Biology subjects

Williams, G.

Publications and source records attributed to Williams, G..

At least 19 recordsLinked to original sources

bioRxiv2026

Schrodinger's mouse: human observation erases a drug-induced behavioral phenotype

Animal studies primarily rely on human monitoring for health and behavioral outcomes. The presence of a human, however, can induce stress and potentially alter experimental results. We sought to answer whether human observation alone is enough to change experimental outcomes and obscure the effect of interest. Our automated home-cage behavioral phenotyping system provided the ideal platform to test this hypothesis. Two cohorts received semaglutide (0.03 mg/kg, intraperitoneally) on separate consecutive days. The first cohort was recorded without inspection after dosing; the second underwent a brief visual health check with no handling. Recordings from the checked cohort on the preceding day, without injection or inspection, provided a matched baseline. A single brief check produced large, time-locked changes across the behavioral repertoire. The changes began before the cage door was opened, indicating a response to experimenter proximity. In addition to adding variance, the semaglutide-treated animals' behavior during observation was more similar to the no-injection baseline than to the semaglutide/no-check reference, transiently erasing the drug phenotype. Brief human observation is therefore not a neutral measurement operation; over the minutes surrounding it, it is a perturbation in itself that is large enough to mask the drug effect it is meant to record.

animal behavior and cognition↗

bioRxiv2026

A foundational in vivo platform for predicting human health outcomes

Rodents remain the workhorse of preclinical drug development, yet often fail to predict human clinical outcomes. Existing alternatives are similarly constrained. Cells in culture cannot recapitulate whole-organism physiology, and larger mammals cannot be studied at comparable throughput. Here we present a scalable, information-dense platform that can predict a drugs long-term human clinical outcomes from 24 hours of rodent behavior. A novel home-cage system continuously records behavior, generating thousands of features per hour. Models are trained on human clinical trial data to map these features onto outcomes including gastrointestinal adverse events, cardiac toxicity, neuropsychiatric side effects, and long-term weight loss. In addition to being an order of magnitude faster, the platform provides more accurate clinical predictions than standard long-term preclinical experiments. The approach readily extends to other outcomes, enabling rodents to serve as quantitative models for human clinical prediction.

pharmacology and toxicology↗

bioRxiv2026

The blueprint of human functional architecture shifts from cognition to anatomy during perturbations of consciousness

Consciousness and cognition arise from the ongoing interactions between brain regions. Synchronous fluctuations of fMRI signals may indicate that two brain regions perform similar cognitive functions, but neural interactions are also constrained by anatomical connectivity and regions molecular, cytoarchitectonic, and metabolic profiles. Here we disentangle the respective contributions of ongoing cognition and multimodal neurobiological constraints in shaping functional connectivity. We jointly contextualise haemodynamic FC against eight distinct multimodal representations of the human connectome: (i) structural connectivity from diffusion tractography; (ii) spatial embedding; (iii) similarity of transcriptional profiles from gene expression; (iv) similarity of receptor profiles from Positron Emission Tomography; (v) laminar profile similarity from histology; (vi) correlated electrophysiological activity from magnetoencephalography; (vii) correlated metabolic activity from PET glucose uptake; (viii) coordinated activation across 123 cognitive operations from the NeuroSynth meta-analytic engine. We demonstrate that cognitive co-activation is the dominant predictor of inter-regional fMRI synchrony in the awake human brain, even when quantified using intracranial electrical stimulation. Crucially, this predominance of cognitive co-activation for shaping functional connectivity is systematically obliterated across five datasets of pharmacological and pathological perturbations of consciousness (chronic disorders of consciousness; anaesthesia with sevoflurane, propofol, or ketamine) when cognition is disconnected from the environment or altogether abolished. Altogether, we show that multimodal predictors of functional architecture shift away from cognitive co-activation and toward anatomicalmolecular constraints during pharmacological and pathological perturbations of consciousness.

neuroscience↗

bioRxiv2026

Chemical genomics screening reveals novel functions for unannotated genes in Vibrio cholerae C6706

Vibrio cholerae, the causative agent of cholera, remains a major global health burden despite ongoing initiatives for vaccination and improved sanitation. Much of the V. cholerae life cycle occurs in aquatic environments, requiring gene functions that enable survival under diverse stresses associated with this niche and during the transition to the human host. Although numerous V. cholerae genome sequences are available, functional annotation across its pan-genome remains incomplete, and many annotated genes lack experimental validation. In this study, we employed a chemical genomics approach to profile fitness phenotypes across 104 diverse stress conditions using a library of 3,026 single-gene mutants of V. cholerae C6706, a widely used research strain. In total, we identified significant growth phenotypes for 1,518 mutants, of which 88 correspond to unannotated (hypothetical or putative) genes. Together, these data provide a comprehensive resource for exploring gene function in V. cholerae, supported by detailed quality metrics and open-access tools to facilitate community-driven discovery. AUTHOR SUMMARYAlthough many bacterial pathogens have been extensively sequenced, we still know relatively little about what many of their genes actually do. In many cases, gene functions are solely predicted by computer algorithms but have not been confirmed in the laboratory, and we can assume that some of those predictions may be incorrect. Chemical genomics -- a method that tests thousands of single-gene mutants under different stresses -- can help reveal what these genes are responsible for. Using this approach, we screened a library of Vibrio cholerae C6706 mutants under 104 different conditions. We found that more than half of the mutants showed measurable effects on growth, including many genes that were previously uncharacterized. Here, we describe our experimental pipeline, present key quality checks, and share how other researchers can use this dataset as a resource to explore V. cholerae mutant phenotypes.

systems biology↗

bioRxiv2025

Integrated Classification of Cortical Cells and Quantitative Projectomic Mapping Unveil Organizational Principles of Brain-Wide Connectomes at Single Cell Level

Molecularly defined cortical cell types have recently been linked to whole neuronal morphology (WNM), particularly those characterized by whole-brain-wide projections, such as intratelencephalic (IT), extratelencephalic (ET), and corticothalamic (CT) neurons. In contrast, classical morphological classifications (e.g., tufted TPC, small tufted SPC, and stellate SSC) are based primarily on local dendrosomatic and axonal structures, especially apical dendrites. This study bridges these perspectives by establishing a new neuronal taxonomy, analyzing the connectomes of defined cortical cell types, and comparing them with those obtained from bulk anterograde injections. Neurons were sparsely labeled via tamoxifen-inducible Cre lines with GFP reporters, and 1,419 WNM cells were comprehensively reconstructed with Vaa3D-TeraVR from [~]15 areas across six functional regions of molecularly labeled brains imaged with 2p-fMOST. These cells were newly classified by integrating current molecular-WNM and classical morphological perspectives, with sample size augmented by 1,455 publicly available WNM cells reconstructed from the Mouse-Light project and CEBSIT. This effort defined ten combined molecular-WNM-classical morphological cell types: L5ET_TPC, L6CT_NPC, L6b_HPC, and seven IT types--L2/3IT_TPC, L4IT_SSC, L4IT_UPC, L4IT_TPC, L5IT_SPC, L6IT_IPC, and L6IT_car3PC. Clustering, quantitative analyses and random Forest classifier objectively validated these types and revealed their distinct connectomes, along with convergent, topographic, and hierarchical organizations across their projection brain regions. At the single-cell level, multiple organizational principles governing cortico-cortical (C-C) and cortico-subcortical (C-subC) connectomes emerged with unprecedented detail, offering a precise GPS-like tool for in vivo recordings and robust datasets for neuronal network modeling. Comparisons with bulk anterograde injection data underscored the limitations of traditional methods in identifying projection targets. Overall, our approach provides significant insights into cortical circuitry and elucidates the complex interplay between neuronal molecular identity, whole morphology, and classical morphological classification.

neuroscience↗

bioRxiv2025

DAGLα/β, 2-AG release, and Parkinson's Disease: Exploring a causal link.

The diacylglycerol lipases, DAGL and DAGL{beta}, hydrolyse diacylglycerol (DAG) to produce 2-arachidonoylglycerol (2-AG), a key endocannabinoid (eCB) and CB/CB2 receptor ligand. While DAGL is well established as a regulator of CB-dependent synaptic plasticity, recent studies have identified DAGLB mutations as a cause of autosomal recessive early-onset Parkinson's disease (PD). Here, we present a comprehensive analysis of DAGL{beta} mRNA expression, demonstrating its co-expression with DAGL mRNA predominantly in excitatory neurons throughout the adult nervous system. We see no evidence for enrichment of the DAGLs or CB transcripts in the striatum or in dopaminergic neurons. We discuss these findings within a review of recent literature that points to a wider involvement of the eCB system in PD. Notably, DAGL-dependent 2-AG release at synapses relies on -synuclein function - a protein central to PD pathophysiology-implicating both DAGLs in PD and pointing to widespread disruption in 2-AG release. Consistent with this, substantial reductions in 2-AG levels have been reported in the cerebrospinal fluid (CSF) of PD patients. Depression, a major non-motor symptom of PD, often precedes the onset of motor deficits by several years. Human and mouse genetic studies suggest that reduced DAGL activity may contribute to depression by impairing 2-AG-mediated CB receptor signalling, which is crucial for synaptic plasticity, stress resilience, and mood regulation. These findings point to a potential causal link between DAGL dysfunction and the non-motor symptoms in PD.

neuroscience↗

bioRxiv2025

Synaptotoxic forms of amyloid-b and a-synuclein act through a common pathway.

It has been suggested that -synuclein (Syn), a major player in Parkinsons disease (PD), plays a role in Alzheimers disease (AD). Several reports have also concluded that Syn and amyloid-{beta} (A{beta}) are mechanistically linked, although how is unclear. Synapse loss is an early feature in both PD and AD and held to be the driver of both diseases. We have previously uncovered a signalling pathway required for A{beta}-driven dendritic spine loss - a non-canonical branch of Wnt signalling known as the Wnt/Planar Cell Polarity (Wnt/PCP) pathway. We asked if a synaptotoxic form of Syn known to impact dendritic spines, the A53T autosomal dominant PD mutant form of Syn (A53T-Syn), might act on synapses through the same pathway. Here, by blocking all Wnt activity with the porcupine inhibitor IWP2, we show that A53T-Syn-driven spine loss is Wnt-dependent. By silencing Daam1, which is unique to Wnt/PCP, we show that A53T-Syn spine loss is Daam1-dependent. Finally, using the pan-ROCK inhibitor fasudil indicates the mechanism also involves ROCK1/2, which Daam1 signals to via RhoA to modulate actin cytoskeletal dynamics within dendritic spines. Together, these observations indicate that A53T-Syn-driven spine loss involves the Wnt/PCP pathway, the same pathway that mediates A{beta} synaptotoxicity. This indicates that A{beta} and Syn are mechanistically connected and that a common pathway is responsible for synapse loss in AD and PD. It also begins to explain why this group of neurodegenerative diseases have many features in common and suggests that drugs which target Wnt/PCP could be of benefit for both AD and PD.

neuroscience↗

bioRxiv2025

Transcription driven repurposing of cardiotonic steroids for Lithium treatment of severe depression

Lithium is prescribed as a mood stabiliser in bipolar disorder and severe depression. However, the mechanism of action of Lithium is unknown and there are major side effects associated with prolonged medication. This motivates a search for safer alternative drug repurposing candidates. Given that the drug mechanism may be encoded in transcriptional changes we have generated the gene expression profile for acute Lithium treatment of cortical neuronal cultures. We found that the Lithium associated transcription response harbours a significant component that is the reverse of that seen in human brain samples from patients with Major Depression, Bipolar Disorder and a mouse model of depression. Interrogating publicly available drug driven expression data we found that cardiotonic steroids drive gene expression in a correlated manner to our acute Lithium profile. An analysis of the psychiatric medication cohort of the Norwegian Prescription Database showed that cardiotonic prescription is associated with a lower incidence of lithium prescription. Our transcriptional and epidemiological observations point towards cardiotonic steroids as possible repurposing candidates for Lithium. These observations motivate a controlled trial to establish a causal connection and genuine therapeutic benefit in the context of depression.

neuroscience↗

bioRxiv2024

Metabolomic profiles of stony coral species from the Dry Tortugas National Park display inter- and intraspecies variation

Coral reefs are experiencing unprecedented loss in coral cover due to increased incidence of disease and bleaching events. Thus, understanding mechanisms of disease susceptibility and resilience, which vary by species, is important. In this regard, untargeted metabolomics serves as an important hypothesis-building tool enabling delineation of molecular factors underlying disease susceptibility or resilience. In this study, we characterize metabolomes of four species of visually healthy stony corals, including Meandrina meandrites, Orbicella faveolata, Colpophyllia natans, and Montastraea cavernosa, collected at least a year before stony coral tissue loss disease reached the Dry Tortugas, Florida and demonstrate that both symbiont and host-derived biochemical pathways vary by species. Metabolomes of Meandrina meandrites displayed minimal intraspecies variability and highest biological activity against coral pathogens when compared to other species in this study. Application of advanced metabolite annotation methods enabled delineation of several pathways underlying interspecies variability. Specifically, endosymbiont-derived vitamin E family compounds, betaine lipids, and host-derived acylcarnitines were among the top predictors of interspecies variability. Since several metabolite features that contributed to inter- and intraspecies variation are synthesized by the endosymbiotic Symbiodiniaceae, which could be a major source of these compounds in corals, our data will guide further investigations into these Symbiodiniaceae-derived pathways. Importance.Previous research profiling gene expression, proteins, and metabolites produced during thermal stress has reported the importance of endosymbiont-derived pathways in coral bleaching resistance. However, our understanding of interspecies variation in these pathways among healthy corals and their role in diseases is limited. We surveyed the metabolomes of four species of healthy corals with differing susceptibilities to the devastating stony coral tissue loss disease and applied advanced annotation approaches in untargeted metabolomics to determine the interspecies variation in host and endosymbiont-derived pathways. Using this approach, we propose the survey of immune markers such as vitamin E family compounds, acylcarnitines, and other metabolites to infer their role in resilience to coral diseases. As time-resolved multi-omics datasets are generated for disease-impacted corals, our approach and findings will be valuable in providing insight into the mechanisms of disease resistance.

systems biology↗

bioRxiv2024

A Predictive Model for Compound-Protein Interactions Based on Concatenated Vectorization

BackgroundLarge data sets of compound activity lend themselves to building predictive models based on compound and target structure. The simplest representation of structure is via vectorisation. Compound fingerprint vectorisation has been successfully employed in predicting compound activity classes. ResultsA vector representation of a protein-compound pair based on a concatenation of the compound fingerprint and the protein triplet vector has been used to train random forest and neural network models on multiple datasets of protein-compound interaction together with compound associated transcription and activity profiles. Results for compound-target predictability are comparable with more complex published methodologies. ConclusionA simple intuitive representation of a protein-compound pair can be employed in a variety of machine learning models to gain a predictive handle on the activity of compounds for which there is no activity data. It is hoped that this transparent approach will prove sufficiently portable and simple to implement that drug discovery will be opened up to the wider research community.

bioinformatics↗

bioRxiv2024

Oxytocin receptor controls distinct components of pair bonding and development in prairie voles

Oxytocin receptor (Oxtr) signaling influences complex social behaviors in diverse species, including social monogamy in prairie voles. How Oxtr regulates specific components of social attachment behaviors and the neural mechanisms mediating them remains unknown. Here, we examine prairie voles lacking Oxtr and demonstrate that pair bonding comprises distinct behavioral modules: the preference for a bonded partner, and the rejection of novel potential mates. Our longitudinal study of social attachment shows that Oxtr sex-specifically influences early interactions between novel partners facilitating the formation of partner preference. Additionally, Oxtr suppresses promiscuity towards novel potential mates following pair bonding, contributing to rejection. Oxtr function regulates coordinated patterns of gene expression in regions implicated in attachment behaviors and regulates the expression of oxytocin in the paraventricular nucleus of the hypothalamus, a principal source of oxytocin. Thus, Oxtr controls genetically separable components of pair bonding behaviors and coordinates development of the neural substrates of attachment.

neuroscience↗

bioRxiv2024

Optogenetic stimulation of dorsal striatum bidirectionally controls seizures

Engagement of the striatum (caudate/putamen) and other basal ganglia nuclei during seizures was first observed over 75 years ago. Basal ganglia output nuclei, and the substantia nigra pars reticulata, in particular, have well-established anti-seizure effects across a large array of experimental models. However, striatal control of seizures is understudied. To address this gap, we used optogenetic approaches to activate and inactivate neurons in the dorsal striatum of Sprague-Dawley rats submitted to the gamma-butyrolactone (GBL) model of absence epilepsy, amygdala kindling model of temporal lobe epilepsy, and pilocarpine-induced Status Epilepticus (SE). All tests were performed on a within-subject basis. Animals were tested in two different light frequencies (5 Hz and 100 Hz). Open-loop (continuous light delivery) optogenetic activation of the dorsal striatal neurons robustly suppressed seizures in all models. On the other hand, optogenetic silencing of the dorsal striatal neurons increased absence seizure expression and facilitated SE onset but had no effect on kindled limbic seizures. In the GBL model, we also verified if the closed- loop strategy (light delivery in response to seizure detection) would be enough to induce antiseizure effects. On-demand light delivery in ChR2-expressing animals reduced SWD duration, while the same approach in ArchT-expressing animals increased SWD duration. These results demonstrated previously unrecognized anti-absence effects associated with striatal continuous and on-demand neuromodulation. Together, these findings document a robust, bidirectional role of the dorsal striatum in the control of seizure generation and propagation in a variety of seizure models, including focal seizure onset and generalized seizures.

neuroscience↗

bioRxiv2024

The choice-wide behavioral association study: data-driven identification of interpretable behavioral components

Behavior contains rich structure across many timescales. However, there is a dearth of methods to identify relevant components, especially over the longer periods required for learning and decision-making. Inspired by the goals and techniques of genome-wide association studies, we present a data-driven method--the choice-wide behavioral association study: CBAS--that systematically identifies such behavioral features. CBAS extracts sequences of actions or choices that either significantly differ between groups or correlate with a covariate of interest, using a powerful resampling-based method to correct for multiple comparisons. We illustrate CBAS through application to tasks performed by flies, rats and humans, showing that it provides unexpected and interpretable information in each case.

neuroscience↗

bioRxiv2024

Pathological mechanisms and candidate therapeutic approaches in the hearing loss of mice carrying human MIR96 mutations

Progressive hearing loss is a common problem in the human population with no effective therapeutics currently available. However, it has a strong genetic contribution, and investigating the genes and regulatory interactions underlying hearing loss offers the possibility of identifying therapeutic candidates. Mutations in regulatory genes are particularly useful for this, and an example is the microRNA miR-96, a transcriptional regulator which controls hair cell maturation. Mice and humans carrying mutations in Mir96 all develop hearing loss, but different mutations result in different physiological, structural and transcriptional phenotypes. Here we present our characterisation of two lines of mice carrying different human mutations knocked-in to Mir96. While mice homozygous for either mutation are profoundly deaf from two weeks old, the heterozygous phenotypes differ markedly, with only one mutation resulting in hearing impairment in heterozygosis. Investigations of the structural phenotype showed that one mutation appears to lead to synaptic defects, while the other has a much more severe effect on the hair cell stereociliary bundles. Transcriptome analyses revealed a wide range of misregulated genes in both mutants which were notably dissimilar. We used the transcriptome analyses to investigate candidate therapeutics, and tested one, finding that it delayed the progression of hearing loss in heterozygous mice. Our work adds further support for the importance of the gain of novel targets in microRNA mutants, and offers a proof of concept for the identification of pharmacological interventions to maintain hearing.

genetics↗

bioRxiv2024

Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873)

Chitons (Polyplacophora) are marine molluscs that can be found worldwide from cold waters to the tropics, and play important ecological roles in the environment. Nevertheless, there remains only two chiton genomes sequenced to date. The chiton Liolophura japonica (Lischke, 1873) is one of the most abundant polyplacophorans found throughout East Asia. Our PacBio HiFi reads and Omni-C sequencing data resulted in a high-quality near chromosome-level genome assembly of [~]609 Mb with a scaffold N50 length of 37.34 Mb (96.1% BUSCO). A total of 28,233 genes were predicted, including 28,010 protein-coding genes. The repeat content (27.89%) was similar to the other Chitonidae species and approximately three times lower than in the genome of the Hanleyidae chiton. The genomic resources provided in this work will help to expand our understanding of the evolution of molluscs and the ecological adaptation of chitons.

genomics↗

bioRxiv2023

Feasibility of intranasal delivery of thin-film freeze-dried monoclonal antibodies

Monoclonal antibodies (mAbs) administered intranasally as dry powders can be potentially applied for the treatment or pre-exposure prevention of viral infections in the upper respiratory tract. However, a method to transform the mAbs from liquid to dry powders suitable for intranasal administration and a device that can spray the dry powders to the desired region of the nasal cavity are needed to fully realize the potentials of the mAbs. Herein, we report that thin-film freeze-drying can be applied to prepare aerosolizable mAb dry powders and that the dry powders can be sprayed into the posterior nasal cavity using Aptar Pharmas Unidose (UDS) Powder Nasal Spray System. AUG-3387, a human-derived mAb that neutralizes the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was used in the present study. First, we prepared AUG-3387 thin-film freeze-dried powders (i.e., TFF AUG-3387 powders) from liquid formulations containing different levels of mAbs. The TFF AUG-3387 powder with the highest solid content (i.e., TFF AUG-3387C powder) was then chosen for further characterization, including the evaluation of the plume geometry, spray pattern, and particle size distribution after the powder was sprayed using the UDS Powder device. Finally, the deposition patterns of the TFF AUG-3387C powder sprayed using the UDS Powder device were studied using 3D-printed nasal replica casts based on an adult model and a child model. It is concluded that it is feasible to intranasally deliver mAbs as dry powders by transforming the mAbs into dry powders using thin-film freeze-drying and then spray the powder using the UDS Powder device.

pharmacology and toxicology↗

bioRxiv2023

SARS-CoV-2 Spike Protein Reduces Burst Activities in Neurons Measured by Micro-Electrode Arrays

SARS-CoV-2 caused a large-scale global pandemic between 2020 and 2022. Despite efforts to understand its biology and mechanisms of pathogenicity, the viral impact on the neurological systems remains unclear. The main goal of this study was to quantify the neurological phenotypes induced by SARS-CoV-2 spike protein in neurons, measured by in-vitro multi-well micro-electrode arrays (MEAs). We extracted the whole-brain neurons from the newborn P1 mice and plated them on multi-well micro-electrode arrays and administered purified recombinant spike proteins (S1 and S2 subunits respectively) from the SARS-CoV-2 virus. The signals from the MEAs were transmitted from an amplifier to a high-performance computer for recording and analysis. We used an in-house developed algorithm to quantify neuronal phenotypes. Among all the phenotypic features analyzed, we discovered that the S1 protein of SARS-CoV-2 decreased the mean burst numbers observed on each electrode; This effect was not observed for the spike 2 protein (S2) and could be rescued by an anti-S1 antibody. Finally, our data strongly suggest that the receptor binding domain (RBD) of S1 is responsible for the reduction of burst activities in neurons. Overall, our results strongly indicate that spike proteins may play an important role in altering neuronal phenotypes, specifically the burst patterns, when neurons are exposed during early development.

microbiology↗

bioRxiv2023

Integrating EM and Patch-seq data: Synaptic connectivity and target specificity of predicted Sst transcriptomic types

Neural circuit function is shaped both by the cell types that comprise the circuit and the connections between those cell types1. Neural cell types have previously been defined by morphology 2, 3, electrophysiology 4, 5, transcriptomic expression 6-8, connectivity 9-13, or even a combination of such modalities 14-16. More recently, the Patch-seq technique has enabled the characterization of morphology (M), electrophysiology (E), and transcriptomic (T) properties from individual cells 17-20. Using this technique, these properties were integrated to define 28, inhibitory multimodal, MET-types in mouse primary visual cortex 21. It is unknown how these MET-types connect within the broader cortical circuitry however. Here we show that we can predict the MET-type identity of inhibitory cells within a large-scale electron microscopy (EM) dataset and these MET-types have distinct ultrastructural features and synapse connectivity patterns. We found that EM Martinotti cells, a well defined morphological cell type 22, 23 known to be Somatostatin positive (Sst+) 24, 25, were successfully predicted to belong to Sst+ MET-types. Each identified MET-type had distinct axon myelination patterns and synapsed onto specific excitatory targets. Our results demonstrate that morphological features can be used to link cell type identities across imaging modalities, which enables further comparison of connectivity in relation to transcriptomic or electrophysiological properties. Furthermore, our results show that MET-types have distinct connectivity patterns, supporting the use of MET-types and connectivity to meaningfully define cell types.

neuroscience↗