Eggleton, BJ & Poulton, CG 2015, 'Acoustic build-up in on-chip stimulated Brillouin scattering', Scientific Reports, vol. 5, no. 1.
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AbstractWe investigate the role of the spatial evolution of the acoustic field in stimulated Brillouin scattering processes in short high-gain structures. When the gain is strong enough that the gain length becomes comparable to the acoustic wave decay length of order 100 microns, standard approximations treating the acoustic field as a local response no longer apply. Treating the acoustic evolution more accurately, we find that the backward SBS gain of sub-millimetre long waveguides is significantly reduced from the value obtained by the conventional treatment because the acoustic mode requires several decay lengths to build up to its nominal value. In addition, the corresponding resonance line is broadened with the development of side bands. In contrast, we argue that intra-mode forward SBS is not expected to show these effects. Our results have implications for several recent proposals and experiments on high-gain stimulated Brillouin scattering in short semiconductor waveguides.

Wong, DCK, Yeoh, WK, De Silva, KSB, Kondyurin, A, Bao, P, Li, WX, Xu, X, Peleckis, G, Dou, SX, Ringer, SP & Zheng, RK 2015, 'Microscopic unravelling of nano-carbon doping in MgB2 superconductors fabricated by diffusion method', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 644, pp. 900-905.
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Wong, DCK, Yeoh, WK, Trimby, PW, De Silva, KSB, Bao, P, Li, WX, Xu, X, Dou, SX, Ringer, SP & Zheng, RK 2015, 'Characterisation of nano-grains in MgB2 superconductors by transmission Kikuchi diffraction', SCRIPTA MATERIALIA, vol. 101, pp. 36-39.
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© 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. We report the first application of the emerging transmission Kikuchi diffraction technique in the scanning electron microscope to investigate nano-grain structures in polycrystalline MgB2 superconductors. Two sintering conditions were considered, and the resulting differences in superconducting properties are correlated to differences in grain structure. A brief comparison to X-ray diffraction results is presented and discussed. This work focusses more on the application of this technique to reveal grain structure, rather than on the detailed differences between the two sintering temperatures.

Wonoputri, V, Gunawan, C, Liu, S, Barraud, N, Yee, LH, Lim, M & Amal, R 2015, 'Copper Complex in Poly(vinyl chloride) as a Nitric Oxide-Generating Catalyst for the Control of Nitrifying Bacterial Biofilms', ACS Applied Materials & Interfaces, vol. 7, no. 40, pp. 22148-22156.
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© 2015 American Chemical Society. In this study, catalytic generation of nitric oxide by a copper(II) complex embedded within a poly(vinyl chloride) matrix in the presence of nitrite (source of nitric oxide) and ascorbic acid (reducing agent) was shown to effectively control the formation and dispersion of nitrifying bacteria biofilms. Amperometric measurements indicated increased and prolonged generation of nitric oxide with the addition of the copper complex when compared to that with nitrite and ascorbic acid alone. The effectiveness of the copper complex-nitrite-ascorbic acid system for biofilm control was quantified using protein analysis, which showed enhanced biofilm suppression when the copper complex was used in comparison to that with nitrite and ascorbic acid treatment alone. Confocal laser scanning microscopy (CLSM) and LIVE/DEAD staining revealed a reduction in cell surface coverage without a loss of viability with the copper complex and up to 5 mM of nitrite and ascorbic acid, suggesting that the nitric oxide generated from the system inhibits proliferation of the cells on surfaces. Induction of nitric oxide production by the copper complex system also triggered the dispersal of pre-established biofilms. However, the addition of a high concentration of nitrite and ascorbic acid to a pre-established biofilm induced bacterial membrane damage and strongly decreased the metabolic activity of planktonic and biofilm cells, as revealed by CLSM with LIVE/DEAD staining and intracellular adenosine triphosphate measurements, respectively. This study highlights the utility of the catalytic generation of nitric oxide for the long-term suppression and removal of nitrifying bacterial biofilms.

Woodcock, S 2015, 'Development of enquiry-oriented learning in the mathematical sciences', ANZIAM JOURNAL, vol. 57, pp. C1-C13.
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Woodcock, S, Manojlovic, B, Baird, ME & Ralph, PJ 2015, 'A POISSON-PARETO MODEL OF CHLOROPHYLL-A FLUORESCENCE SIGNALS IN MARINE ENVIRONMENTS', ANZIAM JOURNAL, vol. 56, no. 4, pp. 373-380.
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© Australian Mathematical Society 2015. Because of its central role in the global carbon cycle, quantifying the biomass of photosynthetic microalgae in the oceans is crucial to our ability to estimate the oceans' carbon drawdown. Many traditional methods of primary production assessment have proven to be extremely time consuming and, consequently, have handled only very small sample sizes. The recent advent of in situ bio-optical sensors, such as the water quality monitor (WQM), is now providing lower cost and higher throughput data on these crucial biological communities. These WQMs, however, only quantify the total fluorescence of all individual cells within their optical sample windows, irrespective of size. In this paper, we further develop an established model, based on Pareto random variables, of the size structure of the microalgae community to understand the effect of the WQMs' sampling and data pooling on their estimates of algal biomass. Unfortunately, evaluating sums of Pareto variables is a notoriously difficult problem. Here, we utilize an approximation for the right-tail of the resulting distribution to derive parameter estimates for the underlying size structure of the microalgae community.

Woodward, KB, Fellows, CS, Mitrovic, SM & Sheldon, F 2015, 'Patterns and bioavailability of soil nutrients and carbon across a gradient of inundation frequencies in a lowland river channel, Murray–Darling Basin, Australia', Agriculture, Ecosystems & Environment, vol. 205, pp. 1-8.
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Wu, WC, Ao, ZM, Yang, CH, Li, S, Wang, GX, Li, CM & Li, S 2015, 'Hydrogenation of silicene with tensile strains', Journal of Materials Chemistry C, vol. 3, no. 11, pp. 2593-2602.
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The energy barrier for hydrogenation of silicene decreases as the strains increase, and the barrier reduces from 1.71 to 0.24 eV when the strain reaches the critical value of 12%. In this way, the reaction time for the hydrogenation of silicene can accelerate significantly from 8.06 × 10¹⁶ to 1.68 × 10⁻⁸ s.

Wyrsch, E, Chowdhury, PR, Abraham, S, Santos, J, Darling, AE, Charles, IG, Chapman, TA & Djordjevic, SP 2015, 'Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs', BMC Genomics, vol. 16, no. 1, pp. 1-11.
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BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) are a major economic threat to pig production globally, with serogroups O8, O9, O45, O101, O138, O139, O141, O149 and O157 implicated as the leading diarrhoeal pathogens affecting pigs below four weeks of age. A multiple antimicrobial resistant ETEC O157 (O157 SvETEC) representative of O157 isolates from a pig farm in New South Wales, Australia that experienced repeated bouts of pre- and post-weaning diarrhoea resulting in multiple fatalities was characterized here. Enterohaemorrhagic E. coli (EHEC) O157:H7 cause both sporadic and widespread outbreaks of foodborne disease, predominantly have a ruminant origin and belong to the ST11 clonal complex. Here, for the first time, we conducted comparative genomic analyses of two epidemiologically-unrelated porcine, disease-causing ETEC O157; E. coli O157 SvETEC and E. coli O157:K88 734/3, and examined their phylogenetic relationship with EHEC O157:H7. RESULTS: O157 SvETEC and O157:K88 734/3 belong to a novel sequence type (ST4245) that comprises part of the ST23 complex and are genetically distinct from EHEC O157. Comparative phylogenetic analysis using PhyloSift shows that E. coli O157 SvETEC and E. coli O157:K88 734/3 group into a single clade and are most similar to the extraintestinal avian pathogenic Escherichia coli (APEC) isolate O78 that clusters within the ST23 complex. Genome content was highly similar between E. coli O157 SvETEC, O157:K88 734/3 and APEC O78, with variability predominantly limited to laterally acquired elements, including prophages, plasmids and antimicrobial resistance gene loci. Putative ETEC virulence factors, including the toxins STb and LT and the K88 (F4) adhesin, were conserved between O157 SvETEC and O157:K88 734/3. The O157 SvETEC isolate also encoded the heat stable enterotoxin STa and a second allele of STb, whilst a prophage within O157:K88 734/3 encoded the serum survival gene bor. Both isolates harbor a large repertoire of antibi...

Xie, X, Ao, Z, Su, D, Zhang, J & Wang, G 2015, 'MoS₂/Graphene Composite Anodes with Enhanced Performance for Sodium‐Ion Batteries: The Role of the Two‐Dimensional Heterointerface', Advanced Functional Materials, vol. 25, no. 9, pp. 1393-1403.
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Graphene has been widely used as conformal nanobuilding blocks to improve the electrochemical performance of layered metal sulfides (MoS2, WS2, SnS, and SnS2) as anode materials for sodium‐ion batteries. However, it still lacks in‐depth understanding of the synergistic effect between these layered sulfides and graphene, which contributes to the enhanced electroactivity for sodium‐ion batteries. Here, MoS2/reduced graphene oxide (RGO) nanocomposites with intimate two‐dimensional heterointerfaces are prepared by a facile one‐pot hydrothermal method. The heterointerfacial area can be effectively tuned by changing the ratio of MoS2 to RGO. When used as anode materials for sodium‐ion batteries, the synergistic effect contributing to the enhanced reversible capacity of MoS2/RGO nanocomposites is closely related with the heterointerfacial area. The computational results demonstrate that Na prefers to be adsorbed on MoS2 in the MoS2/RGO heterostructure rather than intercalate into the MoS2/RGO heterointerface. Interestingly, the MoS2/RGO heterointerfaces can significantly increase the electronic conductivity of MoS2, store more Na ions, while maintaining the high diffusion mobility of Na atoms on MoS2 surface and high electron transfer efficiency from Na to MoS2. It is expected that the efforts to establish the correlation between the two‐dimensional heterointerface and the electrochemical sodium‐ion storage performance offer fundamental understanding for the rational design of layered metal sulfides/graphene composites as high‐performance electrode materials for sodium‐ion batteries.

Xie, X, Chen, S, Sun, B, Wang, C & Wang, G 2015, '3D Networked Tin Oxide/Graphene Aerogel with a Hierarchically Porous Architecture for High-Rate Performance Sodium-Ion Batteries', CHEMSUSCHEM, vol. 8, no. 17, pp. 2948-2955.
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© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Low-cost and sustainable sodium-ion batteries are regarded as a promising technology for large-scale energy storage and conversion. The development of high-rate anode materials is highly desirable for sodium-ion batteries. The optimization of mass transport and electron transfer is crucial in the discovery of electrode materials with good high-rate performances. Herein, we report the synthesis of 3D interconnected SnO2/graphene aerogels with a hierarchically porous structure as anode materials for sodium-ion batteries. The unique 3D architecture was prepared by a facile insitu process, during which cross-linked 3D conductive graphene networks with macro-/meso-sized hierarchical pores were formed and SnO2 nanoparticles were dispersed uniformly on the graphene surface simultaneously. Such a 3D functional architecture not only facilitates the electrode-electrolyte interaction but also provides an efficient electron pathway within the graphene networks. When applied as anode materials in sodium-ion batteries, the as-prepared SnO2/graphene aerogel exhibited high reversible capacity, improved cycling performance compared to SnO2, and promising high-rate capability. Explore the pores: 3D SnO2/graphene aerogels with a hierarchically porous structure are prepared by a facile self-assembly method, in which graphene nanosheets self-bridge to form 3D continuous networks with interconnected porous channels and SnO2 nanoparticles are homogeneously loaded on the graphene nanosheets. The integration of SnO2 nanoparticles leads to fast Na⁺ diffusion and electronic conductivity, giving rise to a promising high-rate performance as anode in sodium-ion batteries.

Xie, X, Kretschmer, K & Wang, G 2015, 'Advances in graphene-based semiconductor photocatalysts for solar energy conversion: fundamentals and materials engineering', NANOSCALE, vol. 7, no. 32, pp. 13278-13292.
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© The Royal Society of Chemistry. Graphene-based semiconductor photocatalysis has been regarded as a promising technology for solar energy storage and conversion. In this review, we summarized recent developments of graphene-based photocatalysts, including preparation of graphene-based photocatalysts, typical key advances in the understanding of graphene functions for photocatalytic activity enhancement and methodologies to regulate the electron transfer efficiency in graphene-based composite photocatalysts, by which we hope to offer enriched information to harvest the utmost fascinating properties of graphene as a platform to construct efficient graphene-based composite photocatalysts for solar-to-energy conversion.

Xie, X, Kretschmer, K, Zhang, J, Sun, B, Su, D & Wang, G 2015, 'Sn@CNT nanopillars grown perpendicularly on carbon paper: A novel free-standing anode for sodium ion batteries', NANO ENERGY, vol. 13, pp. 208-217.
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© 2015 Elsevier Ltd. Sodium-ion batteries have attracted extensive interest for energy storage and conversion as an alternative to lithium-ion batteries. The development of advanced electrode materials is important for the implementation of sodium-ion batteries into practical applications. Herein, we developed a facile soaking-chemical vapour deposition method to grow core-sheath structured Sn@CNT nanopillar arrays on carbon paper with a unique 3D hierarchical architecture as free-standing electrode for sodium-ion batteries. The electrode achieved a reversible capacity of 887μAhcm-2 in the first cycle and good cyclability extending to 100 cycles. The electrode also demonstrated a promising rate capability, which is suitable for high power applications. We also assembled prototype Na-ion full cells, consisting of the as-prepared free-standing Sn@CNT@carbon paper anode and Na0.80Li0.12Ni0.22Mn0.66O2 cathode. The full sodium-ion battery can power LED lights. This work is expected to inspire the development of sustainable sodium-ion batteries for energy storage and conversion.

Xie, X, Su, D, Zhang, J, Chen, S, Mondal, AK & Wang, G 2015, 'A comparative investigation on the effects of nitrogen-doping into graphene on enhancing the electrochemical performance of SnO₂/graphene for sodium-ion batteries', Nanoscale, vol. 7, no. 7, pp. 3164-3172.
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Enhanced electron transfer efficiency plays a dominant role for improving the performance of SnO₂/N-doped graphene for sodium-ion batteries.

Yakkundi, A, Bennett, R, Hernández-Negrete, I, Delalande, J-M, Hanna, M, Lyubomska, O, Arthur, K, Short, A, McKeen, H, Nelson, L, McCrudden, CM, McNally, R, McClements, L, McCarthy, HO, Burns, AJ, Bicknell, R, Kissenpfennig, A & Robson, T 2015, 'FKBPL Is a Critical Antiangiogenic Regulator of Developmental and Pathological Angiogenesis', Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 35, no. 4, pp. 845-854.
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Objective— The antitumor effects of FK506-binding protein like (FKBPL) and its extracellular role in angiogenesis are well characterized; however, its role in physiological/developmental angiogenesis and the effect of FKBPL ablation has not been evaluated. This is important as effects of some angiogenic proteins are dosage dependent. Here we evaluate the regulation of FKBPL secretion under angiogenic stimuli, as well as the effect of FKBPL ablation in angiogenesis using mouse and zebrafish models. Approach and Results— FKBPL is secreted maximally by human microvascular endothelial cells and fibroblasts, and this was specifically downregulated by proangiogenic hypoxic signals, but not by the angiogenic cytokines, VEGF or IL8. FKBPL’s critical role in angiogenesis was supported by our inability to generate an Fkbpl knockout mouse, with embryonic lethality occurring before E8.5. However, whilst Fkbpl heterozygotic embryos showed some vasculature irregularities, the mice developed normally. In murine angiogenesis models, including the ex vivo aortic ring assay, in vivo sponge assay, and tumor growth assay, Fkbpl +/− mice exhibited increased sprouting, enhanced vessel recruitment, and faster tumor growth, respectively, supporting the antiangiogenic function of FKBPL. In zebrafish, knockdown of zFkbpl using morpholinos disrupted the vasculature, and the phenotype was rescued with h FKBPL ...

Yang, J, Liu, C, Li, S, Sun, B, Xiao, J & Jin, Y 2015, 'A new pressure drop model of gas–liquid cyclone with innovative operation mode', Chemical Engineering and Processing: Process Intensification, vol. 95, pp. 256-266.
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Yang, M, Liang, Y, Gui, Q, Zhao, B, Jin, D, Lin, M, Yan, L, You, H, Dai, L & Liu, Y 2015, 'Multifunctional luminescent nanomaterials from NaLa(MoO4)2:Eu3+/Tb3+ with tunable decay lifetimes, emission colors and enhanced cell viability', Scientific Reports, vol. 5, no. 1, pp. 1-12.
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AbstractA facile, but effective, method has been developed for large-scale preparation of NaLa(MoO4)2 nanorods and microflowers co-doped with Eu3+ and Tb3+ ions (abbreviated as: NLM:Ln3+). The as-synthesized nanomaterials possess a pure tetragonal phase with variable morphologies from shuttle-like nanorods to microflowers by controlling the reaction temperature and the amount of ethylene glycol used. Consequently, the resulting nanomaterials exhibit superb luminescent emissions over the visible region from red through yellow to green by simply changing the relative doping ratios of Eu3+ to Tb3+ ions. Biocompatibility study indicates that the addition of NLM:Ln3+ nanomaterials can stimulate the growth of normal human retinal pigment epithelium (ARPE-19) cells. Therefore, the newly-developed NaLa(MoO4)2 nanomaterials hold potentials for a wide range of multifunctional applications, including bioimaging, security protection, optical display, optoelectronics for information storage and cell stimulation.

Yang, ZW, Wang, YD, Liao, JY, Yang, JZ, Qiu, JB & Song, ZG 2015, 'Upconversion Emission Modification and White Light Generation in NaYF₄:Yb³⁺, Er³⁺, Tm³⁺Nanocrystals/Opal Photonic Crystal Composites', IEEE Photonics Journal, vol. 7, no. 6, pp. 1-8.
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© 2009-2012 IEEE. In this paper, we fabricated NaYF4:Yb3+, Er3+, Tm3+ nanocrystal/opal photonic crystal composites by depositing NaYF4:Yb3+, Er3+, Tm3+ nanocrystals on the surface of opal photonic crystals, and we investigated the influence of photonic bandgaps on upconversion (UC) emission properties of NaYF4:Yb 3+, Er3+, Tm3+ nanocrystals. When the photonic bandgaps overlapped with the UC emission bands of NaYF4:Yb 3+, Er3+, Tm3+ nanocrystals on the opal photonic crystal surfaces, the suppression or enhancement of UC emissions was observed due to the Bragg reflection effect of photonic crystal, resulting in the modification of red, green, and blue UC emissions. Thus, white UC emission was realized.

Yao, Q, Li, W, Yu, S, Ma, L, Jin, D, Boccaccini, AR & Liu, Y 2015, 'Multifunctional chitosan/polyvinyl pyrrolidone/45S5 Bioglass® scaffolds for MC3T3-E1 cell stimulation and drug release', Materials Science and Engineering: C, vol. 56, pp. 473-480.
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© 2015 Published by Elsevier B.V. Abstract Novel chitosan-polyvinyl pyrrolidone/45S5 Bioglass® (CS-PVP/BG) scaffolds were prepared via foam replication and chemical cross-linking techniques. The pristine BG, CS-PVP coated BG and genipin cross-linked CS-PVP/BG (G-CS-PVP/BG) scaffolds were synthesized and characterized in terms of chemical composition, physical structure and morphology respectively. Resistance to enzymatic degradation of the scaffold is improved significantly with the use of genipin cross-linked CS-PVP. The bio-effects of scaffolds on MC3T3-E1 osteoblast-like cells were evaluated by studying cell viability, adhesion and proliferation. The CCK-8 assay shows that cell viability on the resulting G-CS-PVP/BG scaffold is improved obviously after cross-linking of genipin. Cell skeleton images exhibit that well-stretched F-actin bundles are obtained on the G-CS-PVP/BG scaffold. SEM results present significant improvement on the cell adhesion and proliferation for cells cultured on the G-CS-PVP/BG scaffold. The drug release performance on the as-synthesized scaffold was studied in a phosphate buffered saline (PBS) solution. Vancomycin is found to be released in burst fashion within 24 h from the pristine BG scaffold, however, the release period from the G-CS-PVP/BG scaffold is enhanced to 7 days, indicating improved drug release properties of the G-CS-PVP/BG scaffold. Our results suggest that the G-CS-PVP/BG scaffolds possess promising physicochemical properties, sustained drug release capability and good biocompatibility for MC3T3-E1 cells' proliferation and adhesion, suggesting their potential applications in areas such as MC3T3-E1 cell stimulation and bone tissue engineering.

Yi, GY, Ma, Y, Spiegelman, D & Carroll, RJ 2015, 'Functional and Structural Methods With Mixed Measurement Error and Misclassification in Covariates', Journal of the American Statistical Association, vol. 110, no. 510, pp. 681-696.
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Yung, R, Rawling, T, Murray, M & Ching, L-M 2015, 'Liquid Chromatography-Tandem Mass Spectrometry Assay Suitable for Quantifying Omega-3 Epoxy-Fatty Acid Analogs in Mouse Brain and Plasma', Journal of Liquid Chromatography & Related Technologies, vol. 38, no. 8, pp. 891-897.
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Metabolites of omega-3 fatty acids can inhibit primary tumor growth, angiogenesis, and tumor metastasis. Effective treatment for brain tumors is an unmet need as many chemotherapies are unable to cross the blood–brain barrier efficiently. As fatty acids are capable of entering the brain, these agents may have potential for treating brain tumors. In this communication a reliable and sensitive LC-MS/MS method was developed and validated for quantitation of ethyl 16-{[(4-methylphenyl)carbamoyl]amino}hexadecanoate (CUT-EE), a urea-based analog of eicosapentaenoic acid. The assay has acceptable intra- and inter-assay accuracy and precision over the range 0.25–125 ng/mL, and a lower limit of quantitation of 0.25 ng/mL. Non-aqueous, mouse brain, and plasma solutions of CUT-EE were stable during short-term and long-term storage, and after three freeze-thaw cycles. This method was applied to determine concentrations of CUT-EE in brain and plasma following administration to mice at 50 mg/kg. CUT-EE was cleared from the plasma within 24 hr, whilst concentrations in the brain increased over 24 hr and remained stable out to 48 hr. The calculated area under the concentration curve in brain was over 100 times greater than that found in plasma, supporting further investigations of CUT-EE for its potential in treating brain cancers.

Yunusa, IAM, Eamus, D, Taylor, D, Whitley, R, Gwenzi, W, Palmer, AR & Li, Z 2015, 'Partitioning of turbulent flux reveals contrasting cooling potential for woody vegetation and grassland during heat waves', QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, vol. 141, no. 692, pp. 2528-2537.
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Zabeau, L, Jensen, CJ, Seeuws, S, Venken, K, Verhee, A, Catteeuw, D, van Loo, G, Chen, H, Walder, K, Hollis, J, Foote, S, Morris, MJ, Van der Heyden, J, Peelman, F, Oldfield, BJ, Rubio, JP, Elewaut, D & Tavernier, J 2015, 'Leptin’s metabolic and immune functions can be uncoupled at the ligand/receptor interaction level', Cellular and Molecular Life Sciences, vol. 72, no. 3, pp. 629-644.
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Zahid, K, Zhao, J-H, Smith, NA, Schumann, U, Fang, Y-Y, Dennis, ES, Zhang, R, Guo, H-S & Wang, M-B 2015, 'Nicotiana Small RNA Sequences Support a Host Genome Origin of Cucumber Mosaic Virus Satellite RNA', PLOS GENETICS, vol. 11, no. 1.
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Zarghami, Z, Maddahfar, M & Ramezani, M 2015, 'Ag@Ag2SO4 nanoparticles: simple microwave-assistance synthesis, characterization and its co-photocatalytic degradation of methylene blue', Journal of Materials Science: Materials in Electronics, vol. 26, no. 9, pp. 6339-6343.
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Zarghami, Z, Ramezani, M & Maddahfar, M 2015, 'Facile hydrothermal synthesis, formation mechanism, and characterization of In(OH)3 nanostructures for preparation of In2O3 nanoparticles using novel starting reagents', Journal of Materials Science: Materials in Electronics, vol. 26, no. 8, pp. 5884-5891.
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Zarghami, Z, Ramezani, M & Maddahfar, M 2015, 'Simple microwave-assisted synthesis of Cu@CuSO4 as co-catalyst of TiO2 for photocatalytic degradation of methylene blue', Materials Letters, vol. 152, pp. 21-24.
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Zavřel, T, Sinetova, MA, Búzová, D, Literáková, P & Červený, J 2015, 'Characterization of a model cyanobacterium Synechocystis sp. PCC 6803 autotrophic growth in a flat‐panel photobioreactor', Engineering in Life Sciences, vol. 15, no. 1, pp. 122-132.
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We characterized the photoautotrophic growth of glucose‐tolerant Synechocystis sp. PCC 6803 in a flat‐panel photobioreactor running on a semicontinuous regime under various lights, temperatures, and influx carbon dioxide concentrations. The maximum reached growth rate was 0.135 h−1, which corresponds to a doubling time of 5.13 h—a growth speed never reported for Synechocystis before. Saturating red light intensity for the strain was 220–360 μmol(photons) m−2 s−1, and we did not observe any photoinhibition up to 660 μmol(photons) m−2 s−1. Synechocystis was able to grow under red light only; however, photons of wavelengths 405–585 and 670–700 nm further improved its growth. Optimal growth temperature was 35°C. Below 32°C, the growth rates decreased linearly with temperature coefficient (Q10) 1.70. Semicontinuous cultivation is known to be efficient for growth characterization and optimization. However, the assumption of correct growth rates calculation—culture exponential growth—is often not fulfilled. The semicontinuous setup in this study was operated as a turbidostat. Accurate online OD measurements with high time‐resolution allowed fast and reliable growth rates determination. Repeating diluting frequencies (up to 18 dilutions per day) were essential for rapid growth stability evaluation. The presented setup provides improvement to previously published semicontinuous characterization strategies by decreasing experimental time requirements and maintaining the culture in exponential growth phase throughout the entire characterization procedure.

Zeng, Y, Li, J, Liu, Q, Qu, Y, Huete, AR, Xu, B, Yin, G & Zhao, J 2015, 'An Optimal Sampling Design for Observing and Validating Long-Term Leaf Area Index with Temporal Variations in Spatial Heterogeneities', REMOTE SENSING, vol. 7, no. 2, pp. 1300-1319.
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Zhand, S, Karami, C, Hosseinzadeh Adli, A, Tabarraei, A, Khodabakhshi, B & Moradi, A 2015, 'Correlation Between Hepatitis B G1896A Precore Mutations and HBeAg in Chronic HBV Patients', Jundishapur Journal of Microbiology, vol. 8, no. 2.
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Zhang, J, Sun, B, Xie, X, Kretschmer, K & Wang, G 2015, 'Enhancement of stability for lithium oxygen batteries by employing electrolytes gelled by poly(vinylidene fluoride-co-hexafluoropropylene) and tetraethylene glycol dimethyl ether', ELECTROCHIMICA ACTA, vol. 183, pp. 56-62.
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© 2015 Elsevier Ltd. All rights reserved. Free-standing gel polymer electrolytes with poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) matrix plasticized with tetraethylene glycol dimethyl ether (TEGDME) were prepared and investigated. The as-prepared gel polymer electrolytes exhibited large operating window and acceptable ionic conductivity. When applied in lithium oxygen batteries, the gel polymer electrolyte could support a high initial discharge capacity of 2988 mAh g-1 when a carbon black electrode without catalyst was used as cathode. Furthermore, the battery with gel polymer electrolyte can last at least 50 cycles in the fixed capacity cycling, displaying an excellent stability. Detailed study reveals that the gelling process is essential for the cycling stability enhancement. With excellent electrochemical properties, the free-standing gel polymer electrolyte presented in this investigation has great application potentials in long-life lithium oxygen batteries.

Zhang, Q, Shuwen, G, Zhang, J, Fane, AG, Kjelleberg, S, Rice, SA & McDougald, D 2015, 'Analysis of microbial community composition in a lab‐scale membrane distillation bioreactor', Journal of Applied Microbiology, vol. 118, no. 4, pp. 940-953.
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© 2015 The Authors published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology. Membrane distillation bioreactors (MDBR) have potential for industrial applications where wastewater is hot or waste heat is available, but the role of micro-organisms in MDBRs has never been determined, and thus was the purpose of this study. Methods and Results: Microbial communities were characterized by bacterial and archaeal 16S and eukaryotic 18S rRNA gene tag-encoded pyrosequencing of DNA obtained from sludge. Taxonomy-independent analysis revealed that bacterial communities had a relatively low richness and diversity, and community composition strongly correlated with conductivity, total nitrogen and bound extracellular polymeric substances (EPS). Taxonomy-dependent analysis revealed that Rubrobacter and Caldalkalibacillus were abundant members of the bacterial community, but no archaea were detected. Eukaryotic communities had a relatively high richness and diversity, and both changes in community composition and abundance of the dominant genus, Candida, correlated with bound EPS. Conclusions: Thermophilic MDBR communities were comprised of a low diversity bacterial community and a highly diverse eukaryotic community with no archea detected. Communities exhibited low resilience to changes in operational parameters. Specifically, retenatate nutrient composition and concentration was strongly correlated with the dominant species. Significance and Impact of the Study: This study provides an understanding of microbial community diversity in an MDBR, which is fundamental to the optimization of reactor performance.

Zhang, T, Hu, Y, Jiang, W, Fang, L, Guan, X, Chen, J, Zhang, J, Saski, CA, Scheffler, BE, Stelly, DM, Hulse-Kemp, AM, Wan, Q, Liu, B, Liu, C, Wang, S, Pan, M, Wang, Y, Wang, D, Ye, W, Chang, L, Zhang, W, Song, Q, Kirkbride, RC, Chen, X, Dennis, E, Llewellyn, DJ, Peterson, DG, Thaxton, P, Jones, DC, Wang, Q, Xu, X, Zhang, H, Wu, H, Zhou, L, Mei, G, Chen, S, Tian, Y, Xiang, D, Li, X, Ding, J, Zuo, Q, Tao, L, Liu, Y, Li, J, Lin, Y, Hui, Y, Cao, Z, Cai, C, Zhu, X, Jiang, Z, Zhou, B, Guo, W, Li, R & Chen, ZJ 2015, 'Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement', NATURE BIOTECHNOLOGY, vol. 33, no. 5, pp. 531-U252.
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© 2015 Nature America, Inc. All rights reserved. Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.

Zhang, X, Cao, J & Carroll, RJ 2015, 'On the Selection of Ordinary Differential Equation Models with Application to Predator-Prey Dynamical Models', Biometrics, vol. 71, no. 1, pp. 131-138.
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Summary We consider model selection and estimation in a context where there are competing ordinary differential equation (ODE) models, and all the models are special cases of a “full” model. We propose a computationally inexpensive approach that employs statistical estimation of the full model, followed by a combination of a least squares approximation (LSA) and the adaptive Lasso. We show the resulting method, here called the LSA method, to be an (asymptotically) oracle model selection method. The finite sample performance of the proposed LSA method is investigated with Monte Carlo simulations, in which we examine the percentage of selecting true ODE models, the efficiency of the parameter estimation compared to simply using the full and true models, and coverage probabilities of the estimated confidence intervals for ODE parameters, all of which have satisfactory performances. Our method is also demonstrated by selecting the best predator-prey ODE to model a lynx and hare population dynamical system among some well-known and biologically interpretable ODE models.

Zhang, X, Zou, G & J. Carroll, R 2015, 'Model averaging based on Kullback-Leibler distance', Statistica Sinica, vol. 25, no. 4, pp. 1583-1598.
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© 2015, Institute of Statistical Science. All rights reserved. This paper proposes a model averaging method based on Kullback-Leibler distance under a homoscedastic normal error term. The resulting model average estimator is proved to be asymptotically optimal. When combining least squares estimators, the model average estimator is shown to have the same large sample properties as the Mallows model average (MMA) estimator developed by Hansen (2007). We show via simulations that, in terms of mean squared prediction error and mean squared parameter estimation error, the proposed model average estimator is more efficient than the MMA estimator and the estimator based on model selection using the corrected Akaike information criterion in small sample situations. A modified version of the new model average estimator is further suggested for the case of heteroscedastic random errors. The method is applied to a data set from the Hong Kong real estate market.

Zhang, Y, Bhadbhade, M, Karatchevtseva, I, Price, JR, Liu, H, Zhang, Z, Kong, L, Cejka, J, Lu, K & Lumpkin, GR 2015, 'Uranium(VI) coordination polymers with pyromellitate ligand: Unique 1D channel structures and diverse fluorescence', JOURNAL OF SOLID STATE CHEMISTRY, vol. 226, pp. 42-49.
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Zhang, Y, Karatchevtseva, I, Price, JR, Aharonovich, I, Kadi, F, Lumpkin, GR & Li, F 2015, 'Uranium(vi) complexes with isonicotinic acid: from monomer to 2D polymer with unique U–N bonding', RSC Advances, vol. 5, no. 42, pp. 33249-33253.
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Two uranium(vi) complexes with isonicotinic acid, exhibiting a monomer and a 2D polymer, have been synthesized and characterized.

Zhao, C, Liu, C, Dai, X, Liu, T, Duan, Z, Liu, L & Mitrovic, SM 2015, 'Separation of the impacts of climate change and human activity on runoff variations', Hydrological Sciences Journal, vol. 60, no. 2, pp. 234-246.
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Zhao, CS, Yang, ST, Liu, CM, Dou, TW, Yang, ZL, Yang, ZY, Liu, XL, Xiang, H, Nie, SY, Zhang, JL, Mitrovic, SM, Yu, Q & Lim, RP 2015, 'Linking hydrologic, physical and chemical habitat environments for the potential assessment of fish community rehabilitation in a developing city', Journal of Hydrology, vol. 523, pp. 384-397.
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© 2015 Elsevier B.V. Aquatic ecological rehabilitation is increasingly attracting considerable public and research attention. An effective method that requires less data and expertise would help in the assessment of rehabilitation potential and in the monitoring of rehabilitation activities as complicated theories and excessive data requirements on assemblage information make many current assessment models expensive and limit their wide use. This paper presents an assessment model for restoration potential which successfully links hydrologic, physical and chemical habitat factors to fish assemblage attributes drawn from monitoring datasets on hydrology, water quality and fish assemblages at a total of 144 sites, where 5084 fish were sampled and tested. In this model three newly developed sub-models, integrated habitat index (. IHSI), integrated ecological niche breadth (. INB) and integrated ecological niche overlap (. INO), are established to study spatial heterogeneity of the restoration potential of fish assemblages based on gradient methods of habitat suitability index and ecological niche models. To reduce uncertainties in the model, as many fish species as possible, including important native fish, were selected as dominant species with monitoring occurring over several seasons to comprehensively select key habitat factors. Furthermore, a detrended correspondence analysis (DCA) was employed prior to a canonical correspondence analysis (CCA) of the data to avoid the 'arc effect' in the selection of key habitat factors. Application of the model to data collected at Jinan City, China proved effective reveals that three lower potential regions that should be targeted in future aquatic ecosystem rehabilitation programs. They were well validated by the distribution of two habitat parameters: river width and transparency. River width positively influenced and transparency negatively influenced fish assemblages. The model can be applied for monitoring the...

Zhao, CS, Yang, ST, Xiang, H, Liu, CM, Zhang, HT, Yang, ZL, Zhang, Y, Sun, Y, Mitrovic, SM, Yu, Q & Lim, RP 2015, 'Hydrologic and water-quality rehabilitation of environments for suitable fish habitat', Journal of Hydrology, vol. 530, pp. 799-814.
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Zhao, Y, Chen, S, Sun, B, Su, D, Huang, X, Liu, H, Yan, Y, Sun, K & Wang, G 2015, 'Graphene-Co3O4 nanocomposite as electrocatalyst with high performance for oxygen evolution reaction', SCIENTIFIC REPORTS, vol. 5.
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Graphene-Co3O4 composite with a unique sandwich-architecture was successfully synthesized and applied as an efficient electrocatalyst for oxygen evolution reaction. Field emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM) analyses confirmed that Co3O4 nanocrystals were homogeneously distributed on both sides of graphene nanosheets. The obtained composite shows enhanced catalytic activities in both alkaline and neutral electrolytes. The onset potential towards the oxygen evolution reaction is 0.406 V (vs. Ag/AgCl) in 1 M KOH solution, and 0.858 V (vs. Ag/AgCl) in neutral phosphate buffer solution (PBS), respectively. The current density of 10 mA/cm2 has been achieved at the overpotential of 313 mV in 1M KOH and 498mV in PBS. The graphene-Co3O4 composite also exhibited an excellent stability in both alkaline and neutral electrolytes. In particular, no obvious current density decay was observed after 10 hours testing in alkaline solution and the morphology of the material was well maintained, which could be ascribed to the synergistic effect of combining Co3O4 and graphene.

Zhao, Y, Sun, B, Huang, X, Liu, H, Su, D, Sun, K & Wang, G 2015, 'Porous graphene wrapped CoO nanoparticles for highly efficient oxygen evolution', JOURNAL OF MATERIALS CHEMISTRY A, vol. 3, no. 10, pp. 5402-5408.
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© The Royal Society of Chemistry 2015. The design of highly efficient, robust and earth-abundant electrocatalysts for the oxygen evolution reaction (OER) is a prodigious challenge for the rapid growth of global energy demand. Herein, an active catalyst composed of porous graphene and cobalt oxide (PGE-CoO) has been synthesized, demonstrating high porosity, large specific surface area and fast charge transport kinetics. The catalyst also exhibits excellent electrochemical performance towards OER with a low onset potential and high catalytic current density. The enhanced catalytic activity could be ascribed to porous structure, high electroactive surface area and strong chemical coupling between graphene and CoO nanoparticles. Moreover, this OER catalyst also shows good stability in the alkaline solution. The high performance and strong durability suggest that the porous structured composite is favorable and promising for water splitting.

Zhao, Y, Xie, X, Zhang, J, Liu, H, Ahn, H-J, Sun, K & Wang, G 2015, 'MoS2 Nanosheets Supported on 3D Graphene Aerogel as a Highly Efficient Catalyst for Hydrogen Evolution', CHEMISTRY-A EUROPEAN JOURNAL, vol. 21, no. 45, pp. 15908-+.
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The development of efficient catalysts for electrochemical hydrogen evolution is essential for energy conversion technologies. Molybdenum disulfide (MoS2 ) has emerged as a promising electrocatalyst for hydrogen evolution reaction, and its performance greatly depends on its exposed edge sites and conductivity. Layered MoS2 nanosheets supported on a 3D graphene aerogel network (GA-MoS2 ) exhibit significant catalytic activity in hydrogen evolution. The GA-MoS2 composite displays a unique 3D architecture with large active surface areas, leading to high catalytic performance with low overpotential, high current density, and good stability.

Zhou, B, Shi, B, Jin, D & Liu, X 2015, 'Controlling upconversion nanocrystals for emerging applications', Nature Nanotechnology, vol. 10, no. 11, pp. 924-936.
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© 2015 Macmillan Publishers Limited. All rights reserved. Lanthanide-doped upconversion nanocrystals enable anti-Stokes emission with pump intensities several orders of magnitude lower than required by conventional nonlinear optical techniques. Their exceptional properties, namely large anti-Stokes shifts, sharp emission spectra and long excited-state lifetimes, have led to a diversity of applications. Here, we review upconversion nanocrystals from the perspective of fundamental concepts and examine the technical challenges in relation to emission colour tuning and luminescence enhancement. In particular, we highlight the advances in functionalization strategies that enable the broad utility of upconversion nanocrystals for multimodal imaging, cancer therapy, volumetric displays and photonics.

Zhou, B, Wei, T, Cai, M, Tian, Y, Zhou, J, Deng, D, Xu, S & Zhang, J 2015, 'Observation of Midinfrared 4-$\mu \text{m}$ Emission in Ho³⁺-Doped Fluoroaluminate Glasses', IEEE Photonics Technology Letters, vol. 27, no. 9, pp. 959-962.
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Ho3+ activated fluoroaluminate glasses were prepared successfully via melt-quenching method. Not only 2- and 2.85-μm emissions but also 4-μm emissions were observed for the first time by 900-nm Ti: sapphire laser pumping. The optimal midinfrared emissions were obtained when Ho3+ concentration reaches 1 mol%. Spectroscopic properties and energy transfer mechanism of Ho3+ were investigated in detail. Results indicate that the prepared glasses possess high midinfrared transmittance (90%), large emission cross sections at 2 μm (7.6 × 10-21 cm2), 2.85 μm (17.6 × 10-21 cm2), and 4 μm (6.87 × 10-21 cm2) together with superior gain properties. It is suggested that Ho3+ activated fluoroaluminate glass is an attractive candidate for midinfrared laser materials application.

Zhou, J, Chen, G, Zhu, Y, Huo, L, Mao, W, Zou, D, Sun, X, Wu, E, Zeng, H, Zhang, J, Zhang, L, Qiu, J & Xu, S 2015, 'Intense multiphoton upconversion of Yb³⁺–Tm³⁺ doped β-NaYF₄ individual nanocrystals by saturation excitation', Journal of Materials Chemistry C, vol. 3, no. 2, pp. 364-369.
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