Biology subjects

Zhang, H.

Publications and source records attributed to Zhang, H..

At least 325 records · Page 18Linked to original sources

bioRxiv2025

Programming Microbe-Computer Interaction for Customized Life-Nonlife and Cross-Life Communication

This extension of human-computer interaction (HCI) paradigm to the non-intelligent microbe-computer interaction (MCI) is attractive for building generalized life-nonlife communication. Main challenges lie in how to construct biohybrid interface within individual MCI unit and thereafter program cross-life communication based on these MCI units. Here, we propose the design and construction of opto-interfaced MCI unit composed of engineered microbes and computer terminals, for enabling quantifiable transduction between microbial signals and digital signals. These units were able to serve as biohybrid sensors, actuators and transceivers, supporting biomonitoring, bio-actuation and microbe-centric bidirectional operations. Based on these functional units, we established programmable cross-life communication architectures capable of unicast, multicast, and logic-gate-driven communication with temporal dynamic control. The architectures were validated in biomedical scenarios including tumor hypoxia biomarking, epidermal heavy metal detoxification, and colitis intervention, demonstrating robust performance in closed-loop diagnostic-therapeutic applications. Additionally, we integrated MCI with an unmanned surface vessel for environmental monitoring, highlighting its cross-domain potential. Collectively, we provide a scalable strategy for building customized life-nonlife and cross-life communication, which is expected as an important complement to internet of things (IoT).

synthetic biology↗

bioRxiv2025

Human SerRS/SIRT2 complex structure reveals cross regulation between translation and NAD+ metabolism

Life at the cellular level depends on effective coordination between diverse processes. Here we uncover a novel cross-regulation between metabolism and translation through a 3.2 [A] cryo-EM structure of human cytosolic seryl-tRNA synthetase (SerRS) bound to sirtuin-2 (SIRT2), an NAD+-dependent deacetylase. This interaction, naturally triggered by the NAD+ metabolite ADP-ribose (ADPR), resembles substrate binding and block SIRT2s active site. Interestingly, SerRS acetylation is not required for this interaction. SIRT2 binding sterically and allosterically impedes tRNA binding to SerRS, lowering charged tRNASer level and protein synthesis activity. Key interaction residues in both proteins emerged simultaneously in vertebrates, suggesting co-evolution for cross-regulation. Given ADPRs accumulation under stress, the ADPR-induced SerRS/SIRT2 interaction likely serves as a cell-protective response.

molecular biology↗

bioRxiv2025

SpaceSequest: A unified pipeline for spatial transcriptomics data analysis

BackgroundSpatial transcriptomics has emerged as one of the most powerful tools for gaining biological insights, enabling researchers to uncover intricate relationships between gene expression patterns and tissue architecture. Recent advances in the field have resulted in a variety of new platforms, including Visium, Visium HD, and Xenium from 10x Genomics, as well as GeoMx and CosMx from NanoString Technologies, which has now been acquired by the Bruker Corporation. However, the existence of diverse spatial transcriptomics platforms and various data formats poses challenges in standardizing data analysis. Thus, there remains a critical gap in the availability of a comprehensive pipeline capable of conducting end-to-end analysis that is necessary to extract biological insights from multiple spatial transcriptomics platforms. ResultsHere, we present SpaceSequest, a tailored pipeline that utilizes cutting-edge computational methodologies to conduct a thorough analysis, enabling the extraction of crucial biological insights from five major spatial transcriptomics technologies. SpaceSequest performs (1) standardized quality control and general data processing, (2) key analyses customized for each spatial platform, (3) automated cell type annotation and deconvolution, and (4) high-quality figure and analysis result generation. In addition, SpaceSequest allows for smooth integration with cellxgene VIP and Quickomics for user-friendly data access and interactive visualization. ConclusionsSpaceSequest is a unified and comprehensive pipeline designed for the analysis, visualization, and publication of spatial transcriptomics data from various platforms. The source code is available at https://github.com/interactivereport/SpaceSequest. To facilitate seamless installation and usage, we have also created a detailed Bookdown tutorial that can be accessed through https://interactivereport.github.io/SpaceSequest/tutorial/docs/index.html.

bioinformatics↗

bioRxiv2025

Water body size shapes body size evolution via subgenomic selection in allopolyploid fish

Allopolyploidization is a major force in species evolution, and studying allopolyploids in diverse environments provides insights into their genetic mechanisms. Here, we investigated how water body size variation influences body size in allopolyploid fish. We used a nascent allopolyploid lineage derived from goldfish (Carassius auratus) and common carp (Cyprinus carpio) and established two populations in small and large water bodies for two generations. Genomic, transcriptomic, and epigenomic analyses revealed that the larger population had higher genetic diversity in subgenome R, while the smaller population had higher diversity in subgenome C. Potential selection regions were associated with growth regulatory genes, suggesting a role for gene regulation in body size adaptation. Dynamic gene expression patterns in various tissues indicated potential mechanisms underlying muscle development and adaptation to smaller water bodies. Furthermore, selection regions were linked to changes in chromatin accessibility, with subgenome R being more susceptible to these changes during genetic divergence. Our findings demonstrate that water body size variation drives body size in allopolyploid fish through subgenomic selection, impacting genetic variation, gene regulation, and epigenetic mechanisms.

genomics↗

bioRxiv2025

Integrated reanalysis of global riverine fish eDNA datasets shows robustness and congruence of biodiversity conclusions

The analysis of environmental DNA (eDNA) has revolutionized biodiversity assessments in aquatic ecosystems, enabling non-invasive monitoring of fish communities across diverse regions. However, the global comparability of these eDNA datasets remains ambiguous due heterogeneous sampling protocols and bioinformatic workflows across studies, particularly regarding the robustness of their conclusions on biodiversity assessments. Here, we conducted a meta-analysis of 58 riverine fish eDNA metabarcoding datasets, covering 1,818 sampling sites worldwide, to evaluate the robustness of eDNA-derived biodiversity patterns. We found that species richness estimates and metrics of community structure derived under a common bioinformatic workflow were overall consistent with those of original analyses, despite the relatively high variability in bioinformatic analyses in the respective original studies. Contrastingly, congruence of species identity varied more extensively across datasets, mostly reflecting different completeness and regional relevance of reference databases. Restricting taxonomic assignment to basin-specific species pools improved species identification accuracy, while datasets lacking publicly accessible or well-curated reference data were more prone to mismatches. Year of sampling had a positive effect on taxonomic congruence, such that more recent studies showed increased robustness, also reflecting improved reference database coverage and enhanced species-level identification over time and overall method congruence in more recent years. Overall, the suitability and potential of eDNA for global biodiversity monitoring is corroborating overall robust biodiversity estimates, irrespective of the bioinformatic approaches. Our study underlines the effectiveness and need of further harmonization of bioinformatic workflows and strengthened region-specific reference databases for improved taxonomic resolution and comparability across studies.

ecology↗

bioRxiv2025

Therapeutic Potential of a Tectorigenin Derivative (TED) in Herpetic Stromal Keratitis: Antiviral and lmmunomodulatory Mechanisms

ObjectivesIn this study, the anti-HSV-1 effects of TED were investigated in vitro and in vivo, its therapeutic efficacy against herpetic stromal keratitis (HSK) was evaluated, and its mechanism of action was examined. MethodsWe assessed the cytotoxicity and anti-HSV-1 activity of TED in Vero cells using CCK-8 and plaque assays. The HSK model mice received TED (2.5, 5, or 15 mg/kg), and symptom progression was monitored. The therapeutic effects were evaluated through HE staining, corneal immunofluorescence, and HSV-1 gB quantification. Mechanistic studies were performed to examine the expression of TLR pathway genes, CD4+/CD8+ T-cell infiltration in the cornea and draining lymph nodes, and dendritic cell activation. ResultsTED showed potent anti-HSV-1 activity in vitro and ameliorated HSK in mice, improving body weight and reducing corneal pathology and the incidence of encephalitis. It decreased HSV-1 loads in the cornea, trigeminal ganglion, and brain while modulating cytokines (downregulating IFN-/{gamma}, TNF-, and IL-1{beta} and upregulating IL-10). TED suppressed the TLR pathway (TLR2/3/9, TRAF6, IRF3, and NF-{kappa}B) in the corneal epithelium and reduced CD4+/CD8+ T-cell and dendritic cell infiltration while increasing the number of CD4+ T cells in the lymph nodes. ConclusionsTED has significant anti-HSV-1 activity and effectively treats HSK by reducing viral loads, improving symptoms, and modulating immune responses through TLR pathway inhibition and immune cell regulation, suggesting its potential as an HSK therapeutic.

pharmacology and toxicology↗

bioRxiv2025

Evolutionary patterns and repeated adaptive strategies of deep-sea anemones

Sea anemones occupy the full depth of the oceans, yet their evolutionary patterns and adaptive strategies to the enigmatic deep sea have remained contentious and poorly resolved. Here, we assemble genomes (n = 13) and transcriptomes for 15 species collected between 432 and 6,000 m and integrate them with all publicly available actiniarian data. Phylogenomic analyses reveal a mosaic topology among deep-sea and shallow-water clades. Using a novel framework that contrasts convergent gene-loss patterns, we show that a large number of light-associated gene families-- including the complete circadian toolkit--were independently deleted after lineages entered the aphotic realm, whereas comparable loss in shallow taxa is negligible, providing decisive support for a shallow-water origin followed by multiple descents. Intriguingly, some deep-sea lineages further streamline energy budgets by recurrent loss or pseudogenisation of key meiotic genes (e.g., Meiosin, Ythdc2, Spo11, Rad21, Mlh3), indicating a shift towards asexual reproduction. Despite this extensive genomic erosion, deep-sea anemones exhibit sophisticated molecular tuning: specific amino-acid substitutions enhance protein stability and activity under deep-sea conditions, while selective expansions of gene families related to neural excitability, membrane systems, etc., likely mitigate the suppressive environmental effects on vital physiological processes. Enzyme activity assays in the yeast system confirm that the deep-sea variants exhibit superior activity and enhanced growth at 4{degrees}C. These results define a "loss-optimization-innovation" triad that underlies bathymetric adaptations and may apply to other deep-sea fauna worldwide.

evolutionary biology↗

bioRxiv2025

MetaFold-RNA: Accurate prediction of RNA secondary structure using a meta-learning-guided deep network

Accurately predicting the secondary structure of ribonucleic acid (RNA) is a critical step toward deciphering its biological roles and engineering novel RNA-based technologies. However, achieving high accuracy and generalization, especially for unseen RNA families, has long remained a central challenge in computational biology. Here we present MetaFold-RNA, a novel meta-learning framework that sets a new state of the art in RNA secondary structure prediction. Instead of relying on a single predictive paradigm, MetaFold-RNA synergizes insights from disparate models through a meta-learning approach and refines predictions via a co-evolutionary optimization process. On the challenging bpRNA-new benchmark, which specifically tests performance on unseen RNA families, MetaFold-RNA surpasses all SOTA methods, outperforming the best previous approach by 7.3%. This breakthrough performance is consistently maintained across other stringent assessments, including the PDB-new dataset and blind CASP predictions. Furthermore, our method demonstrates high robustness by accurately resolving the complex topologies of artificial RNA nanostructures. This work establishes a new performance benchmark, particularly in cross-family generalization, and provides a powerful computational tool for accelerating the study and design of RNA.

bioinformatics↗

bioRxiv2025

Integrative Systems Biology Identifies the AHR Signaling Axis as a Mechanistic Basis for Xiaobi Plaster in Lumbar Disc Degeneration

BackgroundLumbar disc degeneration (LDD) is characterized by chronic inflammation, oxidative stress, and extracellular matrix (ECM) breakdown, yet current therapies provide only symptomatic relief. Xiaobi Plaster (XBG), a traditional Chinese transdermal herbal preparation, has shown clinical benefit, but its molecular mechanisms remain unclear. MethodsWe applied an integrative systems biology framework combining network pharmacology, machine learning, and transcriptomic validation to identify candidate targets of Xiaobi Plaster in LDD. Molecular docking, dynamics simulations, and immune infiltration analysis further elucidated the underlying mechanisms, which were experimentally validated in a rat puncture-induced degeneration model. ResultsThree key targets--AHR, PTPN2, and SOAT1--were identified, with AHR emerging as the central regulator. Differential expression and enrichment analyses highlighted inflammatory and ECM-remodeling pathways, which overlapped with AHR-specific GSEA, underscoring its hub role in integrating immune and redox signaling with matrix turnover. Molecular docking and 100-ns molecular dynamics confirmed rutaecarpine (MOL002662) as the most stable AHR ligand. Transcriptomic data further showed AHR expression correlates with degeneration severity and mast cell infiltration. In vivo qPCR and Western blotting validated upregulation of AHR and supporting roles of PTPN2 and SOAT1 in degenerative discs. ConclusionThis study elucidates the multi-target and multi-pathway mechanisms of XBG in LDD, highlighting AHR as a pivotal therapeutic target modulated by rutaecarpine, with PTPN2 and SOAT1 serving as auxiliary regulators. These findings provide mechanistic insights into the transdermal application of XBG and support the therapeutic relevance of targeting the AHR signaling axis in LDD.

bioinformatics↗

bioRxiv2025

Evolutionary remodeling of non-canonical ORF translation in mammals

Non-canonical open reading frames (ncORFs) are pervasive within transcripts annotated as "non-coding" or "untranslated regions" of mRNAs, yet their landscape under normal physiological conditions remains to be fully resolved, particularly outside humans. Here we applied a stringent and standardized pipeline to hundreds of high-quality ribosome profiling libraries from normal mammalian tissues and cell types, identifying 11,623 human and 16,485 mouse ncORFs. Evolutionary analyses revealed that thousands of ncORFs are subject to coding constraint and exhibit lineage-specific conservation, underscoring their functional potential. Ancient ncORFs are preferentially highly translated, broadly expressed, and enriched for lineage-specific conservation. Co-expression patterns further indicate that many ncORFs, especially ancient ones, are cotranslated with canonical coding sequences, consistent with functions mediated through protein-protein interactions. Together, these findings establish a comprehensive atlas of mammalian ncORFs and provide fundamental insights into their evolutionary dynamics and functional integration within the proteome.

genomics↗

bioRxiv2025

Assembly of the complete horse genome reveals variants associated with reproduction and temperamental traits

A high-quality horse genome assembly is crucial for genetic analysis of equine. Benefiting from long-read sequencing techniques and trio-binning strategy, we assembled a complete telomere-to-telomere horse genome (T2T-horse 1.0) with a size of 2.80 Gb and a base accuracy of more than 99.9999%, comprising a 34.11-Mb entire Y chromosome. T2T-horse 1.0 filled the gaps and corrected errors in previous assemblies, and added 180.30 Mb of previously unresolved regions and 77 new genes compared with the previous reference genome TB-T2T. We identified five types of centromeric satellites and revealed the features of the horse centromeric regions. We characterized the structure of the Y chromosome, and determined the borders of PAR transposed region, and annotated 59 novel genes on Y chromosome of T2T-horse 1.0. Using SNPs in the X-degenerate region of the Y chromosome of T2T-horse 1.0, we performed selection signatures analysis between indigenous horses and horses from intensively selected breeds, and detected the selected genes ARSF and NLGN4Y, which are closely associated with reproduction and temperamental traits, respectively.

genomics↗

bioRxiv2025

The two-component nuclease-active KELShedu system confers broad antiphage activity via abortive infection

Bacteriophages and bacteria engage in a continuous evolutionary arms race, driving the development of intricate bacterial defense systems such as CRISPR-Cas, BREX, Gabija, and Shedu. Here, we characterize a two-component KELShedu system in Escherichia coli that confers resistance to phages via abortive infection. The KELShedu system comprises KELA, a dsDNA-binding protein, and KELB, a metal ion-dependent nuclease harboring the DUF4263 domain. In addition, we find that physiological levels of NTP inhibit the DNA cleavage activity of the KELShedu system, suggesting that KELShedus activation depends on reduced intracellular NTP levels during phage invasion. Our research demonstrates that the KELShedu system responds to nucleotide depletion triggered by phage replication, leading to non-specific degradation of cellular DNA and ultimately inducing abortive infection. These insights into the KELShedu system expand the repertoire of bacterial anti-phage mechanisms and lay the groundwork for novel applications in microbial engineering and therapeutic development. TeaserThe KELShedu system exerts anti-phage function by aborting infection in response to physiological changes following phage infection

microbiology↗

bioRxiv2025

Polyclonal origins of human premalignant colorectal lesions

Cancer is generally thought to be caused by expansion of a single mutant cell1. However, analyses of early colorectal cancer lesions suggest that tumors may instead originate from multiple, genetically distinct cell populations2,3. Detecting polyclonal tumor initiation is challenging in patients, as it requires profiling early-stage lesions before clonal sweeps obscure diversity. To investigate this, we analyzed normal colorectal mucosa, benign and dysplastic premalignant polyps, and malignant adenocarcinomas (123 samples) from six individuals with familial adenomatous polyposis (FAP). Individuals with FAP have a germline heterozygous APC mutation, predisposing them to colorectal cancer and numerous premalignant polyps by early adulthood4. Whole-genome and/or whole-exome sequencing revealed that many premalignant polyps--40% with benign histology and 28% with dysplasia--were composed of multiple genetic lineages that diverged early, consistent with polyclonal origins. This conclusion was reinforced by whole-genome sequencing of single crypts from multiple polyps in additional patients which showed limited sharing of mutations among crypts within the same lesion. In some cases, multiple distinct APC mutations co-existed in different lineages of a single polyp, consistent with polyclonality. These findings reshape our understanding of early neoplastic events, demonstrating that tumor initiation can arise from the convergence of diverse mutant clones. They also suggest that cell-intrinsic growth advantages alone may not fully explain tumor initiation, highlighting the importance of microenvironmental and tissue-level factors in early cancer evolution.

cancer biology↗

bioRxiv2025

Atlas of innate immune responses to experimental cholera and IL22 treatment demonstrates protection by mucus-secreting cells

The diarrheal disease cholera remains a global threat, but there is limited knowledge of the innate immune defenses in the small intestine that protect against the causative agent, Vibrio cholerae. Here, single-cell RNA-sequencing of epithelial and immune cells mapped gene expression patterns in the infant mouse small intestine and revealed changes in response to V. cholerae infection and prophylactic treatment with an IL22 Fc-fusion protein. Infection increased the abundance of an enterocyte subtype with high expression of defense-associated functions and stimulated production of IL22, a cytokine linked to epithelial integrity, from group 3 innate lymphoid cells. Administration of IL22Fc increased production of vibriocidal Reg3{beta} from enterocytes and the abundance of secretory lineage and Muc2-producing goblet cells, which secreted mucus into the intestinal crypts, impairing V. cholerae association with the epithelium. These IL22-mediated responses limited V. cholerae intestinal colonization and protected mice from diarrhea and death. Our findings suggest enterocyte specialization in mucosal defense. SummarySingle cell studies uncovered specialization of epithelial cells in intestinal defense. The epithelial cell-targeting cytokine IL22 protected mice from cholera by promoting the genesis of mucus secreting cells.

microbiology↗

bioRxiv2025

Combining Selenocystine Based Fluorescence Assay with Structural Prediction for Enhanced Detection and Analysis of Cystine Stone Pathology

BackgroundCystine stones, a rare but recurrent type of kidney stones, primarily result from cystinuria, an inherited disorder caused by mutations in the genes SLC3A1 and SLC7A9, which encode renal cystine transporters. These mutations impair cystine reabsorption, resulting in elevated urinary cystine concentrations and stone formation. Current diagnostic methods are limited, particularly for detecting molecular-level dysfunctions. We aimed to develop a nonradioactive method for functional assessment of cystine transporters and mutation-specific pathologies. MethodsWe designed an innovative diagnostic approach combining a selenocystine-based fluorescence assay with structural predictions using AlphaFold to rapidly and accurately assess cystine transporter function and the molecular impacts of genetic mutations. ResultsOur assay demonstrated comparable transport efficiencies of cystine and selenocystine by the SLC3A1/SLC7A9 complex, and effectively differentiated mild, moderate, and severe functional impairments associated with known clinical mutations, including A354T and P482L. Structural modeling further provided mechanistic insights into mutation-induced dysfunctions. ConclusionThis integrated approach--combining a sensitive selenocystine fluorescence assay with AI-powered structural analysis--enables rapid, precise diagnosis of cystinuria variants and delivers mechanistic insights for personalized therapeutic strategies.

genetics↗

bioRxiv2025

An activated wheat CCG10-NLR immune receptor forms an octameric resistosome

Nucleotide-binding and leucine-rich repeat (LRR) receptors (NLRs) are widespread intracellular immune sensors across kingdoms. In plants, the G10-type coiled-coil (CCG10)-NLRs form a distinct phylogenetic clade that remains poorly characterized. Here, we identified a gain-of-function (GOF) mutant of Wheat Autoimmunity 3 (WAI3), designated WAI3GOF, which encodes a constitutively activated CCG10-NLR protein due to an amino acid substitution. Cryo-EM structural analysis revealed that activated WAI3 assembles into a distinctive octameric resistosome. Arabidopsis RPS2, another CCG10-NLR, also forms an octamer, indicating a conserved structural property across monocot and dicot plants. The WAI3 resistosome mediates a prolonged and sustained increase in cytosolic calcium influx, facilitated by a unique channel architecture arising from its divergent CC domain configuration. Notably, this domain arrangement may be shared by many plant NLRs that lack the conserved EDVID motif in their CC domains. Our findings uncover a previously uncharacterized resistosome structure and provide insights into plant immune receptor plasticity.

plant biology↗

bioRxiv2025

Core gastric microbiota linked to pathogenesis and preserved across age stratified cohorts

Mounting evidences reveal a complex microbial niche in gastric environment. Nevertheless, the phylogenetic stability of gastric microbiota remains undetermined. Here, using full-length 16S rRNA and ITS amplicon sequencing applied to gastric brushes from a pediatric endoscopic cohort (n=243), we identified a core microbiota comprising 11 genera, which clustered into two antagonistic communities (CST1A and CST1B). CST1A was enriched in healthy subjects, while CST1B correlated with gastroduodenal disease. Notably, this bipartite architecture arose through bacterial interactions, with fungal taxa demonstrating minimal integration. Further stratified analyses revealed that H. pylori infection preferentially depleted CST1A taxa. The subclusters exhibited divergent metabolic profiles, with CST1A specializing in motility processes and CST1B in nucleotide/peptidoglycan synthesis. Cross-cohort validation of six datasets (n=1,183) confirmed the persistent relevance of the CST1A-CST1B structure across disease stages. Collectively, our findings define a core gastric microbiota established in early life, linked to gastric disease risk, and persisting into adulthood. HighlightsO_LIIdentification of a gastric bacterial network established in early life. C_LIO_LIDysbiosis in two subclusters within the core microbiota is associated with pediatric peptic ulcers. C_LIO_LIHelicobacter pylori infection reduces the abundance of the core microbiota, with a particularly greater inhibitory effect on CST1A. C_LIO_LIThe core microbiota is preserved across age stratified cohorts and is associated with gastric cancer. C_LI

microbiology↗

bioRxiv2025

Exogenous Delivery of Sphingomyelinase Mediates Mesenchymal Stromal Cell-Extracellular Vesicle Biogenesis, Alters Cargo Sorting, and Therapeutic Potency in vitro

Mesenchymal stromal cells (MSCs) exert regenerative and immunomodulatory effects largely through secreted paracrine factors and extracellular vesicles (EVs), which transfer proteins, lipids, and nucleic acids to recipient cells. Lipid composition critically influences EV stability, uptake, and bioactivity. Sphingomyelinase (SMase), an enzyme that hydrolyzes sphingomyelin into ceramide, regulates EV biogenesis by inducing membrane curvature and initiating inward membrane budding. Here, MSCs were treated with SMase, and EVs were isolated and characterized by nanoparticle tracking analysis, miRNA sequencing, lipidomics, and proteomics. SMase treatment increased EV yield and altered lipid, protein, and miRNA cargo linked to TNF- signaling, wound healing, and angiogenesis. Functionally, SMase-EVs suppressed TNF- in macrophages, showed trending increased HUVEC tubular formation, and altered T-cell populations following local delivery in a critical murine oral wound defect model. These findings highlight how enzymatic lipid remodeling modifies MSC-EVs, enhancing their therapeutic potential and informing strategies for optimized EV-based therapies and scalable production.

bioengineering↗