Biology subjects

Williamson, R.

Publications and source records attributed to Williamson, R..

13 recordsLinked to original sources

bioRxiv2026

Self-regulation of neuronal activity in prefrontal cortex

Despite our best efforts to stay focused on a task, our arousal waxes and wanes over time. Lower levels of arousal are typically associated with drowsiness, whereas higher levels are often associated with stress. These changes in arousal move us away from ideal task performance and manifest as fluctuations in neural activity. We asked whether moment-by-moment neurofeedback could be used to counteract neural fluctuations and thereby regulate arousal levels. Here, we developed an intracortical brain-computer interface (BCI) in which animals used visual neurofeedback to maintain neural population activity in prefrontal cortex near a pre-specified activity target. We found animals used moment-to-moment neurofeedback to reduce neural fluctuations on timescales of seconds to hundreds of milliseconds, and that arousal-related regulation of neural activity was associated with BCI use. Our findings suggest that neurofeedback may enhance or restore regulation of neural activity, with potential clinical applications in conditions where such regulation is impaired.

neuroscience↗

bioRxiv2026

ESCRT Machinery Dysfunction in Motor Neurone Disease: TSG101, CHMP2B, and VPS4a Differentially Regulate TDP-43 Pathology, Autophagy, and Exosome Biogenesis

Motor Neurone Disease (MND) is characterised by progressive degeneration of upper and lower motor neurons, accompanied by cytoplasmic mislocalisation and hyperphosphorylation of TDP-43 -- hallmarks that implicate failure of endolysosomal proteostasis. The Endosomal Sorting Complexes Required for Transport (ESCRT) pathway governs multivesicular body (MVB) formation, lysosomal cargo delivery, and autophagosome closure, yet its expression profile in human MND tissue and mechanistic contribution to disease pathology have not been established. Here, we report subunit-specific dysregulation of ESCRT proteins in postmortem motor cortex and spinal cord from MND patients: CHMP2B (ESCRT-III) is significantly upregulated in both regions, whilst TSG101 (ESCRT-I) and VPS37A (ESCRT-I) are significantly downregulated in motor cortex, indicating a region-specific remodelling of the ESCRT network. In a tunicamycin-induced ER stress model using NSC-34 motor neuron-like cells and primary cortical neurons, TSG101 overexpression reduced total and phosphorylated TDP-43, suppressed mTOR signalling, and restored autophagic flux, whereas TSG101 knockdown exacerbated TDP-43 accumulation and cytoplasmic mislocalisation. CHMP2B modulation selectively regulated TDP-43 phosphorylation without altering total TDP-43 levels, consistent with a casein kinase 1-dependent mechanism operating independently of bulk autophagy. Both TSG101 and VPS4a were required to maintain neuronal CD9 tetraspanin localisation to early endosomes; their depletion redirected CD9 to late endosomal and lysosomal compartments under ER stress. Extracellular vesicle characterisation revealed a functional divergence: TSG101 is required for general exosome biogenesis, whereas VPS4a ATPase activity specifically mediates loading of pathological TDP-43 cargo into EVs. Dynamic light scattering confirmed that ER stress and ESCRT modulation produce distinct, condition-specific alterations in EV size and polydispersity. These findings establish ESCRT dysfunction as a multifaceted contributor to MND pathogenesis and identify TSG101, CHMP2B, and VPS4a as mechanistically distinct therapeutic targets warranting preclinical validation.

neuroscience↗

bioRxiv2026

Causes and consequences of unawareness (anosognosia) of tool-action errors after left-hemisphere stroke

Many individuals with limb apraxia after left-hemisphere stroke exhibit a lack of awareness of their tool-related action errors, i.e., unawareness of apraxia (UA; also called anosognosia of apraxia). Little is known about the prevalence of UA, the relationship between UA and apraxia severity, or its underlying mechanisms. Here, we assessed both the causes and consequences of UA. Based on a mechanistic model, we hypothesized that UA may arise because of deficits in representations signaling how tool-related movements should look and feel - a component of action knowledge - and that degradation of this knowledge impedes the detection of mismatches between planned and actual tool-related actions. We further predicted that a consequence of UA is a reduction in error-correction attempts. Fifty-six individuals with chronic LCVA gestured to show how to use tools. Immediately after the gesture production task, participants were asked if they made any errors. All participants also completed an action knowledge task to measure the integrity of tool-related movement goals. Individuals were denoted as exhibiting UA if they performed below a normative cutoff for apraxia yet reported making no errors. Our sample included 21 individuals with apraxia; of these, nearly half (48%) exhibited UA. These two groups made a comparable number of gesture errors and were of equivalent stroke severity, yet individuals with UA had significantly more impaired action knowledge. Additionally, individuals with UA were less likely to attempt to correct their errors compared to individuals who were aware of their apraxia. These data are consistent with the hypothesis that action knowledge (how tool actions look and feel) serves a key role in error detection and awareness of apraxia and may contribute to the difficulties with everyday tasks experienced by many people with apraxia. Abbreviated SummaryThibault et al. show that individuals who are unaware of their tool-use errors (unawareness of apraxia) are selectively impaired at representing how tool-related movements look and feel (action knowledge). Action knowledge may be a central component for the detection of tool-use errors made by individuals with apraxia in everyday tasks. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/715610v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@a935beorg.highwire.dtl.DTLVardef@1075db2org.highwire.dtl.DTLVardef@987485org.highwire.dtl.DTLVardef@109fc62_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

neuroscience↗

bioRxiv2026

A stem cell secretome delays functional decline and supresses inflammation in two distinct models of neurodegeneration.

Alzheimers disease (AD) is a progressive neurodegenerative disorder with a rapidly increasing global prevalence. Current pharmacological interventions offer symptomatic relief but do not modify disease progression. Secretome-based therapeutics have emerged as a potential disease-modifying strategy, given their capacity to influence multiple pathological pathways, including amyloid burden, reactive gliosis, and neuronal survival. Early clinical studies support the safety and potential efficacy of these approaches, indicating mechanisms involving neuroprotection, neurodegeneration, and modulation of neuroinflammation, processes central to AD pathology. In the present study, we investigated the therapeutic efficacy of multipotent stromal cell (MSC)-derived secretomes produced by a specific platform (Secretomix) in two distinct mouse models of neurodegenerative disease: An AD model characterized by amyloid pathology, and a motor neurone disease (MND) model exhibiting TDP-43 protein aggregation. Administration of the MSC secretome resulted in a positive modulation of the behavioural phenotype in the AD model, and reduction in the rate of decline of motor co-ordination (attenuated the progression of motor deficits) in the MND model. In the latter, these functional benefits were accompanied by a measurable reduction in neuroinflammatory responses but without direct alteration of standard neuropathological markers. Additionally, ex vivo assays using human peripheral blood demonstrated broad anti-inflammatory activity of the MSC secretome, providing a potential mechanistic basis for the in vivo observations. Collectively, these findings support further investigation of MSC-derived secretomes as a promising therapeutic approach for neurodegenerative disorders, with relevance across proteinopathies characterised by distinct molecular pathways. Significance StatementHere we demonstrate the efficacy of a stem cell secretome in ameliorating cognitive and behavioural phenotypes in different models of neurodegeneration. These models represent distinct neuropathological features that are unaffected by stem cell secretome treatment but share common features of modulation of inflammation post stem cell secretome treatment. This study highlights the therapeutic potential of stem cell secretomes in the treatment of neurodegenerative conditions with an already existing neuropathology.

neuroscience↗

bioRxiv2025

Evaluation of Engineering Potential in Undomesticated Microbes with VECTOR

Genetic engineering research has predominantly focused on well-characterized organisms like Escherichia coli and Bacillus subtilis, with methods that often fail to translate to other microorganisms. This limitation presents a significant challenge, particularly given the increasing isolation of large microbial collections through high-throughput culturomics. In response, we developed a scalable, high-throughput pipeline to evaluate the engineerability of diverse microbial community members we named VECTOR (Versatile Engineering and Characterization of Transferable Origins and Resistance). We utilized a library of vectors with the Bacterial Expression Vector Archive (BEVA) architecture that included combinations of three antibiotic resistance genes, and three broad host range origins of replication (pBBR1, RK2 and RSF1010) or the restricted host range R6K with an integrative mariner transposon. We tagged each vector with green fluorescent protein and a unique nucleotide barcode. The resulting plasmids were delivered en masse to libraries of undomesticated microbes from plant microbiomes in workflows designed to evaluate their ability to be engineered. Utilizing OD600 and relative fluorescence measurements, we were able to monitor genetic cargo transfer in real time, indicating successfully engineered strains. Next-generation sequencing of plasmid molecular barcodes allowed us to identify specific vector architectures that worked well in particular bacterial strains from a large community. Modifications to the procedure facilitated isolation of engineered microbes. Our results underscore the potential of this approach to rapidly develop toolkits for the efficient engineering of a wide range of cultivatable microorganisms. ImportanceUndomesticated, cultured microbial strains contain a largely untapped reservoir of genetic potential for synthetic biology, and are increasingly being utilized in synthetic communities for microbial ecology research or biotechnology.. However, these strains often have unique physiological or ecological characteristics that make them difficult to engineer using traditional methods. Current approaches are often restricted by inefficient plasmid delivery and integration, which stifles progress in unlocking the promise of undomesticated strains. Our research addresses this challenge by developing VECTOR (Versatile Engineering and Characterization of Transferable Origins and Resistance), a scalable, high-throughput pipeline that utilizes modular vectors and efficient engineering workflows to identify host range and improve plasmid uptake. By optimizing plasmid architectures and pooling them for simultaneous screening across a range of bacterial strains, VECTOR enhances engineering efficiency and opens new avenues for advancements in biotechnology.

synthetic biology↗

bioRxiv2024

BEVA2.0: Modular Assembly of Golden Gate-Compatible Vectors with Expanded Utility for Genetic Engineering

This expansion for the modular vector assembly platform BEVA (Bacterial Expression Vector Archive) introduces 11 new BEVA parts including two new cloning site variants, two new antibiotic resistance modules, three new origins of replication, and four new accessary modules. As a result, the modular system is now doubled in size and expanded in its capacity to produce diverse replicating plasmids. Furthermore, it is now amenable to genetic engineering methods involving genome-manipulation of target strains through deletions or integrations. In addition to introducing the new modules, we provide several BEVA-derived Golden Gate cloning plasmids that are used to validate parts and that may be useful for genetic engineering of proteobacteria and other bacteria. We also introduce new parts to allow compatibility with the CIDAR MoClo parts libraries.

synthetic biology↗

bioRxiv2024

Miniscope Recording Calcium Signals at Hippocampus of Mice Navigating an Odor Plume

Mice navigate an odor plume with a complex spatiotemporal structure in the dark to find the source of odorants. This article describes a protocol to monitor behavior and record Ca2+ transients in dorsal CA1 stratum pyramidale neurons in hippocampus (dCA1) in mice navigating an odor plume in a 50 cm x 50 cm x 25 cm odor arena. An epifluorescence miniscope focused through a GRIN lens imaged Ca2+ transients in dCA1 neurons expressing the calcium sensor GCaMP6f in Thy1-GCaMP6f mice. The paper describes the behavioral protocol to train the mice to perform this odor plume navigation task in an automated odor arena. The methods include a step-by-step procedure for the surgery for GRIN lens implantation and baseplate placement for imaging GCaMP6f in CA1. The article provides information on real-time tracking of the mouse position to automate the start of the trials and delivery of a sugar water reward. In addition, the protocol includes information on using of an interface board to synchronize metadata describing the automation of the odor navigation task and frame times for the miniscope and a digital camera tracking mouse position. Moreover, the methods delineate the pipeline used to process GCaMP6f fluorescence movies by motion correction using NorMCorre followed by identification of regions of interest with EXTRACT. Finally, the paper describes an artificial neural network approach to decode spatial paths from CA1 neural ensemble activity to predict mouse navigation of the odor plume. SUMMARYThis protocol describes how to investigate the brain-behavior relationship in hippocampal CA1 in mice navigating an odor plume. This article provides a step-by-step protocol, including the surgery to access imaging of the hippocampus, behavioral training, miniscope GCaMP6f recording and processing of the brain and behavioral data to decode the mouse position from ROI neural activity.

neuroscience↗

bioRxiv2023

PI4KIII3β inhibition reduces rhinovirus associated cell shedding and ciliary dysfunction

BackgroundPatients with chronic obstructive pulmonary disease (COPD) experience respiratory exacerbations, many of which are associated with rhinoviruses. Current treatment strategies do not target the pathogenic rhinovirus trigger. Research questionWhat is the immediate effect of rhinovirus on the ciliated respiratory epithelium and can viral replication and epithelial toxicity be reduced by targeted PI4KIII{beta} inhibition. MethodsShort (24h) and longer (7 days) rhinovirus infection were explored in primary ciliated airway epithelial cultures from multiple healthy and COPD patients using high-speed video microscopy, viral titration assays and immunofluorescence studies. Ciliated epithelial cultures were pre-treated with a PI4KIII{beta} (GSK533) blocker prior to infection to assess efficacy against rhinovirus. Cytokine and chemokine production were assessed by multiplex immunoassays. ResultsWithin hours of infection rhinovirus co-localised with ciliated cells causing extensive apoptosis-associated shedding of predominantly ciliated cells within 24 hours. Viral replication that peaked at day 1 and cleared by day 7, was associated with dramatic loss of ciliated cells confirmed by reduced ciliary activity and ciliary DNAI2 protein expression. Ciliary beat frequency (CBF) of remaining cilia was significantly reduced by day 7 in cultures from COPD. Infection was partly dependent on PI4KIII{beta} with the GSK533 blocker reducing viral replication while preserving ciliary activity. High levels of pro-inflammatory mediators were secreted by infected cells. ConclusionDecreased ciliation due to rhinovirus infection is likely to impair mucociliary clearance in healthy individuals and COPD patients, contributing to the pathophysiology of COPD exacerbations. PI4KIII{beta} inhibition blocks viral replication, helping to preserve ciliary activity. Take home messageRhinovirus replication in the healthy and COPD respiratory epithelium is mediated by PI4KIII{beta} and intracellular PI4P platform formation. Inhibition of PI4KIII{beta} reduced viral replication and ciliated cell loss.

cell biology↗

bioRxiv2023

Gesture profiles distinguish primary progressive aphasia variants

Primary progressive aphasia (PPA) is a neurodegenerative syndrome characterized by progressive language deficits. There are three main variants of PPA - semantic (svPPA), logopenic (lvPPA), and nonfluent (nfvPPA) - that can be challenging to distinguish. Limb praxis may also be affected in PPA, but it is unclear whether different variants of PPA are associated with differences in gesture production. Prior research with neurotypical individuals indicates that the left temporal lobe is a critical locus of manipulable object and hand posture representations. Moreover, when imitating gestures, individuals whose strokes include the left temporal lobe show reduced benefit of gesture meaning and disproportionate impairment in hand posture as compared to arm kinematics. We tested the hypothesis that svPPA - who typically exhibit primarily temporal lobe atrophy - would differentially show these expected patterns of gesture imitation performance. Nineteen participants with PPA completed meaningful and meaningless gesture imitation tasks, and performance was scored for hand posture and arm kinematics accuracy. Generalized logistic mixed-effect regression models controlling for dementia severity showed overall benefits from gesture meaning, and greater impairments in hand posture than arm kinematics. We also found that svPPA participants were the most impaired in gesture imitation overall. Critically, there was also a significant three-way interaction of group, meaning, and gesture component: only svPPA participants showed relative impairments of hand posture for meaningful gestures as well as meaningless gestures. Thus, unlike lvPPA and nfvPPA, the hand postures of svPPA failed to benefit from gesture meaning. This research extends prior findings on the role of the temporal lobe in hand posture representations associated with manipulable objects, and is the first to indicate that there may be distinct gesture imitation patterns as a function of PPA variant. Characterizing componential gesture deficits in PPA may help to inform differential diagnosis, compensatory communication strategies, and cognitive praxis models of PPA.

neuroscience↗

bioRxiv2022

Genetic architecture and evolution of color variation in American black bears

Color variation is a frequent evolutionary substrate for camouflage in small mammals but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus, exhibits a range of colors including the cinnamon morph which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (P < 10-13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that impaired protein localization and decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos, but is not fixed across the range. HIGHLIGHTSO_LIThe cinnamon morph of American black bears and brown bears have different missense mutations in TYRP1 that account for their similar coloration C_LIO_LITYRP1 variants in American black bears and brown bears are loss-of-function alleles associated with impaired protein localization to melanosomes C_LIO_LIIn American black bears, the variant causing the cinnamon morph arose 9,360 years ago in the western lineage where it provides an adaptive advantage, and has spread northwards and eastwards by migration C_LI

evolutionary biology↗

bioRxiv2022

COVID-19 vaccine booster induces a strong CD8+ T cell response against Omicron variant epitopes in HLA-A*02:01+ individuals

The >30 mutated residues in the Omicron spike protein have led to its rapid classification as a new SARS-CoV-2 variant of concern. As a result, Omicron may escape from the immune system, decreasing the protection provided by COVID-19 vaccines. Preliminary data shows a weaker neutralizing antibody response to Omicron compared to the ancestral SARS-CoV-2 virus, which can be increased after a booster vaccine. Here, we report that CD8+ T cells can recognize Omicron variant epitopes presented by HLA-A*02:01 in both COVID-19 recovered and vaccinated individuals, even 6 months after infection or vaccination. Additionally, the T cell response was stronger for Omicron variant epitopes after the vaccine booster. Altogether, T cells can recognize Omicron variants, especially in vaccinated individuals after the vaccine booster. One-Sentence SummaryCD8+ T cells response against Omicron variant epitopes is stronger after the vaccine booster.

immunology↗

bioRxiv2019

A neural network for online spike classification that improves decoding accuracy

Separating neural signals from noise can improve brain-computer interface performance and stability. However, most algorithms for separating neural action potentials from noise are not suitable for use in real time and have shown mixed effects on decoding performance. With the goal of removing noise that impedes online decoding, we sought to automate the intuition of human spike-sorters to operate in real time with an easily tunable parameter governing the stringency with which spike waveforms are classified. We trained an artificial neural network with one hidden layer on neural waveforms that were hand-labeled as either spikes or noise. The network output was a likelihood metric for each waveform it classified, and we tuned the networks stringency by varying the minimum likelihood value for a waveform to be considered a spike. Using the networks labels to exclude noise waveforms, we decoded remembered target location during a memory-guided saccade task from electrode arrays implanted in prefrontal cortex of rhesus macaque monkeys. The network classified waveforms in real time, and its classifications were qualitatively similar to those of a human spike-sorter. Compared to decoding with threshold crossings, in most sessions we improved decoding performance by removing waveforms with low spike likelihood values. Furthermore, decoding with our networks classifications became more beneficial as time since array implantation increased. Our classifier serves as a feasible preprocessing step, with little risk of harm, that could be applied to both offline neural data analyses and online decoding. New & NoteworthyWhile there are many spike-sorting methods that isolate well-defined single units, these methods typically involve human intervention and have inconsistent effects on decoding. We used human classified neural waveforms as training data to create an artificial neural network that could be tuned to separate spikes from noise that impaired decoding. We found that this network operated in real time and was suitable for both offline data processing and online decoding.

neuroscience↗

bioRxiv2018

Human primary astrocytes increase basal fatty acid oxidation following recurrent low glucose to maintain intracellular nucleotide levels

Hypoglycemia is a major barrier to good glucose control in type 1 diabetes and frequent exposure to hypoglycemia can impair awareness to subsequent bouts of hypoglycemia. The neural changes that occur to reduce a persons awareness of hypoglycemia are poorly defined. Moreover, the molecular mechanisms by which glial cells contribute to hypoglycemia sensing and glucose counterregulation require further investigation. To test whether glia, specifically astrocytes, could detect changes in glucose, we utilized human primary astrocytes (HPA) and U373 astrocytoma cells and exposed them to recurrent low glucose (RLG) in vitro. This allowed measurement, with high specificity and sensitivity, of changes in cellular metabolism following RLG. We report that the AMP-activated protein kinase (AMPK) is activated over a pathophysiologically-relevant glucose concentration range. We observed an increased dependency on fatty acid oxidation for basal mitochondrial metabolism and hallmarks of mitochondrial stress including increased proton leak and reduced coupling efficiency. Relative to glucose availability, lactate release increased during low glucose but this was not modified by RLG, nor were glucose uptake or glycogen levels. Taken together, these data indicate that astrocyte mitochondria are dysfunctional following recurrent low glucose exposure, which could have implications for hypoglycemia glucose counterregulation and/or hypoglycemia awareness.

neuroscience↗