Biochemical Genetics最新文献

Epithelial-mesenchymal transition (EMT) is critical in tumor progression and metastasis, with long non-coding RNAs (lncRNAs) as key regulatory elements. This study explored the association between genetic variants in EMT-related lncRNAs and colorectal cancer (CRC) risk in a Chinese population. A case-control study was conducted involving 1,888 untreated CRC cases and 1,888 cancer-free controls. Multivariate logistic regression models were used to assess effects of SNPs on CRC risk, while expression quantitative trait loci (eQTL) analysis used data from the Genotype-Tissue Expression (GTEx) project, and gene expression was evaluated using The Cancer Genome Atlas (TCGA) database. Four functionally relevant SNPs (AC106786.1 rs76180806, rs2277930, LINC00578 rs28711160, and RP1-193H18.2 rs17823238) were significantly associated with CRC risk (OR = 1.52, 95% CI = 1.26-1.83, P = 1.57 × 10 ^- 2; OR = 1.34, 95% CI = 1.15-1.57, P = 3.30 × 10 ^- 2; OR = 1.21, 95% CI = 1.09-1.33, P = 3.30 × 10 ^- 2; OR = 0.83, 95% CI = 0.75-0.92, P = 3.30 × 10 ^- 2). Notably, rs28711160 exhibited a significant eQTL effect on LINC00578 expression (P = 2.09 × 10^- 5), and LINC00578 expression levels correlated strongly with CRC risk. These findings indicate that genetic variants in EMT-related lncRNAs (AC106786.1, LINC00578, RP1-193H18.2) may contribute to CRC susceptibility and could serve as candidate biomarkers, providing new insights into the genetic architecture of CRC.

The recurring Fibonacci sequence in various biological systems proves that mathematical ideas are frequently mirrored in natural patterns. This work assumes the compelling theory that cattle genomes may exhibit similar periodic and recursive patterns, particularly in regions associated with reproductive fitness. Unregulated crossbreeding can jeopardize indigenous germplasm and disturb natural genomic configurations, endangering genetic diversity and the structural integrity of the genome. We suggest that animal genomes may follow observable mathematical patterns by looking at haplotype and single-nucleotide polymorphism (SNP) distributions. Finding these hidden patterns through whole genome sequencing (WGS) is crucial for rethinking genetic improvement strategies in livestock breeding programs and providing insights into optimising reproductive traits.

This study aimed to identify susceptibility genes of hypertension in Tongdao Dong ethnic group. 38 hypertension candidate genes with their 42 single nucleotide polymorphisms (SNPs) screened from our previous study were selected for genotyping using MALDI-TOF mass spectrometry in a total of 359 participants, including 242 hypertensive patients and 117 healthy controls. The genotype and allele frequencies of these 42 SNPs were compared between the normotensive and hypertensive groups. 7 SNPs (KLK2 rs198972, MGAT1 rs634501, ABCA1 rs2066714, ADRB1 rs1801253, CLCN2 rs2228291, FOLH1 rs202680, and SCNN1G rs5735) exhibiting significant differences in genotypic and/or allelic frequencies between the two groups were subsequently selected for hypertension risk analysis. Logistic regression analysis with adjustment for the same factors revealed that the homozygous mutant GG genotype of MGAT1 SNP rs634501 enhanced the risk of hypertension, whereas carriers of the T minor allele of KLK2 SNP rs198972 showed a decreased risk of hypertension. Association analysis of SNPs with hypertension-related risk factors showed that MGAT1 rs634501 was significantly associated with SBP and DBP. Thus, our study suggests that MGAT1 may be a susceptibility gene for hypertension in the Dong Ethnic Population of Tongdao.

The growing trend of Leishmania major (L. major) infections around the world has raised global concerns due to the lack of efficient vaccines and antiparasitic drugs. In addition, the drug resistance crisis and side effects of chemotherapy remain to be addressed. In the present study, the designed multi-epitope lentiviral vaccine from Leish-F1 (consisting of TSA, Leif, LmSTI1 proteins) was produced. For this purpose, multi-epitope construct was sub-cloned into the pCDH513 lentiviral vector, previously designed in silico. Subsequently, to produce a recombinant lentivirus, PCDH513B-Leish-F1 vector was co-transfected with packaging vectors into HEK293T cells. In order to confirm the gene expression, Western blot technique was performed. Finally, to evaluate the immune responses, the vaccine containing Leish-F1 selected epitopes, and two control groups, phosphate-buffered saline and lentivirus without multiepitope, were injected twice into the Balb/c mice. The enzyme linked immunosorbent assay method deciphered that the vaccinated group had a higher level of IFN (interferon)-γ and IL (interleukin)-4 levels compared to control groups (p < 0.05). Also, the IgG2a and IgG1 antibodies showed a significant increase in the main groups (p < 0.05). The results revealed that the immunization of the Balb/c mice using a multi-epitope lentiviral vaccine led to the stimulation of humoral and cellular responses.

Phylogenetic relationships within Penaeoidea, particularly among taxa of Penaeidae, have long remained controversial. To expand mitogenomic resources for Penaeidae and evaluate the phylogenetic position of Atypopenaeus stenodactylus (Stimpson, 1860), we sequenced and annotated its complete mitochondrial genome and analyzed gene composition, codon usage, tRNA secondary structure, selective pressure, intraspecific mitogenomic variation and phylogenetic relationships. The mitogenome of A. stenodactylus is a typical closed circular double-stranded DNA molecule of 15,933 bp, containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and one D-loop region, with a pronounced A + T bias. Among the 22 tRNAs, all except trnS1, which lacks the DHU arm, formed typical cloverleaf structures, although some showed limited local variation. All 13 PCGs had Ka/Ks values below 1, indicating overall purifying selection; nad6 showed the highest Ka/Ks value, whereas cox1 had the lowest. Comparative analysis of the three available A. stenodactylus mitogenomes, PV007824, PX672768 and PV434778, revealed conserved gene order and low sequence divergence, with variation mainly concentrated in the non-coding D-loop region. Phylogenetic analysis based on 13 PCGs placed A. stenodactylus within Penaeidae and showed close relationships with Metapenaeus, Alcockpenaeopsis, Batepenaeopsis and Trachypenaeus, although traditional Penaeidae monophyly was not recovered. After inclusion of the three conspecific mitogenomes, PV007824, PX672768 and PV434778 clustered together, further supporting the stability of the inferred phylogenetic position. Overall, this study enriches mitogenomic resources for Penaeidae and provides new molecular evidence for resolving phylogenetic relationships within Penaeoidea.

Spatial transcriptomics (ST) has redefined our exploration of tissue-level cellular heterogeneity and spatial architecture; yet accurately pinpointing functional regions within complex, high-dimensional datasets remains a pressing hurdle. To tackle this, we introduce DSSMST, a Deterministic State Space Model for Spatial Transcriptomics, as a self-supervised learning (SSL) framework that integrates a Deterministic State Space Model (DSSM), graph neural networks (GNNs), and contrastive learning. Central to DSSMST is the DSSM module, whose robust dynamic modeling capacity enables it to capture spatial gradient variations and continuous dependencies in ST data-overcoming the limitations of static graph-based approaches-thereby establishing a solid basis for precise spatial domain identification. Complementing this, a customized self-supervised contrastive learning mechanism refines the latent embedding space, empowering the model to better distinguish between subtly differing spatial domain features. This integration effectively elevates the overall accuracy of spatial domain delineation. We assessed DSSMST on multiple representative ST datasets using diverse metrics. Experimental findings reveal that DSSMST achieves leading spatial domain identification accuracy and maintains competitive robustness and generalization across multiple datasets, underscoring its strong potential for advancing ST research. The source code, tutorials, and reproducibility instructions are publicly available at https://github.com/JiruiZhang/DSSMST .

Barbatia virescens is an important economic bivalve along the Chinese coast, but its natural resources have been severely impacted by habitat degradation and overfishing. In this study, we applied RAD-seq to five wild populations and generated 79.48 Gb of raw data, from which 237,101 high-quality SNPs were identified. All populations exhibited relatively high genetic diversity (mean: H_o = 0.158, H_e = 0.248, π = 0.263, and F_IS = 0.290) with low genetic differentiation (F_ST < 0.05). Results from PCA, structure analysis and Neighbor-Joining (NJ) tree supported weak population structure. Relative migration analyses suggested generally high connectivity among populations, although the XP population exhibited comparatively reduced connectivity under stricter network thresholds. The findings provide a basis for sustainable management and the preservation of genetic resources in B. virescens.