Biology subjects

Wang, J.

Publications and source records attributed to Wang, J..

At least 649 records · Page 36Linked to original sources

bioRxiv2025

Temperate phages enhance host fitness via RNA-guided flagellar remodeling

Bacterial flagella drive motility and chemotaxis while also playing critical roles in host-pathogen interactions, as their oligomeric subunit, flagellin, is specifically recognized by the mammalian immune system and flagellotropic bacteriophages. We recently discovered a family of phage-encoded, RNA-guided transcription factors known as TldR that regulate flagellin expression. However, the biological significance for this regulation, particularly in the context of host fitness, remained unknown. By focusing on a human clinical Enterobacter isolate that encodes a Flagellin Remodeling prophage (FR{varphi}), here we show that FR{varphi} exploits the combined action of TldR and its flagellin isoform to dramatically alter the flagellar composition and phenotypic properties of its host. This transformation has striking biological consequences, enhancing bacterial motility and mammalian immune evasion, and structural studies by cryo-EM of host- and prophage-encoded filaments reveal distinct architectures underlying these physiological changes. Moreover, we find that FR{varphi} improves colonization in the murine gut, illustrating the beneficial effect of prophage-mediated flagellar remodeling in a host-associated environment. Remarkably, flagellin-regulating TldR homologs emerged multiple times independently, further highlighting the strong selective pressures that drove evolution of RNA-guided flagellin control. Collectively, our results reveal how RNA-guided transcription factors emerged in a parallel evolutionary path to CRISPR-Cas and were co-opted by phages to remodel the flagellar apparatus and enhance host fitness.

microbiology↗

bioRxiv2025

Hybrid yak-cattle in situ conservation via interspecies somatic cell nuclear transfer at ultra-high-altitude region

Pien-niu, the hybrid offspring of yak (Bos grunniens) and domestic cattle (Bos taurus), possess exceptional adaptability to ultra-high-altitude environments of the Qinghai-Xizang Plateau. In situ conservation is of special significance for ultra-high-altitude region because the offsprings need to possess the ability to adapt to the unique environment. The present study was to clone Pien-niu in Xizang via interspecies somatic cell nuclear transfer (iSCNT) to practice in situ conservation of large animal at ultra-high-altitude region. Ear fibroblast cells were isolated from Pien-niu at Qushui Experimental Station (3650m above sea level), an animal live conservation farm at Xizang, and used as iSCNT donor cells. The iSCNT blastocysts were transferred into the oviduct of surrogate Pien-niu which are maintained at Qushui Experimental Station. A live cloned Pien-niu calf was born on May 12, 2025 and keeps healthy till now. Results of short tandem repeat analysis revealed that the microsatellite loci of cloned calf were completely matched with that of donor fibroblast cells. The successful cloning of Pien-niu can provide a paradigm for in situ germplasm conservation via iSCNT at ultra-high-altitude region.

zoology↗

bioRxiv2025

Formulation and Characterization of Primary Tissue-Derived Microfluidic Droplet-Engineered Organoids

Organoid technology offers a powerful platform for modeling human tissues, studying disease mechanisms, and developing personalized therapies. However, widespread clinical application is hindered by challenges in scalability, reproducibility, and the handling of ultra-small tissue samples typical of clinical biopsies. Here, we present a comprehensive and automated protocol for the formulation and characterization of microfluidic droplet-engineered organoids (DEOs) derived from primary tissue samples. This protocol integrates 3 key stages: (1) Extraction and purification of viable primary cells from ultra-small tissue specimens using the small-Tissue Extraction Device (sTED); (2) High-throughput fabrication of uniform cell-laden microspheres using an integrated microfluidic bioprinter (OrgFab), capable of generating over 100 organoids from just 10 L of bioink; and (3) Rapid organoid characterization using lamination-based processing for single-cell analysis while preserving spatial context. The automated workflow minimizes manual intervention, reducing variability and enhancing reproducibility, making it suitable for high-throughput applications such as drug screening and disease modeling. Our method allows for the generation of patient-derived organoids that closely mimic the native tissue microenvironment, including diverse cell types and structural features, within a significantly reduced timeframe. This 3 stage protocol enhances the use of organoids in personalized medicine by enabling the rapid assessment of drug efficacy in patient-specific models. Here, the integration of advanced techniques supports existing organoid protocols, providing a valuable resource for researchers and clinicians seeking to improve patient outcomes through more efficient and precise organoid-based applications.

bioengineering↗

bioRxiv2025

Pluripotent stem cell-derived siTNK cells attack tumors via a synthetic CD8-CD28 TCR complex

Tumor-associated antigen-specific T cell receptor (TCR)-engineered T cells offer a promising strategy for cancer therapy. Natural killer (NK) cells exhibit broad anti-tumor activity with low side effects but lack the capacity to recognize intracellular antigens. Here, we found that the human pluripotent stem cell (hPSC)-derived iNK cells, unlike tissue-isolated NK cells, expressed all four CD3 subunits at the transcriptome level. We introduced a synthetic gene-expressing complex (SCOTR), encoding a tumor antigen- specific TCR, CD8 coreceptor, and CD28 costimulatory molecule, into hPSCs to generate SCOTR-hPSCs. The SCOTR-hPSCs gave rise to abundant synthetic TCR complex-expressing iNK (siTNK) cells via an organoid induction method. These siTNK cells showed HLA-dependent, antigen-specific cytotoxicity against tumor cells and significantly suppressed tumor growth in tumor xenograft animal models, while also preserving universal non-specific tumor-killing activity. Collectively, siTNK cells, as hPSC-derived hybrid cells with dual features of adaptive T and inherent NK cells, offer an artificial cell source for human immunotherapies.

immunology↗

bioRxiv2025

Accurate Site-specific Folding via Conditional Diffusion Based on Alphafold3

Accurate structure prediction of biomolecular complexes is crucial for understanding biological processes and enabling drug discovery. While AlphaFold3 represents a significant advancement, enhancing its accuracy for specific binding sites remains a challenge. We present SiteAF3, a novel method for accurate site-specific folding via conditional diffusion, built upon the AlphaFold3 framework. SiteAF3 refines the diffusion process by fixing the receptor structure and optionally incorporating binding pocket and hotspot residue information. Comprehensive evaluations on protein-small molecule, protein-peptide, and protein-nucleic acid datasets demonstrate that SiteAF3 consistently outperforms AlphaFold3, achieving higher accuracy in complex structure prediction especially for orphan proteins and allosteric ligands, with reduced computational cost. SiteAF3 offers a user-friendly plug-in compatible with AlphaFold3, providing a valuable tool for more accurate modeling of biomolecular interactions.

bioinformatics↗

bioRxiv2025

SCLC-TumorMiner: A Directly Accessible Genomics Resource for Precision Oncology: Big Data for Small Cells

Small cell lung cancer (SCLC) is among the most aggressive malignancies. Unlike many other cancers, it is not represented in The Cancer Genome Atlas, and available datasets are fragmented across institutions, disease stages, and treatment settings. RNA sequencing provides a powerful and cost-effective approach, but the high dimensionality of transcriptomic data and the heterogeneity of patient cohorts pose significant challenges. To address such challenges, we developed SCLC TumorMiner (https://discover.nci.nih.gov/SclcTumorMinerCDB/), which includes 50 tumor samples from relapse patients at the National Cancer Institute (NCI) and 154 samples from untreated patients at the University of Cologne and Tongji University. SCLC TumorMiner enables molecular classification, genomic pathway analyses, risk stratification, identification of predictive cell-surface biomarkers such as DLL3 or TROP2, and drug-response biomarkers such as SLFN11. SCLC TumorMiner illustrates profound differences between untreated and relapse patient samples. Additionally, "MyPatient", one of SCLC TumorMiners modules, is presented as a medical assistant application prototype.

cancer biology↗

bioRxiv2025

Myocyte Damage and Mass Loss Drives Increasing Water Content, Compliance, and Survival in Septic Cardiomyopathy

Introduction/PurposeDuring the septic cardiomyopathy, the mechanism and relationship to outcome of changes in left ventricular (LV) end diastolic volume (EDV) and ejection fraction (EF) remains obscure. We compared serial changes in LVEF and LVEDV to successive alterations in LV wall ultrastructure, water content, and total mass to investigate whether these measures can explain their basis. MethodsWe performed cardiac magnetic resonance imaging at 0,6,18,30,42,54, and 92h post-bacterial challenge in a large-animal model (n=57) that mimics human septic cardiomyopathy. LV tissue was obtained for electron microscopy (EM) upon death and 66h in sacrificed survivors. ResultsBetween 0-6h post-challenge, LV compliance and EDV reached its greatest decline. Non-survivors (n=18) exhibited significantly greater reductions in LVEDV, along with more myocyte edema, mitochondrial swelling and myofilament fragmentation on EM. This increased tissue damage may explain why non-survivors developed worse LV compliance and a greater decline in LVEDV, which persisted until death. From 6-30h, LVEDV significantly improved to baseline in non-survivors, while survivors experienced [~]20% increases (n=39). Concurrently, there was significant LV mass loss and increases in percent water content that were significantly associated with increases in LVEDV. This is consistent with a passive mechanism for rapidly improving LV compliance and EDV. Full recovery of EF required additional days. We hypothesize the prolonged significant mass loss over 5d reflects an active process for remodeling fragmented myofilaments, eliminating myocyte edema, and mitochondrial swelling, ultimately restoring contractile function. ConclusionThe septic cardiomyopathy constitutes a diffuse ultrastructural injury to myocytes with three phases. Initially, there is a decrease in LVEDV, and EF due to myocyte damage within 6h of bacterial challenge; next, the patient sees a passive LVEDV recovery from 6-30h, where LV mass loss increases relative wall percent water content, which facilitates wall compliance and LVEDV; and lastly, the patient sees mass loss beyond 30h consistent with an active repair mechanism of myocytes, returning systolic function to normal. Therefore, EDV changes are a pathophysiological biomarker for sepsis outcomes. A lower LVEDV indicates persistent unrepairable ultrastructure damage with worsening wall compliance and poorer outcomes. LVEDV dilation is a sign of near-full recovery of ultrastructure injury, augmenting wall compliance and improving outcomes. Clinical ImplicationsWe explain herein why septic cardiomyopathy findings dont have clinical implications like heart failure. Septic patients who exhibit signs of heart failure, low LVEF with high EDVs, are doing well - reflecting mild myocyte injury, effective damaged tissues clearance, increased relative LV wall water content, and compliance. This augments the LVEDV, lowering the LVEF. Septic patients who deteriorate rapidly, contrary to heart failure patients, show high/normal LVEF and low/normal LVEDV. Here, the myocyte damage is severe, leading to insufficient wall repair, and this decreased wall compliance persists, preventing the LV from dilating and making LVEDV low which ultimately raises the LVEF.

physiology↗

bioRxiv2025

Choreography of human mitochondrial leaderless mRNA translation initiation

It remains unclear how human mitochondrial ribosomal subunits assemble into an elongation-competent 55S particle on mRNAs devoid of 5 leader sequences. Here, we reconstituted and directly tracked human mitochondrial translation initiation using real-time single-molecule fluorescence spectroscopy. Corroborated with cryo-EM structural analysis, we show that the initiation factor mtIF2 and initiator fMet-tRNAMet are loaded to the 28S subunit to drive mRNAs binding via 5 start codon recognition. This enables sequential loading of the two ribosomal subunits onto the leaderless mRNA to initiate. In parallel, a preassembled 55S monosome can also be loaded with mtIF2 and fMet-tRNAMet to initiate on the mRNA. Both initiation pathways yield active complexes to enter translation elongation, which is gated by mtIF2. The monosome loading pathway can initiate promiscuously with non-formylated Met-tRNAMet, thus its usage may under tight regulation in cells, e.g. by mtIF3. Our work provides a dynamic framework for the distinct human mitochondrial translation initiation.

biochemistry↗

bioRxiv2025

PromptBio: A Multi-Agent AI Platform for Bioinformatics Data Analysis

PromptBio is a modular AI platform for scalable, reproducible, and user-adaptable bioinformatics analysis, powered by generative AI and natural language interaction. It supports three complementary modes of analysis designed to meet diverse research needs. PromptGenie is a multi-agent system that enables stepwise, human-in-the-loop workflows using prevalidated domain-standard tools. Within PromptGenie, specialized agents--including DataAgent, OmicsAgent, AnalysisAgent, and QAgent--collaborate to manage tasks such as data ingestion, pipeline execution, statistical analysis, and interactive summarization. DiscoverFlow provides integrated, automated workflows for large-scale multi-omics analysis, offering end-to-end execution and streamlined orchestration. ToolsGenie complements these modes by dynamically generating executable bioinformatics code for custom, user-defined analyses, enabling flexibility beyond standardized workflows. PromptGenie and DiscoverFlow leverage a suite of domain-specific tools, including Omics Tools for standardized omics pipelines, Analysis Tools for downstream statistical interpretation, and MLGenie for machine learning and multi-omics modeling. We present the design, capabilities, and validation of these components, highlight their integration into automated and customizable workflows, and discuss extensibility, monitoring, and compliance. PromptBio aims to democratize high-throughput bioinformatics through a large language model-powered, natural language understanding, workflow generation and agent orchestration.

bioinformatics↗

bioRxiv2025

RNA structural heterogeneity in a eukaryotic cell influences its heat shock response

RNA structure-based gene regulation remains under-explored in eukaryotes. While RNA can form different conformations in solution, the extent to which it folds into structure ensembles and how the different conformations regulate gene expression still needs to be fully understood. We coupled the SHAPE compound NAI-N3 with direct RNA sequencing to identify structure modifications along a single RNA molecule (sm-PORE-cupine). Using a combination of base mapping and direct signal alignment, we boosted the percentage of mappable RNA molecules from direct RNA sequencing. Using Bernoulli Mixture Model (BMM) clustering, we show that we can separate RNA structure ensembles from ligand-bound and unbound riboswitches accurately, identify isoform-specific structure ensembles along the SARS-CoV-2 genome, and determine RNA structure ensembles in the transcriptome of a eukaryote, C. albicans, at yeast (30{degrees}C) and hyphae (37{degrees}C) states. We observed that RNAs are more structurally homogenous at 37{degrees}C compared to 30{degrees}C, are more variable in vivo than in vitro, and show higher homogeneity in 3UTRs than in the coding region. We also identified structure ensembles that are associated with changes in translation efficiency and decay in C. albicans at 30{degrees}C and 37{degrees}C and validated translational changes using reporter assays. Our work shows that single-molecule RNA structure probing using direct RNA sequencing can be applied to diverse transcriptomes to study the complexity and function of RNA structures.

molecular biology↗

bioRxiv2025

LoGicAl: Local Ancestry and Genotype Calling Uncertainty-aware Ancestry-specific Allele Frequency Estimation from Admixed Samples

In admixed groups, it is of interest to estimate allele frequencies of their ancestral contributing populations. These ancestry-specific allele frequencies inform genetic drivers of disease etiologies, facilitate genome-wide association study interpretations, enhance polygenic risk prediction and portability, and provide insights into demographic history. Their estimation leverages inferred locus-specific ancestry background, i.e., local ancestry, generated by tools like RFMix. However, existing estimation methods lose accuracy and incur biases by failing to model uncertainty from upstream local ancestry inference and genotype calling. Here, we introduce LoGicAl, a novel likelihood-based method for estimating ancestry-specific allele frequencies from admixed samples, simultaneously accommodating uncertainty from ancestry calling, genotyping, and statistical phasing. We demonstrate that modeling these uncertainties substantially reduces estimation errors, resulting in superior accuracy for both sequence-based and array-based genotyping with different levels of local ancestry inference quality. By integrating an accelerated fixed-point algorithm, LoGicAl achieves high scalability and enhanced computational efficiency compared with existing approaches. Applying LoGicAl to admixed cohorts in the 1000 Genomes Project, we illustrate the benefits of local-ancestry-based allele frequency estimates. Together, LoGicAl contributes to genomic analyses of admixed samples by providing precise and rapid ancestry-specific allele frequency estimates, and to constructing the spatial landscape and dynamics of genetic variations in admixed populations at a finer scale.

genetics↗

bioRxiv2025

Intravital Multimodal Imaging of Human Cortical Organoids for Chronic Stroke Treatment in Mice

Chronic stroke leads to enduring neurological deficits and remains a major clinical challenge. Human induced pluripotent stem cell (hiPSC)-derived cortical organoids (COs) offer promise for regenerative therapies, yet their application in chronic stroke remains understudied, in part due to limited tools for monitoring graft in vivo. Here, we present a Multimodal Imaging Platform for Organoid Tracking (MIPOT), which integrates MRI, bioluminescence imaging, light microscopy, and two-photon fluorescence microscopy to noninvasively track transplanted COs in the post-stroke brain over time. Using MIPOT, we verified precise delivery of COs into cleaned stroke cavities, observed progressive declines in viability within the first 10 days, and introduced labeling methods for functional in vivo tracking of COs at subcellular resolution. By 4 weeks post-transplantation, histological analysis revealed survival of COs in the cerebral cortex. Notably, COs engrafted into the hippocampus displayed enhanced maturation, underscoring the role of local microenvironments in graft integration. MIPOT enables dynamic, noninvasive evaluation of hiPSC COs in chronic stroke, providing a foundation for mechanistic studies and translational development of organoid-based therapies.

neuroscience↗

bioRxiv2025

Buffer Valency Engineering Enables High-concentration and Shelf-stable DNA Transfection Particles for Viral Vector Production

Cost-effective and scalable production is critical for advancing the clinical translation of adeno-associated virus (AAV)-mediated gene therapy. The widely used transient transfection method using plasmid DNA (pDNA)-loaded transfection particles for AAV production faces technical challenges due to instability of the particles and the concentration limits for particle preparation, hindering reproducibility and scalability. Here, we report a streamlined and scalable strategy to generate shelf-stable, highly concentrated pDNA/poly(ethylenimine) (PEI) transfection particles. By incorporating trivalent citrate ions in the dilution buffers, we kinetically modulate electrostatic complexation to achieve uniform nanoparticle assembly and prevent aggregation at high concentrations. This enables a tenfold increase in pDNA concentration in stabilized transfection particles from a typical range of 10-20 g/mL to 200 g/mL, while reducing the required dosing volume from 5-10% to 0.5% of the cell culture medium. The particle assembly process is robust to changes in mixing scale and timing and is compatible with standard workflows. We demonstrate equivalent AAV production efficiencies to standard methods and consistent performance in various production scales, which confirms the practical utility of this assembly method in developing robust, scalable, and cost-effective AAV manufacturing processes.

biochemistry↗

bioRxiv2025

In Silico Screening of Peptide Inhibitors of PHLDA1-Encoded Protein Targeting Cardiovascular Diseases

The PHLDA1-encoded protein (PEP) is a pivotal regulator of cardiomyocyte apoptosis and a promising therapeutic target for cardiovascular diseases. Leveraging in silico approaches, we characterized PEPs structure using AlphaFold3 (AF3) and refined it via molecular dynamics (MD) simulations with various force fields. Kinetic and thermodynamics analysis further confirmed revealed that the Amber99 force field induced the most significant structural change, with the most significant decrease in radius of gyration and lowest potential energy. High-throughput screening of 20 phenylalanine-based dipeptides (FA-FY) revealed sequence-dependent binding to PEP, with FF, FH, FP, and FY exhibiting the maximum count of binders (11, 7, 6, and 6, respectively). Key residues (e.g., L55, C60, E142, E89) formed a continuous binding groove, while FF dipeptides demonstrated cooperative aggregation-enhanced binding. Notably, low-pLDDT regions (< 50) frequently participated in ligand interactions, challenging the rigid "lock-and-key" paradigm and underscoring the role of intrinsic disorder in binding. this work establishes PEP as a tractable target for dipeptide inhibitors and provides a computational framework for designing peptide-based therapeutics against cardiac injury.

pharmacology and toxicology↗

bioRxiv2025

Silencing Proline Dehydrogenases Improves Salt and Drought Tolerance in Gossypium hirsutum

Proline is a key compound that lowers cell water potential, scavenges reactive oxygen species, and stabilizes biomolecules and cell membranes, thus reducing stress-induced damage. Proline dehydrogenase (ProDH), the first rate-limiting enzyme in proline degradation, plays a crucial role in proline accumulation. We explored the role of the GhProDH gene family in regulating physiological responses to stress conditions through transcriptome, metabolome and functional analyses. Overexpression and gene silencing lines in Arabidopsis and cotton revealed that GhProDH2 plays a key role in regulating cottons tolerance to drought and salt stress. GhProDH2-4 improves cottons tolerance to drought and salt stress by engaging in carbon metabolism, glyoxylate cycle, and flavonoid metabolism pathways. These findings highlight the potential role of GhProDH2-4 to improve cotton stress resistance by genetically modifying pathways involved in proline biosynthesis and degradation.

molecular biology↗

bioRxiv2025

Attention robustly dissociates objective performance and subjective visibility reports

Visual experience can sometimes depart from visual performance, providing a powerful lens into the mechanisms generating conscious perception. In one proposed dissociation--subjective inflation--unattended locations in the periphery appear stronger than attended ones despite equated performance. Subjective inflation has played a central role in motivating theories of consciousness that reject the sufficiency of sensory signals for conscious perception. Yet the empirical basis for subjective inflation is limited. Here, in a large-scale adversarial collaboration, we conducted four simultaneously-replicated experiments testing the strength, character, and extent of subjective inflation under inattention. We used a new analytic approach to quantify inattentional inflation over full psychometric functions, beyond single matched-performance levels. We found robust inattentional inflation for contrast-dependent and texture-based perception, at and above the visual threshold. However at suprathreshold, we found inattentional inflation for the overall stimulus but not the specific feature relevant for performance. Finally, we establish the unifying principle that inattentional inflation occurs if and only if attention reduces performance thresholds more than visibility thresholds. Thus what we think we see may regularly exceed what we can visually discriminate, placing constraints on theories of conscious perception.

neuroscience↗

bioRxiv2025

Transcriptome Reprogramming Associated with Autoimmunity Reveals Key Points of the Growth-Defence Trade-off in Arabidopsis thaliana

Growth and defence are inversely correlated processes requiring balance for optimal fitness. While each is well studied, their regulatory trade-offs are less understood. Using DANGEROUS MIX (DM) autoimmune plants with stunted growth in Arabidopsis thaliana, we investigated the balancing act. Transcriptome analysis of three DM cases and pathogen-treated seedlings identified two major modules representing defence and growth. These core modules, comprising 4,712 genes ([~]17% of the transcriptome), were sufficient for projecting the trade-off across immune transcriptome meta-datasets. Removing all three ADR1s, the helper NLRs, reversed the expression patterns of both modules and shifted the trade-off balance. ADR1s had a stronger impact on growth-associated RLK genes than on defence genes. Autoimmune plants also showed greater chromatin accessibility changes in growth loci than in defence loci. Our findings suggest an unexpected mechanism where immune signalling, partly mediated by ADR1s, actively suppresses growth genes, providing a strategy to regulate the growth-defence trade-off.

plant biology↗

bioRxiv2025

Genomic Touchstone: Benchmarking Genomic Language Models in the Context of the Central Dogma

The emergence of genomic language models (gLMs) has revolutionized the analysis of genomic sequences, enabling robust capture of biologically meaningful patterns from DNA sequences for an improved understanding of human genome-wide regulatory programs, variant pathogenicity and therapeutic discovery. Given that DNA serves as the foundational blueprint within the central dogma, the ultimate evaluation of a gLM is its ability to generalize across this entire biological cascade. However, existing evaluations lack this holistic and consistent framework, leaving researchers uncertain about which model best translates sequence understanding into downstream biological prediction. Here we present Genomic Touchstone, a comprehensive benchmark designed to evaluate gLMs across 36 diverse tasks and 88 datasets structured along the central dogmas modalities of DNA, RNA, and protein, encompassing 5.34 billion base pairs of genomic sequences. We evaluate 34 representative models encompassing transformers and convolutional neural networks, as well as emerging efficient architectures such as Hyena and Mamba. Our analysis yield four key insights. First, gLMs achieve comparable or superior performance on RNA and protein tasks compared to models pretrained on these molecules. Second, transformer-based models continue to lead in overall performance, yet efficient sequence models show promising task-specific capabilities and deserve further exploration. Third, the scaling behavior of gLMs remains incompletely understood. While longer input sequences and more diverse pretraining data consistently improve performance, increases in model size do not always translate into better results. Fourth, pretraining strategies, including the choice of training objectives and the composition of pretraining corpora, exert substantial influence on downstream generalization across different genomic contexts. Genomic Touchstone establishes a unified evaluation framework tailored to human genomics. By spanning multiple molecular modalities and biological tasks, it offers a valuable foundation for guiding future gLM design and understanding model generalizability in complex biological contexts.

bioinformatics↗