Biochemical Genetics最新文献

Tall fescue (Festuca arundinacea Schreb.), taxonomically synonymous with Lolium arundinaceum (Schreb.) Darbysh., is a cool-season perennial grass valued for adaptability, forage quality, and stress tolerance. This study evaluated the genetic diversity and population structure of 32 Tunisian spontaneous populations and 3 local varieties using CAAT-box Derived Polymorphism (CBDP) and Conserved DNA-Derived Polymorphism (CDDP) markers. Out of 16 tested primers (8 CBDP and 8 CDDP), 12 (7 CBDP and 5 CDDP) generated reproducible and polymorphic banding patterns, producing a total of 124 bands for CBDP and 121 bands for CDDP. High polymorphism was observed (86.29% for CBDP; 74.38% for CDDP), with a mean polymorphism information content (PIC) of 0.378, confirming the informativeness of both marker systems. Clustering analyses based on CBDP, CDDP, and combined data revealed some grouping tendencies among populations, but these groupings were not strictly associated with geographic origin, bioclimatic stage, or whether populations were spontaneous or cultivated. STRUCTURE analysis suggested two clusters for each marker system, but accessions showed overlapping membership, indicating weak population structure. The combined dataset detected four admixed groups, yet all populations displayed high admixture, reflecting high genetic diversity and extensive gene flow in this outcrossing species. Analysis of molecular variance (AMOVA) indicated that over 97% of the total genetic variation occurred within regions, while PhiPT values were low but significant (P = 0.004). No isolation by distance was detected with the Mantel test (CBDP: r = 0.011, p = 0.419; CDDP: r = 0.087, p = 0.078). This study is the first to apply CBDP and CDDP markers in Tunisian tall fescue populations, demonstrating their efficiency in revealing genetic diversity. The findings highlight substantial genetic diversity among populations within regions and underscore the value of this germplasm for breeding and conservation efforts.

Breast cancer (BC) is the leading cause of cancer mortality in women. The emergence of resistance to radiotherapy (RT) is a great challenge for BC treatment. Discoidin domain receptor 1 (DDR1) can modulate the proliferation, migration, and apoptosis of cancer cells, but its role in RT of BC has not been illuminated. This project evaluated the expression of DDR1 in BC based on single-cell RNA sequencing data. We established RT-resistant strains through radiation and detected the expression of DDR1 using qPCR. The proliferation and apoptosis abilities of BC cells were evaluated using CCK-8, colony formation assay, and flow cytometry. Western blot and IHC were applied to detect the levels of proteins related to the AMPK/SIRT1/PGC-1α pathway. The effect of the DDR1-mediated pathway on resistance to RT in BC was explored in combination with an AMPK inhibitor. DDR1 was highly expressed in BC. In vitro experiments demonstrated that knocking down DDR1 repressed the viability of BC cells during RT, curbed cell proliferation, facilitated apoptosis, and elevated the levels of p-AMPK, SIRT1, and PGC-1α proteins. The addition of an AMPK inhibitor reversed the effects of DDR1 knockdown on cell proliferation and apoptosis. In vivo experiments showed that knocking down DDR1 inhibited tumor growth, and the inhibitory effect was stronger when combined with radiation therapy. This study revealed that the upregulation of DDR1 in BC may reinforce RT resistance by modulating the AMPK/SIRT1/PGC-1α pathway, thus providing a new therapeutic target for improving the sensitivity of BC to RT.

With the increasing complexity of genomic data, traditional classification methods face dual challenges of the "curse of dimensionality" and class imbalance when processing multiple single nucleotide polymorphism (SNP) markers. To address these challenges, this study proposes an innovative approach integrating the Boruta dimensionality reduction algorithm with the Synthetic Minority Over-sampling Technique (SMOTE). The methodology involves two key steps: Feature optimization using the Boruta algorithm to identify the most representative genetic markers, thereby significantly reducing the complexity of high-dimensional data. Application of SMOTE technology to generate synthetic samples, balancing minority class distributions and alleviating data imbalance issues. Experimental results demonstrate that the proposed method outperforms traditional classifiers (Random Forest [RF], K-Nearest Neighbors [KNN], Extreme Gradient Boosting [XGBoost] and Convolutional Neural Network [CNN]) without Boruta-SMOTE integration across multiple metrics including accuracy, precision, recall, and F1-score. This study provides new insights for the conservation of donkey genetic resources, breed improvement, and commercial applications, while offering an effective solution for genomic data classification challenges.

The genetic etiology of hearing loss (HL) in Ecuador remains largely unexplored. This study investigates the spectrum of genetic variants associated with HL in a cohort of 66 Ecuadorian families using Exome or Genome sequencing (ES/GS). We identified pathogenic and likely pathogenic variants underlying HL in 27 families (41%). While variants were detected in 15 different genes, only GJB2 (in 12 families) and TMC1 (in 3 families) variants were identified in more than one family. The NM_004004.6 (GJB2):c.19 C > T (p.Gln7*) and NM_004004.6 (GJB2):c.35delG (p.Gly12Valfs*2) variants were more common than other alleles in GJB2. In some families, we detected variants of uncertain significance (VUS) in well-established HL genes and classified them as "possibly solved" due to their rarity and equivocal functional predictions. This study provides valuable insights into the genetic basis of HL in Ecuador and lays the groundwork for improved regional genetic diagnostics and management.

Streptomyces spp. is a crucial source for the drug discovery and development, especially those from extreme environments. The complete genome was sequenced to uncover the biosynthetic potential of the strain Qhu-M197 producing mithramycin isolated from the alpine meadow of the Qinghai-Tibetan Plateau. The results revealed that the genome consists of one linear chromosome and two plasmids with the size of 9.12 megabases (Mb) and the guanine-cytosine (G + C) content of 71.52%. The phylogenetic analyses of 16S rRNA gene and genome of strain Qhu-M197 suggested the strain belonged to Streptomyces genus, and the closest phylogenetic relationship between the strain Qhu-M197 and S. phaeoluteigriseus DSM 41896^T. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between Qhu-M197 and S. phaeoluteigriseus DSM 41896^T are 97.47% and 84.1%, respectively, indicating that they likely belong to the same species. However, comparative genomic analysis with closely related species reveals that Qhu-M197 may represent a novel strain of S. phaeoluteigriseus, highlighting its potential distinction at the strain level. The biosynthetic gene clusters (BGCs) analyzed by antiSMASH v7.0 revealed that Qhu-M197 had 33 BGCs encoding secondary metabolites. Interestingly, about 64% BGCs show less than 50% similarity to those annotated, which provides new opportunities for the discovery of novel natural products.

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.

Impeding M2 macrophage polarization has been suggested to slow the progression of endometrial cancer (EC). F-box and WD repeat domain containing 7 (FBXW7) reportedly regulates the polarization and migration of macrophages in a multitude of cancers. Our pre-existing bioinformatics predictions showed a negative association between FBXW7 and M2-TAM infiltration in EC. This study aimed to investigate the role of FBXW7 in M2 macrophage polarization in EC by regulating the MYBL2/CCL2 axis. Cancer and adjacent cancerous tissues from patients with EC were collected to detect the differential expression of each factor. CCL2 levels in the cell culture medium were examined using enzyme-linked immunosorbent assay. Immunofluorescence staining was performed to determine the localization of FBXW7 and MYBL2 in EC cells. The number of M2 macrophages marker was determined by flow cytometry. The protein levels of FBXW7, MYBL2, CCL2, CD206, CD163, Arg1, and IL-10 were assessed using western blotting. The ubiquitination level of MYBL2 and the binding relationship between FBXW7 and MYBL2 were verified using co-immunoprecipitation. The effect of FBXW7/MYBL2/CCL2 axis on the malignant progression of EC in vivo was evaluated using tumor xenografts in nude mice. FBXW7 levels were decreased, whereas MYBL2 levels were increased in EC. Overexpression of FBXW7 downregulated CCL2 secretion in EC and inhibited M2 macrophage polarization. FBXW7 promoted the degradation of MYBL2 in a ubiquitination-dependent manner. FBXW7 knockdown inhibited CCL2 secretion by EC cells to restrain M2 macrophage polarization, which was countered by MYBL2 downregulation. In vivo functional assays demonstrated that FBXW7 overexpression significantly suppressed EC xenograft growth and enhanced tumor cell apoptosis. FBXW7 enhanced the ubiquitination and degradation of MYBL2 to reduce CCL2 secretion from EC, which inhibited macrophage polarization to the M2 type.

In Saccharomyces cerevisiae, the AUG codon typically signals translation initiation to set an open reading frame, with a preference for the A^- 3AA/U^- 1(AUG)U^+ 4 sequence context. The mutant eIF5^G31R or eIF2β^S264Y proteins cause translation initiation fidelity defect by initiating translation at a near cognate UUG codon, in addition to the AUG start codon (suppressor of initiation codon; Sui¯ phenotype). However, the critical role of the - 3 to - 1 sequences in selecting the UUG start codon by these Sui¯ mutants is not fully explored. Different HIS4^UUG-LacZ reporter constructs were made with UUG as the start codon and varied nucleotides at the - 3 and - 2 positions or individually at -1 positions. These constructs were transformed to yeast cells having eIF5^G31R or eIF2β^S264Y mutation, and the β-galactosidase activity was measured. The HIS4^UUG-LacZ transcripts carrying a purine (A/G) at the - 3 position showed higher reporter activity than those with a pyrimidine (U/C). Additionally, purines were favored at the - 1 position within an AA (- 3 and - 2) context for efficient UUG start codon selection. Our findings demonstrate that UUG start codon recognition by Sui¯ mutants eIF5^G31R and eIF2β^S264Y is greatly influenced by the surrounding nucleotide context, each showing distinct context preferences. This highlights the nuanced role of sequence context in the near-cognate UUG codon initiation by the Sui¯ mutants.

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.

Grounded on bioinformatics insights, this study investigates the interaction between DEP domain containing 1B (DEPDC1B) and early B cell factor 1 (EBF1), their expression patterns, and their functions in the progression of colon adenocarcinoma (COAD). DEPDC1B was identified as a potential oncogene aberrantly expressed in COAD, and its high expression was detected in COAD cell lines. DEPDC1B silencing in COAD cell lines while blocking epithelial-mesenchymal transition (EMT), dissemination, and expansion of COAD cells in vitro. Additionally, DEPDC1B knockdown suppressed tumorigenic activity and metastasis of mouse CT26 cells in isograft tumor models. EBF1, poorly expressed in COAD, was found to repress DEPDC1B transcription. EBF1 overexpression reduced DEPDC1B expression, thus diminishing the malignant properties of cancer cells. Nevertheless, its tumor-suppressive effects were negated by DEPDC1B restoration. EBF1 presented a promoter hypermethylation pattern in COAD cell lines, in which its expression was restored upon treatment of the methylation inhibitor 5-azacytidine. In conclusion, this study highlights that the hypermethylation of EBF1 leads to transcription activation of DEPDC1B, which promotes cell cycle progression, EMT, and malignant progression in COAD. Restoring EBF1 levels or suppressing DEPDC1B expression may be promising strategies for COAD management.