Biochemical Genetics最新文献

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Understanding the Role of MicroRNAs in Congenital Tooth Agenesis: A Multi-omics Integration.
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-02-22 DOI: 10.1007/s10528-025-11064-9
Prashant Ranjan, Chandra Devi, Neha Verma, Rajesh Bansal, Vinay Kumar Srivastava, Parimal Das
{"title":"Understanding the Role of MicroRNAs in Congenital Tooth Agenesis: A Multi-omics Integration.","authors":"Prashant Ranjan, Chandra Devi, Neha Verma, Rajesh Bansal, Vinay Kumar Srivastava, Parimal Das","doi":"10.1007/s10528-025-11064-9","DOIUrl":"https://doi.org/10.1007/s10528-025-11064-9","url":null,"abstract":"<p><p>This study employs a comprehensive multi-omics approach to investigate the regulatory roles of specific microRNAs (miRNAs) in Congenital Tooth Agenesis (CTA). A total of 58 miRNAs associated with tooth diseases, cancer, and bone development were initially identified through a literature review and analyzed using bioinformatics. Based on target prediction and network analysis, eight miRNAs with strong connectivity and common target genes were shortlisted for further investigation. Blood samples from 10 CTA patients and 5 healthy controls were analyzed for miRNA expression using stem-loop RT-PCR. Four miRNAs-hsa-miR-218-5p, hsa-miR-15b-5p, hsa-miR-200b-3p, and hsa-let-7a-3p-were identified as significantly differentially expressed, marking their first reported involvement in CTA. Notably, hsa-miR-218-5p and hsa-let-7a-3p emerged as novel regulators with no prior associations with CTA or tooth development. To address the limitations of a small sample size, a multi-omics strategy was employed to validate these findings, integrating miRNA expression data with whole exome sequencing (WES), gene expression panels, and metabolomic profiling. The analysis confirmed the association of these four miRNAs with CTA and highlighted their involvement in critical biological pathways such as Wnt signaling, FGF signaling, and PI3 kinase pathways, which are essential for cellular proliferation, differentiation, and tissue morphogenesis. Importantly, the identification of these miRNAs in blood samples, rather than traditional dental tissues, highlights a minimally invasive approach that could aid in the early detection, therapeutic targeting, and personalized management of dental anomalies.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Levels of Talin1 in Platelet-Derived Microvesicles Affect Platelet Activation in Patients with Nonvalvular Atrial Fibrillation.
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-02-21 DOI: 10.1007/s10528-025-11060-z
Zhen Liu, Jun Yang, Hongping Chen, Lihui Zhang
{"title":"Levels of Talin1 in Platelet-Derived Microvesicles Affect Platelet Activation in Patients with Nonvalvular Atrial Fibrillation.","authors":"Zhen Liu, Jun Yang, Hongping Chen, Lihui Zhang","doi":"10.1007/s10528-025-11060-z","DOIUrl":"https://doi.org/10.1007/s10528-025-11060-z","url":null,"abstract":"<p><p>This study evaluated talin1 expression in platelets and platelet-derived microvesicles (PMVs) from nonvalvular atrial fibrillation (NVAF) patients. Meanwhile, this study analyzed the impacts of talin1 expression in PMVs on platelet activation. Twelve healthy controls and 38 NVAF patients were recruited in this study. The levels of talin1 and RAP1B activation were observed in the platelets and PMVs from the participants, and their levels were significantly increased in the NVAF patients compared to the healthy controls (P < 0.01). Talin1 silence in MEG-01 cells was obtained by transfecting talin1 siRNA, and the cells were stimulated by thrombin receptor-activating peptide 6 (TRAP-6) to induce platelet-dense granule secretion. TRAP-6 stimulation increased the talin1 expression and RAP1B activation in the platelet-like particles from MEG-01 cells, but talin1 silence suppressed the TRAP-6-stimulated RAP1B activation and CD62p expression in the platelet-like particle. Moreover, the platelets from healthy donors were activated by the PMVs from the TRAP-6-stimulated MEG-01 cells. However, the decreased talin1 level in the PMVs from MEG-01 cells weakened the platelet activation. This study suggested that talin1 expression in the PMVs affected platelet activation in patients with NVAF.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Study the Expression of Two Circular RNAs, hsa_circ_0003227 and hsa_circ_0001666, in the Primary Breast Cancer Cell Line BT-20 and the Metastatic Breast Cancer Cell Line MCF-7.
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-02-20 DOI: 10.1007/s10528-025-11051-0
Safura Absalan, Hamidreza Vaziri, Mahvash Hadavi
{"title":"Study the Expression of Two Circular RNAs, hsa_circ_0003227 and hsa_circ_0001666, in the Primary Breast Cancer Cell Line BT-20 and the Metastatic Breast Cancer Cell Line MCF-7.","authors":"Safura Absalan, Hamidreza Vaziri, Mahvash Hadavi","doi":"10.1007/s10528-025-11051-0","DOIUrl":"https://doi.org/10.1007/s10528-025-11051-0","url":null,"abstract":"<p><p>Breast cancer is one of the most prevalent cancers globally and remains a significant cause of cancer-related mortality among women despite advancements in early detection and treatment. The heterogeneity of breast cancer arises from a complex interplay of genetic and environmental factors. Early-stage breast cancer is often asymptomatic, with initial signs including subtle changes in breast morphology and localized swelling, emphasizing the need for reliable diagnostic tools for early detection. Recent research has highlighted the potential of molecular biomarkers, particularly non-coding RNAs such as circular RNAs (circRNAs), in cancer diagnosis. CircRNAs, a unique subset of non-coding RNAs, are characterized by their covalently closed-loop structure, which confers exceptional stability and resistance to exonuclease degradation. They are present in various body fluids and have demonstrated regulatory roles in transcription, translation, and as microRNA sponges, making them promising candidates for cancer diagnostics and prognostics. This study focuses on evaluating the diagnostic potential of two circRNAs, hsa_circ_0001666 and hsa_circ_0003227, by examining their expression in normal, tumor, and metastatic breast cancer cell lines. Breast cancer cell lines representing normal (MCF-10A), tumor (MCF-7), and metastatic (BT-20) stages were cultured for analysis. Total RNA was extracted using a column-based RNA extraction kit, and RNA quality was assessed through NanoDrop spectrophotometry and agarose gel electrophoresis. Complementary DNA (cDNA) synthesis was performed using random hexamers, and the expression levels of hsa_circ_0001666 and hsa_circ_0003227 were quantified using Real-Time Quantitative Reverse Transcription PCR (RT-qPCR), with beta-actin serving as the internal control. Statistical analyses were conducted using SPSS software to evaluate differences in expression levels across cell lines. A significant downregulation of hsa_circ_0001666 and hsa_circ_0003227 was observed in tumor and metastatic cell lines compared to normal breast cell lines (P < 0.05). These results suggest that the expression of these circRNAs correlates with the progression of breast cancer, with decreased levels observed as cells transition from normal to tumorigenic and metastatic stages. The findings of this study indicate that hsa_circ_0001666 and hsa_circ_0003227 have potential utility as diagnostic biomarkers for breast cancer. Their significant expression changes across different stages of breast cancer highlight their relevance in early detection and disease monitoring. This study reinforces the potential of RNA-based biomarkers, particularly circRNAs, in cancer diagnosis and treatment. However, in vitro findings require validation in clinical samples and larger cohorts. Future research should explore their roles in breast cancer progression and integration into non-invasive diagnostics.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Complete Mitochondrial Genomes of Babylonia spirata and Babylonia zeylanica (Neogastropoda: Babyloniidae) Provide New Insights into Neogastropoda Phylogeny.
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-02-20 DOI: 10.1007/s10528-025-11055-w
Li Wu, Hongwei Huang, Huai Yang, Yingying Ye, Baoying Guo, Weifeng Wang
{"title":"The Complete Mitochondrial Genomes of Babylonia spirata and Babylonia zeylanica (Neogastropoda: Babyloniidae) Provide New Insights into Neogastropoda Phylogeny.","authors":"Li Wu, Hongwei Huang, Huai Yang, Yingying Ye, Baoying Guo, Weifeng Wang","doi":"10.1007/s10528-025-11055-w","DOIUrl":"https://doi.org/10.1007/s10528-025-11055-w","url":null,"abstract":"<p><p>The genus Babylonia, classified under Mollusca, Gastropoda, Neogastropoda, has been a subject of controversy concerning the phylogenetic relationships within Neogastropoda, a highly intricate group of predatory marine snails. In this study, we sequenced complete mitogenomes of Babylonia spirata and Babylonia zeylanica. Both mitogenomes consist of 37 genes, including 13 PCGs, 22 tRNAs, and 2 rRNAs, which is consistent with the gene numbers observed in most neogastropod snails. We analyzed base content, codon usage preference, and tRNA structure to describe the basic structural features. Additionally, phylogenetic trees were constructed using Maximum Likelihood and Bayesian Inference based on the complete mitogenomes of 43 Neogastropoda species. This analysis revealed that all 19 families formed monophyletic groups, collectively constituting seven monophyletic superfamilies. Moreover, by analyzing the gene arrangement characteristics of these 43 Neogastropoda species, we identified four distinct types of mitochondrial genome arrangements. This study strongly supports the monophyly of Neogastropoda families, contradicting previous molecular studies and providing fundamental insights for further phylogenetic studies in Neogastropoda.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Benazepril Promotes the Proliferation and Differentiation of Urine-Derived Stem Cells from Children with Nephrotic Syndrome During the Chronic Kidney Disease Stage.
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-02-19 DOI: 10.1007/s10528-025-11056-9
Chengqiang Huang, Yuan Yang, Cheng Li, Ling Guo, Ming Liu, Geng Xiong
{"title":"Benazepril Promotes the Proliferation and Differentiation of Urine-Derived Stem Cells from Children with Nephrotic Syndrome During the Chronic Kidney Disease Stage.","authors":"Chengqiang Huang, Yuan Yang, Cheng Li, Ling Guo, Ming Liu, Geng Xiong","doi":"10.1007/s10528-025-11056-9","DOIUrl":"https://doi.org/10.1007/s10528-025-11056-9","url":null,"abstract":"<p><p>Nephrotic Syndrome (NS), especially in the Chronic Kidney Disease (CKD) stage, poses significant challenges in pediatric nephrology. Urine-derived stem cells (USCs) show promise for renal repair and regeneration. While benazepril is commonly used to treat CKD, its impact on USCs from children with NS during the CKD stage is unclear. USCs were isolated from the urine of 6 healthy children and 6 with NS (CKD stage), cultured through passages, and their morphology and cell surface markers were assessed microscopically and by flow cytometry, respectively. USCs were treated with benazepril at concentrations of 1, 10, 20, 40 μmol/L, and proliferation was evaluated using the CCK-8 assay. ROS levels were measured using DCFH-DA probe, and the expression levels of IL-1β, Connexin 43, AEC, ACE2, Ang2, AQP-1 and E-cadherin were analyzed by Western Blot. Tubular epithelial cell differentiation was also examined. USCs could be cultured from both healthy and NS (CKD stage) children, but USCs from NS children only reached passage 5 and exhibited weaker proliferation and differentiation abilities compared to those from healthy children. IL-1β, Connexin 43, ROS,ACE and Ang2 levels were higher in USCs from NS children than in those from healthy children, while ACE2 showed the opposite trend. Treatment with 1 μmol/L benazepril enhanced the proliferation and differentiation ability of USCs from NS children, inhibiting the level of inflammation factors, ROS, ACE and Ang2 while promoting ACE2 expression in these cells. This study offers valuable insights for future USCs applications.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification and Co-expression Analysis of Differentially Expressed LncRNAs and mRNAs Regulate Intramuscular Fat Deposition in Yaks at Two Developmental Stages.
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-02-19 DOI: 10.1007/s10528-025-11046-x
Zhanhong Gao, Quyangangmao Su, Sayed Haidar Abbas Raza, Cristian Piras, Mona N BinMowyna, Majid Al-Zahrani, Charalampos Mavromatis, Raafat T M Makhlof, Mustafa M Senna, Linsheng Gui
{"title":"Identification and Co-expression Analysis of Differentially Expressed LncRNAs and mRNAs Regulate Intramuscular Fat Deposition in Yaks at Two Developmental Stages.","authors":"Zhanhong Gao, Quyangangmao Su, Sayed Haidar Abbas Raza, Cristian Piras, Mona N BinMowyna, Majid Al-Zahrani, Charalampos Mavromatis, Raafat T M Makhlof, Mustafa M Senna, Linsheng Gui","doi":"10.1007/s10528-025-11046-x","DOIUrl":"https://doi.org/10.1007/s10528-025-11046-x","url":null,"abstract":"<p><p>Intramuscular fat (IMF) content is a key indicator of yak meat quality. This study aimed to identify lncRNAs that regulate IMF deposition in yaks. Three male calf yaks (3 months) and three male adult yaks (3 years) were used in the current study. After slaughter, the tissue morphology of the longissimus dorsi (LD) muscle was assessed using a cry-sectioning technique and differentially expressed lncRNAs and mRNAs (DELs and DEMs) were identified using RNA-Seq technology. The diameter and volume of fat droplets were significantly larger and bigger, respectively, in adults than in calves (P < 0.001). A total of 37,790 genes and 16,400 lncRNAs that regulate fat deposition were identified. Among them, 2327 mRNAs and 474 lncRNAs were differentially expressed between calves and adult yaks. DEGs stearoyl-CoA desaturase (SCD), fatty acid synthase (FASN), fatty acid binding protein 4 (FABP4) and fibronectin 1 (FN1) and DELs MSTRG.15795.4 and MSTRG.35028.6 were screened. The enrichment and pathway analysis regulated by the DMEs and DELs were predicted. We found significantly enriched biological processes and pathways involved in fat deposition, including the biosynthesis of unsaturated fatty acids, fatty acid biosynthesis, fatty acid elongation, and the mTOR signaling pathway. Co-expression network of the DELs and related genes, including MSTRG.10268.1-placenta associated 8 (PLAC8), MSTRG.16223.1-galectin 3 (LGALS3), MSTRG.34732.1-glycerol-3-phosphate acyltransferase, mitochondrial (GPAM), MSTRG.11907.11-fibroblast growth factor 1 (FGF1), MSTRG.34342.1-lipase A, lysosomal acid type (LIPA), and MSTRG.1667.2-integrin subunit beta 2 (ITGB2) was constructed. RT-qPCR verified the sequence results. The molecular regulatory mechanisms of lncRNAs on intramuscular fat deposition in yak were further explored.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ssc-miR-361-3p Suppresses Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Replication and Its In Vivo Expression in Mice.
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-02-19 DOI: 10.1007/s10528-025-11054-x
Qinchuan Zhang, Manyi Zhang, Xiao Qi, Jinliang Sheng, Yanming Sun, Yanbing Zhang
{"title":"ssc-miR-361-3p Suppresses Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Replication and Its In Vivo Expression in Mice.","authors":"Qinchuan Zhang, Manyi Zhang, Xiao Qi, Jinliang Sheng, Yanming Sun, Yanbing Zhang","doi":"10.1007/s10528-025-11054-x","DOIUrl":"https://doi.org/10.1007/s10528-025-11054-x","url":null,"abstract":"<p><p>Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically devastating diseases affecting the global pig industry. Host microRNAs directly target viral gene regions to exert their disease-fighting effects. PRRS virus (PRRSV) infection upregulates miR-361-3p expression; however, it is unclear whether it can exert inhibitory effects by directly targeting viral genes. Bioinformatic and experimental findings revealed that miR-361-3p inhibited PRRSV replication by directly targeting the PRRSV ORF1b and ORF1a loci. Intramuscular injection of pcDNA3.1-pri-miR-361 verified the expression of miR-361-3p in mammals. In summary, miR-361-3p plays an important role in infection and may be a promising therapeutic target for PRRS, providing insights into possible drug therapies.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Geniposide Inhibits Non-Small Cell Lung Cancer by Regulating Proliferation, Apoptosis, Invasion, Migration, Epithelial-Mesenchymal Transition, and Cancer Stem-Like Cell Property Via Wnt/β-Catenin Pathway.
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-02-18 DOI: 10.1007/s10528-025-11030-5
Haifa He, Yin Li, Yuan Wang, Man Li
{"title":"Geniposide Inhibits Non-Small Cell Lung Cancer by Regulating Proliferation, Apoptosis, Invasion, Migration, Epithelial-Mesenchymal Transition, and Cancer Stem-Like Cell Property Via Wnt/β-Catenin Pathway.","authors":"Haifa He, Yin Li, Yuan Wang, Man Li","doi":"10.1007/s10528-025-11030-5","DOIUrl":"https://doi.org/10.1007/s10528-025-11030-5","url":null,"abstract":"<p><p>Non-small cell lung cancer (NSCLC) is the leading cause of cancer death worldwide. Geniposide, an active compound of Gardeniae Fructus, has antithrombotic, antitumor, neuroprotective, hepatoprotective, cholestatic, and other effects. The present study aimed to investigate the effects of geniposide on NSCLC cells, as well as its underlying mechanism. Two NSCLC cell lines (H1975 and A549) were treated with different doses of geniposide. The proliferation, apoptosis, migratory and invasive capacities, epithelial-mesenchymal transition (EMT), and stem cell characteristics of NSCLC cells were evaluated using a series of in vitro experiments, including colony formation, flow cytometry, wound healing, transwell, western blotting, and tube formations assays. H1975 cells were subcutaneously injected into nude mice to establish the xenograft tumor models, and the models were intraperitoneally injected with 100 mg/kg geniposide or/and 6 mg/kg SKL2001, an agonist of Wnt pathway. Immunohistochemistry, immunofluorescence, and western blotting analyses of the tumors were performed. Geniposide restrained the proliferation of NSCLC cells, as shown by reduced number of colonies and downregulation of Ki67 and PCNA expression levels. Geniposide promoted apoptosis by reducing Bcl-2 expression and increasing Bax expression. Additionally, geniposide inhibited the migratory and invasive abilities of NSCLC cells as well as reversed the EMT by downregulating vimentin, N-cadherin, snail, and slug and upregulating E-cadherin in the absence or presence of TGF-β1. Furthermore, geniposide attenuated the stem cell characteristics of NSCLC cells. In mechanism, geniposide repressed the activation of Wnt/β-catenin pathway. SKL2001 reversed the anti-NSCLC effects of geniposide in vitro. In the xenograft tumor models, 100 mg/kg geniposide suppressed NSCLC tumor growth, which was reversed by SKL2001 treatment. Overall, geniposide inhibits NSCLC progression by reducing cancer cell proliferation, migration, invasiveness, EMT, and stem cell characteristics. This information might provide novel insights into the potential use of geniposide in lung cancer intervention.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comprehensive Codon Usage Analysis Across Diverse Plant Lineages.
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-02-18 DOI: 10.1007/s10528-025-11053-y
Aasim Majeed, Vikas Sharma, Wahid Ul Rehman, Amitozdeep Kaur, Sreemoyee Das, Josepheena Joseph, Amandeep Singh, Pankaj Bhardwaj
{"title":"Comprehensive Codon Usage Analysis Across Diverse Plant Lineages.","authors":"Aasim Majeed, Vikas Sharma, Wahid Ul Rehman, Amitozdeep Kaur, Sreemoyee Das, Josepheena Joseph, Amandeep Singh, Pankaj Bhardwaj","doi":"10.1007/s10528-025-11053-y","DOIUrl":"https://doi.org/10.1007/s10528-025-11053-y","url":null,"abstract":"<p><p>The variation of codon usage patterns in response to the evolution of organisms is an intriguing question to answer. This study investigated the relevance of the evolutionary events of vascularization and seed production with the codon usage patterns in different plant lineages. We found that the optimal codons of non-vascular lineages generally end with GC, whereas those of the vascular lineages end with AU. Correspondence analysis and model-based clustering showed that the evolution of the codon usage pattern follows the evolutionary event of the vascularization more precisely than that of the seed production. The dinucleotides CpG and TpA were under-represented in all the lineages, whereas the dinucleotide TpG was found over-represented in all the lineages, except algae. Evolutionary-related lineages showed similar codon pair bias. The dinucleotide CpA showed a similar representation as those of its parent codon pairs. Although natural selection predominates over mutational pressure in determining the codon usage bias, the relative influence of mutational pressure is higher in the non-vascular lineages than those in the vascular lineages.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
LncIMF1 Promotes Adipogenesis of Porcine Intramuscular Preadipocyte by Sponging miR-187.
IF 2.1 4区 生物学
Biochemical Genetics Pub Date : 2025-02-17 DOI: 10.1007/s10528-025-11061-y
Ming Feng, Xudong Yi, Ziyi Zhang, Jiahua Zhu, He Yu, Lianxi Ming, Weijun Pang
{"title":"LncIMF1 Promotes Adipogenesis of Porcine Intramuscular Preadipocyte by Sponging miR-187.","authors":"Ming Feng, Xudong Yi, Ziyi Zhang, Jiahua Zhu, He Yu, Lianxi Ming, Weijun Pang","doi":"10.1007/s10528-025-11061-y","DOIUrl":"https://doi.org/10.1007/s10528-025-11061-y","url":null,"abstract":"<p><p>Intramuscular fat, which is closely related to the traits of tenderness, juiciness, and flavor of pork, is regulated by numerous molecular regulatory mechanisms that have been regarded as an important agricultural research area. Long noncoding RNAs (lncRNAs) are emerging regulators involved in adipogenesis due to their functional diversity. In this study, we identified a novel lncRNA related to porcine adipogenesis, named lncIMF1, based on previous RNA sequencing results. Our results suggested that lncIMF1 was most abundantly expressed in adipose tissue and located in both the cytoplasm and nucleus. Besides, lncIMF1 promoted the proliferation and differentiation, while inhibited apoptosis of intramuscular preadipocytes. Moreover, lncIMF1 could act as a molecular sponge for miR-187, inhibiting the binding of miR-187 and SMAD1, thereby promoting the expression of SMAD1 and enhancing the adipogenic differentiation of intramuscular preadipocytes. Additionally, we found that lncIMF1-miR187-SMAD1 axis could activate the p38-mitogen-activated protein kinase (MAPK) pathway. Taken together, our study provided new insights into the role of lncRNAs in the regulation of pork quality.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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