Jan - April 2014
Research & Reviews Journal of
Bioinformatics (RRJoBI)
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STM JOURNALS
I take the privilege to present the print version for the [Volume 1 Issue (1)] of Journal of Bioinformatics. The intension of JoBI is to create an atmosphere that stimulates creativeness, research and growth in the area of Bioinformatics. The development and growth of the mankind is the consequence of brilliant Research done by eminent Scientists and Engineers in every field. JoBI provides an outlet for Research findings and reviews in areas of Bioinformatics found to be relevant for National and International recent developments & research initiative. The aim and scope of the Journal is to provide an academic medium and an important reference for the advancement and dissemination of Research results that support high level learning, teaching and research in the domain of Bioinformatics. Finally, and Authors for their continued support and invaluable contributions and suggestions in the form of authoring I express my sincere gratitude and thanks to our Editorial/ Reviewer board write ups/ reviewing and providing constructive comments for the advancement of the journals. With regards to their due continuous support and co-operation, we have been able to publish quality Research/Reviews findings for our customers base. I hope you will enjoy reading this issue and we welcome your feedback on any aspect of the Journal.
Dr. Archana Mehrotra Director STM Journals
Research & Reviews: A Journal of Bioinformatics
Contents
1. Computational Analysis of Microarray Gene Expression Profiling in Leishmania donovani and Leishmania major Ganesh Chandra Sahoo, Sindhuprava Rana, Manas Ranjan Dikhit, Md Yousuf Ansari, Pradeep Das
1
2. Computational Investigation of nsSNPs of PRSS1 Gene Ekta Kumari, Dhwani Raghaw, Jitendra Singh Rathore
15
3. Detection and Comparative Analysis of Uber-operons of FabZ gene Responsible for Fatty Acid Biosynthesis in Nostoc Punctiforme Cyanobacterium Lakshmi P.T.V., Sathya Priya, Annamalai A.
23
4. Insilico Modelling and Comparative Docking Studies of EWS-FLI1 Responsible for Ewing Sarcoma in Human Beings Lakshmi PTV, Pragna Lakshmi T, Annamalai A
36
Research & Reviews: A Journal of Bioinformatics Volume 1, Issue 1 www.stmjournals.com
Computational Analysis of Microarray Gene Expression Profiling in Leishmania donovani and Leishmania major Ganesh Chandra Sahoo1, 2*, Sindhuprava Rana1, Manas Ranjan Dikhit1, Md Yousuf Ansari1, 2, Pradeep Das1, 2 1
Biomedical Informatics Centre, RMRIMS, (ICMR), Agam Kuan, Patna, India 2 Pharmacoinformatics Department, NIPER, Industrial Area, Hajipur, India
Abstract Leishmaniasis is one of the most deadly diseases in which the human genes are affected and gets altered expression. The genes of Leishmania species which are responsible for causing leishmaniasis are not known yet. The objective behind this study is to know about the genes which are differentially expressed (DE) when macrophage of mice is infected with Leishmania donovani and Leishmania major. It also aims to know the similarities of these DE genes from human genes and predict the genes responsible for leishmaniasis in human. Microarray data analyses allow us to monitor thousands of genes simultaneously. The analyses of microarray data using statistical methods predict the differentially expressed genes in diseased state. Clustering of these genes and functional analysis through GO database accentuate the predictions.
Keywords: Differentially Expressed (DE), Automated Robust Microarray Data Analysis (ARMADA), Perfect Match (PM), Gene Ontology (GO), Clustering
RRJoBI (2014)Š STM Journals 2014. All Rights Reserved
Research & Reviews: A Journal of Bioinformatics Volume 1, Issue 1 www.stmjournals.com
Computational Investigation of nsSNPs of PRSS1 Gene Ekta Kumari*, Dhwani Raghaw, Jitendra Singh Rathore Department: School of Biotechnology, Gautam Buddha University, Greater Noida, Gautam Buddha Nagar, U.P., India
Abstract This research is done for the prioritizing of SNPs of a gene PRSS1 causing hereditary pancreatitis. In this analysis, the authors found out some nsSNPs as less stable, deleterious, probably damaging retain high risk score. It was also predicted that SIFT is fast SNPs server with comparison of PolyPhen2. By Doing its energy calculation and stability prediction, we can also determine the stability of mutant protein, that is ok whether this substitution is stable and heritable as it causes the hereditary pancreatitis. We can also know about its RMSD value which helps in protein modeling in a way by describing its structure features. Prioritizing nsSNPs in the investigation personalized medicine also as every SNPSs id having with their unique amino acid substitution at unique position. Animal models or cell lines to determine if functionality of the protein has indeed been altered today with the help of nsSNPSs analysis and by calculating its stability of protein are under selection pressure as it helps us in predicting phenotype so it may be used in nsSNPs investigation and protein stability prediction in postbiology study.
Keywords: nsSNP, SIFT, mutant protein, protein stability
RRJoBI (2014)Š STM Journals 2014. All Rights Reserved
Research & Reviews: A Journal of Bioinformatics Volume 1, Issue 1 www.stmjournals.com
Detection and Comparative Analysis of Uber-operons of FabZ gene Responsible for Fatty Acid Biosynthesis in Nostoc Punctiforme Cyanobacterium Lakshmi P.T.V.1*, Sathya Priya1, Annamalai A.2 1
Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India Department of Biotechnology, School of Biotechnology and Health Sciences, Karunya University, Karunya Nagar, Coimbatore , Tamil Nadu, India
2
Abstract The increasing price of petroleum products has necessitated the development of alternative fuel energy. The long alkyl chains that represent nature’s ‘petroleum’, are today isolated from microbes, plant and animal oils by amore scalable, controllable and economic routes.Hence, in this perspective, the present study was aimed at exploring the uber-operons of FabZ gene responsible for the synthesis of fatty acid in an aquatic nitrogen-fixing and filamentous cyanobacterium called Nostoc punctiforme. Rearrangement of genomes occur randomly and frequently during evolution. Prokaryotic organisms maintain genes of similar function and that are involved in the same cellular process in clusters of same transcriptional orientation and regulation. The uber-operons are the set of functionally related genes maintained in close proximity in the genome, which assist in genome annotation and the discovery of regulatory elements. Thus, the main objective of the study was to identify the genes those were associated as uber-operon in the fatty acid pathway of Nostoc punctiforme and also to check for its involvement in different pathways based on the ‘neighbourhoods’ assembly and phylogeny.
Keywords: Biofuel, Cyanobacterium
renewable
resources,
Fatty
acids,
Uber-operons,
RRJoBI (2014)© STM Journals 2014. All Rights Reserved
Research & Reviews: A Journal of Bioinformatics Volume 1, Issue 1 www.stmjournals.com
Insilico Modelling and Comparative Docking Studies of EWS-FLI1 Responsible for Ewing Sarcoma in Human Beings Lakshmi PTV1*, Pragna Lakshmi T1, Annamalai A2 1
Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 2 Department of Biotechnology , School of Biotechnology and Health Sciences, Karunya University , Karunya Nagar, Coimbatore , Tamilnadu , India
Abstract Ewing’s sarcoma (EWS) is a small round-cell tumor typically arising in the bones, rarely in soft tissues, of children and adolescents. Patho-genomic translocations involving the EWS gene on chromosome 22 and an ETS-type gene (Fli1) on chromosome 11, are implicated in more than 95% of Ewing’s sarcomas. A chimeric transcript that consists of the N-terminus of EWS i.e., Transcriptional Activation Domain is fused to the C-terminal portion of FLI1 i.e., DNA Binding Domain (DBD). In this present study, the structure of disordered fusion protein, EWS-FLI1 was predicted, modelled and refined. Ligand structures were drawn by using CHEMDRAW and CORINA. Comparative Docking studies were performed for EWS-FLI1 protein with EMODIN and YK-4-279 by using SCHRODINGER. Although, EMODIN and YK-4-279 interacted with the protein by establishing the H-Bonds with SER 316, GLN 326, GLN 328, ASP 430 by the former and with SER 316, ALA 110, and GLN 109 with the later, a common residue of SER 316 was observed to be interacting. However, the docking score and Glide g score of -6.278203 and -6.100573 were observed for EMODIN and YK-4-279 respectively, which revealed EMODIN to be much more effective in presenting the highest value. Molecular Dynamics Simulation was performed to analyse the stability of Docked structure of protein and ligand. For EMODIN, the stabilized structure was formed at 646 ps whereas for YK-4-279, the stabilized structure was formed at 680 ps and RMSD values for EMODIN was comparatively lower than YK-4-279.
Keywords: Ewing sarcoma, disordered fusion protein, natural ligand, comparison, molecular dynamic simulation
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