Biomedical subjects

Jing Gao

Publications and source records attributed to Jing Gao.

9 recordsLinked to original sources

PubMed2026

Decoding gene regulation in plant genomes with artificial intelligence.

One of the central goals of plant functional genomics is to uncover regulatory mechanisms that shape agriculturally important traits to inform crop improvement. Recent advances in machine learning (ML) and artificial intelligence (AI), especially Large Language Models (LLMs), have greatly transformed our ability to derive regulatory information from complex genomics data. This review starts with a brief introduction of recent advances in AI and ML. We then present a plant-focused synthesis of emerging applications of AI- and LLM tools to: (i) predict epigenomic features, regulatory DNA elements, and gene expressions; (ii) infer gene regulatory network; and (iii) estimate post-transcriptional regulation.

Artificial intelligence↗

PubMed2026

Genome-Wide Identification of SSR and InDel Markers and Experimental Validation of SSR Markers for Distinguishing Cold-Tolerant and Cold-Sensitive Lily Cultivars.

In this study, whole-genome resequencing was performed on the cold-tolerant variety ND-6 and the cold-sensitive variety 'Sorbonne'. After evaluation, the Lilium davidii var. unicolor reference genome was selected to analyze SSR distribution characteristics. Whole-genome InDel identification and comparative analysis were conducted for the two varieties, yielding 34,812,909 and 24,497,857 InDels, respectively. Short InDels were predominant, with deletions slightly outnumbering insertions, mostly located in intergenic regions. Twenty pairs of SSR primers were screened and synthesized. Among them, 10 pairs amplified clearly, with a polymorphism rate of 82.6%, effectively distinguishing the two cultivars examined in this study. This study provides systematic data and a reliable marker resource for the analysis of lily genomic variation, laying a foundation for the identification of cold-tolerant germplasm; validation across additional cultivars and individuals will be required to extend their utility to broader germplasm.

cold resistant lilies↗

PubMed2026

Gut microbiota-derived metabolites target C5AR1/KDM2A/HCAR3 axis in inflammatory bowel disease: a multi-machine learning algorithms and molecular docking study.

BACKGROUND: Inflammatory bowel disease (IBD) is a chronic recurrent disorder. Gut microbiota-derived metabolites regulate intestinal homeostasis, but their molecular mechanisms in IBD remain unclear. Current studies lack systematic "microbiota-metabolite-target" network mining with multi-method validation. This study integrates network pharmacology, three machine learning algorithms, and molecular docking to construct this regulatory network in IBD. METHODS: Transcriptome data were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified using limma (p < 0.05, |log2FC| > 0.5). Weighted gene co-expression network analysis (WGCNA) with an optimal soft threshold of β = 7 was performed to identify key module genes. Candidate genes were obtained by intersecting DEGs, gut microbiota-associated genes from the gutMGene database, and WGCNA module genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to explore the functional roles of candidate genes. Core genes were identified using three machine learning algorithms (LASSO, Boruta, and SVM-RFE), followed by protein-protein interaction (PPI) network analysis. Molecular docking was performed to assess the binding affinities between hub proteins and gut microbiota-derived metabolites. RESULTS: A total of 885 DEGs were identified between the IBD and control groups, including 463 upregulated and 422 downregulated genes. WGCNA identified 280 key module genes from the purple and yellow modules. The intersection of DEGs, gut microbiota-associated genes, and WGCNA module genes yielded 19 core candidate genes. PPI network analysis combined with three machine learning algorithms jointly identified C5AR1, KDM2A, and HCAR3 as core hub genes. ROC curve analysis demonstrated that all three hub genes achieved AUC values greater than 0.7 in both the training and validation sets, indicating excellent diagnostic performance for IBD. Enrichment analysis revealed significant associations with the TNF, NF-κB, and IL-17 signaling pathways. Molecular docking confirmed stable binding of C5AR1 with 1,3-Diphenylpropan-2-Ol (-7.87 ± 0.83 kcal·mol-¹) and HCAR3 with 3-Indolepropionic Acid (-6.35 ± 0.70 kcal·mol-¹), both below -5.0 kcal·mol-¹. CONCLUSION: This study first constructs a "gut microbiota-metabolite-hub gene" axis in IBD, providing a computational framework for microbiota-targeted precision therapy, and identifying C5AR1/KDM2A/HCAR3 as computationally predicted diagnostic biomarkers and 1,3-Diphenylpropan-2-Ol/3-Indolepropionic Acid as candidate intervention molecules that warrant further experimental validation.

Molecular Docking Simulation↗

PubMed2026

Placenta-derived Exosomes Mitigate Hypoxia-Induced Trophoblast Apoptosis and Inflammatory Progression via SASH1.

SASH1 is a signal adaptor protein involved in cell growth, apoptosis, and immune regulation, and has been increasingly studied in tumor and immune cells. Emerging evidence suggests that SASH1 plays an important role in inflammatory responses and cellular homeostasis, processes that are closely associated with the development of PE. This study aimed to determine whether SASH1 contributes to trophoblast apoptosis and inflammatory responses in PE and whether P-EXOS exerts protective effects through SASH1 regulation. In this study, three PE-related transcriptomic datasets (GSE75010, GSE10588, and GSE60438) were analyzed to identify shared differentially expressed genes (DEGs), followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Machine learning algorithms were further applied to screen key candidate genes, and single-cell RNA sequencing data were used to characterize cellular heterogeneity in placental tissue and to determine cell type-specific expression patterns. SASH1 was identified as a consensus candidate gene and was significantly upregulated in trophoblast cells from PE samples. In vitro, a hypoxia-treated HTR-8/SVneo trophoblast cell model was established, combined with SASH1 knockdown, SASH1 overexpression, and co-culture with P-EXOS. Functional experiments showed that knockdown of SASH1 significantly suppressed hypoxia-induced trophoblast apoptosis and reduced the secretion of pro-inflammatory cytokines, including IL-6, IL-1β, and TNF-α, whereas SASH1 overexpression promoted apoptosis and inflammatory responses. In addition, P-EXOS treatment markedly reduced SASH1 expression at both mRNA and protein levels and attenuated hypoxia-induced trophoblast injury, while SASH1 overexpression largely abolished these protective effects. Taken together, these findings indicate that SASH1 plays a critical role in trophoblast apoptosis and inflammatory responses in PE. P-EXOS may alleviate hypoxia-induced trophoblastic injury by suppressing SASH1 expression, providing new insights into the molecular mechanisms and potential therapeutic targets for PE.

Trophoblasts↗

PubMed2026

Genome-wide identification and functional analysis of the BES1-like (VfBES1) gene family in Vernicia fordii reveals its role in floral development.

BACKGROUND: Vernicia fordii Hemsl (also known as Tung tree), an significant commercial oil-producing tree species, is a monoecious and diclinous species with male and female flowers on the same inflorescence; however, the molecular mechanisms governing its floral sex determination remain elusive, particularly the genetic basis underlying the skewed female-to-male flower ratio and the evolutionary dynamics of sex-related gene families, which severely restrict targeted breeding for yield enhancement. In the model plant Arabidopsis, the BRI1 EMS SUPPRESSOR 1 (BES1) transcription factor family plays a crucial role in Brassinosteroid (BR) signaling and reproductive development. However, its function remains largely unexplored in woody perennials. RESULTS: In this study, we introduce the genome-wide identification and functional characterization of the BES1-like (VfBES1) gene family in the Tung tree for the first time. Integrative multi-omics approaches reveal seven VfBES1 genes that are clustered into three phylogenetically distinct clades, each characterized by clade-specific motifs and structural simplicity. Segmental duplication events (VfBES1-1/VfBES1-5 and VfBES1-4/VfBES1-7) and promoter cis-element enrichment (hormone-responsive and abiotic stress-related motifs) highlight evolutionary innovation and functional diversification. Spatiotemporal expression profiling reveals VfBES1 genes' tissue- and stage-specific roles. VfBES1-1 predominantly expresses in female flowers and fruits, suggesting its possible roles in late-stage sex maintenance or ovule and fruit development. VfBES1-2 and VfBES1-6 exhibit male flower-specific and early floral developmental activation, respectively. Nuclear-localized VfBES1-6 displays co-expression with VfMYB35-1 gene, which is a regulator of male structure degeneration. CONCLUSIONS: Findings in this study shed light on the regulatory roles of VfBES1 genes in the floral development of the Tung tree, providing a reference for its precision breeding to enhance flowering synchrony and seed productivity. This study also provides a comparative framework for understanding the functional diversity of BES1-like genes in non-model woody plants.

Flowers↗

PubMed2026

Assembly and Characterization of the First Complete Mitochondrial Genome of Tussilago farfara L.: Insights into Biological Functions and Phylogenetic Relationships within the Asteraceae Family.

Tussilago farfara L., a member of the Asteraceae family, is an economically valuable species due to its edible and medicinal properties. To elucidate the structural characteristics, genetic mechanisms, and evolutionary pathways of the organelle genomes of T. farfara, we sequenced, assembled, and annotated its mitochondrial genome for the first time. The complete mitochondrial genome of T. farfara spans 306,024 bp and contains 33 mitochondrial protein-coding genes (PCGs), 3 rRNAs, and 22 tRNAs. Analysis of the nucleotide substitution rate and genetic diversity revealed that most mitochondrial genome genes may have undergone purifying selection, indicating a slow evolutionary rate and a relatively conserved genomic structure. We further identified 13 fragments of chloroplast-derived DNA integrated into the mitochondrial genome, evidencing intracellular gene transfer. Collinearity analysis showed that Arctium lappa shares the most extensive mitochondrial homologous sequences and the highest sequence similarity with T. farfara. Phylogenetic analysis based on the mitochondrial genome helped to clarify the evolutionary and taxonomic position of T. farfara within the Asteraceae family. The mitochondrial genome sequence of T. farfara provides a valuable genomic resource for species identification and for evolutionary studies within the Asteraceae family.

Genome, Mitochondrial↗

PubMed2025

WRKY14-DPB Module Enhances Drought Tolerance by Activating the Expression of UGT84B1 Involved in Hydrolyzable Tannin Biosynthesis.

Drought stress severely limits the growth and development of trees. Tannins, which serve as vital secondary metabolites in plant roots, help mitigate drought stress. The Lauraceae family, which holds major economic and ecological value, faces substantial developmental challenges due to its sensitivity to drought conditions. Despite this, research on the regulatory mechanisms governing tannin-specific accumulation under drought stress remains limited. In this study, we aim to explore how WRKY14 interacts with DPB to regulate the metabolism of hydrolyzable tannin (HT) via the key enzyme UGT84B1, thereby enhancing drought tolerance in Litsea cubeba, a main species within the Lauraceae family. The WRKY-DPB-UGT84B1 module was specifically expressed in roots in response to drought stress. LcUGT84B1 was found to generate 1-O-Galloyl-β-d-glucose in vitro and in overexpressing L. cubeba. Moreover, molecular biology and transformation experiments demonstrated that LcWRKY14 and LcDPB formed a complex that directly bound to the LcUGT84B1 promoter, activating its expression and thereby facilitating HT synthesis. Co-overexpression of LcWRKY14 and LcDPB significantly enhanced drought tolerance by increasing HT accumulation. These findings provide new insights into the regulatory mechanisms of the WRKY-DPB-UGT84B1 module in promoting drought tolerance and offer a potential breeding strategy for developing drought-resistant varieties.

Drought Resistance↗

PubMed2025

Asthma causally affects the brain cortical structure: a Mendelian randomization study.

OBJECTIVE: The potential causal relationship between asthma and brain structures remains uncertain. We performed a two-sample Mendelian randomization to investigate the causal effects of various asthma phenotypes - unspecified asthma, moderate-to-severe asthma, childhood-onset asthma, and adult-onset asthma (AOA) - on cerebral cortex structure. METHODS: We utilized phenotype data derived from genome-wide association studies (GWASs). The ENIGMA Consortium GWAS provided outcome variables for surface area (SA) and thickness across the whole brain and 34 region-specific areas of the cerebral cortex. Using the inverse variance-weighted method as our primary estimation approach, we employed several techniques, including Cochran's Q statistic, the MR-PRESSO global test, MR-Egger, and weighted median, to assess heterogeneity and pleiotropy, thereby ensuring the robustness of our findings. Additionally, we conducted enrichment analyses of gene sets with causal effects on cortical structure and applied bioinformatics techniques to construct interaction networks and identify hub nodes. RESULTS: At the global level, AOA was associated with a significant reduction in full cortical SA (β = -58.49 mm2, p = 0.017). In regional analyses, moderate-to-severe asthma exhibited a more pronounced impact on the cerebral cortex compared to other phenotypes. Enrichment analysis revealed that pathways implicated in brain morphology among asthma patients were primarily linked to immune and inflammation-driven pathways. CONCLUSIONS: Our findings provide new evidence supporting a causal relationship between asthma and alterations in cortical structure, offering potential explanations for cognitive and psychiatric impairments observed in individual post-asthma.

Humans↗

PubMed2025

A positive-sense single-stranded RNA virus acquired a negative-sense open reading frame through recombination.

Although positive- and negative-sense single-stranded RNA viruses are ubiquitous in nature, there is currently no evidence of recombination or reassortment between viruses with these two major forms of genome organization. Here, we describe the discovery of brine shrimp virga-like virus 1 (BSVV1), a novel positive-sense single-stranded RNA virus with a recombinant genome structure derived from two viral phyla with differing genome organizations. The genome of BSVV1 comprises three open reading frames (ORFs). ORF1 resembles the RNA-dependent RNA polymerase of Ips virga-like virus 1 (a positive-sense RNA virus), while ORF2, transcribed in the positive orientation, is related to the glycoprotein of Hubei bunya-like virus 10 and other negative-sense RNA viruses. The predicted ORF3 was unique to BSVV1 without known homologs identified. The presence of the three protein products was verified by mass spectrometry. Notably, our analysis also revealed that BSVV1 is geographically widespread and found in brine shrimp from at least eight countries on four continents. In addition, BSVV1 was successfully cultured and proliferated to high viral loads during brine shrimp development. In sum, we provide compelling evidence of an ancient recombination event between negative- and positive-sense single-stranded RNA viruses, enriching our understanding of the evolution of genome structures in RNA viruses.

Open Reading Frames↗