Biology subjects

Li, D.

Publications and source records attributed to Li, D..

At least 109 records · Page 6Linked to original sources

bioRxiv2026

An AI-Native Biofoundry for Autonomous Enzyme Engineering: Integrating Active Learning with Automated Experimentation

The engineering of enzymes with novel functions is a cornerstone of synthetic biology but remains bottlenecked by the fragmentation between computational design and physical execution. While "self-driving" laboratories promise to resolve this, existing systems often rely on rigid, device-specific scripts that lack the flexibility to handle complex, evolving scientific tasks. Here, we report an AI-native autonomous biofoundry that fundamentally redefines laboratory automation through a "cloud-edge synergistic" architecture. The platform features an Agent-Native control system powered by Large Language Models (LLMs) and the Model Context Protocol (MCP), which bridges the semantic gap between abstract scientific intent and heterogeneous hardware execution. This architecture enables non-experts to orchestrate the entire Design-Build-Test-Learn (DBTL) cycle via natural language. By integrating deep phylogenetic mining, zero-shot protein language models (ESM-2), and supervised active learning, our system efficiently navigates rugged fitness landscapes. As a rigorous proof of concept, we applied this platform to evolve a Family B DNA polymerase for CoolMPS sequencing, a task requiring the incorporation of non-natural 3-blocked nucleotides. In just three autonomous rounds, the platform achieved a hit rate of >66% and identified variants with a 37% reduction in sequencing error rate compared to a commercial reference. This work demonstrates that AI-native infrastructures can not only accelerate trait evolution by orders of magnitude but also provide a scalable, brand-agnostic paradigm for the future of automated scientific discovery.

bioengineering↗

bioRxiv2026

Two tiers of piRNA clusters balance diversification of piRNAs with limitation of off-target effects

PIWI-interacting RNAs (piRNAs) are important factors in the protection of the genome against nucleic acid invaders such as transposons. piRNAs are encoded in the genome in regions known as piRNA clusters, but major questions remain surrounding their regulation. Two such questions are how the piRNA clusters are recognized as piRNA sources, and how the piRNA response can expand from these regions to facilitate the recognition of novel invading sequences without risking the targeting of essential cellular mRNAs. Here, we investigated the piRNA clusters of the planarian S, mediterranea, and found that the clusters differ regarding the PIWI proteins their piRNAs bind to, as well as their chromatin features. We uncovered a subset of piRNA clusters that had unique chromatin features and atypical transcription. piRNAs from these clusters were depleted of genic content, stabilized by 3 methylation and were not dependent on the ping-pong mechanism. We therefore named these clusters Seed clusters. We identified a second set of piRNA clusters that we called Spread clusters, which had features reminiscent of pseudogenes or aberrant genic transcripts. piRNA generation from these clusters relied on ping-pong, and piRNAs largely remained unmethylated. Further, we found that many more regions in the genome generated single ping-pong events, suggesting that ping-pong is used as a means to diversify the collection of piRNA-generating transcripts beyond the Seed clusters. We propose that this two-tiered organization of the piRNA clusters allows the stable targeting of known genomic threats by the piRNAs generated from the Seed clusters, while the flexible generation of additional diverse piRNAs from Spread clusters as well as other aberrant transcripts increases the sequence space probed by the piRNA system. The absence of methylation on these additional piRNAs decreases their lifespan and limits the chances of a run-away response. This two-tiered organization thus solves a core challenge of the piRNA system and may be a widespread feature of piRNA systems across animals.

molecular biology↗

bioRxiv2026

p300/CBP-Driven Acetylation Stabilizes PARP7 to Reinforce Negative Feedback on IFN-I Signaling

Immune suppression within the tumor microenvironment (TME) remains a major barrier to effective immunotherapy, yet the molecular mechanisms that constrain type I interferon (IFN-I) signaling in tumor cells are incompletely understood. PARP7 (also known as TIPARP), a mono-ADP-ribosyltransferase, has been reported to suppress IFN-I signaling by modifying TBK1. Here, we identify PARP7 as a previously unrecognized acetylation substrate of the histone acetyltransferases p300 and CBP. We show that p300/CBP-mediated acetylation of PARP7 at lysine 32 markedly enhances its stability, thereby reinforcing repression of the TBK1-IRF3-STAT1 axis and suppressing IFN-{beta}-induced expression of interferon-stimulated genes, including CXCL10. Beyond their established function as transcriptional co-activators that support tumor cell proliferation, our findings uncover a direct role for p300/CBP in shaping innate antitumor immunity. Pharmacological inhibition of p300/CBP catalytic activity by A-485 abolishes PARP7 acetylation, accelerates its proteasomal turnover, and restores IFN-I signaling. In immunocompetent tumor models, this is accompanied by enhanced CD8+ T-cell infiltration and effector function. Together, these findings define a p300/CBP-PARP7 regulatory axis, uncover a non-canonical role for p300/CBP in innate immune suppression, and nominate this pathway as a tractable target for restoring antitumor immunity.

cancer biology↗

bioRxiv2026

Urban Environments Reshape Reproductive Phenology in Plants Across the Tropics

Plant phenological responses to global change phenomena like urbanization remain understudied in the tropics, hindering predictions regarding the dynamics of tropical ecosystems amid rapid land use changes. Studies of tropical phenology are limited by complexities, like the limited availability of phenological data, especially in urbanized landscapes. Observations recorded on citizen science platforms can overcome this limitation by providing vast, spatially distributed data. In this study, we utilize iNaturalist data to evaluate plant reproductive phenology in tropical urban vs. rural habitats. We first compare iNaturalist data (111533 records) to herbarium collections (217991 records) in order to validate their use, and we then investigate urban-rural phenology differences within 25-km spatial grids for 238 species. Data from iNaturalist and herbaria yield complementary insights, with the former being uniformly distributed between urban and rural settings, and the latter biased towards rural observations. On average, we found species to have significantly longer reproductive duration ({beta} = 11.79 {+/-} 2.83 SE, t = 4.16, p < 10^4), and correspondingly weaker strength of seasonality in urban settings than in nearby rural localities. We also find trait-mediated variation, with seasonal, annual, and herbaceous plants showing more pronounced differences in reproductive duration and seasonality strength. These results suggest that urbanization in tropical landscapes might have important implications for plant demography, with potential consequences for community and ecosystem dynamics. Our work also points to the value of integrating insights from natural history collections with data from citizen science platforms for enabling broad-scale insights into ecological dynamics in tropical urban landscapes.

ecology↗

bioRxiv2026

The RNA Editome of Esophageal Squamous Cell Carcinoma Identifies an ADAR1-CDK13 Editing Feedback Loop Mediating cGAS-STING Activation in Early Tumorigenesis

ObjectiveRNA adenosine-to-inosine (A-to-I) editing, catalyzed by adenosine deaminases acting on RNA (ADARs), is a pervasive post-transcriptional mechanism that expands transcriptomic and proteomic diversity. However, the global landscape of RNA A-to-I editing, as well as its functional and clinical significance in esophageal squamous cell carcinoma (ESCC), remains largely unexplored. This study aimed to systematically characterize the RNA editome of ESCC and elucidate its biological and clinical significance. MethodsWhole-transcriptome sequencing was performed on 121 primary ESCC tumors, with or without lymph node metastasis, together with matched normal tissues, to construct a high-resolution RNA editome. ADAR1-regulated RNA editing events were identified, and their functional consequences were investigated using integrated transcriptomic, phosphoproteomic, and RNA immunoprecipitation sequencing (RIP-seq) analyses. Associations between CDK13 editing, cGAS-STING-interferon-stimulated gene (ISG) signaling, and patient survival were further evaluated. ResultsA total of 222,020 high-confidence RNA editing sites were identified, of which approximately 98% were A-to-I events, including 124,486 ESCC-specific edits predominantly enriched in introns, 3' untranslated regions, and non-coding RNAs, highlighting a pervasive post-transcriptional regulatory layer. RNA A-to-I editing was extensively remodeled and globally up-regulated in non-metastatic ESCC, whereas only minimal changes were observed during lymph node metastasis, indicating that RNA editing alterations predominantly occur during early tumorigenesis. CDK13 emerged as a recurrent ADAR1 target, with RNA editing inversely correlated with CDK13 expression. ADAR1-mediated CDK13 editing established a positive feedback loop associated with enhanced interferon-stimulated gene (ISG) signaling and poorer survival in non-metastatic ESCC. Mechanistically, partial attenuation of CDK13 induced chronic, tumor cell-intrinsic activation of the cGAS-STING-ISG pathway. Integrated multi-omics analyses further revealed that CDK13 regulates phosphorylation networks governing cytoskeleton organization, intracellular trafficking, RNA homeostasis, and immune signaling. ConclusionRNA A-to-I editing represents a dynamic regulatory mechanism driving early ESCC progression and remodeling tumor cell-intrinsic immune signaling. ADAR1-mediated editing of CDK13 provides a mechanistic link between RNA editing and cGAS-STING-ISG pathway activation, revealing potential therapeutic vulnerabilities and supporting its utility as an early prognostic biomarker in ESCC.

cancer biology↗

bioRxiv2026

An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia

The basal ganglia regulate motor, cognitive, and affective behaviors, and their dysfunction underlies diverse neurological and psychiatric disorders. Comprehensive, accessible multi-omics resources are needed to understand the regulatory mechanisms governing basal ganglia cell types. Here we present an open, interactive web-based platform for exploring single-cell multi-omics datasets from basal ganglia, generated using 10X Multiome, snm3C-seq, and Paired-Tag technologies from the BICAN (NIH BRAIN Initiative Cell Atlas Network) consortium. The platform is available at https://basalganglia.epigenomes.net/ and enables integrated visualization of gene expression, chromatin accessibility, DNA methylation, histone modifications, and chromatin conformation across cell types and human, macaque, marmoset, and mouse species, with direct genome browser support and comparative epigenomic functionality. Representative analyses demonstrate cell-type-specific regulatory landscapes, conserved and species-specific regulatory elements, and links between epigenomic regulation and transcription. This resource provides a scalable, community-oriented foundation for advancing basal ganglia biology and interpreting regulatory mechanisms relevant to brain function and disease. HighlightsO_LIIntegrated single-cell epigenomic resource for basal ganglia C_LIO_LIInteractive genome browser enables multi-omics and cross-species exploration C_LIO_LIReveals cell-type-specific and species-specific regulatory landscapes C_LIO_LISupports community access to complex brain epigenomic datasets C_LI

genomics↗

bioRxiv2026

Pan-genome and multi-omics analyses reveal the genomic basis of symbiotic evolution in the mycoheterotrophic medicinal orchid Gastrodia elata

Mycoheterotrophy represents an extreme evolutionary strategy in which plants abandon photosynthesis and become obligately dependent on fungal partners for carbon and nutrients. Gastrodia elata, a medicinal orchid forming long-term symbioses with Armillaria and Mycena, provides a compelling system to investigate the genomic basis of obligate plant-fungus mutualism. Here, we generate a chromosome-level genome assembly (1.09 Gb) of a dark-red G. elata accession and construct a pan-genome from 12 Gastrodia accessions to dissect the evolutionary consequences of mycoheterotrophy. Phylogenomic analyses reveal pervasive hybridization across cultivated germplasm and demonstrate that tuber morphology more accurately reflects intraspecific relationships than stem color, challenging the traditional color-based taxonomy. Comparative genomic analyses reveal a pronounced degeneration of photosynthetic capacity. We detect no intact nuclear-encoded rbcS loci, which would preclude assembly of the Rubisco holoenzyme and thus canonical Calvin-Benson carbon fixation. Notably, a subset of photosynthesis-related genes is retained and transcriptionally active, suggesting their co-option into non-photosynthetic regulatory roles. Despite millions of years of intimate association with fungal partners, we detect no evidence of fungal-derived horizontal gene transfer based on a multi-step phylogenomic validation pipeline, indicating that G. elata-fungus mutualism is sustained through metabolic exchange rather than genetic integration. We further identify the Gastrodia antifungal protein (GAFP) gene family as a key molecular innovation underlying symbiotic homeostasis. The recently derived Class 1 GAFP lineage exhibits distinct domain architecture, tandem expansion, and elevated expression, consistent with enhanced regulation of fungal overgrowth. Finally, we delineate a specialized nutrient-acquisition framework adapted to obligate heterotrophy, in which fungal trehalose hydrolysis supplies hexose carbon via an expanded sugar transporter protein (STP) repertoire, while organic nitrogen is assimilated through amino acid and oligopeptide transporters coupled with urease-mediated conversion, compensating for the loss of nitrate uptake and reduction pathways. Together, these results establish a pan-genomic blueprint for symbiotic adaptation and reductive genome evolution in G. elata.

genomics↗

bioRxiv2026

Cathepsin-dependent amyloid formation drives mechanical rupture of lysosomal membranes

Lysosomal membrane integrity is essential for cellular homeostasis, and its failure drives lysosomal storage disorders (LSD) and neurodegeneration. The dipeptide L-leucyl-L-leucine methyl ester (LLOMe) is widely used to model lysosomal damage, yet its mechanism remains poorly understood. The prevailing view holds that LLOMe polymerizes into membrane-permeabilizing peptide chains within the lysosomal lumen. Using cryo-electron tomography in cultured cells and primary neurons, we visualized the structural basis of LLOMe-induced lysosomal damage. We reveal that LLOMe forms amyloid structures within lysosomes that directly interact with and rupture the limiting membrane through mechanical stress. In vitro reconstitution confirms this amyloid-mediated mechanism. These findings establish a structural paradigm for lysosomal membrane disruption and provide insights into how disease-relevant protein aggregates, implicated in neurodegeneration and LSD, may compromise lysosomal integrity.

cell biology↗

bioRxiv2026

Quantitative Full-length transcriptome analysis by nanopore sequencing with Error-Aware UMI mapping

Comprehensive transcriptome profiling is essential for understanding RNA diversity and regulation, yet accurate identification and quantification of full-length transcript isoforms remain challenging with short-read sequencing technologies. Nanopore sequencing enables direct sequencing of long cDNA molecules and thus offers a powerful solution for full-length transcriptome analysis, but its application to quantitative transcriptomics is limited by PCR amplification bias and the difficulty of unique molecular identifier (UMI) recognition under high sequencing error rates. Here, we developed UMImap, a dedicated pipeline for robust UMI identification, error correction, and deduplication in nanopore data. By integrating transcript-aware UMI correction with long-read isoform assembly, UMImap substantially improves UMI recognition accuracy compared with existing methods and effectively mitigates PCR-induced duplication bias. Using this framework, we identified tens of thousands of full-length transcript isoforms, including a large fraction of previously unannotated isoforms that are significantly longer than reference annotations. Quantitative analyses demonstrate the reliability of UMImap for transcript-level quantification. Functional and pathway enrichment analyses of highly expressed novel isoforms revealed coherent and biologically meaningful patterns, including strong enrichment in RNA processing, splicing, and translation pathways. Our results establish UMImap as an effective solution for UMI-based quantification in nanopore full-length transcriptome sequencing and highlight the potential of long-read sequencing to simultaneously achieve accurate isoform discovery and expression analysis in complex transcriptomes.

bioinformatics↗

bioRxiv2026

Molecular insights into bulk lipid transport from structural studies of the bridge-like protein VPS13A complexed with the scramblase XKR1

In eukaryotes, bridge-like lipid-transfer proteins (BLTPs) are central in mediating vesicle-independent lipid transfer between organelles. BLTPs span the cytosolic space between organelles at contact sites, featuring hydrophobic channels for lipids to travel between membranes. How BLTPs cooperate with partner proteins to orchestrate lipid delivery remains mysterious. Here we used cryo-electron microscopy to visualize a complex comprising the prototypical BLTP VPS13A and the plasma membrane localized scramblase XKR1 at near-atomic resolution. VPS13A interacts with XKR1 via its PH-domain, priming VPS13As bridge-like lipid-transfer domain to deliver lipids directly to the cytosolic leaflet of the acceptor membrane. In molecular dynamics simulations, such arrangement allows for robust lipid transfer, accelerated by membrane properties. Newly delivered lipids can then be equilibrated between leaflets of the membrane bilayer by the scramblase, allowing for membrane growth. Mechanistic insights regarding lipid delivery by VPS13A are directly applicable to all VPS13 proteins and all BLTP family members more broadly.

cell biology↗

bioRxiv2026

Leveraging Human Pangenome for Improved Somatic Variant Detection

Somatic variant detection is technically challenging due to low variant allele fractions, the confounding presence of germline variation, and reference bias. Linear references such as GRCh38 miss sample-specific variation, causing misalignments and incorrect variant calls. Although telomere-to-telomere donor-specific assemblies (DSAs) accurately represent individual genomes, their application is limited by cost and technical barriers. Alternatively, the graph-based human pangenome provides a scalable framework to improve read alignment and perform genome inference. Here, we benchmarked somatic variant detection using GRCh38, graph-based pangenomes, and pangenome-inferred DSAs with a HapMap mixture dataset and the COLO829 melanoma cell line. Pangenome-guided alignment improves read mapping and somatic variant calling accuracy. Furthermore, personalized pangenomes partially reconstruct donor-specific genomic content, improving accuracy, reducing germline contamination, and enabling detection of events in loci absent or poorly represented in GRCh38. These findings demonstrate that graph-based and personalized pangenomes are effective strategies for enhancing somatic variant detection compared with GRCh38.

genomics↗

bioRxiv2025

Discover Potential New Epitopes through Post Translational Modification in Sjogrens Disease

Sjogrens syndrome (SjD) is a chronic autoimmune disorder in which the immune system attacks the glands that produce tears and saliva, leading to symptoms such as dry eyes and dry mouth. If left untreated, SjD can also cause inflammation and damage to other parts of the body, including the skin, lungs, kidneys, and nervous system, and increase the risk of developing lymphoma. The human leukocyte antigen (HLA) class II molecule HLA-DR3 is strongly associated with SjD. To investigate how post-translational modifications (PTMs) influence the presentation of SjD-associated autoantigens by HLA-DR3, we employed a computational framework to analyze the binding of PTM-mimic peptides to HLA-DR3. Our analysis revealed that PTM-mimic substitutions at canonical anchor positions rarely improved predicted binding affinity using the Stabilized Matrix Method, with most modifications resulting in reduced affinity. However, a comprehensive analysis of full-length SjD-associated autoantigen sequences (Ro60, Ro52, La) identified discrete regions with high densities of PTM-eligible anchor sites, specifically, the Ro60 HEAT solenoid, Ro52 RING/B-box/PRY-SPRY modules, and the La motif-RRM1 region, suggesting that PTMs may alter epitope presentation in a sequence-dependent manner. Experimental validation of selected PTM-mimic peptides demonstrated enhanced T cell responses, which were associated with increased binding affinity to HLA-DR3. Structural modeling of a representative complex revealed that PTM-mimic peptides adopt a slightly shifted backbone orientation and altered side-chain positioning, leading to a larger peptide-DR3 interaction interface. These findings provide new insights into the role of PTMs in shaping the immunogenicity of SjD-associated autoantigens and highlight the potential for PTM-mimic peptides to modulate T cell responses in SjD.

immunology↗

bioRxiv2025

Cysteine protease cathepsin B promotes high population density-induced mutagenesis, driving genome evolution and competitive growth in response to the crowding stress

In a wide variety of species from invertebrates to mammals, overpopulation has been shown to induce low fertility and high mortality. Although density-dependent population regulation is widespread in the animal kingdom, the underlying molecular mechanisms remain poorly understood. We show here that C. elegans animals respond to the crowding stress by secreting CPR-4, a homologue of human cathepsin B cysteine protease, to promote chromosomal DNA damage in germ cells, leading to high density-induced deficiencies that include increased embryonic lethality and larval arrest and decreased brood size. CPR-4 mediates these crowding responses through the insulin-like growth factor receptor DAF-2, multiple components in the insulin signaling pathway, and the SKN-1/Nrf transcription factor. Whole genome sequencing analyses of animals from 10 generations of continual growth in the crowded condition reveal that CPR-4-induced DNA damage produces an average of 2.9 more de novo genome mutations per animal per generation and a 75% increase in mutation rate compared with animals grown in the uncrowded condition. CPR-4-induced mutagenesis also facilitates evolution of the genomes through multi-generational crowding selection, leading to biased mutation distributions towards the intergenic regions over the gene bodies and crowd-inducible growth advantage. Our findings suggest that CPR-4 acts as a crucial crowd-responding factor to induce chromosomal DNA damage, leading to density-dependent deficiencies, increased genome mutation rates, and genome evolution and competitive growth of animals in response to the crowding stress.

developmental biology↗

bioRxiv2025

Screening and structural characterization of a nanobody targeting the thermostable green fluorescent protein

Nanobody-fluorescent protein pairs are powerful tools in imaging, protein purification, and structural biology studies. While thermostable GFP (TGP) offers improved characteristics over conventional GFP, nanobodies that specifically recognize TGP remain relatively limited. Here, we report the screening and identification of a synthetic nanobody, Sb32, that binds TGP with nanomolar affinity using the ribosome technique. The crystal structure of the Sb32-TGP complex, solved at 1.82 [A] resolution, revealed an unusual binding mode in which Complementarity Determining Region 2 (CDR2) provides the major contribution, rather than the typically dominant CDR3. Moreover, the interface is stabilized by an extensive hydration network, which compensates for relatively few direct contacts and may explain the fast association and dissociation kinetics observed for this complex. These findings expand the repertoire of TGP-specific nanobodies and highlight an alternative strategy by which nanobodies achieve high affinity. Sb32 provides a new reagent for TGP-based applications, with potential utility in membrane protein purification and structural studies.

biophysics↗

bioRxiv2025

Petal to the metal: The slow road to automating large-scale phenology labeling for herbarium specimens

Herbarium specimens represent critical historical records of plant phenology, yet automating annotation of reproductive structures remains challenging given the diversity of floral morphologies, specimen age and quality, and image quality. Here, we present a machine learning pipeline that uses an ensemble modeling approach to detect flowers on herbarium specimens and deliver these data to the phenology research community. After testing multiple strategies for generating training data, we found in-house expert-curated annotations were essential for producing reliable results. Expert validation found relatively strong accuracy for detecting present floral structures, but still had moderately high false negative rates. Applying the ensemble to our filtered final image dataset of 22 million records resulted in 11.1 million records labeled with flowers present. However, only 2.9 million of these contained complete metadata necessary for downstream phenology research, highlighting the need for full label digitization efforts. Still, this dataset represents a large compilation of historical herbarium-derived phenology records available as a resource for the phenology community. We end by demonstrating how integrating these machine-labeled records into Phenobase, a publicly-available phenology database, expands taxonomic and temporal coverage for large-scale phenological analyses, and discuss remaining challenges and next steps.

ecology↗

bioRxiv2025

Identification of Functional Genetic Components Modulating Toxicity Response to PFOS using Genome-wide CRISPR Screens in HepG2/C3A cells

Perfluorooctane sulfonate (PFOS) poses significant health and environmental risks due to its persistence and widespread use and has been linked to various adverse outcomes, such as liver toxicity. Although the molecular responses and toxicity effects of PFOS exposure have been extensively studied, considerable uncertainty remains regarding the causal mechanisms leading to PFOS-associated adverse effects. To help bridge this gap, we conducted CRISPR screens in HepG2/C3A human liver cells exposed to IC25 (170 {micro}M) of PFOS to identify genes and pathways influencing PFOS-induced cytotoxicity. Using a genome-wide CRISPR knockout library targeting 18,819 genes, we identified 340 candidate genes that modulate PFOS-induced cytotoxicity when genetically disrupted (189 gene disruptions increased sensitivity and 151 gene disruptions increased resistance). From these candidate genes, we individually disrupted two candidate genes, SLC6A9 which encodes the glycine transporter GlyT1, and CPSF2, and confirmed increased resistance to PFOS exposure. Further, molecular docking analysis predicts that PFOS directly binds to GlyT1 and functional inhibition of GlyT1 also increases resistance to PFOS exposure. Gene-Disease outcome association analysis using the Comparative Toxicogenomics Database (CTD) indicated an enrichment of candidate genes associated with cancer-related and liver disease phenotypes. KEGG and STRING enrichment analyses found over representation of several biological pathways including DNA damage response and cell cycle. Lastly, cross-species conservation analysis using the top two validated gene targets found that their pathways were highly conserved in several environmentally relevant species. These findings provide new mechanistic and functional insights into PFOS-induced cytotoxicity, highlight potential molecular targets for toxicity mitigation, and establish a foundation for cross-species toxicogenomic modeling of PFOS health effects.

pharmacology and toxicology↗

bioRxiv2025

A comprehensive evaluation of ultraviolet irradiation at 254 nm and 222 nm in inactivating human noroviruses on surfaces

Human norovirus (hNoV) presents significant public health challenges due to its low infectious dose and environmental persistence. This study compared the inactivation efficacy of ultraviolet C irradiation at 254 nm (UV 254) and far-UVC radiation at 222 nm (UV 222) against four hNoV strains and two surrogate viruses, Tulane virus (TV) and bacteriophage MS2. A symptom scoring assay was developed to assess hNoV infectivity following microinjection into zebrafish embryos, being used in combination with reverse transcriptase quantitative PCR (RT-qPCR), long-range RT-qPCR, and RNase-treated RT-qPCR. With a general laboratory set-up of viruses being suspended in deionized water droplets in Petri dish, UV 222 was demonstrated with comparable, if not superior, performance in reducing hNoV infectivity and RNA integrity, and was significantly more effective than UV 254 in damaging viral capsids. MS2 exhibited inactivation patterns similar to hNoVs, whereas TV was markedly more resistant to UV 222. The performance of UV 222 was consistent in inactivating hydrated viruses on both stainless steel and porcine skin surfaces. However, the efficacy of UV-222 was substantially more reduced when virus inocula were dried or mixed with simulated vomitus containing high levels of organic matter, compared with UV-254. No evidence of viral adaptation or persistent genomic diversification was detected following repeated sublethal UV exposures. Taken together, UV 222 can be regarded as a promising technology in surface disinfection, especially for hNoV control, meantime keeping safe for human exposure. ImportanceHuman norovirus, the main cause of foodborne illness and non-bacterial gastroenteritis, can be transmitted through human-to-human contact. Indirectly, food or food related surfaces are readily contaminated by hNoV, completing the transmission route. So far, no standard cultivation tool is available for detecting viable hNoV, resulting in the challenges of evaluating inactivation effectiveness of various disinfection technologies, including UV 222 treatments. The significance of our study lays in attempts to quantify hNoV infectivity loss of four strains using zebrafish model during UV 222 and 254 treatments, together with the underlying antiviral mechanisms indicated by three different types of reverse transcription qPCR methods. In addition, the concerns over possible emergence of variant were subdued by genome wide sequencing results after consecutive UV exposures and passaging in vivo zebrafish model. SynopsisUV 222 is recommended to be applied after surface cleaning and ideally on moist surfaces.

microbiology↗

bioRxiv2025

CAMP: Coreset Accelerated Metacell Partitioning enables scalable analysis of single-cell data

Scaling metacell inference to atlas-level single-cell datasets demands algorithms that are both computationally efficient and geometrically faithful. We introduce CAMP (Coreset Accelerated Metacell Partitioning), a metacell framework that preserves the intrinsic structure of the cellular manifold while enabling scalable analysis of millions of cells. CAMP leverages coreset-based sampling to construct a small, weighted subset of representative cells that approximates the full dataset with provable geometric guarantees. This formulation transforms metacell construction into a coreset inference problem, reducing runtime and memory complexity by up to an order of magnitude without loss of accuracy. Through extensive experiments, we show that CAMP produces metacells that are compact, well-separated, and biologically coherent, achieving performance on par with or exceeding existing methods including MetaCell, SuperCell, SEACells, and MetaQ. By combining theoretical efficiency with empirical robustness, CAMP establishes coreset acceleration as a principled foundation for scalable, high-fidelity metacell inference in single-cell transcriptomics.

bioinformatics↗