Gene Reports最新文献_第2页

Dynamic DNA methylation of EPHX2 in diabetic kidney disease progression: A potential biomarker EPHX2在糖尿病肾病进展中的动态DNA甲基化：一个潜在的生物标志物

IF 1

Gene Reports Pub Date : 2025-05-02 DOI: 10.1016/j.genrep.2025.102245

Guoxiong Deng , Ziyi Feng , Xiaomu Kong , Peng Gao , Yongwei Jiang , Yi Liu , Meimei Zhao , LiangMa

{"title":"Dynamic DNA methylation of EPHX2 in diabetic kidney disease progression: A potential biomarker","authors":"Guoxiong Deng , Ziyi Feng , Xiaomu Kong , Peng Gao , Yongwei Jiang , Yi Liu , Meimei Zhao , LiangMa","doi":"10.1016/j.genrep.2025.102245","DOIUrl":"10.1016/j.genrep.2025.102245","url":null,"abstract":"<div><h3>Subject</h3><div>To explore the correlation between the methylation level of <em>EPHX2</em> gene with diabetic kidney disease (DKD).</div></div><div><h3>Methods</h3><div>We conducted a case-control study contained 50 pairs of DKD and diabetes mellitus (DM) patients. CpG sites of <em>EPHX2</em> gene around transcription start site are detected using mass spectrometry combined with bisulfite conversation.</div></div><div><h3>Result</h3><div>Significant differences were found in the methylation of <em>EPHX2</em> site 1 (13.59 % vs 19.30 %, <em>P</em> = 0.001), 4(52.81 % vs. 45.2 %, <em>P</em> < 0.001) and 7(41.71 % vs. 48.00 %, <em>P</em> < 0.001) between DKD and diabetes mellitus (DM) patients. Logistic regression showed that for every 1 % increase in site 7 methylation, the risk of DN increased by 56 % (OR = 1.56, 95 %CI:1.26–1.93), suggesting its potential as an independent risk factor. The ROC curve shows that the methylation level of site1,7 have great performance to distinguish DKD and DM (AUC = 0.896, Sensitivity: 91.8 %, specificity: 84.4 %).</div></div><div><h3>Conclusion</h3><div>The DNA methylation levels of <em>EPHX2</em> gene are associated with the occurrence and development of DKD. In addition, changes in DNA methylation levels at sites 1 and 7 of the <em>EPHX2</em> gene may serve as potential biomarkers for the diagnosis of DKD and indicate new strategy to delay the progress of DKD.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102245"},"PeriodicalIF":1.0,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143918264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Forensic and phylogenetic characterization of 24 autosomal STR in the Sindhi population of India 印度信德人24例常染色体STR的法医学和系统发育特征

IF 1

Gene Reports Pub Date : 2025-05-01 DOI: 10.1016/j.genrep.2025.102234

Khushboo Gautam , Chanchal Devnani , Shivani Dixit , Pankaj Shrivastav , Shruti Dasgupta , Madhusudan Reddy Nandineni , Kumarasamy Thangaraj , Rakesh Rawal , Gyaneshwer Chaubey

{"title":"Forensic and phylogenetic characterization of 24 autosomal STR in the Sindhi population of India","authors":"Khushboo Gautam , Chanchal Devnani , Shivani Dixit , Pankaj Shrivastav , Shruti Dasgupta , Madhusudan Reddy Nandineni , Kumarasamy Thangaraj , Rakesh Rawal , Gyaneshwer Chaubey","doi":"10.1016/j.genrep.2025.102234","DOIUrl":"10.1016/j.genrep.2025.102234","url":null,"abstract":"<div><div>Short Tandem Repeats (STR) genotyping is of utmost importance in forensic casework. Thus, this study, for the first time, explores the forensic profile of the Sindhi population of India, a community with deep historical roots in the Indus Valley Civilization, through the analysis of 24 autosomal short tandem repeat (STR) loci. We found a total of 292 alleles for 24 STRs, and for each locus, the number of alleles ranged from 8 to 22. Out of 24 loci analysed, we obtained the highest genetic diversity for SE33 (0.947) and the lowest for TPOX (0.646) loci. We observed the highest Power of Discrimination (PD) for SE33 (0.988) and the lowest for TPOX (0.79) loci. SE33 locus has the highest number of alleles (36), while the CSF1PO, D5S818, TH01, and TPOX loci have the lowest (6 each). Research has revealed a significant genetic link between the Indian Sindhi population and their ancestral homeland. Based on the present analysis, we conclude that these 24 STR makers used in the present study are highly informative for individual identification, paternity testing, and population genetic studies.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102234"},"PeriodicalIF":1.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143890514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

New haplotypes of AvrPi-54 gene detected in Pyricularia oryzae from Malaysia, India and China 马来西亚、印度和中国稻瘟病菌AvrPi-54基因新单倍型的检测

IF 1

Gene Reports Pub Date : 2025-05-01 DOI: 10.1016/j.genrep.2025.102242

Elissa Stella Rafael , Freddy Kuok San Yeo , Walftor Dumin , Surisa Phornvillay , Jun Wah Yap , Najaa Batrisyia Abdullah Zakaria , Lee San Lai

{"title":"New haplotypes of AvrPi-54 gene detected in Pyricularia oryzae from Malaysia, India and China","authors":"Elissa Stella Rafael , Freddy Kuok San Yeo , Walftor Dumin , Surisa Phornvillay , Jun Wah Yap , Najaa Batrisyia Abdullah Zakaria , Lee San Lai","doi":"10.1016/j.genrep.2025.102242","DOIUrl":"10.1016/j.genrep.2025.102242","url":null,"abstract":"<div><div><em>Pyricularia oryzae</em>, the causal agent of rice blast disease, poses a significant threat to rice production. Limited information exists regarding the genetic diversity of <em>Avr</em> genes and the resistance profile of Sarawak rice against <em>P. oryzae</em> isolates in Malaysia. This study aimed to investigate the sequence variation of the <em>AvrPi-54</em> gene in <em>P. oryzae</em> isolates from Sarawak rice, in comparison with sequences available in the National Centre for Biotechnology Information (NCBI) database. A total of 20 <em>P. oryzae</em> isolates were analyzed together with 98 <em>AvrPi-54</em> gene sequences from NCBI. Nine distinct haplotypes were identified, including six novel haplotypes. The <em>AvrPi-54</em> gene was found to be under positive selection pressure. Notably, Sarawak rice exhibited varying levels of susceptibility to <em>P. oryzae</em> isolates carrying the H1 haplotype. Understanding the genetic diversity of <em>AvrPi-54</em> together with other <em>Avr</em> genes is crucial for developing effective strategies to manage <em>P. oryzae</em> in Sarawak, Malaysia.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102242"},"PeriodicalIF":1.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Advancing ovarian cancer management: Role of nucleic acid biomarkers and novel therapeutic approaches 推进卵巢癌管理：核酸生物标志物的作用和新的治疗方法

IF 1

Gene Reports Pub Date : 2025-05-01 DOI: 10.1016/j.genrep.2025.102241

Rutuja Deshmukh, Sharav A. Desai, Vipul P. Patel, Sakshi Narote, Nikita Raut

引用次数: 0

A complete mitochondrial genome-based phylogeny of gooseneck barnacles confirms the sister group relationship between the eastern Pacific Pollicipes elegans and the eastern Atlantic P. pollicipes 鹅颈藤壶的完整线粒体基因组系统发育证实了东太平洋elegans和东大西洋P. policipes之间的姐妹群关系

IF 1

Gene Reports Pub Date : 2025-04-29 DOI: 10.1016/j.genrep.2025.102238

Ruben Alfaro , Guillermo Mantilla , Alan Marín

{"title":"A complete mitochondrial genome-based phylogeny of gooseneck barnacles confirms the sister group relationship between the eastern Pacific Pollicipes elegans and the eastern Atlantic P. pollicipes","authors":"Ruben Alfaro , Guillermo Mantilla , Alan Marín","doi":"10.1016/j.genrep.2025.102238","DOIUrl":"10.1016/j.genrep.2025.102238","url":null,"abstract":"<div><div>Gooseneck barnacles are a fascinating group of crustaceans, and their taxonomic classification has attracted the attention of several specialists, including Charles Darwin, who was the first to note the close relationship between two species of gooseneck barnacles found on the eastern coasts of the Pacific, <em>Pollicipes elegans</em>, and the Atlantic, <em>P. pollicipes</em>. A third species from the eastern Pacific, <em>P. polymerus</em>, is believed to have diverged earlier from this group. Here, we used short-read sequences from GenBank to assemble the first complete mitochondrial genome of <em>P. elegans</em>. This genome was then used to assess the relationships of cirripede species from the superorder Thoracicalcarea through a complete mitochondrial genome-based phylogenetic analysis. Our findings revealed that both <em>P. elegans</em> and <em>P. pollicipes</em> clustered together in a well-supported discrete clade, reinforcing the close relationship between them. On the other hand, <em>P. polymerus</em> emerged as a basal branch within the <em>Pollicipes</em> lineage, indicating its earlier divergence from the group. Further efforts should aim to sequence the complete mitogenomes of other species within the order Pollicipedomorpha. Such endeavors will enable a more comprehensive phylogenetic analysis of this group, whose classification continues to be a subject of debate.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102238"},"PeriodicalIF":1.0,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143886154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SURF1 p.D202H variant is not associated with Leigh syndrome but may contribute to impaired pregnancy outcomes SURF1 p.D202H变异与Leigh综合征无关，但可能导致妊娠结局受损

IF 1

Gene Reports Pub Date : 2025-04-29 DOI: 10.1016/j.genrep.2025.102240

Xingqiang Wei , Junko Otsuki , Miki Fujii , Kaori Kodera , Ai Yamada , Nao Hayashi , Yihsien Enatsu , Kunihiro Enatsu , Noritoshi Enatsu , Yoko Tokura , Satoshi Yamada , Yuri Mizusawa , Eri Okamoto , Shoji Kokeguchi , Toshiroh Iwasaki , Yasuhiro Fujiwara , Mikiya Nakatsuka , Tetsuo Kunieda , Masahide Shiotani

{"title":"SURF1 p.D202H variant is not associated with Leigh syndrome but may contribute to impaired pregnancy outcomes","authors":"Xingqiang Wei , Junko Otsuki , Miki Fujii , Kaori Kodera , Ai Yamada , Nao Hayashi , Yihsien Enatsu , Kunihiro Enatsu , Noritoshi Enatsu , Yoko Tokura , Satoshi Yamada , Yuri Mizusawa , Eri Okamoto , Shoji Kokeguchi , Toshiroh Iwasaki , Yasuhiro Fujiwara , Mikiya Nakatsuka , Tetsuo Kunieda , Masahide Shiotani","doi":"10.1016/j.genrep.2025.102240","DOIUrl":"10.1016/j.genrep.2025.102240","url":null,"abstract":"<div><div>The <em>SURF1</em> gene encodes a mitochondrial protein critical for cytochrome <em>c</em> oxidase (COX) assembly. The c.604G>C (p.D202H) variant, identified in the homozygous state, has conflicting pathogenicity classifications in ClinVar and was found in 6.7 % of individuals with recurrent ART failure or pregnancy loss. This study included 30 Japanese women with infertility, 25 with recurrent ART failure and 5 with recurrent pregnancy loss, and 23 Japanese women with normal fertility, including 12 with successful ART outcomes and 11 with natural conception histories. The median ages of the infertility and control groups were 41.5 and 36 years, respectively. Participants were recruited from Hanabusa Women's Clinic and Okayama University Hospital. Whole-exome sequencing (WES) was performed using DNA extracted from peripheral blood mononuclear cells. Variant prioritization focused on 1136 mitochondrial-related nuclear genes listed in the MitoCarta3.0 database. Analysis was restricted to homozygous missense variants absent in the control group and with minor allele frequency < 0.05 in Japanese databases. <em>SURF1</em> (p.D202H) was significantly enriched in the infertility group compared to population databases. Structural modeling with AlphaFold2 and ChimeraX revealed local hydrogen bonding alterations caused by the substitution of aspartate with histidine at position 202. These findings suggest that while p.D202H is not pathogenic for Leigh syndrome, it may contribute to mitochondrial dysfunction in reproductive tissues. Further investigation into its tissue-specific effects is warranted.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102240"},"PeriodicalIF":1.0,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143903434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comprehensive metagenomic analysis of bacterial diversity and antimicrobial resistance genes in coastal sediments from urbanized Indian cities 印度城市化城市沿海沉积物中细菌多样性和耐药基因的综合宏基因组分析

IF 1

Gene Reports Pub Date : 2025-04-26 DOI: 10.1016/j.genrep.2025.102239

Pradip Sahebrao Gawande , Vajravelu Manigandan , R. Sankar Ganesh , V. Rajesh Kannan , K. Ramu , M.V. Ramana Murthy

{"title":"Comprehensive metagenomic analysis of bacterial diversity and antimicrobial resistance genes in coastal sediments from urbanized Indian cities","authors":"Pradip Sahebrao Gawande , Vajravelu Manigandan , R. Sankar Ganesh , V. Rajesh Kannan , K. Ramu , M.V. Ramana Murthy","doi":"10.1016/j.genrep.2025.102239","DOIUrl":"10.1016/j.genrep.2025.102239","url":null,"abstract":"<div><div>This study presents the comprehensive analysis of bacterial diversity and antimicrobial resistance (AMR) genes in coastal sediments from seven urbanized cities in India: Paradeep (S1), Visakhapatnam (S2), Chennai (S3), Mangalore (S4), Goa (S5), Mumbai (S6), and Veraval (S7). Sediment DNA was sequenced using the Illumina NextSeq-500 platform, assembled with meta-SPAdes, and gene predicted using Prodigal. AMR genes were identified by screening against the CARD database. The results show that Paradeep (S1) and Mumbai (S6) exhibited the highest abundance of both bacterial populations and AMR genes (ARGs). Bacterial diversity revealed that <em>Marinobacter</em> was the most abundant genus in most of the samples, while <em>Qipengyuania</em> and <em>Salegentibacter</em> were prevalent at one location each. A total of 75 types of ARGs (510 counts), including 54 multidrug resistance (MDR) genes, were identified, with <em>Saur_23S_LZD</em> and <em>Ecol_23S_CHL</em> being the most prevalent. BLASTn results of ARGs and network analysis revealed that <em>Ecol_23S_CHL</em> was associated with 42 bacterial species, including human pathogens. This study establishes a baseline for understanding the distribution of ARGs in coastal waters of India and provides valuable insights for future research.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102239"},"PeriodicalIF":1.0,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tissue-specific kinetics of glycerol kinase and its expression pattern in mouse: a comparative analysis 甘油激酶的组织特异性动力学及其在小鼠中的表达模式：比较分析

IF 1

Gene Reports Pub Date : 2025-04-26 DOI: 10.1016/j.genrep.2025.102237

Riva M. Rani, Basukshisha Wanniang, Bidyadhar Das

{"title":"Tissue-specific kinetics of glycerol kinase and its expression pattern in mouse: a comparative analysis","authors":"Riva M. Rani, Basukshisha Wanniang, Bidyadhar Das","doi":"10.1016/j.genrep.2025.102237","DOIUrl":"10.1016/j.genrep.2025.102237","url":null,"abstract":"<div><div>Glycerol kinase (GK) catalyzes the transfer of a phosphate group from ATP to glycerol. GK is the key enzyme for utilizing glycerol as a carbon and energy source. The functionality of GK displays distinctive characteristics based on the tissue type, reflecting the distinct glycerol metabolic pathways in different tissues. Enzyme kinetics and western blot analysis were performed using different mouse tissues to determine the activity and protein expression of GK. The highest specific activities of GK were observed in muscle and heart tissues, with 1.433 U/mg protein and 1.451 U/mg protein, respectively. The enzyme exhibited optimal activity at pH 7.5 and showed consistency in various buffers. The highest <em>V</em>max for ATP was in muscle and heart tissues (3.075 U/mg protein and 2.743 U/mg protein), with the highest <em>K</em>m for ATP in muscle and testis (0.529 mM and 0.582 mM). Additionally, for glycerol, the highest <em>V</em>max was also in muscle and heart tissues (2.970 U/mg protein and 3.220 U/mg protein), with the highest <em>K</em>m in these tissues being 6.496 μM and 7.142 μM, respectively. Western blot analysis indicated that GK is expressed in all tissues analyzed. This study revealed the tissue-specific functionality of GK in various mouse tissues, emphasising its crucial role in glycerol metabolism. This study also provided basic outlines of GK expression patterns in various tissues of mice and may provide important information for the regulation of GK for its critical role in type 2 diabetes mellitus.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102237"},"PeriodicalIF":1.0,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143878778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Analysis of genetic variants of Alox12 (rs9904779) gene in periodontitis and type 2 diabetes mellitus 牙周炎和2型糖尿病患者Alox12 （rs9904779）基因变异分析

IF 1

Gene Reports Pub Date : 2025-04-25 DOI: 10.1016/j.genrep.2025.102236

Nihala Sidhic , Kaniha Sivakumar , Athira Ajith , Usha Subbiah , Bathala Sai Dharani , Shaik Bibijanu , Hakeem Arishiya

{"title":"Analysis of genetic variants of Alox12 (rs9904779) gene in periodontitis and type 2 diabetes mellitus","authors":"Nihala Sidhic , Kaniha Sivakumar , Athira Ajith , Usha Subbiah , Bathala Sai Dharani , Shaik Bibijanu , Hakeem Arishiya","doi":"10.1016/j.genrep.2025.102236","DOIUrl":"10.1016/j.genrep.2025.102236","url":null,"abstract":"<div><h3>Background</h3><div>Periodontitis, a chronic inflammatory disease affecting tooth-supporting structures, shows increased tissue damage in type 2 diabetes patients, highlighting their bidirectional link. The Alox12 gene, encoding arachidonic acid 12-lipoxygenase, plays a role in inflammation and oxidation.</div></div><div><h3>Objective</h3><div>This study investigates Alox12 genetic variants in relation to periodontitis and T2DM.</div></div><div><h3>Method</h3><div>Genotyping of Alox12 rs9904779 in 400 individuals was conducted via PCR-RFLP. Statistical analysis was performed using Epi Info v.7.0, assessing genotype risk via odds ratio (OR) with 95 % CI and <em>p</em> < 0.05 as significant. HWE was evaluated, and genotype/allele frequencies were compared using the Chi-square test. RNA Fold evaluated mRNA structural impacts, while protein-protein docking and visualization were done using pyDOCKWEB.</div></div><div><h3>Results</h3><div>Statistically significant higher prevalence of the heterozygote CG genotype of rs9904779 showed a significant occurrence in the periodontitis patients (OR = 0.13, 95 % CI = 0.062-0.301, <em>p</em> = 0) and periodontitis with T2DM patients (OR = 0.08, 95 % CI = 0.036-0.188, p = 0) when compared to the healthy controls. The mRNA structure stability was found to be better with wild type (−950.68 kcal/mol) than variant (−950.61 kcal/mol). <em>Alox12</em> was found to be interacting with gingipain and the bond length was found to be 12.731 A.</div></div><div><h3>Conclusion</h3><div>The study highlights a significant association between the Alox12 rs9904779 CG genotype and an increased risk of periodontitis and T2DM, suggesting its potential role in disease susceptibility. Additionally, structural and interaction analyses indicate that Alox12 may influence inflammatory pathways, providing insights into its functional impact.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102236"},"PeriodicalIF":1.0,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143935906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Detecting signatures of episodic positive selection based on observed amino acids in hemagglutinin of H3N2 human influenza A virus 基于观察到的H3N2人甲型流感病毒血凝素氨基酸的偶发性阳性选择特征检测

IF 1

Gene Reports Pub Date : 2025-04-24 DOI: 10.1016/j.genrep.2025.102233

Yoshiyuki Suzuki

{"title":"Detecting signatures of episodic positive selection based on observed amino acids in hemagglutinin of H3N2 human influenza A virus","authors":"Yoshiyuki Suzuki","doi":"10.1016/j.genrep.2025.102233","DOIUrl":"10.1016/j.genrep.2025.102233","url":null,"abstract":"<div><div>In the parsimony method for detecting natural selection at amino acid sites of proteins, the numbers of synonymous (<span><math><msub><mi>d</mi><mi>S</mi></msub></math></span>) and nonsynonymous (<span><math><msub><mi>d</mi><mi>N</mi></msub></math></span>) substitutions that have accumulated over the evolutionary history of observed sequences were computed assuming that any amino acid was compatible at each site. Positive selection was inferred to have operated recurrently when the null hypothesis of no selection was rejected with <span><math><msub><mi>d</mi><mi>S</mi></msub><mo><</mo><msub><mi>d</mi><mi>N</mi></msub></math></span>. Here an attempt to detect episodic positive selection within the framework of parsimony method was demonstrated. The <span><math><msub><mi>d</mi><mi>S</mi></msub></math></span> and <span><math><msub><mi>d</mi><mi>N</mi></msub></math></span> values were computed assuming that only the observed amino acids were compatible at each site. Positive selection was inferred to have operated episodically when the null hypothesis of the same fitness effects among observed amino acids was rejected with <span><math><msub><mi>d</mi><mi>S</mi></msub><mo>></mo><msub><mi>d</mi><mi>N</mi></msub></math></span>. In the analysis of 18,444 sequences for hemagglutinin of H3N2 human influenza A virus, recurrent and episodic positive selections were inferred mainly at the sites related to antigenicity. Episodic positive selection was detected particularly at the sites under epistasis. Although it may be necessary to eliminate slightly deleterious amino acids from the population genetic data, the analysis based on observed amino acids may be useful for screening the sites with signatures of episodic positive selection.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102233"},"PeriodicalIF":1.0,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143878689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0