Biology subjects

Ouyang, H.

Publications and source records attributed to Ouyang, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Intermediate Relative Humidity Preserves Respiratory Syncytial Virus via a Semi-Solid Bioaerosol State

Respiratory syncytial virus (RSV) transmission via the aerosol route remains poorly understood, particularly with respect to how evolving virus-laden particles (bioaerosols) microenvironments influence viral survival. Bioaerosol particles contain complex mixtures of organic and inorganic components, and their physicochemical properties change dynamically during evaporation as water is lost upon emission from respiratory activities. These changes directly affect the local environment surrounding embedded virus during both the evaporation stage and the subsequent equilibrium state. However, how these microenvironmental conditions under different relative humidity (RH) levels regulate RSV survival remains unclear. In this study, we quantified RSV survival during the evaporation and early equilibrium stages using a flow-tube system with controlled residence times. Bioaerosols were generated from virus medium alone or supplemented with bovine serum albumin (BSA) or mucin and evaluated under low (35%) and intermediate (61%) RH conditions. Viral infectivity was normalized to RNA copy number to account for particle and sampling losses. At 35% RH, RSV infectivity decreased by one to three orders of magnitude, depending on the solution composition. In contrast, survival was significantly higher at intermediate RH, particularly for virus medium and BSA-supplemented aerosols. Scanning electron microscopy revealed that low RH conditions promote efflorescence, whereas intermediate RH results in viscous or semi-solid particles with higher water content. These observations suggest that efflorescence is associated with enhanced RSV inactivation, while viscous or semi-solid phases tend to preserve RSV in the aerosol state for respirable particles. Overall, RSV infectivity depends strongly on particle chemical composition, phase state (effloresced versus semi-solid), and relative humidity. These results highlight the importance of characterizing particle phase behavior and chemical composition during early aerosol processes to improve mechanistic understanding of viral survival relevant to short-range transmission.

microbiology↗

bioRxiv2026

Telomere-to-telomere gap-free genome assembly integrated with multi-omics uncovers shading mediated regulation of leaf aroma biosynthesis in aromatic crop Pandanus amaryllifolius

Pandanus amaryllifolius is a valuable aromatic crop widely cultivated in tropical forest understories. Here, A telomere-to-telomere, gap-free genome assembly of the Chinese cultivar Taishan Banlan was generated, and the molecular basis underlying shading-mediated regulation of leaf aroma biosynthesis was elucidated for the first time through integrated genomic, transcriptomic, and metabolomic analyses. Volatile metabolomics identified 1599 volatile organic compounds in leaf tissue, with terpenoids as the primary contributors to leaf aroma. Shading modulated the aroma quality of P. amaryllifolius primarily via terpenoid biosynthesis, yielding aroma profiles dominated by sweet, fruity, green, and woody notes. Integrated transcriptomic profiling revealed that terpenoid biosynthesis is co-regulated by structural genes in the MVA/MEP pathways, TPS family members, and key transcription factors, which collectively modulate the biosynthesis and accumulation of the three core differential terpenoids. Our findings provide valuable resources for the targeted genetic improvement and efficient cultivation optimization of P. amaryllifolius.

genomics↗

bioRxiv2026

Organic Components Modulate the Morphology of Respirable Aerovirology Relevant Aerosols

Airborne transmission of pathogens occurs via aerosol particles, whose morphology provides insights into the microenvironments that pathogens experience. Aerosol morphology includes particle size, shape, phase state, and chemical homogeneity, yet systematic studies remain limited. Here, we characterized model bioaerosol morphologies generated from (1) NaCl-organic two-component mixtures, (2) common cell culture media, and (3) artificial respiratory fluids. Particles were collected using a virtual impactor and Andersen cascade impactor and analyzed by scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX). Results show that organic components modulate the morphology: dipalmitoylphosphatidylcholine (DPPC) promotes organic-inorganic phase separation while proteins prohibit formation of large crystals and leads to better mixing among components. At 30% RH with a drying period of 10 seconds, most aerosols appeared desiccated, though NaCl-glucose, DMEM-complete-media and artificial saliva with mucin remained semi-solid or gel-like. Among all formulations examined EMEM-complete-media and artificial saliva (non mucin) show a size-dependent morphology. Our study demonstrates how chemical composition and size alters surrogate bioaerosol phase (semi-solid or solid) and morphology and provides new insights into the microenvironment of aerosol particles for aerovirology investigations.

biochemistry↗

bioRxiv2025

Airflow Determines Natural Airborne Transmission of Tuberculosis in a Guinea Pig Model

Tuberculosis (TB) is transmitted through the air, yet the determinants of natural airborne transmission remain poorly defined. Early twentieth-century guinea pig studies demonstrated efficient airborne transmission of Mycobacterium tuberculosis (Mtb), but this paradigm has not been reestablished in contemporary containment facilities. Here, we show that ventilation can impose airflow constraints that suppress transmission under otherwise permissive conditions. Using a guinea pig model of animal-to-animal exposure, we combined transmission experiments with quantitative airflow measurements and particle transport modeling to explain why some housing configurations fail to support effective exposure. Static environments and excessive unidirectional airflow prevented transmission, whereas controlled low-velocity airflow restored evidence of exposure, including tuberculin skin test conversion, antigen-specific immune responses, and pulmonary inflammation consistent with early infection. These findings identify airflow as a critical constraint on airborne TB transmission and provide a reproducible framework to dissect host, microbial, and environmental determinants of spread.

physiology↗

bioRxiv2025

3' Nucleotide Asymmetry Directs miRNA Strand Selection

Accurate microRNA (miRNA) strand selection is essential for defining the regulatory landscape of the miRNA-induced silencing complex (miRISC). While 5' nucleotide identity and duplex thermodynamics have been proposed to bias strand choice, these features cannot fully explain in vivo strand preferences. Here, we uncover a conserved and previously unrecognized role for 3' nucleotide asymmetry in directing miRNA strand selection in Caenorhabditis elegans and human cells. A favorable 3' terminal nucleotide on the passenger strand promotes selective loading of the opposing guide strand into miRISC, revealing a cooperative interplay between 5' and 3' terminal asymmetries that ensures precise strand discrimination. These findings establish a unified, evolutionarily conserved mechanism for miRNA duplex sorting and expand the fundamental rules governing small RNA biogenesis.

molecular biology↗

bioRxiv2024

Crosslinking-mediated Interactome Analysis Identified PHD2-HIF1α Interaction Hotspots and the Role of PHD2 in Regulating Protein Neddylation

Prolyl Hydroxylase Domain protein 2 (PHD2) targets Hypoxia Inducible Factor alpha subunits (HIF) for oxygen-dependent proline hydroxylation that leads to subsequent ubiquitination and degradation of HIF. In addition to HIF proteins, growing evidence suggested that PHD2 may exert its multifaceted function through hydroxylase-dependent or independent activities. Given the critical role of PHD2 in diverse biological processes, it is important to comprehensively identify potential PHD2 interacting proteins. In this study, we engineered HeLa cells that stably express HTBH-tagged PHD2 to facilitate the identification of PHD2 interactome. Using DSSO-based cross-linking mass spectrometry (XL-MS) technology and LC-MSn analysis, we mapped PHD2-HIF1 interaction hotspots and identified over 300 PHD2 interacting proteins. Furthermore, we validated the COP9 Signalosome (CSN) complex, a major deneddylase complex, as a novel PHD2 interactor. DMOG treatment promoted interaction between PHD2 and CSN complex and enhanced the deneddylase activity of the CSN complex, resulting in increased level of free Cullin and reduced target protein ubiquitination. This mechanism may serve as a negative feedback regulation of the HIF transcription pathway.

biochemistry↗

bioRxiv2024

A Tough Biointerface in Human Knee Empowered by Dynamic Phase-transforming Minerals in Collagenous Matrix

Joining heterogeneous materials in engineered structures remains a daunting challenge because of stress concentration, often resulting in unexpected failures1,2. Studying the structures in organisms that evolved for centuries provides valuable insights that can be instrumental in addressing this mechanical challenge3-5. The human meniscus root-bone interface is a remarkable example known for its exceptional fatigue resistance, toughness and interfacial adhesion properties throughout its lifespan6-8. We studied the multiscale graded mineralization structure designs within the 30-micron soft-hard interface at the root-bone junction and examined its toughening mechanisms. This graded interface with interdigitated structures and exponential modulus increase exhibits a phase transition from amorphous calcium phosphate (ACP) to gradually matured hydroxyapatite (HAP) crystals, mediated by location-specific distributed biomolecules. In coordination with collagen fibril deformation and reorientation, ACP particles debond with collagen and slide to new positions which enable frictional energy dissipation, and HAP particles arrest cracks. The mineral in transforming phases work synergistically to provide interfacial toughening. The presented biointerface model exemplifies human musculoskeletal systems adaptations to mechanical requirements, offering a blueprint for developing tough interfaces in broad applications.

bioengineering↗

bioRxiv2023

Bio-inspired mineralization collagen induce fibrocartilage regeneration after tendon-bone injury by activating Gli1+Dkk3+ progenitor cells

A fibrocartilaginous connection between the tendon and bone, plays a critical role in transferring force from muscle to bone to enable joint movement. However, due to the high mechanical stress it experiences, the enthesis is vulnerable to injury and incapable of regenerating. The spatial relationship and functional basis of the principal components of the fibrocartilage - mineral and collagen - have not been clearly elucidated, which is a significant remaining gap in reconstructing complex architectures for promoting interface tissue regeneration. Here, using three-dimensional electron tomography imaging and high-resolution two-dimensional electron microscopy, we discover that mineral particles form a continuous cross-fibrillar phase within the fibrocartilage region. By developing a "floating mineralization" system, we fabricate a three-layer hydrogel that mimics the hierarchical nano- to micro-scale structure of tendon-bone interface (TBI). The middle layer is noteworthy for its resemblance to the nanostructure of fibrocartilage and its superior ability to induce mineralized fibrochondrogenesis in vitro. Based on motor function analysis, imaging diagnosis, histological staining, immunofluorescence staining, and biomechanics performance, we demonstrate that in situ transplantation of the gradient hydrogel achieved tendon-fibrocartilage-bone synchronous regeneration and result in 68% maximum mechanical recovery at 8-week postoperation. Single-cell RNA sequencing analysis reveals that a unique atlas of in situ stem/progenitor cells is generated during the TBI healing in vivo. Notably, the bio-inspired hydrogel microenvironment drived endogenous Gli1+Dkk3+ progenitor cells, playing a key role in TBI regeneration. Therefore, we have successfully decoded and reconstructed the nanostructure of fibrocartilage, which has great potential in TBI regeneration.

bioengineering↗

bioRxiv2023

Gas tunnel engineering of an iron-based oxygen sensor reprograms cellular hypoxia signaling

Cells have evolved intricate mechanisms for recognizing and responding to changes in oxygen (O2) concentrations. Here, we have reprogrammed cellular hypoxia (low O2) signaling via gas tunnel engineering of prolyl hydroxylase 2 (PHD2), a non-heme iron dependent O2 sensor. Using computational modeling and protein engineering techniques, we identify a gas tunnel and critical residues therein that limit the flow of O2 to PHD2s catalytic core. We show that systematic modification of these residues can open the constriction topology of PHD2s gas tunnel. Using kinetic stopped-flow measurements with NO as a surrogate diatomic gas, we demonstrate up to 3.5-fold enhancement in its association rate to the iron center of tunnel-engineered mutants. Our most effectively designed mutant displays 9-fold enhanced catalytic efficiency (kcat/KM = 830 {+/-} 40 M-1 s-1) in hydroxylating a peptide mimic of hypoxia inducible transcription factor HIF-1, as compared to WT PHD2 (kcat/KM = 90 {+/-} 9 M-1 s-1). Furthermore, transfection of plasmids that express designed PHD2 mutants in HEK-293T mammalian cells reveal significant reduction of HIF-1 and downstream hypoxia response transcripts under hypoxic conditions of 1% O2. Overall, these studies highlight activation of PHD2 as a new pathway to reprogram hypoxia responses and HIF signaling in cells.

biochemistry↗

bioRxiv2023

p120 RasGAP and ZO-2 are essential for Hippo signaling and tumor suppressor function mediated by p190A RhoGAP

ARHGAP35, which encodes p190A RhoGAP (p190A), is a major cancer gene. p190A is a tumor suppressor that activates the Hippo pathway. p190A was originally cloned via direct binding to p120 RasGAP (RasGAP). Here, we determine that a novel interaction of p190A with the tight junction-associated protein ZO-2 is dependent on RasGAP. We establish that both RasGAP and ZO-2 are necessary for p190A to activate LATS kinases, elicit mesenchymal-to-epithelial transition, promote contact inhibition of cell proliferation and suppress tumorigenesis. Moreover, RasGAP and ZO-2 are required for transcriptional modulation by p190A. Finally, we demonstrate that low ARHGAP35 expression is associated with shorter survival in patients with high, but not low, transcript levels of TJP2 encoding ZO-2. Hence, we define a tumor suppressor interactome of p190A that includes ZO-2, an established constituent of the Hippo pathway, and RasGAP, which despite strong association with Ras signaling, is essential for p190A to activate LATS kinases.

cancer biology↗

bioRxiv2023

Reprogramming of lipid secretome in senescent synovial fibroblasts ameliorate osteoarthritis development

Osteoarthritis (OA) is one of the most common causes of physical disability among older people and its incidence increases with age. Removal of the senescent cells (SNCs) delays OA pathologies, but little is known about the SNCs in OA synovium and their roles in OA pathogenesis. Here, we reported that RCAN1+IL1+ double-positive cells represent a senescent subset of synovial fibroblasts which accelerate cartilage degeneration via saturated fatty acids (SFAs). Using single-cell RNA sequencing and synovial organoids, we found that IL1+ senescent synovial fibroblasts mainly located at lining layer of human OA synovium and promote cartilage degeneration. We performed genome-wide CRISPR/Cas9 screens to identify novel regulators of cell-surface bounded IL1 in senescent cells. RCAN1, which was a hit as positive regulator of IL1, governs the cellular senescence and pro-degenerative senescence-associated secretory phenotype (SASP). Mechanistically, we found that RCAN1 mediated the secretion of SFAs from senescent synovial fibroblasts, which promote chondrocytes senescence and cartilage matrix degradation. Intra-articular delivery of synovium-targeted anti-Rcan1 siRNA ameliorates the development of post-traumatic OA in mice, while reducing of SNCs accumulation in synovium and increasing cartilage regeneration. Last, co-culture experiments of human OA cartilage explant with synovial organoids confirmed that RCAN1 silencing in human synovial fibroblasts suppressed chondrocyte senescence and cartilage degradation. Thus, our study revealed a pro-degenerative interaction between RCAN1+IL1+ senescent synovial fibroblasts and chondrocytes through secreted lipid mediators in OA progression. And targeted RCAN1 inhibition in senescent synovium is a promising approach for restore the joint homeostasis.

pathology↗

bioRxiv2022

MSdb: an integrated expression atlas of human musculoskeletal system

We introduce MSdb (https://www.msdb.org.cn), a database for visualization and integrated analysis of next-generation sequencing data from human musculoskeletal system, along with manually curated patient phenotype data. Systematic categorizing, standardized processing and freely accessible knowledge enables the reuse of public data. MSdb provides various types of analysis, including sample-level browsing of metadata information, gene/miRNA expression, and single-cell RNA-seq dataset. In addition, MSdb also allows integrated analysis for cross-samples and cross-omics analysis, including customized differentially-expressed gene/microRNA analysis, microRNA-gene network, scRNA-seq cross-sample/disease integration, and gene regulatory network analysis.

bioinformatics↗

bioRxiv2022

Single-Cell Transcriptomic Analyses of Tumor Ecosystems and Spatial Architectures in Human Small Cell Lung Cancers

Small cell lung cancer (SCLC) is a highly heterogenous disease characterized by aggressive phenotypes and poor prognosis. In order to dissect the cellular components and their spatial distribution in SCLC ecosystems, here we performed single-cell RNA sequencing and spatial transcriptomics analyses of 12 resected human primary SCLCs. Our analysis revealed extensive heterogeneity of both tumor and non-tumor cells, and a predominant immunosuppressive microenvironment. Importantly, multiple hybrid tumor cell states were unmasked, including hybrid SCLC and lung adenocarcinoma cells as well as hybrid tumor and immune cells, indicating high phenotypic plasticity of tumor cells. Moreover, we revealed the cellular origin and evolution of these hybrid tumor cells, and critical roles of tumor-stromal cellular crosstalk in driving the development of hybrid cells. In conclusion, this study deepens our understanding of human SCLC ecosystems and provides rationales to target the hybrid tumor cells and immunosuppressive microenvironment for SCLC therapies.

cancer biology↗

bioRxiv2021

PCBP1 Deficient Pigs Hold the Potential to Inhibit CSFV Infection

Classical swine fever virus (CSFV), pathogen of classic swine fever, has caused severe economic losses worldwide. Poly (rC)-binding protein 1 (PCBP1), interacting with Npro of CSFV, plays a vital role in CSFV growth. Here, our research is the first report to generate PCBP1 knockout pigs via gene editing technology. The PCBP1 knockout pigs exhibited normal birth weight, reproductive-performance traits, and developed normally. Viral challenge results indicated that primary cells isolated from F0 and F1 generation pigs could significantly reduce CSFV infection. Additional mechanism exploration further confirmed that PCBP1 KO mediated antiviral effect is related with the activation of type I interferon. Beyond showing that gene editing strategy can be used to generate PCBP1 KO pigs, our study introduces a valuable animal model for further investigating infection mechanisms of CSFV that help to develop better antiviral solution. ImportanceAs a negative regulator in immune modulation, the effects of PCBP1 on viral replication have been found to be valuable. Here, this study was the first report to generate PCBP1 knockout pigs with normal pregnancy rate and viability. Primary cells isolated from F0 and F1 generation PCBP1 knockout pigs could significantly reduce CSFV infection. The PCBP1 knockout pigs could be used as a natural host models for investigating the effects of PCBP1-mediating critical interactions on viral replication and helping to develop better antiviral solution.

molecular biology↗

bioRxiv2021

Probing neuropeptide volume transmission in vivo by a novel all-optical approach

Neuropeptides are essential signaling molecules in the nervous system involved in modulating neural circuits and behavior. Although hypothesized to signal via volume transmission through G-protein coupled receptors (GPCR), remarkably little is known about their extrasynaptic diffusion. Here, we developed an all-optical approach to probe neuropeptide volume transmission in mouse neocortex. To control neuropeptide release, we engineered photosensitive nanovesicles with somatostatin-14 (SST) that is released with near-infrared light stimulation. To detect SST, we created a new cell-based neurotransmitter fluorescent engineered reporter (CNiFER) using the SST2 GPCR. Under two-photon imaging, we determined the time to activate SST2R at defined distances as well as the maximal distance and loss rate for SST volume transmission in neocortex. Importantly, we determined that SST transmission is significantly faster in neocortex with a chemically degraded extracellular matrix, a diseased condition indicated in neuroinflammation and Parkinsons disease. These new neurotechnologies can reveal important biological signaling processes previously not possible, and provide new opportunities to investigate volume transmission in the brain.

neuroscience↗

bioRxiv2021

PQN-59 antagonizes microRNA-mediated repression and functions in stress granule formation during C. elegans development

microRNAs (miRNAs) are potent regulators of gene expression that function in a variety of developmental and physiological processes by dampening the expression of their target genes at a post-transcriptional level. In many gene regulatory networks (GRNs), miRNAs function in a switch-like manner whereby their expression and activity elicit a transition from one stable pattern of gene expression to a distinct, equally stable pattern required to define a nascent cell fate. While the importance of miRNAs that function in this capacity are clear, we have less of an understanding of the cellular factors and mechanisms that ensure the robustness of this form of regulatory bistability. In a screen to identify suppressors of temporal patterning phenotypes that result from ineffective miRNA-mediated target repression during C. elegans development, we identified pqn-59, an ortholog of human UBAP2L, as a novel factor that antagonizes the activities of multiple heterochronic miRNAs. Specifically, we find that depletion of pqn-59 can restore normal development in animals with reduced miRNA activity. Importantly, inactivation of pqn-59 is not sufficient to bypass the requirement of these regulatory RNAs within the heterochronic GRN. The pqn-59 gene encodes an abundant, cytoplasmically localized and unstructured protein that harbors three essential "prion-like" domains. These domains exhibit LLPS properties in vitro and normally function to limit PQN-59 diffusion in the cytoplasm in vivo. Like human UBAP2L, PQN-59s localization becomes highly dynamic during stress conditions where it re-distributes to cytoplasmic stress granules and is important for their formation. Proteomic analysis of PQN-59 complexes from embryonic extracts indicates that PQN-59 and human UBAP2L interact with orthologous cellular components involved in RNA metabolism and promoting protein translation and that PQN-59 additionally interacts with proteins involved in transcription and intracellular transport. Finally, we demonstrate that pqn-59 depletion results in the stabilization of several mature miRNAs (including those involved in temporal patterning) without altering steady-state pre-miRNAs levels indicating that PQN-59 may ensure the bistability of some GRNs that require miRNA functions by promoting miRNA turnover and, like UBAP2L, enhancing protein translation. AUTHOR SUMMARYBistability plays a central role in many gene regulatory networks (GRNs) that control developmental processes where distinct and mutually exclusive cell fates are generated in a defined order. While genetic analysis has identified a number of gene types that promote these transitions, we know little regarding the mechanisms and players that ensure these decisions are robust. and in many cases, irreversible. We leveraged the robust genetics and phenotypes associated with temporal patterning mutants of C. elegans to identify genes whose depletion would restore normal regulation in animals that express miRNA alleles that do not sufficiently down-regulate their targets. These efforts identified pqn-59, the C. elegans ortholog of the human UBAP2L gene. Like UBAP2L, PQN-59 likely forms a hub for a number of RNA/RNA-binding protein mediated processes in cells including translational activation and in the formation of stress granules in adverse environmental conditions. Finally, we also demonstrate that pqn-59 depletion stabilizes mature miRNA levels further connecting this new family of RNA-binding proteins to translation and miRNA-mediated gene regulation.

developmental biology↗

bioRxiv2020

High-resolution architecture of human epiphysis formation

Human limb skeletal system consists of both bone and cartilage which originated from fetal cartilage. However, the roadmap of chondrocyte divergent differentiation to bone and articular cartilage has yet to be established. Epiphysis possesses articular cartilage, growth plate and the secondary ossification center (SOC), making it an ideal model to uncover the trajectory of chondrocyte divergent differentiation. Here, we mapped differentiation trajectory of human chondrocyte during postnatal finger epiphysis development by using single-cell RNA sequencing. Our results uncovered that chondroprogenitors have two differentiation pathways to hypertrophic chondrocytes during ossification, and one pathway to articular chondrocytes for formation of cartilages. Interestingly, we found that, as an addition to the known typical endochondral ossification path from resting, proliferative to hypertrophic chondrocytes, there was a bypass by which chondroprogenitors differentiate into hypertrophic chondrocytes without proliferative stage. Furthermore, our results revealed two new chondrocyte subpopulations (bypass chondrocytes as it appeared in the ossification bypass, and ID1+ chondroblasts in articular chondrocyte path) during postnatal epiphysis development in addition to six well-known subpopulations. Overall, our study provides a comprehensive roadmap of chondrocyte differentiation in human epiphysis thereby expanding the knowledge of bone and articular cartilage, which could be utilized to design biotherapeutics for bone and articular cartilage regeneration.

developmental biology↗

bioRxiv2020

Eurycomanone regulates lipid metabolism by activating the cAMP/PKA pathway

Eurycoma longifolia Jack (ELJ) contains mainly alkaloids, and quassinoids, which are the main active ingredients. Eurycomanone (EN), one of the most common quassinoids, is said to have beneficial effects on lipid and glucose metabolism. In this study, we investigated the effects of EN on lipolysis by establishing a high-fat animal model in vivo and evaluated its efficacy as a lipolytic and anti-fatty liver agent. Oil red O staining showed morphological changes of 3T3-L1 preadipocytes after EN treatment and confirmed the inhibitory effects of EN on adipocyte differentiation. The mechanism of EN promotes lipolysis in 3T3-L1 cells was analyzed by immunofluorescence, Western blotting, quantitative real-time PCR and siRNA transfection. In C57BL/6J mice fed a high-fat diet, intragastric administration of EN (5 mg/kg and 10 mg/kg) for two weeks, decreased fat droplet mass and size, and reduced fat accumulation in the liver. Furthermore, EN activated PKA and promoted the PKA/hormone sensitive lipase lipolysis signaling pathway, thereby increasing the release of glycerol and free fatty acids from adipocytes. Our findings indicate the potential of EN as a promising alternative pharmacologic agent for the prevention of obesity.

pharmacology and toxicology↗