Biomedical subjects

Lei Huang

Publications and source records attributed to Lei Huang.

4 recordsLinked to original sources

PubMed2026

Multi-omics characterization of flavor profile differences in the Longissimus thoracis between Angus and Hereford cattle.

BACKGROUND: Angus and Hereford cattle are premier breeds widely used in genetic improvement and crossbreeding programs to enhance meat quality, yet the flavor differences between them remain poorly understood. RESULTS: In this study, we performed an integrated analysis using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS)-based volatile metabolomics, lipidomics, and untargeted metabolomics to characterize the flavor profiles of the Longissimus thoracis (LT) muscle from both breeds and to identify potential precursor substances underlying flavor formation. In total, we identified 76 differential volatile organic compounds (VOCs) among the 493 candidate VOCs. By combing relative odor activity value (ROAV) and sensory attribute annotation, 2,3-butanedione which may contribute to the creamy aroma was revealed as the core differential VOC between the two breeds. This finding was robustly validated across SHAP (Shapley additive explanations) analysis, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment, and flavor annotation. Lipidomic analysis revealed 689 differential lipids primarily belonging to classes such as phosphatidylcholine, triglycerides, and phosphatidylethanolamine. Correlation analysis further linked these lipid profiles to flavor, showing that fatty acids (FAs) including FA(19:0), FA(18:2 + O), FA(14:1), FA(16:1), and FA(14:0) were significantly correlated with 2,3-butanedione. Notably, the unsaturated fatty acids (UFAs) in the Longissimus thoracis (LT) of Hereford cattle exhibited higher double bond content compared to Angus cattle, suggesting a greater potential for rich flavor development. Untargeted metabolomics revealed that nine of the 9474 metabolites were significantly correlated with both 2,3-butanedione and FAs, including norepinephrine, l-beta-aspartyl-l-leucine, and artemetin. CONCLUSIONS: Overall, our research has identified differential flavor compounds and potential precursor substances between Angus cattle and Hereford cattle, providing targeted guidance for breed improvement. © 2026 Society of Chemical Industry.

2,3‐butanedione↗

PubMed2025

Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration.

The blastema is key to forming complete tissues in regenerating Dugesia japonica (D. japonica). However, the dynamic changes in cellular compositions and transcription landscapes in blastema during regeneration are understudied. Here, through genome reannotation, 3D spatial transcriptome construction, single-cell RNA sequencing (scRNA-seq), and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) analyses of changes in gene expression and chromatin structures, we delineate key transcription factors regulating the developmental trajectories of major cell clusters in the regenerating head. Importantly, we find that the T cell factor 4 (DjTcf4)-positive cells highly accumulate at wound areas, and its gene network is critical for the proper timing of development during regeneration in multiple progenitor cells. Depletion of DjTcf4 and its target genes leads to singular eye and/or dull tail phenotypes and delays regeneration. Taken together, we build multi-omics atlases in D. japonica and reveal the noncanonical function of the DjTcf4 network in developmental pattern formation, laying a foundation for studies of regeneration in D. japonica.

Animals↗

PubMed2025

Genome-Wide Silencer Screening Reveals Key Silencer Modulating Reprogramming Efficiency in Mouse Induced Pluripotent Stem Cells.

The majority of the mouse genome is composed of non-coding regions, which harbor numerous regulatory sequences essential for gene regulation. While extensive research focuses on enhancers that activate gene expression, the role of silencers that repress gene expression remains less explored. In this study, the first genome-wide identification of silencers in the mouse genome is conducted. In mouse embryonic fibroblasts (MEFs) and embryonic stem cells (mESCs), 89 596 and 115 165 silencers are identified, respectively. These silencers are ubiquitously distributed across the genome and are predominantly associated with low-expression genes. Additionally, these silencers are mainly cell-specific and function by binding to repressive transcription factors (TFs). Further, these silencers are notably enriched with the histone modification H3K9me3. It is observed that the transformation between dual-function silencers and enhancers is correlated with intracellular transcription factor concentrations, accompanied by changes in epigenetic modifications. In terms of biological effects, we have identified silencers that can enhance the induction efficiency of MEFs and influence the pluripotency of mESCs. Collectively, this work offers the first comprehensive silencer landscape in the mouse genome and provides strong evidence for the role of silencers in the induction of induced pluripotent stem cells (iPSCs).

Animals↗

PubMed2025

A rhamnose-rich O-antigen of Paraburkholderia phymatum MP20 is required for symbiosis with Mimosa pudica.

Paraburkholderia phymatum, a β-proteobacterium, forms a nitrogen-fixing symbiosis with many species of the large legume genus Mimosa as well as with common bean (Phaseolus vulgaris L.). Paraburkholderia are considered to have evolved nodulation independently from the well-studied α-proteobacteria symbionts of legumes. However, the detailed mechanisms important for β-rhizobia-legume symbiosis have not yet been determined. In this manuscript, we have sequenced the genome of P. phymatum MP20, a strain isolated from Mimosa pudica nodules, and utilized transposon mutagenesis to identify a mutant that showed delayed and ineffective nodulation of M. pudica. Further analysis revealed that the mutant strain produced an altered lipopolysaccharide lacking rhamnose containing O-antigen. Complementation with the wild-type gene restored the symbiosis. Microscopic analysis of the ineffective nodules showed that the mutant strain did not infect the cortical cells but was restricted to the endodermis. The results suggest that the O-antigen of P. phymatum is important for the bacterial infection of cortical cells and for nodule maturation. Further research will unveil the specific involvement of the glycosyltransferase gene in LPS biosynthesis and its impact on successful nodule formation by P. phymatum.IMPORTANCEThe nitrogen-fixing symbiosis between legumes and rhizobia is important for agricultural and environmental sustainability. The mechanisms of the symbiotic interactions are extensively studied using α-rhizobia. In contrast, mechanisms of symbiotic interactions important for β-rhizobia and their Caesalpinioid (mimosoid) legume hosts are not well known. Here, we describe the genome sequence of P. phymatum MP20, a β-rhizobia isolated from the nodules of M. pudica, and isolation and characterization of a transposon mutant defective in symbiosis. We demonstrate that the O-antigen of the LPS is required for nodulation and symbiotic nitrogen fixation. This study broadens our knowledge of symbiotic interactions in β-rhizobia and will lead to a better understanding of the wider rhizobial-legume symbiosis apart from the α-rhizobia.

Symbiosis↗