Biology subjects

Zhu, C.

Publications and source records attributed to Zhu, C..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Long-read metagenomic sequencing reveals novel lineages and functional diversity in urban soil microbiome

City parks and other urban green spaces can bring significant benefits to the physical and mental health of city residents. However, there is limited knowledge about the microbial communities inhabiting these urban soils. Here, we applied long-read metagenomic sequencing to 58 urban soil samples from two major cities in China, enabling genome-resolved reconstruction of microbial diversity at unprecedented contiguity. We recovered 7,949 medium- and high-quality metagenome-assembled genomes, comprising 4,171 species-level genome bins, of which over 97% represent previously undescribed species. Long-read assemblies revealed extensive secondary metabolic capacity, including more than 30,000 biosynthetic gene clusters, which were highly contiguous compared with those from fragmented short-read assemblies. Beyond secondary metabolism, we uncovered over 2 million small protein families, including hundreds that are strongly enriched in the neighbourhood of defense systems and mobile genetic elements, highlighting their overlooked role in urban soils. These findings expand our understanding of the functional diversity of urban soil microbiomes and provide new insights with implications for urban public health.

bioinformatics↗

bioRxiv2026

CAPZ, but not canonical autophagy, regulates the endosomal-exosomal trafficking of plasma membrane PD-L1

Programmed death-ligand 1 (PD-L1) undergoes continuous endocytosis and intracellular trafficking that regulate its degradation, recycling, and exosomal release. Although PD-L1 internalization is known to depend on RAB5-mediated endocytosis, whether canonical autophagy contributes to its subsequent endosomal trafficking remains unclear. Here we show that the endosomal and exosomal trafficking of cell surface PD-L1 occurs independently of the canonical autophagy machinery. Genetic disruption of core autophagy components, including LC3B, ATG4B, ATG5, and ATG7, did not impair trafficking of internalized PD-L1 to early endosomes, multivesicular bodies, late endosomes, or extracellular vesicles. Pharmacologic inhibition of autophagosome-lysosome fusion enhanced accumulation of PD-L1 within RAB5-and CD63-positive compartments, but this effect persisted in cells lacking LC3B, ATG5, or ATG7, indicating that PD-L1 trafficking through the endosomal-exosomal pathway does not require canonical autophagy. Instead, we identify the actin-capping protein CAPZ as a key regulator of an endosomal maturation checkpoint that controls PD-L1 sorting. Loss of CAPZ impaired progression of PD-L1 from early to late endosomal compartments, reduced PD-L1 incorporation into multivesicular bodies and extracellular vesicles, and redirected PD-L1 toward RAB11-dependent recycling, resulting in increased plasma membrane PD-L1 abundance. These findings establish that PD-L1 membrane fate is determined by CAPZ-dependent endosomal maturation rather than canonical autophagy and identify endosomal trafficking machinery as a critical regulator of immune checkpoint distribution.

cell biology↗

bioRxiv2026

Heat stress-induced condensation of G3BP1 in perinuclear P-bodies in C. elegans' germline

Stress granules (SGs) are essential subcellular assemblies that enable cells to adapt to environmental stress, and their dynamic assembly and disassembly are critical for maintaining cellular homeostasis and reproductive capacity. However, the function and regulation of stress granules in germline cells remain mysterious. In this study, we characterized the function of GTBP-1, the homolog of human G3BP1, in response to heat stress in Caenorhabditis elegans and elucidated its regulation in stress granule dynamics. gtbp-1 mutants exhibit pronounced temperature-dependent biodirectional reproductive characteristics. At lower temperatures, their brood size is higher than that of wild-type animals, whereas at 25 {degrees}C they are completely sterile. GTBP-1 is diffusely distributed at normal culturing temperatures but forms perinuclear stress granules upon heat shock in the germline. While the NTF2 domain is essential for germline stress granule formation, other domains, including the IDR, RRM and RGG, are required for the recovery phase after heat shock. GTBP-1 stress granules colocalize with the P-bodies, but not with other germ granules. The depletion of P-bodies prohibited the perinuclear GTBP-1 stress granule formation. A combination of forward genetic screening together with RNAi-based candidate screening identified the P body components, the RNA helicase LAF-1, the SUMO protein SMO-1, and the mTOR pathway effector RSKS-1(S6K) as key regulators of GTBP-1 germline stress granule formation. Together, this work revealed that germline stress granules may be subjected to multiple layers of regulations and GTBP-1 may safeguards reproductive homeostasis under temperature stress by coordinating germline stress granule condensation. Author SummaryReproduction is particularly vulnerable to environmental stress, yet germ cells must remain functional to ensure fertility. How germ cells protect themselves under stressful conditions is still not well understood. In this study, we used the nematode Caenorhabditis elegans to examine how germ cells respond to heat stress, focusing on GTBP-1, a conserved protein involved in stress granule formation. We found that GTBP-1 plays contrasting roles depending on temperature: under normal conditions it restrains reproduction, whereas under heat stress it becomes essential for maintaining fertility. When animals are exposed to elevated temperature, GTBP-1 rapidly forms granules around the nuclei of germ cells, these granules assemble at sites occupied by processing bodies, another type of RNA-containing structure, revealing a close spatial relationship between two stress-responsive compartments. We also found that this process is regulated by conserved factors involved in RNA regulation and nutrient-responsive signaling. Together, our findings show how germ cells reorganize RNA-protein assemblies to preserve reproductive capacity under stressful conditions.

genetics↗

bioRxiv2026

Antibody Responses Against Coronaviruses in the Wuhan Population

Prolonged circulation of SARS-CoV-2 may broaden population-level neutralizing antibody responses to diverse coronaviruses; however, the extent of this breadth remains unclear. To address this gap, we assessed serum neutralizing activity in 869 individuals from Wuhan, China, including 78 pre-pandemic samples collected in 2017 and 791 post-pandemic samples obtained in 2025. Specifically, using pseudovirus neutralization assays, sera were tested against a panel of coronaviruses, including circulating SARS-CoV-2 Omicron subvariants XFG and NB.1.8.1. Neutralization was measured at a fixed dilution for all samples and by determination of 50% inhibitory dilution (ID50) for selected sera. In parallel, antigenic cartography and genetic distance analyses were applied to relate functional antigenic relationships to spike protein divergence. Our results showed that, compared with pre-pandemic sera, post-pandemic sera exhibited enhanced neutralizing activity against multiple sarbecoviruses and the merbecovirus MjHKU4r-CoV-1, with mean inhibition increases ranging from 1.7% to 76.5% at a 1:20 dilution. Notably, the largest increases from 51.8% to 76.5% were observed against clade 1b sarbecoviruses. In contrast, neutralizing activity against human alphacoronaviruses and MERS-CoV showed no meaningful enhancement. Moreover, neutralizing titers in post-pandemic sera were strongly correlated across sarbecoviruses, particularly among clade 1b viruses. Antigenic mapping further revealed that several zoonotic sarbecoviruses were antigenically closer to ancestral SARS-CoV-2 than contemporary Omicron subvariants, despite substantially greater genetic divergence. Taken together, these findings demonstrate that cumulative SARS-CoV-2 exposure promotes broadly cross-neutralizing antibody responses within the sarbecovirus subgenus and provide a quantitative framework to inform the rational design of pan-sarbecovirus vaccines and antibody-based countermeasures for future coronavirus preparedness.

microbiology↗

bioRxiv2026

Resident cardiac macrophages are not required for normal atrioventricular node conduction

Resident cardiac macrophages are understood to facilitate atrioventricular (AV) node conduction because they purportedly couple to AV node myocytes via connexin43 (Cx43) containing gap junctions. We tested this mechanism using biophysical modelling, high-resolution imaging of mouse and human AV conduction tissue, and pharmacological macrophage depletion. In silico, coupling macrophage membrane phenotypes to HCN4+ AV node myocytes imposed an electrotonic load that suppressed pacemaking and promoted conduction slowing, including stable 2:1 block in strand simulations. Anatomically, HCN4-defined components of the mouse AV conduction axis were essentially devoid of Cx43 and overlap of CD68+ macrophages and Cx43 was negligible in both mouse AV node and human penetrating bundle. Finally, near-complete macrophage depletion with CSF1R inhibition (PLX5622) did not alter AV electrical activity in vivo or ex vivo. Together, these data argue against a physiologically relevant role for Cx43-mediated macrophage-myocyte electrical coupling in normal AV node function. HIGHLIGHTSO_LIModelling predicts that AV node automaticity and conduction would be suppressed if macrophages coupled to AV node myocytes C_LIO_LIThe mouse AV conduction axis is essentially devoid of Cx43, currently considered responsible for macrophage-AV node myocyte coupling C_LIO_LIOverlap of macrophages and Cx43 expression is not discernible in the Cx43-expressing human distal AV node C_LIO_LIMacrophage depletion by CSF1R inhibition does not impact AV electrical activity in vivo or ex vivo C_LI

physiology↗

bioRxiv2026

DynMoCo: a Novel AI Framework to Reveal Modular Substructures of Protein From Molecular Dynamics

Proteins are dynamic molecular machines whose functions are determined by their structures. While static structures can offer initial insights or hypotheses about protein function, they are often insufficient for a detailed mechanistic understanding. Molecular dynamics (MD) simulations provide atomistic view of proteins dynamic motion and conformational change, but the resulting high-dimensional data are challenging to interpret. Traditional summary statistics and dimensionality-reduction methods often focus on global motions and can overlook regional, yet functionally critical motions. Inspired by approaches from social network science, we introduce a novel perspective for analyzing MD simulations through dynamic community detection, where molecules are modeled as time-evolving graphs, and communities of residues or atoms that move coherently or exhibit functional coupling are identified. We present DynMoCo, a novel deep learning framework that integrates graph convolutional networks with recurrent models for end-to-end dynamic community detection on molecular graphs. Given a MD trajectory, DynMoCo identifies spatially grounded substructures, tracks their evolution over time, and can incorporate structural knowledge to ensure physically meaningful communities. We provide a library of custom-written scripts to allow users to extract and visualize these communites on the MD simulated molecules in motion. We demonstrate the method on force-ramp and force-clamp steered MD simulations of three integrin systems, revealing modular substructures within known domains and characterizing their conformational rearrangements during force-induced unbending. By reducing high-dimensional MD data into interpretable communities, this approach offers new insights into the intrinsic organization and dynamic function of complex biomolecular systems. SIGNIFICANCEProteins often perform their functions through dynamic, locally coordinated motions. Molecular dynamics simulations provide detailed views of these motions but produce high-dimensional data that are challenging to analyze and interpret. We present a novel deep learning model that analyzes molecular dynamics simulations data and identifies structurally coherent and potentially functionally related communities, while tracking their temporal evolution. This analysis tool provides a novel way to analyze MD data transforming it into interpretable representations of modular dynamic, enabling discovery of new mechanistic insights and advancing our understanding of how molecular motions drive biological function.

biophysics↗

bioRxiv2026

Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain

Histone modifications underpin the cell-type-specific gene regulatory programs that drive the remarkable cellular diversity of the mammalian brain. Here, we jointly profiled four histone modifications and the transcriptome in 2.5 million nuclei from the adult mouse brain. By integrating these data with chromatin accessibility, DNA methylation, and three-dimensional genome organization, we constructed a unified epigenomic atlas spanning over 100 brain cell subclasses, and assigned active, primed, and repressive chromatin states across 81% of the genome. Active chromatin states marked by combinatorial histone modifications better nominate candidate enhancers with functional support than chromatin accessibility alone, while H3K27me3- and H3K9me3-marked chromatin states delineate distinct modes of cell-type-specific gene repression. Finally, this multimodal resource enables deep learning models that predict cell-type-specific epigenomic features and gene expression from DNA sequence, providing a comprehensive framework for annotating the brain regulatory genome and interpreting non-coding disease risk variants. HIGHLIGHTS- A single-cell epigenome atlas of transcription and four histone modifications across 2.5M mouse brain cells - Multimodal integration maps chromatin states across [~]81% of the adult mouse brain genome - Cell-type-resolved chromatin landscapes reveal regulatory programs mediated by enhancers, Polycomb and H3K9me3 - Deep learning models predict cell-type-specific epigenomic features and gene expression from DNA sequence

genomics↗

bioRxiv2026

Disease diagnosis via sperm motility variations induced by body fluids in bioassay

Precise diagnosis of high-risk conditions such as cardiovascular and cerebrovascular diseases still remains a challenge. We previously developed a microfluidic chip for sperm selection and observed that sperm motility is highly sensitive to environmental changes. Building on this finding, we hypothesized that motility traits of sperm could be differentially modulated by body fluids from healthy versus diseased individuals, thereby serving as potential biomarkers for disease diagnosis. To test this hypothesis, we designed a diagnostic system in which mouse sperm were co-incubated with serum samples from patients with myocardial infarction, cerebral infarction, and pancreatitis, along with matched healthy controls. Key kinematic parameters--including motility rate (MR), curvilinear velocity (VCL), straight-line velocity (VSL), linearity (LIN), and amplitude of lateral head displacement (ALH)--were analyzed using a multiparameter sperm quality analysis system. The results revealed that disease-specific serum induced distinct and reproducible changes in sperm motility patterns, enabling accurate discrimination between healthy and pathological conditions. Evaluation of these motility parameters demonstrated high diagnostic performance, with area under the receiver operating characteristic curve (AUC) values ranging from 0.719 to 0.888. This sperm-based bioassay offers a non-invasive, rapid, and cost-effective platform for disease detection and personalized health assessment, with the potential to complement existing diagnostic approaches.

bioengineering↗

bioRxiv2026

Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia

The basal ganglia play essential roles in motor control, emotion, learning and reward processing. Their dysfunction contributes to many neurological and psychiatric disorders. However, the gene regulatory programs defining basal ganglia cell-type identity and function remain poorly understood, limiting interpretation of disease-associated non-coding variants. Here, we present the first single-cell multiome atlas of histone modifications and transcriptomes across eight basal ganglia regions from neurotypical adult human donors. Joint profiling reveals cell-type-specific deployment of active and repressive cis-regulatory elements and gene regulatory networks, and suggests a combinatorial homeobox transcription factor code underlying cell identity. Integration with matched spatial transcriptomic MERFISH data uncovers regional heterogeneity of epigenomic landscapes. Comparative analysis between human and mouse medium spiny neurons uncovers conservation of core gene regulatory features. This atlas interprets non-coding risk variants of neuropsychiatric disorders and supports the development of a deep learning model to predict gene regulation and functional effects of disease-associated variants. HIGHLIGHTSO_LIJoint single-cell profiling of transcriptomes and three histone modifications across eight human basal ganglia regions characterizes active and repressive chromatin states at cell-type resolution. C_LIO_LICell-type-specific gene regulatory programs decode combinatorial homeobox TF grammar governing the identity and diversification of basal ganglia neurons. C_LIO_LIIntergrative analyses link noncoding neuropsychiatric risk variants to specific cell types, regulatory elements, and candidate target genes. C_LIO_LIA sequence-to-function deep-learning model predicts gene regulation from DNA sequence and prioritizes functional disease-associated variants. C_LI

genomics↗

bioRxiv2026

Progranulin deficiency induces lipid droplet accumulation in microglia via a STAT3-GPAT3 axis

Heterozygous mutations in the progranulin (PGRN) encoding gene GRN cause frontotemporal dementia (FTD), whereas homozygous GRN mutations lead to neuronal ceroid lipofuscinosis (NCL). However, the mechanisms underlying neurodegeneration due to PGRN deficiency remain unclear. In the aged brains or under neurodegenerative conditions, the accumulation of lipid droplets (LDs) in microglia contributes to cellular dysfunction and pro-inflammatory responses, exacerbating neurodegenerative pathology. Here, we investigated how PGRN deficiency induces LD accumulation in microglia. We found that PGRN ablation significantly upregulated triglycerol-3-phosphate acyltransferase 3 (GPAT3), the first and rate-limiting enzyme for triacylglycerol biosynthesis, and increased LD formation in both Grn-/- BV2 microglial cells and Grn-/-mouse brains. Mechanistic study revealed that PGRN deficiency upregulates GPAT3 via stimulating signal transduction and activator of transcription factor 3 (STAT3) signaling. Silencing Gpat3, inhibiting GPAT3 activity with the small molecule inhibitor FSG67, or PGRN restoration reduced LD accumulation and rescued the cytotoxicity of Grn-/- microglia conditional medium (MCM) toward N2a cells. Notably, intraperitoneal administration of FSG67 or AAV-MG1.2-mCx3cr1-mGrn-eGFP-mediated microglia-specific gene therapy reduced microglial LDs and ameliorated behavior phenotypes in Grn-/- mice. Our study elucidates the role of PGRN loss in microglial lipid homeostasis and identifies the STAT3-GPAT3 axis as a potential therapeutic target for LD-associated neurodegenerative diseases.

neuroscience↗

bioRxiv2026

The heat-ramp method to study regulated cell death in a pathogenic yeastCryptococcus neoformans

Human fungal pathogens cause a significant public health burden. While no reliable surveilence data are available, estimations suggest that 1 billion infections and over 2 million deaths are attributable to fungal infections annually worldwide. This drove the World Health Organization to generate a priority list of fungal pathogens for reearch, which includes the yeast Cryptococcus neoformans in a top critical priority. With the rise of drug-resistance and emerging fungal pathogens, new conceptual strategies for antifungal therapies are needed in addition to existing antibiotic development pipelines to meet clinical needs. Intrinsic cell death pathways encoded by pathogenic fungi are largely unstudied but could be leveraged for antifungal therapy analogous to anti-cancer therapeutics that activate apoptosis or other cell death mechanisms. Thus far, molecularly defined fungal cell death mechanisms are best characterized for only a few, predominantly model filamentous species. To extend these studies to pathogenic yeast, here we describe and demonstrate a tunable heat-ramp stimulus that when applied to small volumes of yeast cell suspensions reveals a protracted cell death process in the pathogenic yeast Cryptococcus neoformans. This low cost protocol induces robust and reproducible phenotypes to study gene-dependent mechanisms in laboratory strains and clinical isolates.

microbiology↗

bioRxiv2026

Abalone genomics reveals an ancient asymmetry axis and the multifunctionality of the mantle

Gastropod diversification represents one of the most spectacular evolutionary radiations, underpinned by a fundamentally asymmetric body plan and diverse pigmentation patterns. To understand the genetic underpinnings of these cardinal traits, we constructed a chromosome-level genome assembly for the rainbow abalone, Haliotis iris. Integrating systematic genomics, histoembryology, and molecular assays, we uncover an ancient regulatory axis, conserved for over 544 million years, in which the long non-coding RNA lncRNA1 functions as a competing endogenous RNA to shield pitx transcripts from miRNA-mediated degradation, thereby driving the establishment of asymmetric body patterning, including the mantle. Furthermore, we identify a wnt-mitf-tyr cascade as the driver of melanogenesis and demonstrate that the mantle is the primary site of melanin synthesis. Concurrently, we reveal the mantle as a multifunctional organ possessing mechanosensory capabilities. These findings elucidate the ancient genetic toolkit governing trait evolution in gastropods. TeaserA deeply conserved RNA switch directs gastropod body plans and reveals the mantles hidden talents.

genomics↗

bioRxiv2025

Human heart organoids reveal a regenerative strategy for mitochondrial disease

The human heart is among the most complex tissues to replicate in vitro, with vascular, neuronal, and immune elements shaping its development and function. Here we describe cardiomorphs, self-organising human cardiac organoids that recapitulate the cellular diversity, structural organisation, vascularisation, and innervation of the myocardium and mature along a developmental trajectory from early cardiogenesis to adult tissue. Using patient-derived cardiomorphs, we establish the first three-dimensional human tissue model of Kearns-Sayre syndrome (KSS), a rare mitochondrial disorder characterised by large-scale mtDNA deletions. KSS-cardiomorphs faithfully reproduce disease-associated metabolic, contractile, and ultrastructural hallmarks. Leveraging this platform, we identify Betaxolol, an FDA-approved selective {beta}1-adrenergic antagonist, as a modulator of mitochondrial quality control. Betaxolol increases intracellular oxygenation, selectively eliminates dysfunctional mitochondria via mitophagy, and promotes biogenesis of functional organelles, restoring contractility in KSS tissues. This dual-action, mutation-agnostic mechanism suggests a therapeutic principle with broad relevance to mitochondrial disease, cardiac pathology, and age-associated decline.

cell biology↗

bioRxiv2025

Elevated neuronal TAF15 expression leads to FTD-like phenotype

TAF15, a DNA/RNA-binding protein whose dysfunction in alternative splicing impairs NMDA receptor signaling, can form amyloid fibrils that contribute to neurodegeneration in the neurodegenerative diseases like FTD and ALS, indicating a close involvement of TAF15 in both neuronal physiological function and activation of pathological pathways. However, the relationship between TAF15 expression levels and neurodegeneration, as well as the specific downstream pathways mediating its neurotoxicity, remains unclear. Here, we found a consistent upregulation of TAF15 in prefrontal cortex neurons from patients across multiple FTD and ALS subtypes. Both in vitro and in vivo experiments demonstrated that neuronal TAF15 overexpression triggered oxidative stress, evidenced by reactive oxygen species (ROS) production, leading to neurotoxicity and gliosis. Mice overexpressing TAF15 in medial prefrontal cortex (mPFC) neurons exhibited heightened anxiety and impaired fear memory, mimicking some key features of FTD behavioral abnormalities. Notably, these pathological and behavioral phenotypes are rescued by the antioxidant N-acetylcysteine amide (NACA), indicating that elevated TAF15 level exacerbates neurodegeneration primarily by activating oxidative stress pathways. Together, this work elucidates a novel TAF15-oxidative stress axis in FTD-associated neurodegeneration, providing a conceptual framework for future therapeutic development. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/694105v1_ufig1.gif" ALT="Figure 1000"> View larger version (35K): org.highwire.dtl.DTLVardef@cc581eorg.highwire.dtl.DTLVardef@1ad2129org.highwire.dtl.DTLVardef@15c0fb5org.highwire.dtl.DTLVardef@10b57a6_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsTAF15 is upregulated in prefrontal cortex neurons of patients with FTD and ALS across different subtypes. Elevated TAF15 expression provokes ROS elevation, leading to neurotoxicity and gliosis. Neuronal TAF15 overexpression in the mouse mPFC results in FTD-like anxiety and impaired fear-memory phenotype. Reducing oxidative stress can rescue FTD-like phenotype caused by TAF15 upregulation.

neuroscience↗

bioRxiv2025

A near-complete lamprey genome illuminates ancestral vertebrate innovations

The origin of vertebrates is characterized by a suite of phenotypic innovations, yet the underlying genetic mechanisms remain poorly understood. As a living representative of jawless vertebrates, the lamprey serves as a pivotal model for investigating the genomic basis of early vertebrate evolutioin. Here, we report a near telomere-to-telomere (T2T) genome assembly of the reissner lamprey (Lethenteron reissneri), generated from sperm DNA that is not subject to programmed genome rearrangement. The 1.25 Gb assembly resolves over 97% of chromosome sequences into single contigs, enabling reconstruction of previously inaccessible genomic regions. Centromeres display highly diversified, lamprey-specific repeat units and structural architectures, whereas telomeres contain both conserved and lineage-specific satellite repeats. Deep transcriptomic profiling across representative organs and developmental stages substantially improved genome annotation. Comparative genomic analyses revealed a major expansion of 1,562 gene families at the base of the vertebrate lineage, and they are significantly enriched for functions related to neural development, skeletal formation, and cardiac function, echoing the known phenotypic innovations in vertebrates. Notably, the CDH2 gene family underwent vertebrate-specific copy number expansion and acquired conserved cis-regulatory elements (CREs), highlighting its potential role in shaping the early vertebrate circulatory system. Histological analyses and functional knockout experiments demonstrated that one CDH2 paralog (CDH2_H) is essential for lamprey heart development and chamber formation, playing a critical role in the emergence of the closed circulatory system in early vertebrates. This high-quality lamprey genome provides a foundational resource for dissecting the genetic basis of key innovations that shaped vertebrate evolution.

genomics↗

bioRxiv2025

Symbiosis through lysis: prophage activation underlies Lactiplantibacillus plantarum probiotic function

The release of bacterial bioactive molecules across the gut barrier is a crucial yet poorly understood step in microbe-host molecular dialog. Here we unravel a phage-driven mechanism that enables this process in a symbiont that supports host adaptive growth. In Lactiplantibacillus plantarum NC8 (LpNC8), we identify a stress-inducible prophage, pp2, that undergoes genotoxic-stress-dependent activation in vivo and triggers holin-lysin-mediated lysis. This controlled lytic program produces phage particles together with extracellular vesicles (EVs), enriched in symbiotic cues, including lipoteichoic acids. In a model of beneficial symbiosis, pp2-dependent lysis is strictly required for the ability of LpNC8to support juvenile growth in nutritionally challenged Drosophila melanogaster. Disruption of pp2-dependent lysis abolishes EVs release in vitro and alters the growth-promoting effect in vivo. We show that the acidic region of the Drosophila midgut, but not host antimicrobial peptides nor lysozymes, acts as a physiological trigger of prophage induction: removal of this acidic compartment markedly reduces phage production and impairs LpNC8-mediated growth promotion. These findings demonstrate that host gut physiology regulates prophage activation and reveal prophage-induced lysis as a previously unrecognized mechanism by which a beneficial gut bacterium releases symbiotic cues to support host development during nutritional stress.

microbiology↗

bioRxiv2025

Evaluating the effects of CD8/CD4 on T cell function in terms of TCR-pMHC-coreceptor catch and slip bonds

BackgroundT cells interact with peptide-major histocompatibility complex (pMHC) via the T cell receptor (TCR) and coreceptor CD4 or CD8 depending on the MHC class. These interactions form catch and slip bonds depending on the pMHC activity. Coreceptors and bond profiles impact TCR triggering and antigen discrimination. MethodsBuilt upon our recent correlative analysis of TCR-pMHC catch bond with T cell function, we analyzed 26 pairs of T-cell-pMHC interactions to compare the correlations of their biophysical metrics with antigen-induced T cell responses in two situations: when the coreceptor is prevented vs permitted to bind pMHC. ResultsWe found that the force-based metrics of TCR bond with pMHC perform better than parameters measured in the absence of force either in situ at the T cell membrane or in fluid phase using purified ectodomain proteins as predictors of T cell activation and thymocyte selection in both cases when the contributions of coreceptors are absent and present. Moreover, CD8 or CD4 co-engagement with pMHC systematically increases these metrics and increases TCR sensitivity and specificity, indicating coreceptor-mediated amplification of, or conversion to, catch-bonds that enhances mechanical tuning of TCR responses. ConclusionOur findings highlight the importance of force in antigen recognition by the TCR and reveal that parameters derived from the bond profile, especially in the presence of coreceptor, are more informative predictors of T cell activation compared to conventional affinity-based measurements. These results offer mechanistic insights into the roles of catch bonds and coreceptors in TCR antigen recognition.

immunology↗

bioRxiv2025

Ultra-mild bisulfite outperforms EM-seq for 5-methylcytosine detection with low input DNA

We present Ultra-Mild Bisulfite Sequencing (UMBS-seq), a method for 5-methylcytosine (5mC) detection that minimizes DNA degradation and background noise. UMBS-seq outperforms conventional bisulfite and enzymatic methyl-sequencing (EM-seq) methods in library yield, complexity, and conversion efficiency when applied to low-input DNA samples. In particular, its effectiveness with low-input cell-free DNA (cfDNA) and hybridization-based target capture highlight its potential for clinical applications, including 5mC biomarker detection and early disease diagnosis.

genomics↗