Biology subjects

Gao, Y.

Publications and source records attributed to Gao, Y..

At least 199 records · Page 11Linked to original sources

bioRxiv2025

Particular Amino Acid on Lateral Interface Maintains FtsZ Function Under Acid Stress in Streptococcus mutans

FtsZ is the core protein for cell division in bacteria that can polymerize into Z-rings and drive cytokinesis. Understanding how bacteria maintain the correct function of FtsZ under various environmental stresses is crucial for novel antibacterial drug discovery. Our previous study revealed that the FtsZ in S. mutans has higher self-assembly and GTPase activity under acidic stress, which may be responsible for the cariogenesis of S. mutans. However, the mechanism is still unknown. Here, we further reported the crystal structure of S. mutans FtsZ, revealing a unique lateral interface. Through protein polymerization and GTPase ability assay, we experimentally demonstrated that mutation of Arg68 on this lateral interface significantly reduced the functional activity of FtsZ in an acidic environment. The phenotype assay and rat caries model further showed that mutation of Arg68 effectively inhibited the acid resistance of S. mutans and the occurrence and progress of dental caries in vivo. By employing a molecular dynamics simulation analysis, we conclude that mutation of Arg68 disrupts the conformation change necessary for SmFtsZ polymerization under acidic conditions. Our study proposes a novel mechanism to maintain FtsZ function in bacteria and could be a potential target for antimicrobial drugs to inhibit the growth of S. mutans in an acidic environment. Significance StatementFtsZ is the core protein that drives cytokinesis. Maintaining the self-assembly and GTPase activity of FtsZ plays a critical role in cell growth under environmental stress. Currently, research on FtsZ function maintenance under stress mainly focuses on model organisms, with less on other pathogenic bacteria. This study reveals a novel structural mechanism for the acidic tolerance of FtsZ in S. mutans which survives in strongly acidic surroundings. Meanwhile, Arg68 on the lateral interface of SmFtsZ may be a potential therapeutic target to regulate microecology and combat S. mutans-associated dental caries.

microbiology↗

bioRxiv2025

Single-Cell Genomics Elucidates Molecular Variations and Regulatory Mechanisms in Circulating Immune Cells

The human peripheral blood displays diverse molecular characteristics across populations, understanding the drivers and underlying mechanisms of which remains challenging. Here, we introduce the Chinese Immune Multi-Omics Atlas (CIMA), elucidating sex-, age-, and genetic-related molecular variations by analyzing multi-omics data from 428 adults with over 10 million immune cells. CIMA generated an enhancer-driven gene regulatory network, identifying 237 high-quality regulons and revealing cell type-specific regulatory mechanisms. Additionally, 11,521 lead cis-expression quantitative trait loci (eQTLs) and 46,339 chromatin accessibility QTLs (caQTLs) were identified at cell type level. CIMA also uncovered pleiotropic associations among immune-related disease risk loci, eQTLs, and caQTLs in a cell type-specific manner. Lastly, a novel cell language model, CIMA-CLM, was developed to predict chromatin accessibility and noncoding variant effects using chromatin sequences and gene expressions. This work represents a population-scale multi-omics resource of human immune cells, providing a valuable reference for future investigation of immune-related diseases.

immunology↗

bioRxiv2025

Impact of infusion conditions and anesthesia on CSF tracer dynamics in mouse brain

Tracer imaging has been instrumental in mapping the brains solute transport pathways facilitated by cerebrospinal fluid (CSF) flow. However, the impact of tracer infusion parameters on CSF flow remains incompletely understood. This study evaluated the influence of infusion location, rate, and anesthetic regimens on tracer transport using dynamic contrast-enhanced MRI with Gd-DTPA as a CSF tracer. Infusion rate effects were assessed by administering Gd-DTPA into the cisterna magna (ICM) at two rates under isoflurane anesthesia. Anesthetic effects were evaluated by comparing transport patterns between isoflurane and ketamine/xylazine (K/X) anesthesia at the slower rate. Gd-DTPA transport was also examined after lateral ventricle (ICV) infusion, the primary site of CSF production. The results demonstrate that, besides anesthesia, both the location and rate of infusion substantially affected solute transport within the brain. ICV infusion led to rapid, extensive transport into deep brain regions, while slower ICM infusion resulted in more pronounced transport to dorsal brain regions. Cross-correlation and hierarchical clustering analyses of region-specific Gd-DTPA signal time courses revealed that ICM infusion facilitated transport along periarterial spaces, while ICV infusion favored transport across the ventricular-parenchymal interface. These findings underscore the importance of experimental conditions in influencing tracer kinetics and spatial distribution in the brain.

physiology↗

bioRxiv2025

Preclinical Evaluation of P4B-2412 as Phosphodiesterase 4B Radioligand for Positron Emission Tomography Imaging

Phosphodiesterase 4B (PDE4B) plays a critical role in cAMP hydrolysis and is highly expressed in brain regions associated with neuroinflammation and neurodegenerative disorders. Selective PDE4B radioligands hold significant potential for elucidating disease mechanisms and enabling target occupancy measurements. In this study, we developed [18F]P4B-2412, a novel PDE4B-selective radioligand, and evaluated its utility for PET imaging. [18F]P4B-2412 was synthesized with high radiochemical yield (27.2%), excellent radiochemical purity (99%), and favorable molar activity (66.2 {+/-} 2.5 GBq/mol). In vitro autoradiography revealed high PDE4B binding, while dynamic PET imaging demonstrated high in vivo specificity for PDE4B in rodent brain regions. Notably, [18F]P4B-2412 exhibited excellent metabolic stability in vitro and in vivo. These findings establish [18F]P4B-2412 as a promising PET probe for imaging PDE4B in vivo, offering a valuable tool for investigating neuroinflammation and advancing CNS drug development.

neuroscience↗

bioRxiv2025

Unlocking the Secrets of NSP3: AlphaFold2-assisted Domain Determination in SARS-CoV-2 Protein

Non-structural protein 3 (nsp3) is crucial for the SARS-CoV-2 infection cycle. It is the largest protein of the virus, consisting of roughly 2000 residues, and a major drug target. However, due to its size, disordered regions, and transmembrane domains, the atomic structure of the whole protein has not yet been established. Only 10 out of its 16 domains were individually determined in experiments. Here, we demonstrate how structural bioinformatics, AI-based fold prediction, and traditional experiments complement each other and can shed light on the makeup of this important protein, both in SARS-CoV-2 and related viruses. Our method can be generalized for other multi-domain proteins, so we describe it in detail. Our prediction-based approach reveals a previously undescribed folded domain, which we could confirm experimentally. Our research also suggests a potential function of the nidovirus-wide conserved domain Y1: This domain may be involved in the assembly of nsp3, nsp4, and nsp6 into the hexameric pore, which was discovered by electron tomography and exports RNA into the cytosol. The Y1-hexamer, however, could not be expressed and purified on its own. We also provide a revised domain segmentation and nomenclature of nsp3 domains based on a compilation of previous research and our own findings.

molecular biology↗

bioRxiv2025

Identification of a novel GREMLIN1 uptake pathway in epithelial cells that requires BMP binding

Gremlin1 is a member of a cysteine-knot containing family of secreted antagonists of bone morphogenetic protein signaling. GREM1 binding to BMP targets prevents their engagement with cognate BMP receptors, attenuating BMP-dependent gene expression. Some evidence suggests that GREM1 can directly bind to receptor tyrosine kinases on the plasma membrane, further complicating our understanding of GREM1 biology. To attempt to clarify the modalities of GREM1 signaling, we show that GREM1 protein is produced and secreted by intestinal fibroblasts and endocytosed by neighbouring epithelial cells. GREM1 uptake is a slow process and occurs by both clathrin- and caveolin-mediated endocytosis. Cell membrane heparin sulfate proteoglycans are required for GREM1 binding and uptake, and once internalised, GREM1 appears to localise to the early endosomes. Addition of BMP2 enhanced GREM1 uptake into cells. Remarkably, generation of a BMP-resistant GREM1 mutant abolished GREM1 uptake both in the presence and absence of BMP2. These data suggest that GREM1 binding and uptake into cells requires BMP binding, a process that may contribute to the antagonism of BMP signaling by GREM1. SummaryIn this article, we demonstrate differential GREM1 mRNA versus protein expression in mouse intestine. We also identify a novel GREM1 endocytosis pathway whereby mammalian cells take up GREM1 protein in what appears to be a BMP-dependent mechanism.

cell biology↗

bioRxiv2025

Maturase K forms a plastidial splicing complex with a neofunctionalized branching enzyme

Chloroplast group IIA introns derive from bacterial ribozymes. Their splicing likely requires Maturase K (MatK), which has been largely inaccessible to functional analyses being itself a chloroplast intron-encoded protein. Here we show that MatK physically interacts with a conserved, essential plastid-localized homolog of starch-branching enzymes (BEs), dubbed MATURASE K INTERACTING PROTEIN1 (MKIP1). We demonstrate that MKIP1 proteins have lost BE activity and acquired an insertion enabling direct interaction with the N-terminal region of MatK. Arabidopsis MKIP1 specifically co-precipitates all known intron targets of MatK. Induced MKIP1 silencing results in pale newly emerging leaves, in which the splicing of these intron targets is strongly reduced. Our data suggest that MKIP1 functionally diverged from canonical BEs to facilitate splicing in conjunction with MatK. We propose that the N-terminus of MatK, in turn, has evolved from an RNA-binding domain into a platform for protein interaction, helping its transition towards a general splicing factor.

plant biology↗

bioRxiv2025

Trans-generational maintenance of mitochondrial DNA integrity in oocytes during early folliculogenesis

Mutations in mitochondrial DNA (mtDNA) can lead to mitochondrial and cellular dysfunction. However, recent studies suggest that there is purifying selection against mutant mtDNAs during transgenerational transmission. We investigated the mtDNA dynamics during ovarian follicle development. Using base-editing, we generated mice harboring a 3177 G>A mutation corresponding to the human Leber hereditary optic neuropathy (LHON)-related mtDNA mutation and confirmed the transgenerational reduction of mutant mtDNA. Using a mouse follicle culture system in which pathogenic mtDNA mutations were introduced in vitro followed by mtDNA sequencing and digital PCR, we found this germline heteroplasmy shift during early folliculogenesis was induced by the decrease of mutant mtDNA together with compensatory replication of wild-type mtDNA. In contrast, synonymous mtDNA mutations did not impact the mtDNA dynamics. These findings show that mice can eliminate certain pathogenic mtDNA mutations in the germline during early folliculogenesis, maintaining mitochondrial integrity across generations.

genetics↗

bioRxiv2025

Biochemical Profiling and Structural Basis of ADAR1-Mediated RNA Editing

ADAR1 is a pivotal regulator in RNA-induced immune responses by catalyzing the conversion of adenosine to inosine on double-stranded RNA. Mutations on ADAR1 are associated with human autoimmune disease, and targeting ADAR1 has been proposed for cancer immunotherapy. However, the molecular mechanisms governing ADAR1-mediated RNA editing remain enigmatic. Here, we provide detailed biochemical and structural characterizations of human ADAR1. Our biochemical profiling reveals that ADAR1 editing is both sequence and RNA duplex length-dependent, but can well tolerate mismatches near the editing site. Moreover, our high-resolution structures of ADAR1-RNA complexes, coupled with mutagenesis studies, revealed the molecular basis for RNA binding, substrate selection, dimerization, and the crucial role of the RNA-binding domain 3 for ADAR1 editing. The ADAR1 structures also help explain the potential defects of disease-associated mutations, where biochemical and RNA-sequencing analysis further indicate some of the mutations preferentially impact the editing of RNAs with short duplex. Our findings illustrate the molecular mechanism of ADAR1 editing and provide clues for deciphering its role in immune regulation and drug targeting. HIGHLIGHTSO_LIBiochemical profiling of ADAR1 RNA substrate preference C_LIO_LIAtomic resolution structures of ADAR1 with two physiological RNA substrates C_LIO_LIDisease-related mutations of ADAR1 preferentially impact RNA editing with short dsRNA. C_LIO_LIRNA-binding domain 3 is essential for ADAR1 RNA capture and editing C_LI

biochemistry↗

bioRxiv2024

Exploring the effects of metformin on the body by urine proteome

Metformin is the first-line medication for treating type 2 diabetes mellitus (T2DM), with over 200 million patients taking it daily. Its effects are extensive and play a positive role in multiple areas. Can we explore its effects and potential mechanisms by urine proteome? In this study, a total of 166 differential proteins were identified after rats were given a dose of 150 mg/(kg{middle dot}d) of metformin for 5 consecutive days, including complement component C6, pyruvate kinase, coagulation factor X, growth differentiation factor 15 (GDF15), carboxypeptidase A4, chymotrypsin-like elastase family member 1, and L-lactate dehydrogenase C chain (LDH-C). Several of these proteins have been reported to be directly affected by metformin or associated with the effects of metformin. Several biological pathways enriched by the differential proteins or proteins where the differentially modified peptides are located have been reported to be associated with metformin, including glutathione metabolic process, negative regulation of gluconeogenesis, and renin-angiotensin system. Additionally, some significantly enriched biological pathways that have not been reported to be related to the effects of metformin may provide clues for the study of metformins potential mechanisms. In conclusion, the application of urine proteome offers a comprehensive and systematic approach to exploring both the known and unknown effects of drugs, thus opening a new window to study the mechanisms of metformin.

biochemistry↗

bioRxiv2024

A Linear Mixed Effects Model for Evaluating Synthetic Gene Circuits

A significant advancement in synthetic biology is the development of synthetic gene circuits with predictive Boolean logic. However, there is no universally accepted or applied statistical test to analyze the performance of these circuits. Many basic statistical tests fail to capture the predicted logic (OR, AND, etc.) and most studies neglect statistical analysis entirely. As synthetic gene circuits shift toward advanced applications, primarily in computing, biosensing, and human health, it is critical to standardize the statistical methods used to evaluate gate success. Here, we propose the application of a linear mixed effects model to analyze and quantify genetic Boolean logic gate performance. First, we analyzed 144 currently published Boolean logic gates for trends and used unsupervised machine learning (k-means clustering) to validate the statistical model. Next, we utilized the model to generate estimates for the fixed effect of the ON state, {beta}, as a general descriptor of the Boolean nature of a circuit and used Monte Carlo simulations to recommend sample sizes for evaluating gate performance. Finally, we examined {beta} as a holistic metric for circuit performance using a series of nested repressor OR gates with intentionally degraded performance. We observed a linear correlation between {beta} and the predicted translation rate, highlighting the use of {beta} for the forward design of new Boolean gates. In summary, we utilized a linear mixed effects model to describe synthetic gene circuits and determined that the fixed effect, {beta}, is an appropriate descriptor of gate behavior that can be used to statistically evaluate performance. Significance statementThere is no standard method for statistically evaluating the success of biological Boolean logic gates and common statistical tests are not used or incorrectly applied. We propose the use of a linear mixed effects model to estimate the value for {beta}, a parameter which describes the difference between ON and OFF gate states. A null hypothesis of {beta} = 0 can then be tested to determine if there is a statistically significant difference between the two states.

synthetic biology↗

bioRxiv2024

A novel method for in vivo assessment of soft tissue weight in bivalves

Aquaculture has been playing an increasingly important role in supplying proteins. To satisfy the rapidly growing demands for quality aquatic foods, the efficiency of aquaculture production needs to be improved. One strategy to achieve more efficient aquaculture production is to produce high-yielding seeds through breeding programs, for which in vivo assessment of target traits is indispensable to prevent candidate parents from being sacrificed for measurement and to track dynamically changing yield-related traits. Farmed mollusks, most of which are bivalves, rank the second among all aquatic animals in aquaculture production. Bivalves with heavier soft tissue, the major edible part, are preferable, target species for breeding and farming. A prerequisite for obtaining such species is to make accurate but nondestructive assessments of soft tissue weight, which cannot be accomplished using traditional dissection- or imaging-based methods. To resolve this issue, we take advantage of the complex relationships among shell dimension- and weight-related traits to construct classical, shell dimension- or wet weight-based models and novel, shell surface area-based models for in vivo assessment of soft tissue weight in Zhikong scallop (Chlamys farreri) and yesso scallop (Patinopecten yessoensis). Overall, soft tissue weight estimated by wet weight-involving models are highly correlated with observed values, indicating wet weight as a key proxy for soft tissue weight. While some models incorporating wet weight tend to systematically over- or under-estimate soft tissue weight despite the strong association between actual and estimated values, the novel, shell surface area-based model, MLR-log10Sshell-RR, generates accurate estimates free of systematic biases across populations of different ages for both species, suggesting it as a promising approach for in vivo assessment of soft tissue weight for scallops and other bivalves with bilaterally symmetrical shells.

genetics↗

bioRxiv2024

A Witches' Broom Phytoplasma effector induces stunting by stabilizing a bHLH transcription factor in plants

O_LIPhytoplasmas are specialized phloem-limited bacteria that cause diseases on various crops resulting in significant agricultural losses. This research focuses on the jujube Witches Broom (JWB) phytoplasma and investigates the host-manipulating activity of the effector SJP39. C_LIO_LIWe found that SJP39 directly interacts with the plant transcription factor bHLH87 in the nuclei. SJP39 stabilizes the bHLH87 homologs in A. thaliana and jujube, leading to growth defects in the plants. C_LIO_LITranscriptomic analysis indicates that SJP39 affects the gibberellin (GA) pathway in jujube. We further demonstrate that ZjbHLH87 regulates GA signalling as a negative regulator and SJP39 enhances this regulation. C_LIO_LIThe research offers important insights into the pathogenesis of JWB disease and identified SJP39 as a virulence factor that can contribute to the growth defects caused by JWB phytoplasma infection. These findings open new opportunities to manage JWB and other phytoplasma diseases. C_LI

plant biology↗

bioRxiv2024

PAX2 is Transcriptionally Silenced by a Distinct Mechanism of Epigenetic Reprogramming to Initiate Endometrial Carcinogenesis

In most cancers, including endometrial cancer, tumor suppressor genes harboring inactivating mutations have been systematically cataloged. However, locus-specific epigenetic alterations contributing to cancer initiation and progression remain only partly described, creating knowledge gaps about functionally significant tumor suppressors and underlying mechanisms associated with their inactivation. Here, we show that PAX2 is an endometrial tumor suppressor recurrently inactivated by a distinct epigenetic reprogramming event not associated with promoter hypermethylation. PAX2 is expressed throughout normal endometrial glands; however, microscopic clones with PAX2 protein loss arise spontaneously in adulthood and progress to endometrial precancers and cancers. Here we show that PAX2 protein loss occurs via transcriptional silencing in 80% of endometrial cancers. Mechanistically, transcriptomic, epigenomic, 3D genomic, and machine learning analyses showed that silencing is associated with replacement of open/active chromatin features (H3K27ac/H3K4me3) with inaccessible/repressive features (H3K27me3). The spread of the H3K27me3 signal is restrained by cohesin loops, preventing transcriptional dysregulation of neighboring genes. Functionally, PAX2 loss promoted endometrial carcinogenesis by rewiring the transcriptional landscape via global enhancer reprogramming. Genetically engineered mouse models together with organoid and human cell line studies established Pax2 as an in vivo endometrial tumor suppressor that cooperates with Pten to produce lethal cancers. Our discovery of a specific and recurring epigenetic alteration that transcriptionally silences PAX2 to initiate most endometrial cancers opens new lines of investigation into the origins of endometrial cancer with diverse implications for its diagnosis and treatment. One Sentence SummaryWe demonstrate that PAX2 is silenced by a highly recurrent epigenetic mechanism to initiate most endometrial cancers, establishing a novel mechanism of tumor suppressor inactivation.

cancer biology↗

bioRxiv2024

OmiGA: A Toolkit for Ultra-efficient Molecular Trait Analysis in Complex Populations

Molecular quantitative trait loci (molQTL) mapping is one of the most popular approaches to systematically characterize functional impacts of genomic variants, leading to advanced understanding of the regulatory mechanisms underpinning complex traits and diseases. However, when applied to high-throughput molecular phenotypes, the existing molQTL mapping tools often implement simple linear models, overlooking complex inter-individual relatedness, leading to false positives and insufficient statistical power. Here, we introduce the Omics Genetic Analysis toolkit (OmiGA), an ultra-efficient linear mixed model (LMM) based toolkit, for molQTL mapping in populations with complex relatedness. Both computational simulations and real data analyses demonstrated that OmiGA outperformed the existing popular tools regarding molQTL discovery power, fine mapping of causal variants, colocalization of molQTL and trait associations, and computational efficiency. In summary, we recommend OmiGA for molQTL mapping in populations with complex relatedness, for example, those in the Farm animal Genotype-Tissue Expression (FarmGTEx) project and family-based molQTL studies in humans.

bioinformatics↗

bioRxiv2024

Time-resolved fluorescent proteins towards fluorescence microscopy in the temporal and spectral domains

Fluorescence microscopy has been widely applied in life sciences. While steady-state fluorescence intensity is mostly used, the time-resolved detection mode relying on fluorescence lifetime remains underexplored. Herein, we present a family of time-resolved fluorescent proteins (TRFP). Using a strategy that regulates lifetime without affecting spectra of FPs, we have developed different TRFPs that cover the visible spectrum and a wide range of lifetime. TRFPs are employed in the temporal-spectral resolved microscopy, allowing the simultaneous imaging of 9 different proteins in live cells and correlation of multiple activities to cell cycles. Finally, TRFPs are integrated into multiplexing super-resolution microscopy to concurrently visualize 4 proteins in live cells, acquiring a remarkable 50 nm spatial resolution using lifetime as signal. TRFPs represent a transformative toolset towards fluorescence microscopy in both the temporal and spectral domains. Beyond the multiplexing imaging, TRFPs could introduce unprecedented opportunities of system complexity and quantitative accuracy into biological research.

biochemistry↗

bioRxiv2024

Causal disentanglement for single-cell representations and controllable counterfactual generation

Conducting disentanglement learning on single-cell omics data offers a promising alternative to traditional black-box representation learning by separating the semantic concepts embedded in a biological process. We present CausCell, which incorporates the causal relationships among disentangled concepts within a diffusion model to perform disentanglement learning, with the aim of increasing the explainability, generalizability and controllability of single-cell data, including spatial and temporal omics data, relative to those of the existing black-box representation learning models. Two quantitative evaluation scenarios, i.e., disentanglement and reconstruction, are presented to conduct the first comprehensive single-cell disentanglement learning benchmark, which demonstrates that CausCell outperforms the state-of-the-art methods in both scenarios. Additionally, CausCell can implement controllable generation by intervening with the concepts of single-cell data when given a causal structure. It also has the potential to uncover biological insights by generating counterfactuals from small and noisy single-cell datasets.

bioinformatics↗

bioRxiv2024

Intra-tumor microbiome-based tumor survival indices predict immune interaction and drug sensitivity on pan-cancer scale

Growing research evidence indicates a substantial influence of the intra-tumor microbiome on tumor outcome. However, there is currently no consistent criterion for identifying the association of microbes with tumor progression and response to treatment across various types of cancer. In this study, we concentrate on the intra-tumor microbiome and develop the Tumor Microbiome Survival Index (TMSI), a measure indicative of cancer patient survival risk. Our indices revealed notable distinctions between two stratified risk groups for each of the 10 cancer types and could precisely predict patients overall survival. For each type of cancer, our findings unveiled two distinct gene expression profiles and shed light on the varying patterns of immune and stromal cell enrichment between the two risk groups. Additionally, we noted that the high-TMSI group exhibited substantially elevated IC50 values for a number of drugs, indicating that individuals in the low-TMSI group might experience superior therapeutic effects from chemotherapy. These findings illuminate the complex dynamics between the tumor microbiome, the patients immune reaction, and medical outcomes, thus shedding light on microbiome-based personalized therapeutic interventions. HighlightsO_LIThe TMSI model generates a survival risk score based on the intra-tumor microbiome. C_LIO_LIThe TMSI model predicts survival rates accurately across multiple cancer types. C_LIO_LIMolecular-level analysis highlights distinct immune interactions with tumor microbes. C_LIO_LIHigh-TMSI groups showed altered drug sensitivity and implying potential differences in treatment response. C_LI

bioinformatics↗