Biology subjects

Yang, Q.

Publications and source records attributed to Yang, Q..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Structure basis for single-strand nucleic acid targeting by IscB and variants

Transposon-encoded IscB has been established as the evolutionary ancestor of CRISPR-Cas9. This compact RNA-guided endonuclease has since been engineered for genome editing applications. We previously repurposed IscB and Cas9 as efficient RNA editors by removing their double-stranded DNA recognition module, the TAM/PAM-interacting domain. Here, we report four cryo-EM structures of IscB in complex with single-stranded nucleic acid (ssNA) targets to illuminate its mechanistic underpinnings. Structural analysis reveals that IscB initially facilitates formation of a 10-nt seed duplex with ssNA; however, further base-pairing is blocked by an alternatively positioned HNH nuclease that acts as a conformational roadblock. In this intermediate state, neither HNH nor RuvC is competent for target cleavage: the HNH domain is occluded by the roadblock configuration, while the RuvC active site is obstructed by the guide RNA. Only upon full duplex formation do additional base pairs between the guide RNA and ssNA dislodge the HNH roadblock, simultaneously exposing the RuvC nuclease active site. We propose that an analogous conformational checkpoint governs IscB activity during dsDNA target interrogation. Guided by these structural insights, we introduced mutations to either enhance ssNA binding or relieve the conformational checkpoint, both of which significantly improved RNA-targeting efficiency of IscB.

biochemistry↗

bioRxiv2026

ER-stress signaling and Alzheimer's proteins adjust the quality of human protein synthesis

Proteostasis is the balance of protein synthesis, protein maintenance and protein degradation. Proteostasis is disturbed in neurodegenerative disorders like Alzheimers disease (AD) of the aging human body. Protein synthesis by the ribosome is the most error-prone process in gene expression. If and how the error-rate of protein synthesis is regulated during human aging and contributes to AD is unknown. Here we show that ribosomal error-rate is adapted in cellular models of human aging, but not in mouse aging. This adaptation involves ER-stress signaling and the Alzheimers disease-related proteins amyloid-beta precursor protein and presenilin 1. Our results suggest that ribosomal error-rate is a relevant parameter in human aging and disease.

cell biology↗

bioRxiv2026

Transplanting ANXA1- CD8+ Naive T cells Delay Aging Through Senolysis

Immunosenescence is a hallmark of aging, yet strategies using defined immune subsets to counteract it are largely unexplored. We performed paired scRNA/TCR-seq on CD45 cells from human bone marrow (15 donors, 3-91 years). T cells were the most altered lineage, with CD8 naive T cell contraction and functional impairment. We identified an expanding ANXA1 CD8 naive subset with senescence signatures and impaired function. ANXA1-deficient CD8 T cells exhibited increased resting stemness and enhanced activation/cytotoxicity upon stimulation. ANXA1- cells showed senolytic activity in vitro and reduced senescence burden in vivo. Monthly transfer of syngeneic ANXA1- CD8 naive T cells into aged mice extended median lifespan by >30 weeks, improving cardiac function, bone density, motor coordination, and marrow immune microenvironment. Our study identifies ANXA1 as critical in CD8 naive T cell aging and establishes ANXA1- cell transfer as a strategy to counter immunosenescence and promote healthy aging.

immunology↗

bioRxiv2026

T2T Genome and Population Resequencing Reveal OfCCD4 Alleles Orchestrate Petal Color and Scent in Osmanthus fragrans

Osmanthus fragrans is prized for its floral color and fragrance, both key targets for genetic improvement. However, the lack of a complete genome assembly and comprehensive population structure hinders gene dissection and marker development for breeding. To investigate the genetic basis of color-scent interaction, a telomere-to-telomere (T2T) genome assembly is generated, and whole-genome resequencing of 100 cultivars is performed. Integrative population and metabolomic analyses reveal a trade-off: orange-red ( Aurantiacus) cultivars accumulate high /{beta}-carotene but low aromatic apocarotenoids (/{beta}-ionone), while yellow-white cultivars show the opposite pattern. Divergence mapping identifies OfCCD4 as the major underlying locus. Three alleles are characterized--functional (A), partially functional (aDel), and a frameshift null (aStop)--with aStop strictly co-segregating with the Aurantiacus phenotype. Transient and stable transformations confirm that A and aDel cleave /{beta}-carotene into /{beta}-ionone, while aStop abolishes this activity. A co-dominant PCR marker is developed based on allele-specific polymorphisms. OfCCD4 is thus established as the key regulator of the color-scent trade-off in osmanthus. The identified alleles and molecular marker enable rapid, low-cost genotyping at the seedling stage--offering particular value for marker-assisted selection in ornamental breeding, where extended juvenility makes phenotypic selection highly time- and resource-intensive.

plant biology↗

bioRxiv2026

MATR3 is essential for oocyte growth and maturation quality through a dual molecular mechanism

The molecular mechanisms governing mRNA accumulation during oocyte growth, essential for developmental competence, remain poorly understood. This study investigates the role of Matrin-3 (MATR3), a highly expressed RNA-binding protein in growing oocytes (GOs), using oocyte-specific knockout mouse models and human oocyte maturation arrest (OMA) samples. The results showed that MATR3 was more abundant in GOs than fully-grown oocytes (FGOs), highly expressed in the nucleus of non-surrounded nucleolus (NSN) oocytes, and exited the nucleus during the NSN-to-surrounded nucleolus (SN) transition. In OMA patients, MATR3 nuclear localization was missed, with smaller oocytes than FGOs. Further, Matr3 deletion in mouse GOs caused restricted oocyte growth, global transcription disorders, follicle development failure, blocked GO-granulosa cell communication (via reduced Gdf9 and Radixin expression), and infertility. Mechanistically, MATR3 regulated transcription by recruiting H3K9me2-demethylating lysine-specific demethylase 3B or binding target gene promoters, like Radixin. These findings reveal a critical role of MATR3 in orchestrating transcription and paracrine signaling during oogenesis and suggest its potential as a diagnostic and therapeutic target for OMA.

physiology↗

bioRxiv2026

Artificial Recombination of Nonribosomal Peptide Synthetases Rapidly Evolves Natural Products

Efficient engineering of nonribosomal peptide synthetases (NRPSs) is a key strategy for expanding valuable peptide natural products. Current bioinformatics-guided approaches are often constrained by a set of predefined fusion sites, remaining experimentally challenging in most NRPS systems. Here we present the Recombineering Accelerated Evolution (RACE), which harnesses Red/ET recombineering mediated partially matched homologous recombination to recapitulate recombination-driven NRPS evolution on a highly accelerated timescale. Application of RACE to six known NRPS gene clusters generated 830 recombinants and yielded over 600 novel peptides including novel bis-lipopeptides. These recombinants reveal 112 previously unrecognized recombination fusion sites, providing an extensive landscape for NRPS evolution and more useful resources for guiding NRPS engineering. The RACE establishes a new paradigm for programmable NRPS evolution and enables rapid discovery of bioactive peptides.

synthetic biology↗

bioRxiv2026

Detection of Somatic Point Mutations Directly from Spatial Transcriptomics Enables in vivo Spatiotemporal Lineage Tracing

Spatial transcriptomics reveals tissue organization but lacks in vivo lineage-tracing methods applicable to humans. We introduce SpaceTracer, a computational framework that accurately detects somatic single-nucleotide variants (SNVs) directly from spatial transcriptomics data. By leveraging naturally occurring somatic SNVs, SpaceTracer reconstructs cellular phylogenies within native tissue architecture, enabling the mapping of lineage spread, migration, lineage-coupled expression changes and lineage-aware local interactions. Applied to human cutaneous squamous cell carcinoma, it traced tumor initiation and progressions, uncovered widespread pre-invasive migration of dedifferentiated epithelial cells and characterized mutant B cells migrating from tertiary lymphoid structures (TLS) into the tumor boundary. The framework also reconstructed developmental lineages across multiple tissues and identified tissue-resident mutant immune cells. SpaceTracer thus provides a perturbation-free platform for high-resolution spatiotemporal lineage tracing, offering a transformative tool for elucidating complex biological systems--especially tumor-immune ecosystems--with direct implications for advancing cancer immunotherapy.

bioinformatics↗

bioRxiv2026

PhyloSOLID: Robust phylogeny reconstruction from single-cell data despite inherent error and sparsity

While lineage tracing based on somatic mutations in single-cell sequencing data offers a powerful approach to reconstructing cellular histories in vivo, its reliability is fundamentally limited by pervasive technical artifacts--specifically, high error rates and data sparsity. These issues introduce false phylogenetic signals that corrupt tree topology and lead to spurious evolutionary conclusions. To overcome these limitations, we present PhyloSOLID, a phylogenetic algorithm designed to be inherently robust to these data imperfections. PhyloSOLID employs a progressive scaffolding strategy that begins with graph-based construction of a low-resolution, high-confidence backbone tree from reliable and uniformly covered mutations. This scaffold is then refined through the iterative integration of remaining data, guided by a Bayesian statistical model that penalizes phylogenetic inconsistencies to effectively separate the true evolutionary signal from technical artifacts. Benchmarking on both simulated datasets and multiple ground-truth datasets demonstrates that PhyloSOLID achieves superior lineage reconstruction accuracy over existing methods, for both single-cell RNA-seq and DNA-seq data. Additionally, a user-friendly web interface enables customized quality assessment, artifact removal, and interpretation of lineage structures. PhyloSOLID provides a powerful solution for decoding cellular evolution in developmental and disease contexts.

bioinformatics↗

bioRxiv2026

Unravelling genome-wide mosaic microsatellite mutations at single-cell resolution

Short tandem repeats (STRs), or microsatellites, are highly mutable genomic elements that modulate gene regulations and are implicated in a range of human diseases. However, detecting mosaic STR mutations at single-cell resolution remains challenging due to both technical and biological complexities. To address this, we developed BayesMonSTR, a robust algorithm that enables accurate detection of mosaic STR mutations. Using this tool in single-cell analysis of human tissues, we reveal an accumulation of longer mosaic STR insertions and deletions (indels) in aging mitotic and post-mitotic cells. Strikingly, prefrontal cortex (PFC) neurons accumulate a higher burden of STR mutations than B cells or lung epithelium, with aged neurons exhibiting a particularly pronounced increase in longer STR deletions. These mutations are enriched at transcription start sites (TSSs) and active enhancers of highly expressed genes. Our work establishes a foundation for genome-wide, hypothesis-free discovery of disease-associated mosaic STR mutations and reveals a previously unexplored landscape of mosaic STR variation in development and aging.

bioinformatics↗

bioRxiv2026

RVPSD: A comprehensive and user-friendly web database for RNA viral protein structures

Protein structures are central to understanding the diversity and biological function of RNA viruses. However, few experimentally validated structures of RNA viruses are currently available. To address this gap, we established the RNA Viral Protein Structure Database (RVPSD) that comprises diverse RNA viral protein structures predicted using AlphaFold2. RVPSD integrates taxonomic classification, viral nucleotide and protein sequences, functional annotations, and predicted three-dimensional protein structures to support a systematic exploration of the RNA viral proteomes. Currently, RVPSD comprises a total of 154,716 AlphaFold2-predicted RNA viral protein structures from 5,263 RNA virus species, with 84.9% exhibiting high pLDDT scores (>70) and representing a large-scale and comprehensive resource for RNA viral protein structures. RVPSD also provides a user-friendly web interface, with advanced search, sequence- and structure-based retrieval, interactive 3D visualization, and access and downloading structural data, enabling researchers to perform comparative structural analyses and functional annotation of viral "dark matter".

microbiology↗

bioRxiv2026

Intramuscular Adipose Tissue Accumulation is a Key Determinant of Limb Function in Peripheral Artery Disease

BackgroundPeripheral artery disease (PAD) and its severe form, chronic limb-threatening ischemia (CLTI), significantly impair blood flow to the lower extremities, affecting millions of adults globally. Intramuscular adipose tissue (IMAT) and fibrosis accumulation distinguish patients with CLTI from those with mild PAD, suggesting a role in CLTI pathobiology. However, the functional consequences of IMAT in CLTI remain unclear. MethodsWe compared gastrocnemius muscle samples from patients with PAD/CLTI, intermittent claudication, and non-PAD individuals. We analyzed bulk RNA sequencing, proteomic, lipidomic, and single-cell/nucleus RNA sequencing datasets. Additionally, we used murine models of hindlimb ischemia (HLI) with genetic manipulation of Ppar{gamma}, a key adipogenic transcription factor, specifically in fibro-adipogenic progenitor cells (FAPs), the cellular source of IMAT, to modulate IMAT formation and assessed the impact on limb function and pathology. ResultsPatients with CLTI exhibited significantly elevated expression of adipogenic genes and proteins in muscle specimens when compared to non-PAD controls. Murine models showed that increasing IMAT formation significantly worsened ischemic limb muscle strength and work output. In contrast, preventing IMAT formation significantly improved ischemic limb muscle strength and work output. These findings were consistent across both male and female mice, although females had greater tendency to form IMAT compared with male mice. ConclusionsIMAT accumulation is a key determinant of limb function in PAD/CLTI. Our studies demonstrate that targeting IMAT formation could improve limb function in mice with experimental PAD. Together, these findings suggest that developing strategies to limit or reduce IMAT may improve limb function and walking performance in patients with PAD/CLTI, providing a novel therapeutic avenue to address a critical unmet need. CLINICAL PERSPECTIVEO_ST_ABSWhat is new?C_ST_ABSO_LIIntramuscular adipose tissue accumulation (IMAT) distinguishes patients with chronic limb-threatening ischemia from those with milder peripheral artery disease or those without PAD and directly impairs ischemic limb muscle function. C_LIO_LIGenetic gain- and loss-of-function mouse models demonstrate that increasing IMAT worsens, while preventing IMAT formation improves, ischemic limb strength and performance independent of perfusion. C_LIO_LIAdipogenic signatures in human calf muscle negatively correlates with muscle strength and disease severity, identifying IMAT as a functional biomarker and modifiable target in PAD/CLTI. C_LI What are the clinical implications?O_LIIMAT accumulation represents an underappreciated, non-vascular mechanism contributing to leg dysfunction in PAD/CLTI. C_LIO_LITherapies aimed at limiting or reversing IMAT formation may improve leg strength and walking performance in patients with PAD/CLTI, addressing a critical unmet clinical need. C_LIO_LIIdentifying and targeting cellular pathways regulating IMAT formation from fibro-adipogenic progenitors may complement vascular interventions to enhance functional recovery after revascularization. C_LI

physiology↗

bioRxiv2026

A Manifold-Based Measure of Transcriptional Entropy for Quantifying Aging in Single Cells

Aging reshapes tissues through changes in cellular composition, coordinated transcriptional reprogramming, and loss of transcriptional coordination. Whereas the first two have been characterized across aging tissues, the third remains difficult to quantify. We introduce an unsupervised, first-principles framework for measuring transcriptional dyscoordination in single cells as deviation from a learned, predictable structure accounting for technical noise. Orthogonal validation links transcriptional dyscoordination to classical intrinsic noise and distinguishes it from coordinated change. In controlled perturbations, dyscoordination rises after genotoxic injury and senescence induction, then falls following senolytic depletion. Across mouse, rat, and human tissues, dyscoordination increases with chronological age, especially in regenerative compartments. In human T cells, dyscoordination increases with clonal expansion and effector function yet declines within persisting clones after checkpoint blockade. Cross-modal analyses further link dyscoordination to chromatin-based mitotic age and genome instability. These results identify loss of transcriptional coordination as a distinct and dynamic feature of cellular aging.

genomics↗

bioRxiv2026

A genetically defined midbrain-pontine circuit gates vocal communication

Vocal communication is selectively expressed in social and emotional contexts1-3, suggesting the presence of neural substrates that gate the conversion of internal states into vocal motor output. Although the periaqueductal gray (PAG) is known to be essential for vocalization4-6, the genetic identity and circuit logic of the neurons that initiate and shape vocal signals remain unclear. Here, we identify a genetically defined population of somatostatin-expressing neurons in the lateral and ventrolateral PAG (l/vlPAGSST) that functions as a premotor gate for ultrasonic vocalizations in mice. In vivo calcium imaging shows that l/vlPAGSST neurons are selectively recruited around vocal onset. Manipulating l/vlPAGSST neuron activity bidirectionally regulates vocal output: activation prolongs call duration by coordinating respiratory, laryngeal, and orofacial motor programs, whereas silencing suppresses courtship vocalizations. Projection-specific manipulations further demonstrate that descending glutamatergic, but not neuropeptidergic, output from l/vlPAGSST neurons to the dorsal pontine tegmentum is sufficient to drive vocal production. Together, these findings define a genetically specified midbrain-pontine circuit that gates vocal communication and provides prospective access for linking internal conditions to vocal expressions.

neuroscience↗

bioRxiv2026

Environmental Amino Acid Sensing Regulates the Rate of ASC Translation and NLRP3 Inflammasome Assembly

The NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome is a multiprotein signaling complex that triggers pyroptotic cell death and interleukin (IL)-1 family cytokine release during infection and cell injury. Its assembly is driven by the adaptor protein, apoptosis-associated speck-like protein containing a CARD (ASC), whose filamentation forms a supramolecular speck upon NLRP3 activation to amplify inflammasome signaling. While the NLRP3 inflammasome is well appreciated as a sensor of environmental danger and damage, little is known about how homeostatic environmental factors like dietary metabolites regulate its activity. Here, we find that environmental availability of the branched-chain amino acids (BCAAs), leucine, isoleucine, and valine, controls NLRP3 inflammasome assembly. While ASC is typically viewed as a constitutively expressed, unregulated inflammasome component, we find that Toll-like receptor 4 (TLR4) activation triggers localization of ASC mRNA to the perinuclear space. Moreover, our data demonstrate that ASC undergoes TLR4-driven translational bursting from polyribosomes during inflammasome priming. This translational engagement is dependent on BCAA availability and mechanistic target of rapamycin (mTOR) activity, which regulate the kinetics of inflammasome assembly. In contrast, the translation of NLRP3 and caspase-1 is largely insensitive to these inputs. Furthermore, we find that BCAAs regulate NLRP3 inflammasome activation in both mouse and human macrophages, in the context of bacterial infection, and during lipopolysaccharide (LPS)-induced sepsis in vivo. Altogether, this work unveils a novel inflammasome priming event governed by the amino acid environment. These findings further highlight how the activity of proteins maintained in equilibrium like ASC can be dynamically regulated through rapid changes in mRNA translation.

immunology↗

bioRxiv2026

L-cysteine inhibited the growth of Vibrio parahaemolyticus via increasing the ROS level

The emergence of multidrug-resistant Vibrio parahaemolyticus poses a severe threat to mariculture sustainability, highlighting the urgent need for eco-friendly antimicrobial agents. In this study, we demonstrated that L-Cysteine (L-Cys) functions as an inhibitor of V. parahaemolyticus, with a minimum inhibitory concentration of 7.5 mM. Microscopic observation and viability assays revealed that L-Cys compromises bacterial membrane integrity, ultimately leading to cell death. Further investigation indicated that the antibacterial effect is primarily attributed to the intracellular production of hydrogen sulfide (H2S) generated by L-Cys metabolism. Transcriptomic and biochemical analyses showed that L-Cys induced metabolic reprogramming by suppressing fatty acid {beta}-oxidation, one-carbon metabolism, and antioxidant enzymes. This disruption of redox homeostasis results in accelerated accumulation of reactive oxygen species (ROS). In addition to its antibacterial effect, L-Cys also effectively reduced the virulence factor of bacterial motility. Finally, L-Cys demonstrated broad-spectrum antimicrobial activity against other pathogenic Vibrio species, including V. alginolyticus and V. anguillarum. Our findings suggest that L-Cys is a promising antimicrobial agent inducing ROS to mediate membrane disruption, with the advantages of cost-effectiveness and environmental safety for controlling vibriosis. ImportanceVibrio parahaemolyticus is a significant pathogen in aquaculture and a common cause of seafood-borne gastroenteritis worldwide. The increasing prevalence of antibiotic-resistant strains of this bacterium highlights the need for alternative control agents. This study shows that L-cysteine (L-Cys) inhibits the growth of V. parahaemolyticus. Our data indicate that L-Cys is metabolized to produce hydrogen sulfide, which contributes to the accumulation of ROS and disrupts bacterial membrane integrity. Additionally, L-Cys reduces bacterial motility and shows inhibitory effects against other Vibrio species. These findings suggest that L-Cys may represent a useful agent for managing Vibrio infections in aquaculture settings.

microbiology↗

bioRxiv2026

A Unified and Interpretable Framework for Evaluating Fluorescence Trace Quality in Transcription Kinetics

Quantifying transcriptional dynamics from fluorescence traces is a powerful approach to understanding gene regulation, but such analysis critically depends on the quality of the fluorescence signal. Experimental researchers often lack an objective and computationally simple way to assess trace quality before kinetic modeling. In this study, we fill in this gap via systematically investigating two key factors (i.e., signal-to-noise ratio (SNR) and trace length) using synthetic data generated from a composite-state Hidden Markov Model (cpHMM) simulator. By analyzing thousands of simulated traces, we identified quantitative thresholds (SNR [≥] 30 dB and length [≥] 360) beyond which transcriptional dynamics can be reliably captured for kinetic inference. Building on these findings, we further discovered a unified and easily computable quality indicator based on the difference between the first two autocorrelation lags. A threshold value of approximately 0.07 effectively separates reliable from low quality traces, providing a simple yet robust criterion for data selection. Together, these results establish a practical framework for assessing fluorescence trace reliability, offering experimental researchers an interpretable and computationally efficient tool to ensure data quality prior to transcription kinetics modeling.

bioinformatics↗

bioRxiv2025

MicroGenomer: A Foundation Model for Transferable Microbial Genome Representations Enabling Multi-scale Genomic Understanding and Ecophysiological Trait Prediction

Microorganisms underpin global biogeochemical cycles and represent a vast, underexplored reservoir for sustainable biotechnology and human health. Their diversity, arising from the interplay of numerous genes within holistic genomic contexts, dictates complex ecophysiological traits across varied environments. To bridge the gap between complex genomic sequences and associated biological functions and phenotypic outcomes, we present MicroGenomer, a foundation model for transferable microbial genome representations enabling multi-scale genomic understanding and ecophysiological trait prediction. MicroGenomer leverages a hierarchical training strategy comprising pre-training on large-scale genomic sequences (234.5 billion base pairs), domain-specific mid-training using the GTDB-curated marker gene set, and task-specific post-training. Despite a streamlined architecture of 470 million parameters, MicroGenomer achieves performance on key tasks competitive with models nearly 85 times its size. Advancing beyond established gene-scale encoders, MicroGenomer generates robust embeddings at the genome scale for downstream modeling. Extensive evaluations demonstrate that MicroGenomer effectively captures phylogenetic structures in species space, excelling in geneand genome-scale understanding as well as ecophysiological trait prediction. The practical utility of these capabilities is further demonstrated by targeted wet-lab validation on newly isolated strains, indicating that MicroGenomers predictions provide reliable guidance for biological experiments. Collectively, MicroGenomer offers a high-performance, resource-efficient framework that transforms raw sequence data into actionable biological insights, providing a powerful foundation for microbiome research and biotechnology.

bioinformatics↗

bioRxiv2025

Neural Mechanisms of Willed Attention Control

Cueing paradigms are commonly used to study the neural mechanisms of visual spatial attention control. In these paradigms, each trial starts with an external cue, which instructs the subject to pay covert attention to a spatial location in anticipation of an impending stimulus (instructed attention). Recent work has introduced a new type of cue which prompts the subject to spontaneously decide which spatial location to attend (willed attention). We studied the neural mechanisms of willed attention control by analyzing fMRI and EEG data recorded at two institutions (UF and UC Davis) using the same willed attention paradigm. The findings include: (1) both instructional cues and the choice cue activated the DAN, (2) the choice cue additionally activated a frontoparietal decision network consisting of dorsal anterior cingulate cortex (dACC), anterior insula (AI), anterior prefrontal cortex (APFC), dorsal lateral prefrontal cortex (DLPFC), and inferior parietal lobule (IPL), (3) the decision about where to attend can be decoded in frontoparietal decision network in choice trials but not in instructional trials, and (4) EEG alpha oscillation patterns immediately preceding the choice cue, but not the instructional cues, predicted the postcue direction of attention and the frontoparietal decision network activity. Based on these findings we proposed a model of willed attention control suggesting how the direction of visual spatial attention was decided upon in the absence of external instructions.

neuroscience↗