Biology subjects

Austin, J.

Publications and source records attributed to Austin, J..

13 recordsLinked to original sources

bioRxiv2026

Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes

Mechanistic understanding of viral protein-protein interactions enables global health security and pandemic preparedness, yet experimental characterisation remains difficult, costly, and often restricted to specialised laboratories. Here, we describe an in silico campaign using AlphaFold2 and AlphaFold-Multimer to predict monomers and dimer structures within 2,812 viral proteomes from 23 viral families relevant to human health. We report high-confidence predicted structures of 5,279 hetero-, and 2,749 homo-dimers. Structural clustering of interfaces reduces the set fivefold to 1,598 consolidated by form and function, of which 471 (29.5%) lacked detectable similarity to experimentally determined interfaces in the PDB. These clusters yielded two notable findings: new data on vaccinology-relevant glycoproteins, and accurate prediction of the specificity and cleavage-site recognition of viral proteases, which are targets for anti-viral development. Viral monomers and high-confidence dimers are available for interactive browsing in the Pandemic Preparedness Portal of the AlphaFold Database (https://alphafold.ebi.ac.uk/), and the full dataset is available for bulk download.

bioinformatics↗

bioRxiv2026

Decision analysis in support of proactive planning for chronic wasting disease in Vermont, USA

Chronic wasting disease (CWD), a fatal, transmissible disease in white-tailed deer (Odocoileus virginianus) and related species, is spreading across North America but has not yet been detected in Vermont, United States (U.S.). The Vermont Department of Fish and Wildlife, along with partner agencies, wants to develop a proactive prevention and response plan in anticipation of the eventual detection of the disease. Between September 2023 and September 2025, staff from the U.S. Geological Survey and the University of Vermont facilitated a structured decision-making (SDM) process with seven State and Federal agencies that have jurisdiction over some aspect of CWD management in Vermont. The aim of this process was to generate and evaluate alternative response plans against a range of long-term objectives important to the agencies. To aid in the evaluation of the alternatives, we developed a linked set of models for white-tailed deer population and disease dynamics, hunter participation and health, forest health, economic consequences, and agricultural opportunities related to the actions being contemplated as part of the response plan. We evaluated over 256 different permutations of management actions and used multi-criteria decision analysis, a branch of decision analysis designed to help decision makers navigate tradeoffs among competing objectives, to summarize the performance of those alternative strategies against the desired outcomes. Proactive actions, those designed to slow the arrival of CWD to Vermont, were moderately effective, but the most important proactive action was surveillance to detect the disease early after arrival, which triggered response actions after detection. With the insights generated by the SDM process and the results of the analyses, the participating agencies were able to identify a preferred strategy and outline the elements of a proactive response plan. This report describes the SDM process, the technical details of the modeling work, and the results of the analyses.

ecology↗

bioRxiv2026

Restricting Dietary Isoleucine Promotes Foxo3-Dependent Mitochondrial Respiration by Reducing Caloric Intake

Our prior work demonstrated that lowering dietary branched-chain amino acids (BCAAs) improves cardiac outcomes during pressure overload-induced stress. Here, we identify isoleucine restriction (IleR) as the key driver of this effect. Dietary isoleucine restriction induces hypophagia and weight loss, recapitulating the effects of caloric restriction (CR). Although it does not prevent the initial development of left ventricular hypertrophy, it halts its progression and the decline in ejection fraction compared with controls. This is associated with preservation of electron transport chain (ETC) gene expression, cristae structure, NAD+/NADH levels, and mitochondrial respiratory capacity in cardiomyocytes, which is recapitulated by CR. Mechanistically, both IleR and CR diets increase Foxo3 expression, thereby blocking the decline in expression of its target ETC and mitochondrial genome-encoded genes. Consequently, this improves mitochondrial respiratory capacity and reduces cardiac fibrosis. We conclude that restricting dietary isoleucine improves cardiac health by increasing Foxo3 expression and mitochondrial function via a cell-autonomous mechanism and by reducing caloric intake.

molecular biology↗

bioRxiv2026

Functional assignment of Golgi-associated vesicle tethers to specific membrane recycling pathways

During maturation of a Golgi cisterna, multiple vesicular transport pathways recycle resident Golgi proteins. Recycling vesicles are captured by Golgi-associated tethers. To assign individual tethers to specific recycling pathways in Saccharomyces cerevisiae, we examined tether arrival and departure using kinetic mapping, and we examined tether function using an ectopic tether localization assay. Those approaches yielded mutually consistent results. Our analysis focused on two coiled coil golgin tethers and the multi-subunit tether GARP. At an intermediate stage of cisternal maturation, the golgin Sgm1 tethers proteins that follow an intra-Golgi recycling pathway dependent on COPI. At a late stage of cisternal maturation, GARP and the golgin Imh1 tether trans- Golgi network (TGN) proteins that follow an intra-Golgi recycling pathway dependent on the AP-1 and Ent5 clathrin adaptors. This involvement of GARP in intra-Golgi recycling had not previously been documented. Imh1 also tethers proteins that recycle from prevacuolar endosome compartments to the TGN. Our findings contribute to an integrated model of Golgi membrane traffic.

cell biology↗

bioRxiv2026

Diel remodeling and cellular integration of the nitroplast

Nitrogen-fixing eukaryotes were not believed to exist in nature until the recent discovery of a N2-fixing organelle, or nitroplast, in the marine microalga Braarudosphaera bigelowii. This nitroplast (formerly known as UCYN-A2) has long been recognized as key cyanobacterial contributor to global oceanic N2 fixation. However, how this novel organelle is integrated and regulated within the architecture of a eukaryotic cell remains unclear. Here, we combine multiscale volumetric imaging with cryo-electron tomography to resolve the native architecture, cellular integration, and diel remodeling of the nitroplast in cultured and environmental cells. We find that the nitroplast occupies up to 10% of the cell volume and exhibits close interfaces with multiple host organelles through membrane contact sites, while integration of this metabolically demanding compartment does not disrupt global scaling of host organelles. Interestingly, the chloroplast-to-nitroplast volume ratio is conserved across distinct life stages. Cryo-electron tomography reveals that the nitroplast retains a reinforced four-layer cyanobacterial envelope and is additionally surrounded by two host-derived layers that remodel across the day-night cycle. During daytime N2 fixation, these host-derived barriers become locally discontinuous and the organelle interface becomes enriched with two distinct vesicle populations. Our findings suggest that dynamic control of organelle accessibility through transient membrane gating represents a fundamental strategy by which eukaryotic cells could domesticate new endosymbiotic functions during early organellogenesis.

cell biology↗

bioRxiv2026

AlphaFold Database expands to proteome-scale quaternary structures

Protein function is governed by molecular interactions, yet structural coverage of these interactions remains sparse. The AlphaFold Protein Structure Database (AFDB) transformed access to accurate monomeric protein structures at scale. Here, we expand the AFDB to quaternary structures by predicting 31M candidate homo- and heterodimeric protein complexes, compiled from 4,777 proteomes, including model- and global health organisms. We established confidence criteria via analysis of experimentally determined structures, resulting in 1.81M high-confidence predictions. These models enabled the discovery of emergent structures and topologies not present in monomeric predictions. Additionally, the top 1% of structural clusters accounted for [~]44% of all complexes, and [~]8.3% of clusters were conserved across multiple domains of life, pointing to a substantial fraction of ancient, universally retained assemblies. Structural search highlighted that high-confidence predictions are anchored in experimental multimer space, yet 31.3% extend beyond detectable PDB coverage. These freely accessible proteome-scale predictions facilitate functional and mechanistic hypothesis generation across biology.

synthetic biology↗

bioRxiv2026

Cryo-electron tomography reveals paracellular claudin-15 pores at the tight junction

Tight junctions (TJs) are composed of anastomosing strands between epithelial cells. Members of the claudin family of proteins reside within TJ strands and either seal the paracellular space or assemble into charge and size-selective pathways. Functional studies suggest that claudin-mediated conductance pathways resemble traditional ion channels. However, such postulated pores have not been directly visualized. Using a model claudin deficient epithelium where exogenously introduced EGFP-CLDN15 is the only claudin family member expressed, our investigation sheds light on the arrangement and structure of the postulated claudin pores. Following correlative light and electron microscopical identification of TJs and cryo-electron tomography, we identified series of linearly distributed electron lucent features that locate between two closely apposed plasma membranes of adjacent cells. At these sites, the median spacing between adjacent features is 2.25 nm (IQR = 1.83), with a median 1.66 nm (IQR = 0.92) diameter. In contrast, such features were not observed in claudin deficient model epithelium with exogenous mCherry-ZO-1 expression. These findings agree with the postulated and extensively modeled claudin pores formed within the simple columnar epithelium. This provides the first direct evidence of paracellular pore organization and paves way for future biophysical investigation. SIGNIFICANCEBy combining correlative fluorescence imaging, FIB milling, and cryo-ET within an epithelial system restricted to a single claudin isoform, we were able to visualize repetitive, low-density pore features within CLDN15-containing tight junctions (TJs), structures not previously resolved in intact epithelia. These features were absent in claudin-negative controls and displayed placement and geometry consistent with CLDN15 X-ray crystallography and molecular dynamics models. Quantitative measurements of pore diameter, paracellular gap width, and pore spacing further support their assignment as CLDN15 pores. These findings establish a structurally validated platform for defining claudin pore ultrastructure and provide a foundation for future efforts to compare pore-forming and barrier-forming claudins, understand disease-associated junction remodeling, and guide therapeutic modulation of epithelial barrier function.

physiology↗

bioRxiv2025

COPI-dependent intra-Golgi recycling at an intermediate stageof cisternal maturation

The traffic pathways that recycle resident Golgi proteins during cisternal maturation are not completely defined. We addressed this challenge using the yeast Saccharomyces cerevisiae, in which maturation of individual cisternae can be visualized directly. A new assay captures a specific population of Golgi-derived vesicles at the bud neck, thereby revealing which resident Golgi proteins are carried as cargo in those vesicles. This method supplies evidence for at least three classes of intra-Golgi vesicles with different cargo compositions. Consistent with our previously published data, one class of vesicles mediates a late pathway of intra-Golgi recycling with the aid of the AP-1 and Ent5 clathrin adaptors, and a second class of vesicles mediates an early pathway of intra-Golgi recycling with the aid of the COPI vesicle coat. Here, we identify another COPI-dependent pathway of intra-Golgi recycling and show that it operates kinetically between the two previously known pathways. Thus, intra-Golgi recycling is mediated by multiple COPI-dependent pathways followed by a clathrin-dependent pathway.

cell biology↗

bioRxiv2024

Torque Teno Sus Virus 1: A Potential Surrogate Pathogen to Study Pig-Transmitted Transboundary Animal Diseases

Understanding the epidemiology and transmission dynamics of transboundary animal diseases (TADs) among wild pigs (Sus scrofa) will aid in preventing the introduction or containment of TADs among wild populations. Given challenges associated with studying TADs in free-ranging populations, a surrogate pathogen system for in situ studies of pathogen dynamics would be ideal to elucidate how pathogens may circulate and be maintained within populations, how they may spillover into domestic populations, and how disease spread may be mitigated. We assessed the suitability of Torque teno sus virus 1 (TTSuV1) to serve as a surrogate pathogen for molecular epidemiological studies in wild pigs by investigating the prevalence, persistence, correlation with host health status and genetic variability at two study areas: Archbolds Buck Island Ranch in Florida and Savannah River Site in South Carolina. We then conducted a molecular epidemiological case study within the Archbolds Buck Island Ranch site to determine how analysis of this pathogen could inform transmission studies. Prevalence was high at both study areas (40%, n = 190). Phylogenetic analyses revealed high levels of genetic variability within and between study sites. Our case study showed that pairwise host relatedness and geographic distance were highly correlated to pairwise viral genetic similarity. Molecular epidemiological analyses revealed a distinct pattern of direct transmission from pig to pig occurring within and between family groups. Our results suggest TTSuV1 is highly suitable for molecular epidemiological analyses and will be useful for future in situ studies of transmission dynamics in wild pigs.

ecology↗

bioRxiv2023

Reconstructing colonization dynamics to establish how human activities transformed island biodiversity

AimThe drivers and dynamics of initial human migrations across individual islands and archipelagos are poorly understood, affecting assessments of human-modification of island biodiversity. Here, we describe and test a process-explicit approach for reconstructing human arrival and expansion on islands, which combines archaeological and climate records with high-resolution spatial population models. Using Polynesian colonisation of New Zealand as an example, we show that our new method can generate information crucial for assessing how humans affected biodiversity on islands. InnovationThe transition of islands from prehuman to human dominated ecosystems has typically been assessed by comparing biodiversity before and after time of first arrival, without considering the potential importance of the spatiotemporal dynamics of the human expansion event. Our new approach, which uses pattern-oriented modelling methods to combine inferences of human colonisation dynamics from dated archaeological material with spatially explicit population models, produces validated reconstructions of the pattern and pace of human migration across islands at high spatiotemporal resolutions. From these reconstructions, demographic and environmental drivers of human colonization can be identified, and the role that people had on biodiversity established. Using this technique, we show that closely reconciling inferences of Polynesian colonisation of New Zealand requires there to have been a single founding population of approximately 500 people, arriving between 1233 and 1257 AD, settling multiple areas, and expanding quickly over both North and South islands. The resultant maps of M[a]ori colonisation dynamics provide new opportunities to better determine how human activities transformed biodiversity of New Zealand in space and time. Main conclusionsProcess-explicit models can reconstruct human migration across large islands, producing validated, high resolution spatiotemporal projections of human occupancy and abundance that account for dispersal and population dynamics. This modelling framework should prove effective across any islands and archipelagos where climate and archaeological records are available.

ecology↗

bioRxiv2019

Impute.me: an open source, non-profit tool for using data from DTC genetic testing to calculate and interpret polygenic risk scores.

To date, interpretation of genomic information has focused on single variants conferring disease risk, but most disorders of major public concern have a polygenic architecture. Polygenic risk scores (PRS) give a single measure of disease liability by summarising disease risk across hundreds of thousands of genetic variants. They can be calculated in any genome-wide genotype data-source, using a prediction model based on genome-wide summary statistics from external studies. As genome-wide association studies increase in power, the predictive ability for disease risk will also increase. While PRS are unlikely ever to be fully diagnostic, they may give valuable medical information for risk stratification, prognosis, or treatment response prediction. Public engagement is therefore becoming important on the potential use and acceptability of PRS. However, the current public perception of genetics is that it provides Yes/No answers about the presence/absence of a condition, or the potential for developing a condition, which in not the case for common, complex disorders with of polygenic architecture. Meanwhile, unregulated third-party applications are being developed to satisfy consumer demand for information on the impact of lower risk variants on common diseases that are highly polygenic. Often applications report results from single SNPs and disregard effect size, which is highly inappropriate for common, complex disorders where everybody carries risk variants. Tools are therefore needed to communicate our understanding of genetic predisposition as a continuous trait, where a genetic liability confers risk for disease. Impute.me is one such a tool, whose focus is on education and information on common, complex disorders with polygenetic architecture. Its research-focused open-source website allows users to upload consumer genetics data to obtain PRS, with results reported on a population-level normal distribution. Diseases can only be browsed by ICD10-chapter-location or alphabetically, thus prompting the user to consider genetic risk scores in a medical context of relevance to the individual. Here we present an overview of the implementation of the impute.me site, along with analysis of typical usage-patterns, which may advance public perception of genomic risk and precision medicine.

genetics↗

bioRxiv2019

Sensory Neurons Innervate Peripheral Lymph Nodes and Locally Regulate Gene Expression in Postsynaptic Endothelium, Stromal Cells, and Innate Leukocytes

Immune responses within barrier tissues are regulated, in part, by nociceptors, specialized peripheral sensory neurons that detect noxious stimuli. Previous work has shown that nociceptor ablation not only alters local responses to immune challenge at peripheral sites, but also within draining lymph nodes (LNs). The mechanisms and significance of nociceptor-dependent modulation of LN function are unknown. Indeed, although sympathetic innervation of LNs is well documented, it has been unclear whether the LN parenchyma itself is innervated by sensory neurons. Here, using a combination of high-resolution imaging, retrograde viral tracing, single-cell transcriptomics (scRNA-seq), and optogenetics, we identified and functionally tested a sensory neuro-immune circuit that is preferentially located in the outermost cortex of skin-draining LNs. Transcriptomic profiling revealed that there are at least four discrete subsets of sensory neurons that innervate LNs with a predominance of peptidergic nociceptors, and an innervation pattern that is distinct from that in the surrounding skin. To uncover potential LN-resident communication partners for LN-innervating sensory neurons, we employed scRNA-seq to generate a draft atlas of all murine LN cells and, based on receptor-ligand expression patterns, nominated candidate target populations among stromal and immune cells. Using selective optogenetic stimulation of LN-innervating sensory axons, we directly experimentally tested our inferred connections. Acute neuronal activation triggered rapid transcriptional changes preferentially within our top-ranked putative interacting partners, principally endothelium and other nodal stroma cells, as well as several innate leukocyte populations. Thus, LNs are monitored by a unique population of sensory neurons that possesses immunomodulatory potential.

immunology↗

bioRxiv2018

Dietary folic acid increases neurogenesis in the ventral hippocampus of adult female rats

Folate is an important regulator of hippocampal neurogenesis, and in utero spinal cord development. Both high levels of folic acid and low levels of folate can be harmful to health, as low levels of folate have been linked to several diseases while high folic acid supplements can mask a vitamin B12 deficiency. Depressed patients exhibit folate deficiencies, lower levels of hippocampal neurogenesis, elevated levels of homocysteine, and elevated levels of the stress hormone, cortisol, which may be inter-related. Here, we are interested in whether different doses of natural folate or synthetic folic acid diets can influence neurogenesis in the hippocampus, levels of plasma homocysteine, and serum corticosterone in adult female rats. Adult female Sprague-Dawley rats underwent dietary interventions for 29 days. Animals were randomly assigned to six different dietary groups: folate deficient + succinylsulfathiazole (SST), low 5-methyltetrahydrofolate (5-MTHF), low 5-MTHF + (SST), high 5-MTHF + SST, low folic acid, and high folic acid. SST was added to a subset of the 5-MTHF diets to eliminate folic acid production in the gut. Before and after dietary treatment, blood samples were collected for corticosterone and homocysteine analysis, and brain tissue was collected for neurogenesis analysis. High folic acid and low 5-MTHF without SST increased the number of immature neurons (doublecortin-expressing cells) within the ventral hippocampus compared to folate deficient controls. Low 5-MTHF without SST significantly increased the number of immature neurons compared to low and high 5-MTHF + SST, indicating that SST interfered with elevations in neurogenesis. Low folic acid and high 5-MTHF+SST reduced plasma homocysteine levels compared to controls, but there was no significant effect of diet on serum corticosterone levels. Low folic acid and high 5-MTHF+SST reduced the number of mature new neurons in the ventral hippocampus (BrdU/NeuN-positive cells) compared to folate deficient controls. Overall, folic acid dose-dependently influenced neurogenesis, with low levels decreasing but high levels increasing, neurogenesis in the ventral hippocampus, suggesting this region, which is important for regulating stress, is particularly sensitive to folic acid in diets. Furthermore, the addition of SST negated the effects of 5-MTHF to increase neurogenesis in the ventral hippocampus.

neuroscience↗