MOJ proteomics & bioinformatics最新文献

{"title":"Problem-based learning (PBL), an important paradigm for bioinformatics education","authors":"M. Ling","doi":"10.15406/MOJPB.2017.05.00166","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00166","url":null,"abstract":"one of the final lines for computing advice, at least in my personal experience. As such, I often find myself given problems to solve rather than finding my own problems to tackle. Hence, problem solving becomes a recurring theme over the last one and a half decade. Problem solving as a core skill in bioinformatics is also supported by Jungck et al.3 Therefore, it is imperative that bioinformatics education consists of substantial amount of hands-on and minds-on activities.4","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74180099","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":"Gasotransmitters and Protein Post-Translational Modifications","authors":"Guangdong Yang","doi":"10.15406/MOJPB.2017.05.00165","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00165","url":null,"abstract":"","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"115 1","pages":"1-3"},"PeriodicalIF":0.0,"publicationDate":"2017-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80344401","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":"Computational tools and resources for CRISPR/Cas 9 genome editing method","authors":"Ragothaman M Yennmalli, Siddharth Kalra, Pulkit Srivastava, Vijay Kumar Garlapati","doi":"10.15406/MOJPB.2017.05.00164","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00164","url":null,"abstract":"From an evolutionary point of view, archaea and bacteria have evolved to survive and blossom as communities in active environments that are, in general, stressful and unpredictable. Specifically, the abundance of viruses attacking microorganisms is a constant threat; in addition, the mutation and recombination rates in viruses make them fast-evolving predators. To sustain against such predators, archaea and bacteria have evolved to have a new multilayered defense system that has been identified as CRISPR/Cas9.1 Consequently, many labs have tapped into the potential uses for this method and active research to unravel the mechanism has paved a unique path in the development of targeted genome editing techniques.2 Among the various genome editing methods, TALENs, ZFNs, and CRISPR-Cas9 are the three foremost methods.3","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82327148","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":"Type of stains used in detection of protein in gel","authors":"Alaa A Elnour","doi":"10.15406/MOJPB.2017.05.00163","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00163","url":null,"abstract":"Protein separation by two-dimensional electrophoresis (2DE) is largely used in proteomic approaches because of both high resolution and the availability of powerful image analysis software for gel comparison and compatibility with subsequent protein characterization by mass spectrometry [1]. For these various aspects, the selection of the protein staining procedure is of major importance [2]. Based on two independent biochemical characteristics of proteins, 2DE combines isoelectric focusing, which separates proteins according to their isoelectric point, and SDS-PAGE, which separates them further according to their molecular mass . The next typical steps of the flow of gel-based proteomics are spots visualization and evaluation, expression analysis, and finally protein identification by mass spectrometry. In order to take advantage of the high resolution capacity of 2DE, proteins have to be completely denatured, disaggregated, reduced and solubilized to disrupt molecular interactions and to ensure that each spot represents an individual polypeptide. Proteins can be stained before the open access Materials (pre-electrophoretic protein stain), or after 2DE separation (post-electrophoretic protein stain). Classically, Coomassie blue was the most widely used non-covalent dye for post-electrophoretic protein staining [3]. However, it suffers from a low sensitivity in protein detection, including in the improved colloidal version [4]. In contrast, the other classical protein stain, silver nitrate, displays an excellent sensitivity but could interfere with protein analysis by mass spectrometry [5]. In the last decade, different fluorescent dyes have been introduced [6]. These encompass Sypro Ruby [7], and Ruthenium red-based dyes [8]. However, their present use remains relatively limited, probably due to their cost and/or technical difficulties.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"54 11-12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91501054","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":"Comparison and analysis of different methods for purification of autoimmune antibody reactive with single stranded DNA: a pilot study","authors":"Anna Kats, M. Pavlovic, Ran Chen, Michelle Cavallo, J. Hartmann","doi":"10.15406/MOJPB.2017.05.00161","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00161","url":null,"abstract":"The hallmark of systemic lupus erythematosus (SLE) is the production of an array of IgG and IgM auto-antibodies directed against one or more nuclear components, most commonly double stranded (ds) DNA and/or single stranded (ss) DNA. Both antissDNA and anti-dsDNA antibodies are considered to be involved in disease development based on the fact that both have been eluted from the kidneys of experimental murine models and SLE patients.1 The level of anti-DNA antibodies, both ss and ds, varies in the plasma of different SLE patients, with increased levels coinciding with flares.2–4 Consequently, the level of anti-DNA antibodies in patients’ sera is used to monitor disease activity and progression.3–5 It is still not quite clear which fractions between these two categories of anti-DNA autoantibodies are pathogenic and why.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84225110","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":"Health status of the Indian women-a brief report","authors":"R. Kowsalya, S. Manoharan","doi":"10.15406/MOJPB.2017.05.00162","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00162","url":null,"abstract":"Women’s health concern is influenced by interrelated biological, social, and cultural factors (Figure 1). It is generally expected that women can live longer than men it does not necessarily ensure a better quality of life. Profound studies reported that women are more sickly and disabled than men throughout the life cycle. It has been suggested that women are particularly vulnerable, where basic maternity care is unavailable.1 Due to the involvement of biological factors, women are more prone to sexual exposure of contracting sexually transmitted infections (STIs), including the human immunodeficiency virus (HIV) than do men.2 Moreover an early marriage and childbirth could be responsible for the prevailing wide variation in the socioeconomic status. Profound studies pointed out the voluntary involvement of the community, paramedical workers, NGO, policy makers and teachers in various developmental programs for the removal of poverty and improve the literacy rate among females.3 Nutrition and health education should be strengthened via department of health to improve the nutritional status of mother and child, which are intimately linked.4 A strong and sustained government commitment is therefore needed to improve women’s, health concern.5","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88054544","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":"A smart way for talking with proteins; proteomics","authors":"T. Zengin, Sercan Kiliç, Ufuk Yenigün, Serhat Erdogmus, Ö. Baysal","doi":"10.15406/mojpb.2017.05.00160","DOIUrl":"https://doi.org/10.15406/mojpb.2017.05.00160","url":null,"abstract":"Proteomics is a rapidly tool to identify proteins and map their interactions in a cellular context1 and detailed study of proteins on a genome-wide scale as a key technology.2 These studies relies on dates back to the late 1970s to build databases of proteins using twodimensional gel electrophoresis,3 the term “proteomics” was first introduced in 19954–6 and defined as the large-scale characterization of the entire protein complement of a cell, tissue, or organism.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86642442","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":"Bioinformatic analysis of glycoside hydrolases in the proteomes of mesophilic and thermophilic Actinobacteria","authors":"Kip A. Teegardin, S. James, R. Barabote","doi":"10.15406/mojpb.2017.05.00158","DOIUrl":"https://doi.org/10.15406/mojpb.2017.05.00158","url":null,"abstract":"Petroleum fuels are finite and non-renewable and they pose a significant concern for global climate, sustainability, and international security [1]. Alternative renewable sources of energy are urgently needed to meet the current global challenges. Plants are the most abundant source of renewable carbon on Earth. Plant cell wall (lignocellulose) can be used for the production of renewable, sustainable, and environmentally -clean biofuels [2]. Lignocellulose is mainly composed of polymers of sugars (cellulose and hemicellulose) and phenolic units (lignin). While complex lignocellulose can be converted into liquid fuels thermo-chemically, biological transformation of lignocellulosic polysaccharides using microorganisms and microbial enzymes is an economical and environmentally benign process for sustainable production of biofuels [3,4]. Several microorganisms produce glycoside hydrolase enzymes such as cellulases and xylanases that break down cellulose and xylan (hemicellulose), respectively [5]. Efficient lignocellulose-degrading microorganisms and catalyticallysuperior cellulases and xylanases are of very high value in the bioconversion of lignocellulose into biofuels [6,7]. Actinobacteria are a phylum of Gram-positive bacteria that are found abundantly in soil [8]. They include some of the most prolific lignocellulose-degrading bacteria [9]. Actinobacteria include both mesophilic and thermophilic members. Many new Actinobacteria continue to be isolated and sequenced in bioprospecting studies aimed at identifying new biotechnological targets [10]. Growing number of completely sequenced genomes are being steadily deposited in public databases, which provide an expanding resource for discovering novel targets for biotechnology. Systematic bioinformatic mining of the genomes and predicted proteomes of sequenced Actinobacteria has the potential to reveal novel insights into lignocellulose-degrading enzymes for bioenergy applications [11].","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83681294","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":"Intrinsically disordered proteins as drug targets","authors":"A. Nonell-Canals, Melchor Sánchez-Martínez","doi":"10.15406/MOJPB.2017.05.00157","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00157","url":null,"abstract":"Intrinsically disordered proteins (IDPs) are characterized by a lack of folded structure. Since their identification more than a decade ago, they were designed as potential drug targets. However, nowadays, only few therapeutic molecules have been designed against them. Due to the nature of these proteins bioinformatics methods could have a key role disentangling IDPs related issues, which is key to design new therapeutic agents against them.","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73540717","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":"Density and abundance of the red-capped mangabey (cercocebus torquatus) in omo biosphere reserve and idanre forest reserve, south western Nigeria","authors":"Jacob Oluwafemi Orimaye, Ogunjemite Bg, Agbelusi Ea","doi":"10.15406/MOJPB.2017.05.00156","DOIUrl":"https://doi.org/10.15406/MOJPB.2017.05.00156","url":null,"abstract":"The red-capped mangabey (Cercocebus torquatus) is a partially-terrestrial monkey that occurs from the coastal forests from western Nigeria into southern Cameroon, and within the course of Equatorial Guinea (Rio Muni), and Gabon and the GabonCongo border on the Atlantic shore. Its southern restriction is south of the Ogooue River in Gabon. There had been unconfirmed opinions of its occurrence in Benin, and if it ever did arise it’ll now be extirpated. This species is mainly discovered in excessive wooded area, however it additionally occurs in mangrove, gallery and swamp wooded vicinity. It can also be observed in young secondary forests and close to cultivated regions. Group size has been pronounced to be between 14 and 23 animals in Equatorial Guinea. This species is indexed on Appendix II of CITES and on classification B of the African convention on the Conservation of Nature and Natural Resources. This species is found in some of protected forests in Nigeria, which include: Cross River National Park; Okomu National Park, Douala-Edea Reserve, BanyangMbo Wildlife Sanctuary, Dja Reserve CampoMa’an National Park, and Korup National Park in Cameroon; Sette Cama Forest Reserve and Mayumba, Loango, Moukalaba-Doudou, and Pongara National Parks (Gabon); Conkouati-Douli National Park in Congo; and Monte Allen National Park in Equatorial Guinea [1]. The 2008 IUCN Red List categorized this species as vulnerable [2]. C. torquatus is a large mangabey which was once a common monkey in lowland forests of southwestern Nigeria [3,4]. However, recent study of primates in southwestern Nigeria [5] had disclosed that the animal population had reduced as evident by its little group sizes in several locations across the region. Although Red-capped mangabey got its name from Madagascar, they live solely on the continent of Africa, for instance, their range is fairly restricted, occupying the West and Central Africa to the Congo Basin in Central Africa Republic. Most of their habitats are being destroyed for agricultural purposes and settlements [6].","PeriodicalId":18585,"journal":{"name":"MOJ proteomics & bioinformatics","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85968198","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}