Biology subjects

Wilson, C. G.

Publications and source records attributed to Wilson, C. G..

14 recordsLinked to original sources

bioRxiv2026

Endogenous subthreshold noise and PIP2 tune diastolic coherence across the intact sinoatrial node through stochastic resonance

The heartbeat originates in the sinoatrial (SA) node, where spontaneously firing pacemaker myocytes interact to generate a coherent rhythm. The classical entrainment account is deterministic: the fastest cells entrain the rest, and variability is an error term that coupling suppresses. We proposed previously that the node instead exploits its own noise through stochastic resonance, with rhythm quality peaking at intermediate fluctuation amplitude, and since mapped a metabolic gradient capable of supplying it. Two-photon imaging of the voltage sensor ASAP5 in the intact mouse node resolved the subthreshold regime that tissue-scale mapping averages away. Diastolic coherence followed an inverted-U against endogenous noise amplitude in both poles, with optima 3.5-fold apart, and each pole operated near its own. {beta}-adrenergic stimulation raised noise in both poles to a common level. The inferior pole, which began below its optimum, gained coherence, while the superior pole, already at its optimum, lost interval regularity. Blocking HCN-mediated If with ivabradine lowered superior coherence without changing superior noise, and lowered inferior noise without lowering inferior coherence, dissociating the two coordinates. Thus, coherence is a surface defined by noise and coupled-clock drive. Phosphoinositide 4,5-bisphosphate (PIP2), an ATP-dependent lipid cofactor for HCN channels, increased firing rate and noise in both poles but improved coherence only in the energy-poor inferior node. Prior If block abolished that rescue. Pacemaking is therefore graded by a bioenergetic supply chain that sets the noise, not by entrainment alone. Noise, long treated as a nuisance to be averaged away, is an active ingredient of the pacemaker.

physiology↗

bioRxiv2026

Barrier Immune Memory is Promoted by Intestinal Epithelial Cell Presentation of Injected Bacterial Antigens

The contributions of antigen compartmentalization to recognition differences between CD4 and CD8 T cells have long been appreciated, but little is known of how subcellular localization of different antigens expressed by a single pathogen impacts T cell immunity. By tracking a clonal CD4 T cell response to its cognate epitope shuttled between different virulence proteins of the enteropathogenic bacterium, Citrobacter rodentium (Cr), we find a remarkable bias in the magnitude and quality of the response contingent on whether antigen remains bacterially associated or is introduced into intestinal epithelial cells colonized by the bacterium. Only proteins injected into the cytosol of colonocytes via the type 3 secretion system (T3SS) of Cr were found to recruit robust antigen-specific T cell responses to the infected mucosa and give rise to CD4 resident memory T (Trm) cells that populate the mucosal epithelium--and this required direct presentation of these antigens by infected epithelial cells. Single-cell transcriptomic analyses revealed that sustained, bidirectional epithelial-T cell communication was required both to elicit epithelial barrier-protective T cell help and to promote transcriptional networks that program a tissue-residency rather than central memory fate. These results establish a central role for antigen presentation by non-professional APCs in controlling memory fate decisions by CD4 T cells, with important implications for development of successful mucosal vaccines.

immunology↗

bioRxiv2025

Detecting and quantifying rare sex in natural populations

The distinction between sexual and asexual reproduction is fundamental to eukaryotic evolution. Testing theories about the evolution of reproductive modes first requires knowing whether sex is present or absent in a population. While this seems straightforward, the literature on asexuality reflects a history of shifting claims and uncertainty regarding reproductive mode, especially where sex is potentially rare or cryptic. Here, we develop a new framework to address the challenges in detecting and quantifying sexual reproduction from population genomic data. We first show that commonly calculated population genetic statistics do not reliably distinguish sexual and obligate asexual scenarios if asexuality is accompanied by sex-independent homologous recombination, as emerging evidence indicates is often the case. We then present a new method to quantify the relationship between evolutionary trees and mode of reproduction by classifying local trees for pairs of diploid individuals using ancestral recombination graphs (ARGs). This approach accurately discriminates signatures of genetic exchange and homologous recombination, though some uncertainty remains because of unavoidable biases in the steps needed to reconstruct trees from genome data. We introduce new statistics and simulation models to account for common reconstruction biases and demonstrate their utility by uncovering contrasting reproductive histories in the facultatively sexual budding yeast Saccharomyces cerevisiae. This approach offers the potential for improved quantitative inference of reproductive modes that can readily be extended to a broad range of eukaryotes. Significance StatementDetermining how often, if at all, organisms have sex has implications across biology. Studies often use population genomic data to interrogate the private life of putative asexuals, but the results prove surprisingly inconclusive. We develop a framework to address the challenges in detecting and quantifying rates of sex. New simulation models show how sex-independent recombination, which occurs widely across a range of asexual eukaryotes, causes genetic patterns to resemble sexual populations even when sex is absent. An approach based on ancestral recombination graphs (ARGs) and classification of local trees accounts for these problems and quantifies the remaining uncertainty due to inevitable reconstruction biases. Our framework will enable improved inferences of reproductive mode across a wide range of eukaryotes.

evolutionary biology↗

bioRxiv2025

An Open-Source Image Analysis Method for Quantifying Reporter Fluorescence

Image analysis is a rapidly developing field that provides unique opportunities to characterize and quantify spatial information in images. We study cis-regulatory modules (CRMs), non-coding DNA regions that regulate gene expression, during development using fluorescent reporters in vivo. Characterizing CRM activity during development presents challenges including image segmentation into biologically relevant regions of interest that are not easily distinguishable via common segmentation methods, fluorophore band passing, and variable transfection undermine standardized analysis. To quantify and compare CRM activity levels, we compiled an open-source computer vision tool stack in the form of a Python-based Jupyter notebook and tested four analysis methods to assess their efficacy in quantifying CRM expression in limb development. This Jupyter notebook provides a reproducible, standardized workflow that can be adapted to numerous image analysis applications.

developmental biology↗

bioRxiv2024

Expandable, Functional Hepatocytes Derived from Primary Cells Enable Liver Therapeutics

Liver disease affects millions annually in the United States, with orthotopic transplantation as the only curative option for many patients. However, the scarcity of donor organs highlights a need for alternative cell-based therapies. Hepatocyte-based approaches are promising due to the cells inherent synthetic, metabolic, and detoxifying functions, but they face critical barriers, including the lack of a scalable source of functional hepatocytes and poor engraftment. In this study, we developed a scalable process for expanding primary human hepatocytes (PHHs) while preserving their identity and function. By leveraging heterocellular aggregation with stromal cells, we generated cryopreserved "seed" constructs that maintained viability and function post-thaw. Seeds demonstrated enhanced metabolic and detoxification functions and robust engraftment across multiple anatomic sites outside of the liver. Our approach addresses key limitations of hepatocyte-based therapies, offering a stable, scalable, and clinically viable platform for liver cell therapy applications.

bioengineering↗

bioRxiv2023

A novel subset of colonocytes targeted by Citrobacter rodentium elicits epithelial MHCII-restricted help from CD4 T cells

Interleukin (IL)-22 plays a non-redundant role in immune defense of the intestinal barrier1-3. We recently discovered an indispensable role for T cells, but not ILCs, in sustaining IL-22 signaling required for protection of colonic crypts against invasion during infection by the enteropathogen, Citrobacter rodentium (C.r)4. However, identification of the intestinal epithelial cell (IEC) subsets targeted by T cell-derived IL-22 and how T cell-derived IL-22 sustains activation in IECs are undefined. Here, we identify a novel subset of absorptive IECs in the mid-distal colon that are differentially targeted by C.r and are differentially responsive to IL-22 signaling. Importantly, MHCII expression by these colonocytes was required to elicit T cell-activated IL-22 signaling necessary to resist C.r invasion. Our findings explain the basis for the regionalization of the host response to C.r and demonstrate that epithelial cells must elicit MHCII-dependent help from IL-22-producing T cells to orchestrate immune protection in the intestines.

immunology↗

bioRxiv2023

COVID-19 and silent hypoxemia in a minimal closed-loop model of the respiratory rhythm generator

Silent hypoxemia, or happy hypoxia, is a puzzling phenomenon in which patients who have contracted COVID-19 exhibit very low oxygen saturation (SaO2 < 80%) but do not experience discomfort in breathing. The mechanism by which this blunted response to hypoxia occurs is unknown. We have previously shown that a computational model (Diekman et al., 2017, J. Neurophysiol) of the respiratory neural network can be used to test hypotheses focused on changes in chemosensory inputs to the central pattern generator (CPG). We hypothesize that altered chemosensory function at the level of the carotid bodies and/or the nucleus tractus solitarii are responsible for the blunted response to hypoxia. Here, we use our model to explore this hypothesis by altering the properties of the gain function representing oxygen sensing inputs to the CPG. We then vary other parameters in the model and show that oxygen carrying capacity is the most salient factor for producing silent hypoxemia. We call for clinicians to measure hematocrit as a clinical index of altered physiology in response to COVID-19 infection.

physiology↗

bioRxiv2021

Bdelloid rotifers use hundreds of horizontally acquired genes against fungal pathogens

Obligately asexual lineages are typically rare and short-lived. According to one hypothesis, they adapt too slowly to withstand relentlessly coevolving pathogens. Bdelloid rotifers seem to have avoided this fate, by enduring millions of years without males or sex. We investigated whether bdelloids unusual capacity to acquire non-metazoan genes horizontally has enhanced their resistance to pathogens. We found that horizontally transferred genes are three times more likely than native genes to be upregulated in response to a natural fungal pathogen. This enrichment was twofold stronger than that elicited by a physical stressor (desiccation), and the genes showed little overlap. Among hundreds of upregulated non-metazoan genes were RNA ligases putatively involved in resisting fungal toxins and glucanases predicted to bind to fungal cell walls, acquired from bacteria. Our results provide evidence that bdelloids mitigate a predicted challenge of long-term asexuality in part through their ability to acquire and deploy so many foreign genes.

evolutionary biology↗

bioRxiv2020

Evolutionary dynamics of transposable elements in bdelloid rotifers

Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates where males are thus far unknown. Contrary to expectations, we find a diverse range of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms, but we report that bdelloids share a large and unusual expansion of genes involved in RNAi-mediated TE suppression. This suggests that enhanced cellular defence mechanisms might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.

evolutionary biology↗

bioRxiv2020

Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex

DHTKD1 is the E1 component of the 2-oxoadipic acid dehydrogenase complex (OADHc), which functions in the L-lysine degradation pathway. Mutations in DHTKD1 have been associated with 2-aminoadipic and 2-oxoadipic aciduria, Charcot-Marie-Tooth disease type 2Q (CMT2Q) and eosinophilic esophagitis (EoE). A crystal structure and inhibitors of DHTKD1 could improve the understanding of these clinically distinct disorders, but are currently not available. Here we report the identification of adipoylphosphonic acid and tenatoprazole as DHTKD1 inhibitors using targeted and high throughput screening, respectively. We furthermore elucidate the DHTKD1 crystal structure with thiamin diphosphate bound at 2.1 [A]. The protein assembles as a dimer with residues from both monomers contributing to cofactor binding. We also report the impact of ten DHTKD1 missense mutations on the encoded proteins by enzyme kinetics, thermal stability and structural modeling. Some DHTKD1 variants displayed impaired folding (S777P and S862I), whereas other substitutions rendered the enzyme inactive (L234G, R715C and R455Q) or affected the thermal stability and catalytic efficiency (V360A and P773L). Three variants (R163Q, Q305H and G729R) surprisingly showed wild type like properties. Our work provides a structural basis for further understanding of the function of DHTKD1 and a starting point for selective small molecule inhibitors of the enzyme, which could help tease apart the role of this enzyme in several human pathologies.

biochemistry↗

bioRxiv2019

Size, not temperature, drives cyclopoid copepod predation of invasive mosquito larvae

During range expansion, invasive species can experience new thermal regimes. Differences between the thermal performance of local and invasive species can alter species interactions, including predator-prey interactions. The Asian tiger mosquito, Aedes albopictus, is a known vector of several viral diseases of public health importance. It has successfully invaded many regions across the globe and currently threatens to invade regions of the UK where conditions would support seasonal activity. We assessed the functional response and predation efficiency (percentage of prey consumed) of the cyclopoid copepods Macrocyclops albidus and Megacyclops viridis from South East England, UK against newly-hatched French Ae. albopictus larvae across a relevant temperature range (15, 20, and 25{degrees}C). Predator-absent controls were included in all experiments to account for background prey mortality. We found that both M. albidus and M. viridis display type II functional response curves, and that both would therefore be suitable biocontrol agents in the event of an Ae. albopictus invasion in the UK. No significant effect of temperature on the predation interaction was detected by either type of analysis. However, the predation efficiency analysis did show differences due to predator species. The results suggest that M. viridis would be a superior predator against invasive Ae. albopictus larvae due to the larger size of this copepod species, relative to M. albidus. Our work highlights the importance of size relationships in predicting interactions between invading prey and local predators.

ecology↗

bioRxiv2019

Adipocyte JAK2 mediates aging-associated metabolic liver disease and progression to hepatocellular carcinoma

Non-alcoholic fatty liver disease (NAFLD) and steatohepatitis (NASH) are liver manifestations of the metabolic syndrome and can progress to hepatocellular carcinoma (HCC). Loss of Growth Hormone (GH) signaling is reported to predispose to NAFLD and NASH through direct actions on the liver. Here, we report that aged mice lacking hepatocyte Jak2 (JAK2L), an obligate transducer of Growth Hormone (GH) signaling, spontaneously develop the full spectrum of phenotypes found in patients with metabolic liver disease, beginning with insulin resistance and lipodystrophy and manifesting as NAFLD, NASH and even HCC, independent of dietary intervention. Remarkably, insulin resistance, metabolic liver disease, and carcinogenesis are prevented in JAK2L mice via concomitant deletion of adipocyte Jak2 (JAK2LA). Further, we demonstrate that GH increases hepatic lipid burden but does so indirectly via signaling through adipocyte JAK2. Collectively, these data establish adipocytes as the mediator of GH-induced metabolic liver disease and carcinogenesis. In addition, we report a new spontaneous model of NAFLD, NASH, and HCC that recapitulates the natural sequelae of human insulin resistance-associated disease progression. The work presented here suggests a attention be paid towards inhibition of adipocyte GH signaling as a therapeutic target of metabolic liver disease.

physiology↗

bioRxiv2017

Comparative genomics of bdelloid rotifers: evaluating the effects of asexuality and desiccation tolerance on genome evolution

Bdelloid rotifers are microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasized desiccation as the cause of several unusual genomic features in this group. Here, we evaluate the relative effects of asexuality and desiccation tolerance on genome evolution by comparing whole genome sequences for three bdelloid species: Adineta ricciae (desiccation tolerant), Rotaria macrura and Rotaria magnacalcarata (both desiccation intolerant) to the only published bdelloid genome to date, that of Adineta vaga (also desiccation tolerant). We find that tetraploidy is conserved among all four bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is low, well within the range observed between alleles in obligately sexual, diploid animals. In addition, we find that homologous regions in A. ricciae are largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. These findings are contrary to current understanding of the role of desiccation in shaping the bdelloid genome, and indicate that various features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous findings of high levels of horizontally transferred non-metazoan genes encoded in both desiccating and non-desiccating bdelloid species, and show that this is a unique feature of bdelloids among related animal phyla. Comparisons within bdelloids and to other desiccation-tolerant animals, however, again call into question the purported role of desiccation in horizontal transfer.

evolutionary biology↗

bioRxiv2017

Evidence for "inter- and intraspecific horizontal genetic transfers" between anciently asexual bdelloid rotifers is explained by cross-contamination

Bdelloid rotifers are microscopic invertebrates thought to have evolved for millions of years without sexual reproduction. They have attracted the attention of biologists puzzled by the maintenance of sex among nearly all other eukaryotes. Bdelloid genomes have an unusually high proportion of horizontally acquired non-metazoan genes. This well-substantiated finding has invited speculation that homologous horizontal transfer between rotifers also may occur, perhaps even 'replacing' sex. A 2016 study in Current Biology claimed to supply evidence for this hypothesis. The authors sampled rotifers of the genus Adineta from natural populations and sequenced one mitochondrial and four nuclear loci. For several samples, species assignments were incongruent among loci, which the authors interpreted as evidence of \"interspecific genetic exchanges\". Here, we use sequencing chromatograms supplied by the authors to demonstrate that samples treated as individuals actually contained two or more divergent mitochondrial and ribosomal sequences, indicating contamination with DNA from additional animals belonging to the supposed \"donor species\". We also show that \"exchanged\" molecules share only 75% sequence homology, a degree of divergence incompatible with established mechanisms of recombination and genomic features of Adineta. These findings are parsimoniously explained by cross-contamination of tubes with animals or DNA from different species. Given the proportion of tubes contaminated in this way, we show by calculation that evidence for \"intraspecific horizontal exchange\" in the same dataset is explained by contamination with conspecific DNA. On the clear evidence of these analyses, the 2016 study provides no reliable support for the hypothesis of horizontal genetic transfer between or within these bdelloid species.

evolutionary biology↗