Biology subjects

Wang, B.

Publications and source records attributed to Wang, B..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Metal Coordination Dynamics Governs Selective Epoxidation in Hyoscyamine 6β-Hydroxylase: Integrated Experimental and Computational Insights

Iron(II)- and 2-oxoglutarate-dependent (Fe(II)/2OG) enzymes catalyze a wide range of C-H bond activation and functionalization reactions and play essential roles in biosynthesis and metabolic regulation. Despite extensive mechanistic studies, the principles governing selectivity between canonical hydroxylation and alternative transformations remain incompletely understood. Here, we investigate the catalytic mechanism of hyoscyamine 6{beta}-hydroxylase (H6H), a Fe(II)/2OG-dependent oxygenase that sequentially catalyzes the 6{beta}-hydroxylation of hyoscyamine followed by 6,7-exo-epoxidation of 6{beta}-hydroxyhyoscyamine to generate scopolamine. Combined molecular dynamics and QM/MM calculations reveal that an inline Fe(IV)-oxo intermediate initiates hydrogen atom abstraction from the substrate C7 position. The resulting Fe(III)-OH species subsequently deprotonates the substrate hydroxyl group in a process coupled to substrate coordination to the iron center and an in-line-to-off-line rearrangement of the Fe(III)-OH moiety. This coordination dynamics machinery is further supported by the observed chlorination reactivity on the same substrate. Importantly, this coordination switch favors epoxide formation over hydroxyl rebound, thereby directing the reaction toward selective epoxidation. Further computational analysis of the L290F variant demonstrates that steric constraints imposed by L290 are essential for suppressing hydroxylation, revealing a bidirectional regulatory mechanism governing epoxidation/hydroxylation selectivity. Whereas iron coordination dynamics promote epoxidation reactivity, precise substrate positioning and protein-derived steric effects suppress the competing hydroxylation pathway. These findings are consistent with available experimental observations and establish metal coordination dynamics as a key determinant of selective C-H functionalization in Fe(II)/2OG enzymes.

biochemistry↗

bioRxiv2026

The Drosophila IR20a Integrates L-arginine and Salt Signals via Distinct Subunit Assemblies

Amino acids and sodium salt are essential nutrients that frequently occur together in natural food sources. While animals typically employ distinct receptor subfamilies for specific taste modalities, the molecular mechanisms that integrate these concurrent nutritional signals at the peripheral level remain poorly understood. Here, we identify the Drosophila Ionotropic Receptor IR20a as a multimodal tuning receptor required for the detection of both the amino acid arginine and low NaCl salt. We find that IR20a is expressed in a subset of IR76b-positive gustatory receptor neurons (GRNs) distinct from GRNs dedicated to sweet or bitter taste. Mutation analysis and heterologous expression experiments demonstrate that IR20a functions combinatorially: it pairs with the core receptor IR25a to detect arginine, whereas the additional recruitment of IR76b is required to confer sensitivity to low salt. Crucially, we establish that IR20a/IR25a complex mediates synergistic responses to arginine-salt mixtures, thereby enhancing feeding preference. Furthermore, we reveal that IR20a provides a tonic, state-independent nutrient signal that operates in parallel to the starvation-modulated IR56b pathway to regulate NaCl feeding. Together, our studies uncover a molecular logic in which combinatorial assembly of receptor complexes enables the peripheral integration of complex nutritional signals.

neuroscience↗

bioRxiv2026

Shared binding sites for the chromosomal architectural protein Su(Hw) mediate physical interactions between Drosophila TAD boundaries

The head-to-tail pairing of the nhomie and homie boundaries is responsible for the formation of a stem-loop TAD (topologically associated domain) that encompasses the even-skipped (eve) gene and its regulatory elements. TAD boundaries like homie and nhomie have partner preferences and one mechanism thought to be important in linking compatible boundaries is shared binding sites for the same architectural protein. Both eve boundaries have a single binding site for the polydactyl zinc finger protein Su(Hw). Here we have investigated the role of the shared Su(Hw) sites in the long-distance regulation of a dual reporter by the eve enhancers. Consistent with this mechanism, we find that when the transgene nhomie or homie boundary has a mutation in the Su(Hw) binding site, reporter activation by the eve enhancers is severely compromised. Using MicroC we show the mutating the single Su(Hw) substantially weakens the ability of the nhomie and homie boundaries in the transgene to physically pair with the two endogenous eve boundaries. Su(Hw) binding sites are not, however, sufficient as the gypsy su(Hw) insulator is unable to support long-distance regulation. In a less demanding transvection assay mutations in the nhomie and homie Su(hw) site have only a modest effect on regulatory interactions. The eve boundaries can mediate transvection with the gypsy insulator; however. they are not compatible with the dCTCF Fab-8 boundary even in the transvection assay. Finally, we show that the regulatory and physical interactions of the nhomie boundary in the transgene and the two endogenous eve boundaries are incompatible with the popular cohesin-loop extrusion model.

genetics↗

bioRxiv2026

Microbiota-derived TMAO links PM2.5 exposure to cognitive impairment: A gut liver brain axis

Although fine particulate matter (PM2.5) is linked to cognitive impairment, the mechanistic links between pulmonary exposure and neurodegeneration remain poorly understood. This study investigates the role of the gut-liver-brain axis in mediating PM2.5-induced neurotoxicity. We demonstrate that three weeks of intratracheal PM2.5 instillation in mice causes significant memory deficits, impaired hippocampal adult neurogenesis, and reduced synaptic plasticity in both sexes. Metagenomic analysis revealed that PM2.5 alters gut microbiota composition, specifically by upregulating pathways involved in trimethylamine (TMA) synthesis. This microbial shift led to a systemic increase in the metabolite trimethylamine N-oxide (TMAO) and its accumulation in the hippocampus. Mechanistic experiments revealed that TMAO drives neurotoxicity by activating the hippocampal PERK-mediated endoplasmic reticulum (ER) stress pathway. Critically, these deficits were reversed by suppressing hepatic TMAO production via either pharmacological inhibitors or genetic knockdown. Additionally, hippocampal-specific PERK silencing or dietary resveratrol intervention attenuated hippocampal ER stress, thereby protecting against PM2.5-induced cognitive and hippocampal impairments. These results identify the microbial metabolite TMAO as a key mediator of air pollution-related neurotoxicity and highlight the gut-liver-brain axis as a promising therapeutic strategy to counteract the neurological impacts of air pollution.

animal behavior and cognition↗

bioRxiv2026

A fungal pathogen effector that shapes host plant microbiota kills bacteria through lipoteichoic acid binding and membrane disruption

Antimicrobial proteins are ancient and widespread molecules that contribute to survival across all domains of life. We previously showed that fungal plant pathogens secrete antimicrobial proteins to suppress antagonistic members of the host microbiota and thereby promote host colonization. The soil-borne plant pathogen Verticillium dahliae employs the bactericidal protein VdAve1 for this purpose. Here, we elucidate the mode of action of VdAve1 and define its mechanism as a distinct type of antimicrobial activity. Nuclear magnetic resonance (NMR) analysis revealed that VdAve1 adopts a jelly-roll barrel-like fold. Functionally, VdAve1 disrupts bacterial plasma membranes, and synthetic peptides derived from its positively charged regions retain antimicrobial activity, indicating that these regions contribute to its function. We further show that the bacterial model system Bacillus subtilis responds to VdAve1 by modifying teichoic acids, and that loss of these modifications increases bacterial sensitivity. Consistent with this, VdAve1 binds lipoteichoic acid (LTA), a major component of the Gram-positive cell wall. Together, our findings support a model in which VdAve1 binds LTA to localize at the bacterial surface, where it perturbs the plasma membrane, leading to membrane collapse and cell death. SIGNIFICANCE STATEMENTPlant-pathogenic microbes secrete effector proteins to promote host colonization. While these proteins are typically studied for their roles in host manipulation, some affect host-associated microbial communities by exhibiting antimicrobial activity. However, their modes of action remain largely unexplored. The fungal plant pathogen Verticillium dahliae secretes the antimicrobial effector VdAve1 to inhibit bacterial antagonists in the host microbiota. Here, we characterize the mode of action of VdAve1. We show that VdAve1 binds lipoteichoic acid, a major component of the cell wall of Gram-positive bacteria. This promotes VdAve1 accumulation close to the plasma membrane, and through electrostatic interactions it disrupts the plasma membrane. We further determine VdAve1 structure by NMR, revealing VdAve1 adopts a {beta}-barrel-like fold. Together, our findings show the mechanism by which a fungal effector inhibits bacterial growth and thereby how it may influence host-associated bacterial communities.

microbiology↗

bioRxiv2026

A Time-Sequenced Three-Drug-Loaded Microneedle Patch for the Prevention of Vein Graft Restenosis After Coronary Artery Bypass Grafting

Coronary artery bypass grafting (CABG) is the recommended treatment for severe coronary heart disease; however, restenosis of great saphenous vein grafts continues to limit long-term outcomes because of early thrombosis, mid-term intimal hyperplasia, and late atherosclerosis. To address these sequential pathological processes, this study develops a perivascular drug-loaded microneedle (MN) patch capable of controlled chronological release of tirofiban, rapamycin, and rosuvastatin. The MN patch exhibits uniform conical microneedles (height: 700-800 {micro}m), nanoparticle size of 125 nm, sufficient mechanical strength (1.07 N/needle) for venous intimal penetration, excellent biocompatibility, and no detectable cytotoxicity or hemolysis. In a mouse model of venous graft transplantation, the device significantly reduces early platelet thrombus formation (23.3% to 10%), alleviates mid-term intimal hyperplasia (intimal thickness: 0.84 mm to 0.45 mm at 4 weeks), and improves long-term graft patency with blood flow increasing from 13.1 to 65.8 mL/min at 32 weeks while reducing long-term mortality. Mechanistically, RNA sequencing and functional analyses demonstrate that excessive glycolysis-driven smooth muscle cell proliferation, coupled with abnormal endothelial cell apoptosis, constitutes the core mechanism underlying mid- to long-term restenosis, which the MN device effectively suppresses. This integrated MN patch provides a localised therapeutic strategy for preventing restenosis and improving long-term CABG outcomes. Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/726718v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@1de0e6borg.highwire.dtl.DTLVardef@184a846org.highwire.dtl.DTLVardef@43a50forg.highwire.dtl.DTLVardef@109bb85_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Decoding Immune Reconstitution Failure in People Living with HIV through Single-cell Genomics

Immune non-responders (INRs), a subset of people living with HIV (PLWH), fail to achieve full immune reconstitution and remain at increased risk of morbidity, mortality, and non-AIDS-related illnesses. As the mechanisms underlying this impaired immune recovery remain poorly understood, we performed single-cell multi-omics profiling on peripheral blood mononuclear cells from 43 INRs, 47 immune responders and 53 healthy donors. Our dataset comprises 2,744,009 transcriptomes and 1,226,658 chromatin-accessibility profiles across 58 identified immune cell types. INRs exhibited markedly elevated inflammatory signaling, increased apoptotic activity, and dysregulation of immune-activating ligand-receptor interactions. Additionally, we identified 2,996 interaction cis-eGenes and 5,938 cis-caPeaks, and validated key cell type-specific cis-xQTL effects associated with immune reconstitution failure. Furthermore, we identified 3,551 sc-eQTLs and 872 cell-state interaction eQTLs (ieQTLs) in CD4+ T cells. A genotype-specific upregulation of OAS3 in INRs, likely regulated by STAT1, was identified based on these results. We developed scPRISM (single cell Predictive Reconstitution Immune Status Model), a multi-modal framework that integrates scRNA-seq and scATAC-seq data to perform the dual tasks of differentiating disease states and predicting gene expression from chromatin accessibility, thereby deciphering the cell type-specific cis-regulatory basis of the disease. Our study delineates the transcriptional and epigenomic landscape of immune dysregulation in INRs and provides new genetic insights into HIV-associated immune reconstitution failure. These findings offer a foundation for developing biomarkers and precision therapies to restore immune function in PLWH.

genetics↗

bioRxiv2026

A Screen To Identify Protein Phosphatases with Roles in Circadian Period, Temperature Compensation and Output in the Neurospora Circadian Clock

The circadian clock is a highly conserved evolutionary advantage which allows organisms to anticipate regular changes in daily environmental conditions. Clocks from fungi to mammals rely on a transcription-translation feedback loop (TTFL) mechanism. Phosphorylation is understood to be a critical regulatory step for maintaining the period of the circadian clock and feedback loop closure. The role of kinases in the Neurospora clock has been examined extensively; however, phosphatases have not been systematically interrogated. By re-examining the Neurospora genome using current informatic tools we identified the 30 genes previously identified as encoding protein phosphatases as well as 13 novel genes, and we assessed the function of the core circadian clock in 39 non-essential phosphatases using a real-time luciferase reporter. We observed both period lengthening and shortening effects, which are not restricted to a single phosphatase family or fold. All but one deletion mutant maintained a rhythmic core clock. In addition, we observed a new temperature compensation defect in the previously studied knockout of phosphatase pph-4, the result of nutritional growth conditions.

genetics↗

bioRxiv2026

A Bioprinted Head and Neck Cancer Organoid-Based Platform for Evaluating Multimodal Therapies

Treatment of advanced head and neck squamous cell carcinoma (HNSCC) often involves radiotherapy combined with chemotherapy, targeted therapy, or immunotherapy. However, due to its anatomical and molecular heterogeneity, identifying the most effective treatment for each patient remains a major clinical challenge. To address this need, we developed a high-throughput organoid-based drug screening platform that uses patient-derived organoids to assess candidate treatment regimens. We validated the platform by establishing bioprinted 3D organoids of human HNSCC cell lines and exposing them to X-ray radiation in combination with various small-molecule drugs and biologics. We quantified viability using ATP release assays and assessed extracellular matrix (ECM) invasion with a machine learning-based brightfield image analysis pipeline. Proof-of-concept experiments with HPV-negative HNSCC lines (HN30 and HN31, established from primary and metastatic disease from the same patient) and HPV-positive HNSCC cells (SCC154) revealed different therapy agents that can radiosensitize each cell line. Image analysis showed that copanlisib, afatinib, and ibrutinib could limit ECM invasion of HN31, while the AKT inhibitor ipatasertib promotes invasion of HN30 cells, consistent with previous studies. Application of the platform to patient-derived HPV+ oropharyngeal tumor organoids showed that they shared sensitivity to several agents while also exhibiting differences against certain therapies. Cetuximab, sorafenib, and nedisertib significantly radiosensitized organoids from two clinical samples. This work demonstrates the feasibility of performing sensitivity screening by integrating bioprinting, conventional viability assays, and advanced image analysis techniques. This platform has the potential to enable a personalized therapeutic pipeline for patients with advanced HNSCC, optimizing responses to radiotherapy and targeted agents to improve clinical outcomes while avoiding modulators that may promote tumor invasion.

cancer biology↗

bioRxiv2026

TBI-166 inhibits DlaT and LpdC, exhibiting synergistic effects with Bedaquiline and Pyrazinamide against Mycobacterium tuberculosis

Tuberculosis (TB), particularly drug-resistant tuberculosis (DR-TB), remains a critical global challenge and underscores the urgent need for novel drugs and innovative combination regimens with distinct mechanisms of action. Here, we characterize an all-oral three-drug regimen comprising TBI-166, bedaquiline(BDQ), and pyrazinamide(PZA), which displays strong synergistic antimicrobial activity in vitro against both replicating and non-replicating Mycobacterium tuberculosis (MTB) and has previously shown superior bactericidal and sterilizing efficacy to standard HRZ and BPaL regimens in murine TB models(1). Time-kill studies demonstrate that the triple regimen outperforms dual-drug combinations, accelerating bacterial clearance across multiple physiological states. Mechanistic investigations revealed that the TBI-166-BDQ-PZA combination induces a comprehensive collapse of energy and redox homeostasis, marked by profound ATP depletion, robust accumulation of reactive oxygen species (ROS), and marked disruption of the intracellular NAD(H) pool. TBI-166, a novel riminophenazine analogue of clofazimine (CFZ) currently in phase II clinical trials, emerged as a key contributor to this metabolic stress. Metabolomic profiling and {superscript 1}3C-based flux analysis show that TBI-166 slows glycolysis and the tricarboxylic acid (TCA) cycle while enhancing flux through the pentose phosphate and nicotinate pathways, thereby lowering the NADH/NAD ratio and diminishing MTB metabolic flexibility under environmental stress. In parallel, TBI-166 downregulates the dormancy regulator DosR and its regulon, further compromising adaptation to non-replicating states. Multi-omics analyses, together with biochemical and biophysical assays, identify the pyruvate dehydrogenase complex (PDHc) components DlaT and LpdC as direct molecular targets of TBI-166, with drug binding leading to potent inhibition of their enzymatic activities. Collectively, these findings define the mechanism of action of TBI-166 and provide a molecular rationale for its inclusion in potent, all-oral, short-course regimens. More broadly, they highlight the therapeutic potential of metabolically targeted combinations that destabilize energy metabolism, redox balance, and metabolic adaptability to improve DR-TB treatment outcomes.

microbiology↗

bioRxiv2026

NuGraph: Graph-Based Reasoning over 3D Primitives for Nucleus Segmentation Correction

Correcting segmentation errors in large-scale 3D nuclei reconstructions requires reasoning about which fragments belong to the same nucleus across densely packed regions. Existing correction methods rely on local pairwise fragment matching, which cannot resolve the global topology of nuclear clusters and fails to recover missing morphology. We propose NO_SCPLOWUC_SCPLOWGO_SCPLOWRAPHC_SCPLOW, a graph-based reasoning framework that operates over atomic 3D primitives obtained by decomposing erroneous masks. NO_SCPLOWUC_SCPLOWGO_SCPLOWRAPHC_SCPLOW encodes primitive geometry via a 3D point-cloud backbone and performs global relational reasoning through graph attention, capturing inter-primitive dependencies across entire clusters rather than isolated pairs. A primitive-proposal contrastive loss aligns local primitive features with nucleuslevel semantics, improving grouping accuracy in dense regions. The resulting proposals are then refined by a shaperefinement network that predicts signed distance fields to restore smooth morphology. To train without manual error annotations, we develop a self-supervised data engine that synthesizes realistic segmentation errors from clean nuclei labels. To benchmark correction at brain scale, we curate NucEMFix, the first brain-wide EM benchmark of nuclei error cases across FAFB and MICrONS (8,000+ annotated error nuclei). NO_SCPLOWUC_SCPLOWGO_SCPLOWRAPHC_SCPLOW attains 87.99% F1 on NucEMFix-F (FAFB) and 86.20% on NucEMFix-M (MICrONS), outperforming both re-segmentation baselines (e.g., +8.6% over nnU-Net) and pairwise correction methods, while reducing curation effort by over 100x relative to manual proofreading. Code and data are available at https://mingzhiwang618.github.io/NucEMFix.

neuroscience↗

bioRxiv2026

Microbial network rewiring mediates the function-biosafety trade-off in transboundary Pamir lakes

The Pamir Plateau is a transboundary water tower whose source lakes serve as critical biogeochemical hubs with implications for downstream freshwater security. However, it remains unclear how environmental shifts in these high-altitude lakes reshape the microbial communities that drive ecosystem functioning and water safety. Here, we conducted a multi-omics survey across 20 lakes spanning Chinese and Tajikistani Pamir. Our results revealed that prokaryotes exhibited lower diversity but higher among-lake connectivity in China, while eukaryotes showed higher diversity but stronger dispersal limitation. These contrasting biogeographic responses triggered profound rewiring of microbial associations. Under intensified anthropogenic pressures, Chinese cross-kingdom networks decoupled from environmental constraints and became more centralized and complex. Conversely, Tajikistani lakes maintained more modular networks governed by hydrochemical filtering. Critically, this rewiring mediated a trade-off between multifunctionality and potential biosafety risk, with higher element cycling abundances in Chinese lakes, whereas Tajikistani lakes harbored larger biosafety burden dominated by virulence, pathogen, and toxic-algae potential. Incorporating network topology also substantially improved the prediction of these ecological consequences. These findings highlight the importance of network-informed monitoring and management strategies to safeguard ecosystem sustainability in transboundary Pamir lakes under global change.

microbiology↗

bioRxiv2026

Piezo3 is a novel mechanosensitive Piezo ion channel in vertebrates

Mechanosensing and mechanotransduction are essential for all living cells. In mammals, Piezo1 and Piezo2 are two mechanically activated cation channels that serve as mechanosensors for a variety of physiological and pathological processes, ranging from touch sensing to sickle cell disease. These two channels are well evolutionarily conserved, and orthologous genes can be traced back to the origin of vertebrates, which underwent whole-genome duplications (WGDs). The number of paralogous genes originating from the vertebrate WGD varies across gene families. Thus, whether there are more PIEZO paralogous genes in vertebrates remains understudied. Here, we identified piezo3, a new paralog of the piezo gene family, and analyzed its evolutionary history using phylogenetic and synteny analyses. The piezo3 gene is present in most vertebrate lineages but absent in birds and most mammals, likely due to nonfunctionalization after WGDs. In addition, we demonstrated that this channel could mediate calcium flux in response to mechanical stimuli in HEK293T cells, suggesting that Piezo3 exhibits PIEZO1/2-like activation and conduction channel functions. Our CRISPR mutation analysis revealed that the zebrafish piezo3 gene is not developmentally essential, possibly because its expression overlaps with other PIEZO channels. Mutant zebrafish showed elevated sensitivity to mechanical force and increased locomotor activity under (photopic) light illumination. Our results suggest that this new mechanical-sensing Piezo channel is widespread in vertebrates and may be critical for vertebrate adaptation by modulating mechanical sensing and light responses during evolution. SIGNIFICANCEAll living cells must sense mechanical forces, whether endogenous or exogenous, and respond to them by transforming these forces into biological signals, which is essential to a wide range of cellular processes, including cell division, growth, and differentiation. PIEZO channels are well-characterized, critical, versatile mechanotransducers for touch and pain physiology and for human diseases. Currently, PIEZO1 and PIEZO2 are the only two known PIEZO channels in most vertebrates. In zebrafish, there are two Piezo2 channels (Piezo2a and Piezo2b) due to extra genome duplication in the ray-finned fishes. Here, we report Piezo3 channel, a long-missing paralog of Piezo1 and Piezo2, in most vertebrates. This channel is present in the majority of vertebrate lineages, except for most birds and mammals. The zebrafish piezo3 gene is expressed during early embryogenesis, and mutation of this gene leads to zebrafish larvae responding to tapping mechanical force and light with active movement. The widespread distribution of this Piezo3 channel across most vertebrate species, but its absence in birds and most mammals, suggests it may play important roles in vertebrate physiology and evolution.

evolutionary biology↗

bioRxiv2026

Resolving the oak tree of life: comparing RADseq and whole genome resequencing methods for oak phylogenetics

Forest trees pose numerous potential challenges to phylogenomic inference. Their large effective population sizes and relatively long generation times lead to deep allele coalescence and consequently incomplete lineage sorting (ILS), which biases inferences of divergence times toward older ages and introduces gene tree discordance. Deep phylogenetic divergences, reaching back into the Paleocene, introduce reference-mapping biases. Introgression--the movement of genes between lineages--may result in different phylogenies being inferred depending on which individuals are included in analysis, even if the plurality of the genome favors the divergence history unaffected by introgression. These factors influence phylogenetic inference across the Tree of Life but are particularly prevalent in forest trees. Oaks (Quercus) are notable for all three influences. In addition, our knowledge of the oak phylogeny is currently based strongly on restriction site associated DNA sequencing (RADseq) datasets published over the past decade, which may introduce additional sources of uncertainty. In this chapter, we analyze a 322-species RADseq dataset and genome resequencing data from across the genus to address sources of uncertainty in our understanding of the global oak phylogeny, which we hope will serve as a model for other research groups working on comparable woody plant groups.

evolutionary biology↗

bioRxiv2026

The ω subunit stabilizes transcribing RNA polymerase to balance processivity and collision resolution

The ubiquitous subunit of RNA polymerase (RNAP), {omega}/RPB6, is traditionally viewed as an assembly chaperone or bacterial {sigma}-factor competition modulator. This study redefines the role of Escherichia coli {omega}, encoded by the rpoZ gene. Unexpectedly,{Delta} rpoZ strain does not exhibit major defects in {sigma}S-dependent stress responses, indicating its primary function lies elsewhere. Our CRISPRi screen suggested that losing {omega} may promote survival during transcription-replication conflicts. Consistently, we show that loss of {omega} sensitizes RNAP to termination, reduces RNAP processivity, and suppresses toxic effects of DNA-damaging agents in strains lacking functional DksA, Rho, or SeqA; DksA and Rho promote the release of stalled RNAP from nucleic acids, while SeqA prevents aberrant replication initiation. These findings suggest that loss of {omega} facilitates the removal of stalled RNAP, preventing catastrophic replisome collisions. We propose that {omega}/RPB6 homologs may balance RNAP processivity with controlled release to preserve genome integrity across all domains of life.

genetics↗

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↗

bioRxiv2026

G-SPRI: A Structure-Centric Graph Model for Comprehensive Prediction of Cancer Driver Events from Missense Mutations

In silico approaches for predicting the functional impact of missense mutations are critical for interpreting personal genomes and identifying disease-related biomarkers. Existing methods largely rely on sequence-based information or intuitive structural features, but often overlook the complex biophysical patterns encoded in protein 3D structures. Here, we present G-SPRI, a multilevel framework built on a novel alpha-shape protein graph that accurately captures residue connectivity from atomic-resolution geometry and enables precise message passing around mutation sites. Using this graph representation, G-SPRI integrates wild-type structural properties and mutation-specific perturbation signals derived from the Protein Data Bank (PDB) universe to support graph-based learning for distinguishing pathogenic from benign missense variants. G-SPRI performs strongly across multiple key tasks. On the binary prediction benchmark, G-SPRI delivers improved pathogenicity prediction for individual mutations. By integrating mutation recurrence across the pan-cancer cohort, G-SPRI recovers more known cancer driver genes than state-of-the-art methods from more than 2.3 million mutations. Furthermore, by jointly quantifying site-specific pathogenicity and co-clustering influence within higher-order structural organization units, G-SPRI provides comprehensive evidence for pinpointing likely driver mutations and structurally susceptible regions within disease genes.

bioinformatics↗

bioRxiv2026

ArchaicSeeker 3.0: A deep-learning framework for scalable, haplotype-resolved inference of archaic introgression

Archaic introgression has left a significant mark on human genetic diversity, but reliably identifying introgressed segments remains a major challenge, especially with complex demographic histories and limited sample sizes. Existing methods often rely on demographic assumptions or cohort-specific parameter fitting, which compromises robustness and scalability. We introduce ArchaicSeeker 3.0 (AS3), a deep-learning framework designed for haplotype-resolved detection of archaic introgression. AS3 integrates a tract-scale sequence model with an overlap-aware reassembly approach and boundary refinement, enabling accurate, boundary-coherent reconstruction of introgressed segments across diverse genomic contexts. By leveraging a simulation-trained model, AS3 avoids inference-time recalibration, offering stable performance across unrepresented demographic scenarios and small cohorts. In extensive simulations, AS3 outperforms existing methods in precision, recall, and F1 score, while providing more continuous segments with accurate boundary localization. It demonstrates robustness in small-target regimes and varying marker densities. Applied to 3,453 genomes from 209 populations, AS3 shows strong concordance with existing introgression callers and identifies additional introgressed regions, including high-frequency AS3-specific introgressed segments supported by locus-level haplotype and phylogenetic analyses. AS3 provides a scalable, robust solution for detecting archaic introgression from single individuals to large biobank datasets, marking a significant advancement in the field of local ancestry inference and opening new possibilities for the study of human evolutionary genetics. ArchaicSeeker 3.0 is available at https://github.com/Shuhua-Group/ArchaicSeeker3.0.

bioinformatics↗