Biology subjects

Stevenson, M.

Publications and source records attributed to Stevenson, M..

8 recordsLinked to original sources

bioRxiv2026

Index-agnostic oblique plane light sheet microscopy of centimetre-scale cleared tissues at subcellular resolution

We present cleared-tissue direct-view oblique plane microscopy (CtDvOPM), which enables optically sectioned subcellular resolution imaging of centimetre-scale tissues at high throughput over the full range of clearing media refractive indices (n = 1.33-1.56). CtDvOPM can image conventionally-mounted expanded, aqueous or non-aqueous cleared tissue samples at up to 2 {micro}m lateral by 14 {micro}m axial resolution over a 10.1 mm x 25.0 mm x 6.8 mm (x x y x z) sample volume without image tiling, at up to 400 million voxels per second.

biophysics↗

bioRxiv2024

"The Metagenomics Days": a simplified workshop on amplicon sequencing analysis with open cloud bioinformatics for eDNA and Microbiomes

The "Metagenomics Days" event was organized to enhance understanding of metagenomics and microbiome analysis among participants new to the field. This paper presents an evaluation of the courses impact through a comprehensive survey administered before and after the event. We assessed participants prior knowledge, experience with bioinformatics tools, and confidence levels regarding key concepts in microbiome analysis. Word clouds generated from open-ended survey responses provided additional insights into participants interests and pre-course familiarity with metagenomic tools and concepts. Surveys results showed substantial improvements in participants confidence, particularly in building bioinformatics pipelines (+41%), understanding diversity metrics (+44.1%), and applying microbiome analysis concepts (+34.8%). Similarly, understanding of core topics like cloud computing (+28%), bioinformatics workflows (+34%), and 16S rRNA gene variable regions (+27.5%) increased significantly. The courses impact on knowledge retention was also evaluated, with participants achieving an average of 64.87% correct responses, with 25.76% unsure answers and only 9.35% incorrect responses, highlighting the effectiveness of the course in enhancing comprehension. Overall, the survey results indicate a significant increase in participants confidence and knowledge acquisition, particularly in the areas of cloud computing, diversity metrics, and bioinformatics pipelines. These improvements in confidence and knowledge acquisition underscore the effectiveness of the course in bridging knowledge gaps and preparing participants for future research in the complex and rapidly evolving fields of metagenomics and microbiome analysis.

bioinformatics↗

bioRxiv2024

The effect of climate change on the spread of predicted bluetongue in Australian livestock

IntroductionThe frequency of vector-borne disease in human and animal populations has increased in recent years leading to concerns that even greater increases will occur as a result of climate change, driven by changes in the geographic distribution of insect vector habitat areas. In this study we investigate the effect of climate change on the expected spread of bluetongue (a viral disease of ruminants spread by Culicoides midges) using the Australian Animal Disease Spread model (AADIS). MethodsEstimates of average daily temperature across Australia for 2015 were obtained from the Australian Bureau of Meteorology. Predicted average daily temperatures using the CanESM2 model (emission scenario RCP 8.5) for 2025 and 2035 at a resolution of 5 km x 5 km were obtained from the Australian Climate Futures decision-support tool, managed by CSIRO. Two study areas in Australia were selected: the first in North Queensland and the second in Northern New South Wales. A total of 24 outbreak scenarios were run: mid-summer and mid-winter incursions for each study area for 2015, 2025 and 2035 with direct movement of animals in the AADIS model disabled and enabled for each. Model results were expressed as the number bluetongue-positive herds, (herds in which at least one animal was BTV positive) at the end of each 365 day simulation period. ResultsFor North Queensland, there was little change in the median predicted number of bluetongue positive herds for mid-summer and mid-winter 2025 and 2035 incursions (compared with 2015) and a moderate increase in the variability of predicted outbreak sizes when direct animal movements were disabled. For Northern New South Wales there were moderate increases in both the predicted number of bluetongue positive herds and the variability of predicted outbreak sizes for 2025 and 2035, compared with 2015. Compared with the direct animal movement disabled scenarios, there were marked increases in the predicted number of bluetongue positive herds as a function of simulation year for North Queensland. For Northern New south Wales this trend was not as distinct, but as for the direct movement disabled scenarios, the variability of predicted outbreak sizes for the 2035 incursions were greater than the variability of predicted outbreak sizes for the 2015 incursions. ConclusionClimate change will result in a greater portion of the land area of Australia with conditions suitable for Culicoides midges. Our findings show that under conditions of climate change and an outbreak of virulent bluetongue in Australia, the rapid imposition of effective restrictions of animal movement will be the single most important control measure to limit further spread of disease.

ecology↗

bioRxiv2024

Adult Single-nucleus Neuronal Transcriptomes of Insulin Signaling Mutants Reveal Regulators of Behavior and Learning

The insulin/insulin-like signaling (IIS) pathway regulates many of C. elegans adult functions, including learning and memory1. While whole-worm and tissue-specific transcriptomic analyses have identified IIS targets2,3, a higher-resolution single-cell approach is required to identify changes that confer neuron-specific improvements in the long-lived insulin receptor mutant, daf-2. To understand how behaviors that are controlled by a small number of neurons change in daf-2 mutants, we used the deep resolution of single-nucleus RNA sequencing to define each neuron types transcriptome in adult wild-type and daf-2 mutants. First, we found surprising differences between wild-type L4 larval neurons and young adult neurons in chemoreceptor expression, synaptic genes, and learning and memory genes. These Day 1 adult neuron transcriptomes allowed us to identify adult AWC-specific regulators of chemosensory function and to predict neuron-to-neuron peptide/receptor pairs. We then identified gene expression changes that correlate with daf-2s improved cognitive functions, particularly in the AWC sensory neuron that controls learning and associative memory4, and used behavioral assays to test their roles in cognitive function. Combining deep single-neuron transcriptomics, genetic manipulation, and behavioral analyses enabled us to identify genes that may function in a single adult neuron to control behavior, including conserved genes that function in learning and memory. One-Sentence SummarySingle-nucleus sequencing of adult wild-type and daf-2 C. elegans neurons reveals functionally relevant transcriptional changes, including regulators of chemosensation, learning, and memory.

neuroscience↗

bioRxiv2023

SIV clearance from neonatal macaques following transient CCR5 depletion

SUMMARY PARAGRAPHTreatment of people with HIV (PWH) with antiretroviral therapy (ART) results in sustained suppression of viremia, but HIV persists indefinitely as integrated provirus in CD4-expressing cells. Intact persistent provirus, the "rebound competent viral reservoir" (RCVR), is the primary obstacle to achieving a cure. Most variants of HIV enter CD4+ T cells by binding to the chemokine receptor, CCR5. The RCVR has been successfully depleted only in a handful of PWH following cytotoxic chemotherapy and bone marrow transplantation from donors with a mutation in CCR5. Here we show that long-term SIV remission and apparent cure can be achieved for infant macaques via targeted depletion of potential reservoir cells that express CCR5. Neonatal rhesus macaques were infected with virulent SIVmac251, then treated with ART beginning one week after infection, followed by treatment with either a CCR5/CD3-bispecific or a CD4-specific antibody, both of which depleted target cells and increased the rate of plasma viremia decrease. Upon subsequent cessation of ART, three of seven animals treated with CCR5/CD3-bispecific antibody rebounded quickly and two rebounded 3 or 6 months later. Remarkably, the other two animals remained aviremic and efforts to detect replication-competent virus were unsuccessful. Our results show that bispecific antibody treatment can achieve meaningful SIV reservoir depletion and suggest that functional HIV cure might be achievable for recently infected individuals having a restricted reservoir.

immunology↗

bioRxiv2022

Modelling the spread of resistance to Varroa in Australian feral honeybee populations

Australia is the only country where Western honeybees, Apis mellifera, are not infested with the mite Varroa destructor. Hence, a collapse in the feral honeybee population, brought about by an incursion and spread of V. destructor, would have serious consequences for Australian horticulture given its dependence on managed and feral honeybees for pollination. Managing Varroa in commercial colonies is well understood and can be achieved, although at significant bee-health costs, by using miticides. Protecting the feral population in the event of a Varroa incursion is much more difficult, but nevertheless imperative. One way to mitigate against collapse of the feral population is to seed it with Varroa-resistant queens, so as to accelerate the spread of resistance. We developed a simulation model of the spread of Varroa-resistance in feral honeybee populations following the introduction of Varroa-resistant queens into the managed population. We show that, compared with a do-nothing scenario, seeding the managed honeybee population with Varroa-resistant queens was only effective in decreasing the length of time for the feral honeybee population to recover when the size of the managed resistant population was large compared to the size of the feral population. This situation may be achievable in some urban areas where numbers of managed colonies are high and habitat for feral colonies is limited.

evolutionary biology↗

bioRxiv2020

Ap2s1 mutation in mice causes familial hypocalciuric hypercalcemia type 3

Mutations of the adaptor protein-2 sigma subunit (AP2S1) gene which encodes AP2{sigma}2, a component of the ubiquitous AP2 heterotetrameric complex involved in endosomal trafficking of the calcium-sensing receptor (CaSR), cause familial hypocalciuric hypercalcemia type 3 (FHH3). FHH3 patients have heterozygous AP2S1 missense Arg15 mutations (p.Arg15Cys, p.Arg15His or p.Arg15Leu) with marked hypercalcemia and occasional hypophosphatemia and osteomalacia. To further characterise the phenotypic spectrum and calcitropic pathophysiology of FHH3, we used CRISPR/Cas9 genome editing to generate mice harboring the AP2S1 p.Arg15Leu mutation, which causes the most severe FHH3 phenotype. Heterozygous (Ap2s1+/L15) mice were viable, and had marked hypercalcemia, hypermagnesemia, hypophosphatemia, and increased plasma concentrations of parathyroid hormone, fibroblast growth factor 23 and alkaline phosphatase activity, but normal pro-collagen type 1 N-terminal pro-peptide and 1,25 dihydroxyvitamin D. Homozygous (Ap2s1L15/L15) mice invariably died perinatally. The AP2S1 p.Arg15Leu mutation impaired protein-protein interactions between AP2{sigma}2 and the other AP2 subunits, and the CaSR. Cinacalcet, a CaSR allosteric activator, ameliorated the hypercalcemia and elevated PTH concentrations, but not the diminished AP2{sigma}2-CaSR interaction. Thus, our studies have established a mouse model with a germline loss-of-function AP2S1 mutation that is representative for FHH3 in humans, and demonstrated that cinacalcet corrects the abnormalities of plasma calcium and PTH.

genetics↗

bioRxiv2020

A chemical tool for improved culture of human pluripotent stem cells

The large-scale and cost-effective production of quality-controlled human pluripotent stem cells (hPSC) for use in cell therapy and drug discovery requires chemically-defined xenobiotic-free culture systems that enable easy and homogeneous expansion of pluripotent cells. Through phenotypic screening, we have identified a small molecule, OXS8360 (an optimized derivative of (-)-Indolactam V ((-)-ILV)), that stably disrupts hPSC cell-cell contacts. Proliferation of hPSC in OXS8360 is normal, as are pluripotency signatures, directed differentiation to hallmark lineages and karyotype over extended passaging. In 3D culture, OXS8360-treated hPSC form smaller, more uniform aggregates, that are easier to dissociate, greatly facilitating expansion. The mode of action of OXS8360 involves disruption of the localisation of the cell-cell adhesion molecule E-cadherin, via activation of unconventional Protein Kinase C isoforms. OXS8360 media supplementation is therefore able to yield more uniform, disaggregated 2D and 3D hPSC cultures, providing the hPSC field with an affordable tool to improve hPSC quality and scalability.

cell biology↗