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Biochemistry, Genetics and Molecular Biology >
Indian Journal of Bioinformatics and Biotechnology
Publisher:Indian society for Education and Environment
Editor in chief:Prof.Natarajan Gajendran
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Diversity Of 2, 4 Dichlorobiphenyl Degrading Consortium Of Pseudomonas Isolates Gsa And Gsb For Degradation Of Poly Chlorinated Biphenyl Congeners
Author:Shobha K Jayanna, Devaraja Gayathri, Somaraja Palegar Krishnappa.
Volume: 4 | Issue no: 3-2016 | Pagination: 1-5
Objective: Polychlorinated biphenyls (PCB) are persistent organic pollutants that are widely distributed in the environment. PCBs are aromatic compounds have more than 210 congeners, nonvolatile, chemically inert and do not undergo oxidation, reduction or addition reactions, elimination or electrophilic substitution reactions except under extreme conditions. Their improper disposal in storage and disposal area has negative impact on the ecosystem. Although Chemical methods are available for the degradation, they tend to emit more toxic chemicals. Alternative the biological methods are safer and cost effective. In this context, 2, 4 Dichlorobiphenyl, (a PCB congener) degrading bacterial isolates which have been evaluated for substrate affinity using PCB congener mix. Methods: In the present study, 2, 3, 5, 6 tetrachlorobiphenyls and 3, 5, 3, 5 tetrachlorobiphenyl in PCB congener mix degradation by previously characterised Pseudomonas isolates GSa and GSb was studied using GC-MS. Findings: Two constantly overlapping bacterial isolates identified as Pseudomonas sp., capable of degrading 2, 4 Chlorobiphenyl degrading, showed its diversity of degrading other PCB congener mix. On GC-MS analysis of the cell free extract showed 60 and 70% degradation as per the ECD values. Applications: Therefore, the present paper is first of its kind, as 2, 4 CB degrading Pseudomonads in tern degrade other PCB congeners perhaps showing wide application on in situ bioremediation since the contaminated site contains variety of congeners.
Comparative Studies On Type Iii Polyketide Synthase Proteins Of "Indian Bael" And "Indian Gooseberry": An In Silico Approach
Author:Aiswarya G, Mallika V, E.V Soniya.
Volume: 4 | Issue no: 2-2016 | Pagination: 1-7
Objectives: Type III polyketide synthases are homodimeric enzyme having imperative roles in the production of plant metabolites known as polyketides. In pharmacologically relevant 'Bael' and 'Gooseberry' plants, the type III polyketide synthases are reported to have different functional activity. Methods: A concise comparative bioinformatic analysis was carried out on two type III polyketide synthase proteins of medicinally important 'Indian Bael' and 'Indian Gooseberry'. The study has been performed using different computational tools in order to analyze the structure and function-correlation from their respective nucleotide sequences and corresponding protein sequences. Physico-chemical properties, sequence conservation and secondary structural details were studied based on various bioinformatics tools and techniques. Findings: Different bioinformatics tools have been used to understand both sequence and structural divergence. Initial sequence analysis of bael and gooseberry type III polyketide synthases showed that they shared 87.2% similarity and 73.7% identity. Both sequence showed high degree of sequence conservation with few exceptions. Pairwise distance analysis confirmed that evolutionary distance between gooseberry and bael type III PKS is high. Phylogenetic analysis showed clear clustering pattern, which also suggested its evolutionary relationship among different type III polyketide synthases. The results suggested that both the enzymes might have evolved from a common ancestor and functional diverged in the course of evolution. These studies will be helpful to the researchers to study the functional divergence and substrate binding mechanism of type III PKS. Applications: Understanding the sequence conservation and evolutionary relationship among the two different type III polyketide synthases of Bael and Gooseberry, which may contribute to the further proteomics studies.
Bioinformaticsgene Expression Analysis Of Stromal Cellsthat Are Educated By Mda-Mb-231 Metastatic Breast Cancer Cell Line
Author:Dabirihamed, M. Soltanibahram, Dokanehiifard Sadat, Shabaninejadzahra, Yousefifatemeh, Amin Jahanbakhshi.
Volume: 4 | Issue no: 2-2016 | Pagination: 1-9
Background/Objectives: Cancer microenvironment play important and dynamic role in cancer cell survival, growth and migration. Cancer educated stromal cells that are located in its microenvironment, prepare adapted situation for cancer cells and feed them to better growing and migration. We intended to find stromal cell genes that are affected by cancer cell secreted macromolecules and also to find the secreted miRNAs that are potentially involved in stromal cells adaptation. Methods/Statistical analysis:Here, we analyzed the microarray expression data of three cell types (fibroblast, myoepithelial and MSCs) that have been educated through co-culture with MDA-MB-231 metastatic breast cancer cell line. Findings:Results indicated that the expression of 138 genes has been significantly altered in all three cell types after culturing with MDA-MB-231 cell line. Bioinformatics analysis indicated that these genes are involved in many biological processes including: Cadherin signaling pathway, glycolysis, hypoxia response via HIF activation, VEGF signaling pathway and cell adhesion. We also carried out integrated analysis for top five vesicular miRNAs secreted by MDA-MB-231 cells and their predicted targets in Mesenchymal Stem Cells. Our analysis suggested that vesicular hsamiR-106b may target protocadherin transcripts in MSCs, which are involved in cell adhesion. Improvements/Applications:Overall, our investigation emphasizes on 138 stromal cell genes to be affected by cancer cells and also hsa-miR-106b as a potential mediator of this effect.
Ontogenetic Memory Of The Cell
Author:Sreenile V. Chirala.
Volume: 4 | Issue no: 1-2016 | Pagination: 1-5
Objective: A hypothesis is presented here, that 'in the ontogenetic growth-aging process from conception to death of an organism, each cell has a reducing predefined finite reproductive potential and somatic life span of its own, defined by its temporal occurrence within the life-cycle of the organism'. Methods : Phenomenological and Reductionist observations. Different species of living organisms have different species-specific finite life spans. In each of the species different cell lines have finite replicative potential, and, different cells have different life-spans. Findings: The growth-aging process of ontogeny unfolds in a specific biocybernatic process. Either in the native state or explanted or transplanted or cloned or grafted state, the cell has memory of its original age and its remaining replicative potential and somatic life span. Applications : are in the selection of cell in animal cloning, cell line in tissue transplantation, and the donor for organ transplantation and plant grafting.
In-Silico Analysis Of Cds For Snorkel Genes Of Oryza Sativa Using Bioinformatics Tools And Techniques In Deep Water Rice
Author:Pragnya Paramita Jena, Pranati Swain, Gayatri Gouda
Volume: 3 | Issue no: 2-2014 | Pagination: 70-76
Background: Prolonged submergence stress is a serious consequence in rice. The CDS regions of Snorkel protein were considered for the study. Method: A brief comparative analysis has been performed by using several bioinformatics tools and techniques in order to understand the physico-chemical properties, secondary structures of conserved protein regions, multiple sequence alignment, homology models, and backbone confirmation for generated homology models. Findings: The objective of this study was to understand the similarity among all these four CDS regions. Different bioinformatics tools PROTPARAM, CFFFSP server, CLC genomic workbench, MODELLER, RAMPAGE has been used to understand both structural and comparative differences. This insilco analysis will helpful to researchers to study more on the networking mechanism between sub1 introgressed lines and snorkel introgressed lines and mechanism involve when both the gene are introgressed together in single variety. Application/Improvements: understanding the network mechanism in snorkel introgressed lines.
Modeling The Interaction Of Trehalose-6-Phosphate Synthase And Udp-Glucose Bycomputational Methods
Author:J. Sarvanan, Sourav Dutta, Asit B. Mandal
Volume: 3 | Issue no: 2-2014 | Pagination: 55-69
Background:Trehalose, an integral component of the cell-wall glycolipids of Mycobacteriumis an unusual nonreducing disaccharide, which plays a variety of biological roles from food storage to cellular protection under diverse environmental stresses (e.g. high pressure, heat-shock, reactive oxygen species, free radicals etc.). Primary enzymatic route to trehalose first involves the transfer of glucose from an UDP-glucose donor to glucose-6-phosphate to form alpha, alpha-1 and 1 trehalose-6-phosphate. It serves as a stress protectant in a range of organisms especially in resurrection of plants and many microorganisms. In addition, the principal role of trehalose is as an important metabolite due to its unique properties like high hydrophobicity, chemical stability, non-hygroscopic glass formation and no internal hydrogen bond formation is worthy to mention. Methods: MODELLER, a command-line bioinformatics tools and various other bioinformatics programmes and servers like RAMPAGE, PRO-CHECK, Dallite, Errat, Verify 3D were used for analysis and validation of final structures created through homology modeling. Results: The present work was done for virtual screening of the enzyme Trehalose-6-Phosphate Synthase and studying the interaction with ligand UDP. The crystal structure of TPS-UDP glucose was used for studying the proteinligand interaction. Further homology modeling of the protein was done in detail by deploying basic operation of Argus Lab; Chimer graphics interface to display and manipulate modeled protein. Application: We report here virtual screening of the enzyme Trehalose-6-Phosphate Synthase to unzip protein-ligand interaction through homology search or comparative modeling to pinpoint potential of the modeled/created protein and to analyze and validate the final structures using various informatics tools.
Human Immunodeficiency Virus -1: A Brief Overview Of Virology, Diagnosis, Pathogenesis And Treatment
Author:Radhika Ramachandran, Piramanayagam Shanmughavel
Volume: 3 | Issue no: 2-2014 | Pagination: 45-54
This article intends to present important aspects related to HIV which would serve as an introduction to beginner's of HIV research. A brief overview of the structure, genome organization and the function of viral proteins of HIV-1 required for viral infection and replication are presented. The genetic diversity of HIV-1 along with its diagnosis and pathogenesis, host immune response, transmission routes and prevention methods are also summarized. Finally, the treatments against HIV-1 and drug resistance are briefly discussed. The ratio of different routes of HIV transmission from infected person to a healthy person and the effectiveness of their preventive measures are summarized. The review also describes about HAART, newer therapies like microbicides and vaccines.
Development Of Iridology System Database For Colon Disorders Identification Using Image Processing
Author:Rossi Passarella, Erwin, M. Fachrurrozi And Sutarno
Volume: 2 | Issue no: 6-2013 | Pagination: 101-103
Iridology is an art of knowledge to detect a specific disease of human body from the iris. The detection will tell each individual organ when it has low or high performance (abnormal). The iris reveals conditions change of every part of the body. Every organ and part of the body are represented in the iris in a well-defined area. The objective of research is to develop an iris database of colon disorder based on the map of iridology. This map is represented as a diagnosis tool to detect the common colon disorder. In developing the database, Sixty (60) subjects were enrolled in the study where 35 subjects had histologically proven problem in colon disorder, and 25 were control subject. To extract the iris, the image processing methods such Hough transform, segmentation and normalization were applied in this research. The conclusion of this paper is the proposed an iris database for helping medical doctor in detecting colon disorder using image processing.
Molecular Docking Analysis Of Sorbitol Dehydrogenase Using Ligandfit Algorithm
Author:V.G.Vidhya, Anusha Bhaskar, S.Vijayasr
Volume: 2 | Issue no: 5-2013 | Pagination: 96-99
Diabetic retinopathy is a major cause of visual impairment worldwide. The polyol pathway is a two step metabolic process in which the enzyme aldose reductase reduces glucose to sorbitol using NADPH as a cofactor; Sorbitol is then metabolized to fructose by sorbitol dehydrogenase (SORD) that uses NAD+ as cofactor. Human sorbitol dehydrogenase is a tetramer of identical, catalytically active sububits. Recent evidence suggests that the inhibition of both sorbitol and fructose is required to achieve beneficial effects in diabetic retinopathy. In our present study the molecular docking analysis of sorbitol dehydrogenase was carried out using Accelyr's Discovery studio software (uses LIGANDFIT algorithm). The binding affinity of several ligands to the target protein was calculated based on the dock scores obtained. It was found that out of 210 compounds 21 ligands docked to SORD whereas 17 ligands failed to dock and 59 ligands were found to be without hits. Among the 21 ligands, Dithiodialanine had greater binding affinity with the receptor thereby it can be recommended as a drug for the treatment of diabetic retinopathy.
Analytical Study Of Plasmodium Yoelii Yoelii
Volume: 2 | Issue no: 5-2013 | Pagination: 88-94
Protein sequence of Plasmodium yoelii yoelii "prt_seq No definition line found" was extracted from GenPept database (ACCESSION: EAA21357), used to predict its hydrophobic, atomic and amino acid composition, PEST region, solvent accessibility, molecular mass, theoretical pI and finally catalytic site detail was identified with their three dimensional structure. Analysis was made using several bioinformatics tool. PEST region was indentified using pestfind tool, whose abundant availability indicates intracellular half-lives of less than two hour. Hydrophobicity was checked using  to know it's buried or exposed state in terms of solvent accessibility, also used to find its different physical and chemical properties, secondary structure composition using Hidden Markov models, formation of disulphide bond, effect of point mutation prediction using heat map representation and finally catalytic site identification were made. Online Active site prediction was made using web server , where given protein sequence was matched with server's library of catalytic site, resulting in twenty six identified region with maximum score of 0.015 with Orotidine "5-monophosphate decarboxylase" and minimum score of 0.004 with "Endo-alpha-sialidase". Molecular weight of retrieved protein sequence was found to be 32049.9 and Theoretical Pi value was 6.08, protein close to given Pi and molecular mass was matched using TagIdent web server , which reveal 126466 protein. The Instability Index was computed to be 36.19 which classifies the protein as stable and the Aliphatic Index showing relative value occupied by aliphatic side chain (alanine, valine, isoleucine, and leucine) was 80.77. The three dimensional structure of catalytic site was visualized using Jmol software.
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