Biochemical Genetics最新文献

The capacity for biofilm formation, along with the acquisition of antimicrobial resistance, could be the primary factors enhancing the persistence and spread of Acinetobacter baumannii (AB). We aimed to identify the trends in molecular epidemiology of AB isolated from western Iran. Ninety-nine pathogenic AB isolates were collected from patients in three major hospitals in Sanandaj and Kermanshah (the capitals of Kurdistan and Kermanshah provinces in western Iran, respectively) in one year. Isolates were tested for the presence of class D and B carbapenemases, integrons, and biofilm-associated genes, and their genetic diversity was initially investigated using enterobacterial repetitive intergenic consensus (ERIC) analysis, followed by multilocus sequence typing (MLST) and plasmid profiling. Of the 99 isolates, 91.9% showed resistance to carbapenems. The most common class D and class B carbapenemases were OXA-24-like and VIM type, respectively. The bap, bfmR, and ompA biofilm-related genes were present in all isolates. Class 1 integron was only identified in 10.1% of isolates and contained the sugar dehydrogenase gene cassette. By ERIC, Cluster C was found in three hospitals, and Clone A in two hospitals. By MLST, isolates in Cluster C and Clone A were assigned to ST78 and ST2125, respectively. Plasmid profiling of Cluster C and Clone A isolates showed similar plasmid profiles. Our research offers insights into the epidemiology of AB circulating in western Iran during recent years. The results may suggest a possible inter-hospital spread of these strains; however, further research is needed. We document for the first time the emergence of ST2125 and ST78 in Iran.

Laeonereis acuta is a polychaete species typically found at high abundance in estuarine and coastal lagoon environments. Due to its association with polluted habitats, it is commonly used in ecotoxicological studies. Moreover, its occurrence in spatially discontinuous environments with high environmental variability makes it a suitable model for evolutionary studies of local adaptation, genetic landscape, and early stages of speciation. This study aimed to develop primers and characterize microsatellite markers for L. acuta sampled from three coastal lagoons in southwestern Brazil. A total of 10 loci were characterized based on the genotyping of 40 individuals. The number of alleles per locus ranged from 2 to 19. Evidence of null alleles was detected at five loci, although their frequency decreased when coastal lagoons were analyzed separately. When considering all individuals as a single population, five loci showed positive and significant F_IS values, and seven loci deviated from Hardy-Weinberg equilibrium. Maricá and Guarapina exhibited heterozygote excess at several loci, whereas Jaconé showed evidence of population genetic isolation. The 10 microsatellite loci were polymorphic and suitable for population genetic analysis in L. acuta, although these patterns may not necessarily be representative of other geographic regions. These markers may contribute to ecotoxicological studies by clarifying whether physiological responses to pollutants are associated with genetic differentiation among populations. Furthermore, they provide valuable tools for investigating genetic structure and connectivity in discontinuous environments.

Systemic sclerosis (SSc) is a chronic, autoimmune, fibrotic disorder involving immune dysregulation, vascular abnormalities and progressive fibrosis. Although oxidative stress and defective DNA repair have been implicated in its pathogenesis, the impact of vitamin D on DNA repair pathways remains unclear. This study aimed to investigate the expression of DNA repair enzymes in SSc, explore their relationship with vitamin D status and assess the effects of vitamin D supplementation on the transcriptional expression of these enzymes. Peripheral blood samples were collected from 52 female patients with SSc and 31 age-matched healthy controls (HCs). Gene expression levels of base excision repair (BER) enzymes (APE1 and OGG1) and nucleotide excision repair (NER) enzymes (XPA and XPC) were analyzed. Serum vitamin D levels were measured and correlated with disease activity scores. In a prospective arm of the study, patients received six months of vitamin D supplementation and their DNA repair capacity was evaluated pre- and post-intervention. Baseline expression of APE1 and OGG1 was significantly lower in SSc patients than in HCs, whereas expression of the NER genes remained unchanged, indicating selective impairment of the BER pathway. Vitamin D deficiency was prevalent in SSc and inversely correlated with disease severity. Supplementation significantly increased serum vitamin D levels and up-regulated APE1 and OGG1 expression; while NER genes remained unaffected. These findings are consistent with evidence of elevated oxidative DNA lesions in SSc and support a mechanistic link between BER activity and the repair of oxidative DNA damage. SSc patients exhibit reduced transcription of BER-specific enzymes associated with vitamin D deficiency andrestoration of vitamin D levels partially rescues BER enzyme expression. These findingshighlight a potentially modifiable axis linking micronutrient status, genomic stability and disease activity and provide a rationale for investigating vitamin D optimization as an adjunctive strategy to enhance DNA repair and potentially attenuate inflammatory and fibrotic processes in SSc.

BK polyomavirus (BKV) infection, a common complication following kidney transplantation, can lead to BKV-associated nephropathy (BKVN). Molecular genetic studies have classified BKV into four genotypes (I-IV); however, comprehensive molecular characterization of BKV strains circulating in China remains limited. This study aimed to elucidate the predominant subtypes and clinical infection characteristics of BKV strains among kidney transplant recipients in Yunnan, a province in southwestern China. PCR-amplified BKV DNA sequences from kidney transplant recipients were aligned with reference strains and subjected to phylogenetic analysis. The viral VP1 gene was successfully amplified from 180 participants, spanning 16 ethnic groups. Genotype I was the predominant viral strain (56.66%, 102/180), followed by genotype IV (43.33%, 78/180), while genotypes II and III were not detected. Among genotypic subtypes, IVc-1 was most prevalent (40.0%, 72/180), followed by Ic (38.3%, 69/180) and Ib-1 (18.3%, 33/180). IVa-1 and IVa-2 were rare, identified in only 0.6% (n = 1) and 2.2% (n = 4) of cases, respectively. No significant differences in sex, age, BKVN incidence, BK viremia, or viruria were observed between patients with BKV-I and BKV-IV infections. Among the five confirmed BKVN cases, two were genotyped as subtype Ic, one as Ib-1, and two as IVc-1. Clinical phenotypes were also comparable between patients with BKV-I and BKV-IV infections. This study represents the largest single-center sequencing analysis of BKV in kidney transplant recipients in China, offering a valuable genomic resource for future research.

Rhizobial bacteria are known for their ability to fix nitrogen for leguminous plants and their essential function for sustainable agriculture. This study characterizes the taxonomic status and functional potential of the Bradyrhizobium B64 isolate using integrated genomic and molecular approaches. The whole genome of the B64 isolate was sequenced via Illumina paired-end technology. Species delimitation was performed using average nucleotide identity (ANI) and digital DNA-DNA Hybridization (dDDH). The NodD1 protein structure was modeled using AlphaFold3 and validated by Ramachandran plot analysis. Molecular docking was then conducted to evaluate interactions between NodD1 and four signaling flavonoids: Apigenin, Daidzein, Genistein, and Naringenin. Genomic analysis revealed a maximum ANI of 94.4% and dDDH values between 51.4 and 62.4%. Since these values fall below the standard prokaryotic thresholds (ANI < 95%; dDDH < 70%), the B64 isolate is identified as a novel species. Physiological assays confirmed nitrogen fixation (1.97 ppm), IAA production (3.67 ppm), and phosphate solubilization (26.10 ppm). Structural validation showed 100% of NodD1 residues in allowed regions, ensuring high model reliability. Docking simulations demonstrated strong binding affinities across all flavonoids, with binding free energies ranging from - 8.8 to - 9.0 kcal/mol. Daidzein exhibited the highest thermodynamic stability (- 9.0 kcal/mol), whereas apigenin showed the most extensive residue interaction network. The B64 isolate is a novel Bradyrhizobium species with a high symbiotic capacity. The stable NodD1-flavonoid interactions provide a molecular basis for efficient nodulation, positioning B64 as a promising candidate for developing lipo-chitooligosaccharide (LCO)-based biofertilizers.

To elucidate the molecular mechanism by which long non-coding RNA CCAT1 (LncRNA CCAT1) promotes colorectal cancer (CRC) progression via regulation of microRNA miR-490-3p and Voltage-Dependent Anion Channel 1 (VDAC1), thereby activating glycolysis. In vitro, LncRNA CCAT1, miR-490-3p, and VDAC1 expression in CRC cell lines (HT-29, SW620, SW480, HCT116) and normal colonic epithelial cells (NCM460) was quantified by qRT-PCR. Selected lines underwent CCAT1, miR-490-3p, or VDAC1 overexpression/knockdown. Dual-luciferase assays confirmed interactions between CCAT1 and miR-490-3p, and between miR-490-3p and VDAC1. Cell proliferation was assessed by CCK-8 and colony formation assays; glucose consumption, ATP production, and lactate secretion were measured by ELISA. In vivo, nude mice received subcutaneous xenografts of modified HT-29 cells. Tumor growth, body weight, histopathology, apoptosis, glycolysis-related gene/protein expression (VDAC1, Hexokinase 2 [HK2], Pyruvate Kinase M2 [PKM2], Glucose Transporter 2 [GLUT2]), and glucose metabolism were evaluated. CCAT1 was significantly upregulated in CRC cells. Its knockdown suppressed proliferation and glycolysis, whereas overexpression had the opposite effect. CCAT1 acted as a competing endogenous RNA for miR-490-3p, alleviating miR-490-3p-mediated repression of VDAC1, leading to VDAC1 upregulation. Overexpressing miR-490-3p or silencing VDAC1 inhibited CRC cell proliferation and glycolysis. In vivo, CCAT1 or VDAC1 knockdown reduced tumor growth and altered glycolysis-related gene/protein expression. LncRNA CCAT1 promotes CRC progression by sponging miR-490-3p to upregulate VDAC1, thereby activating glycolysis. The CCAT1/miR-490-3p/VDAC1 axis may serve as a promising diagnostic and therapeutic target in CRC.

Diabetic foot ulcer (DFU) is a severe complication of diabetes mellitus (DM), contributing significantly to morbidity and healthcare burden. Kerala, a South Indian state, has a high prevalence of diabetes, yet limited data exist on the genetic risk factors for DFU in this population. In this study, we assessed the association of four common vitamin D receptor (VDR) gene polymorphisms-rs7975232 (ApaI), rs731236 (TaqI), rs1544410 (BsmI), and rs2228570 (FokI)-with DFU in Kerala population. Mean serum 25-hydroxyvitamin D 25(OH)D) levels were 17.7 ± 14.2 ng/mL in the DFU group, 19.5 ± 12.4 ng/mL in the DM group, and 20.6 ± 13.9 ng/mL in the control group. Although the mean 25(OH)D levels did not differ significantly among the groups, the prevalence of vitamin D deficiency was significantly higher in the DFU group than in the DM and control groups (χ² = 6.03, P = 0.04), indicating a greater burden of vitamin D deficiency among patients with diabetic foot ulcers. Among the SNPs studied, rs731236 and rs1544410 showed significant associations with DFU. The AG genotype of rs731236 was associated with a reduced risk of DFU compared to both DM patients and non-diabetic Controls (p < 0.05, OR = 0.51). Similarly, the TC genotype of rs1544410 showed a protective association (p = 0.0219, OR = 0.51). No significant associations were found for rs2228570 and rs7975232. Functional docking analysis of rs2228570 indicated favourable calcitriol binding to both VDR isoforms, with slightly higher affinity for the shorter 424 aa variant (- 7.8 vs. - 7.7 kcal/mol). these findings suggest that vitamin D deficiency and genetic variation in the VDR gene, particularly rs731236 and rs1544410, may contribute to susceptibility to diabetic foot ulcer in the Kerala population, warranting further validation in larger, multicentre studies and functional investigations.

Viral infections in the female reproductive tract pose significant risks to fertility; however, their specific impacts on ovulated oocytes and the role of the surrounding cumulus cells remain unclear. In this study, we examined viral infection experiments and gene expression analyses to investigate the cell type-specific antiviral responses of mouse cumulus-oocyte complexes (COCs) using vesicular stomatitis virus (VSV) as a model RNA virus. Although ovulated oocytes expressed the cytosolic viral receptor retinoic acid-inducible gene-I, they lacked melanoma differentiation-associated gene 5 and laboratory of genetics and physiology 2 gene, which are present in cumulus cells. Exposure of COCs to VSV significantly impaired preimplantation development, reducing cleavage and blastocyst formation rates. Interestingly, no direct viral infection was detected in oocytes or early embryos, possibly due to the physical barrier of the zona pellucida. Direct exposure of denuded oocytes to VSV failed to induce antiviral gene expression or developmental defects. In contrast, co-culturing uninfected oocytes with VSV-infected cumulus cells resulted in developmental impairment. Infected cumulus cells exhibited robust antiviral responses and significantly upregulated retinoic acid-inducible gene-i, interferon-b, interleukin (Il)-6, and tumor necrosis factor-a levels. Correspondingly, oocytes and zygotes expressed the IL-6 receptor subunits Il6ra and Gp130. Overall, viral infection of cumulus cells impaired oocyte developmental competence via indirect paracrine signaling and identified IL-6 as a candidate mediator. These findings provide insights into the mechanisms by which the maternal inflammatory microenvironment influences early embryonic success and highlight the protective yet vulnerable nature of COCs during viral challenge.

Marfan syndrome (MFS) aortopathy involves extracellular matrix disruption, altered mechanical cues, and maladaptive vascular smooth muscle cell (VSMC) remodeling. However, the mechanosensitive regulators associated with MFS-related VSMC dysfunction remain unclear. This study aimed to identify and validate mechanosensitive candidate genes in MFS aortopathy. Public VSMC transcriptomic data from GSE128101 were re-analyzed to identify differentially expressed genes (DEGs). Protein-protein interaction analysis, functional enrichment, and minimum redundancy maximum relevance analysis were used to prioritize mechanosensitive candidates. Candidate genes were examined in independent MFS-related datasets and validated by qRT-PCR in primary aortic medial VSMCs from MFS patients and donor controls. TRPV4 localization was assessed by immunofluorescence. TRPV4 function was evaluated in primary human aortic smooth muscle cells using overexpression and siRNA-mediated knockdown, followed by proliferation, wound-closure, inflammatory cytokine, and NF-κB pathway assays. A total of 436 DEGs were identified in MFS-derived aortic VSMCs. Functional analyses highlighted extracellular matrix remodeling, mechanotransduction-related, inflammatory, and cytoskeleton-associated pathways. TRPV4 was the top-ranked mechanosensitive candidate, with TRPM5 also identified as an overlapping candidate. qRT-PCR confirmed increased TRPV4 and TRPM5 expression in MFS-derived VSMCs. MFS-derived VSMCs also showed elevated inflammatory gene expression and enhanced membrane-associated TRPV4 localization. In vitro, TRPV4 overexpression promoted proliferation, wound closure, inflammatory cytokine secretion, and NF-κB pathway phosphorylation, whereas TRPV4 knockdown showed opposite effects. These exploratory findings identify TRPV4 as a leading mechanosensitive candidate associated with MFS-related VSMC remodeling and inflammatory activation. Larger cohorts, MFS-specific models, and direct mechanistic assays are required to determine its biomarker or therapeutic relevance.

Camellia drupifera is an economically important woody oil plant rich in edible seed oil. High-quality and well-developed floral buds are key determinants of its yield. However, studies on the regulatory mechanisms underlying its floral bud development remain relatively limited. In this study, proteomics and metabolomics profiles, along with physiological traits, tested during the final three developmental stages of floral buds. The results showed that the contents of indole-3-acetic acid (IAA), abscisic acid (ABA), and 1-aminocyclopropane-1-carboxylic acid (ACC, a precursor of ethylene) decreased significantly in the second (GZII) and third (GZIII) stages. Gibberellin 3 (GA3) maintained a relatively stable content in GZII with a slight decrease, but decreased significantly in GZIII. These changes in hormone contents may promote the growth of stamens and pistils. During the transition among the three floral bud developmental stages, the relative water content, superoxide dismutase (SOD) activity, soluble sugar content, and soluble protein content decreased significantly, accompanied by an increase in hydrogen peroxide (H₂O₂) content. Integration of differentially accumulated metabolites (DAMs) and differentially expressed proteins (DEPs) analysis showed that the upregulated proteins in the energy metabolism pathway, including pyruvate kinase (PK), citrate synthase (CS), succinate dehydrogenase (SDH), aldolase (ALDO), and hexokinase (HK), promoted the production of adenosine triphosphate (ATP)-a critical energy source for the entire floral development process, including plant hormone synthesis. The decreased IAA content might be attributed to the downregulation of enzymes involved in tryptophan metabolism, such as aldehyde dehydrogenase (ALDH), 3-dehydroquinate dehydratase/shikimate dehydrogenase (aroDE), and chorismate mutase/prephenate dehydratase (aroH). The contents of ABA and GA3 were affected by the downregulation of 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (ispH). Furthermore, the contents of anthocyanins (antioxidant metabolites) decreased significantly in GZII and GZIII, which was caused by the downregulation of key enzymes in the anthocyanin synthesis pathway, including 4-coumarate-CoA ligase (4CL), flavonoid 3'-hydroxylase (F3'H), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), and anthocyanidin synthase (ANS). This study provides a foundation for further investigating the regulatory metabolites and enzymes involved in C. drupifera floral bud development, and lays a theoretical basis for solving the problem of flower abscission in C. drupifera.