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bioRxiv, which is pronounced as "bio-archive," is a no-cost online platform where researchers can share and distribute unpublished preprints in the life sciences field.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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Male mice prefer to live on their own

1 week ago | biorxiv.org | Jennifer Davies |Megan Jackson |Justyna K. Hinchcliffe |Michael Mendl

AbstractAround the world, guidance for the management of laboratory mice recommends social housing (1-3). However, fighting in male mice represents a major animal welfare and scientific issue. Despite the risks of stress and injury and associated welfare costs of in-cage aggression, we currently prioritise group housing. In this study we first validated a trans-species behavioural biomarker of affective state for mice using a chronic corticosterone model of depression.
High-Throughput Multiomics Profiling of Model Systems Using the AVITI24 Platform

1 week ago | biorxiv.org | Tyler Lopez |Daniel Honigfort |Adeline Yen Mah |Connor Thompson

New Results High-Throughput Multiomics Profiling of Model Systems Using the AVITI24 Platform Tyler Lopez, Daniel Honigfort, Adeline Mah, Connor Thompson, Vivian Dien, Mariam Dawood, Eva Frankel, Derek Fuller, Claudia Jamison, Ryan Kelley, Jean Kwon, Yu Liu, Pin Ren, Sanchari Saha, Haosen Wang, Jennifer Wong, Da Zhao, Minna Abtahi, Andrew Altomare, Rosi Bajari, Ava Bellizzi, Sierra Bracamonte, Alex Bradfield, Colin Brown-Greaves, Chris Bui, Katia Charov, Rodger Constandse, Kim Cullion, West...
A bacterial CARD-NLR immune system controls the release of gene transfer agents

1 week ago | biorxiv.org | Emma Banks |Pavol Bardy |Ngat T. Tran |Phuong Nguyen |Phương Nguyên

AbstractBacteria have evolved a wide array of immune systems to detect and defend against external threats including mobile genetic elements (MGEs) such as bacteriophages, plasmids, and transposons. MGEs are often selfish, exploiting their bacterial hosts to propagate, however they can also provide adaptive advantages through horizontal gene transfer.
Medium-sized protein language models perform well at transfer learning on realistic datasets

1 week ago | biorxiv.org | Luiz Vieira |Morgan C. Handojo |Claus O. Wilke

AbstractProtein language models (pLMs) can offer deep insights into evolutionary and structural properties of proteins. While larger models, such as the 15 billion parameter model ESM-2, promise to capture more complex patterns in sequence space, they also present practical challenges due to their high dimensionality and high computational cost.
Drug screen reveals new potent host-targeted antivirals against Mpox virus

1 week ago | biorxiv.org | Vaithilingaraja Arumugaswami |Robert Damoiseaux |Ashok Kumar |Arjit Vijey Jeyachandran

AbstractMpox virus (MPXV), a re-emerging zoonotic threat, has caused outbreaks in non-endemic regions through respiratory, sexual, and close-contact transmission. The increased transmissibility of Clade IIb fueled the 2022 global outbreak, with 2024 Clade Ib spread in the Democratic Republic of Congo further escalating concern. Both outbreaks were declared public health emergencies by the WHO.
Peptidic tryptophan halogenation by a promiscuous flavin-dependent enzyme

1 week ago | biorxiv.org | Andrew Rice |Mayuresh G Gadgil |Paola Bisignano |Richard Stein

AbstractAmino acids undergo numerous enzymatic modifications. However, the broad applicability of amino acid-modifying enzymes for synthetic purposes is limited by narrow substrate scope and often unknown regulatory or accessory factor requirements. Here, we characterize ChlH, a flavin-dependent halogenase (FDH) from the chlorolassin biosynthetic gene cluster.
miRNA-mRNA network analysis identifies PAX5 as a potential regulator of adaptive immune response in COPD

1 week ago | biorxiv.org | Michele Gentili |Margherita De Marzio |Brian P. Hobbs |Craig P. Hersh

AbstractMicro-ribonucleic acids (miRNAs) are key post-transcriptional regulators of the immune system and may play a role in Chronic Obstructive Pulmonary Disease (COPD). In this paper, we constructed subject-specific miRNA-mRNA regulatory networks using bulk and deconvoluted whole blood RNA-sequencing, whole blood miRNA-sequencing, and B-cell receptor-sequencing data from up to 570 miRNAs, 11,859 mRNAs, and 3,190 participants in the COPDGene study.
Targeting the canonical ER stress IRE1α/XBP1 pathway counteracts pancreatic cancer-induced skeletal muscle wasting

1 week ago | biorxiv.org | Aniket Joshi |Anh Tuan Vuong |Bowen Xu |Ravi Singh

AbstractCancer-driven cachexia is a deleterious syndrome which involves progressive loss of skeletal muscle mass with or without fat loss, fatigue, and weakness that cannot be reversed by nutritional intake. Recent studies have shown deregulation of endoplasmic reticulum (ER)-induced unfolded protein response (UPR) pathways in skeletal muscles in various catabolic conditions, including cancer growth.
The epigenomic landscape of single vascular cells reflects developmental origin and identifies disease risk loci

1 week ago | biorxiv.org | Chad S. Weldy |Soumya Kundu |Joao Monteiro |Wenduo Gu

AbstractVascular sites have distinct susceptibility to atherosclerosis and aneurysm, yet the biological underpinning of vascular site-specific disease risk is largely unknown. Vascular tissues have different developmental origins that may influence global chromatin accessibility, and understanding differential chromatin accessibility, gene expression profiles, and gene regulatory networks (GRN) on single cell resolution may give key insight into vascular site-specific disease risk.
Multiomic clocks to predict phenotypic age in mice

1 week ago | biorxiv.org | Daniel Vera |Patrick Griffin |David Leigh |Jason Kras

AbstractBiological age refers to a person's overall health in aging, as distinct from their chronological age. Diverse measures of biological age, referred to as clocks, have been developed in recent years and enable risk assessments, and an estimation of the efficacy of longevity interventions in animals and humans. While most clocks are trained to predict chronological age, clocks have been developed to predict more complex composite biological age outcomes, at least in humans.