Biology subjects

Davis, R.

Publications and source records attributed to Davis, R..

13 recordsLinked to original sources

bioRxiv2026

Machine learning-based image analysis of Parkinson's disease iPS-derived neurons predicts genotype and reveals mitochondria-lysosome abnormalities

Mitochondrial and lysosomal dysfunction are central features of Parkinsons disease (PD) across major genetic forms including PRKN, SNCA, and LRRK2. We applied cell morphomics, a machine-learning-based framework combining high-content imaging with quantitative feature extraction, to analyse mitochondrial and lysosomal morphology at single-cell resolution in iPS cell-derived cortical neurons from PD patients and healthy controls (13 lines total). Supervised machine-learning models distinguished PD neurons from controls with high accuracy (AUC = 0.87) and reliably separated individual genotypes. Feature importance and attribution analysis revealed genotype-specific organelle biases, with mitochondrial features dominating classification in PRKN neurons, balanced mitochondrial and lysosomal contributions in SNCA neurons, and a greater lysosomal contribution in LRRK2 neurons. Multi-class models retained strong performance, and findings were reproduced across two independent laboratories using different dyes and imaging conditions. These results demonstrate that morphomics provides a robust and scalable framework to quantify genotype-specific organelle abnormalities in PD neurons and supports its application for cellular stratification and biomarker discovery.

neuroscience↗

bioRxiv2026

The role of relA-mediated stringent response on the nutritional, environmental, antimicrobial resistance and biofilm formation in Klebsiella pneumoniae and its effect on Drosophila melanogaster survival

The stringent response has far-reaching consequences, with links to antimicrobial resistance, stress and virulence. This study assessed the role of relA in nutritional, environmental and antimicrobial stress in Klebsiella pneumoniae, the extent of polysaccharide capsule and biofilm formation, and the pathogenic effect on Drosophila melanogaster. Two single mutants (KP03DrelA and KPPR1DrelA) obtained using the Lambda Red Recombinase Technique were the focus of analyses. We assessed environmental (ethanol, osmotic, heat) and nutritional stress (carbon, phosphate, amino acid) tolerance, capsule formation, and cell size determination in wild-type (WT) and mutant bacteria. Biofilm and agar plate susceptibility assays were performed on both starved and non-starved strains using gentamicin and ceftazidime, and stress response genes were analyzed. Drosophila melanogaster was used to examine the pathogenic effect of the presence or deletion of relA on fly survival. DrelA mutants had reduced fitness to environmental and nutritional stress compared to WT strains. Mutant strains cell lengths were elongated and lacked a capsule versus WT and non-starved strains, and mutant strains exhibited enhanced biofilm formation or survival in the presence of ceftazidime and gentamicin. Stress response genes rpoD, phoR, phoU and pstB were absent during starvation, but rpoS was detected in C-, C+PO+ and serine hydroxamate (SHX) media; mrkA gene was not detected during starvation. Lastly, the animal model proved to be effective in showing infection levels associated with the presence of the relA gene.

molecular biology↗

bioRxiv2025

A typology of Australian terrestrial bird communities

AimIncreasing interest in holistic measurement of the response of fauna communities to interventions requires suitable community condition metrics. However, the development of such metrics is hindered by the absence of broad-scale typologies at suitable spatial and ecological resolutions. We aimed to derive a preliminary typology of terrestrial bird communities for Australia, based on bird co-occurrence data, and describe and map the likely distribution of each community type across the continent. LocationMainland Australia, continental islands Time period1973-2022 Major taxa studiedAves MethodsWe used fine-scale co-occurrence data from standard 2-ha surveys in BirdLife Australias citizen-science database. After filtering to reduce bias, we used hierarchical clustering followed by iterative consultation with experts to identify reliably distinct and recognisable terrestrial bird communities across Australia. We used Maxent to model the likely distributions of each community, and developed community descriptions based on each communitys composition and distribution. ResultsThe resultant typology included 29 reliably distinct and recognisable bird communities with major clusters corresponding with seven broad geographical regions. The distributions of bird communities did not correspond tightly to the boundaries of major vegetation groups, with most communities occurring across multiple vegetation types. Main ConclusionsOur preliminary typology of bird communities provides a standard classification at a continental scale. It newly defines distinct bird communities as entities for which condition benchmarks can be established to allow assessment of their conservation status and monitoring of change over time. Refinement will enable cryptic communities in areas with sparse data to be identified. The method could be translated to other regions where adequate coverage of data in the form of standardised surveys of fauna are available. Vast biodiversity datasets delivered through citizen science programs provide the opportunity to develop such typologies for fauna communities, as a precursor to developing targeted and informative community condition metrics.

ecology↗

bioRxiv2024

Single-stranded DNA binding protein hitches a ride with the Escherichia coli YoaA-χ helicase

The Escherichia coli XPD/Rad3-like helicase, YoaA, and DNA polymerase III subunit, {chi}, are involved in E. coli DNA damage tolerance and repair. YoaA and {chi} promote tolerance to the DNA chain-terminator, 3{square}-azidothymidine (AZT), and together form the functional helicase complex, YoaA-{chi}. How YoaA-{chi} contributes to DNA damage tolerance is not well understood. E. coli single-stranded DNA binding protein (SSB) accumulates at stalled replication forks, and the SSB-{chi} interaction is required to promote AZT tolerance via an unknown mechanism. YoaA-{chi} and SSB interactions were investigated in vitro to better understand this DNA damage tolerance mechanism, and we discovered YoaA-{chi} and SSB have a functional interaction. SSB confers a substrate-specific effect on the helicase activity of YoaA-{chi}, barely affecting YoaA-{chi} on an overhang DNA substrate but inhibiting YoaA-{chi} on forked DNA. A paralog helicase, DinG, unwinds SSB-bound DNA in a similar manner to YoaA-{chi} on the substrates tested. Through use of ensemble experiments, we believe SSB binds behind YoaA-{chi} relative to the DNA ds/ss junction and show via single-molecule assays that SSB translocates along ssDNA with YoaA-{chi}. This is, to our knowledge, the first demonstration of a mechanoenzyme pulling SSB along ssDNA.

biochemistry↗

bioRxiv2024

Oxidative Stress is a shared characteristic of ME/CFS and Long COVID

More than 65 million individuals worldwide are estimated to have Long COVID (LC), a complex multisystemic condition, wherein patients of all ages report fatigue, post-exertional malaise, and other symptoms resembling myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS). With no current treatments or reliable diagnostic markers, there is an urgent need to define the molecular underpinnings of these conditions. By studying bioenergetic characteristics of peripheral blood lymphocytes in over 16 healthy controls, 15 ME/CFS, and 15 LC, we find both ME/CFS and LC donors exhibit signs of elevated oxidative stress, relative to healthy controls, especially in the memory subset. Using a combination of flow cytometry, bulk RNA-seq analysis, mass spectrometry, and systems chemistry analysis, we also observed aberrations in ROS clearance pathways including elevated glutathione levels, decreases in mitochondrial superoxide dismutase levels, and glutathione peroxidase 4 mediated lipid oxidative damage. Critically, these changes in redox pathways show striking sex-specific trends. While females diagnosed with ME/CFS exhibit higher total ROS and mitochondrial calcium levels, males with an ME/CFS diagnosis have normal ROS levels, but larger changes in lipid oxidative damage. Further analyses show that higher ROS levels correlates with hyperproliferation of T cells in females, consistent with the known role of elevated ROS levels in the initiation of proliferation. This hyperproliferation of T cells can be attenuated by metformin, suggesting this FDA-approved drug as a possible treatment, as also suggested by a recent clinical study of LC patients. Thus, we report that both ME/CFS and LC are mechanistically related and could be diagnosed with quantitative blood cell measurements. We also suggest that effective, patient tailored drugs might be discovered using standard lymphocyte stimulation assays.

immunology↗

bioRxiv2024

The effect of a harmful algal bloom (Karenia selliformis) on the benthic invertebrate community and the sea otter (Enhydra lutris) diet in eastern Hokkaido.

In recent decades, the locally extinct sea otter (Enhydra lutris lutris) has been recolonizing the coast of eastern Hokkaido. Their diet includes benthic invertebrates such as bivalves, sea urchins, snails, and chitons. In the fall of 2021, a harmful algal bloom (HAB) of Karenia selliformis occurred across Hokkaidos northern and eastern coasts, leading to a massive mortality of sea urchins. This dinoflagellate produces a neurotoxin (gymnodimine) implicated in shellfish poisoning. To determine the effect of the HAB on the marine community, we conducted benthic surveys using SCUBA and visually monitored the prey items of the sea otters in the affected area from 2020 to 2023. Following the HAB, we observed an 82% decrease in benthic sea urchin density (number m2), leading to their complete absence from the diet of sea otters. Conversely, bivalve density increased six-fold, accompanied by a nearly two-fold rise in their percentage in the sea otters diet. Minimal changes were observed in the density of chitons and snails, with no significant alteration in the sea otters diet. Despite these changes, the impact of the HAB on otters dietary preferences was temporary, as the percentage of dietary sea urchins began recovering one year later. Sea otters augmented their diet with bivalves to compensate for the reduced availability of sea urchins during the HAB with no apparent effects on the number of sea otters or their health. Our results highlight the adaptability of sea otters to adjust their diet according to prey availability.

ecology↗

bioRxiv2023

Avian influenza viruses in wild birds in Canada following incursion of the highly pathogenic H5N1 virus from Eurasia in 2021/2022

Following detection of novel highly pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b in Newfoundland, Canada in late 2021, avian influenza surveillance in wild birds was scaled-up across Canada. Herein, we present results of Canadas Interagency Surveillance Program for Avian Influenza in wild birds during the first year (November 2021 - November 2022) following the incursions of HPAIV from Eurasia. Key objectives of the surveillance program were to (i) detect the presence, distribution and spread of HPAIV and other avian influenza viruses (AIVs), (ii) detect wild bird morbidity and mortality associated with HPAIV, (iii) identify the range of wild bird species infected by HPAIV, and (iv) characterize detected AIV. A total of 6,246 sick and dead wild birds were tested, of which 27.4% were HPAIV positive across 12 taxonomic orders and 80 species. Geographically, HPAIV detections occurred in all Canadian provinces and territories, with the highest numbers in the Atlantic and Central flyways. Temporally, peak detections differed across flyways, though the national peak occurred in April 2022. In an additional 11,295 asymptomatic harvested or live captured wild birds, 5.2% were HPAIV positive across 3 taxonomic orders and 19 species. Whole genome sequencing identified HPAIV of Eurasian origin as most prevalent in the Atlantic flyway, along with multiple reassortants of mixed Eurasian and North American origins distributed across Canada, with moderate structuring at the flyway scale. Wild birds were victims and reservoirs of HPAIV H5N1 2.3.4.4b, underscoring the importance of surveillance encompassing samples from sick and dead, as well as live and harvested birds to provide insights into the dynamics and potential impacts of the HPAIV H5N1 outbreak. This dramatic shift in presence and distribution of HPAIV in wild birds in Canada highlights a need for sustained investment in wild bird surveillance and collaboration across One Health partners.

zoology↗

bioRxiv2023

Total Chemical Synthesis of Glycosylated TREM2 Ectodomain

Mutations in a microglia-associated gene TREM2 increase the risk of Alzheimers disease. Currently, structural and functional studies of TREM2 mainly rely on recombinant TREM2 proteins expressed from mammalian cells. However, using this method, it is difficult to achieve site-specific labeling. Here we present the total chemical synthesis of the 116 amino-acid TREM2 ectodomain. Rigorous structural analysis ensured correct structural fold after refolding. Treating microglial cells with refolded synthetic TREM2 enhanced microglial phagocytosis, proliferation, and survival. We also prepared TREM2 constructs with defined glycosylation patterns and found that glycosylation at N79 is critical to the thermal stability of TREM2. This method will provide access to TREM2 constructs with site-specific labeling, such as fluorescent labeling, reactive chemical handles, and enrichment handles, to further advance our understanding of TREM2 in Alzheimers disease.

biochemistry↗

bioRxiv2022

Comparative genetic study of the colony structure and colony spatial distribution between the higher termite Amitermes parvulus and the lower, subterranean termite Reticulitermes flavipes in an urban environment

In insects, ecological competition has often resulted in phenotypic changes and modifications to foraging areas. In termites - and social insects as a whole - colonies cannot easily escape competition through the relocation of their colony. In these species, the outcomes of inter and intra-specific competition are influenced by different life history traits, such as colony size, breeding system (number and types of reproductives), food preference, tunneling patterns, nest site selection, and antagonism between colonies. Here, we investigated variation in breeding system and spatial distribution among colonies of a higher termite Amitermes parvulus and a subterranean termite Reticulitermes flavipes within an urban landscape. We first developed microsatellite markers as a tool to study these life history traits in A. parvulus. Second, we assessed competitive exclusion or tolerance of A. parvulus and R. flavipes colonies by determining their fine-scale distribution using monitoring stations on a grid site, and their large-scale distribution across an urban landscape. Third, we investigated the breeding system of A. parvulus colonies. We showed that the numerous colonies of R. flavipes inhabiting a restricted area contrast with the few, but spatially expansive colonies of A. parvulus, suggesting these species face different degrees of intra-specific competition. We showed that colonies of A. parvulus frequently merged together, and all of them were headed by inbred neotenic reproductives, two characteristics rarely observed in higher termites. Overall, our study revealed drastic differences in colony structure, breeding systems and foraging ranges between the two species. These differences may reflect differences in food preference and food availability between the two species allowing their co-existence within the same urban environment.

evolutionary biology↗

bioRxiv2022

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant Small ORFs and Functional Microproteins

The absence of thousands of recently annotated small open reading frame (smORF)-encoded peptides and small proteins (microproteins) from databases has precluded their analysis in metabolism and metabolic disease. Given the outsized importance of small proteins and peptides such as insulin, leptin, amylin, glucagon, and glucagon-like peptide-1 (GLP-1) in metabolism, microproteins are a potentially rich source of uncharacterized metabolic regulators. Here, we annotate smORFs in primary differentiated brown, white, and beige mouse adipose cells. Ribosome profiling (Ribo-Seq) detected a total of 3,877 unannotated smORFs. Analysis of RNA-Seq datasets revealed diet-regulated smORF expression in adipose tissues, and validated the adipose translation of the feeding-neuron marker gene Gm8773. Gm8773 encodes the mouse homolog of FAM237B, a neurosecretory protein that stimulates food intake and promotes weight gain in chickens. Testing of recombinant mFAM237B produced similar orexigenic activity in mice further supporting a role for FAM237B as a metabolic regulator and potentially part of the brain-adipose axis. Furthermore, we demonstrated that data independent acquisition mass spectrometry (DIA-MS) proteomics can provide a sensitive, flexible, and quantitative platform for identifying microproteins by mass spectrometry. Using this system led to the detection of 58 microproteins from cell culture and an additional 33 from mouse plasma. The proteomics data established the anti-inflammatory microprotein AW112010 as a circulating factor, and found that plasma levels of a microprotein translated from a FRS2 uORF is elevated in older obese mice. Together, the data highlight the value of this database in examining understudied smORFs and microproteins in metabolic research and identifying additional regulators of metabolism.

systems biology↗

bioRxiv2021

An alphavirus replicon-based vaccine expressing a stabilized Spike antigen induces sterile immunity and prevents transmission of SARS-CoV-2 between cats

Early in the global SARS-CoV-2 pandemic concerns were raised regarding infection of other animal hosts and whether these could play a significant role in the viral epidemiology. Infection of animals could be detrimental by causing clinical disease but also of concern if they become a viral reservoir allowing further mutations, plus having the potential to infect other animals or humans. The first reported animals to be infected both under experimental conditions and from anecdotal field evidence were cats described in China early in 2020. Given the concerns this finding raised and the close contacts between humans and cats, we aimed to determine whether a vaccine candidate could be developed that was suitable for use in multiple susceptible animal species and whether this vaccine could reduce infection of cats in addition to preventing spread to other cats. Here we report that a Replicon Particle (RP) vaccine based on Venezuelan equine encephalitis virus (VEEV), known to be safe and efficacious for use in a variety of animals, expressing a stabilised Spike antigen, could induce neutralising antibody titers in guinea pigs and cats. After two intramuscular vaccinations, virus neutralising antibodies were detected in the respiratory tract of the guinea pigs and a cell mediated immune response was induced. The design of the SARS-CoV-2 antigen was shown to be critical in developing a strong neutralising antibody response. Vaccination of cats was able to induce a serum neutralising antibody response which lasted for the course of the experiment. Interestingly, in contrast to control animals, infectious virus could not be detected in oropharyngeal or nasal swabs of vaccinated cats after challenge. Moreover, the challenged control cats spread the virus to in-contact cats whereas the vaccinated cats did not transmit virus. The results show that the RP vaccine induces sterile immunity preventing SARS-CoV-2 infection and transmission. This data suggests that this RP vaccine could be a multi-species vaccine useful for preventing spread to and between other animals should that approach be required.

microbiology↗

bioRxiv2021

Predicted distribution of a rare and understudied forest carnivore: Humboldt martens (Martes caurina humboldtensis)

BackgroundA suite of mammalian species have experienced range contractions following European settlement and post-settlement development of the North American continent. For example, while North American martens (American marten, Martes americana; Pacific marten, M. caurina) generally have a broad range across northern latitudes, local populations have experienced substantial reductions in distribution and some extant populations are small and geographically isolated. The Humboldt marten (M. c. humboldtensis), a subspecies of Pacific marten that occurs in coastal Oregon and northern California, was recently designated as federally threatened in part due to its reduced distribution. To inform strategic conservation actions, we assessed Humboldt marten occurrence by compiling all known records from their range. MethodsWe compiled Humboldt marten locations since their rediscover to present (1,692 marten locations, 1996-2020). We spatially-thinned locations to 500-m to assess correlations with variables across contemporary Humboldt marten distribution (n=384). Using maximum entropy modeling (Maxent), we created distribution models with variables optimized for spatial scale; pre-selected scales were associated with marten ecology (50 to 1170 m radius). Marten locations were most correlated with abiotic factors (e.g., precipitation), which are unalterable and therefore uninformative within the context of restoration or management actions. Thus, we created variables to focus on hypothesized marten habitat relationships, including understory conditions such as predicted suitability of shrub species. ResultsHumboldt marten locations were positively associated with increased shrub cover (salal (Gautheria shallon), mast producing trees), increased pine (Pinus sp) overstory cover and precipitation at home-range spatial scales, areas with low and high amounts of canopy cover and slope, and cooler August temperatures. Unlike other recent literature on the species, we found little evidence that Humboldt marten locations were associated with old growth structural indices, perhaps because of a potential mismatch in the association between this index and shrub cover. As with any species distribution model, there were gaps in predicted distribution where Humboldt martens have been located during more recent surveys, for instance the southeastern portion of Oregons coast range. Conservation efforts and our assessment of potential risks to Humboldt marten populations would benefit from additional information on range extent, population sizes, and fine-scale habitat use. Like many rare and lesser-known species, this case study provides an example of how limited information can provide differing interpretations, emphasizing the need for study-level replication in ecology.

ecology↗

bioRxiv2017

Versatile open software to quantify cardiomyocyte and cardiac muscle contraction in vitro and in vivo

Contraction of muscle reflects its physiological state. Methods to quantify contraction are often complex, expensive and tailored to specific models or recording conditions, or require specialist knowledge for data extraction. Here we describe an automated, open-source software tool (MUSCLEMOTION) adaptable for use with standard laboratory and clinical imaging equipment that enables quantitative analysis of normal cardiac contraction, disease phenotypes and pharmacological responses. MUSCLEMOTION allowed rapid and easy measurement of contractility in (i) single cardiomyocytes from primary adult heart and human pluripotent stem cells, (ii) multicellular 2D-cardiomyocyte cultures, 3D engineered heart tissues and cardiac organoids/microtissues in vitro and (iii) intact hearts of zebrafish and humans in vivo. Good correlation was found with conventional measures of contraction in each system. Thus, using a single method for processing video recordings, we obtained reliable pharmacological data and measures of cardiac disease phenotype in experimental cell- and animal models and human echocardiograms.

physiology↗