{"title":"A Stress Response Program at the Origin of Evolutionary Innovation in the Skin","authors":"L. Eckhart, F. Ehrlich, E. Tschachler","doi":"10.1177/1176934319862246","DOIUrl":"https://doi.org/10.1177/1176934319862246","url":null,"abstract":"The skin epithelium, ie, the epidermis, of dolphins and whales (cetaceans) is up to 50 times thicker than that of humans and other mammals living on land. Recently, comparative genomics revealed further striking differences in the cytoskeleton of the outer layers of the epidermis in aquatic and terrestrial mammals. Cetaceans lack the cytoskeletal keratins, which make up more than half of the total protein mass in the cornified epidermal layer of terrestrial mammals under homeostatic conditions. By contrast, orthologs of stress-inducible epithelial keratins are conserved in cetaceans and these keratins are constitutively expressed in their skin. Thus, the epidermal stress response program of a terrestrial common ancestor of modern mammals has become the default program of epidermal differentiation and a central component of the unique cutaneous organization of cetaceans. We propose that phenotypic plasticity during stress responses plays important roles in the evolution of the skin.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"s2-2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124183098","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}
Yongchun Zuo, Yu Chang, Shenghui Huang, Lei Zheng, Lei Yang, G. Cao
{"title":"iDEF-PseRAAC: Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor","authors":"Yongchun Zuo, Yu Chang, Shenghui Huang, Lei Zheng, Lei Yang, G. Cao","doi":"10.1177/1176934319867088","DOIUrl":"https://doi.org/10.1177/1176934319867088","url":null,"abstract":"Defensins as 1 of major classes of host defense peptides play a significant role in the innate immunity, which are extremely evolved in almost all living organisms. Developing high-throughput computational methods can accurately help in designing drugs or medical means to defense against pathogens. To take up such a challenge, an up-to-date server based on rigorous benchmark dataset, referred to as iDEF-PseRAAC, was designed for predicting the defensin family in this study. By extracting primary sequence compositions based on different types of reduced amino acid alphabet, it was calculated that the best overall accuracy of the selected feature subset was achieved to 92.38%. Therefore, we can conclude that the information provided by abundant types of amino acid reduction will provide efficient and rational methodology for defensin identification. And, a free online server is freely available for academic users at http://bioinfor.imu.edu.cn/idpf. We hold expectations that iDEF-PseRAAC may be a promising weapon for the function annotation about the defensins protein.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128946378","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}
Sofia B. Mohamed, Talal A Adlan, Nagla A Khalafalla, Nusiba I Abdalla, Zainab Sa Ali, Abdella Munir Ka, Mohamed M. Hassan, Mohammed A. Elnour
{"title":"Proteomics and Docking Study Targeting Penicillin-Binding Protein and Penicillin-Binding Protein2a of Methicillin-Resistant Staphylococcus aureus Strain SO-1977 Isolated from Sudan","authors":"Sofia B. Mohamed, Talal A Adlan, Nagla A Khalafalla, Nusiba I Abdalla, Zainab Sa Ali, Abdella Munir Ka, Mohamed M. Hassan, Mohammed A. Elnour","doi":"10.1177/1176934319864945","DOIUrl":"https://doi.org/10.1177/1176934319864945","url":null,"abstract":"Whole genome sequencing of methicillin-resistant Staphylococcus aureus (MRSA) strain isolated from Sudan has led to a great deal of information, which allows the identification and characterization of some pivotal proteins. The objective of this study was to investigate the penicillin-binding proteins, PBP and PBP2a, of SO-1977 strain to have insights about their physicochemical properties and to assess and describe the interaction of some phytochemicals against them in silico. PBP and PBP2a from MRSA’s Sudan strain were found to be of great resemblance with some other strains. G246E single-nucleotide polymorphism was reported and identified in the allosteric binding site positioned in the non-penicillin-binding domain. The docked compounds demonstrated good binding energies and hydrogen bond interactions with residue Ser404 which plays crucial roles in β-lactam activity. This finding would contribute significantly to designing effective β-lactam drugs, to combat and treat β-lactam–resistant bacteria in the future.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"70 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131153899","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}
{"title":"In Silico Analysis of Hepatitis B Virus Genotype D Subgenotype D1 Circulating in Pakistan, China, and India","authors":"Muneeb Bahar, M. T. Pervez, Akhtar Ali, M. Babar","doi":"10.1177/1176934319861337","DOIUrl":"https://doi.org/10.1177/1176934319861337","url":null,"abstract":"The focus of this study was the computational analysis of hepatitis B virus (HBV) genotype D subgenotype D1 in Pakistan, China, and India. In total, 54 complete genome sequences of HBV genotype D subgenotype D1 were downloaded from National Center for Biotechnology Information (NCBI). Of these, 6 complete genome sequences were from Pakistan, 14 were from China, and 34 were from India. Sequence alignment showed less than 4% divergence in these sequences. C and X genes showed divergence of less than 3%. Comparison over the S gene showed more than 97% similarity among the nucleotide sequences of genotype D subgenotype D1. The identity and similarity matrix of 54 nucleotide sequences of HBV genotype D subgenotype D1 from Pakistan, China, and India revealed more than 93% identity and 93% similarity. Phylogenetic analysis highlighted that complete genome isolates of HBV circulating in Pakistan had the closest evolutionary relationship with its neighboring countries China and India. China’s (HQ833466) and Pakistan’s (AB583680.1) isolates shared the same ancestor. Gene structure analysis showed that “P” gene exons were the longest, about three-fourth of the genome size, whereas gene “S” had the second longest coding regions with 2 exons and 1 intron. However, “C” and “X” genes had 1 smallest exon. X proteins had proven role in spreading of the HBV infection diseases. For HBx analysis, 1 X protein sequence of HBV genotype D subgenotype D1 belonging to each country was obtained. Homology models of the 3 X proteins generated using SWISS-MODEL revealed GMQE (Global Model Quality Estimation) = 0.1. Global and local quality estimate scores including Z-scores for Qualitative Model Energy Analysis (QMEAN) C-beta, all-atom, solvation, and torsion energy scores were similar indicating good quality, accuracy, and reliability of the predicted models. Three-dimensional (3D) visualization showed similar structures and Ramachandran plots showed a high percentage of protein residues into the favorable region for X protein models.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123495194","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}
{"title":"Versatile Quality Control Methods for Nanopore Sequencing","authors":"D. Bolognini, R. Semeraro, A. Magi","doi":"10.1177/1176934319863068","DOIUrl":"https://doi.org/10.1177/1176934319863068","url":null,"abstract":"Third-generation sequencing using nanopores as biosensors has recently emerged as a strategy capable to overcome next-generation sequencing drawbacks and pitfalls. Assessing the quality of the data produced by nanopore sequencing platforms is essential to decide how useful these may be in making biological discoveries. Here, we briefly contextualized NanoR, a quality control method for nanopore sequencing data we developed, in the scenario of preexistent similar tools. We also illustrated 2 quality control pipelines, readily applicable to nanopore sequencing data, respectively, based on NanoR and PyPore, a second quality control method published by our group.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121525717","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}
Artur Kumar, Arun Panja, A. Sundar, Boškovic, Borko Caetano, Daniel Chang, Hsueh-Wei Cheng, D. Prandi, Davide Santesmasses, D. Sekar, D. Moraes, Evandro Matsuda, Fumio Dussart, Francois Casalino, Gabriella Daetwyler, Hans Yang, Haixuan Wang, Haohan Hashimoto, Tetsuo Li, Hengde Hilu, Kh Lin, Hao Hou, C. Seim, I. Wolters, Jaap Hily, Jean-Michel Martini, Johannes W. R. Tang, Jijun Jensen, Louise Puchades, Leonor Bollu, L. Serafim, Luísa Nunes, Lw Lu, Tomoaki Yamashiro, Tadashi Greiff, V. Parada, Victor Gu, Wanjun Liu, Weiguo Wellmer, Frank Karlowski, Wojciech Yu, Xiaolin Yau, Stephen S T Nakamura, Yoji Tepe, Yah Ma, Yunlong Zhao
{"title":"Diversified Variants of Astrovirus MLB2 in Patients Following Hematopoietic Stem Cell Transplantation and the Evolutionary Rates and Patterns of the Virus","authors":"K. Guo, Li-li Li, Qing Zhang, Jie-mei Yu, Yan Ye","doi":"10.1177/1176934319864922","DOIUrl":"https://doi.org/10.1177/1176934319864922","url":null,"abstract":"We assessed the quasispecies heterogeneity of a human astrovirus MLB2 (HAstV-MLB2-YJMGK) in immunocompromised patients following hematopoietic stem cell transplantation and performed genetic and evolutionary analyses of HAstV isolates circulating worldwide. The result showed that the virus had diversified variants and a strong positive selection in the patient, indicating that such patients may be a reservoir for astrovirus. The time to the most recent common ancestor of MLB2 and classic HAstVs was around 1800 years, and it has a decline in effective population size of HAstVs in the late 100 years.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134633452","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}
Katja Nowick, Maria Beatriz Walter Costa, C. Höner zu Siederdissen, P. Stadler
{"title":"Selection Pressures on RNA Sequences and Structures","authors":"Katja Nowick, Maria Beatriz Walter Costa, C. Höner zu Siederdissen, P. Stadler","doi":"10.1177/1176934319871919","DOIUrl":"https://doi.org/10.1177/1176934319871919","url":null,"abstract":"With the discovery of increasingly more functional noncoding RNAs (ncRNAs), it becomes eminent to more strongly consider them as important players during species evolution. Although tests for negative selection of ncRNAs already exist since the beginning of this century, the SSS-test is the first one for also investigating positive selection. When analyzing selection in ncRNAs, it should be taken into account that selection pressures can independently act on sequence and structure. We applied the SSS-test to explore the evolution of ncRNAs in primates and identified more than 100 long noncoding RNAs (lncRNAs) that might evolve under positive selection in humans. With this test, it is now possible to more thoroughly include ncRNAs into evolutionary studies.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129230194","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}
{"title":"Gene Families, Epistasis and the Amino Acid Preferences of Protein Homologs","authors":"E. Ferrada","doi":"10.1177/1176934319870485","DOIUrl":"https://doi.org/10.1177/1176934319870485","url":null,"abstract":"In order to preserve structure and function, proteins tend to preferentially conserve amino acids at particular sites along the sequence. Because mutations can affect structure and function, the question arises whether the preference of a protein site for a particular amino acid varies between protein homologs, and to what extent that variation depends on sequence divergence. Answering these questions can help in the development of models of sequence evolution, as well as provide insights on the dependence of the fitness effects of mutations on the genetic background of sequences, a phenomenon known as epistasis. Here, I comment on recent computational work providing a systematic analysis of the extent to which the amino acid preferences of proteins depend on the background mutations of protein homologs.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125250739","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}
{"title":"Molecular Docking of Broad-Spectrum Antibodies on Hemagglutinins of Influenza A Virus","authors":"Khanh Le, Phuc-Chau Do, Rommie E. Amaro, Ly Le","doi":"10.1177/1176934319876938","DOIUrl":"https://doi.org/10.1177/1176934319876938","url":null,"abstract":"Influenza A has caused several deadly pandemics throughout human history. The virus is often resistant to developed treatments because of its genetic drift or shift property. Broad-spectrum antibodies show a promising potential to overcome the resistance of influenza viruses. In silico studies on broad-reactive antibodies and their interactions with hemagglutinins might shed light on the rational design of a universal vaccine. In this study, 11 broad-spectrum antibodies (or antigen-binding fragments) and 14 hemagglutinins of H3N2 and H5N1 strains were docked and analyzed to provide information about the construction of the scaffold for using universal antibodies against the influenza A virus. Antigen-binding fragments that have high number of appearances in the top 3 within each H3 and H5 subtypes were chosen for protein-protein interaction analysis. The results show that while the hydrogen bond is important for Ab/Fab binding to H3, the H5-Ab/Fab system may need cation-pi interaction for a strong interaction.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"46 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123237138","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}
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