Current Issue : July - September Volume : 2015 Issue Number : 3 Articles : 5 Articles
Ebola virus (EBOV) is a deadly virus that has caused several fatal outbreaks. Recently it caused another outbreak and resulted in\nthousands afflicted cases. Effective and approved vaccine or therapeutic treatment against this virus is still absent. In this study,\nwe aimed to predict B-cell epitopes from several EBOV encoded proteins which may aid in developing new antibody-based\ntherapeutics or viral antigen detection method against this virus. Multiple sequence alignment (MSA) was performed for the\nidentification of conserved region among glycoprotein (GP), nucleoprotein (NP), and viral structural proteins (VP40, VP35, and\nVP24) of EBOV. Next, different consensus immunogenic and conserved sites were predicted from the conserved region(s) using\nvarious computational tools which are available in Immune Epitope Database (IEDB). Among GP, NP, VP40, VP35, and VP30\nprotein, only NP gave a 100% conserved GEQYQQLR B-cell epitope that fulfills the ideal features of an effective B-cell epitope and\ncould lead a way in themilieu of Ebola treatment. However, successful in vivo and in vitro studies are prerequisite to determine the\nactual potency of our predicted epitope and establishing it as a preventing medication against all the fatal strains of EBOV....
Impaired insulin signaling has been thought of as important step in both Alzheimer�s disease (AD) and type 2 diabetes mellitus\n(T2DM). Posttranslational modifications (PTMs) regulate functions and interaction of insulin with insulin receptors substrates\n(IRSs) and activate insulin signaling downstream pathways via autophosphorylation on several tyrosine (TYR) residues on IRSs.\nTwo important insulin receptor substrates 1 and 2 are widely expressed in human, and alternative phosphorylation on their serine\n(Ser) and threonine (Thr) residues has been known to block the Tyr phosphorylation of IRSs, thus inhibiting insulin signaling and\npromoting insulin resistance. Like phosphorylation, O-glycosylation modification is important PTMand inhibits phosphorylation\non same or neighboring Ser/Thr residues, often called Yin Yang sites. Both IRS-1 and IRS-2 have been shown to be O-glycosylated;\nhowever exact sites are not determined yet. In this study, by using neuronal network based prediction methods, we found more\nthan 50 Ser/Thr residues that have potential to be O-glycosylated and may act as possible sites as well. Moreover, alternative\nphosphorylation and O-glycosylation on IRS-1 Ser-312, 984, 1037, and 1101 may act as possible therapeutic targets to minimize\nthe risk of AD and T2DM....
Complex informational spectrum analysis for protein sequences (CISAPS) and its web-based server are developed and presented.\nAs recent studies show, only the use of the absolute spectrumin the analysis of protein sequences using the informational spectrum\nanalysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including\nabsolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case\nstudy in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes\ncan present similarities or differences according to the features extracted from CISAPS web server. These associations are probable\nto be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as\nzero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino\nacid indices where each one represents a different property to performthe analysis. This web-based server enables researchers with\nlittle knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work....
Phosphorylation is a protein posttranslational modification. It is responsible of the activation/inactivation of disease-related\npathways, thanks to its role of ââ?¬Å?molecular switch.ââ?¬Â The study of phosphorylated proteins becomes a key point for the proteomic\nanalyses focused on the identification of diagnostic/therapeutic targets. Liquid chromatography coupled to tandem mass\nspectrometry (LC-MS/MS) is themost widely used analytical approach. Although unmodified peptides are automatically identified\nby consolidated algorithms, phosphopeptides still require automated tools to avoid time-consuming manual interpretation. To\nimprove phosphopeptide identification efficiency, a novel procedure was developed and implemented in a Perl/C tool called\nPhosphoHunter, here proposed and evaluated. It includes a preliminary heuristic step for filtering out the MS/MS spectra\nproduced by nonphosphorylated peptides before sequence identification. Amethod to assess the statistical significance of identified\nphosphopeptides was also formulated. PhosphoHunter performance was tested on a dataset of 1500 MS/MS spectra and it was\ncompared with two other tools:Mascot and Inspect. Comparisons demonstrated that a strong point of PhosphoHunter is sensitivity,\nsuggesting that it is able to identify real phosphopeptides with superior performance. Performance indexes depend on a single\nparameter (intensity threshold) that users can tune according to the study aim. All the three tools localized >90% of phosphosites...
Online literatures are increasing in a tremendous rate. Biological domain is one of the fast growing domains. Biological researchers\nface a problem finding what they are searching for effectively and efficiently. The aim of this research is to find documents that\ncontain any combination of biological process and/or molecular function and/or cellular component. This research proposes a\nframework that helps researchers to retrieve meaningful documents related to their asserted terms based on gene ontology (GO).\nThe system utilizes GO by semantically decomposing it into three subontologies (cellular component, biological process, and\nmolecular function). Researcher has the flexibility to choose searching terms from any combination of the three subontologies.\nDocument annotation is taking a place in this research to create an index of biological terms in documents to speed the searching\nprocess. Query expansion is used to infer semantically related terms to asserted terms. It increases the search meaningful results\nusing the term synonyms and term relationships. The system uses a ranking method to order the retrieved documents based on\nthe ranking weights. The proposed system achieves researchers� needs to find documents that fit the asserted terms semantically....
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