Biomedical subjects
Publications and source records attributed to Cong Li.
Residual PSC detection follows ultra‑trace‑analysis principles. LOD supports qualitative assessment. Assays employ PSC‑specific markers and proper references, with adaptation to differentiated cell populations from diverse PSC sources.
Flavonoids are central to abiotic stress responses, yet the specific signaling roles and evolutionary dynamics of flavonoid biosynthetic intermediates in crop drought adaptation remain elusive. Here, we demonstrate that dihydrokaempferol (DHK) and dihydroquercetin (DHQ), specific intermediate products of the soybean flavanone 3-hydroxylases GmF3H1/2, function as potent signaling molecules that mitigate drought stress. Exogenous DHK/DHQ promoted abscisic acid-dependent stomatal closure and enhanced drought tolerance across diverse dicot species, including soybean and tobacco, highlighting a broadly conserved stress-mitigating signaling mechanism. CRISPR/Cas9-generated gmf3hs double mutants exhibited severe drought hypersensitivity due to compromised redox homeostasis and defective stomatal regulation, which could be specifically rescued by DHK/DHQ application. Furthermore, the loss of GmF3H triggered a distinct reproductive trade-off under stress, leading to increased pod initiation but severe filling defects. Multiomics network analysis revealed extensive rewiring of broader stress-responsive pathways and identified upstream transcription factors, among which GmPHL11 directly binds to and activates the GmF3H1 promoter; overexpression of GmPHL11 promoted DHK accumulation and enhanced drought stress tolerance in soybean hairy roots. Finally, population genomic analyses demonstrated that the GmF3H1H1 haplotype, which confers superior enzymatic activity and robust root growth under drought stress, might have undergone positive selection during soybean domestication. Collectively, our findings redefine the role of GmF3H-derived specific intermediates as potent signaling molecules, providing comprehensive mechanistic and evolutionary insights into flavonoid-mediated drought resilience, developmental trade-offs, and molecular breeding in crops.
INTRODUCTION: Cartilage defects (CDs) are orthopedic conditions with limited regenerative potential. This study aimed to identify endoplasmic reticulum (ER) stress-related biomarkers and construct a diagnostic model to enhance the early detection of CD. METHODS: This study analyzed the transcriptomic dataset GSE129147 to identify ER stressrelated differentially expressed genes (ERSRDEGs) between CD and control tissues using the limma package (version 3.58.1). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were employed for functional enrichment. Immune infiltration was assessed using cell-type identification, which involved estimating the relative subsets of RNA transcripts and single-sample gene set enrichment analysis. Diagnostic models were constructed using logistic regression, support vector machine, and least absolute shrinkage and selection operator regression. RESULTS: Twenty ERSRDEGs were identified, with CYBB, ATP6V1A, and TNFRSF12A significantly upregulated in CD samples. GO and KEGG analyses highlighted oxidative stress response and extracellular matrix remodeling as key mechanisms in CD pathogenesis. Immune analysis revealed an increase in regulatory T cells and a reduction in CD8. T cells. TNFRSF12A showed strong immune associations and, together with TWIST1 and ATP6V1A, formed the final preliminary diagnostic model. The preliminary LASSO model achieved satisfactory predictive accuracy (AUC: 0.7-0.9). DISCUSSION: These findings suggest that ER stress and immune imbalance jointly contribute to cartilage degeneration. The identified genes, particularly TNFRSF12A, TWIST1, and ATP6V1A, not only serve as potential biomarkers but also provide preliminary evidence for new mechanistic insights into stress-immune crosstalk in CD. CONCLUSION: This study reveals the key roles of ER stress and immune dysregulation in CDs. Moreover, the ERSRDEG-based diagnostic model provides preliminary bioinformatics evidence and potential molecular indicators for targeted diagnostics and therapies.
OBJECTIVES: Integrons facilitate the capture and expression of exogenous genes, including antimicrobial resistance (AMR) genes. This study aimed to detect the presence of integrons, examine their genomic structure and location, and analyse integron-associated AMR, virulence and stress response genes in Salmonella using WGS. METHODS: WGS data from 193 Salmonella strains, representing 38 serotypes isolated from food animals and related meat products (2001-2019), were analysed using bioinformatic tools to assess integron presence and characterize their genomic architectures. RESULTS: Of 193 isolates, 116 (60.1%) harboured class 1 and/or class 2 integrons. Class 1 integrons alone were detected in 105 isolates, with some containing multiple copies. One S. Infantis isolate harboured only class 2 integrons, whereas 10 others contained both classes. No class 3-5 integrons were found. Twenty-seven class 1 integrons were chromosomal; the rest were plasmid-associated, linked to various plasmid incompatibility (Inc) types. Sixty-nine distinct AMR genes conferring resistance to 11 antimicrobial classes were found in integron cassettes or integron-associated plasmids. Genes linked to resistance to quaternary ammonium compounds and heavy metals, as well as ISs and transposons, were also identified. Significant virulence and stress response genes and proteins such as groES-groEL, LysR and EAL (glutamate, alanine and leucine) were common in integron cassettes. CONCLUSIONS: Class 1 integrons are prevalent in MDR Salmonella isolates from food animals and related meat products and are linked to diverse plasmid types. Their association with AMR, virulence and stress response genes underscores their role in AMR dissemination, and bacterial adaptation and pathogenicity.
Understanding the genetic mechanism of cold adaptation in cashmere goats and dairy goats is very important to improve their production performance. The purpose of this study was to comprehensively analyze the genetic basis of goat adaptation to cold environments, clarify the impact of environmental factors on genome diversity, and lay the foundation for breeding goat breeds to adapt to climate change. A total of 240 dairy goats were subjected to genome resequencing, and the whole genome sequencing data of 57 individuals from 6 published breeds were incorporated. By integrating multiple approaches such as phylogenetic analysis, population structure analysis, gene flow and population history exploration, selection signal analysis, and genome-environment association analysis, an in-depth investigation was carried out. Phylogenetic analysis unraveled the genetic relationships and differentiation patterns among dairy goats and other goat breeds. Through signal analysis (θπ, FST, XP-CLR), we identified numerous candidate genes associated with cold adaptation in dairy goats (STRIP1, ALX3, HTR4, NTRK2, MRPL11, PELI3, DPP3, BBS1) and cashmere goats (MED12L, MARC2, MARC1, DSG3, C6H4orf22, CHD7, MYPN, KIAA0825, MITF). Genome-environment association (GEA) analysis confirmed the link between these genes and environmental factors. Moreover, a detailed analysis of the critical genes C6H4orf22 and STRIP1 demonstrated their significant roles in the geographical variations of cold adaptation and allele frequency differences among different breeds. This study contributes to understanding the genetic basis of cold adaptation, providing crucial theoretical support for precision breeding programs aimed at improving production performance in cold regions by leveraging adaptive alleles, thereby ensuring sustainable animal husbandry.
Pre-mRNA, produced by eukaryotic DNA transcription, undergoes splicing by the spliceosome, which removes introns and joins exons to form mRNA. The spliceosome is a large and highly dynamic molecular machine. Its core components include five small nuclear ribonucleoproteins (snRNPs) and the various spliceosome-related proteins. The conserved Smith (Sm) complex and the Sm-like proteins (LSm) serve as primary components of the snRNPs. Sm proteins are involved in processes such as pre-mRNA splicing and mRNA degradation, which can regulate gene expression, thereby influencing plant growth, development, and stress responses. While 25 Sm proteins have been identified in rice, their specific roles in regulating rice growth and development remain unclear. In this study, we employed the CRISPR/Cas9 system to edit 15 OsSm genes, and 13 mutants were obtained, with mutation rates ranging from 20.83 to 83.87%. In comparison to the wild type (WT), the mutants exhibited dwarfism, reduced tiller numbers, lower seed-setting rates or sterility, and increased susceptibility to diseases. One Sm mutant, ossmf-2, exhibited dwarfism, delayed flowering, and small grains. Through transcriptome analysis, three target genes, OsMRG702, OsRGG2, and OsLA1, were identified. Mutations of the OsSmF protein may lead to the abnormal splicing of these genes and finally lead to the inhibition of growth and development. Our study first edited the OsSm genes and generated a mutant library in rice. Most of the mutants exhibited abnormal growth and development, underscoring the essential roles of OsSm proteins in rice physiology. Furthermore, this work addresses a critical gap in the functional characterization of Sm proteins in rice. The resulting mutant collection offers valuable germplasm resources and lays a theoretical foundation for elucidating the molecular regulatory networks involving spliceosomal components and their target genes in the control of crop growth, development, and reproduction.
The circadian system plays a pivotal role in facilitating the ability of crop plants to respond and adapt to fluctuations in their immediate environment effectively. Despite the increasing comprehension of PSEUDO-RESPONSE REGULATORs and their involvement in the regulation of diverse biological processes, including circadian rhythms, photoperiodic control of flowering, and responses to abiotic stress, the transcriptional networks associated with these factors in soybean (Glycine max (L.) Merr.) remain incompletely characterized. In this study, we provide empirical evidence highlighting the significance of GmPRR3b as a crucial mediator in regulating the circadian clock, drought stress response, and abscisic acid (ABA) signaling pathway in soybeans. A comprehensive analysis of DNA affinity purification sequencing and transcriptome data identified 795 putative target genes directly regulated by GmPRR3b. Among them, a total of 570 exhibited a significant correlation with the response to drought, and eight genes were involved in both the biosynthesis and signaling pathways of ABA. Notably, GmPRR3b played a pivotal role in the negative regulation of the drought response in soybeans by suppressing the expression of abscisic acid-responsive element-binding factor 3 (GmABF3). Additionally, the overexpression of GmABF3 exhibited an increased ability to tolerate drought conditions, and it also restored the hypersensitive phenotype of the GmPRR3b overexpressor. Consistently, studies on the manipulation of GmPRR3b gene expression and genome editing in plants revealed contrasting reactions to drought stress. The findings of our study collectively provide compelling evidence that emphasizes the significant contribution of the GmPRR3b-GmABF3 module in enhancing drought tolerance in soybean plants. Moreover, the transcriptional network of GmPRR3b provides valuable insights into the intricate interactions between this gene and the fundamental biological processes associated with plant adaptation to diverse environmental conditions.