Biology subjects

Wang, Y.-L.

Publications and source records attributed to Wang, Y.-L..

12 recordsLinked to original sources

bioRxiv2026

Microglial pruning of extinction-ensemble synapses preserves fear memory

Fear extinction suppresses learned fear without erasing the original memory, yet how competing fear and extinction ensembles are selectively updated remains unknown. Here, we show that microglia preserve fear memory by selectively editing extinction-ensemble synapses during retrieval. In medial prefrontal cortex, microglial processes, but not somata, expand, ramify, and tighten their engagement with extinction-ensemble dendrites and spines, where they preferentially engulf excitatory postsynaptic material and bias spine remodeling toward elimination. This selectivity is instructed by local find-me, eat-me, and dont-eat-me cues: purinergic signaling recruits microglial processes, phosphatidylserine exposure licenses engulfment of extinction-ensemble synapses, and CD47-SIRP protects fear ensembles from removal. Weakening microglial recruitment or engulfment, or removing this protection, accelerates extinction without impairing fear acquisition. These findings identify microglial processes as active gatekeepers of ensemble competition and reveal a neuroimmune mechanism that preserves fear memory by limiting extinction. In BriefDuring memory updating, microglial processes selectively engage extinction-ensemble synapses rather than globally pruning active circuits. Local recruitment, engulfment, and protection cues determine this choice, allowing microglia to preserve fear memory by limiting extinction. HighlightsO_LIExtinction retrieval selectively recruits microglial processes to extinction ensembles. C_LIO_LIMicroglia preferentially engulf excitatory postsynaptic material from extinction ensembles. C_LIO_LILocal "find-me," "eat-me," and "dont-eat-me" cues determine synapse selection. C_LIO_LIDisrupting microglial pruning facilitates extinction without impairing fear learning. C_LI

neuroscience↗

bioRxiv2026

Conservation Blind Spot: The Critical Role of Larval Stage in Assessing Extinction Risk

In an era of severe global biodiversity threats, understanding the link between species traits and their endangerment helps uncover causes of risk and infer threats to understudied species. Most animals have complex life cycles with distinct stages that may face stage-specific threats. Current conservation frameworks rely heavily on adult traits, potentially misjudging extinction risk. Using Chinese anurans as a model, we integrated functional traits from both adult and tadpole stages to examine their association with extinction risk. We found that body size positively correlates with risk in both stages. Microhabitat use related with extinction risk in tadpoles but shows no significant link in adults. Adult relative tympanum diameter and head length also correlate with extinction risk. These results indicate that species vulnerability is correlated with multi-stage traits, with both shared and stage-specific threats. Conservation based solely on adult traits may fail to accurately assess species threats. We call for integrating a whole-life-history perspective into biodiversity assessment and conservation to more effectively address the global biodiversity crisis.

ecology↗

bioRxiv2025

Dynamic Spiral Artery Remodeling in Early Human Pregnancy: An Analysis of Specimens Collected with a Standardized Protocol

Human uterine spiral artery remodeling (SAR) is a tightly regulated process involving complex interactions between interstitial and endovascular extravillous trophoblasts (iEVTs and enEVTs) and diverse maternal decidual cell populations. However, the intrinsic spatiotemporal dynamics of SAR in human placentation remain poorly understood, largely due to the limited availability of high-quality maternal-fetal interface specimens. Electively terminated early pregnancies offer a valuable resource for studying SAR in situ, yet inconsistent methods for distinguishing fragmented villous and decidual tissues have hindered reproducibility and interpretation. Herein we present a standardized protocol for the classification and characterization of high-quality maternal-fetal interface specimens from elective terminations by integrating stereomicroscopic evaluation with confirmation by immunohistochemistry and immunofluorescence microscopy. Combined with multiplex immunofluorescence imaging with cell-type- specific markers, this approach enabled precise spatial mapping and quantification of key morphological and cellular events in SAR from gestational weeks 5 to 10. Our analyses reveal that SAR initiates as early as week 5 with extraluminal recruitment of natural killer (NK) cells, followed by the formation of tightly packed EVT plugs within the lumens of spiral arteries in the decidua compacta; these plugs progressively extend deeper into the vessels and gradually loosen as gestation progresses. Notably, enEVTs appear to acquire NK cell-like phenotypes that may facilitate the displacement of endothelial and smooth muscle cells, promoting progressive vessel dilation. In summary, we provide a robust and reproducible method for assessing physiological SAR in early human pregnancy, supporting the adoption of our methodology in future studies of pathological SAR and related pregnancy disorders. Summary SentenceA standardized protocol for classifying maternal-fetal interface specimens from electively aborted materials at gestational weeks 5-10 was developed to quantify the spatiotemporal spiral artery remodeling dynamics in early human pregnancy. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=176 HEIGHT=200 SRC="FIGDIR/small/682615v2_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@ad6f1eorg.highwire.dtl.DTLVardef@5a3dcborg.highwire.dtl.DTLVardef@8f06b7org.highwire.dtl.DTLVardef@1f877_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

StCEL-based platform enables detection and sequencing of native sialoglycoRNA

Glycosylated RNAs (glycoRNAs) are an emerging class of biomolecules characterized by glycans attached to RNA molecules. Currently, glycoRNA detection remains largely confined to cellular models, substantially impeding its functional characterization and clinical translation. Here, we developed sialyltransferase-mediated chemical enzymatic labeling (StCEL), in which azido-modified sialic acid was transferred to the natural sialic acid on sialoglycoRNA, enabling the detection of native sialoglycoRNA across diverse biological samples with high specificity and sensitivity. Using StCEL, we found that sialoglycoRNA was significantly upregulated in multiple cancer types. StCEL combined with a microplate reader was applied to detect sialoglycoRNA in large-scale samples, revealing that elevated sialoglycoRNA levels correlate positively with tumor malignancy and poor patient prognosis. Furthermore, StCEL-based sialoglycoRNA enrichment and sequencing identified dysregulated sialoglycoRNAs in tumor tissues. Collectively, StCEL establishes a multifunctional platform that enables sensitive and specific detection of sialoglycoRNA, alongside sequencing analysis, demonstrating significant potential for clinical translation.

molecular biology↗

bioRxiv2025

Lethal effects of phyllosphere fungi associated with local plants on invasive plant Ageratina adenophora seedlings

Native community resistance to plant invasion may reflect microbial effects on invader establishment. Here, we compared the effects of the aboveground and belowground microbes and leaf functional traits of 25 native plant species on the germination and survival of invader Ageratina adenophora. Results show that leaf physical and chemical traits vary among plant species and shape the aboveground microbial community. Local plants more phylogenetically close to A. adenophora harbour more similar pathogen communities to those A. adenophora. The aboveground tissue inoculations had more adverse effects on A. adenophora establishment by delaying germination time and decreasing the germination rate and seedling survival than did soil inoculations; aboveground tissues from local plants, which are more closely related to A. adenophora, cause longer germination times and greater seedling mortality of A. adenophora. Moreover, local plant aboveground fungi, rather than bacteria, adversely impact seedling survival, and most of the detrimental fungal pathogen ASVs are specialists. Several strains isolated from dead seedlings caused by aboveground tissue inoculations belonging to Alternaria, Fusarium and Stagonosporopsis were verified to kill more than 60% of A. adenophora seedlings and thus have great potential as biocontrol agents for A. adenophora. This is the first study to provide evidence for the effects of phylogenetic relatedness and leaf traits (both functional and microbial) on local community resistance to invaders through the regulation of germination and seedling survival.

ecology↗

bioRxiv2024

Massively Parallel Polyribosome Profiling Reveals Translation Defects of Human Disease-Relevant UTR Mutations

The untranslated regions (UTRs) of mRNAs harbor regulatory elements influencing translation efficiency. Although 3.7% of disease-relevant human mutations occur in UTRs, their exact role in pathogenesis remains unclear. Through metagene analysis, we mapped pathogenic UTR mutations to regions near coding sequences, with a focus on the upstream open reading frame (uORF) initiation site. Subsequently, we utilized massively parallel poly(ribo)some profiling to compare the ribosome associations of 6,555 pairs of wildtype and mutant UTR fragments. We identified 46 UTR variants that altered polysome profiles, with enrichment in pathogenic mutations. Both univariate analysis and the elastic net regression model highlighted the significance of motifs of short repeated sequences, including SRSF2 binding sites, as mutation hotspots that lead to aberrant translation. Furthermore, these polysome-shifting mutations exhibited considerable impact on RNA secondary structures, particularly for upstream AUG-containing 5 UTRs. Integrating these features, our model achieved high accuracy (AUROC > 0.8) in predicting polysome-shifting mutations in the test dataset. Additionally, several lines of evidence indicate that changes in uORF usage underlie the translation deficiency arising from these mutations. Illustrating this, we demonstrate that a pathogenic mutation in the IRF6 5 UTR suppresses translation of the primary open reading frame by creating a uORF. Remarkably, site- directed ADAR editing of the mutant mRNA rescued this translation deficiency. Overall, our study provides insights into the molecular mechanisms of UTR mutations and their links to clinical impacts through translation defects. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/589132v2_ufig1.gif" ALT="Figure 1000"> View larger version (50K): org.highwire.dtl.DTLVardef@57217corg.highwire.dtl.DTLVardef@575410org.highwire.dtl.DTLVardef@15013bforg.highwire.dtl.DTLVardef@408840_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2024

Multiplexed Assays of Human Disease-relevant Mutations Reveal UTR Dinucleotide Composition as a Major Determinant of RNA Stability

UTRs contain crucial regulatory elements for RNA stability, translation and localization, so their integrity is indispensable for gene expression. Approximately 3.7% of genetic variants associated with diseases occur in UTRs, yet a comprehensive understanding of UTR variant functions remains limited due to inefficient experimental and computational assessment methods. To systematically evaluate the effects of UTR variants on RNA stability, we established a massively parallel reporter assay on 6,555 UTR variants reported in human disease databases. We examined the RNA degradation patterns mediated by the UTR library in two cell lines, and then applied LASSO regression to model the influential regulators of RNA stability. We found that UA dinucleotides and UA-rich motifs are the most prominent destabilizing element. Gain of UA dinucleotide outlined mutant UTRs with reduced stability. Studies on endogenous transcripts indicate that high UA-dinucleotide ratios in UTRs promote RNA degradation. Conversely, elevated GC content and protein binding on UA dinucleotides protect high-UA RNA from degradation. Further analysis reveals polarized roles of UA- dinucleotide-binding proteins in RNA protection and degradation. Furthermore, the UA- dinucleotide ratio of both UTRs is a common characteristic of genes in innate immune response pathways, implying a coordinated stability regulation through UTRs at the transcriptomic level. We also demonstrate that stability-altering UTRs are associated with changes in biobank-based health indices, underscoring the importance of precise UTR regulation for wellness. Our study highlights the importance of RNA stability regulation through UTR primary sequences, paving the way for further exploration of their implications in gene networks and precision medicine.

genetics↗

bioRxiv2024

Distinct effects of phyllosphere and rhizosphere microbes on invader Ageratina adenophora during its early life stages

Microbes strongly affect invasive plant growth. However, how the phyllosphere and rhizosphere soil microbes distinctively affect seedling mortality and the growth of invasive plants across ontogeny under varying soil nutrient levels remains unclear. In this study, we used the invader Ageratina adenophora to evaluate these effects in plant growth chambers. We found that leaf litter harboured more potential pathogens and thus had more adverse effects on seed germination and seedling survival than soil inoculation. Microbial inoculation at different growth stages altered the microbial community and microbial functions of seedlings, and earlier inoculation had a more adverse effect on seedling survival and growth. In most cases, the soil nutrient level did not affect microbe-mediated seedling growth and the relative abundance of the microbial community and functions involved in seedling growth. The effects of some microbial genera on seedling survival are distinct from those on growth. Moreover, the A. adenophora seedling-killing effects of fungal strains isolated from dead seedlings by nonsterile leaf inoculation litter exhibited significant phylogenetic signals, by which strains of Allophoma and Alternaria generally caused high seedling mortality. Our study stresses the essential role of A. adenophora litter microbes in population establishment by regulating seedling density and growth.

plant biology↗

bioRxiv2023

Understanding the biosynthesis of human IgMs through a combinatorial expression of mutant subunits that affect different assembly steps

Polymeric IgMs are secreted from plasma cells abundantly despite their structural complexity and intricate multimerization steps. To gain new insights into IgMs assembly mechanics that underwrite the high-level secretion, we characterized the biosynthetic process of a natural human IgM, SAM-6, using a recombinant HEK293 cell system. By creating a series of mutant subunits that differentially disrupt specific sets of inter-chain disulfide bonds, we assessed their effects on various aspects of IgM biosynthesis in 48 different mutant subunit combinations. The analysis included the visualization of intracellular biosynthetic events such as steady-state subcellular subunit distribution, secretory trafficking bottlenecks, and the ER-associated Russell body formation by fluorescent microscopy. We also characterized various extracellular events including secreted IgM product quality, secretion output, and the release of various assembly intermediates using biochemical and biophysical assays. In this combinatorial mutagenesis approach, we unexpectedly found that the loss of multiple inter-chain disulfide bonds, including the one between HC and {lambda}LC subunits, was tolerated in polymeric IgM formation and secretion. This finding revealed the vital role of underlying non-covalent protein-protein association not only during the orchestration of initial subunit interactions but also in maintaining the polymeric IgM product integrity during ER quality control steps, secretory pathway trafficking, and secretion. We suggest that the IgM assembly process is inherently robust and has a stopgap that permits the secretion of polymeric IgM even when not all the prescribed inter-chain disulfide bonds are formed. This study holistically presents the requirements and exemptions in polymeric IgM biosynthesis by encompassing the characterization of intracellular and extracellular events and the roles of covalent and non-covalent interactions. These findings can guide antibody engineering strategy when designing IgM-based multivalent modalities.

cell biology↗

bioRxiv2022

Antimicrobial Susceptibility Test by Surface-enhanced Raman Scattering of Bacterial Metabolites directly from Positive Blood Cultures

Effective management of sepsis requires timely administration of appropriate antibiotics; therefore, a reliable and rapid antimicrobial susceptibility test (AST) is crucial. To meet clinical needs, we developed a novel AST, referred to as SERS-AST, based on the surface-enhanced Raman Scattering (SERS) technology. In this study, we applied SERS-AST to eight most common pathogens causing bacteremia, including Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, E. faecium, Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae, and Acinetobacter baumannii. Seven different antibiotics were tested, including oxacillin, levofloxacin, vancomycin, ampicillin, cefotaxime, ceftazidime, levofloxacin, and imipenem. SERS-AST determines antibiotic susceptibility of bacteria directly from positive blood cultures based on variations in bacterial SERS signals derived from secreted purines and their derivatives. The whole process could be completed within 4 hours, and the agreement rates between SERS-AST and VITEK 2 results were 96% for Gram-positive bacteria and 97% for Gram-negative bacteria.

microbiology↗

bioRxiv2020

Longitudinal single-cell immune profiling revealed distinct innate immune response in asymptomatic COVID-19 patients

Recent studies have characterized the single-cell immune landscape of host immune response of coronavirus disease 2019 (COVID-19), specifically focus on the severe condition. However, the immune response in mild or even asymptomatic patients remains unclear. Here, we performed longitudinal single-cell transcriptome sequencing and T cell/B cell receptor sequencing on 3 healthy donors and 10 COVID-19 patients with asymptomatic, moderate, and severe conditions. We found asymptomatic patients displayed distinct innate immune responses, including increased CD56briCD16- NK subset, which was nearly missing in severe condition and enrichment of a new Th2-like cell type/state expressing a ciliated cell marker. Unlike that in moderate condition, asymptomatic patients lacked clonal expansion of effector CD8+ T cells but had a robust effector CD4+ T cell clonal expansion, coincide with previously detected SARS-CoV-2-reactive CD4+ T cells in unexposed individuals. Moreover, NK and effector T cells in asymptomatic patients have upregulated cytokine related genes, such as IFNG and XCL2. Our data suggest early innate immune response and type I immunity may contribute to the asymptomatic phenotype in COVID-19 disease, which could in turn deepen our understanding of severe COVID-19 and guide early prediction and therapeutics.

immunology↗

bioRxiv2020

Traction Force Microscopy by Deep Learning

Cells interact mechanically with their surrounding by exerting forces and sensing forces or force-induced displacements. Traction force microscopy (TFM), purported to map cell-generated forces or stresses, represents an important tool that has powered the rapid advances in mechanobiology. However, to solve the ill-posted mathematical problem, its implementation has involved regularization and the associated compromises in accuracy and resolution. Here we applied neural network-based deep learning as a novel approach for TFM. We modified a network for processing images to process vector fields of stress and strain. Furthermore, we adapted a mathematical model for cell migration to generate large sets of simulated stresses and strains for training the network. We found that deep learning-based TFM yielded results qualitatively similar to those from conventional methods but at a higher accuracy and resolution. The speed and performance of deep learning TFM make it an appealing alternative to conventional methods for characterizing mechanical interactions between cells and the environment. Statement of SignificanceTraction Force Microscopy has served as a fundamental driving force for mechanobiology. However, its nature as an ill-posed inverse problem has posed serious challenges for conventional mathematical approaches. The present study, facilitated by large sets of simulated stresses and strains, describes a novel approach using deep learning for the calculation of traction stress distribution. By adapting the UNet neural network for handling vector fields, we show that deep learning is able to minimize much of the limitations of conventional approaches to generate results with speed, accuracy, and resolution.

biophysics↗