Evolutionary Bioinformatics最新文献

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Identification of Key Genes and Pathways in Gefitinib-Resistant Lung Adenocarcinoma using Bioinformatics Analysis. 利用生物信息学分析鉴定吉非替尼耐药肺腺癌的关键基因和途径。
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2021-06-11 eCollection Date: 2021-01-01 DOI: 10.1177/11769343211023767
Kailin Mao, Fang Lin, Yingai Zhang, Hailong Zhou
{"title":"Identification of Key Genes and Pathways in Gefitinib-Resistant Lung Adenocarcinoma using Bioinformatics Analysis.","authors":"Kailin Mao,&nbsp;Fang Lin,&nbsp;Yingai Zhang,&nbsp;Hailong Zhou","doi":"10.1177/11769343211023767","DOIUrl":"10.1177/11769343211023767","url":null,"abstract":"<p><p>Gefitinib resistance is a serious threat in the treatment of patients with non-small cell lung cancer (NSCLC). Elucidating the underlying mechanisms and developing effective therapies to overcome gefitinib resistance is urgently needed. The differentially expressed genes (DEGs) were screened from the gene expression profile GSE122005 between gefitinib-sensitive and resistant samples. GO and KEGG analyses were performed with DAVID. The protein-protein interaction (PPI) network was established to visualize DEGs and screen hub genes. The functional roles of CCL20 in lung adenocarcinoma (LUAD) were examined using gene set enrichment analysis (GSEA). Functional analysis revealed that the DEGs were mainly concentrated in inflammatory, cell chemotaxis, and PI3K signal regulation. Ten hub genes were identified based on the PPI network. The survival analysis of the hub genes showed that CCL20 had a significant effect on the prognosis of LUAD patients. GSEA analysis showed that CCL20 high expression group was mainly enriched in cytokine-related signaling pathways. In conclusion, our analysis suggests that changes in inflammation and cytokine-related signaling pathways are closely related to gefitinib resistance in patients with lung cancer. The CCL20 gene may promote the formation of gefitinib resistance, which may serve as a new biomarker for predicting gefitinib resistance in patients with lung cancer.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/11769343211023767","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39112216","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: 4
Insights into Bacterial Community Involved in Bioremediation of Aged Oil-Contaminated Soil in Arid Environment. 对干旱环境中老化石油污染土壤生物修复中细菌群落的见解。
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2021-06-08 DOI: 10.1177/11769343211016887
Rita Rahmeh, Abrar Akbar, Vinod Kumar, Hamad Al-Mansour, Mohamed Kishk, Nisar Ahmed, Mustafa Al-Shamali, Anwar Boota, Zainab Al-Ballam, Anisha Shajan, Naser Al-Okla
{"title":"Insights into Bacterial Community Involved in Bioremediation of Aged Oil-Contaminated Soil in Arid Environment.","authors":"Rita Rahmeh,&nbsp;Abrar Akbar,&nbsp;Vinod Kumar,&nbsp;Hamad Al-Mansour,&nbsp;Mohamed Kishk,&nbsp;Nisar Ahmed,&nbsp;Mustafa Al-Shamali,&nbsp;Anwar Boota,&nbsp;Zainab Al-Ballam,&nbsp;Anisha Shajan,&nbsp;Naser Al-Okla","doi":"10.1177/11769343211016887","DOIUrl":"10.1177/11769343211016887","url":null,"abstract":"<p><p>Soil contamination by hydrocarbons due to oil spills has become a global concern and it has more implications in oil producing regions. Biostimulation is considered as one of the promising remediation techniques that can be adopted to enhance the rate of degradation of crude oil. The soil microbial consortia play a critical role in governing the biodegradation of total petroleum hydrocarbons (TPHs), in particular polycyclic aromatic hydrocarbons (PAHs). In this study, the degradation pattern of TPHs and PAHs of Kuwait soil biopiles was measured at three-month intervals. Then, the microbial consortium associated with oil degradation at each interval was revealed through 16S rRNA based next generation sequencing. Rapid degradation of TPHs and most of the PAHs was noticed at the first 3 months of biostimulation with a degradation rate of pyrene significantly higher compared to other PAHs counterparts. The taxonomic profiling of individual stages of remediation revealed that, biostimulation of the investigated soil favored the growth of <i>Proteobacteria, Alphaprotobacteria, Chloroflexi, Chlorobi</i>, and <i>Acidobacteria</i> groups. These findings provide a key step towards the restoration of oil-contaminated lands in the arid environment.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/11769343211016887","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39020516","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: 4
Analysis of Emerging Variants in Structured Regions of the SARS-CoV-2 Genome. SARS-CoV-2基因组结构区域新出现的变异分析
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2021-05-05 eCollection Date: 2021-01-01 DOI: 10.1177/11769343211014167
Sean P Ryder, Brittany R Morgan, Peren Coskun, Katianna Antkowiak, Francesca Massi
{"title":"Analysis of Emerging Variants in Structured Regions of the SARS-CoV-2 Genome.","authors":"Sean P Ryder,&nbsp;Brittany R Morgan,&nbsp;Peren Coskun,&nbsp;Katianna Antkowiak,&nbsp;Francesca Massi","doi":"10.1177/11769343211014167","DOIUrl":"https://doi.org/10.1177/11769343211014167","url":null,"abstract":"<p><p>The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has motivated a widespread effort to understand its epidemiology and pathogenic mechanisms. Modern high-throughput sequencing technology has led to the deposition of vast numbers of SARS-CoV-2 genome sequences in curated repositories, which have been useful in mapping the spread of the virus around the globe. They also provide a unique opportunity to observe virus evolution in real time. Here, we evaluate two sets of SARS-CoV-2 genomic sequences to identify emerging variants within structured cis-regulatory elements of the SARS-CoV-2 genome. Overall, 20 variants are present at a minor allele frequency of at least 0.5%. Several enhance the stability of Stem Loop 1 in the 5' untranslated region (UTR), including a group of co-occurring variants that extend its length. One appears to modulate the stability of the frameshifting pseudoknot between ORF1a and ORF1b, and another perturbs a bi-ss molecular switch in the 3'UTR. Finally, 5 variants destabilize structured elements within the 3'UTR hypervariable region, including the S2M (stem loop 2 m) selfish genetic element, raising questions as to the functional relevance of these structures in viral replication. Two of the most abundant variants appear to be caused by RNA editing, suggesting host-viral defense contributes to SARS-CoV-2 genome heterogeneity. Our analysis has implications for the development of therapeutics that target viral cis-regulatory RNA structures or sequences.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/11769343211014167","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38933380","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: 12
The Missing Piece: Recent Approaches Investigating the Antimicrobial Mode of Action of Essential Oils. 缺失的部分:最近的方法调查抗菌模式的作用的精油。
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2021-05-04 eCollection Date: 2021-01-01 DOI: 10.1177/1176934320938391
Shun-Kai Yang, Ngai-Paing Tan, Chun-Wie Chong, Aisha Abushelaibi, Swee-Hua-Erin Lim, Kok-Song Lai
{"title":"The Missing Piece: Recent Approaches Investigating the Antimicrobial Mode of Action of Essential Oils.","authors":"Shun-Kai Yang,&nbsp;Ngai-Paing Tan,&nbsp;Chun-Wie Chong,&nbsp;Aisha Abushelaibi,&nbsp;Swee-Hua-Erin Lim,&nbsp;Kok-Song Lai","doi":"10.1177/1176934320938391","DOIUrl":"https://doi.org/10.1177/1176934320938391","url":null,"abstract":"<p><p>Antibiotic resistance is a major global health issue that has seen alarming rates of increase in all parts of the world over the past two decades. The surge in antibiotic resistance has resulted in longer hospital stays, higher medical costs, and elevated mortality rates. Constant attempts have been made to discover newer and more effective antimicrobials to reduce the severity of antibiotic resistance. Plant secondary metabolites, such as essential oils, have been the major focus due to their complexity and bioactive nature. However, the underlying mechanism of their antimicrobial effect remains largely unknown. Understanding the antimicrobial mode of action of essential oils is crucial in developing potential strategies for the use of essential oils in a clinical setting. Recent advances in genomics and proteomics have enhanced our understanding of the antimicrobial mode of action of essential oils. We might well be at the dawn of completing a mystery on how essential oils carry out their antimicrobial activities. Therefore, an overview of essential oils with regard to their antimicrobial activities and mode of action is discussed in this review. Recent approaches used in identifying the antimicrobial mode of action of essential oils, specifically from the perspective of genomics and proteomics, are also synthesized. Based on the information gathered from this review, we offer recommendations for future strategies and prospects for the study of essential oils and their function as antimicrobials.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1176934320938391","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38933378","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: 18
Identification and Analysis of Aux/IAA Family in Acer rubrum. 红叶复叶槭 Aux/IAA 家族的鉴定和分析
IF 1.7 4区 生物学
Evolutionary Bioinformatics Pub Date : 2021-04-12 eCollection Date: 2021-01-01 DOI: 10.1177/1176934321994127
Wenpeng Zhu, Manyu Zhang, Jianyi Li, Hewen Zhao, Wei Ge, Kezhong Zhang
{"title":"Identification and Analysis of <i>Aux/IAA</i> Family in <i>Acer rubrum</i>.","authors":"Wenpeng Zhu, Manyu Zhang, Jianyi Li, Hewen Zhao, Wei Ge, Kezhong Zhang","doi":"10.1177/1176934321994127","DOIUrl":"10.1177/1176934321994127","url":null,"abstract":"<p><p>The phytohormone auxin are important in all aspects of plant growth and development. The <i>Auxin/Indole-3-Acetic Acid</i> (<i>Aux/IAA</i>) gene responds to auxin induction as auxin early response gene family. Despite the physiological importance of the <i>Aux/IAA</i> gene, a systematic analysis of the <i>Aux/IAA</i> gene in <i>Acer rubrum</i> has not been reported. This paper describes the characterization of <i>Acer rubrum Aux/IAA</i> genes at the transcriptomic level and <i>Acer yangbiense Aux/IAA</i> genes at the genomic level, with 17 <i>Acer rubrum AUX/IAA</i> genes <i>(ArAux/IAA)</i> and 23 <i>Acer yangbiense Aux/IAA (AyAux/IAA)</i> genes identified. Phylogenetic analysis shows that <i>AyAux/IAA</i> and <i>ArAux/IAA</i> family genes can be subdivided into 4 groups and show strong evolutionary conservatism. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to test the expression profile of <i>ArAux/IAA</i> genes in different tissues under indole-3-acetic acid (IAA) treatment. Most <i>ArAux/IAA</i> genes are responsive to exogenous auxin and have tissue-specific expression. Overall, these results will provide molecular-level insights into auxin metabolism, transport, and signaling in <i>Acer</i> species.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2021-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0a/b4/10.1177_1176934321994127.PMC8044571.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38954026","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
Weighted gene co-expression network analysis of hub genes in lung adenocarcinoma. 肺腺癌中心基因的加权基因共表达网络分析。
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2021-04-12 eCollection Date: 2021-01-01 DOI: 10.1177/11769343211009898
Xuan Luo, Lei Feng, WenBo Xu, XueJing Bai, MengNa Wu
{"title":"Weighted gene co-expression network analysis of hub genes in lung adenocarcinoma.","authors":"Xuan Luo,&nbsp;Lei Feng,&nbsp;WenBo Xu,&nbsp;XueJing Bai,&nbsp;MengNa Wu","doi":"10.1177/11769343211009898","DOIUrl":"https://doi.org/10.1177/11769343211009898","url":null,"abstract":"<p><p>Lung adenocarcinoma (LUAD) is a tumor with high incidence. This study aimed to identify the central genes of LUAD. LUAD were analyzed by weighted gene co-expression network (WGCNA), and differentially expressed genes (DEGs) were identified. Samples were obtained from The Cancer Genome Atlas (TCGA) and Genotype Tissue Expression (GTEx) databases and included 515 LUAD samples and 347 normal samples. The WGCNA algorithm generated a total of 10 modules. The top 2 modules (MEturquoise and MEblue) with the highest correlation to LUAD were selected. Ten Hub genes (IL6, CDH1, PECAM1, SPP1, THBS1, HGF, SNCA, CDH5, CAV1, and DLC1) were screened in the intersecting genes of DEGs and WGCNA (MEturquoise and MEblue). Only SPP1 was correlated with LUAD poor survival, indicating that SPP1 may be a key Hub gene for LUAD. The competing endogenous RNA (ceRNA) network was constructed to analyze the regulatory relationship of Hub genes, and SPP1 may be directly regulated by 4 microRNAs (miRNAs) and indirectly regulated by 49 long noncoding RNAs (lncRNAs).</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/11769343211009898","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38838907","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: 10
Grafting Methionine on 1F1 Ab Increases the Broad-Activity on HA Structural-Conserved Residues of H1, H2, and H3 Influenza a Viruses. 在1F1 Ab上接枝蛋氨酸增加了H1、H2和H3甲型流感病毒HA结构保守残基的广谱活性。
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2021-03-16 eCollection Date: 2021-01-01 DOI: 10.1177/11769343211003082
Hoa Thanh Le, Phuc-Chau Do, Ly Le
{"title":"Grafting Methionine on 1F1 Ab Increases the Broad-Activity on HA Structural-Conserved Residues of H1, H2, and H3 Influenza a Viruses.","authors":"Hoa Thanh Le,&nbsp;Phuc-Chau Do,&nbsp;Ly Le","doi":"10.1177/11769343211003082","DOIUrl":"https://doi.org/10.1177/11769343211003082","url":null,"abstract":"<p><p>A high level of mutation enables the influenza A virus to resist antibiotics previously effective against the influenza A virus. A portion of the structure of hemagglutinin HA is assumed to be well-conserved to maintain its role in cellular fusion, and the structure tends to be more conserved than sequence. We designed peptide inhibitors to target the conserved residues on the HA surface, which were identified based on structural alignment. Most of the conserved and strongly similar residues are located in the receptor-binding and esterase regions on the HA1 domain In a later step, fragments of anti-HA antibodies were gathered and screened for the binding ability to the found conserved residues. As a result, Methionine amino acid got the best docking score within the -2.8 Å radius of Van der Waals when it is interacting with Tyrosine, Arginine, and Glutamic acid. Then, the binding affinity and spectrum of the fragments were enhanced by grafting hotspot amino acid into the fragments to form peptide inhibitors. Our peptide inhibitor was able to form in silico contact with a structurally conserved region across H1, H2, and H3 HA, with the binding site at the boundary between HA1 and HA2 domains, spreading across different monomers, suggesting a new target for designing broad-spectrum antibody and vaccine. This research presents an affordable method to design broad-spectrum peptide inhibitors using fragments of an antibody as a scaffold.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/11769343211003082","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25555273","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
The Functional Classification of ORF8 in SARS-CoV-2 Replication, Immune Evasion, and Viral Pathogenesis Inferred through Phylogenetic Profiling. ORF8在SARS-CoV-2复制、免疫逃避和病毒发病机制中的功能分类
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2021-03-15 eCollection Date: 2021-01-01 DOI: 10.1177/11769343211003079
Muhamad Fahmi, Hiromu Kitagawa, Gen Yasui, Yukihiko Kubota, Masahiro Ito
{"title":"The Functional Classification of ORF8 in SARS-CoV-2 Replication, Immune Evasion, and Viral Pathogenesis Inferred through Phylogenetic Profiling.","authors":"Muhamad Fahmi, Hiromu Kitagawa, Gen Yasui, Yukihiko Kubota, Masahiro Ito","doi":"10.1177/11769343211003079","DOIUrl":"10.1177/11769343211003079","url":null,"abstract":"<p><p><i>ORF8</i> is a highly variable genomic region of SARS-CoV-2. Although non-essential and the precise functions are unknown, it has been suggested that this protein assists in SARS-CoV-2 replication in the early secretory pathway and in immune evasion. We utilized the binding partners of SARS-CoV-2 proteins in human HEK293T cells and performed genome-wide phylogenetic profiling and clustering analyses in 446 eukaryotic species to predict and discover ORF8 binding partners that share associated functional mechanisms based on co-evolution. Results classified 47 ORF8 binding partner proteins into 3 clusters (groups 1-3), which were conserved in vertebrates (group 1), metazoan (group 2), and eukaryotes (group 3). Gene ontology analysis indicated that group 1 had no significant associated biological processes, while groups 2 and 3 were associated with glycoprotein biosynthesis process and ubiquitin-dependent endoplasmic reticulum-associated degradation pathways, respectively. Collectively, our results classified potential genes that might be associated with SARS-CoV-2 viral pathogenesis, specifically related to acute respiratory distress syndrome, and the secretory pathway. Here, we discuss the possible role of ORF8 in viral pathogenesis and in assisting viral replication and immune evasion via secretory pathway, as well as the possible factors associated with the rapid evolution of ORF8.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/11769343211003079","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25540618","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: 8
Plasmodium falciparum Malaria Parasites in Ghana Show Signatures of Balancing Selection at Artemisinin Resistance Predisposing Background Genes. 加纳恶性疟原虫显示青蒿素抗性易感背景基因的平衡选择特征。
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2021-03-03 eCollection Date: 2021-01-01 DOI: 10.1177/1176934321999640
Kwesi Z Tandoh, Lucas Amenga-Etego, Neils B Quashie, Gordon Awandare, Michael Wilson, Nancy O Duah-Quashie
{"title":"<i>Plasmodium falciparum</i> Malaria Parasites in Ghana Show Signatures of Balancing Selection at Artemisinin Resistance Predisposing Background Genes.","authors":"Kwesi Z Tandoh,&nbsp;Lucas Amenga-Etego,&nbsp;Neils B Quashie,&nbsp;Gordon Awandare,&nbsp;Michael Wilson,&nbsp;Nancy O Duah-Quashie","doi":"10.1177/1176934321999640","DOIUrl":"https://doi.org/10.1177/1176934321999640","url":null,"abstract":"<p><p>Sub-Saharan Africa is courting the risk of artemisinin resistance (ARTr) emerging in <i>Plasmodium falciparum</i> malaria parasites. Current molecular surveillance efforts for ARTr have been built on the utility of <i>P. falciparum</i> kelch13 (<i>pfk13</i>) validated molecular markers. However, whether these molecular markers will serve the purpose of early detection of artemisinin-resistant parasites in Ghana is hinged on a <i>pfk13</i> dependent evolution. Here, we tested the hypothesis that the background <i>pfk13</i> genome may be present before the <i>pfk13</i> ARTr-conferring variant(s) is selected and that signatures of balancing selection on these genomic loci may serve as an early warning signal of ARTr. We analyzed 12 198 single nucleotide polymorphisms (SNPs) in Ghanaian clinical isolates in the Pf3K MalariaGEN dataset that passed a stringent filtering regimen. We identified signatures of balancing selection in 2 genes (phosphatidylinositol 4-kinase and chloroquine resistance transporter) previously reported as background loci for ARTr. These genes showed statistically significant and high positive values for Tajima's D, Fu and Li's F, and Fu and Li's D. This indicates that the biodiversity required to establish a <i>pfk13</i> background genome may have been primed in clinical isolates of <i>P. falciparum</i> from Ghana as of 2010. Despite the absence of ARTr in Ghana to date, our finding supports the current use of <i>pfk13</i> for molecular surveillance of ARTr in Ghana and highlights the potential utility of monitoring malaria parasite populations for balancing selection in ARTr precursor background genes as early warning molecular signatures for the emergence of ARTr.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1176934321999640","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25500098","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: 4
Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi). 圈养高原鼢鼠肠道菌群的变化
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2021-02-27 eCollection Date: 2021-01-01 DOI: 10.1177/1176934321996353
Daoxin Liu, Pengfei Song, Jingyan Yan, Haijing Wang, Zhenyuan Cai, Jiuxiang Xie, Tongzuo Zhang
{"title":"Gut Microbiome Changes in Captive Plateau Zokors (<i>Eospalax baileyi</i>).","authors":"Daoxin Liu,&nbsp;Pengfei Song,&nbsp;Jingyan Yan,&nbsp;Haijing Wang,&nbsp;Zhenyuan Cai,&nbsp;Jiuxiang Xie,&nbsp;Tongzuo Zhang","doi":"10.1177/1176934321996353","DOIUrl":"https://doi.org/10.1177/1176934321996353","url":null,"abstract":"<p><p>Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor (<i>Eospalax baileyi</i>), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference (<i>P</i> < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2021-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1176934321996353","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38995356","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: 3
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