Biology subjects

Zhou, Z.

Publications and source records attributed to Zhou, Z..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

Healthcare Infrastructure Shapes Evolutionary Trade-offs and Geographic Dissemination of Multidrug-Resistant Acinetobacter baumannii

Antimicrobial-resistant pathogens pose an existential threat to modern medicine, yet the evolutionary forces driving their adaptation in healthcare systems remain largely unexplored. We revealed that hospital network architecture functions as a primary selective pressure, driving pathogen evolution through infrastructure-dependent virulence-transmission trade-offs. Phylogenomic analysis of 5,023 Acinetobacter baumannii isolates across Chinas centralized healthcare system identifies two co-existing evolutionary strategies: a virulence-optimized clade (ESL2.4) that spread slowly (20.4 km per year) in low-connectivity hospitals, and a transmission-optimized clade (ESL2.5) that disseminate rapidly (65.2 km per year) through mega-city healthcare hubs, likely attributed to its capsule conversion and increased upper respiratory colonization. Comparative analysis with European A. baumannii populations demonstrates that healthcare connectivity, not geography, governs pathogen distribution through convergent genomic adaptations. Our simulation suggests competitive asymmetries of the two clades, following the ecotype principle and enabling stable coexistence. The COVID-19 pandemic provided a natural experiment validating these mechanisms: outpatient restrictions reduced transmission-optimized lineage spread by 89%, while virulence-optimized lineage persisted through inpatient networks. These findings establish healthcare infrastructure as a critical evolutionary driver with immediate implications for predicting and controlling antimicrobial resistance emergence across diverse healthcare systems.

microbiology↗

bioRxiv2026

Stepwise DNA unwinding gates TnpB genome-editing activity

TnpB is a compact RNA-guided endonuclease and evolutionary ancestor of CRISPR-Cas12 that offers a promising platform for genome engineering. However, the genome-editing activity of TnpBs remains limited and its underlying determinants are poorly understood. Here, we used biochemical and single-molecule assays to examine the DNA-unwinding mechanism of Youngiibacter multivorans TnpB (Ymu1 TnpB). DNA unwinding proceeds through a discrete, long-lived partially unwound intermediate state before reaching a fully unwound open state. The open state forms inefficiently and collapses readily in the absence of negative supercoiling. An optimized variant, Ymu1-WFR, stabilizes formation of both the intermediate and open states, resulting in enhanced DNA cleavage in vitro and increased genome editing in plants. These findings identify the physical basis for the observed minimal activities of natural TnpBs, revealing how stabilizing specific unwinding states enables efficient DNA targeting.

biochemistry↗

bioRxiv2025

STEAP4+ neutrophils: a promising circulating biomarker for lung metastasis

As the leading contributor to cancer-related mortality, metastasis often evades detection until advanced stages, underscoring the critical need for early predictive biomarkers. Neutrophils are naturally circulating sentinels that have been implicated in pioneering pre-metastatic niche formation in distant organs. Nevertheless, their heterogeneity within evolving metastatic microenvironments remains poorly characterized. Here, through dynamically delineating neutrophil subsets via single-cell transcriptomics, we identified a conserved feature of lung metastasis in breast cancer and other cancer models. Among the core genes, a cell surface marker, STEAP4, was selected and validated to indicate lung metastases at both RNA and protein levels. In both humans and mice, these STEAP4+ neutrophils were detectable not only in lung metastatases but also in the circulation. Clinically, the abundance of circulating STEAP4+ neutrophils robustly discriminates patients with lung metastasis from those with localized primary tumor. Our findings uncover STEAP4+ neutrophils as a promising biomarker and lay the groundwork for a non-invasive, blood-based diagnostic strategy for metastatic disease.

cancer biology↗

bioRxiv2025

Structure and evolution-guided design of minimal RNA-guided nucleases

The design of RNA-guided nucleases with properties not limited by evolution can expand programmable genome editing capabilities. However, generating diverse multi-domain proteins with robust enzymatic properties remains challenging. Here we use an artificial intelligence-driven strategy that couples structure-guided inverse protein folding with evolution-informed residue constraints to generate active, divergent variants of TnpB, a minimal CRISPR-Cas12-like nuclease. High-throughput functional screening of AI-generated variants yielded editors that retained or exceeded wild-type activity in bacterial, plant and human cells. Cryo-EM-based structure determination of the most divergent active variant revealed new stabilizing contacts in the RNA/DNA interfaces across conformational states, demonstrating the design potential of this approach. Together these results establish a strategy for creating non-natural RNA-guided nucleases and conformationally active nucleic acid binders, enlarging the designable protein space. One-sentence abstractAn evolution- and structure-conditioned model enables design of active RNA-guided nucleases with new nucleic acid contacts resolved by cryo-EM.

synthetic biology↗

bioRxiv2025

A foundation model for microbial growth dynamics

Microbial growth dynamics contain rich information about microbial populations, which support applications from antibiotic testing to microbiome engineering. However, the high dimensionality of growth data and the scarcity of large, task-specific datasets have limited generalizable modeling analysis across systems. Here, we develop a foundation model for microbial growth dynamics. It is a large-scale, self-supervised representation model trained on [~]370,000 experimental and simulated growth curves spanning diverse microbial species, environmental conditions, and community contexts. The model learns lower-dimensional latent embeddings that capture essential dynamical features of raw growth data and enable accurate reconstruction of these data. The concise representations enhance predictive performance in diverse downstream applications. Using these embedding, we achieve few-shot learning for antibiotic classification and concentration prediction, accurate forecasting of simulated and experimental communities, and inference of total abundance from relative-abundance data. By extracting transferable representations from heterogeneous datasets, our model provides a general framework for analyzing and predicting microbial community dynamics from limited measurements.

synthetic biology↗

bioRxiv2025

Single-cell transcriptomics reveals spaceflight-induced accelerated aging and impaired recovery in the murine bone marrow

Spaceflight induces physiological changes that resemble accelerated aging, however, how age influences bone marrow response at the cellular level remains poorly understood. Here, we perform single-cell transcriptomic profiling of murine femur and humerus bone marrow from young (12-week-old) and old (29-week-old) mice that underwent a 32-day spaceflight mission followed by a 24-day Earth recovery, with age-matched ground controls. Our analysis reveals that, compared with young cohorts, old mice exhibit persistent dysregulation after spaceflight, most prominently in erythroid and B cell lineages. In erythroid cells, old flight mice show pronounced aging signatures, characterized by impaired maturation, inhibited mitophagy, and increased oxidative stress. In B cells, old flight mice show dysregulation associated with failure of the AP-1 stress-response pathway and complete collapse of the intercellular CXCL signaling network. Our findings dissect the age-dependent effects of spaceflight on the bone marrow hematopoietic and immune system at single-cell resolution, and demonstrate that spaceflight imposes a disproportionate burden on the aged hematopoietic system and blunts post-flight recovery. These insights provide candidate pathways and biomarkers for health monitoring and countermeasures in long-duration missions.

bioinformatics↗

bioRxiv2025

CREG1 promotes autophagy and protects the heart against nutritional stress-induced injury and age-associated hypertrophy, fibrosis and diastolic dysfunction

BackgroundCellular repressor of E1A-stimulated genes 1 (CREG1) is an evolutionarily conserved endolysosomal glycoprotein that enhances lysosomal biogenesis and autophagy, suppresses proliferation, and promotes differentiation. A prior gene targeting strategy that produced truncated N-terminal fragments resulted in embryonic lethality, limiting the ability to assess the physiological role of complete CREG1 loss. We hypothesized that CREG1 regulates cardiac autophagy, thereby maintaining cardiac structure and function under both physiological and stress conditions. MethodsWe generated true Creg1 knockout (KO) mice by deleting the entire open reading frame and established a gain-of-function model by inserting human CREG1 into the Rosa26 locus. Cardiac structure and function were assessed in global and cardiomyocyte-specific Creg1 knockout (cmCreg1KO) and knock-in (cmCREG1KI) mice. Autophagy was evaluated using biochemical assays, immunofluorescence, electron microscopy, and the CAG-EGFP-RFP-LC3 reporter analysis. ResultsGlobal Creg1 knockout mice developed progressive cardiac hypertrophy, fibrosis, and diastolic dysfunction at [~]80 weeks of age. At younger ages, CREG1 deficiency increased susceptibility to nutritional stress, resulting in mitochondrial damage and myofiber disruption in cardiomyocytes. cmCreg1KO mice exhibited dilated cardiomyopathy, left atrial thrombosis, and lethality around 50 weeks of age; however, interpretation of disease severity is confounded by Myh6-Cre-associated cardiotoxicity, which may mask additional pathogenic effects attributable to CREG1 loss. In contrast, cmCREG1KI mice demonstrated enhanced exercise capacity under nutritional stress. Mechanistically, CREG1 was localized to endolysosomal and autophagosomal compartments. Loss of CREG1 impaired autophagy flux and mitophagy, likely due to defective autophagosome membrane expansion and degradation. In contrast, CREG1 overexpression enhanced autophagy in cardiomyocytes. ConclusionsCREG1 is a key regulator of cardiac autophagy, protecting the heart against nutritional stress-induced injury and age-associated cardiac hypertrophy, fibrosis, and diastolic dysfunction. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/687936v1_ufig1.gif" ALT="Figure 1000"> View larger version (60K): org.highwire.dtl.DTLVardef@1b9fc05org.highwire.dtl.DTLVardef@150e48aorg.highwire.dtl.DTLVardef@1cc47adorg.highwire.dtl.DTLVardef@75ed53_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Skull Bone Marrow Drainage and Its Associations with Inflammation, Sleep Quality, and Cognitive Performance

BackgroundRecent studies using human craniotomy samples and murine models have revealed channels that connect the inner skull cortex to the skull marrow cavities. While cerebrospinal fluid (CSF) tracer access to skull bone marrow has been described in CSF circulation disorders, evidence on regional patterns and clinical correlates in broader clinical cohorts is limited. MethodsThree-dimensional imaging was performed at baseline, 4.5, 15, and 39 hours post-gadolinium administration in 87 patients with neurological conditions. Signal changes in skull bone marrow near the superior sagittal sinus, lateral fissure, and cisterna magna were recorded. CSF drainage function was characterized as the percentage changes in the signal unit ratio within the skull bone marrow from baseline to time points post administration of gadolinium. ResultsThe tracer drained from CSF into the skull bone marrow, highlighting the drainage variations nearby different regions. Reduced drainage was associated with female sex, hypertension, diabetes, and elevated neutrophil levels (p < 0.05). Drainage near the superior sagittal sinus was inversely associated with sleep quality and positively associated with cognitive scores, and partially accounted for the association of sleep quality with cognitive function (indirect effect {Delta}{beta} = -0.092; bootstrap 95% CI -0.195 to -0.004; proportion mediated {approx} 38%). ConclusionThese results support the presence of skull bone marrow adjacent routes for CSF tracer movement and suggest that skull bone marrow tracer dynamics relate to systemic inflammation, sleep quality, and cognitive performance in this clinical cohort.

neuroscience↗

bioRxiv2025

MicroRNA156 and its targeted SPL genes interact with the photoperiod, vernalization, and gibberellin pathways to regulate wheat heading time

Heading time has a large impact on adaptation to different environments and crop productivity. In this study, we characterized the effect of the endogenous age pathway on heading time and its interactions with the photoperiod and vernalization pathways in the leaves of tetraploid wheat (Triticum turgidum ssp. durum). Plants with reduced levels of microRNA156 or increased expression of its downstream targets, the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes SPL3, SPL4, and SPL13 exhibited accelerated heading time, with stronger effects under suboptimal inductive conditions. Earlier heading was associated with the upregulation of miR172 and flowering-promoting genes VRN1, FUL2, and FT1 and the downregulation of flowering-repressing genes AP2L1 and VRN2. Additionally, we uncovered complex interactions among SPL, SQUAMOSA (VRN1 and FUL2) and DELLA proteins that modulate wheat heading time. We showed that DELLA proteins, which are negative regulators in the gibberellic acid pathway, can interact with SPL proteins reducing their ability to induce flowering. We also discovered previously unknown interactions between SQUAMOSA and DELLA proteins in wheat that compete with the DELLA-SPL interactions, likely reducing DELLAs ability to repress SPL3 and SPL4 activity. Since SPL3 and SPL4 directly promote VRN1 and FUL2 transcription, these interactions generate a positive regulatory feedback loop that accelerates wheat heading time. Finally, we developed dominant miR156-resistant alleles rSPL3, rSPL4, and rSPL13 that accelerate wheat heading time under both optimal and suboptimal inductive conditions. These publicly available genetic resources can be used to fine tune heading time and improve wheat adaptation to changing environments. Significance statementWheat heading time is critical for adaptation to diverse environments. We generated dominant mutations for the SPL3, SPL4 and SPL13 genes that accelerate heading time. Different combinations of these mutations can be used to modulate heading time and improve wheat adaptation to changing environments.

plant biology↗

bioRxiv2025

Dynamical memory underlies prolonged plasmid persistence after transient antibiotic treatment

Plasmids play critical roles in spreading and maintaining antimicrobial resistance (AMR). They often exhibit prolonged persistence upon antibiotic treatment, even when they impose substantial burden on their hosts. This persistence has been primarily attributed to rapid horizontal transfer or low plasmid cost. However, these mechanisms cannot account for the slow decay of burdensome plasmids with poor mobility. Here, we show that the decoupling of time scales between slow segregation loss and fast growth competition leads to a slow-down in plasmid abundance decay at high initial plasmid abundance, reminiscent of the ghost effect from nonlinear dynamical systems. Integrating theory, simulations, and quantitative experiments across clonal populations and multi-species bacterial communities, we demonstrate that a transient antibiotic pulse can eliminate plasmid-free cells and create a ghost state that extends plasmid persistence from days to months. Our research reveals a generalizable mechanism for the prolonged ecological memory of antibiotic exposure and underscores the need for proactive strategies to curb the spread of AMR.

microbiology↗

bioRxiv2025

Evolutionary landscape of oral microbiome over 100,000 years

The human oral microbiome represents an intimate and enduring partnership between host and microbial communities, yet its evolutionary trajectory across deep time remains largely uncovered. Here we reconstruct the global history of the oral microbiome over 102,400 years using a global collection of 1854 oral samples spanning 61 countries. We reveal that major cultural transitions of the Neolithic Revolution, industrialization, and recent medical advances have driven a directional, globally coordinated co-evolution of oral microbial ecology, function, and population structure. Network analysis identifies two universal microbial modules of dental calculus modules: the commensal-enriched DCM1 module and the pathogen-enriched DCM2, both exhibiting progressive ecological polarization. DCM2 surged around 4,000 years ago with agricultural intensification but subsequently declined in modern European populations while persisting at high levels in African and some American groups, a geographic divide mirroring socioeconomic inequities. Species-level analyses demonstrate widespread directional changes, with obligate anaerobes declining as aerotolerant taxa expand, reflecting a carbohydrate-associated functional remodeling toward starch metabolism. Phylogenomic reconstruction reveals contrasting evolutionary trajectories. Pauljensenia mediterranea experienced near-extinction following a severe bottleneck, while Actinomyces israelii underwent a selective sweep with rapid population expansion 1,000 years ago. Critically, the oral resistome has accelerated in the antibiotic era, resulting in [~]33-50-fold surge of highly mobile, clinically relevant antimicrobial resistance genes in the last century, with Streptococcus acting as a central hub of dissemination. Collectively, these results position the oral microbiome as an active participant that has co-evolved with human subsistence, urbanization and medical practice, with direct implications for global oral health, antimicrobial resistance and interventions aimed at restoring resilient microbial states.

microbiology↗

bioRxiv2025

TSProm: Deciphering the Genomic Context of Tissue Specificity

Characterizing tissue-specific (TSp) gene expression is crucial for understanding development and disease; however, traditional expression-based methods often overlook the latent "regulatory grammar" embedded in the non-coding DNA, particularly in distal promoter regions. Here, we introduce TSProm, a framework that specializes a DNA foundation model (DNABERT2) to decipher the long-range regulatory logic of TSp promoters at the gene isoform level. The contributions of our work are two-fold. First, we propose a novel comparative design that trains two distinct models, A: for general promoter biology and B: for TSp regulation. These models enable the precise isolation of sequence motifs around the transcription start site that uniquely define tissue identity. Second, we introduce a comprehensive explainable AI (xAI) module that integrates attention-based discovery with model-agnostic SHAP analysis to provide robust, cross-validated interpretations of learned features. Applying this framework to human brain, liver, and testis promoters, we identified and validated clinically relevant transcription factors (TFs) in the brain, including SP1, MYC, and HES6, and confirmed their known roles in diseases such as gliomas and neuroblastomas. Our analysis further revealed that C2H2 Zinc Finger proteins are a dominant feature of the global landscape of TSp gene regulation. TSProm provides a novel and interpretable framework for identifying TSp gene regulatory elements, offering powerful computational tools for the study of tissue-specific gene regulation in normal and disease conditions.

bioinformatics↗

bioRxiv2025

Development of Collagenous Filaments with Tuneable Mechanical Properties Using a 3D Bioprinter and Molecular Crowding

Engineering collagen constructs that replicate the mechanical strength and biological functionality of load-bearing tissues like tendon remains a significant challenge. This study establishes a scalable and accessible biofabrication method that combines the precision of a commercial 3D bioprinter with the physicochemical principles of molecular crowding. Using an acidic collagen solution in combination with a hypertonic polyethylene glycol (PEG) bath, we systematically investigate how modulating pulling speed and nozzle diameter dictates the final filament properties. Our results demonstrate that faster pulling speeds and smaller nozzle diameters produce thinner, more densely packed filaments. High-resolution scanning electron microscopy (SEM) and polarised light microscopy reveal a tuneable transition in surface morphology, from a disordered isotropic state to a highly ordered phase, quantitatively confirmed by a sharp increase in birefringence. Critically, we demonstrate the preservation of collagens native, periodic 66 nm d-banding, an essential motif for cell interaction. This structural refinement translates to a dramatic enhancement of mechanical performance, with the strongest filaments achieving an ultimate tensile strength of 0.64 GPa and a Youngs modulus of 8.9 GPa, values that surpass native tendon. Furthermore, the fabricated filaments are highly biocompatible and bio-instructive, promoting robust alignment and elongation of mesenchymal stem cells. This work provides a direct link between bioprocess parameters and the resulting hierarchical structure, offering a versatile platform for fabricating high performance, biomimetic materials for regenerative medicine.

bioengineering↗

bioRxiv2025

MDFIC2 is a sensory neuron-specific PIEZO channel auxiliary subunit

PIEZO channels are critical for sensory mechanotransduction. While MyoD-family inhibitor proteins were identified as PIEZO1 auxiliary subunits, their broader regulatory roles, particularly in sensory cells, remained unclear. Here we demonstrate native MDFIC and MDFI regulate endogenous PIEZO channel currents in various non-sensory cell types. However, neither MDFIC nor MDFI are expressed in primary sensory neurons. In these cell types we identified an uncharacterised member of this family, Mdfic2/Gm765, that shares the ability to physically bind to PIEZO1 and PIEZO2. MDFIC2 is selectively expressed in subsets of mechanosensitive neurons, including dorsal root ganglia, trigeminal ganglia, and vagal sensory neurons. Like its paralogues, MDFIC2 alters PIEZO1/2 mechanosensitivity and inactivation kinetics, converting them into high-threshold slowly inactivating mechanoreceptors. Extensive cryo-EM reveals a conserved binding pocket for these auxiliary subunits in the pore modules of both PIEZO1 and PIEZO2 mediated by the post-translationally modified distal C-termini of MyoD-family inhibitor proteins. This provides a comprehensive structural and functional characterisation of MyoD-family inhibitor proteins as PIEZO1/2 channel regulators and offers new insights into sensory physiology and mechanical pain mechanisms.

biophysics↗

bioRxiv2025

Hemin Inhibits the Activation of STING in Macrophages by Inducing HO-1, Promoting Endometriosis Development

IntroductionEndometriosis (EMS) is an estrogen-dependent inflammatory disorder characterized by immune dysregulation. This condition profoundly affects the quality of life and reproductive health of nearly 200 million women of reproductive age worldwide and poses significant clinical challenges due to lack of diagnosis tools and effective treatment. Peritoneal macrophages play a central role in promoting the initiation and progression of EMS. Bioinformatics studies have indicated that the STimulator of INterferon Gene (STING) was downregulated in the macrophages in EMS, and this influenced their polarization and functional. However, the specific contribution of STING pathway alterations to EMS pathogenesis remains unclear. MethodsWe integrated scRNA-seq data from EMS patients and healthy controls-including lesions, eutopic endometrium, non-lesional tissue, and peritoneal fluid from EMS patients and healthy controls(n = 19,291 total samples)-to analyze macrophage STING expression and function. Mouse EMS model was generated by injecting uterus fragments into WT or STING-/- mice. Peritoneal fluid was collected and macrophage proportions and subtypes were assessed via flow cytometry. Macrophages were depleted in STING-/- mice prior to EMS induction to evaluate their role in disease progression. In vitro, hemin was used to treat macrophages to investigate how heme oxygenase-1 (HO-1) modulates the STING pathway, assessed through immunoblotting, co-immunoprecipitation, ELISA, and multiplex immunofluorescence. ResultsBioinformatic analysis revealed that macrophages within the EMS lesions are primarily derived from peritoneal macrophages and exhibit decreased STING expression, which correlated negatively with HO-1. STING-/- mice developed more numerous and larger EMS lesions, accompanied by a decreased proportion of large peritoneal macrophages and an increase in small peritoneal macrophages. A marked elevation in M2-type macrophages within the lesions was detected in STING-/- mice. In vitro, hemin-induced HO-1 suppressed STING pathway activation in macrophages. Mechanistically, HO-1 inhibited the translocation of STING from the endoplasmic reticulum to the Golgi, thereby suppressing STING signaling and facilitating EMS. ConclusionMacrophages are essential for lesion formation in STING-/- mice. In vitro, hemin promotes EMS progression via HO-1 - mediated suppression of the STING pathway. Our findings identify the heme-HO-1-STING axis as a key immunomodulatory pathway in EMS and suggest its potential as a therapeutic target. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/683839v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@6901beorg.highwire.dtl.DTLVardef@1f18d44org.highwire.dtl.DTLVardef@1716f6forg.highwire.dtl.DTLVardef@4ae22d_HPS_FORMAT_FIGEXP M_FIG Graphical abstract (Created in BioRender.com) Retrograde menstruation leads to the accumulation of heme in the peritoneal cavity, which upregulates HO-1 expression in peritoneal macrophages. HO-1 inhibits the translocation of STING from the endoplasmic reticulum to the Golgi apparatus in macrophages, thereby suppressing the STING pathway and promoting the development and progression of EMS. The progression of EMS, in turn, reinforces this mechanism, creating a self-sustaining vicious cycle. C_FIG

immunology↗

bioRxiv2025

Graph-based tracing of dynamically functioning gene circuits in cell fate decisions with isoform resolution

Transcription factor (TF) regulatory networks govern complex cellular processes, yet their inference from single-cell transcriptomes is hindered by TFs low abundance, tissue-specific functions, and isoform diversity. We evaluated the utility of transcription factor activity (TFA) to infer TF-TF interactions, demonstrating its superiority over expression-based methods in capturing tissue-specific, high-fidelity regulatory relationships. Using simulated and real-world transcriptomes across human hematopoiesis and early embryonic development, we validated TFAs ability to render regulatory relationships. Through utilizing the concept of propagated regulome, we uncovered TFAs utility in retrospectively resolving dynamic regulatory circuits. To address regulome limitations, we developed an embryonic stem cell-specific Consensus REgulome Database (CRED) with isoform resolution, revealing functional heterogeneity among TF isoforms. Applied to human preimplantation single-cell datasets, CRED outperformed existing regulomes, identifying isoform-specific regulators and tracing regulatory modules despite severe dropouts. Our work unleashes TFA as a robust tool for reconstructing TF networks and highlights the importance of transited, isoform-level, cell-type-specific analysis in unraveling transcriptional regulatory circuits. HighlightsO_LITFA (Transcription Factor Activity) renders regulatory relationships with high fidelity compared to expression. C_LIO_LIUsing transited regulons enables TFA to retrospectively resolve dynamic regulatory interactions in cell fate decisions. C_LIO_LIAn integrated ESC-specific transited regulome database reveals isoform-level heterogeneity. C_LIO_LITFA successfully identifies key TF regulatory modules during human preimplantation from datasets with severe dropout. C_LI

systems biology↗

bioRxiv2025

ProSiteHunter: A unified framework for sequence-based prediction of protein-nucleic acid and protein-protein binding sites

Accurate prediction of protein binding sites is essential for elucidating protein function, understanding molecular interaction mechanisms, and facilitating drug design. However, existing sequence-based approaches are often designed for specific binding-site types and therefore lack generality, whereas structure-based methods typically rely on high-quality structural models, limiting their applicability. Here, we introduce ProSiteHunter, a unified sequence-based framework for protein binding-site prediction, which integrates a fine-tuned protein language model (SiteT5) with a multi-source feature-fusion network that incorporates evolutionary, geometric, and statistical features, while employing bidirectional semantics, local associations, and global dependencies for comprehensive binding-site characterization. The method was systematically evaluated on diverse binding sites prediction tasks, where ProSiteHunter achieved a 39.1% average improvement in PRAUC for protein-DNA/RNA/protein tasks and a 7.4% PRAUC enhancement on the particularly challenging antibody-antigen task over state-of-the-art methods. Moreover, ProSiteHunter is capable of identifying local flexible sites that complement AlphaFold3 predictions and improving the accuracy of antibody-antigen interaction prediction. These results highlight ProSiteHunter as an efficient and unified approach for accurate and robust prediction of diverse protein binding sites.

bioinformatics↗

bioRxiv2025

A newly identified Duck orbivirus as the etiological agent of egg-production decline in Chinese breeder ducks

The genus Orbivirus comprises double-stranded RNA viruses, many of which are transmitted by arthropods and cause febrile, hemorrhagic, or reproductive diseases in animals. In recent years, unexplained outbreaks characterized by marked egg-production decline have occurred in breeder duck flocks in China. To identify the causative agent, samples were collected from affected farms in multiple regions across China between 2022 and 2025. Representative samples were analyzed by high-throughput sequencing, followed by phylogenetic analysis, transmission electron microscopy, host cell infection assays, and animal challenge experiments. A previously unreported Orbivirus, designated Duck orbivirus (DORV), was identified. Epidemiological investigation indicated that outbreaks mainly affected breeder ducks during the peak laying period (21-55 weeks of age), with higher incidence in summer and autumn. The DORV genome contains ten double-stranded RNA segments encoding seven structural and five nonstructural proteins. Phylogenetic analysis showed that DORV is closely related to Parrys Lagoon virus (PLV) and Corriparta virus (CORV). Electron microscopy revealed icosahedral particles 30-40 nm in diameter. DORV replicated efficiently in DEF, DEL and C6/36 cells but not in MDCK and LMH cells, suggesting a restricted host range with potential arthropod-borne features. Infection of breeder ducks with DORV-SD01 reduced egg production by 30-40% and caused lesions in the ovary, liver, and spleen. This study describes a novel duck-origin Orbivirus linked to egg-production decline, offering new etiological insights and extending the host spectrum of Orbivirus. The results provide a foundation for future surveillance and prevention of emerging waterfowl diseases.

microbiology↗