Biology subjects

Wang, J.

Publications and source records attributed to Wang, J..

At least 253 records · Page 14Linked to original sources

bioRxiv2026

A Sandwich-Structured Silk Fibroin Mesh with ROS-Responsive and Immunoregulatory Functions for Pelvic Floor Repair

Current biodegradable meshes for pelvic floor repair are constrained by a limited ability to actively modulate the hostile immune microenvironment following implantation. To address these challenges, we developed a functionalized degradable silk fibroin mesh (SFM) integrated with a reactive oxygen species (ROS)-responsive nanocomposite hydrogel. The resulting composite mesh, SFM@Gel-NP, features a "hydrogel-mesh-hydrogel" sandwich structure, wherein the hydrogel layers are loaded with self-assembled nanoparticles (NP-H-CRFP) for the co-delivery of the STING inhibitor H-151 and the ROS-scavenging agent catechin. This design provides immediate mechanical reinforcement while enabling microenvironment-triggered drug release. In vitro, NP-H-CRFP demonstrated efficient cellular uptake, significant ROS clearance, and effective attenuation of macrophage inflammation and apoptosis. In vivo, SFM@Gel-NP remodeled the local immune milieu by inhibiting the ROS/cGAS-STING/NF-{kappa}B axis, thereby promoting a shift from pro-inflammatory M1 toward pro-regenerative M2 macrophage polarization. This immunomodulatory effect, coupled with enhanced and well-organized collagen deposition--particularly of early type III collagen--resulted in improved tissue integration and repair. This work presents a novel strategy that combines structural reinforcement with active immune regulation, offering a promising next-generation solution for durable and functional pelvic floor reconstruction.

bioengineering↗

bioRxiv2026

A paradigm for skilled forelimb reaching by head-restrained mice

Forelimb reaching tasks are widely used in neuroscience across species. In mice, pellet reaching is especially useful because it requires fine motor control. However, few automated pellet-delivery systems are well suited for head-restrained reaching, where pellet position must be highly consistent. Here we present a complete pipeline for head-restrained, or head-fixed, forelimb reaching in mice. The pipeline includes a simple customizable pellet-presentation rig, an effective training protocol, and analysis code to detect reaches and classify their outcomes. To demonstrate pipeline utility, we quantified interruption of an ongoing reach. The temporal requirement for initiating cancellation was dependent on the phase of the reach, lengthening significantly as the reach neared completion. These results show that the pipeline can resolve fine phase-dependent features of skilled behavior and provide a practical framework for studying motor control in head-restrained mice.

neuroscience↗

bioRxiv2026

Recursive mutational robustness in cancer through intra- and inter-genic compensation

Mutational robustness is a fundamental property of biological systems allowing phenotypic stability against genotypic perturbation. At the gene level, this is primarily attributed to inter-genic functional redundancy driven by paralogs. Here, we show that intra-genic functional redundancy, driven by alternatively spliced isoforms, is another prevalent source of mutational robustness. Integrating isoform-resolved pan-cancer genomics and transcriptomics data across tumors and cancer cell lines, we show that alternative isoforms often bypass deleterious somatic mutations. Mutation-skipping isoforms exhibit compensatory upregulation indicative of robustness against deleterious effects, especially in highly expressed genes. We found that intra-genic robustness is strongly associated with perturbation tolerance, is highly context-specific and, notably, can be complemented and augmented recursively by inter-genic robustness. Non-tumour-suppressor genes generally show higher robustness than tumour suppressor genes, and intra-genic compensation of their mutations is associated with worse disease outcome in most cancer types. Furthermore, intra-genic compensation by mutation-skipping isoforms associates with differential isoform usage among proximal interactors, suggesting restorative protein interaction rewiring at isoform-level. Mechanistically, self-transcriptional adaptation (self-TA) following nonsense-mediated decay of perturbed isoforms provides an explanation for the observed up-regulation of mutation-skipping isoforms. Overall, the proposed recursive mutational robustness framework opens new avenues for deeper mechanistic investigation into cancer evolution and identification of selective vulnerabilities in cancer cells. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/727768v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1b0f79aorg.highwire.dtl.DTLVardef@14fa261org.highwire.dtl.DTLVardef@12da16aorg.highwire.dtl.DTLVardef@c03dee_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2026

An AI-agent-orchestrated grey-box Transformer framework for sparse pharmacokinetic curve reconstruction and pharmacometric model initialization

Clinical pharmacokinetic (PK) modelling is constrained by sparse sampling, limited general-isability of single-drug models, and labour-intensive workflows, making it difficult to infer complete drug exposure from limited concentration observations. We present the Pharmacokinetic Foundation Model (PKFM), a grey-box Transformer framework pre-trained across 32 drugs that reconstructs concentration-time profiles from sparse concentration observations, dosing events, molecular descriptors, and physiological covariates while preserving output interpretability. In representative oral PK curves, three sparse input points recovered the principal absorption-elimination trajectory, achieving coefficient of determination (R2) = 0.992 for Midazolam oral and R2 = 0.990 for Verapamil oral. Using reconstructed curves in NONMEM (nonlinear mixed-effects modelling) improved covariance stability and individual prediction accuracy. Contrastive-learning embeddings supported Top-10 physiologically based pharmacokinetic (PBPK) candidate retrieval, with 75.6% of observations within the 2-fold range. A pharmacometrics-informed AI Agent (PM Agent) outperformed general-purpose programming tools in stability and pairwise win rate on a standardised modelling benchmark, with each run requiring human pharmaco-metrician confirmation before downstream use. These results support cross-drug pre-trained PK models as an information-completion layer for sparse PK evidence and a structured scaffold for the modelling workflow; clinical or regulatory use requires prospective validation, broader external benchmarking, and independent expert assessment.

pharmacology and toxicology↗

bioRxiv2026

Cobamide-Dependent Dichloromethane Fermentation by Dehalobacter Reveals a Hidden Acetogenic Route for Organohalide Biotransformation

Halogenated one-carbon (C1) compounds, such as dichloromethane (DCM), drive critical fluxes in global carbon and halogen cycles. While the genus Dehalobacter is canonically defined by obligate organohalide respiration, its physiological and ecological roles in anaerobic C1 metabolism have remained fundamentally ambiguous. Here, we document a paradigm-shifting metabolic capacity within a sediment-derived microbial consortium: the autonomous fermentation of DCM by a novel population, Candidatus Dehalobacter formatiformans strain J1. Over successive transfers, strain J1 outcompeted co-existing Dehalobacterium formicoaceticum to become the overwhelmingly dominant population (>80% relative abundance), converting DCM stoichiometrically to acetate and formate (4:1) without auxiliary substrates. Genome-resolved metagenomics revealed that strain J1 couples a distinct mec gene cassette--mediating methyl-transfer reactions during DCM activation--to a complete Wood-Ljungdahl pathway for efficient C1 assimilation. Crucially, strain J1 lacks the complete genetic repertoire for de novo cobamide biosynthesis. Physiological validation confirmed that this fermentative pathway is strictly dependent on exogenous cobamides, exposing a profound reliance on community cross-feeding. These findings reveal an unexpected acetogenic lifestyle within Dehalobacter, a lineage historically viewed as comprising obligate organohalide-respiring bacteria. More broadly, this work identifies cobamide-dependent methyl-transfer metabolism as an ecological control on anaerobic DCM fermentation and expands the known roles of Dehalobacter in carbon-halogen cycling in anoxic environments.

microbiology↗

bioRxiv2026

The in vivo inhibitory function of the MHC-I alpha3 domain/CD8alpha interaction

The interaction between the Major Histocompatibility Complex Class I (MHC-I) 3 domain and CD8 has classically been viewed as a positive coreceptor interaction that stabilizes TCR signaling during antigen recognition. However, its physiological function in mature peripheral CD8+ T cells in vivo remains incompletely understood. Here, we identify the MHC-I 3 domain-CD8 interaction as a previously unrecognized inhibitory pathway that tonically restrains peripheral CD8+ T-cell activation and maintains T-cell tolerance in vivo. Antibody-mediated disruption of the MHC-I 3 domain-CD8 interaction induced spontaneous activation of peripheral CD8+ T cells without impairing their survival, lowered the threshold for antigen-induced activation, and enhanced responsiveness to cognate peptide stimulation. In peptide-induced OT-I T-cell anergy models, blockade of either H-2Db or H-2Kb 3 domain interactions with CD8 prevented the induction of anergy and restored responsiveness of previously anergic T cells. Notably, blockade of the H-2Kb 3 domain enhanced OT-I responses despite simultaneously disrupting the classical positive coreceptor interaction within the TCR-peptide-MHC complex, indicating that tonic inhibitory signaling mediated by the MHC-I 3 domain predominates under these conditions. Together, these findings redefine the classical MHC-I-CD8 interaction as a bidirectional pathway that not only supports antigen recognition but also imposes tonic inhibitory control over peripheral CD8+ T cells. These results identify the MHC-I 3 domain-CD8 axis as a potential target for reversing T-cell tolerance and enhancing antitumor or antiviral immunity.

immunology↗

bioRxiv2026

IID-KG: An ontology-aligned literature-derived knowledge graph for infectious and immune-mediated diseases

Infectious and immune-mediated diseases (IIDs) represent a broad and rapidly expanding biomedical literature domain in which scalable evidence extraction, disease ontology refinement, and interpretable knowledge integration are essential for biomedical discovery. We constructed an IID-specific biomedical knowledge graph (IID KG) from PubMed abstracts and PMC full-text articles by integrating nested named entity recognition, ontology-guided identifier assignment, full-text relation extraction, and relation-resolution strategies. A gold-standard corpus of 500 PubMed abstracts and 8 PMC full-text articles was manually annotated for nested biomedical entities across six entity types. The resulting models were applied to 30,128,068 PubMed abstracts and 1,385,500 IID-related PMC full-text articles. A unified IID ontology was developed from 411,341 disease terms using hierarchical text classification, large language model-based refinement, ontology cross-referencing, and expert review, yielding 179,657 confirmed MeSH mappings. The final IID KG contains approximately 1,837,513 unique entities and 16,295,390 unique relations across eight relation types. The resource was released publicly together with repurposing workflows, supporting ontology-aligned literature mining, disease mechanism analysis, and drug-repurposing hypothesis generation for IID research.

bioinformatics↗

bioRxiv2026

Biosynthesis of bisbenzylisoquinoline alkaloids

Bisbenzylisoquinoline alkaloids (bisBIAs) are pharmacologically valuable plant metabolites with complex stereochemical architectures, yet the catalytic principles governing their assembly have remained largely unclear. Here, we elucidate the enzymatic pathway to cyclic bisBIAs and uncover a non-canonical redox-mediated mechanism for post-assembly stereochemical control. We identify cytochrome P450 enzymes that catalyze regioselective oxidative dimerization and macrocyclization of benzylisoquinoline monomers, establishing the macrocyclic scaffold. Subsequent stereochemical specification is achieved by a paired oxidase-reductase module that selectively epimerizes a single stereocenter through a transient imine formation, converting (R,S)-configured intermediates to (S,S)-products. Reconstitution of the pathway in yeast enabled production of both native bisBIAs and non-natural analogs, demonstrating pathway modularity and engineering potential. These results establish the biochemical principle underlying bisBIA biosynthesis and provide a framework for programmable biosynthesis of these complex natural products.

biochemistry↗

bioRxiv2026

Molecular Characterization of T-Lineage Acute Lymphoblastic Leukemia by an Optimal-Transport Based Multi-Omics Integration Framework

T-lineage acute lymphoblastic leukemia (T-ALL) is an aggressive pediatric malignancy characterized by complex heterogeneity across multiple molecular layers. Accurate subtyping is essential for understanding disease mechanisms, risk stratification, and guiding targeted therapeutic strategies. However, current diagnostic approaches are labor-intensive and time-consuming, and existing computational methods are limited by reliance on single-modality data or simple integration strategies. Effective integration of heterogeneous multi-omics data remains a major computational challenge. We present OTTER (Optimal Transport-based Transcriptomics and gEnomics Representation fusion), a novel multi-modal deep learning framework that jointly models RNA-seq gene expression and somatic genomic variant data for T-ALL molecular characterization. OTTER encodes each omics modality through a modality-specific variational autoencoder and aligns the resulting latent representations using Gromov-Wasserstein optimal transport (GW-OT), which preserves the internal geometric structure of each modality without requiring a shared feature space. We applied OTTER to the Childrens Oncology Group (COG) AALL0434 cohort comprising 1,309 patients across 17 T-ALL subtypes. Gradient-based feature importance and cross-omics interaction analysis were performed on the holdout set to identify subtype-driving molecular features and cross-modal coordinated programs. OTTER provides a principled, biologically interpretable, and computationally effective framework for multi-omics-driven T-ALL molecular characterization. By leveraging GW-OT for geometry-preserving cross-modal alignment and gradient-based interpretability for cross-omics interaction profiling, OTTER goes beyond single-modality approaches to uncover the coordinated molecular landscape of T-ALL. The framework is generalizable to other cancers and multi-omics integration tasks.

bioinformatics↗

bioRxiv2026

Atlas-Level Single-Cell and Spatial Transcriptomics Data Integration via PRIME

Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) have enabled atlas-scale cellular cartography, with consortium efforts now assembling millions of cells across diverse tissues, donors, and technologies to build comprehensive references for cell identify and disease mechanism, yet the scientific value of these atlases hinges on robust computational integration across heterogeneous data sources. Unlike pairwise batch correction, atlas-level integration must jointly reconcile heterogeneous and often hierarchically nested batch effects across many datasets whose cell-type compositions are highly imbalanced, all while preserving subtle biological variation and remaining computationally tractable at the scale of millions of cells. Existing approaches often prioritize either batch mixing or preservation of local biological structure, and most cannot natively accommodate spatial coordinates. Here we introduce PRIME (Projection-based Robust Integration via Manifold Embedding), an ensemble integration framework that combines random-projection-based consensus anchoring, graph-Laplacian correction, and optional spatial-neighborhood regularization. Across multiple random projections of the expression manifold, PRIME uses consensus voting to keep only cell pairs that repeatedly matched, reducing false anchors caused by projection-specific distortions. For ST, PRIME couples this expression-based anchor graph with a coordinate-derived spatial neighborhood graph in a unified graph-Laplacian objective with closed-form solution, enabling simultaneous cross-batch alignment and local spatial coherence. Based on extensive benchmarking spanning diverse datasets, we show that PRIME consistently outperforms state-of-the-art methods in both batch correction and biological conservation across scRNA-seq and ST integration scenarios and downstream tasks including trajectory inference, spatial-domain preservation, and perturbation-response analysis. Particularly, when integrating a human hematopoiesis benchmark spanning eight donors and approximately 33,000 cells, PRIME preserves biologically coherent developmental trajectories in human hematopoiesis. It also maintains cortical laminar architecture across dorsolateral prefrontal cortex sections in a ST dataset and recovers known drug-target relationships in a perturbation atlas of more than 1 million cells while suppressing batch-associated confounders. Together, these results establish PRIME as a versatile and scalable framework for atlas-level integration of scRNA-seq and ST across diverse biological applications.

bioinformatics↗

bioRxiv2026

Cholangiocyte RUNX1 Orchestrates Fibrogenic and Inflammatory Signaling to Drive Biliary Fibrosis

IntroductionBiliary fibrosis and inflammation are central to the pathogenesis of cholangiopathies such as primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC). Inflammatory and fibrogenic stimuli, such as transforming growth factor-{beta} (TGF{beta}) and lipopolysaccharide (LPS) signaling, drive these processes, but their underlying transcriptional mechanisms in cholangiocytes remain incompletely defined. We investigated the role of Runt-related transcription factor 1 (RUNX1) as a transcriptional co-regulator of fibroinflammatory signaling in cholangiocytes. MethodsHuman PSC-derived cholangiocytes (PSC-Cs) and mouse large biliary epithelial cells (MLEs) were subjected to RUNX1 knockdown or pharmacologic inhibition (Ro5-3335 or AI-10-104). Cytokine secretion was profiled by Luminex multiplexing; RUNX1 genomic binding and protein interactome were assessed by ChIP-qPCR, ChIP-seq, and LC-MS/MS. In vivo, Mdr2-/- mice received Ro5-3335, and cholangiocyte-selective Runx1 knockout mice (Krt19-CreERT) were challenged with a DDC diet, followed by evaluation of fibrosis and inflammation. ResultsRUNX1 expression was significantly increased in cholangiocytes from PSC and PBC patients, and Mdr2-/- mice. RUNX1 knockdown or inhibition reduced IL6, TNF, and other proinflammatory cytokines in PSC-Cs and attenuated TGF{beta}-, LPS-, and TNF-induced Il6 and Ccl2 expression in MLEs. ChIP-qPCR and ChIP-seq revealed TGF{beta}-induced RUNX1 binding to the Il6 promoter and 727 additional genomic sites enriched for fibrosis and inflammatory pathways; predicted upstream regulators included TGF{beta}, TNF, and NF{kappa}B signaling. Proteomic analysis identified TGF{beta}-induced RUNX1 interactions with SMAD2 and NF{kappa}B2. In vivo, Ro5-3335 treatment in Mdr2-/- mice reduced hepatic collagen, ECM gene expression, immune cell infiltration, and serum liver injury markers and bile acids. Similarly, cholangiocyte-specific Runx1 deletion mitigated fibrosis, inflammation, and liver injury in DDC-fed mice. ConclusionRUNX1 is a central transcriptional hub integrating TGF{beta} and inflammatory signals in cholangiocytes. Its inhibition attenuates biliary fibrosis and inflammation in cholestatic models, supporting RUNX1 as a potential therapeutic target in fibroinflammatory cholangiopathies.

physiology↗

bioRxiv2026

Divergent scalp-to-region distance alteration patterns in autism spectrum disorders, Parkinson's disease and Alzheimer's disease

Brain stimulation is increasingly recognized as an effective and important therapeutic intervention for many brain diseases. Distance between the scalp and other brain regions is a pivotal variable for neurostimulation planning and the development of new techniques, but alterations in the distance between the scalp and other regions in brain diseases are largely unknown. In this study, we developed an automatic pipeline to calculate scalp-to-region distance (SRD) values from T1 MR images and applied it to a total of 1382 participants, including patients with autism spectrum disorder (ASD), Parkinsons disease (PD), Alzheimers disease (AD), and cognitively normal controls (CNs). Cloud points were uniformly sampled on the automatically extracted scalp surface and cortex surface, on which the point-wise distance maps were generated. The brain was then coregistered with the BCI-DNI atlas, and SRD value for each brain region was extracted. Analysis of covariance (ANCOVA) was performed for SRD in each brain region, with age and sex as covariates. Compared with CNs, ASD patients showed widespread SRD decreases across the brain with prominent involvement of the frontal lobe, especially the orbitofrontal cortex and adjacent regions. In contrast, in AD patients, significantly increased SRD values were observed in various regions of the frontal gyrus. No significant SRD alteration was found in PD patients after correction. The automatic SRD calculation pipeline and the different patterns of SRD alterations in these diseases might be helpful for future neurostimulation planning in clinical practice. HighlightsO_LIAutomatic pipeline enables scalp-to-region distance (SRD) measurement, facilitates brain stimulation planning. C_LIO_LIASD patients show widespread SRD decreases, especially in the orbitofrontal cortex and adjacent regions. C_LIO_LIAD patients present increased SRD in the frontal gyrus and decreased SRD in the parahippocampal gyrus. C_LI

neuroscience↗

bioRxiv2026

CAD rewires nucleotide metabolism to drive oxidative stress in myocardial ischemia/reperfusion injury

Myocardial ischemia/reperfusion (I/R) injury is a major determinant of infarct size and clinical outcome, yet effective therapies remain limited. Although metabolic remodeling is central to I/R pathology, the contribution of nucleotide biosynthesis remains unclear. Here, we identify CAD, the multifunctional rate-limiting enzyme of de novo pyrimidine biosynthesis, as a previously unrecognized regulator of myocardial reperfusion injury. CAD activation exacerbated cardiomyocyte death during simulated I/R, whereas CAD knockdown or pharmacological inhibition was protective in vitro. Mechanistically, CAD enhanced dihydroorotate dehydrogenase (DHODH)-dependent electron transfer, increased the CoQH2/CoQ ratio, and promoted complex I reverse electron transport (RET), thereby amplifying mitochondrial ROS. In parallel, CAD suppressed de novo purine synthesis, causing purine insufficiency, DIS3L-dependent RNA decay, and cytosolic ROS. Importantly, cardiomyocyte-specific CAD deletion protected against cardiac I/R injury in vivo. Together, these findings establish CAD as a metabolic hub linking nucleotide flux to dual-compartment ROS signaling and identify nucleotide metabolism as a therapeutic vulnerability in myocardial I/R injury. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/725578v1_ufig1.gif" ALT="Figure 1"> View larger version (87K): org.highwire.dtl.DTLVardef@14c4fedorg.highwire.dtl.DTLVardef@1138ed2org.highwire.dtl.DTLVardef@1057d8borg.highwire.dtl.DTLVardef@17546bd_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Binary partitioning of human brain organization due to divergent human cytoskeletal evolution

CHRFAM7A is a biallelic uniquely human fusion gene present in 99.3% of humans. The direct and inverted alleles likely emerged independently in Africa and East Asia. We uncovered that the inverted allele regulates ULK4 expression through genetic epistasis. The increase in long to short ULK4 isoform ratio enhances -tubulin acetylation leading to microtubule (MT) cytoskeleton phenotypes (cell body: microtubule rich projections; neurite: de-bundling; growth cone: fanning with MT invasion). The MT cytoskeleton gain of function enhances neuronal arborization and functional connectivity in the human brain. Considering that the previously reported direct allele leads to actin cytoskeleton gain of function, we propose that CHRFAM7A alleles represent binary human genetic background through divergent evolution of the cytoskeleton. In the human brain the two alleles represent distinct brain organization: the direct allele enhances microstructure as measured by diffusion tensor imaging while the inverted allele increases functional connectivity with increased small world propensity. The two types of brain organization likely represent different susceptibility to neuropsychiatric disease and may underlie the allelic disease associations. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/725959v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@a84e75org.highwire.dtl.DTLVardef@1b712d9org.highwire.dtl.DTLVardef@367c01org.highwire.dtl.DTLVardef@1074dc4_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Structural Basis of Ligand-Specific Orthosteric-Allosteric Coupling and Sensory Tuning in the Human Bitter Taste Receptor TAS2R14

The bitter taste receptor TAS2R14 recognizes hundreds of structurally diverse ligands, yet the mechanisms governing its broad promiscuity, graded agonist efficacy, and multi-site regulation remain unclear. Here, we report cryo-EM structures of TAS2R14-Gi1 complexes bound to 3,5-diiodosalicylic acid (DA), flufenamic acid (FA) and aristolochic acid (AA) at resolutions of 2.44 [A], 2.39 [A], and 2.69 [A], with a clear efficacy hierarchy of AA > FA > DA. Transmembrane helix 6 (TM6) acts as a core regulatory hub, with agonist binding triggering 12 [A] lever-like TM6 rearrangements to reshape receptor interfaces and modulate G-protein coupling strength. We also identify cholesterol hemisuccinate (CHS) as a new TAS2R14 orthosteric agonist, selectively potentiating DA-mediated signaling potency by [~]5-fold via allosteric-orthosteric coupling without affecting FA or AA. Our findings show TM6 dynamics unify TAS2R14s key functional features, advancing insights into bitter receptor activation and sterol regulation.

molecular biology↗

bioRxiv2026

Bacteroidales on Harvesters: Baseline Prevalence and Abundance

Fresh produce encounters pathogens at various stages of production and supply, with the harvesting process serving as one of these stages. To evaluate contamination associated with harvesting, we systematically swabbed zone 1 harvester surfaces and quantified Bacteroidales as a fecal biomarker using quantitative polymerase chain reaction (qPCR). Baseline contamination was dominated by non-detects, with occasional low-level detections (<25 copies/cm2) near the assay limit of detection (LoD). Detection occurred more frequently post-harvest (overall [~]4% pre-harvest and 10% post-harvest), while microbial loads remained low, indicating that harvesting primarily affected the likelihood of low-level contamination rather than increasing contamination abundance. Additionally, we developed and field-deployed a portable loop- mediated isothermal amplification (LAMP) assay for rapid harvester hygiene assessment and benchmarked its field performance against qPCR. Together, these results support a practical molecular tool for monitoring fecal contamination and informing cleaning and sanitization decisions.

bioengineering↗

bioRxiv2026

A weak-interaction model defines the cell-autonomous function of DNA methylation in gastrulation

DNA methylation is essential for mammalian embryonic development, yet its functional implications remain debated. Here, we introduce a quantitative model that reconciles conflicting perspectives on the roles of methylation in genome regulation and cell specification. Using single-cell multiome analysis in chimeric and whole embryo mutants during mouse gastrulation and organogenesis, we separate cell-autonomous from indirect effects of methylation and demethylation machinery. We show that while the transcriptional and chromatin programs defining basic lineages can be established independently of methylation, the fidelity of differentiated states is severely impaired in its absence. Specifically, we identify hundreds of genes and thousands of cis-regulatory elements (CREs) dependent on methylation for precise regulation. CRE accessibility alterations in methylation mutants are linked with CpG dinucleotide content, and correlate with multiple transcription factor binding motifs. Our data support a weak-interaction model in which DNA methylation moderates, but does not block or instruct the potency of trans-acting regulatory machineries genome-wide.

genomics↗

bioRxiv2026

Benthic diatoms navigate shear flows via hydrodynamic rolling and active gliding

Navigating fluid flow is a fundamental challenge for microbial life across diverse aquatic environments. While rheotaxis in swimming microorganisms has been extensively studied, it remains unresolved whether near-bed shear merely perturbs gliding motility or instead provides directional cues for active navigation on surfaces. Here we show that the benthic diatom Navicula cryptocephala utilises a purely mechanical strategy to achieve downstream rheotaxis and anisotropic spreading on submerged surfaces. Single-cell ellipsoidal tracking reveals a direction-dependent angular response that reorients gliding cells towards the downstream direction. Using interference reflection microscopy, we further reveal that shear induces rolling of obliquely gliding cells, laterally shifting the cell-substrate contact site. This shift renders raphe-based propulsion non-collinear with substrate friction, generating a downstream-restoring yaw torque. Crucially, our results rule out alternative explanations based on longitudinal shifts of the raphe contact site or direct hydrodynamic yaw torque. A minimal stochastic model confirms that this mechanical reorientation alone is sufficient to reproduce the observed drift and diffusion patterns, without invoking either orientation-dependent switching between motility states or orientation-dependent dwell times of those states. Our findings uncover a mechanism by which ambient shear is converted into directional guidance for active surface motility, providing new insights into microbial transport, retention, and resilience on submerged surfaces.

biophysics↗