Biochemical Genetics[JOURNAL]
Sun
200 papers
Pediococcus acidilactici WSP-AZM23: Genomic Insights, In Vitro Probiotic Potential, and Computational Analysis for Biotherapeutic Applications.
Akmaliyah R, Mustopa AZ, Budiarti S … +5 more , Mubarik NR, Mamangkey J, Putranto WS, Pratama R, Maladan Y
Biochem Genet · 2026 Apr · PMID 41931223 · Publisher ↗
Probiotics are increasingly recognized for their therapeutic potential and health-promoting properties. This study characterized a novel probiotic strain, WSP-AZM23, isolated from Etawa goat milk. Molecular identificatio...
Probiotics are increasingly recognized for their therapeutic potential and health-promoting properties. This study characterized a novel probiotic strain, WSP-AZM23, isolated from Etawa goat milk. Molecular identification assigned the strain to Pediococcus acidilactici. Whole-genome sequencing revealed a single circular chromosome of 2,007,629 bp. Genome annotation confirmed the absence of virulence-associated determinants and identified genes linked to probiotic functionality, including acid and bile salt tolerance, extracellular protease production, type III polyketide synthase (T3PKS)-related proteins, auto-aggregation capacity, and biosynthetic pathways for secondary metabolites with predicted antioxidant, anti-inflammatory, and antidiabetic activities. The genome also contains type II CRISPR-associated genes (csn2, cas1, cas2, and cas9), indicating adaptive immune defense systems. Molecular docking analysis supported the predicted bioactivities of selected metabolites against relevant therapeutic targets. Antioxidant activity was evaluated using NADPH oxidase 4 (NOX4; PDB ID: 5O0X), anti-inflammatory potential using cyclooxygenase-2 (COX-2; PDB ID: 6BL4), and antidiabetic activity using human intestinal α-glucosidase (PDB ID: 3W37), a key enzyme in postprandial carbohydrate digestion. The occurrence of P. acidilactici strain WSP-AZM23 in sourdough and local dairy products further supports its ecological adaptability and potential application as a candidate biotherapeutic strain.
Development and Characterization of Microsatellite Markers for the Euryhaline Polychaete Laeonereis acuta (Annelida: Nereididae) in the Southwestern Brazilian Coast.
Carvalho PCE, Paiva PC, Seixas VC
Biochem Genet · 2026 Mar · PMID 41910901 · Publisher ↗
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. Mor...
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 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.
Mitogenome of Rhabdophis swinhonis (Squamata: Colubridae): Its Comparative Description and Phylogenetic Position Within Colubridae.
Su Y, Luo J, Wu F … +3 more , Song H, Wang J, Zhu G
Biochem Genet · 2026 Mar · PMID 41910900 · Publisher ↗
Rhabdophis swinhonis (GÜNTHER, 1868) remains understudied due to its narrow distribution and scarcity. This study aimed to sequence and characterize its mitochondrial genome to provide essential genetic data for understa...
Rhabdophis swinhonis (GÜNTHER, 1868) remains understudied due to its narrow distribution and scarcity. This study aimed to sequence and characterize its mitochondrial genome to provide essential genetic data for understanding its evolution and conservation. We sequenced the complete mitochondrial genome of R. swinhonis. The mitogenome is 18,525 bp long and contains 37 typical mitochondrial genes and 2 control regions. Most genes are encoded on the H-chain, including 12 protein-coding genes (excluding ND6 on the L-chain). Phylogenetic analysis robustly places R. swinhonis within Rhabdophis, forming a sister clade to R. chiwen with maximal support (BI/ML = 1.0/100%). This study reports the first complete mitochondrial genome of R. swinhonis, confirming its phylogenetic position consistent with prior genus-level studies. The findings provide fundamental genetic resources crucial for future research on the species’ evolutionary history and conservation strategies.
STOML2 Knockdown Amplifies PINK1/Parkin-Dependent Mitophagy in Colorectal Cancer.
Cheng T, Zhao X, Ruan Y
Biochem Genet · 2026 Mar · PMID 41893974 · Publisher ↗
Colorectal cancer (CRC) remains a major cause of cancer death. STOML2 can orchestrate mitophagy in pancreatic cancer cells. Herein, this study probed whether STOML2 modulated cell mitophagy in CRC. STOML2 expression in C...
Colorectal cancer (CRC) remains a major cause of cancer death. STOML2 can orchestrate mitophagy in pancreatic cancer cells. Herein, this study probed whether STOML2 modulated cell mitophagy in CRC. STOML2 expression in CRC was analyzed using databases and measured in CRC cells and tissues. Following STOML2 knockdown in CRC cells, CCK-8 assay was utilized for detecting cell viability, Transwell assay for measuring cell invasion and migration, and flow cytometry for testing apoptosis. Meanwhile, mitochondrial membrane potential (MMP) and adenosine triphosphate (ATP) levels were examined using JC-1 probes and kits. PINK1, Parkin, LC3II/I, and p62 protein levels were determined by Western blot, and Bax, Bcl-2, and Caspase 3 mRNA levels were analyzed by RT-qPCR. TOM20 and LC3 co-expression was tested by immunofluorescence. Rescue experiments were conducted with an inhibitor of mitophagy (3-methyladenine) and STOML2 knockdown. STOML2 was highly expressed in CRC. STOML2 knockdown diminished CRC cell proliferation, invasion, and migration while augmenting apoptosis. Additionally, STOML2 knockdown reduced MMP, ATP contents, and p62 expression and enhanced LC3II/I, PINK1, and Parkin expression and co-expression of TOM20 and LC3II/I in CRC cells. Treatment with 3-MA reversed the promotion of mitophagy in CRC cells caused by STOML2 knockdown. Simultaneous knockdown of PINK1 in STOML2-knockdown cells effectively reversed STOML2-induced decreases in p62, increases in the LC3II/I ratio, and enhanced co-localization of mitochondria and autophagosomes. STOML2 knockdown suppresses cell proliferation, invasion, and migration and promotes mitophagy and apoptosis by inhibiting the PINK1/Parkin pathway.
Whole Mitochondrial Genome Analysis Highlights India's Role in Pig Domestication and Maternal Lineage Diversification.
Ahlawat S, Sharma U, Singh KV … +7 more , Arora R, Sharma R, Singh A, Mohan NH, Banik S, Kn R, Venkatachalapathy RT
Biochem Genet · 2026 Mar · PMID 41893973 · Publisher ↗
The mitochondrial genome is a powerful molecular marker for investigating genetic diversity, evolutionary relationships, and maternal lineage in livestock species. This study provides a comprehensive assessment of matern...
The mitochondrial genome is a powerful molecular marker for investigating genetic diversity, evolutionary relationships, and maternal lineage in livestock species. This study provides a comprehensive assessment of maternal genetic diversity in Indian pig populations based on complete mitochondrial genome analysis of 73 samples representing 13 indigenous breeds: Agonda Goan, Doom, Ghoongroo, Manipuri Black, Niang Megha, Mali, Banda, Ghurrah, Purnea, Nicobari, Tenyi Vo, Wak Chambil, and Andamani, along with non-descript Ankamali pigs from Kerala. Mitochondrial genome lengths ranged from 16,609 to 16,620 bp and included 13 protein-coding genes, 22 tRNAs, two rRNAs, and a control region. A total of 63 distinct haplotypes were identified, with high haplotype diversity (0.996) and moderate nucleotide diversity (0.007). Hierarchical AMOVA revealed moderate maternal structuring, with 49.18% of variation within populations and 10.35% among geographically defined groups. Phylogenetic analyses showed clear genetic separation between pigs and closely related species, reflecting deep evolutionary divergence. Indian wild pigs formed a strongly supported, distinct cluster, clearly differentiated from Indian domestic pigs as well as domestic and wild pigs from other regions. Most Indian domestic pig mitogenomes clustered within the Asian clade (A), encompassing haplogroups A2, A1b, D1a1, D1a1a, D1b, D1c3, D1d, D2, D3, and D4. Evidence of European maternal introgression was detected in Agonda Goan, Doom, and Purnea pigs, indicating historical influences of trade, migration, or crossbreeding. Median-joining network analysis of the complete D-loop region independently corroborated whole-mitogenome phylogenetic patterns. Overall, these findings highlight Indian wild pigs as an important ancestral reservoir contributing to global porcine genetic diversity.
Characterizing 46,XY Differences of Sex Development: Novel Genetic Variants and Diagnostic Pitfalls in a Single-Center Cohort.
Hassan HA, Essawi M, Elaidy A … +4 more , Eissa N, Mekkawy M, Kamel A, Mazen I
Biochem Genet · 2026 Mar · PMID 41893972 · Publisher ↗
46,XY Differences of Sex Development (DSD) present major diagnostic challenges in consanguineous populations like Egypt, where genetic causes remain poorly characterized despite high prevalence. This study investigates t...
46,XY Differences of Sex Development (DSD) present major diagnostic challenges in consanguineous populations like Egypt, where genetic causes remain poorly characterized despite high prevalence. This study investigates the molecular spectrum and regional epidemiology of 46,XY DSD in Egypt to identify novel variants and improve diagnosis. Thirty-seven Egyptian patients with 46,XY DSD underwent clinical evaluation and hormonal profiling. We performed targeted genetic sequencing of key genes (SRD5A2, AR, HSD17B3, NR5A1, SRY, and WT1), and exome sequencing (ES) for cases that remained undiagnosed. We also reviewed previously reported Egyptian cases to build a comprehensive picture of the genetic landscape. Molecular diagnosis was achieved in 67% (25/37) of patients, including eleven novel variants in AR, SRD5A2, HSD17B3, and ZNRF3. Combining with prior data (n = 113), 5α-reductase deficiency was most frequent (52%), followed by AIS (23%) and 17β-HSDD (12%). Consanguinity was high (69%), with regional clustering in Upper Egypt and Sinai. Diagnostic delays were prominent in CAIS and 17β-HSDD cases. This study identified eleven novel pathogenic variants and provided further evidence implicating ZNRF3 as a candidate gene in Egyptian 46,XY DSD patients. We confirmed 5α-reductase deficiency (52%) as the predominant etiology and demonstrated that ES significantly improves diagnostic yield. Key challenges included limited LC-MS/MS availability for steroid profiling and regional disparities in diagnostic resources. Future efforts should prioritize ES implementation and multicenter collaborations to address diagnostic delays.
Tannic Acid Inhibits Lung Adenocarcinoma Progression by Suppressing MMP-2-Mediated Epithelial-Mesenchymal Transition.
Lin M, Zhou Y, Wang Y … +5 more , Yan H, Qin X, Zhong X, Yang G, Liu Q
Biochem Genet · 2026 Mar · PMID 41880115 · Publisher ↗
This study explores the antitumor effect of tannic acid (TA), a natural polyphenol derived from gallnuts, on lung adenocarcinoma (LUAD), with a focus on its impact on epithelial-mesenchymal transition (EMT) and matrix me...
This study explores the antitumor effect of tannic acid (TA), a natural polyphenol derived from gallnuts, on lung adenocarcinoma (LUAD), with a focus on its impact on epithelial-mesenchymal transition (EMT) and matrix metalloproteinase-2 (MMP-2). We employed CCK-8, wound healing, and Transwell assays to assess the effects of TA on the malignant behaviors of A549 LUAD cells. Western blot (WB) and immunofluorescence were used to examine EMT-related protein expression. Molecular docking was used to analyze TA-MMP-2 binding interaction. RT-qPCR, WB, and MMP-2 activity assay were applied to evaluate the expression and enzymatic activity of MMP-2. An MMP-2-overexpressing cell model was established to clarify its role in TA-mediated antitumor activity. Furthermore, an A549 subcutaneous xenograft model was employed to verify the in vivo antitumor efficacy of TA and its impact on MMP-2. TA markedly suppressed the viability, migration, and invasion of LUAD cells, downregulated the EMT-associated transcription factors Twist and Snail, downregulated N-cadherin and vimentin, and upregulated E-cadherin. Molecular docking indicated stable binding of TA to MMP-2 via multiple hydrogen bonds. TA downregulated MMP-2 at both mRNA and protein levels and suppressed its enzymatic activity. Overexpression of MMP-2 partially reversed the inhibitory effects of TA on cell viability, migration, invasion, and EMT. In vivo, TA markedly suppressed tumor growth, reduced MMP-2 expression, and inhibited EMT, whereas MMP-2 overexpression attenuated these antitumor effects. In conclusion, TA suppresses LUAD progression by inhibiting MMP-2 expression and activity, thereby interfering with the EMT process. MMP-2 is a key target of TA, suggesting its potential as a therapeutic agent.
Chemical Complementarities of Neuroblastoma Tumor-Resident TCR CDR3s and CMV Antigens are Associated with a Better Outcome.
Rigby KL, Jain R, Gozlan EC … +5 more , Kacsoh DB, Singh T, Chobrutskiy A, Chobrutskiy BI, Blanck G
Biochem Genet · 2026 Mar · PMID 41880114 · Publisher ↗
A likely immune response to a virus can be detected via the presence of TCR CDR3s that (a) exactly match CDR3s known to bind viral antigens or (b) represent chemical complementarity to viral antigens. Previous studies, b...
A likely immune response to a virus can be detected via the presence of TCR CDR3s that (a) exactly match CDR3s known to bind viral antigens or (b) represent chemical complementarity to viral antigens. Previous studies, based on genomics approaches to characterizing anti-CMV TCR CDR3s in patient blood samples, have indicated the possibility that a systemic CMV infection is associated with worse outcomes for NBL, as well as for breast cancer. Thus, the association of NBL tumor-resident anti-CMV TCR CDR3s and patient outcomes was evaluated here, with results indicating that high levels of chemical complementarity between tumor-resident TCR CDR3s and CMV antigens represented a better outcome. This is in apparent contrast to results obtained via the previous study of blood sourced, anti-CMV TCR CDR3s representing a worse outcome. This study identified gene expression values associated with the tumor-specific anti-CMV TCR CDR3s, representing exact matches to known anti-CMV TCR CDR3s, which may assist in identifying a potential underlying mechanism effecting the better outcomes associated with the tumor-resident, anti-CMV TCR CDR3s. Overall, results here raise the question of whether an anti-CMV response directly against the tumor, or within the tumor microenvironment, is involved in reductions in tumor progression or responsiveness to treatment?
Study on the Role of Galectin-3 in Sepsis.
Pan W, Zhao J, Liu F … +4 more , Liu Q, Chen Q, Zhu G, Cheng Y
Biochem Genet · 2026 Mar · PMID 41880113 · Publisher ↗
To elucidate the role of galectin-3 (Gal-3) in sepsis, bacterial sepsis models were established in wild-type infant mice and Gal-3 knockout (Gal-3⁻/⁻) mice. Macrophage phagocytic function and maturation were systematical...
To elucidate the role of galectin-3 (Gal-3) in sepsis, bacterial sepsis models were established in wild-type infant mice and Gal-3 knockout (Gal-3⁻/⁻) mice. Macrophage phagocytic function and maturation were systematically compared between the two groups. Sepsis was induced by intraperitoneal injection of Salmonella typhimurium (2.5 × 106 colony-forming units [CFU]/mouse) into 2-week-old wild-type (n = 20) and Gal-3⁻/⁻ mice (n = 20). Macrophage cytokine production, including interleukin (IL)-8, tumor necrosis factor (TNF)-α, and IL-10, was quantified by enzyme-linked immunosorbent assay (ELISA). Bacterial clearance was evaluated by peripheral blood CFU enumeration, and intracellular bactericidal activity was assessed in macrophages co-incubated with S. typhimurium. To examine phagocytic maturation, bacteria labeled with pH-sensitive and pH-insensitive fluorescent probes were used, and phagosome acidification was analyzed by flow cytometry. Compared with wild-type controls, Gal-3⁻/⁻ macrophages exhibited no significant changes in IL-8 or TNF-α expression (P > 0.05) but showed a marked reduction in IL-10 levels (P < 0.05). In parallel, Gal-3⁻/⁻ mice displayed significantly impaired bacterial clearance and intracellular killing capacity (P < 0.05). Defective phagosome acidification and reduced phagosome-lysosome fusion were observed in Gal-3-deficient macrophages, rendering Gal-3⁻/⁻ mice more susceptible to bacterial sepsis. Collectively, these results indicate that Gal-3 is a key regulator of macrophage phagocytic maturation and antimicrobial defense during sepsis. IMPACT STATEMENT: This study identifies galectin-3 as a critical regulator of phagosome acidification and bacterial clearance during sepsis. Loss of galectin-3 disrupts immune homeostasis, characterized by impaired intracellular bacterial killing and reduced IL-10 production, rather than a global increase in pro-inflammatory cytokines. These findings suggest that galectin-3 contributes to sepsis progression by modulating immunoregulatory balance and highlight its potential value for immune endotype stratification and therapeutic targeting.
AI-PlaNet: An Integrative Platform for Machine Learning-Based Discovery of Abiotic Stress-Responsive Genes in Cucurbit Crops.
Huang C
Biochem Genet · 2026 Mar · PMID 41880112 · Publisher ↗
Abiotic stress poses a significant threat to cucurbit crop productivity under climate change. While numerous transcriptomic datasets have been generated for cucumber, melon, and watermelon under drought, heat, and salt c...
Abiotic stress poses a significant threat to cucurbit crop productivity under climate change. While numerous transcriptomic datasets have been generated for cucumber, melon, and watermelon under drought, heat, and salt conditions, these data remain fragmented and difficult to interpret across species and stress types. Here, we present AI-PlaNet, a resource platform for multi-omics integration and machine learning–based discovery of stress-responsive genes in cucurbits. We curated and standardized 328 RNA-seq samples from nine independent studies and constructed co-expression networks to identify stress-associated modules. Through multi-species comparative analysis, we identified 134 conserved hub genes across drought, salt, and heat stress. Integrating metabolomic data further revealed transcription–metabolism coordination, particularly during key time points in drought response. Using gradient boosting models trained on promoter features, network metrics, and expression dynamics, we achieved high prediction accuracy (AUC = 0.94) for classifying core stress genes. SHAP analysis enabled interpretable feature attribution, highlighting ABRE motif density and hub connectivity as key predictors. AI-PlaNet includes an interactive visualization panel that links gene expression, co-expression context, and model-based priority scores. This platform provides a reusable and expandable framework for abiotic stress gene mining in cucurbits and offers valuable resources to support functional genomics and stress-resilient breeding strategies.
Novel Models to Predict Pregnancy for Patients Receiving In-Vitro-Fertilization Embryo Transfer: The Significance of Clinical Indicators and Key Gene Expression in the Endometrium.
Shi C, Wang YB, Shen H … +4 more , Gao FM, Fu M, Chen X, Han HJ
Biochem Genet · 2026 Mar · PMID 41870819 · Publisher ↗
This study aimed to discover key genes associated with the in-vitro-fertilization embryo transfer (IVF‑ET) outcomes and develop new prediction models, as well as potential drugs. We enrolled the following infertile women...
This study aimed to discover key genes associated with the in-vitro-fertilization embryo transfer (IVF‑ET) outcomes and develop new prediction models, as well as potential drugs. We enrolled the following infertile women who received IVF-ET between Sep 8, 2018, and Oct 19, 2021. The endometrial biopsy was performed for RNA sequencing. The differentially expressed genes (DEGs) were identified, based on which two models were developed for prediction of clinical pregnancy and live birth. Besides, we screened key pregnancy-lower and pregnancy-higher genes and identified candidate drugs that modulate the expression of key genes. Overall, 147 patients received IVF-ET, including 92 patients in the pregnancy group and 55 in the no-pregnancy group. We initially identified 180 differentially expressed genes (DEGs) between pregnancy and no-pregnancy groups, including 131 pregnancy-lower and 49 pregnancy-higher genes. After covariate-adjusted sensitivity analyses (age, RIF status, right-side AFC, and cycle type), 168 of these DEGs (93.3%) remained significant with consistent effect direction, and this 168-gene panel was used for all downstream predictive modelling and drug-repositioning analyses. Using the expression level of 17 genes and one clinical feature (recurrent implantation failure history), we developed a logistic regression model that achieved an apparent 100% classification accuracy in this internal dataset. Another live-birth prediction model was constructed using the expression of 20 genes and three clinical features (ovulation disorder, antral follicle count on the right side, and primary infertility), which also reached an apparent 100% accuracy in this internal cohort. Lastly, we screened key risk genes for drug mining, and four drugs may be beneficial for IVF‑ET: cyclosporine, acetaminophen, tretinoin, and estradiol. Combining key genes and clinical features, we developed two models with satisfactory apparent accuracy for predicting pregnancy and live birth. Based on the key genes, we further proposed four candidate drugs (cyclosporine, acetaminophen, tretinoin, and estradiol) that may have potential to improve IVF-ET outcomes and warrant further validation.
Genome-Wide Characterization of β-Glucosidase (TaBGLU) Genes in Bread Wheat and Their Expression Under Drought, Cold, and Combined Stress.
Alwutayd KM, Shami A, Alqudah AM … +1 more , Thabet SG
Biochem Genet · 2026 Mar · PMID 41854831 · Publisher ↗
Glycoside hydrolase 1 (GH1) β-glucosidases were known to activate hormone conjugates and defense metabolites, yet their genomic organization and stress-response dynamics in wheat remained incompletely defined. We therefo...
Glycoside hydrolase 1 (GH1) β-glucosidases were known to activate hormone conjugates and defense metabolites, yet their genomic organization and stress-response dynamics in wheat remained incompletely defined. We therefore performed an integrated characterization of TaBGLUs spanning phylogeny, gene structure and conserved motifs, subcellular localization, promoter cis-elements, Gene Ontology enrichment, protein-protein interaction networks, and targeted expression profiling. Wheat TaBGLUs partitioned into well-supported clades that shared canonical GH1 catalytic residues and a largely conserved motif scaffold. Subcellular localization predictions indicated predominant nuclear and chloroplast targeting, with a smaller cohort directed to secretory or endomembrane compartments. Promoters were enriched for light-responsive, hormone-related (ABA, JA/SA, auxin, GA) and stress-associated (MYB/WRKY, heat, low temperature) cis-elements, and functional annotations were consistent with roles in carbohydrate and cell-wall metabolism, hormone homeostasis, and defense. Network analysis revealed a densely connected TaBGLU submodule embedded within broader carbohydrate and defense interaction networks, suggesting coordinated or cooperative functions. Expression profiling under cold, drought, and combined drought and cold demonstrated broad stress inducibility, with early activation detected by 6 h, cold-responsive maxima typically at 12 h, drought-responsive peaks predominating at 24 h, and combined stress eliciting both earlier and more sustained expression maxima between 12-24 h. Representative strongly responsive genes included TaBGLU20, TaBGLU44, TaBGLU6, and TaBGLU23, which showed pronounced late induction under combined stress, TaBGLU30, which exhibited an earlier combined-stress peak, and TaBGLU12, which displayed a marked late drought-specific response. Taken together, this integrated genomic, regulatory, and expression atlas refined the wheat BGLU repertoire relative to previous gene model inventories, highlighted candidate TaBGLUs with central network positions and strong stress inducibility, and provided concrete entry points for functional validation and breeding for improved stress resilience.
The Biochemical and Genetic Effects of Lavandula angustifolia and Medical Ozone Treatments on Acute Liver Toxicity.
Taş İZ, Kolcuoğlu D, Tükenmez M … +5 more , Altiner N, Acar E, Çolak E, Sari İ, Öner Ç
Biochem Genet · 2026 Mar · PMID 41854830 · Publisher ↗
This study aimed to investigate the effects of Lavandula angustifolia oil and medical ozone on the gene expressions of CYP1A1, CYP1A2, CYP2B1, and CYP3A1, as well as on the levels of Malondialdehyde (MDA), and the activi...
This study aimed to investigate the effects of Lavandula angustifolia oil and medical ozone on the gene expressions of CYP1A1, CYP1A2, CYP2B1, and CYP3A1, as well as on the levels of Malondialdehyde (MDA), and the activities of Superoxide Dismutase (SOD) and Catalase (CAT) enzymes on acute liver toxicity. Experimental groups were established by separating 10-week-old 28 Wistar male rats, each weighing between 350 and 450 g, into four groups of seven rats each. Gene expression levels were determined using RT-qPCR. MDA measured in the tissue samples by the thiobarbituric acid method. SOD and CAT enzyme activities measured spectrophotometrically. CYP1A1 fold regulation significantly decreased in the Lavandula (p = 0.012), and medical ozone (p = 0.044) groups compared to the control group. However, changes in the combination group were not statistically significant compared to the control group (p = 0.133). There were no significant differences in the fold regulations of CYP1A2, CYP2B1, and CYP3A1 among any groups (p > 0.05). MDA levels were significantly lower in the Lavandula, and medical ozone groups compared to the control group (p = 0.001). CAT enzyme activity did not show significant differences in the Lavandula (p = 0.096) and medical ozone groups (p = 0.103) but decreased significantly in the combination group (p = 0.031). SOD enzyme activity did not show significant differences among the groups (p = 0.112). Lavandula and medical ozone treatments significantly reduced CYP1A1 gene expression and MDA levels, which may indicate their potential in reducing oxidative stress. These findings highlight the complexity of combined therapies and suggest possible interactions or suppressive effects between the agents, which have not been previously reported.
Comparative Evaluation of Floral Traits, Color Coordinates, and Bioactive Potential in Crossandra (Crossandra infundibuliformis L.) Genotypes.
Mahesh Reddy D, Safeena SA, Arivalagan M … +5 more , Srinivas PT, Naveen Kumar P, Chandrashekar N, Sonavane P, Monika GC
Biochem Genet · 2026 Mar · PMID 41838260 · Publisher ↗
Crossandra (Crossandra infundibuliformis L.) is an important ornamental crop widely cultivated for its aesthetic appeal, loose flower and use in traditional medicine. Wide variability exits among crossandra genotypes, pr...
Crossandra (Crossandra infundibuliformis L.) is an important ornamental crop widely cultivated for its aesthetic appeal, loose flower and use in traditional medicine. Wide variability exits among crossandra genotypes, primarily in flower color, and pigment content. In the present study, sixteen Crossandra genotypes were evaluated floral morphological traits, CIELAB color coordinates, total carotenoid content, total phenolic content (TPC), total flavonoid content (TFC), and antioxidant potential (DPPH and FRAP assays). Significant variability was observed across genotypes for flower length (3.03–4.58 cm), flower diameter (1.22–3.77 cm), and 100 flower fresh weight (3.01–8.32 g). Color parameters (L*, a*, b*, hue, and chroma) showed vide variation, reflecting differences from pale greenish to dark orange petals. The total carotenoid content ranged from 0.12 to 11.20 mg/g dry weight and was positively correlated with color intensity. TPC varied between 32.99 and 78.51 mg GAE/g, and the TFC ranged from 9.60 to 25.01 mg CE/g. The antioxidant activity also showed significant variation. Correlation analysis revealed strong positive relationships between antioxidant potential and phenolic/flavonoid content. Principal component analysis (PCA) revealed three major components explaining 92.41% of the total variance, separating floral morphology, pigmentation, and phytochemical traits. Two-way hierarchical clustering grouped genotypes into distinct clusters, effectively differentiated ornamental traits from biochemical traits. These findings offer valuable insights for the targeted selection of crossandra genotypes for ornamental breeding or functional applications as a natural source of antioxidants and bioactive compounds.
HIF-1α and YBX1 Mediated Up-Regulation of NonO/p54nrb in Prostate Cancer Cells.
Aydoğan Türkoğlu S, Baysal S, Ercevahir M … +3 more , Poyrazli F, Yeşildirek YV, Köçkar F
Biochem Genet · 2026 Mar · PMID 41824197 · Publisher ↗
This study examines the effect of hypoxia, a pivotal factor in prostate carcinogenesis, on the cellular roles of NonO/p54nrb and YBX1 proteins. NonO/p54nrb is a part of the paraspeckle protein, a nuclear domain that is e...
This study examines the effect of hypoxia, a pivotal factor in prostate carcinogenesis, on the cellular roles of NonO/p54nrb and YBX1 proteins. NonO/p54nrb is a part of the paraspeckle protein, a nuclear domain that is encoded by the NONO gene in humans and has been demonstrated to interact with the Androgen receptor, SFPQ, and SPI1. In the nucleus, NonO/p54nrb is involved in a variety of processes, such as transcription initiation, RNA processing, transcription elongation, and termination while YBX1, binds to both DNA and RNA. Elevated levels of YBX1 and HIF-1α have been observed in prostate carcinoma. The expression profile of NonO/p54nrb was assessed using sqRT-PCR in HUVEC and a panel of nine diverse cancer cell lines from various tissues (prostate, breast, colon, liver, pancreas, and bone). The PC3 prostate cancer cell line exhibited the highest level of NonO/p54nrb expression. A hypoxic microenvironment was successfully induced with the mimetic agent CoCl2, with its confirmation obtained by quantifying HIF-1α mRNA levels via Real-Time PCR. To assess the activity of the NonO/p54nrb promoter, a series of 5’ deletion constructs − 730/+529; -516/+529; -336/+529 and − 159/+529 were cloned into the pMetLuc luciferase vector. The basal transcriptional activity of NonO/p54nrb promoter constructs increased under hypoxic conditions at 48 h. Hypoxic up-regulation was also observed at both mRNA and protein levels. The study also analyzed the effect of exogenously produced YBX1 transcription factor on NonO/p54nrb mRNA and protein levels. An upregulation was also observed in all YBX1-transfected promoter fragments. The findings from our study indicate that NonO/p54nrb is transcriptionally upregulated by HIF-1 in PC-3 cell line. Furthermore, the YBX1 transcription factor enhances NonO/p54nrb expression under both normoxic and hypoxic conditions, with a more pronounced increase observed specifically during hypoxia.
MiR-342-3p Attenuates Inflammation and Pyroptosis in Severe Community-Acquired Pneumonia by Targeting EP300.
Song B, Xu R, Cui C … +3 more , Rao S, Liu Y, Yang Y
Biochem Genet · 2026 Mar · PMID 41824196 · Publisher ↗
Community-acquired pneumonia (CAP), particularly severe CAP (SCAP), poses a significant clinical challenge with high mortality. MicroRNAs, including miR-342-3p, have been implicated in various pulmonary diseases, suggest...
Community-acquired pneumonia (CAP), particularly severe CAP (SCAP), poses a significant clinical challenge with high mortality. MicroRNAs, including miR-342-3p, have been implicated in various pulmonary diseases, suggesting a potential role in SCAP. To examine the expression, functional mechanisms, and clinical relevance of miR-342-3p in SCAP. Bioinformatic analysis was performed on two independent GEO datasets (GSE196399 and GSE136390). Serum miR-342-3p levels were measured in a clinical cohort of 109 SCAP patients and 109 healthy controls by RT-qPCR, and its correlation with clinical prognosis was analyzed. An in vitro pneumonia model was established using LPS-stimulated MRC-5 cells. Gain-of-function experiments of miR-342-3p were achieved through mimic transfection. MiR-342-3p's involvement in inflammation, cytotoxicity, and pyroptosis was assessed via ELISA, western blot, CCK-8, and LDH assays. The interaction between miR-342-3p and EP300 was confirmed by dual-luciferase reporter and RNA pull-down assays, and its functional role was confirmed through rescue experiments. The downregulation of miR-342-3p in SCAP patient serum correlated with increased mortality. In vitro, miR-342-3p overexpression reduced LPS-induced inflammation and pyroptosis. Bioinformatics analysis confirmed that histone acetyltransferase EP300 is a candidate target gene for miR-342-3p. Mechanistically, miR-342-3p directly targeted and negatively regulated EP300. Overexpression of EP300 abolished the anti-inflammatory and anti-pyroptotic effects of miR-342-3p through the activation of NF-κB p65. MiR-342-3p acts as a protective factor in SCAP by targeting EP300 to inhibit inflammation and pyroptosis. These results indicate the potential of miR-342-3p as a biomarker and therapeutic target in SCAP.
Investigation of Fatty Acid Metabolism-Associated Molecular CPOX and the Underlying Mechanism in Follicular Lymphoma.
He J, Wang F, Shen C … +1 more , Zhang K
Biochem Genet · 2026 Mar · PMID 41811681 · Publisher ↗
Dysregulated lipid metabolism is a key driver of follicular lymphoma (FL). This study aimed to explore the lipid metabolism-related genes (LMRGs) and clarify the underlying roles and mechanisms in FL. Bioinformatics meth...
Dysregulated lipid metabolism is a key driver of follicular lymphoma (FL). This study aimed to explore the lipid metabolism-related genes (LMRGs) and clarify the underlying roles and mechanisms in FL. Bioinformatics methods, including differential analysis, WGCNA, machine learning, and Mendelian randomization, were utilized to select the LMRGs in FL. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to investigate the function of the key LMRG. Receiver operator characteristic (ROC) was used to evaluate the diagnostic value of the key gene CPOX. A pan-cancer analysis investigated CPOX's expression level and immune correlations. In vitro experiments using FL cell lines (WSU-FSCCL, DOHH2) validated CPOX expression, and CPOX knockdown in DOHH2 cells was used to assess its impact on viability, migration, invasion, and fatty acid metabolism. CPOX was confirmed to be a risk factor, significantly overexpressed in FL, and exhibited effective diagnostic ability in FL (AUC = 0.731). Functional analysis linked CPOX to mitochondrial function, oxidative phosphorylation, and heme metabolic process. Pan-cancer indicated the dysregulated CPOX across multiple cancers and closely correlation with immune characteristics. Experimentally, CPOX was higher in the more invasive DOHH2 cells; and CPOX knockdown suppressed FL progression and reduced lipid droplet formation, triglyceride, total cholesterol, and free fatty acid levels. In conclusion, this study fills the gap in understanding the significance of lipid metabolism-related molecules in FL, and innovatively proposes that CPOX is a risk factor for FL. Knockdown of CPOX inhibits the FL progression, which is regulated by fatty acid metabolism.
Unveiling the Link Between Expression of Aspartate Kinase2 (ask2) Gene and Accumulation of Methionine in Developing Maize Kernels.
Duo H, Chhabra R, Zunjare RU … +4 more , Sharma G, Mishra SJ, Muthusamy V, Hossain F
Biochem Genet · 2026 Mar · PMID 41803573 · Publisher ↗
Traditional maize grains, used in human diets and animal feeds, are deficient in methionine (an essential amino acid), which severely affects growth and development. Aspartate kinase2 (ask2) gene plays a pivotal role in...
Traditional maize grains, used in human diets and animal feeds, are deficient in methionine (an essential amino acid), which severely affects growth and development. Aspartate kinase2 (ask2) gene plays a pivotal role in the accumulation of methionine in maize kernels. Here, we studied the temporal expression dynamics of ask2 gene and accumulation of methionine in maize kernel among inbreds with the mutant (ask2) and wild-type (ask2) allele at 20-, 30- and 40-days after pollination (DAP). The inbreds (PMI-PV5-ask2 and PMI-PV6-ask2) with mutant ask2 gene were developed through marker-assisted introgression into two elite inbreds (PMI-PV5 and PMI-PV6) with wild-type (ask2) allele. An average of 4.30-fold change was observed among ask2 mutant inbreds over inbreds possessing the wild-type ask2 allele at 20-DAP.. Gene expression of ask2 gene showed decreasing pattern with peak expression at 20-DAP (0.255) and decreases towards 30- (0.072) and 40-DAP (0.030). The ask2-based inbreds showed higher methionine (0.370% in flour) over original versions (0.346% in flour) at 20-DAP. DAP contributed the most (77.29%) to total variance for methionine, followed by genotype (17.68%) and genotype × DAP interaction (3.95%). The highest accumulation of methionine was observed at 20-DAP (0.354%) and decreased at 30-DAP (0.255%), with the least at 40-DAP (0.219%). Strong positive correlation (r = 0.763, p < 0.01) was observed between the transcript abundance and methionine accumulation over the kernel growth stages. Results revealed deeper insights into the regulation and accumulation of methionine in maize endosperm. This is the first report on the expression dynamics of ask2 gene and its association with accumulation of methionine across developmental stages of maize kernel. The results assume great significance in the pursuit to develop high methionine maize cultivars to alleviate protein energy malnutrition, especially in developing countries.
Endothelial Cell Differentiation-Related CircRNAs Drive the Differentiation of Vascular Endothelial Cells.
Sun Y, Yin Z, Huang Y … +4 more , Chen Y, Yin H, Zhang Y, Jin W
Biochem Genet · 2026 Mar · PMID 41779083 · Publisher ↗
The emergence and progression of a range of cardiovascular and cerebrovascular conditions are linked to endothelial dysfunction. Nevertheless, the specific pathways leading to damage in vascular endothelium remain to be...
The emergence and progression of a range of cardiovascular and cerebrovascular conditions are linked to endothelial dysfunction. Nevertheless, the specific pathways leading to damage in vascular endothelium remain to be elucidated. This study aimed to investigate the function and mechanisms of endothelial cell differentiation-related circular RNAs (circRNAs) in the differentiation of vascular endothelial cells. First, we screened for differentially expressed circRNAs (DECs) and genes (DEGs) during the differentiation of induced pluripotent stem cells (iPSCs) into endothelial cells, using human umbilical vein endothelial cells (HUVECs) as a reference model. Next, we predicted miRNAs associated with DECs and identified core genes related to the differentiation of stem cells into endothelial cells. Then, we verified the expression of endothelial cell differentiation-related circRNAs and the competing endogenous RNA (ceRNA) axis at the cellular and organoid level. Finally, we explored the ceRNA regulatory axis. Six core genes were initially identified, but we focused on a disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9). At the cellular level, hsa_circ_0000010, hsa_circ_0005875, hsa_circ_0090122, and ADAMTS9 mRNA and protein levels were significantly increased in the HUVEC group, while hsa_circ_0000161, hsa_circ_0002824, hsa_circ_0074944, TXNIP mRNA, hsa-miR-548az-5p, and hsa-miR-548t-5p levels were significantly decreased compared to the iPSC group. At the organoid level, during the differentiation of stem cells into endothelial cells, hsa_circ_0090122 and ADAMTS9 mRNA and protein levels were increased, while hsa-miR-548az-5p and hsa-miR-548t-5p levels were decreased. Among the candidates, hsa_circ_0090122 and its related miRNAs (hsa-miR-548az-5p/hsa-miR-548t-5p) were prioritized because their expression changes were the most pronounced and directionally consistent with ADAMTS9, both in bioinformatic screening and validation experiments. Hsa_circ_0090122 may play a significant role in driving endothelial differentiation by regulating ADAMTS9 expression through competitive interaction with hsa-miR-548az-5p and hsa-miR-548t-5p.
Silencing of HAVCR2 Attenuates Skeletal Muscle Ischemia-Reperfusion Injury by Inhibiting Oxidative Stress.
Wang H, Li P, Xiong X … +1 more , Gao Y
Biochem Genet · 2026 Mar · PMID 41779082 · Publisher ↗
Skeletal muscle ischemia-reperfusion (IR) injury is a common clinical condition associated with oxidative stress and inflammation that leads to muscle damage and multi-organ failure. However, the molecular mechanisms und...
Skeletal muscle ischemia-reperfusion (IR) injury is a common clinical condition associated with oxidative stress and inflammation that leads to muscle damage and multi-organ failure. However, the molecular mechanisms underlying its pathogenesis remain incompletely understood. R software and the limma package were used to analyze mRNA expression profiles from the GSE275811 dataset. Hub genes were identified using the protein-protein interaction (PPI) network, support vector machine-recursive feature elimination (SVM-RFE), and least absolute shrinkage and selection operator (LASSO) regression analysis, and their diagnostic performances were assessed using receiver operating characteristic (ROC) curves. The roles of hepatitis A virus cellular receptor 2 (HAVCR2) were explored in IR-induced Sprague-Dawley rat models and in vitro hypoxia-reoxygenation (HR)-treated human umbilical vein endothelial cells (HUVECs). A total of 188 differentially expressed genes (DEGs) were screened, primarily enriched in pathways associated with immune responses and inflammation regulation. CX3CR1, HAVCR2, IL1B, LYZ2, and PTPRC were identified as key genes with potential to distinguish between normal and IR samples. HAVCR2 silencing alleviated rat muscle fiber disruption, inflammatory infiltration, and oxidative stress, with reduced levels of ROS, MDA, IL-6, and TNF-α and elevated levels of GSH, SOD, MnSOD, and CAT. Similarly, HAVCR2 knockdown conferred protective effects in HUVECs subjected to HR injury, improving cell viability, enhancing migratory ability, and restoring antioxidant defenses. HAVCR2 knockdown inhibited oxidative stress in the skeletal muscle IR, suggesting that targeting HAVCR2 represents a promising therapeutic strategy for skeletal muscle IR injury.
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