bioRxiv

bioRxiv, which is pronounced as "bio-archive," is a no-cost online platform where researchers can share and distribute unpublished preprints in the life sciences field. This service is managed by Cold Spring Harbor Laboratory, a non-profit organization focused on research and education. By uploading their preprints to bioRxiv, authors can quickly share their discoveries with the scientific community and gather feedback on their draft manuscripts before they submit them to academic journals.

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Unbiased recording of clonal potency reveals species-specific regulation of mammalian intestine

1 week ago | biorxiv.org | Mirazul Islam |Matthew Bechard |Yilin Yang |Alan Simmons

AbstractThe mammalian intestine regenerates rapidly after damage, yet the clonal dynamics and species-specific regulation of different populations remain poorly understood. Here we used synthetic or naturally occurring DNA alterations to reconstruct clonal histories of the mouse and human intestinal epithelium at single-cell resolution. In mice, we uncovered the clonal architecture of different cell types and their roles in regeneration, supporting a hierarchical regenerative response model.
SAMP-Score: A morphology-based machine learning classification method for screening pro-senescence compounds in p16 positive cancer cells

1 week ago | biorxiv.org | Ryan Wallis |Bethany Hughes |Madeleine Moore |Emily O'Sullivan

AbstractBackgroundSenescence identification is rendered challenging due to a lack of universally available biomarkers. This represents a bottleneck in efforts to develop pro-senescence therapeutics - agents designed to induce the arrest of cellular proliferation associated with a senescence response in cancer cells for therapeutic gain.
Prophage regulation of Shewanella fidelis 3313 motility and biofilm formation: implications for gut colonization dynamics in Ciona robusta

1 week ago | biorxiv.org | Ojas NATARAJAN |Susanne L Gibboney |Morgan Young |Shen Jean Lim

AbstractLysogens, bacteria with one or more viruses (prophages) integrated into their genomes, are abundant in the gut of animals. Prophages often influence bacterial traits; however, the influence of prophages on the gut microbiota-host immune axis in animals remains poorly understood. Here, we investigate the influence of the prophage SfPat on Shewanella fidelis 3313, a persistent member of the gut microbiome of the model marine tunicate, Ciona robusta.
A Thiopurine-like Mutagenic Process Defines TGCT Subtypes

1 week ago | biorxiv.org | Kevin Brown |Jun Zhong |Adriana Miranda |Mengyan Zhang

AbstractTesticular germ cell tumors (TGCTs) are the most common malignancy in young men, exhibit a unique developmental origin and exceptional chemosensitivity. However, the molecular distinctions between TGCT subtypes remain poorly understood. Here we present a comprehensive genomic analysis of 252 treatment-naive primary TGCTs, integrating deep whole-genome sequencing with matched transcriptomic and epigenomic data.
Duration of immunity following infection with moderately virulent ASFV

1 week ago | biorxiv.org | Virginia Friedrichs |Paul Deutschmann |Kerstin Wernike |Tessa Carrau

AbstractAfrican swine fever virus (ASFV) poses a significant threat to pork production and wild pig populations worldwide. The study assessed the long-term fate and immunity of animals recovering from a moderately virulent ASFV infection, following the principles of a duration of immunity study for live vaccines. Pigs inoculated with the moderately virulent ASFV strain 'Estonia14' largely developed mild clinical signs and only transient viremia.
Improved Allele Frequencies in gnomAD through Local Ancestry Inference

1 week ago | biorxiv.org | Pragati Kore |Michael Wilson |Grace Tiao |Katherine R Chao

AbstractThe Genome Aggregation Database (gnomAD) is a foundational resource for allele frequency data, widely used in genomic research and clinical interpretation. However, traditional estimates rely on individual-level genetic ancestry groupings that may obscure variation in recently admixed populations.
Methane-fed microbial communities enriched from field-grown rice support diverse heterotrophic bacteria

1 week ago | biorxiv.org | Elena Perry |Aqib Hasnain |Benjamin Cole |Hans K. Carlson

AbstractRice paddies naturally host significant populations of methanotrophs, due to the production of methane in flooded soils. However, relatively little is known about how the activity of these bacteria impacts the structure of the broader microbial community in this important agricultural environment. To address this question, we passaged 51 microbial aerobic enrichment cultures from rice rhizosphere, root, and stem samples in a chemically-defined medium with methane as sole electron donor.
Single-cell transcriptomics showed that maternal PCB exposure dysregulated ER stress-mediated cell type-specific responses in the liver of female offspring

1 week ago | biorxiv.org | Joe Lim |Youjun Suh |Xueshu Li |Rebecca Wilson

AbstractPolychlorinated biphenyls (PCBs) are persistent environmental toxicants that bioaccumulate in the food chain and readily cross the placenta, raising concerns for developmental toxicity. While PCB exposure has been associated with metabolic and neurodevelopmental disorders, its cell type-specific effects on liver development remain poorly understood.
Breast Cancer Clustering Integrating Complete Gene Expression Profiles and Genetic Ancestry

2 weeks ago | biorxiv.org | Johanna Stepanian |Alejandro Mejía-García |Carlos Orozco |Jorge Duitama

AbstractBreast cancer (BC) remains the leading cause of cancer-related mortality among women globally. Precise subtyping of BC is critical for optimizing treatment strategies. This study explored the capacity of bulk RNA-seq data to improve breast cancer characterization by analysis of complete expression profiles. We analyzed RNA-seq 274 tumor samples and six healthy tissue samples from diverse geographical origins.
Regulation of essential hepatocyte functions and identity by super-enhancers in health and disease

2 weeks ago | biorxiv.org | Tao Lin |Chenjun Huang |Chenhao Tong |Wentao Xu

AbstractPhysiologically, hepatocytes perform an estimated 500 essential liver functions to ensure systemic homeostasis. The mechanisms how hepatocytes maintain these numerous crucial functions in response to physiological and pathophysiological challenges are largely unknown. In this study, we found that vital liver function genes (e.g., HNF4A, ALB, coagulation factors, and SLC2A2) in hepatocytes possess super-enhancers.