School of BioSciences - Research Publications

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    Adjacent crop type impacts potential pollinator communities and their pollination services in remnants of natural vegetation
    Reynolds, VA ; Cunningham, SA ; Rader, R ; Mayfield, MM ; Andersen, A (WILEY, 2022-04-26)
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    Altered SOD1 maturation and post-translational modification in amyotrophic lateral sclerosis spinal cord.
    Trist, BG ; Genoud, S ; Roudeau, S ; Rookyard, A ; Abdeen, A ; Cottam, V ; Hare, DJ ; White, M ; Altvater, J ; Fifita, JA ; Hogan, A ; Grima, N ; Blair, IP ; Kysenius, K ; Crouch, PJ ; Carmona, A ; Rufin, Y ; Claverol, S ; Van Malderen, S ; Falkenberg, G ; Paterson, DJ ; Smith, B ; Troakes, C ; Vance, C ; Shaw, CE ; Al-Sarraj, S ; Cordwell, S ; Halliday, G ; Ortega, R ; Double, KL (Oxford University Press (OUP), 2022-09-14)
    Aberrant self-assembly and toxicity of wild-type and mutant superoxide dismutase 1 (SOD1) has been widely examined in silico, in vitro and in transgenic animal models of amyotrophic lateral sclerosis. Detailed examination of the protein in disease-affected tissues from amyotrophic lateral sclerosis patients, however, remains scarce. We used histological, biochemical and analytical techniques to profile alterations to SOD1 protein deposition, subcellular localization, maturation and post-translational modification in post-mortem spinal cord tissues from amyotrophic lateral sclerosis cases and controls. Tissues were dissected into ventral and dorsal spinal cord grey matter to assess the specificity of alterations within regions of motor neuron degeneration. We provide evidence of the mislocalization and accumulation of structurally disordered, immature SOD1 protein conformers in spinal cord motor neurons of SOD1-linked and non-SOD1-linked familial amyotrophic lateral sclerosis cases, and sporadic amyotrophic lateral sclerosis cases, compared with control motor neurons. These changes were collectively associated with instability and mismetallation of enzymatically active SOD1 dimers, as well as alterations to SOD1 post-translational modifications and molecular chaperones governing SOD1 maturation. Atypical changes to SOD1 protein were largely restricted to regions of neurodegeneration in amyotrophic lateral sclerosis cases, and clearly differentiated all forms of amyotrophic lateral sclerosis from controls. Substantial heterogeneity in the presence of these changes was also observed between amyotrophic lateral sclerosis cases. Our data demonstrate that varying forms of SOD1 proteinopathy are a common feature of all forms of amyotrophic lateral sclerosis, and support the presence of one or more convergent biochemical pathways leading to SOD1 proteinopathy in amyotrophic lateral sclerosis. Most of these alterations are specific to regions of neurodegeneration, and may therefore constitute valid targets for therapeutic development.
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    Seasonal and daily activity of non-native sambar deer in and around high-elevation peatlands, south-eastern Australia
    Comte, S ; Thomas, E ; Bengsen, AJ ; Bennett, A ; Davis, NE ; Freney, S ; Jackson, SM ; White, M ; Forsyth, DM ; Brown, D ; Taylor, A (CSIRO PUBLISHING, 2022-05-26)
    Context Of the six species of non-native deer present in Australia, the sambar deer is the largest and has been identified as a major threat to high-elevation peatlands in south-eastern Australia. However, little is known about sambar deer activity in high-elevation peatlands. Aims The aims of this study were to quantify sambar deer activity (including wallowing) seasonally and daily in response to biotic and abiotic variables, and how activity was impacted by ground-based shooting. Methods To estimate sambar deer activity, camera traps were continuously deployed for 4 years in two ~4300-ha areas in Alpine National Park, Victoria, south-eastern Australia. One area was subject to management operations using ground-based shooting to target deer and the other was not. Monthly activity of sambar deer was modelled using biotic (woody vegetation cover), abiotic (snow depth, aspect, slope, distance to water, road and peatland) and management (treatment versus non-treatment) covariates. Additional camera traps were deployed to monitor sambar deer activity at wallows. Key results Sambar deer activity decreased when snow depth increased (between July and September), and was highest in easterly and northerly aspects with dense woody vegetation close to high-elevation peatlands and roads. During our 4-year study, sambar deer activity decreased in the treatment area but increased in the non-treatment area. Sambar deer exhibited a crepuscular diel cycle, with greatest activity around sunset. Only male sambar deer were observed to wallow, with most wallowing occurring in the afternoon during October–June. Conclusions Sambar deer utilised high-elevation peatlands during October–June. Daily activity was crepuscular and was greatest in dense tree cover close to roads. Ground-based shooting reduced sambar deer activity in and around high-elevation peatlands. Implications Control operations targeting sambar deer at high elevations in south-eastern Australia should be conducted during October–June. Outside this period sambar deer appear to use lower-elevation habitats. The effectiveness of ground-based shooting could be improved by focusing this control action around sunset (when sambar deer are most active) and in places with dense vegetation close to roads and high-elevation peatlands.
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    N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon
    Kuang, W ; Sanow, S ; Kelm, JM ; Muller Linow, M ; Andeer, P ; Kohlheyer, D ; Northen, T ; Vogel, JP ; Watt, M ; Arsova, B ; Janni, M (OXFORD UNIV PRESS, 2022-05-05)
    Nitrogen (N) fixation in cereals by root-associated bacteria is a promising solution for reducing use of chemical N fertilizers in agriculture. However, plant and bacterial responses are unpredictable across environments. We hypothesized that cereal responses to N-fixing bacteria are dynamic, depending on N supply and time. To quantify the dynamics, a gnotobiotic, fabricated ecosystem (EcoFAB) was adapted to analyse N mass balance, to image shoot and root growth, and to measure gene expression of Brachypodium distachyon inoculated with the N-fixing bacterium Herbaspirillum seropedicae. Phenotyping throughput of EcoFAB-N was 25-30 plants h-1 with open software and imaging systems. Herbaspirillum seropedicae inoculation of B. distachyon shifted root and shoot growth, nitrate versus ammonium uptake, and gene expression with time; directions and magnitude depended on N availability. Primary roots were longer and root hairs shorter regardless of N, with stronger changes at low N. At higher N, H. seropedicae provided 11% of the total plant N that came from sources other than the seed or the nutrient solution. The time-resolved phenotypic and molecular data point to distinct modes of action: at 5 mM NH4NO3 the benefit appears through N fixation, while at 0.5 mM NH4NO3 the mechanism appears to be plant physiological, with H. seropedicae promoting uptake of N from the root medium.Future work could fine-tune plant and root-associated microorganisms to growth and nutrient dynamics.
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    Advanced microscopy and novel methods in microbiology
    Kurtböke, DI ; Meyer, W ; Blackall, LL (CSIRO Publishing, 2022)
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    Effects of Ocean Warming on the Underexplored Members of the Coral Microbiome
    Maire, J ; Buerger, P ; Chan, WY ; Deore, P ; Dungan, AM ; Nitschke, MR ; van Oppen, MJH (OXFORD UNIV PRESS INC, 2022-03-08)
    The climate crisis is one of the most significant threats to marine ecosystems. It is leading to severe increases in sea surface temperatures and in the frequency and magnitude of marine heatwaves. These changing conditions are directly impacting coral reef ecosystems, which are among the most biodiverse ecosystems on Earth. Coral-associated symbionts are particularly affected because summer heatwaves cause coral bleaching-the loss of endosymbiotic microalgae (Symbiodiniaceae) from coral tissues, leading to coral starvation and death. Coral-associated Symbiodiniaceae and bacteria have been extensively studied in the context of climate change, especially in terms of community diversity and dynamics. However, data on other microorganisms and their response to climate change are scarce. Here, we review current knowledge on how increasing temperatures affect understudied coral-associated microorganisms such as archaea, fungi, viruses, and protists other than Symbiodiniaceae, as well as microbe-microbe interactions. We show that the coral-microbe symbiosis equilibrium is at risk under current and predicted future climate change and argue that coral reef conservation initiatives should include microbe-focused approaches.
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    Novel methods for spatial prioritization with applications in conservation, land use planning and ecological impact avoidance
    Moilanen, A ; Lehtinen, P ; Kohonen, I ; Jalkanen, J ; Virtanen, EA ; Kujala, H (WILEY, 2022-02-25)
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    Roles of the apicoplast across the life cycles of rodent and human malaria parasites
    Buchanan, HD ; Goodman, CD ; McFadden, GI (WILEY, 2022-09-30)
    Malaria parasites are diheteroxenous, requiring two hosts-a vertebrate and a mosquito-to complete their life cycle. Mosquitoes are the definitive host where malaria parasite sex occurs, and vertebrates are the intermediate host, supporting asexual amplification and more significant geographic spread. In this review, we examine the roles of a single malaria parasite compartment, the relict plastid known as the apicoplast, at each life cycle stage. We focus mainly on two malaria parasite species-Plasmodium falciparum and P. berghei-comparing the changing, yet ever crucial, roles of their apicoplasts.
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    Guidelines for standardizing the application of discriminant analysis of principal components to genotype data
    Thia, JA (WILEY, 2022-09-07)
    Despite the popularity of discriminant analysis of principal components (DAPC) for studying population structure, there has been little discussion of best practice for this method. In this work, I provide guidelines for standardizing the application of DAPC to genotype data sets. An often overlooked fact is that DAPC generates a model describing genetic differences among a set of populations defined by a researcher. Appropriate parameterization of this model is critical for obtaining biologically meaningful results. I show that the number of leading PC axes used as predictors of among-population differences, paxes , should not exceed the k-1 biologically informative PC axes that are expected for k effective populations in a genotype data set. This k-1 criterion for paxes specification is more appropriate compared to the widely used proportional variance criterion, which often results in a choice of paxes  ≫ k-1. DAPC parameterized with no more than the leading k-1 PC axes: (i) is more parsimonious; (ii) captures maximal among-population variation on biologically relevant predictors; (iii) is less sensitive to unintended interpretations of population structure; and (iv) is more generally applicable to independent sample sets. Assessing model fit should be routine practice and aids interpretation of population structure. It is imperative that researchers articulate their study goals, that is, testing a priori expectations vs. studying de novo inferred populations, because this has implications on how their DAPC results should be interpreted. The discussion and practical recommendations in this work provide the molecular ecology community with a roadmap for using DAPC in population genetic investigations.