Biology subjects

Chamberlain, M.

Publications and source records attributed to Chamberlain, M..

7 recordsLinked to original sources

bioRxiv2026

The Metabolome of Drosophila Reveals Exercise-Induced Stress and Anti-Inflammatory Response

Exercise is a known remedy for metabolic disorders, including obesity and type II diabetes. In humans and some model organisms, exercise is classified into different types and intensities based on the mode of exercise and the devices used. Since Drosophila has emerged as a model for exercise research, several devices have been developed for exercise training. These devices vary in mechanisms of operation; for example, the Power Tower (PT) uses a repeated drop-and-hit mechanism, and the TreadWheel (TW) uses end-over-end rotation. This variation in mechanisms that trigger the negative geotaxis of flies could impact exercise outcomes, and it remains unclear how this variation drives the response of flies to exercise training. Stress is a known response to exercise in humans and mice. Stress in Drosophila can be induced by various conditions, including heat, cold, chemical exposure, and other environmental stressors, but there is little information on exercise-induced stress. It is also unclear whether different devices elicit distinct stress responses or whether the exercise-induced stress response is similar to other stress responses (e.g., thermal, chemical). To explore the effects of device, sex, and genotype on multiple metabolic pathways, we used an untargeted metabolomics approach to further elucidate the molecular mechanisms of exercise. As no studies have directly examined the exercise metabolome of Drosophila, this study is the first to explore the metabolome of flies post-exercise. Our results revealed that exercising on different devices elicits varying responses and reshapes the metabolome of flies. We also identified specific small compounds that may be linked to stress and inflammatory response more in the PT-exercised flies than in the TW-exercised flies. Overall, the exercise device effect interacted with sex effect and genotype, such that male and female flies have different metabolite compositions post-exercise on TW and PT.

Molecular Biology↗

bioRxiv2025

Modeling human phenotypes in the nematode C. elegans during an undergraduate developmental biology course

Caenorhabditis elegans is a widely used model organism in biomedical research due to its genetic tractability, short life cycle, and conservation of many developmental processes with humans. In this study, undergraduate students conducted nine independent experiments during a Developmental Biology course to model human phenotypes using C. elegans. Each group selected a human phenotype of interest, identified a gene associated with the phenotype, and then determined the orthologous or homologous gene in C. elegans. By obtaining mutants and designing phenotypic assays, students investigated the extent to which the worm models could recapitulate aspects of the human condition. This collective work highlights both the potential and limitations of C. elegans as a model for human phenotypic variation and disease and demonstrates the value of undergraduate inquiry as a catalyst for scientific engagement and research-based learning.

scientific communication and education↗

bioRxiv2025

Role of RSPO3 in Estrogen-mediated Sex Differences in Body Fat Distribution: A Single-cell Data-driven Study

Obesity is a global health concern affecting more than one-third of the adult population worldwide. Epidemiological studies indicate that body fat distribution, more than overall adiposity, is a key risk factor for obesity-related diseases. Genome-wide association studies revealed that RSPO3 is associated with body fat distribution. Additionally, marked sex differences in body fat distribution are largely influenced by estrogen, suggesting that exploring the relationship between estrogen and RSPO3 expression may illuminate the mechanisms underlying the sexual dimorphism of fat distribution. We revisited a comprehensive set of gene expression data from humans and mice to explore these mechanisms. We assessed RSPO3 expression in male and female adipose tissues and utilized single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics to examine RSPO3s function within different tissues. Our findings confirmed significantly higher RSPO3 expression in male adipose tissue compared to female. Furthermore, our data for the first time suggest that estrogen plays a crucial role in fat distribution, as blocking estrogen signaling upregulates RSPO3 expression. In mouse liver, we observed a correlation between sex-specific ADK overexpression and RSPO3 expression, resulting in increased obesity and hepatocyte expansion via WNT/{beta}-catenin signaling in male mice. This study sheds light on how estrogen influences sexual dimorphism in fat distribution and underscores RSPO3s vital role in this process. These insights open new avenues for targeted therapeutic interventions addressing obesity and metabolic diseases with a focus on sex-specific factors.

bioinformatics↗

bioRxiv2023

The Septin Cytoskeleton is Required for Plasma Membrane Repair

Mammalian cells are frequently exposed to mechanical and biochemical stressors resulting in plasma membrane injuries. Repair mechanisms reseal the plasma membrane to restore homeostasis and prevent cell death. In the present work, a silencing RNA screen was performed to uncover plasma membrane repair mechanisms of cells exposed to a pore-forming toxin (listeriolysin O). This screen identified molecules previously known to repair the injured plasma membrane such as annexin A2 (ANXA2) as well as novel plasma membrane repair candidate proteins. Of the novel candidates, we focused on septin 7 (SEPT7) because the septins are an important family of conserved eukaryotic cytoskeletal proteins. Using diverse experimental approaches, we established for the first time that SEPT7 plays a general role in plasma membrane repair of cells perforated by pore-forming toxins and mechanical wounding. Remarkably, upon cell injury, the septin cytoskeleton is extensively redistributed in a Ca2+-dependent fashion, a hallmark of plasma membrane repair machineries. The septins reorganize into subplasmalemmal domains arranged as knob and loop (or ring) structures containing F-actin, myosin II, and annexin A2 (ANXA2) and protrude from the cell surface. Importantly, the formation of these domains correlates with the plasma membrane repair efficiency. Super-resolution microscopy shows that septins and actin are arranged in intertwined filaments associated with ANXA2. Silencing SEPT7 expression prevented the formation of the F-actin/myosin II/ANXA2 domains, however, silencing expression of ANXA2 had no observable effect on their formation. These results highlight the key structural role of the septins in remodeling the plasma membrane and in the recruitment of the repair molecule ANXA2. Collectively, our data support a novel model in which the septin cytoskeleton acts as a scaffold to promote the formation of plasma membrane repair domains containing contractile F-actin and annexin A2.

cell biology↗

bioRxiv2021

Cell type classification and discovery across diseases, technologies and tissues reveals conserved gene signatures and enables standardized single-cell readouts

Autoimmune diseases are a major cause of mortality1,2. Current treatments often yield severe insult to host tissue. It is hypothesized that improved "precision medicine" therapies will target pathogenic cells selectively and thus reduce or eliminate severe side effects, and potentially induce robust immune tolerance3. However, it remains challenging to systematically identify which cellular phenotypes are present in cellular ensembles. Here, we present a novel machine learning approach, Signac, which uses neural networks trained with flow-sorted gene expression data to classify cellular phenotypes in single cell RNA-sequencing data. We demonstrate that Signac accurately classified single cell RNA-sequencing data across diseases, technologies, species and tissues. Then we applied Signac to identify known and novel immune-relevant precision medicine candidate drug targets (n = 12) in rheumatoid arthritis. A full release of this workflow can be found at our GitHub repository (https://github.com/mathewchamberlain/Signac).

immunology↗

bioRxiv2019

An optimized workflow for single-cell transcriptomics and repertoire profiling of purified lymphocytes from clinical samples.

Establishing clinically relevant single-cell (SC) transcriptomic workflows from cryopreserved tissue is essential to move this emerging immune monitoring technology from the bench to the bedside. Improper sample preparation leads to detrimental cascades, resulting in loss of precious time, money and finally compromised data. There is an urgent need to establish protocols specifically designed to overcome the inevitable variations in sample quality resulting from uncontrollable factors in a clinical setting. Here, we explore sample preparation techniques relevant to a range of clinically relevant scenarios, where SC gene expression and repertoire analysis are applied to a cryopreserved sample derived from a small amount of blood, with unknown or partially known preservation history. We compare a total of ten cell-counting, viability-improvement, and lymphocyte-enrichment methods to highlight a number of unexpected findings. Trypan blue-based automated counters, typically recommended for single-cell sample quantitation, consistently overestimate viability. Advanced sample clean-up procedures significantly impact total cell yield, while only modestly increasing viability. Finally, while pre-enrichment of B cells from whole peripheral blood mononuclear cells (PBMCs) results in the most reliable BCR repertoire data, comparable T-cell enrichment strategies distort the ratio of CD4+ and CD8+ cells. Furthermore, we provide high-resolution analysis of gene expression and clonotype repertoire of different B cell subtypes. Together these observations provide both qualitative and quantitative sample preparation guidelines that increase the chances of obtaining high-quality single-cell transcriptomic and repertoire data from human PBMCs in a variety of clinical settings.

immunology↗

bioRxiv2019

Alternative transcription cycle for bacterial RNA polymerase

RNA polymerases (RNAPs) transcribe genes through a cycle of recruitment to promoter DNA, initiation, elongation, and termination. After termination, RNAP is thought to initiate the next round of transcription by detaching from DNA and rebinding a new promoter. We used single-molecule fluorescence microscopy to observe individual RNAP molecules after transcript release at a terminator. Following termination, RNAP almost always remained bound to DNA and sometimes exhibited one-dimensional sliding over thousands of basepairs. Unexpectedly, the DNA-bound RNAP often restarted transcription, usually in reverse direction, thus producing an antisense transcript. Furthermore, we report evidence of this \"secondary initiation\" in live cells, using genome-wide RNA sequencing. These findings reveal an alternative transcription cycle that allows RNAP to reinitiate without dissociating from DNA, which is likely to have important implications for gene regulation.

biophysics↗