Evolutionary Bioinformatics最新文献

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An Intron of Invertebrate Microphthalmia Transcription Factor Gene Is Evolved from a Longer Ancestral Sequence. 无脊椎动物小眼症转录因子基因内含子由较长的祖先序列进化而来。
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2021-01-22 eCollection Date: 2021-01-01 DOI: 10.1177/1176934320988558
Jun-Ming Mao, Yong Wang, Liu Yang, Qin Yao, Ke-Ping Chen
{"title":"An Intron of Invertebrate Microphthalmia Transcription Factor Gene Is Evolved from a Longer Ancestral Sequence.","authors":"Jun-Ming Mao,&nbsp;Yong Wang,&nbsp;Liu Yang,&nbsp;Qin Yao,&nbsp;Ke-Ping Chen","doi":"10.1177/1176934320988558","DOIUrl":"https://doi.org/10.1177/1176934320988558","url":null,"abstract":"<p><p>Introns are highly variable in number and size. Sequence simulation is an effective method to elucidate intron evolution patterns. Previously, we have reported that introns are more likely to evolve through mutation-and-deletion (MD) rather than through mutation-and-insertion (MI). In the present study, we further studied evolution models by allowing insertion in the MD model and by allowing deletion in the MI model at various frequencies. It was found that all deletion-biased models with proper parameter settings could generate sequences with attributes matchable to 16 invertebrate introns from the microphthalmia transcription factor gene, whereas all insertion-biased models with any parameter settings failed to generate such sequences. We conclude that the examined invertebrate introns may have evolved from a longer ancestral sequence in a deletion-biased pattern. The constructed models are useful for studying the evolution of introns from other genes and/or from other taxonomic groups. (C++ scripts of all deletion- and insertion-biased models are available upon request.).</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"17 ","pages":"1176934320988558"},"PeriodicalIF":2.6,"publicationDate":"2021-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1176934320988558","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25340834","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
NLPEI: A Novel Self-Interacting Protein Prediction Model Based on Natural Language Processing and Evolutionary Information. NLPEI:一种基于自然语言处理和进化信息的自相互作用蛋白质预测模型。
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2020-12-26 eCollection Date: 2020-01-01 DOI: 10.1177/1176934320984171
Li-Na Jia, Xin Yan, Zhu-Hong You, Xi Zhou, Li-Ping Li, Lei Wang, Ke-Jian Song
{"title":"NLPEI: A Novel Self-Interacting Protein Prediction Model Based on Natural Language Processing and Evolutionary Information.","authors":"Li-Na Jia,&nbsp;Xin Yan,&nbsp;Zhu-Hong You,&nbsp;Xi Zhou,&nbsp;Li-Ping Li,&nbsp;Lei Wang,&nbsp;Ke-Jian Song","doi":"10.1177/1176934320984171","DOIUrl":"https://doi.org/10.1177/1176934320984171","url":null,"abstract":"<p><p>The study of protein self-interactions (SIPs) can not only reveal the function of proteins at the molecular level, but is also crucial to understand activities such as growth, development, differentiation, and apoptosis, providing an important theoretical basis for exploring the mechanism of major diseases. With the rapid advances in biotechnology, a large number of SIPs have been discovered. However, due to the long period and high cost inherent to biological experiments, the gap between the identification of SIPs and the accumulation of data is growing. Therefore, fast and accurate computational methods are needed to effectively predict SIPs. In this study, we designed a new method, NLPEI, for predicting SIPs based on natural language understanding theory and evolutionary information. Specifically, we first understand the protein sequence as natural language and use natural language processing algorithms to extract its features. Then, we use the Position-Specific Scoring Matrix (PSSM) to represent the evolutionary information of the protein and extract its features through the Stacked Auto-Encoder (SAE) algorithm of deep learning. Finally, we fuse the natural language features of proteins with evolutionary features and make accurate predictions by Extreme Learning Machine (ELM) classifier. In the SIPs gold standard data sets of human and yeast, NLPEI achieved 94.19% and 91.29% prediction accuracy. Compared with different classifier models, different feature models, and other existing methods, NLPEI obtained the best results. These experimental results indicated that NLPEI is an effective tool for predicting SIPs and can provide reliable candidates for biological experiments.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"16 ","pages":"1176934320984171"},"PeriodicalIF":2.6,"publicationDate":"2020-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1176934320984171","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38853529","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
Analysis of Adaptive Evolution and Coevolution of rbcL Gene in the Genus Hildenbrandia (Rhodophyta). 红藻属rbcL基因的适应进化与协同进化分析。
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2020-12-16 eCollection Date: 2020-01-01 DOI: 10.1177/1176934320977862
Nan Fangru, Han Yuxin, Liu Xudong, Feng Jia, Lv Junping, Liu Qi, Xie Shulian
{"title":"Analysis of Adaptive Evolution and Coevolution of <i>rbc</i>L Gene in the Genus <i>Hildenbrandia</i> (Rhodophyta).","authors":"Nan Fangru,&nbsp;Han Yuxin,&nbsp;Liu Xudong,&nbsp;Feng Jia,&nbsp;Lv Junping,&nbsp;Liu Qi,&nbsp;Xie Shulian","doi":"10.1177/1176934320977862","DOIUrl":"https://doi.org/10.1177/1176934320977862","url":null,"abstract":"<p><p>The adaptive evolution and coevolution of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (<i>rbc</i>L) gene in the genus <i>Hildenbrandia</i> were studied based on phylogenetic tree construction and the physicochemical properties and the secondary structures of protein encoded by <i>rbc</i>L (Rubisco large subunit) were analyzed. The amino acids compositions and grand average of hydropathicity of freshwater <i>H. rivularis</i> and marine <i>H. rubra</i> were similar. Rubisco large subunit of <i>Hildenbrandia</i> was hydrophilic and the secondary structure was primarily composed of α-helixes and β-sheets, revealing the relatively stable structure of this protein. The predicted phosphorylation sites in <i>H. rivularis</i> and <i>H. rubra</i> were 33 and 36, respectively. No positive selection sites were detected in the genus <i>Hildenbrandia</i>, implying that <i>rbc</i>L gene evolved either neutrally or under purifying selection. A total of 41 coevolutionary groups were detected in the Rubisco large subunit of <i>Hildenbrandia</i> and the coevolving sites are in closer proximity in 3-dimensional structure of the protein. Despite the long evolutionary history, <i>rbc</i>L gene in genus <i>Hildenbrandia</i> under different environments is rather conservative.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"16 ","pages":"1176934320977862"},"PeriodicalIF":2.6,"publicationDate":"2020-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1176934320977862","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39132480","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: 1
Hypergraph Clustering Based on Game-Theory for Mining Microbial High-Order Interaction Module. 基于博弈论的超图聚类用于挖掘微生物高阶交互模块
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2020-12-04 eCollection Date: 2020-01-01 DOI: 10.1177/1176934320970572
Limin Yu, Xianjun Shen, Jincai Yang, Kaiping Wei, Duo Zhong, Ruilong Xiang
{"title":"Hypergraph Clustering Based on Game-Theory for Mining Microbial High-Order Interaction Module.","authors":"Limin Yu, Xianjun Shen, Jincai Yang, Kaiping Wei, Duo Zhong, Ruilong Xiang","doi":"10.1177/1176934320970572","DOIUrl":"10.1177/1176934320970572","url":null,"abstract":"<p><p>Microbial community is ubiquitous in nature, which has a great impact on the living environment and human health. All these effects of microbial communities on the environment and their hosts are often referred to as the functions of these communities, which depend largely on the composition of the communities. The study of microbial higher-order module can help us understand the dynamic development and evolution process of microbial community and explore community function. Considering that traditional clustering methods depend on the number of clusters or the influence of data that does not belong to any cluster, this paper proposes a hypergraph clustering algorithm based on game theory to mine the microbial high-order interaction module (HCGI), and the hypergraph clustering problem naturally turns into a clustering game problem, the partition of network modules is transformed into finding the critical point of evolutionary stability strategy (ESS). The experimental results show HCGI does not depend on the number of classes, and can get more conservative and better quality microbial clustering module, which provides reference for researchers and saves time and cost. The source code of HCGI in this paper can be downloaded from https://github.com/ylm0505/HCGI.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"16 ","pages":"1176934320970572"},"PeriodicalIF":2.6,"publicationDate":"2020-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/24/ac/10.1177_1176934320970572.PMC7720323.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38718028","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
Alteration of the Gut Microbiome in Normal and Overweight School Children from Selangor with Lactobacillus Fermented Milk Administration. 雪兰莪州正常和超重学龄儿童肠道微生物群的改变与乳杆菌发酵乳的应用。
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2020-11-23 eCollection Date: 2020-01-01 DOI: 10.1177/1176934320965943
Narcisse Joseph, Jonathan B Clayton, Susan L Hoops, Carter A Linhardt, Amalia Mohd Hashim, Barakatun Nisak Mohd Yusof, Suresh Kumar, Syafinaz Amin Nordin
{"title":"Alteration of the Gut Microbiome in Normal and Overweight School Children from Selangor with <i>Lactobacillus</i> Fermented Milk Administration.","authors":"Narcisse Joseph,&nbsp;Jonathan B Clayton,&nbsp;Susan L Hoops,&nbsp;Carter A Linhardt,&nbsp;Amalia Mohd Hashim,&nbsp;Barakatun Nisak Mohd Yusof,&nbsp;Suresh Kumar,&nbsp;Syafinaz Amin Nordin","doi":"10.1177/1176934320965943","DOIUrl":"https://doi.org/10.1177/1176934320965943","url":null,"abstract":"<p><p>Childhood obesity is a serious public health problem worldwide. Perturbations in the gut microbiota composition have been associated with the development of obesity in both children and adults. Probiotics, on the other hand, are proven to restore the composition of the gut microbiome which helps reduce the development of obesity. However, data on the effect of probiotics on gut microbiota and its association with childhood obesity is limited. This study aims to determine the effect of probiotics supplement intervention on gut microbiota profiles in obese and normal-weight children. A total of 37 children, 17 normal weight, and 20 overweight school children from a government school in Selangor were selected to participate in this study. Participants were further divided into intervention and control groups. The intervention groups received daily probiotic drinks while the control groups continued eating their typical diet. Fecal samples were collected from the participants for DNA extraction. The hypervariable V3 and V4 regions of 16S rRNA gene were amplified and sequenced using the Illumina MiSeq platform. No significant differences in alpha diversity were observed between normal weight and obese children in terms of the Shannon Index for evenness or species richness. However, a higher intervention effect on alpha diversity was observed among normal-weight participants compared to obese. The participants' microbiome was found to fluctuate throughout the study. Analysis of the taxa at species level showed an increase in <i>Bacteroides ovatus</i> among the normal weight cohort. Genus-level comparison revealed a rise in genus <i>Lachnospira</i> and <i>Ruminococcus</i> in the overweight participants after intervention, compared to the normal-weight participants. The probiotics intervention causes an alteration in gut microbiota composition in both normal and overweight children. Though the association could not be defined statistically, this study has provided an improved understanding of the intervention effect of probiotics on gut microbiome dysbiosis in an underrepresented population.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"16 ","pages":"1176934320965943"},"PeriodicalIF":2.6,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1176934320965943","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38678530","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
New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. SARS-CoV-2蛋白组突变变化的新途径涉及对病毒复制和释放重要的内在紊乱区域
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2020-10-23 eCollection Date: 2020-01-01 DOI: 10.1177/1176934320965149
Tre Tomaszewski, Ryan S DeVries, Mengyi Dong, Gitanshu Bhatia, Miles D Norsworthy, Xuying Zheng, Gustavo Caetano-Anollés
{"title":"New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release.","authors":"Tre Tomaszewski,&nbsp;Ryan S DeVries,&nbsp;Mengyi Dong,&nbsp;Gitanshu Bhatia,&nbsp;Miles D Norsworthy,&nbsp;Xuying Zheng,&nbsp;Gustavo Caetano-Anollés","doi":"10.1177/1176934320965149","DOIUrl":"https://doi.org/10.1177/1176934320965149","url":null,"abstract":"<p><p>The massive worldwide spread of the SARS-CoV-2 virus is fueling the COVID-19 pandemic. Since the first whole-genome sequence was published in January 2020, a growing database of tens of thousands of viral genomes has been constructed. This offers opportunities to study pathways of molecular change in the expanding viral population that can help identify molecular culprits of virulence and virus spread. Here we investigate the genomic accumulation of mutations at various time points of the early pandemic to identify changes in mutationally highly active genomic regions that are occurring worldwide. We used the Wuhan NC_045512.2 sequence as a reference and sampled 15 342 indexed sequences from GISAID, translating them into proteins and grouping them by month of deposition. The per-position amino acid frequencies and Shannon entropies of the coding sequences were calculated for each month, and a map of intrinsic disorder regions and binding sites was generated. The analysis revealed dominant variants, most of which were located in loop regions and on the surface of the proteins. Mutation entropy decreased between March and April of 2020 after steady increases at several sites, including the D614G mutation site of the spike (S) protein that was previously found associated with higher case fatality rates and at sites of the NSP12 polymerase and the NSP13 helicase proteins. Notable expanding mutations include R203K and G204R of the nucleocapsid (N) protein inter-domain linker region and G251V of the viroporin encoded by ORF3a between March and April. The regions spanning these mutations exhibited significant intrinsic disorder, which was enhanced and decreased by the N-protein and viroporin 3a protein mutations, respectively. These results predict an ongoing mutational shift from the spike and replication complex to other regions, especially to encoded molecules known to represent major β-interferon antagonists. The study provides valuable information for therapeutics and vaccine design, as well as insight into mutation tendencies that could facilitate preventive control.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"16 ","pages":"1176934320965149"},"PeriodicalIF":2.6,"publicationDate":"2020-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1176934320965149","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38570973","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: 37
Vesicle Transport in Plants: A Revised Phylogeny of SNARE Proteins. 植物的囊泡转运:对SNARE蛋白系统发育的修正。
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2020-10-15 eCollection Date: 2020-01-01 DOI: 10.1177/1176934320956575
Xiaoyan Gu, Adrian Brennan, Wenbin Wei, Guangqin Guo, Keith Lindsey
{"title":"Vesicle Transport in Plants: A Revised Phylogeny of SNARE Proteins.","authors":"Xiaoyan Gu, Adrian Brennan, Wenbin Wei, Guangqin Guo, Keith Lindsey","doi":"10.1177/1176934320956575","DOIUrl":"10.1177/1176934320956575","url":null,"abstract":"<p><p>Communication systems within and between plant cells involve the transfer of ions and molecules between compartments, and are essential for development and responses to biotic and abiotic stresses. This in turn requires the regulated movement and fusion of membrane systems with their associated cargo. Recent advances in genomics has provided new resources with which to investigate the evolutionary relationships between membrane proteins across plant species. Members of the soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are known to play important roles in vesicle trafficking across plant, animal and microbial species. Using recent public expression and transcriptomic data from 9 representative green plants, we investigated the evolution of the SNARE classes and linked protein changes to functional specialization (expression patterns). We identified an additional 3 putative SNARE genes in the model plant <i>Arabidopsis</i>. We found that all SNARE classes have expanded in number to a greater or lesser degree alongside the evolution of multicellularity, and that within-species expansions are also common. These gene expansions appear to be associated with the accumulation of amino acid changes and with sub-functionalization of SNARE family members to different tissues. These results provide an insight into SNARE protein evolution and functional specialization. The work provides a platform for hypothesis-building and future research into the precise functions of these proteins in plant development and responses to the environment.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"16 ","pages":"1176934320956575"},"PeriodicalIF":2.6,"publicationDate":"2020-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7573729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38634879","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
Cathepsin F of Teladorsagia circumcincta is a recently evolved cysteine protease. 组织蛋白酶F是一种新近进化的半胱氨酸蛋白酶。
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2020-10-10 eCollection Date: 2020-01-01 DOI: 10.1177/1176934320962521
Sarah Sloan, Caitlin Jenvey, Callum Cairns, Michael Stear
{"title":"Cathepsin F of <i>Teladorsagia circumcincta</i> is a recently evolved cysteine protease.","authors":"Sarah Sloan,&nbsp;Caitlin Jenvey,&nbsp;Callum Cairns,&nbsp;Michael Stear","doi":"10.1177/1176934320962521","DOIUrl":"https://doi.org/10.1177/1176934320962521","url":null,"abstract":"<p><p>Parasitic cysteine proteases are involved in parasite stage transition, invasion of host tissues, nutrient uptake, and immune evasion. The cysteine protease cathepsin F is the most abundant protein produced by fourth-stage larvae (L4) of the nematode <i>Teladorsagia circumcincta</i>, while its transcript is only detectable in L4 and adults. <i>T. circumcincta</i> cathepsin F is a recently evolved cysteine protease that does not fall clearly into either of the cathepsin L or F subfamilies. This protein exhibits characteristics of both cathepsins F and L, and its phylogenetic relationship to its closest homologs is distant, including proteins of closely related nematodes of the same subfamily.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"16 ","pages":"1176934320962521"},"PeriodicalIF":2.6,"publicationDate":"2020-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1176934320962521","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38526966","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
Identification of Hub Genes and Potential Molecular Mechanisms in Patients with HBV-Associated Acute Liver Failure. 乙肝病毒相关急性肝衰竭患者Hub基因的鉴定及其潜在分子机制
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2020-10-10 eCollection Date: 2020-01-01 DOI: 10.1177/1176934320943901
Ying Sun, Haitao Yu, Fangfang Li, Liqiang Lan, Daxin He, Haijun Zhao, Dachuan Qi
{"title":"Identification of Hub Genes and Potential Molecular Mechanisms in Patients with HBV-Associated Acute Liver Failure.","authors":"Ying Sun,&nbsp;Haitao Yu,&nbsp;Fangfang Li,&nbsp;Liqiang Lan,&nbsp;Daxin He,&nbsp;Haijun Zhao,&nbsp;Dachuan Qi","doi":"10.1177/1176934320943901","DOIUrl":"https://doi.org/10.1177/1176934320943901","url":null,"abstract":"<p><p>Hepatitis B virus (HBV) infection is a major cause of acute liver failure (ALF) in China, and mortality rates are high among patients who do not receive a matched liver transplant. This study aimed to determine potential mechanisms involved in HBV-ALF pathogenesis. Gene expression profiles under access numbers GSE38941 and GSE14668 were downloaded from the Gene Expression Omnibus database, including cohorts of HBV-ALF liver tissue and normal samples. Differentially expressed genes (DEGs) with false discovery rates (FDR) <0.05 and |log<sub>2</sub>(fold change)| >1 as thresholds were screened using the Limma package. Gene modules associated with stable disease were mined using weighed gene co-expression network analysis (WGCNA). A co-expression network was constructed and DEGs were analyzed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. A gene-based network was constructed to explore major factors associated with disease progression. We identified 2238 overlapping DEGs as crucial gene cohorts in ALF development. Based on a WGCNA algorithm, 10 modules (modules 1-10) were obtained that ranged from 75 to 1078 genes per module. Cyclin-dependent kinase 1 (<i>CDK1</i>), cyclin B1 (<i>CCNB1</i>), and cell-division cycle protein 20 (<i>CDC20</i>) hub genes were screened using the co-expression network. Furthermore, 17 GO terms and 6 KEGG pathways were identified, such as cell division, immune response process, and antigen processing and presentation. Two overlapping signaling pathways that are crucial factors in HBV-ALF were screened using the Comprehensive Toxicogenomics Database (CTD). Several candidate genes including <i>HLA-E, B2M, HLA-DPA1</i>, and <i>SYK</i> were associated with HBV-ALF progression. Natural killer cell-mediated cytotoxicity and antigen presentation contributed to the progression of HBV-ALF. The <i>HLA-E, B2M, HLA-DPA1</i>, and <i>SYK</i> genes play critical roles in the pathogenesis and development of HBV-ALF.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"16 ","pages":"1176934320943901"},"PeriodicalIF":2.6,"publicationDate":"2020-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1176934320943901","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38526964","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: 2
Does Ulcerative Colitis Influence the Inter-individual Heterogeneity of the Human Intestinal Mucosal Microbiome? 溃疡性结肠炎是否影响人类肠道黏膜微生物组的个体间异质性?
IF 2.6 4区 生物学
Evolutionary Bioinformatics Pub Date : 2020-10-10 eCollection Date: 2020-01-01 DOI: 10.1177/1176934320948848
Yang Sun, Lianwei Li, Aiyun Lai, Wanmeng Xiao, Kunhua Wang, Lan Wang, Junkun Niu, Juan Luo, Hongju Chen, Lin Dai, Yinglei Miao
{"title":"Does Ulcerative Colitis Influence the Inter-individual Heterogeneity of the Human Intestinal Mucosal Microbiome?","authors":"Yang Sun,&nbsp;Lianwei Li,&nbsp;Aiyun Lai,&nbsp;Wanmeng Xiao,&nbsp;Kunhua Wang,&nbsp;Lan Wang,&nbsp;Junkun Niu,&nbsp;Juan Luo,&nbsp;Hongju Chen,&nbsp;Lin Dai,&nbsp;Yinglei Miao","doi":"10.1177/1176934320948848","DOIUrl":"https://doi.org/10.1177/1176934320948848","url":null,"abstract":"<p><p>The dysbiosis of the gut microbiome associated with ulcerative colitis (UC) has been extensively studied in recent years. However, the question of whether UC influences the spatial heterogeneity of the human gut mucosal microbiome has not been addressed. Spatial heterogeneity (specifically, the inter-individual heterogeneity in microbial species abundances) is one of the most important characterizations at both population and community scales, and can be assessed and interpreted by Taylor's power law (TPL) and its community-scale extensions (TPLEs). Due to the high mobility of microbes, it is difficult to investigate their spatial heterogeneity explicitly; however, TPLE offers an effective approach to implicitly analyze the microbial communities. Here, we investigated the influence of UC on the spatial heterogeneity of the gut microbiome with intestinal mucosal microbiome samples collected from 28 UC patients and healthy controls. Specifically, we applied Type-I TPLE for measuring community spatial heterogeneity and Type-III TPLE for measuring mixed-species population heterogeneity to evaluate the heterogeneity changes of the mucosal microbiome induced by UC at both the community and species scales. We further used permutation test to determine the possible differences between UC patients and healthy controls in heterogeneity scaling parameters. Results showed that UC did not significantly influence gut mucosal microbiome heterogeneity at either the community or mixed-species levels. These findings demonstrated significant resilience of the human gut microbiome and confirmed a prediction of TPLE: that the inter-subject heterogeneity scaling parameter of the gut microbiome is an intrinsic property to humans, invariant with UC disease.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":"16 ","pages":"1176934320948848"},"PeriodicalIF":2.6,"publicationDate":"2020-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1177/1176934320948848","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38526965","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: 2
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