Nucleosides, Nucleotides & Nucleic Acids最新文献

{"title":"Like pashtun like haplogroup.","authors":"Jabbar Khan, Zia Ur Rehman, Zafar Uddin, Zahid Rauf, Li Yuchun, Muzammil Ahmad Khan, Muhammad Muzammal","doi":"10.1080/15257770.2025.2482827","DOIUrl":"https://doi.org/10.1080/15257770.2025.2482827","url":null,"abstract":"<p><p>The hypervariable HVS-I and HVS-II regions of mitochondrial genome of 124 longevity individuals (age <b>≥</b> 90 years) and 46 non-longevity individuals (age <b>≤</b> 65 years) of purely Pashtun ethnicity were characterized for forensic purposes. Blood samples were collected from southern belt of Khyber Pakhtunkhwa (KP) province. For exploring the genetic architect of mitochondrial DNA of Pashtun longevity individuals. Sequence analysis revealed 16 major haplogroups and 56 sub-haplogroups in longevity persons and, 12 and 29 major and sub-haplogroups in non-longevity persons respectively. The 3 most common major haplogroups in longevity individuals were [M (25.0%), J (14.51%), D and U (13 = 10.48% each)], while in non-longevity human, these were [M (17.39%), H & T (15.21% each), and D (13.04%)]. Nineteen unique point mutations were identified not reported previously in reference sequence. More interestingly, the position of mutations found in non-longevity individuals were not observed in longevity individuals and vice versa. Data presented here may contribute to the accuracy of forensic mtDNA comparisons in the Pashtun of Pakistan. Social, cultural and unique territorial factors contribute to heterogeneous nature of Pashtun ethnic group.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-15"},"PeriodicalIF":1.1,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143701112","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}

{"title":"Research on correlations of miR-374a-5p expression with progression and prognosis of prostate cancer.","authors":"Ke Lv, Haiyan Pan, Hui Yao","doi":"10.1080/15257770.2025.2481947","DOIUrl":"https://doi.org/10.1080/15257770.2025.2481947","url":null,"abstract":"<p><p>Prostate cancer (PCa) is a frequently occurring malignant tumor affecting male reproductive system. miR-374a-5p was identified to participate in regulation of several tumors. The aim of the research was to discuss the influence for miR-374a-5p upon PCa progression and prognosis. A total of 112 PCa and 110 benign prostatic hyperplasia tissue samples were collected for the study. Real-time quantitative polymerase chain reaction was adopted to examine miR-374a-5p level in PCa tissues and cells. Kaplan-Meier and Cox model were applied to evaluate prognostic significance of miR-374a-5p for PCa. CCK8 and Transwell assays were carried out to analyze the efficacy of miR-374a-5p in PCa cell proliferation, migration and invasion. miR-374a-5p was under-expressed in PCa tissues and cells. Low expression of miR-374a-5p is linked to less favorable prognosis in PCa sufferers. Additionally, Cox analysis revealed that miR-374a-5p and TNM stage were two independent prognostic factors for PCa. Cellular assays showed that upregulating miR-374a-5p suppressed PCa cell proliferation, migration, and invasion.</p><p><p>Conversely, knockdown of miR-374a-5p facilitated PCa cell proliferation, migration, and invasion. miR-374a-5p expression decreased in PCa and was remarkably related to poor prognosis in PCa patients. miR-374a-5p acts in PCa by inhibiting cell proliferation, migration, and invasion. Consequently, miR-374a-5p has potential to act as a prognostic biomarker and a target for clinical therapeutic intervention in PCa.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-12"},"PeriodicalIF":1.1,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692817","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}

{"title":"miR-103 promotes esophageal squamous cell carcinoma metastasis by targeting FOXP1.","authors":"Min Huang, Jun Cai, Hai Zeng, Yan Zhu, Fan Zhang, Shuang Li","doi":"10.1080/15257770.2025.2478980","DOIUrl":"https://doi.org/10.1080/15257770.2025.2478980","url":null,"abstract":"<p><p>Esophageal squamous cell carcinoma (ESCC), a prevalent malignancy within the digestive tract, is associated with a significantly high mortality rate. MicroRNAs were already demonstrated to work in a wide range of tumors. The objective of the present research was to elucidate the involvement of miR-103 in the pathogenesis of ESCC and to explore its underlying mechanisms of action. Real-time quantitative polymerase chain reaction was used to detect miR-103 expressions in ESCC tissues and cells. The clinical significance of these expressions was assessed by a series of statistical analyses. Transwell assay was used to study the impact of miR-103 on migration and invasion ability of ESCC cells. Furthermore, a dual luciferase reporter gene method was adopted to study the association of miR-103 with the targeting of forkhead box protein 1 (FOXP1). miR-103 was significantly up-regulation in ESCC tissues and cell lines. Clinically, high miR-103 expression was associated with negative prognosis in ESCC. The low miR-103 expression significantly inhibited cell proliferation, migration and invasion in ESCC cell lines. Furthermore, miR-103 regulated the mechanism of action of ESCC by targeting FOXP1. In this study, we found that miR-103 may serve as a biomarker for ESCC prognosis. miR-103 may promote ESCC cell metastasis by targeting FOXP1. These studies may elucidate the potential of miR-103 as a novel target for the treatment of ESCC.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-14"},"PeriodicalIF":1.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674296","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}

{"title":"Short-read next-generation sequencing of 16s rRNA gene amplicons for characterizing amplicon sequence variants (ASVs) and determination of gene copy numbers using ion Torrent platform.","authors":"Mukesh K Jogi, Sristy Shikha, Pushpendra Singh, Shreyansh, Aranya Paul, Vijay Nema, Akshay Shankar, Mohammad Sajid, Anil Kumar, Brijendra K Kashayap, Mausumi Bharadwaj, Shalini Singh, Pramod Kumar","doi":"10.1080/15257770.2025.2479620","DOIUrl":"https://doi.org/10.1080/15257770.2025.2479620","url":null,"abstract":"<p><p>The short-amplicon sequencing of hypervariable regions of 16S rRNA gene is the widely used method for bacterial identification and microbiota profiling. Bacteria possess multiple copies of 16S rRNA gene and may contain single nucleotide variations (SNPs) or amplicon sequence variants (ASVs). The ASVs based determination of microbial taxa can be better representation over operational taxonomic units (OTUs). Illumina based NGS platforms are mostly used to define the ASVs whereas Ion-torrent platform is commonly used for diagnostic purposes. We aimed to identify bacterial isolates having ASVs and infer the copy numbers of16S rRNA gene using short read sequencing performed on the Ion Gene Studio S5 NGS platform. The V2-V3 regions of 16S rRNA gene were amplified from the bacterial isolates and subjected to NGS. Further, the sequences produced by NGS were compared with those generated from Sanger sequencing. The bacterial isolates were identified and characterize during ASVs. The copy number of the 16S rRNA gene was established in Gram-negative isolates. Assigning bacterial taxa based on ASVs would provide a more accurate representation of the variant data.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-14"},"PeriodicalIF":1.1,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657993","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}

{"title":"Histone chaperones as potential epidrug targets against cancer.","authors":"Sonam Malik, Pramod Kumar, Chander Prakash Yadav, Dinesh Kumar, Anuj Kumar","doi":"10.1080/15257770.2025.2476597","DOIUrl":"https://doi.org/10.1080/15257770.2025.2476597","url":null,"abstract":"<p><p>Epigenetic modifications play a crucial role in various diseases, including cancer. Targeting chromatin modulators to normalize these epigenetic markers is a promising avenue for overcoming cancer drug resistance and improving treatment efficacy. Histone chaperones, implicated in cancer due to their imperfect compensatory mechanisms, represent potential targets for epidrugs. To identify these targets, we performed enrichment and network analyses of histone chaperone interactions, both among themselves and with other proteins. This approach provided insights into structure-function relationships. The selective binding of histone chaperones to canonical histones highlights their potential as epidrugs targets. Network analysis of common histone chaperones identified key hub proteins: HSP90AB1, RBBP4, NPM1, DAXX, and SET. These hub proteins, particularly RBBP4, which formed the largest protein cluster was found associated with oncogenesis, suggesting RBBP4 as prime candidates for therapeutic intervention. Druggability prediction of these hub protein pockets further identified RBBP4 as the most promising target, with Ritonavir emerging as a potential epidrugs. These findings provide a crucial foundation for future epidrugs discovery targeting cancer.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-15"},"PeriodicalIF":1.1,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586398","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}

{"title":"Bioinformatics analysis of differentially expressed genes in hyperplastic scars using microarray data.","authors":"Jiayue Ding, Chun Xiang","doi":"10.1080/15257770.2025.2466427","DOIUrl":"https://doi.org/10.1080/15257770.2025.2466427","url":null,"abstract":"<p><strong>Objective: </strong>Using DNA microarray technology, we compared the differences in mRNA expression profiles between human hypertrophic scars (HTS) and normal skin tissues. Analyzing the differential genes in bioinformatics, to explore the pathogenesis of HTS at the molecular level, and to provide new targets for clinical treatment of HTS.</p><p><strong>Methods: </strong>Three HTS samples and their adjacent normal skin samples were collected. The extraction of total RNA was performed for cDNA microarray analysis. The screening of differentially expressed genes was carried out by using Genespring 10.0 software, and cluster analysis was performed between HTS and normal skin groups within the group, and Gene Ontology (GO) and biological pathway analysis were performed for differentially expressed genes by using DAVID Bioinformatics Resources 6.7.</p><p><strong>Results: </strong>In the 3 HTS samples, 3832 mRNAs overlapped in 3 HTS samples with more than 2-fold changes, 1920 mRNAs with more than 2-fold up-regulation, 1912 mRNAs with more than 2-fold down-regulation, 18 mRNAs with more than 5-fold up-regulation, and 29 mRNAs with more than 5-fold down-regulation. The results of the GO analysis showed that CDKN1C, CDKN2A, CTNNA3, COL6A3, HOXB4 and other differentially expressed genes are closely related to biological processes such as cell cycle, cell proliferation, and cell adhesion. The kegg pathway enrichment analysis showed that TGF-β1, CDKN1C, CDKN2A, CDC14A, ITGB6, EGF and other differentially expressed genes are mainly involved in the formation of adhesion plaques, β transforming factor signaling pathways, cell cycle signaling pathways, P53 signaling pathways, and tumor-related signaling pathways.</p><p><strong>Conclusion: </strong>The mRNA expression profile of human HTS samples showed significant changes compared to normal skin samples. TGF-β1, SMAD2, SMAD7, BAX, IGF2, COL1A1, COL1A2, MMPs, CDC14A, ITGB6, EGF, CDKN1C, CDKN2A, CTNNA3, HOXA3 and other related genes involved in biological processes, molecular functions, signaling pathways may be closely related to the occurrence and development of hypertrophic scars.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-13"},"PeriodicalIF":1.1,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573348","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}

{"title":"Nano calcium zincate-assisted synthesis of benzo[<i>d</i>]thiazol-2-yl phenylisoxazoles: quantum computational, <i>in silico</i> molecular docking simulations and DNA interaction.","authors":"A K Smitha, V Srinivasa Murthy, B Vinay Kumar, M Sennappan, A H Shridhar, Lohit Naik, K Yogendra, N Madhusudhana","doi":"10.1080/15257770.2025.2473442","DOIUrl":"10.1080/15257770.2025.2473442","url":null,"abstract":"<p><p>This study introduces a new and simple method for the synthesis of a series of 3-(benzo[<i>d</i>]thiazol-2-yl)-5-phenylisoxazole derivatives 3(a-f), and examines its potential interactions with DNA. The synthesis includes the reaction of 2-aminobenzenethiol (1) with a variety of substituted 5-phenylisoxazole-3-carbaldehydes 2(a-f) in the presence of a cost-effective and reusable nanocatalyst, Calcium-Zincate (CaZnO₂). The CaZnO₂ catalyst showed a consistent and long-lasting catalytic activity over several reaction cycles and retained its unique heterogeneous properties. The resulting compounds were characterized in detail using various spectroscopic and analytical techniques in order to confirm their structures. In addition, the interaction of these synthesized compounds with calf thymus-DNA (CT-DNA) using absorption spectroscopy and viscosity measurements was assessed. <i>In silico</i> docking studies were performed to predict their binding affinity with human DNA (PDB ID: 1G3X). The compounds were further analyzed using the Density Functional Theory (DFT) with the B3LYP functional and the 6-31 G(d) basis set in chloroform, with the results aligning closely with the experimental findings. Furthermore, the compounds ability to cleave PUC19 DNA was assessed, along with their photoinduced nuclease activity under UV-visible light, confirmed by photo-induced cleavage assays.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-26"},"PeriodicalIF":1.1,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567814","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}

{"title":"Association between <i>TMEM132D</i> gene polymorphisms and depressive symptoms in Qingdao Chinese elderly.","authors":"Shumin Chen, Kaiwen Cui, Dongfeng Zhang","doi":"10.1080/15257770.2025.2474587","DOIUrl":"https://doi.org/10.1080/15257770.2025.2474587","url":null,"abstract":"<p><p>The relationship between <i>TMEM132D</i> and depressive symptoms in community populations has not been investigated. Therefore, we explored the association between <i>TMEM132D</i> gene polymorphism and depressive symptoms based on data from a community sample of older adults in Qingdao. A total of 863 older adults were included in this study to examine the relationship between 12 SNPs and depressive symptoms. Depressive symptoms were assessed using the Patient Health Questionnaire-9. Logistic regression analysis was used to analyze the relationship between SNPs and depressive symptoms based on five genetic models. Finally, linkage disequilibrium analysis was performed, and haplotype domains were constructed. We discovered a statistically significant difference between groups with and without depressive symptoms in the genotype and allele frequencies of rs2292723. In addition, multivariate logistic regression showed that rs2292723 and rs2170820 were positively associated with depressive symptoms, and rs61944776 was negatively associated with depressive symptoms. Finally, we found that the haplotype \"CTC\" of rs2292723, rs492759, and rs61944776 was significantly associated with depressive symptoms by haplotype analysis. Our study suggested that <i>TMEM132D</i> was associated with depressive symptoms, which supplemented the role of the <i>TMEM132D</i> gene in psychiatric disorders.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-14"},"PeriodicalIF":1.1,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567813","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}

{"title":"Glucose depletion reduces cholesterol intracellular accumulation in ABCB1-dependent mechanism.","authors":"Mohammad Fayyad-Kazan, Rana Awada, Hussein Fayyad-Kazan, Zeina Soayfane","doi":"10.1080/15257770.2025.2473436","DOIUrl":"https://doi.org/10.1080/15257770.2025.2473436","url":null,"abstract":"<p><p>Lipids and glucose are important components of energy metabolism closely linked to each other. Glucose regulates cholesterol uptake <i>via</i> regulating the expression of different membrane transport proteins including NPC1L1, SR-B1 and ATP-binding cassette (ABC) transporters. Here, we explored further the mechanism underlying glucose-mediated regulation of cholesterol absorption and secretion. Caco-2 cells were cultivated in glucose-repletion versus glucose-depletion conditions. Quantitative real-time PCR and western blot were performed to assess mRNA and protein levels of different transporters. The amount of 25-NBD cholesterol uptake and the activity of P-gp (ABCB1) protein were measured by direct fluorometry and Rhodamine 123 efflux assay, respectively. Glucose-depleted Caco-2 cells showed lower NPC1L1 expression accompanied by reduced cholesterol uptake when compared to glucose-repleted cells. This effect was associated with an increase in the apical secretion of cholesterol compared with the basal secretion. In addition, glucose depletion upregulated both the expression level and activity of ABCB1, an apical pole transporter. However, the expression levels of ABCG5/G8, an apical sterol dimer transporter as well as ABCA1, a basal cholesterol transporter, were unchanged. The knockdown of ABCB1 in Caco-2 cells increased the intracellular accumulation of cholesterol. Glucose depletion reduces cholesterol accumulation in intestinal cells upon inducing its apical removal <i>via</i> ABCB1-dependent mechanism.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-16"},"PeriodicalIF":1.1,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557490","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}

{"title":"Precise control model of the epidemic: a cross-sectional study.","authors":"Mingyun Jiang, Ruiqi Liu, Weiping Yao, Shuang Li, Xiaodong Liang, Haibo Zhang","doi":"10.1080/15257770.2025.2470736","DOIUrl":"https://doi.org/10.1080/15257770.2025.2470736","url":null,"abstract":"<p><strong>Objectives: </strong>Coronavirus disease 2019 (COVID-19) is the most influential public health emergency worldwide. Controlling viral infection with people's health and reducing the impact on people's freedom is difficult at present. The precise control of COVID-19 in a city may be a suitable solution.</p><p><strong>Methods: </strong>An anonymous cross-sectional survey was conducted among Hangzhou people between 1 January and 28 February 2022. We organized the classification, incidence rate and mortality of COVID-19. And we introduced the discovery process of Omicron, health code of four colors, the epidemiological investigation and the policies of government in Hangzhou. This paper discusses various measures taken against Omicron in Hangzhou, China, which are effective methods to deal with such public health emergencies.</p><p><strong>Conclusions: </strong>Hangzhou quickly controlled the epidemic through precise control. As of February 1, Hangzhou had 115 confirmed cases with total population is 12.204 million. The rate of severe and death is 0%. Hangzhou's new model of precise control provides an important reference for the global city's response to COVID-19 and the reduction in losses caused by COVID-19. The COVID-19 Omicron variant outbreak indicates that people will still face unpredictable health risks in the future. Precise control is one of the best ways to effectively manage an epidemic, minimize its severity, and reduce losses in all aspects.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-14"},"PeriodicalIF":1.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143542741","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}