Biology subjects

Hunter, J.

Publications and source records attributed to Hunter, J..

7 recordsLinked to original sources

bioRxiv2026

VesSynth: Tubes Are All You Need for Robust Cross-Scale Cross-Modal 3D Vessel Segmentation

The cerebral vasculature is central to brain function, with alterations linked to numerous cerebrovascular and neurological disorders. Yet, no single imaging modality can capture the entire cerebral vascular network in humans. Instead, an array of techniques are sensitized to different spatial scales, while trading off resolution for coverage. Magnetic Resonance Imaging (MRI) typically resolves only large pial vessels, while high-resolution microscopy allows micrometer-scale vessels to be mapped over limited spatial extents. These techniques must therefore be combined to obtain a complete mapping of the cerebral angioarchitecture, which underscores the need for automatic, cross-modal vessel segmentation. Here, we introduce VesSynth, a flexible vessel segmentation framework that achieves state-of-the-art accuracy across multiple modalities and spatial resolutions (MR, optical and X-ray imaging), despite being trained entirely on synthetic data. By enabling consistent vascular mapping across scales, this framework paves the way to comprehensive investigation of cerebrovascular organization and its role in health and disease.

bioengineering↗

bioRxiv2026

Early-Stage Corticostriatal Circuit Hyperactivity Impairs Cholinergic Function and Cognitive Flexibility in an Alzheimer's Model

Cognitive flexibility deficits are a hallmark of early-stage Alzheimers disease (AD), but the underlying circuit mechanisms remain poorly understood. Here, we show that the 5xFAD mouse model of AD neuropathology exhibited early deficits in instrumental reversal learning, indicating cognitive inflexibility preceding spatial memory deficits. This impairment was associated with excessive neuronal reactivation in the medial prefrontal cortex (mPFC) and dorsomedial striatum (DMS), key regions for goal-directed behavior. Electrophysiological recordings revealed that mPFC neurons in young 5xFAD mice were hyperexcitable and received elevated excitatory input. Moreover, the mPFC-to-direct pathway medium spiny neuron (dMSN) circuit and the dMSNs themselves were selectively hyperactive. These hyperactive dMSNs exerted increased inhibitory control over cholinergic interneurons (CINs) in the DMS, coinciding with reduced CIN firing and diminished striatal acetylcholine (ACh) release. Critically, sustained chemogenetic inhibition of the mPFC-to-DMS circuit in 5xFAD mice reduced cortical A{beta} accumulation, normalized glutamatergic transmission in both the mPFC and DMS, restored striatal ACh levels, and rescued reversal learning deficits. Together, these findings identify a hyperactive mPFC-to-DMS circuit that disrupts corticostriatal and cholinergic signaling, contributing to cognitive inflexibility in 5xFAD mice. Targeting this circuit may offer a therapeutic strategy to preserve cognitive function in the early stages of AD. HighlightsO_LI5xFAD mice exhibit early cognitive deficits in instrumental reversal learning. C_LIO_LImPFC neurons and corticostriatal circuits are hyperactive, while cholinergic neurons are hypoactive in 5xFAD mice. C_LIO_LISustained inhibition of mPFC-to-DMS circuit hyperactivity normalizes glutamatergic transmission and slows A{beta} accumulation in 5xFAD mice. C_LIO_LISustained inhibition of the mPFC-to-DMS circuit rescues reversal learning deficits in 5xFAD mice. C_LI

neuroscience↗

bioRxiv2024

End of preservation normothermic machine perfusion of porcine kidneys after ischaemic injury reprograms metabolism and induces fibrosis after transplant despite unchanged function: insights from the renal proteome.

Normothermic machine perfusion (NMP) after initial hypothermic preservation of donor kidneys prior to transplantation is becoming a clinical reality, but the precise molecular mechanisms through which the graft is impacted remain only partially characterised. Using an unbiased proteomic methodology, we found that auto transplantation of is chaemically injured porcine kidneys resulted in an activation of the stress response 14 days after transplantation, as well as in selective changes in the proteins responsible for the metabolism of organic acids. The addition of 4 hours of NMP at the end of organ preservation (endNMP) resulted in coordinated changes to the renal proteome at 14 days when compared with the effect of transplant after preservation by hypothermic machine perfusion alone: most notably increased fibrosis and widespread additional reprogramming of metabolism. These findings were supported by intersection with single cell transcriptomics data which suggested an enrichment of proteins predominantly expressed in fibroblasts in kidneys with end of preservation NMP 14 days post-transplant compared to healthy kidneys. Our data showed that the addition of endNMP to existing preservation strategies resulted in a different molecular phenotype after transplantation, despite unchanged filtration function. In addition to potentially conferring benefits, NMP may also result in potentially detrimental molecular changes and thus protocols should be carefully evaluated to derive optimal clinical outcomes.

physiology↗

bioRxiv2022

Integrating inflammatory biomarker analysis and artificial intelligence-enabled image-based profiling to identify drug targets for intestinal fibrosis

Intestinal fibrosis is a common complication of several enteropathies with inflammatory bowel disease being the major cause. The progression of intestinal fibrosis may lead to intestinal stenosis and obstruction. Even with an increased understanding of tissue fibrogenesis, there are no approved treatments for intestinal fibrosis. Historically, drug discovery for diseases like intestinal fibrosis has been impeded by a lack of screenable cellular phenotypes. Here we applied Cell Painting, a scalable image-based morphology assay, augmented with machine learning algorithms to identify small molecules that were able to morphologically reverse the activated fibrotic phenotype of intestinal myofibroblasts under pro-fibrotic TNF stimulus. In combination with measuring CXCL10, a common pro-inflammatory cytokine in intestinal fibrosis, we carried out a high-throughput small molecule chemogenomics screen of approximately 5000 compounds with known targets or mechanisms, which have achieved clinical stage or approval by the FDA. Through the use of two divergent analytical methods, we identified several compounds and target classes that are potentially able to treat intestinal fibrosis. The phenotypic screening platform described here represents significant improvements in identifying a wide range of drug targets over conventional methods by integrating morphological analyses and artificial intelligence using pathologically-relevant cells and disease-relevant stimuli.

pharmacology and toxicology↗

bioRxiv2020

HIV cell-to-cell spread slows evolution of drug resistance

Many enveloped viruses such as HIV have evolved to transmit by two infection modes: cell-free infection and cell-to-cell spread. Cell-to-cell spread is highly efficient as it involves directed viral transmission from the infected to the uninfected cell. In contrast, cell-free infection relies on chance encounters between the virion and cell. Despite the higher efficiency of cell-to-cell spread, there is substantial transmission by cell-free infection in conjunction with cell-to-cell spread. A possible reason is that cell-free infection offers a selective advantage by increasing sensitivity to factors interfering with infection, hence accelerating evolution of resistance relative to cell-to-cell spread alone. Here we investigated whether a combination of cell-free infection and cell-to-cell spread confers a selective advantage in experimental evolution to an antiretroviral drug. We maintained HIV infection using coculture of infected with uninfected cells in the face of moderate inhibition by the reverse transcriptase inhibitor efavirenz. We tested the effect on the rate of drug resistance evolution of replacing one coculture infection cycle with an infection cycle involving cell-free infection only, and observed earlier evolution of drug resistance mutations to efavirenz. When we increased selective pressure by adding a second reverse transcriptase inhibitor, emtricitabine, infection with the cell-free step consistently evolved multidrug resistance to both drugs and was able to replicate. In contrast, infection without a cell-free step mostly failed to evolve multidrug resistance. Therefore, HIV cell-to-cell spread decreases the ability of HIV to rapidly evolve resistance to inhibitors, which is conferred by cell-free infection. Author summaryCell-to-cell spread of HIV differs from cell-free, diffusion-based HIV infection in that viral transmission is directed from the infected to the uninfected cell through cellular interactions. Cell-to-cell spread has been recognized as a highly efficient infection mode that is able to surmount inhibition by antibodies and antiretroviral drugs. However, the effect of HIV cell-to-cell spread on the rate of evolution of viral resistance to infection inhibitors has not been studied. Here we used experimental evolution to investigate the effect of cell-to-cell spread versus cell-free infection on the emergence of drug resistance mutations to one or a combination of antiretroviral drugs. We found that replacing one infection cycle in experimental evolution with cell-free infection, where the filtered supernatant from infected cells, but not the cellular fraction, is used as the viral source, results in more rapid evolution of resistance. The consequences are that multidrug resistance consistently evolves with a cell-free viral cycle, but not when infection is solely by coculture of infected and uninfected cells. A possible consequence is that in environments where HIV cell-to-cell spread may predominate and some residual viral replication occurs in the face of ART, the emergence of drug resistance mutations would be delayed.

evolutionary biology↗

bioRxiv2018

Temporal Control of Transcription by Zelda in living Drosophila embryos

Abstract/introPioneer factors have the exquisite ability to engage their target sites at nucleosomal DNA, which leads to a local remodeling of chromatin and the establishment of a transcriptional competence. However, the direct impact of enhancer priming by pioneer factors on the temporal control of gene expression and on mitotic memory remains elusive. In Drosophila embryos, the maternally deposited activator Zelda (Zld) exhibits key pioneer factor properties and indeed regulates the awakening of the zygotic genome. The analysis of thousands of endogenous Zld bound regions in various genetic contexts, as well as the study of isolated synthetic enhancers with static approaches, led to the proposal that Zld could act as a quantitative developmental timer. Here we employ quantitative live imaging methods and mathematical modeling to directly test the effect of Zld on temporal coordination in gene activation and on mitotic memory. Using an automatic tracking software, we quantified the timing of activation in hundreds of nuclei and their progeny in Drosophila embryos. We demonstrate that increasing the number of Zld binding sites accelerates the kinetics of transcriptional activation regardless of their past transcriptional state. In spite of its known pioneering activities, we show that Zld is not a mitotic bookmarker and is neither necessary nor sufficient to foster mitotic memory. Fluorescent recovery after photo-bleaching and fluorescent correlation spectroscopy experiments reveal that, Zld is highly dynamic and exhibits transient binding to chromatin. We propose that Zld low binding rates could be compensated for by local accumulation of Zld in nuclear microenvironments in vivo, thus allowing rapid and coordinated gene activation.

developmental biology↗

bioRxiv2017

Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death

HIV has been reported to be cytotoxic in vitro and in lymph node infection models. Using a computational approach, we found that partial inhibition of transmission which involves multiple virions per cell could lead to increased numbers of live infected cells if the number of viral DNA copies remains above one after inhibition, as eliminating the surplus viral copies reduces cell death. Using a cell line, we observed increased numbers of live infected cells when infection was partially inhibited with the antiretroviral efavirenz or neutralizing antibody. We then used efavirenz at concentrations reported in lymph nodes to inhibit lymph node infection by partially resistant HIV mutants. We observed more live infected lymph node cells, but with fewer HIV DNA copies per cell, relative to no drug. Hence, counterintuitively, limited attenuation of HIV transmission per cell may increase live infected cell numbers in environments where the force of infection is high.

bioinformatics↗