Biology subjects

Hu, W.

Publications and source records attributed to Hu, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

NgBR controls hepatic adiponectin signaling competence through KAT7-dependent chromatin regulation

Adiponectin signaling is essential for hepatic glucose homeostasis, yet the molecular basis of adiponectin receptor responsiveness remains incompletely understood. Here, we identify the Nogo-B receptor (NgBR; NUS1) as a regulator of hepatic adiponectin sensitivity. Across human, cynomolgus monkey, and mouse datasets, hepatic NgBR expression is consistently reduced in obesity-associated diabetes, indicating a conserved metabolic signature. Hepatocyte-specific NgBR deletion abolishes the metabolic effects of the adiponectin agonist AdipoRon, resulting in impaired AMPK activation, persistent gluconeogenesis, and ceramide accumulation. Mechanistically, NgBR loss suppresses KAT7 expression and reduces histone acetylation at AdipoR1 and AdipoR2 promoters, thereby limiting receptor expression. Adeno-associated virus (AAV)-mediated restoration of hepatic NgBR reinstates KAT7-dependent chromatin activation, adiponectin receptor expression, and glucose homeostasis. These findings support a hepatocellular mechanism in which NgBR maintains adiponectin receptor competence and suggest a potential therapeutic strategy for restoring adiponectin responsiveness in metabolic disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/726643v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@117fa66org.highwire.dtl.DTLVardef@1385297org.highwire.dtl.DTLVardef@b64369org.highwire.dtl.DTLVardef@3dd55_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Phase-Separated RNA Condensates Govern Cas13 Target Accessibility and Cleavage

RNA-guided CRISPR-Cas13 nucleases must efficiently locate and target specific transcripts amidst the millions of other RNA molecules that are spatially regulated in the cell. Yet the mechanisms by which Cas13 finds its targets within this crowded, compartmentalized environment remain elusive. Here, we show that diverse Cas13 orthologs assemble into distinct cytoplasmic granules in a crRNA-concentration dependent manner. These granules exhibit hallmark features of phase-separated condensates, displaying liquid-like viscoelasticity and dynamic molecular exchange with the cytoplasm, as demonstrated by FRAP analysis in both human and bacterial cells. Molecular profiling revealed that Cas13 co-localizes with polyadenylated RNAs and noncoding RNAs within condensates that display markers of canonical RNA granules. Biochemical purification coupled with RNA sequencing shows Cas13 associated with thousands of transcripts within condensates, likely mediated by electrostatic interactions with its positively charged surface. Notably, Cas13 retains catalytic activity within these condensates, efficiently cleaving co-localized targets, whereas RNA species excluded from the condensates remain largely protected from Cas13 cleavage. This data indicates that condensate-based spatial organization facilitates efficient sampling and binding of diverse RNA targets by concentrating Cas13 and its substrates within a confined, liquid-like compartment. Together, our findings uncover a conserved spatial mechanism regulating Cas13 activity across bacterial and mammalian cells, where localization within RNA dense granules governs Cas13 activity in cells.

molecular biology↗

bioRxiv2026

Intragenic suppressor screen of YHB identifies novel and known loss-of-function alleles of Arabidopsis phytochrome B

The red/far-red sensing photoreceptor phytochrome B (phyB) governs multifaceted plant development and responses to light and temperature stimuli. PhyB photoconversion between red-absorbing, inactive Pr and far red-absorbing, active Pfr states, imparted by its covalently bound bilin chromophore, enables rapid switching and plasticity of phyB signaling activities. The phyBY276H variant (YHB) is photochemically inert but adopts a constitutively active Pfr-like structure regardless of light conditions, which becomes a versatile model to dissect phyB signaling mechanisms. Here, we conducted a large-scale EMS mutagenesis screen on YHB-expressing transgenic lines, mining intragenic suppressor mutations that would unveil critical residues for phyB structure-function relationships. Comparative analyses of 26 nonsense variants suggested modular organization of phyB overall structure and dispensability of the C-terminal HKRD domain for phyB signaling. Amongst fourteen novel and nine known loss-of-function missense variants identified herein, G284E was of particular interest for its fully suppressed constitutive activity in darkness and its restored photochemistry and light responsiveness. The G284E mutation was further tested to also nullify another constitutively active phyBY303V allele by eliminating chromophore attachment. P309L was the sole variant identified which fully suppressed YHB in both dark and light conditions. C402Y profoundly elicited YHB protein instability. Three variants G118R, C402Y and G538D markedly reduced chromophorylation levels of YHB. Although the chromophore binding site variant C357Y was a strong loss-of-function allele, it retained residual signaling activity with respect to PIF3 protein turnover in dark-grown seedlings, presumably due to its ability to noncovalently bind chromophore. Two tandem prolines (P799, P800) proved critical to YHB structural integrity/stability as well as signaling activity. In summary, these diverse variants shed new insights into multiple levels by which the YHB (and thereby phyB) signaling is initiated, tuned, and disseminated.

plant biology↗

bioRxiv2026

Gut microbiota-derived indole-3-propionic acid preserves dorsal hippocampal catecholamines to prevent post-stroke cognitive impairment

BackgroundGut dysbiosis has been increasingly implicated in post-stroke cognitive impairment (PSCI), yet the causal contribution and therapeutic potential of gut microbiota-derived metabolites remain unclear. This study aimed to identify key microbiota-derived metabolites involved in PSCI and to elucidate their underlying mechanisms. ResultsWe found that both PSCI patients and middle cerebral artery occlusion (MCAO) mice exhibited distinct gut microbial alterations, characterized by a marked reduction in tryptophan-metabolizing bacteria and indole-3-propionic acid (IPA), a gut microbiota-derived tryptophan metabolite. Exogenous IPA administration alleviated PSCI-like phenotypes in MCAO mice. Mechanistically, IPA preserved tyrosine hydroxylase-positive (Th) fibers and catecholamine levels in the dorsal hippocampus. Further analyses showed that IPA binds to the adaptor protein Ywhab, promotes ERK activation, and enhances neuronal survival, thereby counteracting neuronal apoptosis-associated inflammation and subsequent Th fiber degeneration. ConclusionThese findings identify IPA as a gut microbiota-derived neuromodulator that mitigates PSCI by preserving dorsal hippocampal catecholaminergic transmission. IPA may therefore serve as a promising predictive biomarker and therapeutic candidate for PSCI.

neuroscience↗

bioRxiv2026

YIPPEE/YPEL5 regulates circadian period by modulating PER ubiquitination and stability

Circadian clocks rely on evolutionarily conserved transcriptional-translational feedback loops to align physiology and behavior with the 24-hour day-night cycle. Post-translational modifications, especially ubiquitination, critically control core clock protein stability and circadian pace. In both fruit flies and mammals, the abundance of key pacemaker protein PERIOD (PER/PER2) must be tightly regulated to sustain circadian rhythms. However, the canonical phosphorylation-dependent pathway cannot fully account for turnover of PER in Drosophila. Here we identify Yippee as a critical regulator of PER level through a genetic screen of downregulating ubiquitination pathways. Knockdown of Yippee in circadian pacemaker neurons significantly lengthens the circadian period by [~]2 hours and elevates PER levels. Indeed, YIPPEE physically interacts with PER in fly head. Mechanistically, its mammalian homolog YPEL5 binds PER2, promotes K63-linked polyubiquitination and proteasomal degradation of PER2 independently of FASP-region phosphorylation. Lastly, downregulating YPEL5/Ypel5 prolongs circadian periods in human U2OS cells and mice. Our findings reveal an evolutionarily conserved mechanism in which Yippee/YPEL5 regulates circadian rhythms by mediating ubiquitin-dependent degradation of PER/PER2.

molecular biology↗

bioRxiv2026

Target RNA abundance controls the collateral activity of RfxCas13d in human cells and zebrafish embryos

Collateral RNA cleavage by CRISPR-Cas13 effectors presents a critical obstacle to their application in biological research and therapeutics, yet the molecular determinants of this activity remain poorly understood. Here, we systematically investigate the collateral activity of various Cas13 variants in human cells in vitro and zebrafish embryos in vivo. Among these nucleases, RfxCas13d displays robust collateral activity that is highly dependent on target abundance. Targeting moderately expressed RNAs activates only a limited subset of RfxCas13d molecules, resulting in selective degradation of ectopically expressed transcripts, while endogenous RNAs remain largely protected. This selectivity indicates higher accessibility to exogenous RNAs through spatial proximity and temporal colocalization with activated RfxCas13d nuclease domains. In contrast, the recognition of highly abundant RNA targets drives simultaneous activation of a large fraction of cellular RfxCas13d, leading to widespread collateral cleavage of cellular RNAs, disruption of proteome homeostasis, and consequent cell toxicity and developmental defects in zebrafish embryos. Notably, transgenic zebrafish with target RNA expression restricted to endothelial or neuronal cell lineages exhibit localized collateral activity, leading to tissue-specific developmental abnormalities and motility deficits. These findings reveal that RfxCas13ds collateral activity is threshold-dependent, with abundant target RNA acting as a molecular switch for widespread collateral RNA degradation. This work underscores the need for careful consideration of target abundance when deploying RfxCas13d, and highlights PspCas13b as an alternative for RNA silencing free of collateral activity.

molecular biology↗

bioRxiv2026

Meaning-based guidance of attention in rhesus monkeys during naturalistic scene viewing

In humans and other primates, high-acuity vision is restricted to the fovea, requiring frequent saccadic eye movements to sample visual information, a process known as overt attention. Classical visual salience theory explains how low-level image features guide these movements, but recent human studies have shown that overt attention is also strongly guided by scene meaning--the spatial distribution of semantic informativeness. Whether this form of attentional guidance is uniquely human or shared across primate vision remains unknown. Here, we addressed this question by recording eye movements from two rhesus macaques freely viewing naturalistic indoor scenes. Fixation selection was modeled using meaning maps alongside image-based salience maps and center proximity. In both monkeys, meaning robustly predicted fixation selection after controlling for visual salience and center bias. Moreover, high-meaning regions captured attention independently of visual salience, whereas salience played an increasingly important role as meaning decreased. While this prioritization of meaningful regions remained robust across environments, familiarity broadened visual exploration by increasing the likelihood of fixating less meaningful areas. Finally, the influence of meaning on fixation selection strengthened with attentional engagement. These findings suggest that meaning-based attention is an evolutionarily conserved component of primate vision and establish a behavioral foundation for investigating its neural mechanisms.

animal behavior and cognition↗

bioRxiv2026

Co-evolution of Oncogenic KRAS Signaling and LILRBhigh Macrophages Drives Pancreatic Cancer Recurrence

Pancreatic ductal adenocarcinoma (PDAC) frequently recurs after surgical resection, indicating that residual disease is sustained by coordinated tumor-microenvironment interactions. To define the biological basis of recurrence, we leverage large-scale clinical data from 2,710 patients, deeply characterized multi-omics profiling (whole-exome, bulk RNA, and single-nucleus sequencing) of 36 matched primary and locally recurrent PDACs, an in-house multiplex spatial imaging cohort of 190 patients, and extensive public datasets. Recurrent tumors were characterized by increased KRAS mutant allele dosage and reinforced KRAS signaling, accompanied by expansion of basal-like malignant cell states. In parallel, we identified an immunosuppressive macrophage population marked by high LILRB expression that spatially co-localized with KRAS-activated tumor cells. Functional studies showed that LILRB4+ macrophages enhanced tumor cell plasticity and progression, whereas inhibition of macrophage LILRB4 suppressed these phenotypes. Notably, a first-in-class human anti-LILRB4 antibody reduced macrophage-driven tumor traits, and dual targeting of KRAS signaling and LILRB4 achieved superior tumor control in macrophage-containing mouse models. These findings reveal a co-evolved tumor-immune niche underlying PDAC recurrence and nominate the KRAS-LILRB4 axis as a therapeutic vulnerability.

cancer biology↗

bioRxiv2026

Retrotransposons Promote Clonal Hematopoiesis Through Aging-Related Stromal Inflammation

Clonal hematopoiesis (CH) is an age-related phenomenon driven by the expansion of mutant hematopoietic stem cell (HSC) clones, most commonly harboring mutations in DNMT3A. While inflammation is known to promote CH, the upstream triggers of this inflammatory state remain unclear. We show that aging selectively upregulates retrotransposons in the non-hematopoietic cell compartment of the murine bone marrow, particularly in mesenchymal stromal cells. Using in vivo competitive transplant models, we demonstrate that retrotransposon-induced inflammation cell-extrinsically promotes Dnmt3a-mutant HSC expansion. This competitive advantage arises from mutant HSC resistance to inflammation-driven cell cycle perturbations. Mechanistically, we show that retrotransposon activation induces type I interferon signaling via viral mimicry, such that stromal knockdown of either Irf3 or Sting abrogates the competitive advantage of Dnmt3a-mutant HSCs. Our findings establish stromal-selective retrotransposon reactivation as a previously unrecognized, non-cell-autonomous source of inflammation that contributes to age-associated CH. Key PointsO_LIRetrotransposons remodel the aging niche through viral mimicry pathways to promote Dnmt3a-mutant clonal hematopoiesis. C_LIO_LIRetrotransposon-mediated inflammation impairs wild-type HSC fitness, while Dnmt3a-mutant HSCs resist inflammatory changes. C_LI

cancer biology↗

bioRxiv2026

Unwinding of RNA G-quadruplexes induces mouse and human totipotency

Totipotent stem cells (TotiSCs) have significant application prospects in regenerative medicine and assisted reproductive technologies. The mRNAs of totipotency-related genes are rich in G-quadruplex (G4) structures, while the G4 density of pluripotency-related genes mRNAs is relatively low, suggesting a potential functional link between RNA G4s and the totipotent state. Nevertheless, how G4s are involved in the establishment or maintenance of mouse and human totipotency remains poorly understood. Here, we demonstrate that FC3, a small-molecule RNA G4 unwinder, enables efficient induction and maintenance of mouse and human TotiSCs (mG4TotiSCs and hG4TotiSCs). These FC3-induced TotiSCs closely recapitulate the molecular features of 2-cell-stage blastomeres via transcriptomic and epigenomic profiling. Functionally, both mG4TotiSCs and hG4TotiSCs exhibit totipotent capacity: they differentiate into embryonic and extraembryonic lineages in vitro and in chimeric embryos; moreover, they autonomously self-organize into blastocyst-like structures without exogenous signalling. Mechanistically, we identify that Gata2 mRNA, a G4-containing transcript, is essential for FC3-mediated reprogramming. Genetic disruption of Gata2 would abolish totipotency induction. Collectively, RNA G4 unwinding is a new regulatory axis governing totipotency acquisition and maintenance, providing insight into the functional interplay between nucleic acid secondary structures and cell fate plasticity.

cell biology↗

bioRxiv2026

Nonanticoagulated Heparin Derivatives Mediate Goblet Cell Differentiation to Restore the Mucosal Barrier for Ulcerative Colitis Therapy

Epithelial mucus barrier dysfunction is a pathological hallmark of ulcerative colitis (UC), yet current clinical therapeutic strategies primarily suppress inflammation, lacking reliable approaches for restoration of the mucosal layer. Here, through a systematic screen of our established library of deanticoagulated heparins, we identified NALHP, a non-anticoagulant low-molecular-weight heparin derivative, and its representative fraction S6 as orally active epithelial repair-promoting glycans. NALHP/S6 restored crypt architecture, mucus production and epithelial barrier integrity in experimental colitis. In UC patient-derived colonic organoids, NALHP/S6 reduced aberrant stem/proliferative programs while promoting secretory, absorptive and junctional maturation. Single-cell transcriptomics and temporal validation identified a transient repair-secretory transitional state (RSTS) positioned between classical Wnt-associated stemness and mature barrier-forming epithelial states. Transcriptomic analysis revealed coordinated attenuation of Wnt and Notch signaling, whereas pharmacological reactivation of these pathways opposed NALHP/S6-induced epithelial state progression. These findings define mucosal repair as a regulated epithelial-state transition and identify NALHP/S6 as glycan-based modulators capable of restoring this progression in UC epithelium.

pathology↗

bioRxiv2026

Antibody-Dependent Heterotypic Syncytia Drive COVID-19 Inflammation and Disease Progression

Severe COVID-19 is characterized by profound immune dysregulation and excessive inflammation. Aberrant myeloid responses drive hyperinflammation, yet the precise mechanisms remain elusive. Here, we demonstrate that certain spike antibodies promote the formation of heterotypic syncytia between monocytes/macrophages and virus-infected pneumocytes, leading to excessive inflammatory cytokine release. This antibody-dependent syncytium formation requires Fc{gamma}RI (CD64) and ADAM10, as well as the assembly of the six-helix bundle by the spike S2 subunit. Notably, these syncytia exhibit a stronger proinflammatory signature compared to virus-infected epithelial cells. In vivo, sub-neutralizing antibody concentrations amplified inflammation and exacerbated disease in SARS-CoV-2-infected mice without increasing viral burden. Furthermore, scRNA-seq of postmortem lung tissues from COVID-19 patients implicated the monocyte/macrophage-derived syncytia as a key cellular source of inflammatory cytokines. Together, these findings define a novel mechanism of antibody-dependent enhancement of inflammation that helps explain the hyperinflammatory responses in severe COVID-19 and suggest new therapeutic opportunities targeting this pathway.

immunology↗

bioRxiv2026

CD28 Co-stimulation Is Organized by Signaling Condensates and Counteracted by PD-1

T cell activation relies on the coordinated integration of TCR and co-signaling pathways, yet how these signals are physically organized remains unclear. Here, we demonstrate that CD28 co-stimulation is driven by a phase-separation mechanism in which the CD28 intracellular domain (ICD) forms signaling condensates with the Src-family kinase Lck. Ligand engagement promotes the CD28 ICD accessibility, and triggers rapid CD28/Lck condensation, enhancing CD28 phosphorylation, cytoskeletal polarization, and cytokine production. We further identify PD-1 as a graded regulator of this process: monophosphorylated PD-1 is recruited into CD28/Lck condensates, whereas di-phosphorylated PD-1 competitively binds the CD28 ICD and dissolves these assemblies. CD28 and PD-1 ICDs also undergo condensation directly, revealing a dynamic and compositionally heterogeneous signaling system. Guided by this competitive phase-separation mechanism, we engineer CD28 ICD mutants that preserve Lck condensation while resisting PD-1-mediated disruption. Incorporation of these condensation-selective mutants into CAR constructs confers resistance to inhibitory signaling and enhances antitumor efficacy in vivo. These findings establish phase separation as a central organizing principle of CD28 co-stimulation and provide a biophysical framework for engineering more resilient therapeutic T cells.

immunology↗

bioRxiv2026

A transcriptional regulator gene TRG1 of Trichoderma longibrachiatum is involved in the regulation of peptaibols synthesis

Trichoderma species are recognized for their robust biocontrol capacity, primarily due to the production of peptaibols, potent secondary metabolites that exhibit antibacterial properties, induce cell apoptosis, and enhance plant disease resistance. To elucidate the regulatory mechanism of peptaibol synthesis, we investigated the role of a transcription regulator gene TRG1 (designated as TLTRG1), which we identified within a non-ribosomal peptide synthetase (NRPS) gene cluster of T. longibrachiatum SMF2. We successfully created a{Delta} TRG1 gene knockout mutantusing homologous recombination. Phenotypic analysis indicated that the{Delta} TRG1 mutant maintained wild-type growth rate, colony morphology, and spore production. However,{Delta} TRG1 exhibited a significantly reduced inhibition rate against the plant pathogen Botrytis cinerea and a lower efficacy in controlling gray mold on detached rose leaves. High-performance liquid chromatography (HPLC) analysis provided direct molecular evidence, showing that peptaibol production in the mutant was 2.5 times lower than that of the wild-type strain. These findings conclusively establish that TRG1 functions as a key positive transcriptional regulator essential for high-yield peptaibol biosynthesis by modulating NRPS gene expression. This gene represents a critical molecular target for bioengineering strategies aimed at enhancing the biocontrol efficacy of Trichoderma strains. The Importance sectionTrichoderma species are known to produce peptaibols, which exhibit antibacterial properties, induce cell apoptosis, and enhance plant disease resistance. However, the mechanisms underlying the biosynthesis and regulation of peptaibols remain unclear. In this study, we investigated the role of a transcription regulator gene located within a non-ribosomal peptide synthetase (NRPS) gene cluster of T. longibrachiatum SMF2, which we designated as TLTRG1 (TRG1). Phenotypic analysis indicated the inhibition rate of {Delta}TRG1 against Botrytis cinerea and its effectiveness in controlling gray mold were significantly reduced compared to the WT strain. High-performance liquid chromatography (HPLC) analysis revealed that the production of peptaibols in the mutant was significantly decreased. These findings suggest that the TRG1 gene may play a crucial role in regulating the expression of NRPS genes, thereby affecting the biosynthesis of peptaibols. Therefore, it can be concluded that the gene TRG1 is a molecular target for bioengineering strains with enhanced biocontrol efficacy.

microbiology↗

bioRxiv2025

Synchronized Latency Reversal and Immune Clearance by a Multifunctional Fusion Protein Enables HIV-1 Reservoir Reduction

Strategies that concurrently reactivate latent reservoirs and enhance immune-mediated clearance hold significant promise for achieving an HIV cure. Here, we developed hyperIL-15xsCD4-Fc (15xsCD4-Fc), a fusion protein that integrates latency reactivation, targeted immune engagement, and effector-mediated killing into a single molecule. This agent not only potently reverses HIV-1 latency in CD4+ T cells from people living with HIV-1 (PLWH) through coordinated IL-15 receptor signaling and sCD4-mediated HIV-1 envelope (Env) engagement, but also enhances antigen-specific CD8+ T cell response in PBMCs derived from PLWH. Furthermore, 15xsCD4-Fc enables Env-specific elimination of reactivated latently infected cells by NK cells while preventing off-target cytotoxicity. In PBMCs from PLWH, 15xsCD4-Fc reduced replication-competent HIV-1 DNA by 93.8%. In antiretroviral treated HIV-1-infected humanized mice, the molecule demonstrated both safety and efficacy in diminishing viral reservoir in lymphoid organs. This spatiotemporally coupled approach to reservoir exposure and immune recognition establishes a clinically viable strategy for clearing the HIV-1 reservoir. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/693434v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@8f8f0org.highwire.dtl.DTLVardef@10f63f7org.highwire.dtl.DTLVardef@16c1de2org.highwire.dtl.DTLVardef@11e1787_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Quantitative MRI Reveals Bone Marrow Regeneration Following Targeted Marrow Irradiation and Transplantation in a Sickle Cell Disease Model

Sickle cell disease (SCD) is associated with chronic bone marrow stress, altered hematopoiesis, and reduced adiposity. Whether marrow-selective conditioning followed by transplantation normalizes these abnormalities remains unclear. We investigated bone marrow remodeling in Townes mice by comparing SCD control (SCD-Con) with mice that received total marrow irradiation (TMI) followed by bone marrow transplantation (SCD-TMI-BMT). Multiparametric micro-MRI at 7 T quantified proton density water fraction (PDWF), proton density fat fraction (PDFF), and R2*(1/T2*), and micro-CT assessed trabecular structure in the femur. SCD-Con marrow showed higher water content (elevated PDWF), reduced adiposity (lower PDFF), and imaging features consistent with erythroid hyperplasia and elevated iron burden (shorter T2* with reciprocal increase in R2*). In contrast, SCD-TMI-BMT mice demonstrated smaller R2*, reduced PDWF, and partial restoration of adiposity, accompanied by reciprocal shifts in R2*, consistent with decreased cellular iron and marrow remodeling. Micro-CT revealed an improved trabecular architecture after BMT compared to SCD control. MRI imaging biomarkers aligned with histologic evidence of reduced cellularity and larger adipocyte voids. In conclusion, a TMI-BMT SCD model promotes partial normalization of the marrow microenvironment. Multiparametric MRI with micro-CT provides a practical, non-invasive framework for monitoring marrow remodeling and skeletal health after curative therapy.

bioengineering↗

bioRxiv2025

Genome-wide CRISPR screen reveals PEX11B as a host restriction factor against ORFV through membrane fluidity regulation

Host-pathogen interactions are shaped by cellular restriction factors that direct antiviral defenses. We built the first ovine genome-wide CRISPR knockout library in sheep testis (OA3.Ts) cells, targeting all protein-coding genes. Using this platform, we identified PEX11B, a peroxisomal membrane regulatory protein, as a strong restriction factor against orf virus (ORFV) infection. Removing PEX11B increased viral susceptibility and triggered severe cytopathic effects with membrane fusion and syncytia formation. Mechanistic studies showed that PEX11B knockout harmed peroxisomal integrity and disrupted lipid metabolism. This led to greater plasma membrane fluidity, creating a proviral environment that allowed more viral entry and replication. These results reveal a new antiviral function for PEX11B in blocking viral infection and underscore the importance of peroxisomal regulation in host-virus interactions.

microbiology↗

bioRxiv2025

Identification of QTLs for Internode Length and Diameter Associated with Lodging Resistance in Rice

Lodging is a significant challenge in rice production, particularly for high-yielding cultivars. Previous research has shown that stem characteristics, such as internode length and diameter, are key determinants of lodging resistance. However, the genetic mechanisms controlling these traits remain poorly understood. To investigate the genetic basis of lodging-related stem traits, a recombinant inbred line (RIL) population was developed from a cross between Zhenshan 97 and C309, two rice varieties with contrasting stem architectures. A high-density genetic linkage map was constructed using 3,307 bin markers generated by next-generation sequencing. Comprehensive phenotypic analysis was conducted for heading date, internode length, and diameter. A total of 54 quantitative trait loci (QTLs) were identified across the genome. Importantly, 15 pleiotropic QTLs were detected, each affecting multiple internode-related traits. These pleiotropic loci include well-known functional genes such as SCM2 and Gn1a, as well as several novel loci potentially involved in regulating stem strength and lodging resistance. Additionally, RNA-Seq analysis was performed to identify candidate genes associated with these traits. Among the 1,263 expressed genes within the 15 pleiotropic QTL regions, 183 differentially expressed genes were identified. LOC_Os06g11130 was highlighted as a key gene for further investigation. Haplotype analysis and linkage disequilibrium analysis revealed significant haplotype variation in LOC_Os06g11130, further confirming its potential role in lodging resistance. This study enhances our understanding of the genetic architecture of internode traits associated with lodging resistance in rice. The identification of pleiotropic and major-effect QTLs provides valuable genetic resources for marker-assisted selection and genomic breeding, with the potential to improve lodging resistance in high-yielding rice cultivars. These findings contribute to the development of rice varieties that balance high yield potential with enhanced lodging resistance.

genetics↗