Biology subjects

Thompson, C.

Publications and source records attributed to Thompson, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Correlative In Situ Cryo-ET Reveals Cellular and Viral Remodeling Associated with Selective HIV-1 Core Nuclear Import

Lentiviruses like HIV-1 infect non-dividing cells by traversing the nuclear pore, but studying this process has been challenging due to its scarcity and dynamic nature in infected cells. Here, we developed a robust cell-permeabilization system that recapitulates HIV-1 nuclear import and established an integrated cryo-correlative workflow combining cryo-CLEM, cryo-FIB, and cryo-ET for targeted imaging of this process. These advancements enabled the successful capture of 1,899 HIV-1 cores at various stages of nuclear import. Statistical and structural analyses of native wild-type and mutant cores revealed that HIV-1 nuclear import depends on both capsid elasticity and nuclear pore adaptability, as well as nuclear factors such as CPSF6. Brittle cores fail to enter the nuclear pore complex (NPC), while CPSF6-binding-deficient cores stall inside the NPC, resulting in impaired nuclear import. Intriguingly, nuclear pores function as selective filters favoring the import of smaller, tube-shaped cores. Our study opens new avenues for dissecting the biochemistry and structural biology of HIV-1 nuclear import as well as downstream events including core uncoating and potentially integration, with unprecedented detail.

microbiology↗

bioRxiv2025

Using The Cancer Genome Atlas from cBioPortal to Develop Genomic Datasets for Machine Learning Assisted Cancer Treatment

Predicting the impact of genetic mutations is crucial for understanding diseases like cancer. Polymorphism Phenotyping (PolyPhen) and Sorting Intolerant From Tolerant (SIFT) are key tools for assessing how amino acid substitutions affect protein function and mutation pathogenicity. To our knowledge, no ready-to-use genomic dataset exists for prediction models to identify potentially harmful mutations, which could support research and clinical decisions. This study develops genomic and non-genomic datasets using The Cancer Genome Atlas (TCGA) from cBioPortal and applies machine learning models to predict PolyPhen and SIFT scores. We explore three classification models: Random Forest (RF), Extreme Gradient Boosting (XGBoost), and an ensemble RF-XGBoost model. Experimental results show that genomic data yields more accurate predictions than non-genomic data. The ensemble RF-XGBoost model performs best on genomic data, achieving average accuracies of 88.43% for PolyPhen and 95.13% for SIFT, highlighting the potential of artificial intelligence in genetic mutation analysis for disease treatment.

genomics↗

bioRxiv2025

Astrocyte Ca2+ activity regulates node of Ranvier length in the white matter

Nodes of Ranvier generate action potentials along myelinated axons, but it is unclear whether they can modulate neural circuit function. Computer modelling previously predicted that adjusting node length can control axonal conduction speed1, but it is unknown whether mechanisms controlling nodal structure operate in the healthy brain. Here, in brain slices and in intact white matter tracts of live mice, we found that nodes elongate and shorten, while an overall stable mean node length is maintained. Changes in node length were only detected in nodes that were flanked by compact myelin sheaths and, in brains of juvenile mice, neuronal activity caused the nodes to elongate. This occurred via astrocyte Ca2+-mediated adenosine generation, targeting myelin sheath A2b receptors which raised oligodendrocyte cyclic AMP levels. This activated NKCC1 cotransporters present in the myelin of the paranodes flanking the nodes, the expression of which was higher in the brains of juvenile mice compared to adults. NKCC1 activation elevated the membrane conductance of the myelin sheaths and reduced the length of the paranodal ends of the internodes, which was associated with node elongation that is predicted to slow action potential propagation. Thus, nodal dynamics may continuously tune information flow along myelinated axons and drive activity-dependent white matter plasticity.

neuroscience↗

bioRxiv2025

Linage priming and cell type proportioning depends on the interplay between stochastic and deterministic factors

Isogenic cells can break symmetry and adopt different fates, even when exposed to a seemingly identical environment. This deeply conserved phenomenon allows unicellular organisms to pre-empt dynamically changing environments and is central to the evolution of multicellularity. It is thought that cells are primed towards different lineages by cell-cell variation, although the underlying mechanisms are poorly understood. To address this, we exploit the tractability of the social amoeba Dictyostelium discoideum, where cell fate choice also does not depend on spatial cues. We develop and test a model to explain quantitative experimental single cell observations of probabilistic differentiation. The model suggests that cell cycle position affects lineage choice, as previously shown, but that stochastic cell-cell variation also plays a key role. Single cell sequencing reveals genes that exhibit cell type specific expression or genes that affect fate choice exhibit extensive stochastic cell-cell expression variation. Like lineage priming genes in ESCs, they are associated with specific epigenetic modifications, which when perturbed affect their expression and disrupt fate choice. We suggest the integration of stochastic and deterministic inputs represents an adaptive mechanism to increase developmental robustness against perturbations that affect deterministic signals.

developmental biology↗

bioRxiv2024

Novel symbionts reveal amoebae as significant hosts for environmental chlamydiae

Chlamydiae represent a diverse group of obligate intracellular bacteria with elusive hosts in environmental settings. This study used one of the largest collections of wild amoebae (Dictyostelium discoideum and D. giganteum, 106 clones) collected over the past two decades to screen for novel environmental chlamydiae. We found that novel environmental chlamydiae are prevalent in two wild Dictyostelium species and assembled 42 novel chlamydiae metagenome-assembled genomes (MAGs). The MAGs represent three chlamydiae species previously only reported using 16S sequencing. Their genomes are divergent enough from other species to warrant placing them in two new genera (tentatively called Ca. Dictychlamydia sp. LF1, Ca. Dictychlamydia sp. LF2, and Ca. Feichlamydia sp. LF3). In addition, these chlamydiae species show strong host specificity with two Dictyostelium amoeba hosts, except one amoeba sample. Ca. Dictychlamydia sp. LF1 and Ca. Feichlamydia sp. LF3 was exclusively observed in D. discoideum, while Ca. Dictychlamydia sp. LF2 was found only in D. giganteum. Phylogenetic and comparative genomic analyses suggest that all three chlamydiae are close to arthropod-associated chlamydiae and likely have some intermediate characteristics between previously reported amoeba-associated and vertebrate-associated chlamydiae. This study significantly broadens our understanding of the chlamydial host range and underscores the role of amoebae as vital hosts for environmental chlamydiae.

microbiology↗

bioRxiv2023

A highly resolved multiplex network reveals the structural role of insects and plants in terrestrial food webs

Comparative studies suggest remarkable similarities among food webs across habitats, including systematic changes in their structure with diversity and complexity (scale-dependence). However, historic aboveground terrestrial food webs (ATFWs) have coarsely grouped plants and insects such that these webs are generally small, and herbivory is disproportionately underrepresented compared to vertebrate predator-prey interactions. Furthermore, terrestrial herbivory is thought to be structured by unique processes compared to size-structured feeding in other systems. Here, we present the richest ATFW to date, including [~]580,000 feeding links among [~]3,800 taxonomic species, sourced from [~]27,000 expert-vetted interaction records annotated as feeding upon one of six different resource types: leaves, flowers, seeds, wood, prey, and carrion. By comparison to historical ATFWs and null ecological hypotheses, we show that our temperate forest web displays a potentially unique structure characterized by two properties: a) a large fraction of carnivory interactions dominated by a small number of hyper-generalist, opportunistic bird and bat predators, and b) a smaller fraction of herbivory interactions dominated by a hyper-rich community of insects with variably-sized but highly-specific diets. We attribute our findings to the large-scale, even resolution of vertebrate, insect, and plant guilds in our food web.

ecology↗

bioRxiv2023

Serial Lift-Out - Sampling the Molecular Anatomy of Whole Organisms

Cryo-focused ion beam milling of frozen-hydrated cells and subsequent cryo-electron tomography (cryo-ET) has enabled the structural elucidation of macromolecular complexes directly inside cells. Application of the technique to multicellular organisms and tissues, however, is still limited by sample preparation. While high-pressure freezing enables the vitrification of thicker samples, it prolongs subsequent preparation due to increased thinning times and the need for extraction procedures. Additionally, thinning removes large portions of the specimen, restricting the imageable volume to the thickness of the final lamella, typically < 300 nm. Here, we introduce Serial Lift-Out, an enhanced lift-out technique that increases throughput and obtainable contextual information by preparing multiple sections from single transfers. We apply Serial Lift-Out to C. elegans L1 larvae yielding a cryo-ET dataset sampling the worms anterior-posterior axis and resolve its ribosome structure to 7 [A], illustrating how Serial Lift-Out enables the study of multicellular molecular anatomy.

biophysics↗

bioRxiv2023

A local ATR-dependent checkpoint pathway is activated by a site-specific replication fork block in human cells

When replication forks encounter DNA lesions that cause polymerase stalling a checkpoint pathway is activated. The ATR-dependent intra-S checkpoint pathway mediates detection and processing of sites of replication fork stalling to maintain genomic integrity. Several factors involved in the global checkpoint pathway have been identified, but the response to a single replication fork barrier (RFB) is poorly understood. We utilized the E.coli-based Tus-Ter system in human MCF7 cells and showed that the Tus protein binding to TerB sequences creates an efficient site-specific RFB. The single fork RFB was sufficient to activate a local, but not global, ATR-dependent checkpoint response that leads to phosphorylation and accumulation of DNA damage sensor protein {gamma}H2AX, confined locally to within a kilobase of the site of stalling. These data support a model of local management of fork stalling, which allows global replication at sites other than the RFB to continue to progress without delay.

molecular biology↗

bioRxiv2023

Microbiome induced complement synthesized in the gut protects against enteric infections

Canonically, complement is a serum-based host defense system that protects against systemic microbial invasion. Little is known about the production and function of complement components on mucosal surfaces. Here we show gut complement component 3 (C3), central to complement function, is regulated by the composition of the microbiota in healthy humans and mice, leading to host-specific gut C3 levels. Stromal cells in intestinal lymphoid follicles (LFs) are the predominant source of intestinal C3. During enteric infection with Citrobacter rodentium or enterohemorrhagic Escherichia coli, luminal C3 levels increase significantly and are required for protection. C. rodentium is remarkably more invasive to the gut epithelium of C3-deficient mice than of wild-type mice. In the gut, C3-mediated phagocytosis of C. rodentium functions to clear pathogens. Our study reveals that variations in gut microbiota determine individuals intestinal mucosal C3 levels, dominantly produced by LF stromal cells, which directly correlate with protection against enteric infection. HighlightsO_LIGut complement component 3 (C3) is induced by the microbiome in healthy humans and mice at a microbiota-specific level. C_LIO_LIGut stromal cells located in intestinal lymphoid follicles are a major source of luminal C3 C_LIO_LIDuring enteric infections with Citrobacter rodentium or enterohemorrhagic Escherichia coli, gut luminal C3 levels increase and are required for protection. C_LIO_LIC. rodentium is significantly more invasive of the gut epithelium in C3-deficient mice when compared to WT mice. C_LIO_LIIn the gut, C3-mediated opsonophagocytosis of C. rodentium functions to clear pathogens. C_LI

immunology↗

bioRxiv2022

Plasmid manipulation of bacterial behaviour through translational regulatory crosstalk

Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator controlling the host proteome through direct interaction with host mRNAs and interference with the hosts translational regulatory network. This mRNA interference leads to largescale proteomic changes in metabolic genes, key regulators and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle. Significance StatementPlasmids are recognised for their important role in bacterial evolution as drivers of horizontal gene transfer. Less well understood are the effects of plasmids upon bacterial behaviours by manipulating the expression of key bacterial phenotypes. Until now, examples of plasmid manipulation of their bacterial hosts were limited to highly targeted transcriptional control of a few related traits. In contrast, here we describe the first plasmid global translational regulator evolved to control the bacterial behavioural switch from a motile to a sessile lifestyle and bacterial metabolism, mediated through manipulation of the bacterial proteome. Moreover, this global translational regulator is common across divergent plasmids in a wide range of bacterial host taxa, suggesting that plasmids may commonly control bacterial lifestyle in the clinic, agricultural fields, and beyond.

microbiology↗

bioRxiv2022

Endocytosis at Extremes: Formation and Internalization of Giant Clathrin-coated Pits Under Elevated Membrane Tension

Internalization of clathrin-coated vesicles from the plasma membrane constitutes the major endocytic route for receptors and their ligands. Dynamic and structural properties of endocytic clathrin coats are regulated by the mechanical properties of the plasma membrane. Here, we used conventional fluorescence imaging and multiple modes of structured illumination microscopy (SIM) to image formation of endocytic clathrin coats within live cells and tissues of developing fruit fly embryos. High resolution in both spatial and temporal domains allowed us to detect and characterize distinct classes of clathrin-coated structures. For the first time, we show that membrane tension induces formation of giant coated pits (GCPs) that can be up to two orders of magnitude larger than the canonical clathrin-coated pits. GCPs take longer to form but their mechanism of curvature generation is the same as the canonical pits. We also demonstrate that GCPs can split into smaller fragments during internalization. Considering the supporting roles played by actin filament dynamics in clathrin-mediated endocytosis under mechanically stringent conditions, we suggest that local changes in the coat curvature driven by actin machinery can drive splitting and internalization of GCPs.

biophysics↗

bioRxiv2021

Single Cell Enhancer Activity Maps Neuronal Lineages in Embryonic Mouse Basal Ganglia

Enhancers integrate transcription factor signaling pathways that drive cell fate specification in the developing brain. We used single cell RNA-sequencing (scRNA-seq) to capture enhancer activity at single cell resolution and delineate specification of cells labeled by enhancers in mouse medial, lateral, and caudal ganglionic eminences (MGE, LGE, and CGE) at embryonic day (E)11.5. We combine enhancer-based reporter labeling with single-cell transcriptional readout to characterize enhancer activity and define cell populations in vivo. Seven enhancers had diverse activities in specific progenitor and neuronal populations within the GEs. We then applied enhancer-based labeling, scRNA-seq, and analysis of in situ hybridization (ISH) data to distinguish subtypes of MGE-derived GABAergic and cholinergic projection neurons and interneurons. This work demonstrates how the power of scRNA-seq can be extended by enhancer-based labelling and leveraging ISH data and reveals novel lineage specification paths underlying patterning of developing mouse brain.

neuroscience↗

bioRxiv2020

Transcriptional Network Orchestrating Regional Patterning of Cortical Progenitors

We uncovered a transcription factor (TF) network that regulates cortical regional patterning. Screening the expression of hundreds of TFs in the developing mouse cortex identified 38 TFs that are expressed in gradients in the ventricular zone (VZ). We tested whether their cortical expression was altered in mutant mice with known patterning defects (Emx2, Nr2f1 and Pax6), which enabled us to define a cortical regionalization TF network (CRTFN). To identify genomic programming underlying this network, we performed TF ChIP-seq and chromatin-looping conformation to identify enhancer-gene interactions. To map enhancers involved in regional patterning of cortical progenitors, we performed assays for epigenomic marks and DNA accessibility in VZ cells purified from wild-type and patterning mutant mice. This integrated approach has identified a CRTFN and VZ enhancers involved in cortical regional patterning.

neuroscience↗

bioRxiv2020

High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States

SARS-CoV-2 is constantly evolving. Prior studies have focused on high case-density locations, such as the Northern and Western metropolitan areas in the U.S. This study demonstrates continued SARS-CoV-2 evolution in a suburban Southern U.S. region by high-density amplicon sequencing of symptomatic cases. 57% of strains carried the spike D614G variant. The presence of D614G was associated with a higher genome copy number and its prevalence expanded with time. Four strains carried a deletion in a predicted stem loop of the 3 untranslated region. The data are consistent with community spread within the local population and the larger continental U.S. No strain had mutations in the target sites used in common diagnostic assays. The data instill confidence in the sensitivity of current tests and validate "testing by sequencing" as a new option to uncover cases, particularly those not conforming to the standard clinical presentation of COVID-19. This study contributes to the understanding of COVID-19 by providing an extensive set of genomes from a non-urban setting and further informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the U.S.

microbiology↗

bioRxiv2020

Pleiotropy-guided transcriptome imputation from normal and tumor tissues identifies new candidate susceptibility genes for breast and ovarian cancer

Familial, genome-wide association (GWAS), and sequencing studies and genetic correlation analyses have progressively unraveled the shared or pleiotropic germline genetics of breast and ovarian cancer. In this study, we aimed to leverage this shared germline genetics to improve the power of transcriptome-wide association studies (TWAS) to identify candidate breast cancer and ovarian cancer susceptibility genes. We built gene expression prediction models using the PrediXcan method in 681 breast and 295 ovarian tumors from The Cancer Genome Atlas and 211 breast and 99 ovarian normal tissue samples from the Genotype-Tissue Expression project and integrated these with GWAS meta-analysis data from the Breast Cancer Association Consortium (122,977 cases/105,974 controls) and the Ovarian Cancer Association Consortium (22,406 cases/40,941 controls). The integration was achieved through novel application of a pleiotropy-guided conditional/conjunction false discovery rate approach for the first time in the setting of a TWAS. This identified 14 new candidate breast cancer susceptibility genes spanning 11 genomic regions and 8 new candidate ovarian cancer susceptibility genes spanning 5 genomic regions at conjunction FDR < 0.05 that were > 1 Mb away from known breast and/or ovarian cancer susceptibility loci. We also identified 38 candidate breast cancer susceptibility genes and 17 candidate ovarian cancer susceptibility genes at conjunction FDR < 0.05 at known breast and/or ovarian susceptibility loci. Overlaying candidate causal risk variants identified by GWAS fine mapping onto expression prediction models for genes at known loci suggested that the association for 55% of these genes was driven by the underlying GWAS signal. SignificanceThe 22 new genes identified by our cross-cancer analysis represent promising candidates that further elucidate the role of the transcriptome in mediating germline breast and ovarian cancer risk.

genetics↗

bioRxiv2020

Abundance and Distribution of Heterelmis cf. glabra (Coleoptera: Elmidae) within Dolan Falls Preserve and the Devils River State Natural Area, Texas, USA

The Devils River watershed in south-central Texas has baseflows entirely attributable to groundwater primarily sourced from the Edwards-Trinity and Edwards Aquifers. The largest known populations of a species of riffle beetle, Heterelmis cf. glabra, are located in springs associated with the upper Devils River. The focus of this study was to 1) determine site-level abundances of H. cf. glabra using open system N-mixture models, 2) test mesohabitat associations of members in the riffle beetle family Elmidae and, 3) measure and examine abiotic and habitat associations for adult and larval beetles within the study area. We sampled 32 spring sources to determine occupancy and abundance of adult and larval riffle beetles (Elmidae) within the study area. Spring sources were mapped and categorized by type (orifice, upwelling, group of springs, or seep). Basic water chemistry and flow rate categorization were also performed at each site. Model results suggest that rainfall, flow and site are important for detection of H. cf. glabra. Based on our results, regular monitoring of these 32 sites using these methods, is recommended to conduct hypotheses tests on covariates influencing abundance. Such baseline information will be important in measuring impacts to this and other spring-associated species as the habitats of this region are impacted by natural or anthropogenic phenomena.

ecology↗

bioRxiv2019

Equilin does not affect thyroid hormone signaling in the developing Xenopus laevis tadpole brain

Toxcast/Tox21 is a massive federally run research effort dedicated to better understanding the potential toxicity of thousands of compounds in a high throughput manner. Among this list of compounds is equilin, an estrogen-like compound that was flagged as a potential thyroid hormone agonist. Here we examine if equilin acts like a thyroid hormone agonist on cellular and molecular mechanisms of brain development in Xenopus laevis tadpoles. To examine the effect of equilin, tadpoles were divided into eight groups and received 4 days of exposure. The experimental groups were as follows: 1 L, 10 L, and 100 L of equilin, 1 L, 10M, and 100 M of 17-{beta} estradiol as an estrogen control, 15 g/mL thyroxine (T4) as a thyroid hormone control, and a no-exposure control. After 4 days of treatment, animals were treated with CldU to label dividing cells for 2hr and then euthanized in MS-222. After fixation, body length was measured and the brains dissected out. IHC was performed on brains for CldU to label proliferating neural progenitor cells. Brains were then whole-mounted and analyzed using confocal microscopy. We found that equilin did not increase the number of dividing progenitor cells in a T4-like manner. Instead, equilin decreased proliferation in a dose-dependent manner, as did estradiol. The same paradigm was performed separately staining for caspase-3 and h2ax, finding that equilin increased cell death in contrast to CNTL and T4. In another experiment, RNA was extracted from tadpole brains in each group and qPCR was performed to assess change in expression of thyroid hormone-sensitive genes, Equilin did not affect gene expression in a thyroid hormone-like manner. Our data indicate that equilin does not act as a thyroid hormone agonist in the Xenopus laevis nervous system but instead acts similarly to estradiol. Our data strongly suggest that equilin is not a TH disruptor, contrary to the findings of the ToxCast/Tox21 dataset.

neuroscience↗

bioRxiv2019

REMI-seq: Development of methods and resources for functional genomics in Dictyostelium

Genomes can be sequenced with relative ease, but ascribing gene function remains a major challenge. Genetically tractable model systems are crucial to meet this challenge. One powerful model is the social amoeba Dictyostelium discoideum, a eukaryotic microbe widely used to study diverse questions in cell, developmental and evolutionary biology. However, its utility is hampered by the inefficiency with which sequence, transcriptome or proteome variation can be linked to phenotype. To address this, we have developed methods (REMI-seq) to (1) generate a near genome-wide resource of individual mutants (2) allow large-scale parallel phenotyping. We demonstrate that integrating these resources allows novel regulators of cell migration, phagocytosis and macropinocytosis to be rapidly identified. Therefore, these methods and resources provide a step change for high throughput gene discovery in a key model system, and the study of genes affecting traits associated with higher eukaryotes.

genomics↗