Biology subjects

Yue, L.

Publications and source records attributed to Yue, L..

At least 19 recordsLinked to original sources

bioRxiv2026

The Arabidopsis outward K+ channel GORK mediates flg22-induced K+ efflux and stomatal closure

Transient K+ efflux occurs rapidly following pathogen-associated molecular pattern (PAMP) perception by pattern recognition receptors (PRRs) as part of pattern-triggered immunity (PTI). However, the molecular identities of the K+ channels responsible for PTI-associated K+ efflux and the mechanisms linking immune signaling to K+ channel regulation remain largely unknown. Here, we show that the channel GUARD CELL OUTWARD RECTIFYING K+ (GORK) is required for K+ efflux and stomatal closure induced by flg22, a model PAMP derived from bacterial flagellin. BOTRYTIS-INDUCED KINASE 1 (BIK1), a receptor-like cytoplasmic kinase associated with immune receptor complexes that functions as a central regulator of PTI, interacts with GORK and phosphorylates the channel on the conserved T199 residue in vitro. Electrophysiological analyses indicate that BIK1 inhibits GORK activity in a kinase-dependent manner and that T199 plays an essential role for GORK function. Together, this study identifies GORK as the key K+ channel executing rapid PTI-associated K+ efflux and associated stomatal closure, thus shedding light on the mechanisms of early immune signaling.

plant biology↗

bioRxiv2026

Effects of Glutamate Delta 1 Receptor (GluD1) Deletion on the Ultrastructural Features of Corticostriatal and Thalamostriatal Synapses in Mice

The glutamate delta 1 receptor (GluD1) represents a unique subtype of ionotropic glutamate receptors that is strongly expressed in the mammalian striatum. Disruptions of the GRID1 gene, which encodes GluD1, have been associated with neuropsychiatric disorders, including schizophrenia and autism spectrum disorder; however, the role of GluD1 in the brain remains poorly understood. Previous studies in mice have demonstrated that the knockout of striatal GluD1 led to fear-conditioning deficits and depressive-like behaviors. Furthermore, these mice exhibited reduced excitatory input to the striatum due to a loss of thalamostriatal innervation, whereas corticostriatal innervation was unaffected. In this study, we examined whether changes in synapse morphology contribute to the observed functional deficits. We found that the ablation of GluD1 does not affect synaptic targeting patterns of corticostriatal and thalamostriatal terminals, using transmission electron microscopy. We further utilized three-dimensional reconstruction to obtain quantitative data on synapse ultrastructure and found no significant changes in corticostriatal and thalamostriatal synaptic components, including the presynaptic terminal volume, postsynaptic density area and morphology, and postsynaptic dendritic spine volume. These findings support a model in which GluD1 regulates input-specific circuit organization and synaptic connectivity rather than the structural morphology of individual synapses.

neuroscience↗

bioRxiv2026

MorphOTU: A universal image-based framework for delineating biodiversity discovery

Biodiversity can be quantified only after organisms are assigned to reproducible units, yet most individuals encountered in nature lack reliable species-level identifications. Molecular operational taxonomic units can organize unnamed diversity, whereas image-based approaches generally depend on predefined species levels. Here, we show that operational biodiversity units can be derived directly from phenotypes. We developed morphOTU, a framework combining self-supervised representation learning, operational metric supervision, and adaptive hierarchical clustering to organize specimen images in continuous phenotypic space. Across five benchmark datasets comprising flowers, wood anatomy, and beetle habitus, morphOTUs recovered coherent species-level structure and produced -diversity estimates close to those obtained from expert identifications. This structure remained informative when species were excluded from representation learning, when labeled data were sparse, and per-species sampling was limited. In a heterogeneous field-survey dataset of 4,717 insects representing 269 species across 12 orders, fine-tuning on only 28 common species produced diversity estimates close to expert labels (Shannon index, 3.75 versus 3.53). Visual explanations localized variation to biologically meaningful structures, including body outliers, surface sculpture, floral symmetry, and wood vessels. Morphological units therefore provide an operational layer for organizing and quantifying biodiversity before, alongside, or in the absence of formal species names.

bioinformatics↗

bioRxiv2026

MTB-KB: A Curated Knowledgebase of Mycobacterium tuberculosis Related Studies

Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), has regained its position as the worlds leading killer among infectious diseases. Despite extensive research progress across epidemiology, diagnosis, drug development, treatment regimens, vaccines, drug resistance, virulence factors, and immune mechanisms, MTB-related knowledge remains fragmented across thousands of publications, limiting its effective use. To address this gap, we present MTB-KB, a literature-curated knowledgebase that systematically integrates high-impact findings from eight major sections of TB research. The current release contains 75,170 associations from 1,246 publications, covering 18,439 entities standardized using authoritative databases and WHO-endorsed classifications. A central feature is the interactive knowledge graph, which links cross-section associations to reveal and infer MTB-host interactions, treatment strategies, and vaccine development opportunities. MTB-KB also provides a user-friendly interface with browsing, advanced search, and statistical visualization. Overall, by consolidating dispersed MTB knowledge into a structured and accessible platform, MTB-KB provides a valuable resource for researchers, clinicians, and policymakers, supporting both basic and clinical TB research, enabling evidence-based TB prevention, diagnosis, and treatment, and contributing to global elimination efforts. MTB-KB is accessible at https://ngdc.cncb.ac.cn/mtbkb/.

bioinformatics↗

bioRxiv2025

Tracking the Evolutionary Patterns of RNA Modifications from Bryophyte to Flowering Plants by Mass Spectrometry

RNA modifications are critical for the regulation of gene expression. Comprehensive profiling of RNA modifications is a prerequisite for unravelling their identities and functions. The plant hormone auxin plays pivotal roles in regulating plant growth, development, and environmental responses. In contrast to the extensive studies in animals, there is a paucity of knowledge regarding the existence and functions of RNA modifications in plants. This is due to the low abundance of modified ribonucleosides and the lack of accurate analytical methods. This study employs a state-of-the-art hydrophilic interaction liquid chromatography-tandem-mass spectrometry (HILIC-MS/MS) platform to achieve the sensitive detection of 12 nucleosides at the pM to nM level. Utilizing this platform, we were able to identify N4,2-O-dimethylcytidine (m4Cm) in plants by LC-MS/MS for the first time, which provided direct evidence for the widespread of this modification in plants. Moreover, a comprehensive investigation was undertaken to examine the 12 types of RNA modifications and their response patterns to auxin in a range of prototype plants, spanning from bryophyte (Marchantia polymorpha) to flowering plants (Arabidopsis thaliana, Oryza sativa, and Zea mays). The evolutionary patterns of the 12 RNA modifications were depicted from bryophyte to flowering plants, and their potential functions in plant growth, development, and auxin responses were revealed.

biochemistry↗

bioRxiv2025

Spatial distribution of the proteome in human body and cancers

A comprehensive spatial distribution of the proteome in human body and cancers is fundamental for understanding human biology and diseases including cancers. Here, we present an anatomically resolved human proteome derived from 1781 benign and malignant samples from 58 major tissue types encompassing 251 specific tissues and 25 carcinomas. Based on a spectral library covering over 75% of the human protein-coding genes with 208 understudied and 82 missing proteins characterized, we quantified over 13,000 proteins in these samples using data-independent acquisition proteomics. This data resource presents the so far most comprehensive quantitative proteomic landscape of human tissues and common carcinomas. It allows systematic evaluation of tissue-specific drug responses, identification of drug candidates that may be repurposed as antineoplastics, and discovery of novel targets for anticancer therapy. This resource, available as an online knowledgebase, refines our knowledge of spatial distribution of the human proteome and tumor-specific protein modulation.

systems biology↗

bioRxiv2025

Leopard Cats Occupied Human Settlements in China for 3,500 years before the Arrival of Domestic cats in 600-900 CE around the Tang Dynasty

The earliest cats in human settlements in China were not domestic cats (Felis catus), but native leopard cats (Prionailurus bengalensis). To trace when and how domestic cats arrived in East Asia, we analyzed 22 feline bones from 14 sites across China spanning 5,000 years. Nuclear and mitochondrial genomes revealed that leopard cats began occupying anthropogenic scenes around 5,400 years ago and last appeared in 150 CE. Following several centuries gap of archeological feline remains, the first known domestic cat (706-883 CE) in China was identified in Shaanxi during the Tang Dynasty. Genomic analysis suggested a white or partially white coat and a link to a contemporaneous domestic cat from Kazakhstan, indicating a likely dispersal route via the Silk Road. The two felids once independently occupied ancient anthropogenic environments in China but followed divergent paths and reached different destinations in human-animal interactions.

evolutionary biology↗

bioRxiv2025

C. elegans interprets dietary quality through context-dependent serotonergic modulation

Animals sense their metabolic needs to guide foraging decisions using neuronal pathways that are only partly understood. Here, we systematically investigate how foraging in the nematode Caenorhabditis elegans is influenced by its bacterial diet, E. coli. By screening C. elegans behavior on 3983 E. coli knockout strains, we identified 22 E. coli metabolic mutants that are aversive to C. elegans in a long-term foraging assay. These include the global metabolic regulator CRP and genes affecting cysteine synthesis, vitamin B6 synthesis, and iron uptake. Serotonin, a neurotransmitter associated with feeding in many animals, allows C. elegans to distinguish wild-type E. coli from these "mediocre" diets through bidirectional signaling. Serotonin produced by the ADF serotonergic neurons supports attraction to wild-type E. coli with the serotonin receptor genes ser-4 and ser-5, whereas serotonin produced by the NSM serotonergic neurons differentially drives aversion to two mediocre diets through four serotonin receptor genes, ser-1, ser-7, mod-1, and lgc-50. Serotonin receptors act in multiple target neurons, including octopamine-producing neurons that suppress aversion across all diets. In addition, dopamine promotes aversion, in part by inhibiting octopaminergic neurons. These results reveal interactions between neuromodulatory circuits in the context-dependent evaluation of dietary quality.

neuroscience↗

bioRxiv2024

Cytoplasmic calcium influx mediated by Lr14a regulates stomatal immunity against leaf rust in wheat

The race-specific resistance gene Lr14a in wheat confers a unique type of heterogenous resistance reaction. It encodes an ankyrin-repeat transmembrane domain protein that confers immunity against the fungal pathogen Puccinia triticina. Here, we show that Lr14a functions as a calcium-permeable channel, mediating cytoplasmic Ca{superscript 2} influx that is crucial for leaf rust resistance in wheat. Infection with avirulent isolates induced Lr14a expression predominantly in mesophyll cells while triggering cell death in guard cells in wheat. This study revealed a mechanism by which the product of an R gene regulates stomatal immunity non-cell autonomously through the mediation of calcium signaling.

plant biology↗

bioRxiv2024

Cost-effective DNA storage with DNA movable type

In the face of exponential data growth, DNA-based storage offers a promising solution for preserving big-data. However, most existing DNA storage methods, akin to traditional block printing, require costly chemical synthesis for each individual data file, adopting a sequential, one-time-use synthesis approach. To overcome these limitations, we introduce a novel, cost-effective "DNA-Movable-Type Storage" system, inspired by movable type printing. This system utilizes pre-fabricated DNA movable types-short, double-stranded DNA oligonucleotides encoding specific payload, address, and checksum data. These DNA-MTs are enzymatically ligated/assembled into cohesive sequences, termed "DNA movable type blocks", streamlining the assembly process with the automated BISHENG-1 DNA-MT inkjet printer. Using BISHENG-1, we successfully printed, assembled, stored and accurately retrieved 43.7 KB of data files in diverse formats (text, image, audio, and video) in vitro and in vivo, using only 350 DNA-MTs. Notably, each DNA-MT, synthesized once (2 OD), can be used up to 10,000 times, reducing costs to 122 $/MB-outperforming existing DNA storage methods. This innovation circumvents the need to synthesize entire DNA sequences encoding files from scratch, offering significant cost and efficiency advantages. Furthermore, it has considerable untapped potential to advance a robust DNA storage system, better meeting the extensive data storage demands of the big-data era.

bioinformatics↗

bioRxiv2024

Hematopoietic stem cell division is governed by distinct RUNX1 binding partners.

A defined number of hematopoietic stem cell (HSC) clones are born during development and expand to form the pool of adult stem cells. An intricate balance between self-renewal and differentiation of these HSCs supports hematopoiesis for life. HSC fate is determined by complex transcription factor networks that drive cell-type specific gene programs. The transcription factor RUNX1 is required for definitive hematopoiesis, and mutations in Runx1 have been shown to reduce clonal diversity. The RUNX1 cofactor, CBFy, stabilizes RUNX1 binding to DNA, and disruption of their interaction alters downstream gene expression. Chemical screening for modulators of Runx1 and HSC expansion in zebrafish led us to identify a new mechanism for the RUNX1 inhibitor, Ro5-3335. We found that Ro5-3335 increased HSC divisions in zebrafish, and animals transplanted with Ro5-3335 treated cells had enhanced chimerism compared to untreated cells. Using human CD34+ cells, we show that Ro5-3335 remodels the RUNX1 transcription complex by binding to ELF1, independent of CBFy. This allows specific expression of cell cycle and hematopoietic genes that enhance HSC self-renewal and prevent differentiation. Furthermore, we provide the first evidence to show that it is possible to pharmacologically increase the number of stem cell clones in vivo, revealing a previously unknown mechanism for enhancing clonal diversity. Our studies have revealed a mechanism by which binding partners of RUNX1 determine cell fate, with ELF transcription factors guiding cell division. This information could lead to treatments that enhance clonal diversity for blood diseases.

cell biology↗

bioRxiv2024

CD13 Activation Assembles Signaling Complexes that Promote the Formation of Tunneling Nanotubes in Endothelial Cells

Transmembrane CD13 assembles protein complexes at the plasma membrane to enable diverse cellular processes such as cell-cell adhesion, focal adhesion turnover, endocytosis and recycling of cell surface proteins. In this study, we demonstrate a novel CD13-dependent assembly platform that regulates phosphoinositide (PI) signal transduction during the formation of Tunneling Nanotubes (TNTs). TNTs are actin-based, membrane-delimited bridges that facilitate intercellular communication by connecting distant cells to physically transfer subcellular cargoes. TNTs form between various cell types under stress conditions, but few molecular TNT-inducers exist. Human Kaposis sarcoma-derived endothelial cells (KSECs) readily form stress-induced TNTs capable of transferring Ca2+ and membrane molecules between cells, with clear accumulation of CD13 and actin at the base of the protrusions. Alternatively, CD13-null KSECs form fewer TNTs and Ca2+ transfer is markedly reduced. Mechanistically, CD13-mediated TNT formation requires activation of CD13, Src, FAK and Cdc42 to allow tethering of the IQGAP1 and ARF6 complex at the membrane to activate the phosphatidylinositol-4-phosphate-5-kinase PI5K. This increases local phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) levels to promote the actin-polymerization and membrane protrusion necessary for TNT formation. Therefore, CD13 is a novel molecular PIP regulator and TNT trigger that will facilitate the dissection of downstream pathways and mechanisms regulating TNT formation.

cell biology↗

bioRxiv2023

metaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis

BackgroundAnalysis of mass spectrometry-based metaproteomic data, in particular large-scale data-independent acquisition MS (DIA-MS) data, remains a computational challenge. Here, we aim to develop a software tool for efficiently constructing spectral libraries and analyzing extensive datasets of DIA-based metaproteomics. ResultsWe present a computational pipeline called metaExpertPro for metaproteomics data analysis. This pipeline encompasses spectral library generation using data-dependent acquisition MS (DDA-MS), protein identification and quantification using DIA-MS, functional and taxonomic annotation, as well as quantitative matrix generation for both microbiota and hosts. To enhance accessibility and ease of use, all modules and dependencies are encapsulated within a Docker container. By integrating FragPipe and DIA-NN, metaExpertPro offers compatibility with both Orbitrap-based and PASEF-based DDA and DIA data. To evaluate the depth and accuracy of identification and quantification, we conducted extensive assessments using human fecal samples and benchmark tests. Performance tests conducted on human fecal samples demonstrated that metaExpertPro quantified an average of 45,000 peptides in a 60-minute diaPASEF injection. Notably, metaExpertPro outperformed three existing software tools by characterizing a higher number of peptides and proteins. Importantly, metaExpertPro maintained a low factual False Discovery Rate (FDR) of less than 5% for protein groups across four benchmark tests. Applying a filter of five peptides per genus, metaExpertPro achieved relatively high accuracy (F-score = 0.67-0.90) in genus diversity and demonstrated a high correlation (rSpearman = 0.73-0.82) between the measured and true genus relative abundance in benchmark tests. Additionally, the quantitative results at the protein, taxonomy, and function levels exhibited high reproducibility and consistency across the commonly adopted public human gut microbial protein databases IGC and UHGP. In a metaproteomic analysis of dyslipidemia patients, metaExpertPro revealed characteristic alterations in microbial functions and potential interactions between the microbiota and the host. ConclusionsmetaExpertPro presents a robust one-stop computational solution for constructing metaproteomics spectral libraries, analyzing DIA-MS data, and annotating taxonomic as well as functional data.

microbiology↗

bioRxiv2023

PPARγ controls ESCRT-dependent fibroblast-like synoviocyte exosome biogenesis and Alleviates Chondrocyte Osteoarthritis Mediated by Exosomal ANXA1

Osteoarthritis (OA) is characterized by synovitis, cartilage degeneration and exercise therapy has been recognized as first line therapy. The exercise related exosome involved in the interaction between fibroblast-like synoviocytes (FLSs) and chondrocytes could be a novel promising strategy for treating OA. In this study, PPAR{gamma} was upregulated in FLSs under exercise by single cell transcriptome sequencing. Then, we investigated the underlying mechanisms of PPAR{gamma}-treated FLSs derived exosome on OA in vivo and vitro. Our data revealed that overexpression PPAR{gamma} FLSs derived exosome could ameliorate the OA severity in vivo and vitro. But knockdown PPAR{gamma} FLSs derived exosome aggravate OA. Moreover, we found PPAR{gamma} controls the endosomal sorting complex required for the transport (ESCRT)-dependent exosome biogenesis pathway. Annexin A1 (ANXA1) was enriched in OE-PPAR{gamma} exosome by quantitative proteomics. By Chip-qPCR and Co-IP methods, PPAR{gamma} and its coactivator -1 (PGC-1) acts with ESCRT subunits including HRS, STAM1, TSG101, CHMP7 and promotes their association to cargo ANXA1. As a therapeutic cargo, exosomal ANXA1 was confirmed be internalization by chondrocyte via exosome labeled experiment and ANXA1 could inhibit the phospharylation of ERK to activate the autophagy and decrease chondrocyte apoptosis. While the ANXA1 receptor blocker BOC-2 could reverse the therapic effect. In conclusion, PPAR{gamma}/ESCRT - FLSs exosomal ANXA1 - ERK axis provides a deeper theoretical basis for exercise therapy of OA and a new idea for the clinical transformation of exosomes into OA therapy.

cell biology↗

bioRxiv2023

Single-cell transcriptome analysis reveals the cellular atlas of human intracranial aneurysm and highlights inflammation features associated with aneurysm rupture

Intracranial aneurysm (IA) is pouch-like pathological dilations of cerebral arteries, which often affects middle-aged people and culminates in life-threatening hemorrhagic stroke. A deeper knowledge of the cellular and gene expression perturbations in human IA tissue deepens our understanding of disease mechanisms and facilitates developing pharmacological targets for unruptured IA. In this study, 21,332 qualified cells were obtained from cell-sparse ruptured and unruptured human IA tissues and a detailed cellular profile was determined, including conventional endothelial cells, smooth muscle cells (SMC), fibroblasts and the newly identified pericytes. Notably, striking proportion of immune cells were identified in IA tissue, with the number of monocyte/macrophages and neutrophils being remarkably higher in ruptured IA. By leveraging external datasets and machine learning algorithms, a subset of macrophages characterized by high expression of CCL3 and CXCL3, and transcriptional activation of NF-{kappa}B and HIVEP2 was identified as the cell most associated with IA rupture. Further, the interactome of CCL3/CXCL3 macrophages disclosed their role in regulating vascular cell survival and orchestrating inflammation. In summary, this study illustrated the profile and interactions of vascular and immune cells in human IA tissue and the opportunities for targeting local chronic inflammation.

cell biology↗

bioRxiv2023

Structural insights into regulation of TRPM7 divalent cation uptake by the small GTPase ARL15

Cystathionine-{beta}-synthase (CBS)-pair domain divalent metal cation transport mediators (CNNMs) are an evolutionarily conserved family of magnesium transporters. They promote efflux of Mg2+ ions on their own or uptake of divalent cations when coupled to the transient receptor potential ion channel subfamily M member 7 (TRPM7). Recently, ADP-ribosylation factor-like GTPase 15 (ARL15) has been identified as CNNM binding partner and an inhibitor of divalent cation influx by TRPM7. Here, we characterize ARL15 as a GTP-binding protein and demonstrate that it binds the CNNM CBS-pair domain with low micromolar affinity. The crystal structure of the complex between ARL15 GTPase domain and CNNM2 CBS-pair domain reveals the molecular determinants of the interaction and allowed the identification of mutations in ARL15 and CNNM2 mutations that abrogate binding. Loss of CNNM binding prevented ARL15 suppression of TRPM7 channel activity in support of previous reports that the proteins function as a ternary complex. Binding experiments with phosphatase of regenerating liver 2 (PRL2 or PTP4A2) revealed that ARL15 and PRLs compete for binding CNNM, suggesting antagonistic regulation of divalent cation transport by the two proteins.

biochemistry↗

bioRxiv2023

DPHL v2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.

A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS)-based proteomics. DPHL v1, a previous pan-human library built from 1096 data-dependent acquisition (DDA) MS data of 16 human tissue types, allows quantifying 10,943 proteins. However, a major limitation of DPHL v1 is the lack of semi-tryptic peptides and protein isoforms, which are abundant in clinical specimens. Here, we generated DPHL v2 from 1608 DDA-MS data acquired using Orbitrap mass spectrometers. The data included 586 DDA-MS newly acquired from 17 tissue types, while 1022 files were derived from DPHL v1. DPHL v2 thus comprises data from 24 sample types, including several cancer types (lung, breast, kidney, and prostate cancer, among others). We generated four variants of DPHL v2 to include semi-tryptic peptides and protein isoforms. DPHL v2 was then applied to a publicly available colorectal cancer dataset with 286 DIA-MS files. The numbers of identified and significantly dysregulated proteins increased by at least 21.7% and 14.2%, respectively, compared with DPHL v1. Our findings show that the increased human proteome coverage of DPHL v2 provides larger pools of potential protein biomarkers.

bioinformatics↗

bioRxiv2022

Integrative genetic analysis identifies FLVCR1 as an essential component of choline transport in mammals

Genome-wide association studies (GWAS) of serum metabolites have the potential to uncover genes that influence human metabolism. Here, we combined an integrative genetic analysis associating serum metabolites to membrane transporters with a coessentiality map of metabolic genes. This analysis revealed a connection between feline leukemia virus subgroup C cellular receptor 1 (FLVCR1) - a plasma membrane protein - and phosphocholine, a downstream metabolite of choline metabolism. Loss of FLVCR1 in human cells and in mice strongly impairs choline metabolism due to a block in choline import. Consistently, CRISPR-based genetic screens identified several components of the membrane phospholipid machinery as synthetic lethal with FLVCR1 loss. Finally, cells lacking FLVCR1 exhibit mitochondrial defects and upregulate the integrated stress response (ISR) through heme regulated inhibitors kinase (HRI). Altogether, these findings identify FLVCR1 as a universal mediator of choline transport in mammals and provide a platform to discover substrates for unknown metabolite transporters.

cell biology↗