Evolutionary Bioinformatics最新文献_第2页

HNF4A-Bridging the Gap Between Intestinal Metaplasia and Gastric Cancer HNF4A--弥合肠增生与胃癌之间的鸿沟

IF 2.6 4区生物学

Evolutionary Bioinformatics Pub Date : 2024-04-26 DOI: 10.1177/11769343241249017

Yihang Zhao, Hong Tang, Jianhua Xu, Feifei Sun, Yuanyuan Zhao, Yang Li

{"title":"HNF4A-Bridging the Gap Between Intestinal Metaplasia and Gastric Cancer","authors":"Yihang Zhao, Hong Tang, Jianhua Xu, Feifei Sun, Yuanyuan Zhao, Yang Li","doi":"10.1177/11769343241249017","DOIUrl":"https://doi.org/10.1177/11769343241249017","url":null,"abstract":"Background:Intestinal metaplasia (IM) of gastric epithelium has traditionally been regarded as an irreversible stage in the process of the Correa cascade. Exploring the potential molecular mechanism of IM is significant for effective gastric cancer prevention.Methods:The GSE78523 dataset, obtained from the Gene Expression Omnibus (GEO) database, was analyzed using RStudio software to identify the differently expressed genes (DEGs) between IM tissues and normal gastric epithelial tissues. Subsequently, gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, Gene Set Enrichment Analysis (GESA), and protein-protein interaction (PPI) analysis were used to find potential genes. Additionally, the screened genes were analyzed for clinical, immunological, and genetic correlation aspects using single gene clinical correlation analysis (UALCAN), Tumor–Immune System Interactions Database (TISIDB), and validated through western blot experiments.Results:Enrichment analysis showed that the lipid metabolic pathway was significantly associated with IM tissues and the apolipoprotein B ( APOB) gene was identified in the subsequent analysis. Experiment results and correlation analysis showed that the expression of APOB was higher in IM tissues than in normal tissues. This elevated expression of APOB was also found to be associated with the expression levels of hepatocyte nuclear factor 4A ( HNF4A) gene. HNF4A was also found to be associated with immune cell infiltration to gastric cancer and was linked to the prognosis of gastric cancer patients. Moreover, HNF4A was also highly expressed in both IM tissues and gastric cancer cells.Conclusion:Our findings indicate that HNF4A regulates the microenvironment of lipid metabolism in IM tissues by targeting APOB. Higher expression of HNF4A tends to lead to a worse prognosis in gastric cancer patients implying it may serve as a predictive indicator for the progression from IM to gastric cancer.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140803734","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

Genomic Characterization of IS6110 Insertions in Mycobacterium orygis 鸟疫分枝杆菌 IS6110 插入的基因组特征

IF 2.6 4区生物学

Evolutionary Bioinformatics Pub Date : 2024-04-05 DOI: 10.1177/11769343241240558

Ahmed Kabir Refaya, Umashankar Vetrivel, Kannan Palaniyandi

{"title":"Genomic Characterization of IS6110 Insertions in Mycobacterium orygis","authors":"Ahmed Kabir Refaya, Umashankar Vetrivel, Kannan Palaniyandi","doi":"10.1177/11769343241240558","DOIUrl":"https://doi.org/10.1177/11769343241240558","url":null,"abstract":"Mycobacterium orygis, a subspecies of the Mycobacterium tuberculosis complex (MTBC), has emerged as a significant concern in the context of One Health, with implications for zoonosis or zooanthroponosis or both. MTBC strains are characterized by the unique insertion element IS 6110, which is widely used as a diagnostic marker. IS 6110 transposition drives genetic modifications in MTBC, imparting genome plasticity and profound biological consequences. While IS 6110 insertions are customarily found in the MTBC genomes, the evolutionary trajectory of strains seems to correlate with the number of IS 6110 copies, indicating enhanced adaptability with increasing copy numbers. Here, we present a comprehensive analysis of IS 6110 insertions in the M. orygis genome, utilizing ISMapper, and elucidate their genetic consequences in promoting successful host adaptation. Our study encompasses a panel of 67 paired-end reads, comprising 11 isolates from our laboratory and 56 sequences downloaded from public databases. Among these sequences, 91% exhibited high-copy, 4.5% low-copy, and 4.5% lacked IS 6110 insertions. We identified 255 insertion loci, including 141 intragenic and 114 intergenic insertions. Most of these loci were either unique or shared among a limited number of isolates, potentially influencing strain behavior. Furthermore, we conducted gene ontology and pathway analysis, using eggNOG-mapper 5.0, on the protein sequences disrupted by IS 6110 insertions, revealing 63 genes involved in diverse functions of Gene Ontology and 45 genes participating in various KEGG pathways. Our findings offer novel insights into IS 6110 insertions, their preferential insertion regions, and their impact on metabolic processes and pathways, providing valuable knowledge on the genetic changes underpinning IS 6110 transposition in M. orygis.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140579546","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

Large-scale Pan Genomic Analysis of Mycobacterium tuberculosis Reveals Key Insights Into Molecular Evolutionary Rate of Specific Processes and Functions. 结核分枝杆菌的大规模泛基因组分析揭示了特定过程和功能的分子进化速度的关键信息。

IF 1.7 4区生物学

Evolutionary Bioinformatics Pub Date : 2024-03-25 eCollection Date: 2024-01-01 DOI: 10.1177/11769343241239463

Eshan Bundhoo, Anisah W Ghoorah, Yasmina Jaufeerally-Fakim

{"title":"Large-scale Pan Genomic Analysis of Mycobacterium tuberculosis Reveals Key Insights Into Molecular Evolutionary Rate of Specific Processes and Functions.","authors":"Eshan Bundhoo, Anisah W Ghoorah, Yasmina Jaufeerally-Fakim","doi":"10.1177/11769343241239463","DOIUrl":"10.1177/11769343241239463","url":null,"abstract":"Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), an infectious disease that is a major killer worldwide. Due to selection pressure caused by the use of antibacterial drugs, Mtb is characterised by mutational events that have given rise to multi drug resistant (MDR) and extensively drug resistant (XDR) phenotypes. The rate at which mutations occur is an important factor in the study of molecular evolution, and it helps understand gene evolution. Within the same species, different protein-coding genes evolve at different rates. To estimate the rates of molecular evolution of protein-coding genes, a commonly used parameter is the ratio dN/dS, where dN is the rate of non-synonymous substitutions and dS is the rate of synonymous substitutions. Here, we determined the estimated rates of molecular evolution of select biological processes and molecular functions across 264 strains of Mtb. We also investigated the molecular evolutionary rates of core genes of Mtb by computing the dN/dS values, and estimated the pan genome of the 264 strains of Mtb. Our results show that the cellular amino acid metabolic process and the kinase activity function evolve at a significantly higher rate, while the carbohydrate metabolic process evolves at a significantly lower rate for M. tuberculosis. These high rates of evolution correlate well with Mtb physiology and pathogenicity. We further propose that the core genome of M. tuberculosis likely experiences varying rates of molecular evolution which may drive an interplay between core genome and accessory genome during M. tuberculosis evolution.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10964447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140295209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Draft Genome Sequence of Pantoea sp. Strain MHSD4, a Bacterial Endophyte With Bioremediation Potential. 具有生物修复潜力的内生细菌 Pantoea sp.

IF 2.6 4区生物学

Evolutionary Bioinformatics Pub Date : 2024-03-13 eCollection Date: 2024-01-01 DOI: 10.1177/11769343231217908

Dimpho Michelle Morobane, Khuthadzo Tshishonga, Mahloro Hope Serepa-Dlamini

引用次数: 0

A Comprehensive Analysis of 3 Moroccan Genomes Revealed Contributions From Both African and European Ancestries. 对 3 个摩洛哥人基因组的综合分析表明，非洲和欧洲血统都有贡献。

IF 2.6 4区生物学

Evolutionary Bioinformatics Pub Date : 2024-02-06 eCollection Date: 2024-01-01 DOI: 10.1177/11769343241229278

Nasma Boumajdi, Houda Bendani, Souad Kartti, Tarek Alouane, Lahcen Belyamani, Azeddine Ibrahimi

{"title":"A Comprehensive Analysis of 3 Moroccan Genomes Revealed Contributions From Both African and European Ancestries.","authors":"Nasma Boumajdi, Houda Bendani, Souad Kartti, Tarek Alouane, Lahcen Belyamani, Azeddine Ibrahimi","doi":"10.1177/11769343241229278","DOIUrl":"10.1177/11769343241229278","url":null,"abstract":"Genetic variations in the human genome represent the differences in DNA sequence within individuals. This highlights the important role of whole human genome sequencing which has become the keystone for precision medicine and disease prediction. Morocco is an important hub for studying human population migration and mixing history. This study presents the analysis of 3 Moroccan genomes; the variant analysis revealed 6 379 606 single nucleotide variants (SNVs) and 1 050 577 small InDels. Of those identified SNVs, 219 152 were novel, with 1233 occurring in coding regions, and 5580 non-synonymous single nucleotide variants (nsSNP) variants were predicted to affect protein functions. The InDels produced 1055 coding variants and 454 non-3n length variants, and their size ranged from -49 and 49 bp. We further analysed the gene pathways of 8 novel coding variants found in the 3 genomes and revealed 5 genes involved in various diseases and biological pathways. We found that the Moroccan genomes share 92.78% of African ancestry, and 92.86% of Non-Finnish European ancestry, according to the gnomAD database. Then, population structure inference, by admixture analysis and network-based approach, revealed that the studied genomes form a mixed population structure, highlighting the increased genetic diversity in Morocco.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10848790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139703947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Screening and Validation of Key Genes of Autophagy in Acute Myocardial Infarction Based on Bioinformatics. 基于生物信息学的急性心肌梗死自噬关键基因的筛选与验证

IF 2.6 4区生物学

Evolutionary Bioinformatics Pub Date : 2024-01-30 eCollection Date: 2024-01-01 DOI: 10.1177/11769343241227331

Yingjie Geng, Yu'e Han, Shujuan Wang, Jia Qi, Xiaoli Bi

{"title":"Screening and Validation of Key Genes of Autophagy in Acute Myocardial Infarction Based on Bioinformatics.","authors":"Yingjie Geng, Yu'e Han, Shujuan Wang, Jia Qi, Xiaoli Bi","doi":"10.1177/11769343241227331","DOIUrl":"10.1177/11769343241227331","url":null,"abstract":"Aims: Autophagy plays a significant role in the development of acute myocardial infarction (AMI), and cardiomyocyte autophagy is of major importance in maintaining cardiac function. We aimed to identify key genes associated with autophagy in AMI through bioinformatics analysis and verify them through clinical validation.Materials and methods: We downloaded an AMI expression profile dataset GSE166780 from Gene Expression Omnibus (GEO). Autophagy-associated genes potentially differentially expressed in AMI were screened using R software. Then, to identify key autophagy-related genes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, protein-protein interaction (PPI) analysis, Receiver Operating Characteristic (ROC) curve analysis, and correlation analysis were performed on the differentially expressed autophagy-related genes in AMI. Finally, we used quantificational real-time polymerase chain reaction (qRT-PCR) to verify the RNA expression of the screened key genes.Results: TSC2, HSPA8, and HIF1A were screened out as key autophagy-related genes. qRT-PCR results showed that the expression levels of HSPA8 and TSC2 in AMI blood samples were lower, while the expression level of HIF1A was higher than that in the healthy controls.Conclusions: TSC2, HSPA8, and HIF1A were identified as key autophagy-related genes in this study. They may influence the development of AMI through autophagy. These findings may help deepen our understanding of AMI and may be useful for the treatment of AMI.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10832399/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139681764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phylogenetic Analysis Provides Insight Into the Molecular Evolution of Nociception and Pain-Related Proteins. 系统发育分析为痛觉和疼痛相关蛋白的分子进化提供了洞察力。

IF 2.6 4区生物学

Evolutionary Bioinformatics Pub Date : 2023-12-14 eCollection Date: 2023-01-01 DOI: 10.1177/11769343231216914

Rujun Zhai, Qian Wang

{"title":"Phylogenetic Analysis Provides Insight Into the Molecular Evolution of Nociception and Pain-Related Proteins.","authors":"Rujun Zhai, Qian Wang","doi":"10.1177/11769343231216914","DOIUrl":"https://doi.org/10.1177/11769343231216914","url":null,"abstract":"Nociception and pain sensation are important neural processes in humans to avoid injury. Many proteins are involved in nociception and pain sensation in humans; however, the evolution of these proteins in animals is unknown. Here, we chose nociception- and pain-related proteins, including G protein-coupled receptors (GPCRs), ion channels (ICs), and neuropeptides (NPs), which are reportedly associated with nociception and pain in humans, and identified their homologs in various animals by BLAST, phylogenetic analysis and protein architecture comparison to reveal their evolution from protozoans to humans. We found that the homologs of transient receptor potential channel A 1 (TRPA1), TRAPM, acid-sensing IC (ASIC), and voltage-dependent calcium channel (VDCC) first appear in Porifera. Substance-P receptor 1 (TACR1) emerged from Coelenterata. Somatostatin receptor type 2 (SSTR2), TRPV1 and voltage-dependent sodium channels (VDSC) appear in Platyhelminthes. Calcitonin gene-related peptide receptor (CGRPR) was first identified in Nematoda. However, opioid receptors (OPRs) and most NPs were discovered only in vertebrates and exist from agnatha to humans. The results demonstrated that homologs of nociception and pain-related ICs exist from lower animal phyla to high animal phyla, and that most of the GPCRs originate from low to high phyla sequentially, whereas OPRs and NPs are newly evolved in vertebrates, which provides hints of the evolution of nociception and pain-related proteins in animals and humans.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10725132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138812717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computer-Assisted Drug Discovery of a Novel Theobromine Derivative as an EGFR Protein-Targeted Apoptosis Inducer. 计算机辅助药物发现一种新的可可碱衍生物作为EGFR蛋白靶向细胞凋亡诱导剂。

IF 1.7 4区生物学

Evolutionary Bioinformatics Pub Date : 2023-12-01 eCollection Date: 2023-01-01 DOI: 10.1177/11769343231217916

Ibrahim H Eissa, Reda G Yousef, Eslam B Elkaeed, Aisha A Alsfouk, Dalal Z Husein, Ibrahim M Ibrahim, Hesham A El-Mahdy, Hazem Elkady, Ahmed M Metwaly

{"title":"Computer-Assisted Drug Discovery of a Novel Theobromine Derivative as an EGFR Protein-Targeted Apoptosis Inducer.","authors":"Ibrahim H Eissa, Reda G Yousef, Eslam B Elkaeed, Aisha A Alsfouk, Dalal Z Husein, Ibrahim M Ibrahim, Hesham A El-Mahdy, Hazem Elkady, Ahmed M Metwaly","doi":"10.1177/11769343231217916","DOIUrl":"10.1177/11769343231217916","url":null,"abstract":"The overexpression of the Epidermal Growth Factor Receptor (EGFR) marks it as a pivotal target in cancer treatment, with the aim of reducing its proliferation and inducing apoptosis. This study aimed at the CADD of a new apoptotic EGFR inhibitor. The natural alkaloid, theobromine, was used as a starting point to obtain a new semisynthetic (di-ortho-chloro acetamide) derivative (T-1-DOCA). Firstly, T-1-DOCA's total electron density, energy gap, reactivity indices, and electrostatic surface potential were determined by DFT calculations, Then, molecular docking studies were carried out to predict the potential of T-1-DOCA against wild and mutant EGFR proteins. T-1-DOCA's correct binding was further confirmed by molecular dynamics (MD) over 100 ns, MM-GPSA, and PLIP experiments. In vitro, T-1-DOCA showed noticeable efficacy compared to erlotinib by suppressing EGFRWT and EGFRT790M with IC50 values of 56.94 and 269.01 nM, respectively. T-1-DOCA inhibited also the proliferation of H1975 and HCT-116 malignant cell lines, exhibiting IC50 values of 14.12 and 23.39 µM, with selectivity indices of 6.8 and 4.1, respectively, indicating its anticancer potential and general safety. The apoptotic effects of T-1-DOCA were indicated by flow cytometric analysis and were further confirmed through its potential to increase the levels of BAX, Casp3, and Casp9, and decrease Bcl-2 levels. In conclusion, T-1-DOCA, a new apoptotic EGFR inhibitor, was designed and evaluated both computationally and experimentally. The results suggest that T-1-DOCA is a promising candidate for further development as an anti-cancer drug.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10693208/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138479082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Toward a Better Understanding of G4 Evolution in the 3 Living Kingdoms. 更好地理解三个生物王国的G4进化。

IF 2.6 4区生物学

Evolutionary Bioinformatics Pub Date : 2023-12-01 eCollection Date: 2023-01-01 DOI: 10.1177/11769343231212075

Anaïs Vannutelli, Aïda Ouangraoua, Jean-Pierre Perreault

{"title":"Toward a Better Understanding of G4 Evolution in the 3 Living Kingdoms.","authors":"Anaïs Vannutelli, Aïda Ouangraoua, Jean-Pierre Perreault","doi":"10.1177/11769343231212075","DOIUrl":"10.1177/11769343231212075","url":null,"abstract":"Background: G-quadruplexes (G4s) are secondary structures in DNA and RNA that impact various cellular processes, such as transcription, splicing, and translation. Due to their numerous functions, G4s are involved in many diseases, making their study important. Yet, G4s evolution remains largely unknown, due to their low sequence similarity and the poor quality of their sequence alignments across several species. To address this, we designed a strategy that avoids direct G4s alignment to study G4s evolution in the 3 species kingdoms. We also explored the coevolution between RBPs and G4s. Methods: We retrieved one-to-one orthologous genes from the Ensembl Compara database and computed groups of one-to-one orthologous genes. For each group, we aligned gene sequences and identified G4 families as groups of overlapping G4s in the alignment. We analyzed these G4 families using Count, a tool to infer feature evolution into a gene or a species tree. Additionally, we utilized these G4 families to predict G4s by homology. To establish a control dataset, we performed mono-, di- and tri-nucleotide shuffling. Results: Only a few conserved G4s occur among all living kingdoms. In eukaryotes, G4s exhibit slight conservation among vertebrates, and few are conserved between plants. In archaea and bacteria, at most, only 2 G4s are common. The G4 homology-based prediction increases the number of conserved G4s in common ancestors. The coevolution between RNA-binding proteins and G4s was investigated and revealed a modest impact of RNA-binding proteins evolution on G4 evolution. However, the details of this relationship remain unclear. Conclusion: Even if G4 evolution still eludes us, the present study provides key information to compute groups of homologous G4 and to reveal the evolution history of G4 families.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10693206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138479083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Retrospective Phylodynamic and Phylogeographic Analysis of the Bluetongue Virus in Tunisia. 突尼斯蓝舌病病毒的系统动力学和系统地理学回顾性分析。

IF 2.6 4区生物学

Evolutionary Bioinformatics Pub Date : 2023-11-27 eCollection Date: 2023-01-01 DOI: 10.1177/11769343231212266

Oussema Souiai, Marwa Arbi, Mariem Hanachi, Ameny Sallami, Imen Larbi, Melek Chaouch, Emna Harigua-Souiai, Alia Benkahla

{"title":"Retrospective Phylodynamic and Phylogeographic Analysis of the Bluetongue Virus in Tunisia.","authors":"Oussema Souiai, Marwa Arbi, Mariem Hanachi, Ameny Sallami, Imen Larbi, Melek Chaouch, Emna Harigua-Souiai, Alia Benkahla","doi":"10.1177/11769343231212266","DOIUrl":"10.1177/11769343231212266","url":null,"abstract":"Bluetongue virus (BTV) is an arbovirus considered as a major threat for the global livestock economy. Since 1999, Tunisia has experienced several incursions of BTV, during which numerous cases of infection and mortality have been reported. However, the geographical origin and epidemiological characteristics of these incursions remained unclear. To understand the evolutionary history of BTV emergence in Tunisia, we extracted from Genbank the segment 6 sequences of 7 BTV strains isolated in Tunisia during the period 2000 to 2017 and blasted them to obtain a final dataset of 67 sequences. We subjected the dataset to a Bayesian phylogeography framework inferring geographical origin and serotype as phylodynamic models. Our results suggest that BTV-2 was first introduced in Tunisia in the 1960s and that since 1990s, the country has witnessed the emergence of other typical and atypical BTV serotypes notably BTV-1, BTV-3 and BTV-Y. The reported serotypes have a diverse geographical origin and have been transmitted to Tunisia from countries in the Mediterranean Basin. Interserotype reassortments have been identified among BTV-1, BTV-2 and BTV-Y. This study has provided new insights on the temporal and geographical origin of BTV in Tunisia, suggesting the contribution of animal trade and environment conditions in virus spread.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10683408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138464103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0