Biochemical Genetics最新文献

Shilajit, a natural product with a documented history of use in traditional medicine for millennia, poses considerable challenges in elucidating its biological origin and pharmacological properties. In this study, a multidisciplinary approach integrating DNA metabarcoding and biochemical profiling was employed to investigate processed shilajit samples from the Pamir-Alai Mountains. Environmental DNA analysis identified 50 plant taxa across taxonomic levels ranging from order to species, indicating substantial botanical contributions to shilajit's composition. Among the identified taxa, Apiaceae and Asteraceae were the most represented families, while Vincetoxicum rossicum, Populus alba, and Quercus suber were the dominant species detected through metabarcoding analysis. Complementary biochemical analyses demonstrated notable antioxidant capacity and the presence of diverse bioactive compounds. Furthermore, oxidative stress-related biomarkers (NO, MDA, and GSH) were evaluated in the brain tissue of healthy rats following shilajit administration. No statistically significant differences were observed between the control and shilajit treated groups, suggesting that shilajit maintains physiological oxidative balance in healthy brain tissue. These findings provide important baseline biochemical data and support future investigations of shilajit's biological effects in validated oxidative stress and neurological disease models.

Ficus carica L. is an economically important fruit crop widely cultivated in the Mediterranean region. In this study, genetic diversity and population structure were investigated in 72 F. carica genotypes collected from the Derecik and Çukurca regions of Hakkâri province, Türkiye, using 15 highly polymorphic Start Codon Targeted (SCoT) markers. A total of 481 amplification bands were obtained, of which 475 were polymorphic, resulting in a high average polymorphism rate of 98.60%. Genetic diversity indices indicated substantial variation among the genotypes, with a mean effective number of alleles of 1.53, gene diversity of 0.31, and Shannon information index of 0.47. The average genetic distance among genotypes was 0.37, with the highest pairwise distance (0.721) observed between genotypes HC4 and HD7. Analysis of molecular variance (AMOVA) revealed that most genetic variation was distributed within populations (93%), whereas only 7% was among populations. Bayesian STRUCTURE analysis identified two distinct genetic clusters corresponding largely to geographic origin, with 22 genotypes (30.56%) classified as admixed based on a membership coefficient threshold of < 0.70. Principal coordinate analysis (PcoA) clearly separated genotypes according to their sampling locations, where Axis 1 and Axis 2 explained 24.31% and 15.07% of the total genetic variation, respectively. Overall, these findings demonstrate the effectiveness of SCoT markers in assessing genetic diversity and population structure in F. carica germplasm from southeastern Türkiye. Future studies should use codominant markers (SSRs and SNPs) expand geographic sampling, and adopt open data repositories to enhance conservation and breeding strategies.

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.

The economic importance of the sea urchin Glyptocidaris crenularis drives the need to elucidate the genetic mechanisms controlling its sex differentiation and development, a key step for enabling targeted genetic improvement. This study presents a chromosome-scale genome assembly for G. crenularis characterized by 22 chromosome-length scaffolds and a total length of 787.45 Mb. The phylogenetic tree revealed that G. crenularis diverged early among sea urchins. Synteny analysis among species suggested that superscaffold 10 might be the sex chromosome. Subsequent transcriptomic profiling further revealed 273 genes (298 transcripts) on chromosome 10 whose expression differed significantly between testis and ovary tissues. The genomic resources established in this study provide a foundation for investigating the population genetics, evolution, and functional mechanisms of this species, while the identified sex chromosomes and candidate genes pave the way for elucidating the molecular basis of sex determination in sea urchins.

Recurrent pregnancy loss (RPL) is characterized by two or more consecutive pregnancy losses, often associated with genetic, immunological, endocrine, and anatomical abnormalities. Among these, chromosomal abnormalities, including aneuploidies and submicroscopic copy number variations (CNVs), play a critical role in adverse pregnancy outcomes. A total of 125 fetal specimens were collected, of which 118 were included after applying predefined exclusion criteria. DNA isolated from products of conception and fetal tissues was subjected to quantitative fluorescent PCR (QF-PCR) for rapid aneuploidy screening. A subset of 30 samples with selected QF-PCR outcomes underwent array comparative genomic hybridization (aCGH). Identified CNVs were interpreted according to ACMG/ClinGen guidelines, followed by bioinformatics analyses using FunRich, WebGestalt, KEGG, and STRING to explore functional annotations and pathway enrichment. Among 118 samples, QF-PCR identified aneuploidy in 36 cases (30.5%), including monosomy (n = 20) and trisomy (n = 16), while 82 cases were reported as normal. Maternal age showed a significant association with chromosomal abnormalities (p < 0.05), and a weak negative correlation was observed between gestational age and aneuploidy risk (r = - 0.238, p = 0.008855). In the aCGH cohort (n = 30), clinically relevant CNVs were identified, including pathogenic and likely pathogenic variants, as well as variants of uncertain significance (VOUS). Notably, genes such as CFHR3, TNFRSF4, UGT2B17, CD24, MSR1, and the PSG gene family were implicated. Functional enrichment analysis revealed involvement in immune-inflammatory pathways, endocrine regulation, lipid metabolism, extracellular matrix remodeling, and placental development. This study demonstrates the enhanced diagnostic utility of combining aCGH with QF-PCR for identifying chromosomal abnormalities in RPL. However, the observed associations between CNVs and biological pathways are exploratory in nature and require validation in larger, well-powered cohorts.

Long non-coding RNAs (lncRNAs) are key regulators in hepatocellular carcinoma (HCC) progression, yet the function of lncRNA GAS5 in HCC remains controversial. GAS5 expression was analyzed across multiple public datasets. Overexpression experiments were performed in HCC cells to evaluate GAS5's biological role. Bioinformatic prediction, luciferase reporter experiments, and rescue assays were used to elucidate the molecular mechanism. Xenograft mice were established to confirm GAS5's in vivo effects. GAS5 levels were markedly reduced in HCC tissues. Excessive GAS5 suppressed cell viability and colony formation, induced G0/G1 arrest, promoted apoptosis, and inhibited migration and invasion. Mechanistically, GAS5 functioned as a competing endogenous RNA to inhibit miR-18a-5p and restore the expression of the tumor suppressor CADM2. The direct interactions between GAS5 and miR-18a-5p, and between miR-18a-5p and the CADM2 3'-UTR, were validated by luciferase assays. Rescue assays demonstrated that miR-18a-5p overexpression or CADM2 silencing reversed the tumor-suppressive effects of GAS5. In the xenograft mice, excessive GAS5 significantly impaired tumorigenesis and modulated apoptosis- and EMT-related markers. GAS5 suppresses HCC by modulating the miR-18a-5p-CADM2 axis. Our findings offer a new perspective into HCC tumorigenesis and suggest that GAS5 and its downstream network may serve as potential therapeutic targets.

We aimed to investigate whether secretory carrier membrane protein 3 (SCAMP3) knockdown could attenuate hypoxic pulmonary hypertension (HPH) potentially involving WW domain-containing E3 ubiquitin protein ligase 1 (WWP1). Fifty mice were randomly assigned to a blank group, an HPH group, a small interference (si)-negative control (NC) group, a si-SCAMP3 group and a si-SCAMP3 + si-WWP1 group (n = 10 per group). Pulmonary function, right ventricular systolic pressure (RVSP) and the Fulton index [RV/(LV + S)] were measured. Hematoxylin-eosin staining was performed to evaluate pulmonary vascular morphology and the pulmonary vascular remodeling indexes were calculated. Compared with the normoxia group, the hypoxia group exhibited significantly increased SCAMP3 relative expression, OD₄₅₀ value and SCAMP3 protein expression in HPASMCs, while the apoptosis rate and WWP1 protein expression were significantly decreased (P < 0.05). Compared with the hypoxia group, the hypoxia + si-SCAMP3 group showed significantly reduced SCAMP3 relative expression, OD₄₅₀ value and SCAMP3 protein expression, but significantly increased apoptosis rate and WWP1 protein expression (P < 0.05). Compared with the hypoxia + si-SCAMP3 group, the hypoxia + si-SCAMP3 + si-WWP1 group exhibited partial restoration of SCAMP3 expression increased OD₄₅₀ value and SCAMP3 protein expression, and decreased apoptosis rate and WWP1 protein expression (P < 0.05). These findings suggest that SCAMP3 knockdown may inhibit hypoxia-induced proliferation and promote apoptosis potentially involving WWP1, thereby alleviating pulmonary vascular remodeling in HPH mice.

Circular RNAs (circRNAs) have emerged as important regulators of tumor progression; however, their roles in papillary thyroid carcinoma (PTC) remain incompletely understood. In this study, we investigated the expression, biological function, and molecular mechanism of circGABRB2_006 in PTC. CircGABRB2_006 was significantly upregulated in PTC tissues and cell lines and was associated with aggressive clinicopathological characteristics, including increased tumor number, larger tumor size, advanced TNM stage, and lymph node metastasis. Functional assays demonstrated that circGABRB2_006 promoted PTC cell proliferation, migration, invasion, epithelial-mesenchymal transition (EMT), tumor growth, and pulmonary metastasis, whereas its silencing exerted the opposite effects. Mechanistically, circGABRB2_006 predominantly localized in the cytoplasm and acted as a molecular sponge for miR-296-5p, thereby relieving miR-296-5p-mediated repression of fibroblast growth factor receptor 1 (FGFR1). Rescue experiments further confirmed that the oncogenic effects of circGABRB2_006 were largely dependent on the miR-296-5p/FGFR1 axis. Collectively, these findings demonstrate that circGABRB2_006 drives malignant progression of PTC through the miR-296-5p/FGFR1 signaling axis, highlighting its potential as a biomarker and therapeutic target in PTC.

Heart failure is a leading cause of hospitalization worldwide, and evaluating the severity of heart failure often relies on the ejection fraction. Matrix metalloproteinases (MMPs) are crucial for tissue remodeling, and their dysregulation is linked to various pathologies, including cardiovascular diseases. Prior studies have demonstrated that MMP-9 gene deletion can promote angiogenesis, attenuate inflammation, and prevent vascular leakiness. Although MMP-9 is known to contribute to heart failure, it remains unclear whether the lack of the MMP-9 gene impacts heart failure with reduced ejection fraction (HFrEF) by preserving EF. We investigated whether removing the MMP-9 gene can help maintain ejection fraction during the transition from diastolic to systolic heart failure. To test the hypothesis, surgical creation of an arteriovenous fistula (AVF) was made between the abdominal aorta and inferior vena cava ~ 0.5 cm below the left kidney of the mice using a 25-gauge needle to create a chronic volume overload, a "single-hit" model of HFrEF. The mice were grouped into four separate categories: (i) Wild type (WT) sham, (ii) WT-AVF, (iii) MMP9-KO-sham, and (iv) MMP9-KO-AVF. The "in-gel" zymography technique quantified proteolytic activity on substrate gels. Protein expression levels of heart tissues were assessed by the Western blots. The multi-organ injury was assessed using tissue-specific creatine kinase isoforms, and cardiac function-related datasets were collected using an ultrasound procedure and myobath. The results showed that MMP-9 gene ablation preserves ejection fraction during HFrEF by enhancing the processes of (a) cell synthesis, adhesion, and contraction signaling, (b) mitigating multi-organ injury, (c) mitigating mitophagy, and (d) mitigating endocardial endothelial myocyte uncoupling.

Lumbar disc degeneration (LDD) is a major cause of chronic low back pain, and current treatments only provide symptomatic relief. This study aimed to investigate the role of miR-4632-5p and its target MAP3K11 in the pathogenesis of LDD. Bioinformatics analysis was used to predict target genes of miR-4632-5p. LDD tissues (n=22) and normal intervertebral disc (IVD) tissues (n=19) were collected to detect the expression of miR-4632-5p and MAP3K11 by RT-qPCR. A dual-luciferase reporter assay validated their direct interaction. In vitro, TNF-α-induced human nucleus pulposus cells (HNPCs) degeneration models were used to evaluate the effects of miR-4632-5p/MAP3K11 on cell viability, apoptosis, oxidative stress, and inflammatory cytokine secretion via CCK-8, flow cytometry, and ELISA. miR-4632-5p was significantly downregulated in LDD tissues, whereas MAP3K11 was upregulated (P<0.0001), and their expression showed a strong negative correlation (r=-0.82, P<0.0001). miR-4632-5p targeted the 3'UTR of MAP3K11, reducing dual luciferase activity by 35.9% (P<0.001). Overexpression of miR-4632-5p alleviated TNF-α-induced HNPC injury by enhancing cell viability, reducing the apoptotic rate by approximately 26%, improving redox homeostasis (lower MDA/ROS, higher SOD), and reduced the secretion of pro-inflammatory cytokines (IL-6, IL-1β, IL-8, IL-17) by 19%-25% (all P<0.001). These effects were abolished by concurrent MAP3K11 overexpression. Western blotting confirmed that miR-4632-5p reduced MAP3K11 protein levels and inhibited TNF-α-induced NF-κB p65 phosphorylation. In summary, the dysregulated expression of miR-4632-5p and MAP3K11 suggests their potential as exploratory biomarker candidates for LDD, and the miR-4632-5p/MAP3K11 axis represents a preliminary candidate strategy for LDD treatment.