Biology subjects

Hall, J.

Publications and source records attributed to Hall, J..

At least 19 recordsLinked to original sources

bioRxiv2026

A qualitative and quantitative framework for the characterization of protein-RNA interactions by cross-linking mass spectrometry (XL-MS)

Protein-RNA interactions regulate nearly all levels of gene expression. Their characterization at the molecular basis is critical for understanding the function of protein-RNA complexes, both in cell homeostasis and pathology. Yet, molecular interactions underlying the formation of these complexes remain understudied. UV cross-linking mass spectrometry (XL-MS) is one of the leading approaches for in vitro identification of protein-RNA contact sites, and for providing structural information in the form of distance constraints crucial for the refinement of structural models. Our previously published CLIR-MS method enables qualitative characterization of protein-RNA interactions at residue-specific resolution but was not designed for highly accurate quantitative interpretation. Here, we present a XL-MS workflow based on irradiation with UV light that combines data-dependent acquisition (DDA) and parallel reaction monitoring (PRM) for simultaneous detection and characterization of protein-RNA interaction sites at residue-specific resolution, followed by label-free quantification of cross-linked products. We successfully apply our combined workflow to in vitro reconstituted protein-RNA complexes formed by the proteins TDP-43 and FOX1. We report on novel RNA interaction sites located in the oligomerization interface of the N-terminal domain (NTD) of TDP-43, and characterize quantitatively the process of RNA-induced monomerization of the NTD in an RNA titration experiment. We also investigate temperature-dependent differences in the efficiency of cross-link formation in the FOX1 complex. Our framework offers a unique and novel approach to comparative quantification of protein-RNA cross-links, overcoming the limitations imposed by conventional UV XL-MS methods.

biophysics↗

bioRxiv2026

Metatranscriptomic Identification of Co- and Incidental Infections in Marine Turtles Reveals Complex Disease Aetiologies

Traditional veterinary pathology investigations on wild animals generally conclude a primary cause of death based on a combination of observed clinical signs, gross and microscopic lesions, microbial culture and PCR. However, these methods may fail to capture the broader microbial community of the host. We employed metatranscriptomic sequencing to characterise the potential pathobiome of necropsied marine turtles, comparing these findings with corresponding veterinary pathology reports. Tissue samples were collected from 76 individuals spanning three species of marine turtles -- the green turtle (Chelonia mydas), the hawksbill turtle (Eretmochelys imbricata), and the loggerhead turtle (Caretta caretta) -- across the coastline of New South Wales, Australia. Reported causes of mortality ranged from infectious disease to trauma. We identified a diverse range of parasites within the genera Neospirochis, Hapalotrema, Paraorgymatobothrium, Eimeria and Callitetrarhynchus, and bacteria including the genera Aeromonas, Clostridium, and Vibrio. Novel viruses of the families Astroviridae, Caliciviridae, Hepaciviridae, Hepeviridae, Nyamivirdae, Orthomyxoviridae, Picobirnaviridae and Rhabdoviridae were also identified. In cases where infectious disease was noted in the pathology report, we frequently observed high pathogen read counts consistent with the listed primary diagnoses. However, we also detected a range of incidental infections involving eukaryotic parasites, bacteria, and viruses. The diversity of infectious agents detected in marine turtles suggests that the observed disease outcomes are unlikely to be driven by a single causative agent, but rather by complex interactions between host health, the pathobiome, and environmental stressors. We discuss the potential implications for turtle health and conservation.

molecular biology↗

bioRxiv2026

Metagenomic identification of novel Hepaciviridae in Australian birds reveals pegivirus recombination

The Hepaciviridae family of RNA viruses have a wide range of hosts including arthropods, fish, birds and mammals. Birds are well documented reservoirs of these viruses, owing to their physiological and ecological characteristics that facilitates rapid transmission through populations. To expand our understanding of the avian virome, with a particular focus on the identification of novel hepaciviruses, we performed metatranscriptomic sequencing on tissues taken from Australian endemic birds such as emus, pelicans as well as migratory birds (shearwater and albatross sp., egrets, herons and cuckoos) found deceased in New South Wales, Australia between 2021 and 2025. From these data we identified two novel pegiviruses -- shearwater and Australian pelican pegivirus (denoted SWPgV and APPgV) -- that provided phylogenetic evidence of a putative recombination event, reflected in incongruent tree topologies. SWPgV and APPgV form a sister clade with previously described avian-associated pegiviruses in NS3 phylogenetic trees, yet fell as a unique basal group in phylogenies based on NS5B. The lack of a clear parental lineage in NS5B domains suggests that additional divergent avian-associated pegiviruses have yet to be identified. In addition, we discovered two novel orthohepaciviruses herein named short-tailed shearwater and emu orthohepacivirus (STSHpV and EHpV) that are related to other avian-associated orthohepaciviruses, indicative of a long avian association, as well as a confirmed case of pegivirus and orthohepacivirus co-infection. Combined, these avian hepacivirus findings demonstrate the importance of tissue-based viral discovery studies in uncovering novel virus species and understanding their complex evolutionary histories.

microbiology↗

bioRxiv2026

Single-cell mapping of the fallopian tube reveals a genomically unstable secretory cell state enriched in carriers of germline BRCA1/2 mutations

Carriers of germline BRCA1 or BRCA2 alterations have a substantially increased lifetime risk of high-grade serous ovarian carcinoma (HGSOC), which originates from the secretory cells of the fallopian tube. However, comparative multi-omic analyses of bulk fallopian tube tissue from BRCA1/2 carriers and the general population have, to date, revealed only limited differences. New molecular biomarkers of early malignant transformation in the FT are needed to enable non-surgical cancer interception in high-risk individuals through window-of-opportunity trials prior to risk-reducing surgery. We performed a comprehensive single-cell, multi-regional analysis of fallopian tubes from 34 women, including 15 carriers of germline BRCA1/2 alterations. Using a metacell-based approach applied to single-cell transcriptomic data, we identify both established and previously unrecognised cellular populations, and characterise phenotypic variation associated with menopausal status, menstrual cycle phase, hormonal contraception use, and anatomical region of the fallopian tube. Menopause was associated with depletion of ciliated cells, whilst both secretory (SEC) and ciliated epithelial cells (CEC) shifted to a glandular phenotype in the luteal phase. Previous hormonal contraception usage had lasting effects including depletion of CD163-positive tissue resident macrophages and progesterone-specific increase of MHC-II expression in SECs. Metacell analysis further identified distinct subpopulations of SECs, most frequently in BRCA1/2 carriers, characterised by high TP53 expression and markedly elevated histone levels. This phenotype is consistent with replication stress, cell-cycle arrest, and activation of innate immune signalling pathways. Protein-level validation in matched samples showed enrichment of cells with increased {gamma}H2AX expression and persistent 53BP1 foci in BRCA1/2 carriers. Together our data supports the role of BRCA1/2 in maintaining genomic integrity and a BRCA1/2 haploinsufficient phenotype characterised by increased replication stress in the fallopian tube epithelium. Our findings provide evidence for distinct immune responses in users of hormonal contraception and demonstrate early events in malignant transformation. They establish potential biomarkers in microscopically normal FT and a framework for measurement of cancer risk with the goal of enabling molecularly informed cancer interception in high-risk individuals.

cancer biology↗

bioRxiv2026

Modeling quantifies in vivo neutralization, Fc-mediated killing, and resistance in human clinical trials of five anti-HIV broadly neutralizing antibodies

Broadly neutralizing antibodies (bnAbs) are a promising intervention for HIV prevention, therapy, and cure. bnAb optimization requires precise quantification of in vivo functions, many of which cannot be directly measured in humans. We therefore performed a mathematical modeling meta-analysis which integrated four clinical trials and reproduced serial bnAb concentrations, viral loads, and bnAb sensitivities (IC50) in 43 viremic trial participants who received an infusion of VRC01, VRC01LS, VRC07-523LS, 3BNC117 or 10-1074. We compared >300 mathematical models for their ability to recapitulate multi-strain HIV dynamics following bnAb infusion. For each bnAb, our best model identified a scaling factor of 36-462 to project in vivo activity from in vitro IC50, quantified Fc-mediated infected cell killing in humans over time, and projected the timing of bnAb-resistant strain emergence. Using this holistic profile, VRC07-523-LS was generally optimal.

immunology↗

bioRxiv2026

Hidden diversity and expanded host range of sarthroviruses, including terrestrial vertebrates

The Sarthroviridae are a family of highly compact satellite RNA viruses comprising one recognised species, extra small virus (XSV). Macrobrachium rosenbergii nodavirus (MrNV) is the associated helper virus of XSV and their co-infection has been linked to white tail disease in freshwater prawns globally, although the role of XSV is remains unclear. Here, we describe the discovery and characterisation of ten novel, highly divergent sarthrovirus species from a range of hosts and environments within a small geographical region in Australia. These comprise novel sarthroviruses associated with marine sponges, seal and dingo faeces, environmental marine sediment samples and Indo-Pacific geckos (Hemidactylus garnotii). All the novel viruses possess only a capsid protein, consistent with the genome of XSV, yet exhibit substantial sequence divergence. Notably, some sarthrovirus variants seem to utilise different replication systems despite being genetically identical and present in the same host species. Sequences from nodaviruses, which could plausibly act as helpers, were associated with some, but not all, the sarthroviruses identified here. Phylogenetic analyses support the expansion of the Sarthroviridae into multiple distinct lineages, comprising at least seven genera. Collectively, these findings reveal a broader ecological distribution and evolutionary diversity of sarthroviruses and highlight the possibility of alternative replication strategies and tissue tropism in diverse animal host. SignificanceSarthoviruses are small ([~]800 nucleotides) satellite RNA viruses associated with a nodavirus of crustaceans that acts as a helper. To date, the only known sarthovirus is extra small virus (XSV), which also represents the sole species within the Sarthroviridae. Here, we report the detection of ten divergent sarthroviruses sampled from diverse animal hosts, including vertebrates, that expand the family to 11 species and at least seven genera. These viruses were detected from various host taxa and environmental samples from a confined geographical region in eastern Australia, suggesting that they are ecologically connected. Notably, we did not detect nodaviruses in all samples containing sarthroviruses, suggesting that different viruses may act as helpers for sarthovirus replication.

microbiology↗

bioRxiv2026

Monoclonal nephritic factors reveal insights into C3 convertase dynamics and dysregulation

C3- and C5-nephritic factors are potent but poorly understood autoantibodies that dysregulate complement convertases. To date, their underlying mechanisms of action, epitopes, and sequences remain unknown. To address this knowledge gap, we immune profiled B cells from a nephritic factor-positive C3 glomerulopathy patient and identified the first monoclonal C3- and C5-nephritic factors. We present the structure of a C3-nephritic factor bound to a C3 convertase with the convertase protease domain unexpectedly rotated and inhibited. This rotation advances our understanding of complement convertase progression and decay, explains disease-associated convertase variants, and reveals the molecular mechanism by which nephritic factors can either activate or inhibit convertase activity. We also detail heterogeneity within and between C3- and C5-nephritic factors in terms of convertase binding, stabilizing capacity, regulator inhibition, fluid-phase activation, and disease contribution. These findings improve stratification of patients with C3 glomerulopathy, redefine basic C3 convertase dynamics, and provide insights into antibody-mediated modulation of the complement system.

immunology↗

bioRxiv2026

Detection and genomic characterisation of a novel hantavirus in Australian dolphins

We report the detection of a novel hantavirus in the lung tissue of two diseased Australian dolphins with histopathological changes. Phylogenetic analysis placed this virus within the genus Mobatvirus. This highlights the ability of hantaviruses to infect non-terrestrial mammals and the potential role of marine mammals as one health sentinels.

microbiology↗

bioRxiv2026

SYBR Gold staining of single stranded nucleic acids is strongly influenced by the presence of guanosines

SYBR Gold is one of the most strongly fluorescent members of the SYBR family of asymmetrical cyanine dyes commonly used for staining double and single-stranded DNA and RNA. The dye fluorescence increases dramatically upon nucleic acid binding. The primary mode of binding to double-stranded DNA is through intercalation between the base-paired deoxyribonucleotides, while the precise mode of binding to single-stranded DNA and to RNA is less well understood. Here we show that the fluorescence activity of SYBR Gold is strongly influenced by the presence of guanines in single-stranded nucleic acids. We expect this insight to aid in the evaluation of SYBR Gold-based measurements of nucleic acid abundance and spark further studies into the binding behaviour of the SYBR family dyes.

molecular biology↗

bioRxiv2026

Precision mapping and molecular contextualization of surgical outcome epicenters in temporal lobe epilepsy

AO_SCPLOWBSTRACTC_SCPLOWTemporal lobe epilepsy is the most common drug-resistant epilepsy, with surgical resection offering the primary path to seizure freedom. Despite standardized approaches, a substantial proportion of patients experience seizure recurrence, and the neurobiological substrates underlying these divergent outcomes remain unclear. We applied an individualized normative modeling framework to multimodal preoperative MRI data in a group that subsequently underwent surgical resection, to characterize patient-specific structural deviations and identify disease epicenters. Patients who became seizure-free exhibited spatially coherent abnormalities localized to the hippocampus and ipsilateral association regions, anchored in agranular limbic territories and enriched for genes linked to calcium-dependent signaling. Non-seizure-free patients, on the other hand, showed a more heterogeneous and distributed pattern of deviations, consistent with a "temporal-plus" network organization, and broader neuromodulatory dysregulation. Crucially, overlap between resected tissue and network-defined epicenters was closely associated with seizure freedom, independent of total resection volume. These findings provide a multiscale framework for precision surgical planning, shifting the focus from standardized tissue removal to targeted disconnection of patient-specific pathological hubs.

neuroscience↗

bioRxiv2026

p70 ribosomal protein S6 Kinase (p70S6K) as a potential peripheral biomarker for mental symptoms in 16p11.2 deletion and duplication syndromes

Neurodevelopmental disorders (NDDs) encompass heterogeneous cognitive, motor, and psychiatric manifestations that typically require extensive behavioural assessments for characterization. Individuals carrying 16p11.2 copy number variations (CNVs), including both deletions and duplications, represent a relatively common NDD subgroup marked by wide variability in psychiatric symptoms, as well as metabolic and peripheral abnormalities, complicating prediction of disease trajectory and treatment response. The identification of biomarkers in easily accessible tissues, such as peripheral blood mononuclear cells (PBMCs), could provide valuable tools for diagnosis and prognosis, yet remains an unmet clinical need. Converging evidence implicates dysregulation of ubiquitous signalling pathways, including ERK and mTOR cascades, in altered protein synthesis across both idiopathic and genetic NDDs. Here, using a hypothesis-driven screening approach, we examined candidate peripheral biomarkers in individuals with 16p11.2 deletions and duplications. We identified a significant reduction of ribosomal protein S6 kinase (p70S6K) levels in PBMCs across both genotypes. Notably, the magnitude of p70S6K reduction correlated with the severity of autistic symptoms independently of CNV genotype. In parallel, MAPK3/ERK1 protein levels mirrored gene dosage, showing increased expression in duplication carriers and reduced levels in deletion carriers, in accordance with the genotype. Collectively, these findings indicate that peripheral molecular alterations may support clinical stratification and suggest that p70S6K represents a promising biomarker for symptom severity and potentially treatment responsiveness in NDD patients carrying 16p11.2 CNVs.

neuroscience↗

bioRxiv2026

Beyond alignment: synergistic integration is required for multimodal cell foundation models

The vision of a "virtual cell"--a computational model that simulates biological function across modalities and scales--has become a defining goal in computational biology. While powerful unimodal foundation models exist, the lack of large-scale paired data prohibits the joint training of multimodal approaches. This scarcity favors compositional foundation models (CFMs): architectures that fuse frozen unimodal experts via a learned interface. However, it remains unclear when this multimodal fusion adds task-relevant information beyond the strongest unimodal representation and when it merely aggregates redundant signal. Here, we introduce the Synergistic Information Score (SIS), a metric grounded in partial information decomposition (PID), that quantifies the information gain achievable only through cross-modal interactions. Extending theoretical results from self-supervised learning, we show that standard alignment-based fusion objectives on frozen encoders inherently collapse to detecting linear redundancies, limiting their ability to capture nonlinear synergistic states. This distinction is directly relevant for tasks aiming to link tissue morphology and gene expression. Benchmarking ten fusion methods on spatial transcriptomics datasets, we use SIS to demonstrate that tasks dominated by linear redundancies are sufficiently served by unimodal baselines, whereas complex niche definitions benefit from synergy-aware integration objectives that enable cross-modal interactions beyond linear alignment. Finally, we perform a scaling analysis which highlights that fine-tuning a dominant unimodal expert is the most sample-efficient path for standard tasks, suggesting that the benefits of multimodal frameworks only emerge when tasks depend on information distributed across modalities. Together, these results establish that building towards a virtual cell will require a fundamental shift from alignment objectives that emphasize shared structure to synergy-maximizing integration that preserves and exploits complementary cross-modal signal.

bioinformatics↗

bioRxiv2026

Predicting evolutionary rate as a pretraining task improves genome language model representations

Genome language models (gLM) have the potential to further understanding of regulatory genomics without requiring labeled data. Most gLMs are pretrained using sequence reconstruction tasks inspired by natural language processing, but recent studies have shown that these gLMs often fail to capture biological signal. To overcome this, we introduce pretraining tasks that predict the rate of evolution. These tasks are designed so that they can be composed with sequence reconstruction, enabling a controlled comparison of predicting sequence only, evolutionary rate only, or both. To address gaps in existing evaluations, we developed a suite of biologically grounded benchmarks. Across these tasks, and for established variant effect prediction benchmarks, models pretrained on both sequence and evolutionary rate outperform those trained on sequence alone, and training on evolutionary rate can make the even the relatively small models in our work competitive with much larger existing gLMs for some tasks. These results establish evolution as a key training target for genome-scale models.

genomics↗

bioRxiv2026

Functional genomics identifies therapeutic options, biomarkers, and resistance mechanisms for high-grade gliomas

High-grade gliomas (HGGs) are aggressive tumors with poor outcomes and limited treatment options. Here, we combined genomic and transcriptomic tumor profiling with drug testing in a patient-derived 3-dimensional culture model to identify individualized treatments and predictive biomarkers. Activity of single agents targeting frequently dysregulated glioma pathways was relatively poor ex vivo and generally reflected historical patient data. However, compounds targeting PI3K, epigenetic, and survival/senescence signaling were effective in some cases. Drug sensitivity correlated with transcriptional rather than genomic features and suggested heterogeneity as a resistance mechanism. Bromodomain and extraterminal domain inhibition was particularly effective in tumors enriched in the mesenchymal transcriptional subtype, promoted proneural transition, and was overcome by upregulated PI3K signaling. Notably, combinations were largely effective, with 6 strategies exhibiting stronger efficacy than corresponding single agents in most cases (58-77%). This study identifies HGG vulnerabilities and associated biomarkers, resistance mechanisms, and effective combination strategies that warrant further clinical validation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/701806v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@cdb75corg.highwire.dtl.DTLVardef@1c133e6org.highwire.dtl.DTLVardef@1365153org.highwire.dtl.DTLVardef@11543a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

The Hemodynamic Response Function Varies Across Anatomical Location and Pathology in the Epileptic Brain

The hemodynamic response function (HRF) links neuronal activity to functional magnetic resonance imaging (fMRI) signals. While most fMRI studies use a "canonical" HRF, increasing evidence from studies of healthy subjects suggests that the HRF depends on anatomical location and disease states. Here, we investigate how HRF variability relates to anatomical location and pathology in the epileptic brain, using a large simultaneous electroencephalogram and fMRI dataset. Applying HRF deconvolution and temporal decomposition, we built the first whole-brain HRF library specific to epilepsy, identifying four distinct shape groups. We mapped HRF features across parcellations of two atlases using novel Bayesian hierarchical models. In non-epileptogenic regions, HRF shape and spatial distributions align with findings from healthy subjects. Within pathological regions, they vary significantly according to pathology. Our results indicate that HRF variability is associated with pathology, in addition to its dependence on anatomical location, motivating region- and pathology-based HRF modulation in epilepsy studies.

neuroscience↗

bioRxiv2025

Gain and loss of function changes in CACNA1C affect neuronal networks through divergent pathways

BackgroundCACNA1C encodes the pore-forming subunit of the L-type calcium channel Cav1.2. Common variants in CACNA1C are associated with psychiatric disorders, while rare single-nucleotide variants cause CACNA1C-related disorder (CRD), a multi-system disorder with symptoms that include autism spectrum disorder (ASD), intellectual disability and seizures. However, the cellular mechanisms linking CACNA1C dysfunction to neurodevelopmental phenotypes remain poorly understood. MethodsWe generated isogenic CACNA1C loss-of-function (LoF) induced pluripotent stem cell (iPSC) lines and reprogrammed a line from an individual carrying a novel gain-of-function (GoF) variant in CACNA1C. Neuronal activity was assessed using multi-electrode arrays (MEA), pharmacological manipulation, and gene expression analysis. Early developmental phenotypes were examined using qRT-PCR, immunocytochemistry, and RNA sequencing. ResultsLoF and GoF patient-derived neurons displayed opposing alterations in network dynamics. Pharmacological and molecular assays indicated that these network differences were associated with dysregulated GABAergic signalling. Early developmental analysis revealed that loss of CACNA1C altered rosette morphology, CREB phosphorylation, and transcriptional programs related to axonogenesis and synaptic signalling, indicating effects on neuronal differentiation. The patient line exhibited opposing phenotypes, reflecting variant-specific effects. ConclusionsThese findings demonstrate that Cav1.2 regulates excitatory-inhibitory balance, network organization, and aspects of neurodevelopment. Divergent effects of LoF and GoF variants highlight how altered Cav1.2 signalling contributes to variable neurodevelopmental phenotypes, including ASD and epilepsy, and establish a framework for defining CACNA1C variant effects in human neurons.

neuroscience↗

bioRxiv2025

Sleep fragmentation drives local, network-specific epileptic activity in human epilepsy

Sleep has complex links with epileptic activity, yet the causal role of sleep instability in driving and modulating pathological discharges in the human brain remains incompletely understood. Here we directly examine this by characterising the fine-scale temporal coupling between experimentally induced sleep arousals and interictal epileptiform discharges (IEDs), using combined stereo-electroencephalography and polysomnography recordings in patients with epilepsy. Sleep arousals triggered rapid IED increases, with effects gated by anatomical region and sleep stage. Increases were confined to neocortical regions and occurred during both non-rapid eye movement stage 2 (N2) and stage 3 (N3) sleep, with a larger effect observed in N2. IED increases did not differ between the seizure-onset zone and surrounding regions. Despite elevating IED counts, arousals did not alter IED spatial propagation, indicating state-dependent enhancement of local cortical excitability without recruitment of broader epileptic networks. These findings establish a causal role for sleep instability in actively driving pathological activity on fine-grained spatiotemporal scales, and highlight sleep stabilisation as a promising therapeutic strategy to reduce epileptic burden and preserve cortical network function.

neuroscience↗

bioRxiv2025

Sex Dependent Effects of Minocycline on Contextual Fear Memory

Recent studies have highlighted the crucial role of microglia in fear learning and memory. This supports the potential therapeutic value of the anti-inflammatory agent minocycline, which regulates microglial activity, in psychiatric disorders involving dysregulated emotional memory. To assess the impact of minocycline during a tractable intervention window, we examined its acute systemic effects on the reconsolidation, extinction, and forgetting of contextual fear memory (CFM) in rats. Our findings show that the effects of minocycline on fear memory and anxiety-like behaviours depend on sex, memory activation (i.e., whether it was retrieved), and memory age. In males with recently acquired CFM, minocycline given before retrieval enhanced extinction and reduced fear expression. When administered without retrieval, it disrupted passive forgetting, increasing evoked fear behaviour. This extinction-enhancing effect did not occur with older (28-day) memories rather it strengthened CFM through enhancing reconsolidation. In contrast, in females, minocycline increased the expression of recent fear memories regardless of retrieval, without affecting extinction or forgetting. This elevated fear expression appeared linked to heightened anxiety-like behaviour. These findings suggest that minocycline, or other microglia-targeting agents, would need to be used in a highly selective and targeted manner to therapeutically modulate pathological fear memories. Minocycline may be beneficial as an adjunct to exposure therapy in men explicitly retrieving recent fear or trauma-related memories, but outside these conditions, it may worsen fear expression. These results help explain the mixed findings from therapeutic trials using minocycline in psychiatry and support the application of a more precision approach in any future applications.

animal behavior and cognition↗