Biology subjects

Xing, C.

Publications and source records attributed to Xing, C..

At least 19 recordsLinked to original sources

bioRxiv2026

A minimally modified AAV9 variant (AAV9fyhr) for enhanced CNS gene delivery by intra-CSF administration.

Adeno-associated virus (AAV) mediated gene therapies continue to show promise for the treatment of genetic diseases. However, delivery and safety still represent significant prohibitive barriers restricting translation of these delivery modalities to humans. We describe a novel AAV9 variant, AAV9fyhr or FYHR, identified from screening a controlled randomization point mutation AAV9 library in mice and nonhuman primates followed by directed evolution of in vivo CNS-derived libraries screened in human iPSC differentiated cortical neurons. Capsid variants of interest were identified by coupling long read sequencing and computational structure modeling. Structure-function analysis of our lead candidate reveal that two targeted amino acid changes are sufficient to result in beneficial pleiotropic effects across viral stability, cell surface attachment, and gene delivery. We developed a novel multiplexed barcoding reporter system, enabling a time and cost-effective option to gather spatially resolved single cell capsid validation data in mice and nonhuman primates. When administered intrathecally, AAV9fyhr exhibits 2-to-6-fold higher gene delivery across several tissues in the CNS while minimally altering the tropism to peripheral tissues in comparison to AAV9. These findings demonstrate the potential of whole capsid engineering for the rational development of translational next generation AAV capsids.

bioengineering↗

bioRxiv2026

Convergent activity but divergent anxiety dimensions in male and female C57BL/6 mice across the open field and elevated plus maze

Anxiety disorders are among the most common psychiatric illnesses, with a significantly higher prevalence in females than in males. The open field (OF) and the elevated plus maze (EPM) are the two assays used most often to model anxiety-like behavior in mice. It is usually assumed that they index a common underlying trait, yet few studies have investigated this in a large group of male and female mice using an advanced analytical approach. The goal of these studies was to determine sex differences in locomotor activity and anxiety-like behavior in the OF and the EPM, and to establish which behavioral parameters correlate between the tests. Adult male and female C57BL/6 mice (n = 61; 29 male, 32 female) were given a single 15 min session in the OF, analyzed as a whole and in three consecutive 5 min blocks, and a single 5 min EPM trial. Males and females did not differ on any OF measure over the cumulative 15-minute session. Locomotion and stereotypy declined over time with females habituating faster than males while center exploration did increase. In the EPM, females made more closed-arm entries than males while open-arm exploration was identical. Every significant correlation between the two tests involved an activity measure. All four pairs formed between OF and EPM activity parameters were significant whereas none of the six pairs formed between OF center parameters and EPM open-arm parameters were significant. Hierarchical clustering revealed the same structure, placing the activity measures of both tests in one cluster, the EPM open-arm measures in a second, and the two OF center measures in a third. The cross-test activity correlation was strongest during the initial five minutes of the OF and weakened as the session progressed. These studies indicate that the OF and EPM yield convergent measures of activity, but divergent measures of anxiety-like behavior.

animal behavior and cognition↗

bioRxiv2026

AB-Free Kava and its Kavalactones Suppress Cigarette Smoke- and Lipopolysaccharide-Induced Lung Inflammation: Efficacy and Mechanisms

Cigarette smoke-induced lung inflammation is a central driver of pulmonary diseases. The limited efficacy of current anti-inflammatory agents underscores the need for structurally novel therapeutics with distinct mechanisms. We recently demonstrated that AB-free kava, a flavokavains A/B-depleted formulation from Piper methysticum containing six major kavalactones, effectively suppresses cigarette smoke-induced lung inflammation in mice. This study aims to identify the bioactive constituent(s) and elucidate underlying mechanisms. These kavalactones revealed a clear structure-activity relationship in suppressing lipopolysaccharide (LPS)-stimulated prostaglandin E2 (PGE2) production in macrophages with desmethoxyyangonin (DMY) as the most potent kavalactone whereas dihydrokavain (DHK, a structurally similar analog) with minimal activity. DMY also effectively reduced LPS-induced interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-) production while DHK was ineffective. Mechanistically, DMY, but not DHK, attenuated COX-2 induction and reduced phosphorylation of cAMP response element-binding protein (CREB). Pharmacological inhibition of protein kinase A (PKA) similarly reduced p-CREB, COX-2 and PGE2, supporting a PKA-dependent CREB/COX-2 signaling in mediating PGE2 suppression while these effects were independent of nuclear factor kappa B (NF-{kappa}B) and activator protein 1 (AP-1) signaling. Similar results were observed for DMY and DHK in attenuating cigarette smoke condensate-induced proinflammatory pathways and PGE2 production. Consistently, DMY demonstrated significant in vivo efficacy in suppressing cigarette smoke-induced lung inflammation while DHK was not effective. Interestingly, dihydromethysticin (DHM) demonstrated the greatest in vivo anti-inflammatory efficacy, although it only exhibited moderate in vitro potency, likely due to its superior bioavailability over DMY. Concordantly, cigarette smoke exposure elevated p-CREB and COX-2 expressions in mouse lungs, which were attenuated by AB-free kava and its bioactive kavalactones with the extent of suppression correlating with their in vivo anti-inflammatory efficacy. DHM effectively suppressed LPS-induced neutrophil accumulation in mouse lungs as well. Collectively, these studies identify bioactive kavalactones in AB-free kava that suppress cigarette smoke- and LPS-induced lung inflammation through the modulation of the PKA/CREB/COX-2 signaling axis, providing a foundation for developing structurally distinct anti-inflammatory agents, particularly targeting smoke-induced inflammation and associated pulmonary diseases.

immunology↗

bioRxiv2026

AB-Free Kava Reduces Anxiety-Like Behavior Without Preventing Nicotine-Induced Exploration Suppression in Mice

Tobacco use is the leading preventable cause of death worldwide. Anxiety increases the risk for smoking, and smoking in turn increases the risk for anxiety disorders. There is therefore a need to identify interventions that reduce anxiety, in general and in the context of smoking, without producing sedation. Kava (Piper methysticum), a natural product with a long history of indigenous use, has been shown to have anxiolytic and calming effects and reduce nicotine withdrawal. The current study examined whether kava without the hepatotoxic flavokavains A and B (AB-free) could reduce anxiety-like behavior in mice repeatedly treated with nicotine. Male and female C57BL/6NCrl mice received either a control diet or an AB-free kava-supplemented diet and underwent two blocks of nicotine treatments. Mice underwent a first block of five every-other-day injections of nicotine (0.5 mg/kg) or saline, with open field testing after each injection, followed one week later by a nicotine challenge. A second block of injections was given using the same injection schedule, followed by a second challenge one week later, and two weeks afterward mice received a final challenge in a novel open field. During the first treatment block, AB-free kava significantly increased center time overall, an effect most pronounced in saline-treated animals, and increased locomotor activity, while nicotine decreased both measures. During the second challenge, nicotine reduced center time but not locomotor activity, and AB-free kava increased center time in saline-treated animals only. During the final challenge, nicotine reduced both measures, whereas AB-free kava increased center time regardless of nicotine treatment, and kava-treated animals also showed a near-significant increase in center entries. These results suggest that AB-free kava reduces anxiety-like behavior without inducing sedation but does not prevent nicotine-induced suppression of exploratory behavior.

pharmacology and toxicology↗

bioRxiv2026

TRACER navigates rearrangement-driven sesterterpene chemical space via multimodal enzyme-product representation learning

Skeletal rearrangement drives the immense structural complexity of terpene, yet predicting it remains a formidable challenge due to sequence-function decoupling in terpene synthases. Here, we established TRACER (terpene rearrangement annotation via co-attentive enzyme-product representation), a multimodal framework mapping the latent associations between sequence-derived enzyme representations and product chemotypes. Retrospective validation proved TRACERs exceptional precision in predicting compound classes and discriminating skeletal rearrangement (SR) from non-skeletal rearrangement (NSR) pathways. TRACER-guided genome mining characterized two bifunctional synthases, FsPS and AcPS, uncovering four unprecedented carbon skeletons. Density functional theory calculations deciphered these cyclization cascades, pinpointing a critical 5/6/11 tricyclic intermediate as the key branching node for scaffold diversification. Mutagenesis and molecular dynamics simulations suggested that E305 in FsPS enables rearrangement by maintaining active-site water exclusion, whereas its alanine mutation causes premature carbocation quenching. Collectively, this work establishes a predictive paradigm for the rational discovery and mechanistic elucidation of complex terpene architectures.

synthetic biology↗

bioRxiv2026

HER2 mutation-derived neoantigens in NSCLC as actionable targets for TCR therapy

HER2 mutations are oncogenic drivers in 1-6% of non-small cell lung cancers (NSCLC), but therapeutic resistance limits the durability of current HER2-targeted treatments. Here, we identify T-cell receptors (TCRs) targeting recurrent HER2 hotspot mutations as a potential immunotherapeutic strategy for HER2-mutant NSCLC. Using neoepitope prediction and antigen-specific T-cell enrichment, we isolated HLA-A*02:01restricted TCRs recognizing HER2 A775insYVMA, S310F, and G776delinsVC mutations, collectively covering approximately 60% of HER2-mutant NSCLC. These TCRs selectively recognized mutant HER2 epitopes without detectable wild-type reactivity and some displayed cross-recognition of related hotspot variants, expanding the spectrum of targetable tumors. The G776delinsVC-specific TCR also exhibited co-receptorindependent activity showcased by its ability to activate CD4+ T cells. Importantly, timelapse single-cell flow cytometry analyses demonstrated that TCR-engineered T cells repeatedly reacquired activated polyfunctional states following serial antigen stimulation, while serial tumor rechallenge assays confirmed sustained cytotoxic activity across multiple rounds of tumor killing. These findings identify recurrent HER2 mutations as shared immunotherapeutic targets and provide a foundation for the development of TCR-based therapies for HER2-mutant NSCLC.

immunology↗

bioRxiv2026

Multiscale harmonization and semantic integration of biomedical data enable biological insights through immersive exploration

Single-cell atlassing efforts like the Human BioMolecular Atlas Program (HuBMAP) and the Cellular Senescence Network (SenNet) are producing multiscale datasets across the healthy, adult, human body, but this data is typically explored only on 2D screens with limited 3D affordances, even though understanding a cells location within a tissue, organ, and body requires reasoning across many orders of spatial magnitude. The Human Reference Atlas (HRA) provides standard terminologies and a Common Coordinate Framework (CCF) for harmonizing such data spatially and semantically. Building on the HRA Organ Gallery in virtual reality (VR) application, we present "HRA: Powers of Ten," which integrates, harmonizes, and visualizes biological data from these efforts immersively in VR using a Multiscale Elevator System that lets users descend, like riding an elevator through an inverted skyscraper, from a whole body view of 81 reference organs to datasets across 5 organs (lymph node, brain, large intestine, small intestine, liver), 5 assay types (CODEX, Visium, v-CyCIF, Xenium, SBF-SEM), and 4 spatial scales. Contributed by Data Providers, these VR scenes enable biological insights into senescence patterns, cellular neighborhoods, 3D tissue reconstruction, and subcellular liver architecture. A standard operating procedure supports adding further datasets. Freely available on the Meta Store to over 20 million headset owners, the application, data, and code are open-source.

bioinformatics↗

bioRxiv2026

OmicOS: A Comprehensive Omics Ecosystem Infrastructure and Agent System for the AI Era

Biology has accumulated a vast ecosystem of omics methods, but much of this ecosystem remains built for expert humans rather than scientific agents. Methods are scattered across Python packages, R/Bioconductor and CRAN workflows, command-line tools, incompatible data containers and implicit object states, making even routine analyses difficult for an AI system to choose, execute and verify reliably. Here we introduce OmicOS, a comprehensive omics ecosystem infrastructure and agent system that turns OmicVerse V2, an open-source omics community, into an executable foundation for agentic biology. OmicVerse V2 provides the community substrate: scalable AnnDataOOM-compatible rust backends, agent-friendly Python algorithms for single-cell, spatial, bulk and multi-omics analysis, interfaces to single-cell foundation models, and Python-native reconstructions of historically R-centred Bioconductor/CRAN-style workflows. OmicOS makes this substrate actionable by registering analytical functions as state-aware capability contracts, allowing agents to inspect live data objects, select valid methods, execute controlled workflows and record provenance. The result is not a fixed pipeline, but a programmable omics environment in which agents compose real analyses from verified community methods rather than inventing tools. Across external and purpose-built benchmarks, OmicOS ranked first among the evaluated systems, reaching 81.2% on BiomniBench. Adding OmicVerse to a minimal agent improved task completion by up to 34.2 percentage points with qwen-3.6-35b, and controlled ablations showed that the gains came from registry-grounded execution rather than from larger models, documentation retrieval or unrestricted tool exposure. The same infrastructure scaled to atlas-sized data, reproduced R-centred workflows in Python and converted external pathology software into agent-usable skills. In a discovery task starting from a whole-body spatial map and the term "Alzheimers disease", OmicOS composed a non-canonical workflow that integrated spatial expression, genetic association, eQTL and colocalization evidence to nominate a colon epithelial risk axis centred on PICALM, CD2AP and CR1. Together, OmicVerse and OmicOS define an open foundation for AI-era omics, showing how a community of biological methods can be transformed into a reliable, extensible and agent-operable system for discovery. HighlightO_LIOmicVerse 2.0 consolidates 694 methods spanning 11 omics domains into agent-callable high-level APIs. C_LIO_LIRebuildR automatically reconstructs and evolves R/Bioconductor methods as Python-native implementations under output-equivalence gates. C_LIO_LIOmicOS establishes a state-of-the-art omics agent harness, ranking first on general omics benchmarks across models and substantially improving the analytical capability of local open-source models. C_LIO_LICompositional use of ecosystem modules nominates a colon epithelial axis associated with Alzheimers disease risk. C_LIO_LIExternal algorithm packages supporting automatic iterative evolution can be integrated into the OmicOS ecosystem. C_LI

bioinformatics↗

bioRxiv2026

Protein Response to ACL Injury in Humans Show Early Cartilage Remodeling and Differences by Sex

ObjectiveAnterior cruciate ligament (ACL) tears increase the risk for developing posttraumatic osteoarthritis (PTOA). Females have greater risk for both. However, studies defining sex-specific protein responses in human cartilage after ACL injury are lacking. We hypothesize that articular cartilages response to an injurious environment differs depending on sex. DesignWe compared the proteomic profiles of normal cartilage with injured cartilage harvested from the intercondylar area during ACL surgery. Sex-specific injury effects were estimated through contrasts between Injured Male and Normal Male and between Injured Female and Normal Female. Pathway enrichment analysis was done using gene ontology (GO) and compared against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Extracellular matrix (ECM) proteins were further analyzed using the Matrisome AnalyzeR. ResultsFrom the 2,188 proteins identified, males and females shared 1,121 upregulated and 23 downregulated proteins in injured compared to normal cartilage. Analysis of ECM proteins and enriched pathways revealed mostly similar male and female responses to an injurious environment, with evidence of early cartilage remodeling in both sexes. Nevertheless, more than 240 proteins were affected specifically by sex, and significant sex differences were found in inflammation, ECM-related, and metabolic pathways. Males were enriched mostly in "ECM-receptor interaction", while females were enriched in "Citrate cycle (TCA cycle)", "Fatty acid degradation", and "Fatty acid metabolism" pathways. ConclusionArticular cartilage shows signs of remodeling soon after ACL injury, even when only exposed to an injurious environment rather than being physically impacted. Sex differences were observed in inflammation, metabolic pathways, and ECM synthesis.

biochemistry↗

bioRxiv2026

Multiscale volume electron microscopy of the human liver maps vascular-cellular architecture, organelle dynamics and inter-organelle communication

The human liver depends on multiscale structural organization from vasculature to cells to organelles to perform its diverse metabolic functions. A unified three-dimensional view linking these hierarchical scales in intact human tissue would be useful for better understanding these levels and how they relate to each other. We present a high-resolution volume electron microscopy reconstruction of human periportal liver tissue (152 x 140 x 33 {micro}m3 at 8 nm pixel size) acquired by serial block-face scanning electron microscopy. Using a multiscale deep learning approach, we performed automated segmentation across the entire volume, enabling comprehensive annotation of vasculature, cells, and organelles. Quantitative analysis of bile duct architecture revealed coordinated scaling between lumen geometry and cholangiocyte number and size. Sinusoidal capillary branches exhibited distinct structural profiles with differential endothelial coverage. Analysis of 35,790 complete mitochondria identified substantial morphological heterogeneity, with elongated mitochondria displaying preferential endoplasmic reticulum (ER) contacts at narrowing sites, a pattern consistent with ER-mediated fission or fusion. This multiscale reconstruction establishes an ultrastructural reference for the healthy human liver and provides a quantitative framework for investigating hepatic physiology and disease.

cell biology↗

bioRxiv2026

GMIP-PLSR: A Nextflow Pipeline for GWAS and Multi-Omics Integration in Gene Prioritization Using PLSR

Genome-wide association studies (GWAS) have significantly advanced our understanding of complex traits and diseases, but their interpretive power remains limited due to challenges in identifying causal genes and pathways. Integrating GWAS with multi-omics data--such as gene expression, protein-protein interactions, and gene-pathway networks have the potential to enhance biological insights and improve gene prioritization. To fulfill this potential and need, we developed the GWAS & Multi-omics Integration Pipeline (GMIP), a flexible and scalable framework that incorporates widely used tools such as PoPS, MAGMA, and benchmarker to enrich GWAS findings. However, PoPS suffers from multicollinearity in its features, which can impact performance. To overcome this, we introduce GMIP-PLSR, an extension of GMIP that uses Partial Least Squares Regression (PLSR) to manage multicollinearity effectively. We applied GMIP-PLSR across multiple GWAS datasets, demonstrating superior performance over PoPS in most cases. In a case study on NAFLD, GMIP-PLSR, using features derived from both disease-specific scRNA-seq and general PoPS features, identified gene sets with higher heritability and stronger enrichment in known NAFLD pathways, confirming its ability to enhance GWAS findings. Built on Nextflow, GMIP is computationally efficient, adaptable to diverse research environments, and provides a robust solution for gene reprioritization in post-GWAS analyses. GMIP-PLSR is available at https://github.com/mohammedmsk/GMIP.

bioinformatics↗

bioRxiv2026

Barrier Immune Memory is Promoted by Intestinal Epithelial Cell Presentation of Injected Bacterial Antigens

The contributions of antigen compartmentalization to recognition differences between CD4 and CD8 T cells have long been appreciated, but little is known of how subcellular localization of different antigens expressed by a single pathogen impacts T cell immunity. By tracking a clonal CD4 T cell response to its cognate epitope shuttled between different virulence proteins of the enteropathogenic bacterium, Citrobacter rodentium (Cr), we find a remarkable bias in the magnitude and quality of the response contingent on whether antigen remains bacterially associated or is introduced into intestinal epithelial cells colonized by the bacterium. Only proteins injected into the cytosol of colonocytes via the type 3 secretion system (T3SS) of Cr were found to recruit robust antigen-specific T cell responses to the infected mucosa and give rise to CD4 resident memory T (Trm) cells that populate the mucosal epithelium--and this required direct presentation of these antigens by infected epithelial cells. Single-cell transcriptomic analyses revealed that sustained, bidirectional epithelial-T cell communication was required both to elicit epithelial barrier-protective T cell help and to promote transcriptional networks that program a tissue-residency rather than central memory fate. These results establish a central role for antigen presentation by non-professional APCs in controlling memory fate decisions by CD4 T cells, with important implications for development of successful mucosal vaccines.

immunology↗

bioRxiv2026

OmicClaw: executable and reproducible natural-language multi-omics analysis over the unified OmicVerse ecosystem.

Advances in bulk, single-cell and spatial omics have transformed biological discovery, yet analysis remains fragmented across packages with incompatible interfaces, heterogeneous dependencies and limited workflow reproducibility. Here, we present OmicClaw, an executable natural-language framework for multi-omics analysis built on the unified OmicVerse ecosystem and the J.A.R.V.I.S. runtime. OmicVerse organizes upstream processing, preprocessing, single-cell, spatial, bulk-transcriptomic and foundation-model workflows into a shared AnnData-centered interface spanning more than 100 methods. J.A.R.V.I.S. converts this ecosystem into a bounded analytical action space through a registry-grounded, state-aware and recoverable execution layer that validates prerequisites, preserves provenance and supports iterative repair, while enabling conversational, notebook and visual interfaces to operate over the same live analytical state. Rather than relying on unconstrained code generation, OmicClaw translates user requests into traceable workflows over live omics objects. Across a benchmark of 15 tasks spanning scRNA-seq, spatial transcriptomics, RNA velocity, scATAC-seq, CITE-seq and multiome analysis, ov.Agent improved rubric-based performance over bare one-shot large language model baselines, particularly for long-horizon multi-step workflows. OmicClaw further supports external agent access through an MCP-compatible server and a beginner-friendly web platform for interactive analysis, code execution and million-scale visualization. Together, OmicClaw provides a practical foundation for reproducible human-AI collaboration in modern multi-omics research

bioinformatics↗

bioRxiv2026

3D Cell-Matrix Mechanical Interaction Models for Cancer Invasion and Drug Evaluation

Cancer cells breach the extracellular matrix (ECM) using both protease-driven degradation and force-driven physical remodeling, yet most anti-metastatic drug screens still rely on biochemical assays that overlook cell-matrix mechanical reciprocity. Here, we present a fully synthetic 3D invasion platform based on cellular force-responsive polyisocyanide (PIC) hydrogels that isolates biophysical invasion mechanisms. Cell-generated forces align and densify the PIC fibrous network, reproducing hallmark matrix remodeling seen in the tumor microenvironment. A constitutive model, parameterized by the critical stress for strain stiffening effect, links matrix nonlinear elasticity to pericellular stiffening, long-range mechanotransmission, and intercellular coupling. Using this system, we show that breast cancer cells invade by pulling and pushing the network even when matrix metalloproteinases are inhibited, revealing a physical bypass of protease blockade. Accordingly, broad-spectrum metalloproteinase inhibitors that suppress invasion in Matrigel fail to inhibit invasion here, exposing a limitation of current drug-evaluation pipelines. In co-culture, cancer-associated fibroblasts markedly accelerate invasion by generating aligned fiber tracks through higher contractility, implicating CAF-driven mechanical remodeling as a key route for breaching barriers during metastasis. The platform is thermoresponsive, compatible with standard Transwell formats, enables direct imaging of fiber architecture and invasion fronts, and decouples biophysical from biochemical cues for mechanism-aware, animal-free assessment of anti-metastatic therapies.

cancer biology↗

bioRxiv2025

BMP-Smad1/9 signaling is required for PGC proliferation in zebrafish

The specification and maintenance of germ cell lineage are vital for reproductive development and heredity. The germ cell fate in some species, such as zebrafish and Xenopus, is determined by maternally supplied germ plasm, whereas in mammals it is induced by bone morphogenetic protein (BMP) signaling after implantation. It remains elusive whether BMP signaling is implicated in zebrafish germ cell development. Here, we demonstrate that, in zebrafish, BMP-Smad1/9 signaling is required for primordial germ cell (PGC) maintenance but not for PGC fate determination or migration. BMP inhibitor treatment or whole-embryo smad1/9 knockdown reduces the number of PGCs. To investigate cell-autonomous roles of BMP-Smad1/9 in PGCs, we generated PGC-specific smad1/9 knockouts using a double-transgenic approach with PGC-specific expression of Cas9 and ubiquitous expression of guide RNAs (gRNAs). Loss of Smad1/9 in PGCs leads to impaired PGC proliferation and increased apoptosis, resulting in reduced PGC numbers and adult sex bias. Moreover, transcriptome analysis of smad1-deficient PGCs revealed no significant changes in the expression of PGC-specific genes, but a marked upregulation of genes involved in cell cycle checkpoints and DNA damage repair. Notably, ectopic ATR-pChk1 activation in smad1-cKO PGCs validates cell cycle defects and DNA replication stress. ATR inhibition restores PGC numbers in mutant embryos. Collectively, these findings underscore a critical role of BMP-Smad1/9 signaling in zebrafish PGC population maintenance, while it is dispensable for PGC fate determination and migration.

developmental biology↗

bioRxiv2025

RNA viruses in water shape the viromes of shrimp and fish in aquaculture systems

Aquatic environments host immense RNA viral diversity, yet the extent to which waterborne viruses influence the virome of aquatic animals remains unclear. Here, we conducted a comprehensive longitudinal metatranscriptomic analysis of water, shrimp, and fish across multiple culture stages in aquaculture systems. We identified 3,211 RNA viruses spanning 21 viral supergroups, with 97.4% representing novel species. Water exhibited the greatest viral diversity (3,093 species), followed by shrimp (1,280) and fish (398), with most viruses detected in shrimp and fish also detected in water. Diversity analyses revealed increasing richness and significant compositional shifts in 92 high-abundance viruses (>1,000 RPM) across culture stages. Viral abundance in aquatic animals was strongly correlated with that in water, and the temporal trajectories of the 16 most abundant viruses were closely synchronized between water and shrimp. Furthermore, 337 virus species were shared among shrimp and two fish species, of which 309 were present in water. These findings demonstrated that RNA viruses in water shape the composition and dynamics of aquatic animal viromes, underscoring the importance of water virome surveillance and management for disease prevention in shrimp aquaculture.

microbiology↗

bioRxiv2025

Stage- and tissue-specific gene editing using 4-OHT inducible Cas9 in whole organism

Vertebrate genes usually function in specific tissues at specific stages, and thus their functional studies require conditional knockout or editing. In the zebrafish, spatiotemporally inducible genome editing, especially during early embryonic development, is still challenging. Here, we report inducible Cas9-based gene editing in specific cell types at desired stages in zebrafish. We show that the nCas9ERT2 fusion protein consisting of Cas9 and estrogen receptor flanked by two nuclear localization signals is normally located in the cytoplasm and efficiently translocated into the nucleus upon 4-hydroxytamoxifen (4-OHT) treatment in cultured cells or embryos. As a proof-of-concept, we demonstrate that target genes in primordial germ cells or germ cells of transgenic zebrafish embryos or adults with stable expression of nCas9ERT2 and gene-specific guide RNAs (gRNAs) can be induced to mutate by application of 4-OHT. This inducible nCas9ERT2 system also works in mouse early embryos. Thus, this inducible gene editing approach will be another choice for studying the temporospatial function of genes at the organismal level. Hence, the inducible nCas9ERT2 system expands the tissue- and stage-specific gene editing toolkit.

developmental biology↗

bioRxiv2025

Identification of α-azacyclic acetamide-based inhibitors of P. falciparum Na+ pump (PfATP4) with fast-killing asexual blood-stage antimalarial activity by phenotypic screening

Malaria treatments are compromised by drug resistance, creating an urgent need to discover new drugs. We used a phenotypic high-throughput screening (HTS) platform to identify new antimalarials, uncovering three related pyrrole-, indole-, and indoline-based series with a shared -azacyclic acetamide core. These compounds showed fast-killing activity on asexual blood-stage Plasmodium falciparum parasites, were not cytotoxic, and disrupted parasite intracellular pH and Na+ regulation similarly to cipargamin (KAE609), a clinically advanced inhibitor of the P. falciparum Na+ pump (PfATP4). PfATP4 is localized to the parasite plasma membrane and is essential for maintaining a low cytosolic Na+ concentration. Resistance selections on P. falciparum parasites with two -azacyclic acetamide analogs identified mutations in PfATP4, and cross-resistance was observed across the -azacyclic acetamides and KAE609, confirming PfATP4 as the target. PfATP4 is a well-established antimalarial target, and identification of additional PfATP4 inhibitors provides alternative avenues to disrupt its function.

microbiology↗