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ThesisItem Open Access UNDERSTANDING THE MOLECULAR INTERACTION OFATP WITH MITOGEN ACTIVATED PROTIEN KINASE 1(Orissa Univesrity of Agriculture and Technology; Bhubaneswar, 2006) Mohanty, Eliza; Jagadev, P.N"Abstract Mitogen-activated protein kinases (MAPKs) are a group of serine/threonine kinases which are activated in response to a diverse array of extracellular stimuli and mediate signal transduction from the cell surface to the nucleus. It has been demonstrated that MAPKs are activated by external stimuli including chemotherapeutic agents, growth factors and reproductive hormones in ovarian surface epithelial cells. Thus, the MAPK signaling pathway may play an important role in the regulation of proliferation, survival and apoptosis in response to these external stimuli in ovarian cancer. In this article, an activation of the MAPK signaling cascade by several key reproductive hormones and growth factors in epithelial ovarian cancer is reviewed. ATP is the natural ligand for MAP kinase 1, it causes the activation of MAP kinase. Adenosine triphosphate (ATP) has been implicated in the regulation of cell proliferation and activation ofMAPK pathway in ovarian cancer cells. The aim of the study is to understand how ATP binds with Mitogen Activated Protein Kinase 1.1 have modeled 10 structures of MAPK1 by using the template Mus musculus(lLEW} having sequence identity 50% and gaps of 2% using the software lVIODELLER. From this a structure with least energy and highest score was selected. This modelled protein (MAPKI) is taken for the further experiment. The ATP and this modelled protein (MAP~l) ~e .docked by using the software InsightII. It includes potential fixing, energy mmlmlzatlOn and then docking the minimized structure."ThesisItem Open Access DESIGN AND SYNTHESIS OF 6, 6-FUSED HETEROCYCLIC AMIDES AS RAF KINASE INHIBITORS AND 7-0XOPYRROLOPYRIDINE-DERIVED DPP4INHIBITORSMITIGATION CYP AND HERG LIABILITIES VIA INTRODUCTION OF POLAR FUNCTIONALITIES IN THE ACTIVE SITE(Orissa Univesrity of Agriculture and Technology; Bhubaneswar, 2012) Nath, Ipsita; Balabantaray, Sucharita"Cancer is a broad group of various diseases, all involving unregulated cell growth. In cancer, cells divide and grow uncontrollably. B-Raf is a member of the Raf kinase family of serine/threonine-specific protein kinases. This protein plays a role in regulating the MAP kinaselERKs signaling pathway, which affects cell division, differentiation, and secretion. The BRAF gene may be mutated and as a consequence, the normal functioning of the B-Raf protein may be altered. Celiain inherited BRAF mutations cause birth defects. Alternatively, other acquired mutations (oncogene) in adults may cause cancer. BRAF (v-raf murine sarcoma viral oncogene homolog B 1) has attracted considerable interest in recent years as such a potential therapeutic target for the identification and development of a new generation of anticancer drugs. Dipeptidyl peptidase-4 (DPP4) is a protein in humans, encoded by the DPP4 gene. DPP4 plays a major role in glucose metabolism. It is responsible for the degradation of incretins such as GLP-l. Inhibitors of dipeptidyl peptidase 4, also DPP-4 inhibitors or gliptins, are a class of oral hypoglycaemic that block DPP-4. They can be used to treat diabetes mellitus type 2. Dipeptidyl peptidase-4 inhibitors (DPP-4 inhibitors) are enzyme inhibitors that inhibit the enzyme dipeptidyl peptidase-4 (DPP-4) and are a potent treatment for type 2 diabetes. Inhibition of the DPP-4 enzyme prolongs and enhances the activity of incretins that play an important role in insulin secretion and blood glucose control regulation."ThesisItem Open Access IDENTIFICATION OF PUTATIVE RESIDUES IN FERREDOXIN RESPONSIBLE FOR SALT STRESS TOLERANCE(Orissa Univesrity of Agriculture and Technology; Bhubaneswar, 2012) Pallabi, Mohanty; Ratha, Suryanarayan"Salt stress is a severe environmental abiotic stress. Ferredoxin(Fe2-S2) is an non haeme electn transferring protein diversely found in almost all organisms acts as a salt tolerant protein during hypersaline condition In Halobacterium salinarum. Therefore, the aim of this study was to find out the probable amino acid residues in ferredoxin taking part in salt stress tolerance in halophilic microbes and plants. To achieve this, initially, similarity search for ferredoxin H salinarum was carried out and the homologous proteins in halophilic microbes and plants were selected for the study. Conserved residues at sequence level were detected through multiple sequence alignment. The structural conservedness of those residues was confirmed by in silico proteomics analysis. The results showed that the residues viz. Alanine and Aspartate were found strongly conserved at defined position identified as a putative key residue in ferredoxin that is responsible for salt stress tolerance."ThesisItem Open Access HOMOLOGOUS PROTEIN SEQUENCE CLASSIFICATION BY SUPPORT VECTOR MACHINES(Orissa Univesrity of Agriculture and Technology; Bhubaneswar, 2012) Bej, Aritra; Balabantaray, Sucharita"Protein homology is concerned about the proteins which have a common evolution ancestor. These homologous proteins share common structural and sequential features among them. These structural similarities lead them to have common biological functions. But the problem arises with those homologous proteins which are sequentially and structurally similar but functionally distinct. Classification of such proteins based on their sequence information is a challenging task. So that Support Vector Machines is introduced as a method for classification of those functionally distinct classes. Studies are conducted on two homologous proteins i.e. epimerase and dehydratase of short-chain dehydrogenase/reductase superfamily. These two proteins share 25%-45% sequence identity. But the mechanisms of action of these two proteins are same in the first step but different from the second step. These distinct functional properties may arise due to some sequence patterns present in their sequences. For classification of these two group based on their sequence properties is concerned with finding those dissimilarity among those two groups. Those unique patterns increase the distance between them. So the distance is a valuable parameter for classification. These distance function is further used to construct the feature vectors for further use in Support Vector Machines. Support Vector Machine was first trained with the training set and generates models which are further used for test set classification. The test set is classified with some level of accuracy. 93.44% sequences of test set are classified successfully. This result is further compared with HMM result to construct a comparative analysis of these two methods. The overall accuracy level in SVM based classification is 98.77% which is higher than the accuracy of HMM result i.e. 98.36%. This suggests usefulness of SVM in classification of proteins with greater accuracy."ThesisItem Open Access SEQUENCING & IN SILICO ANALYSIS OF 16 S r-RNA OF Escherichia coli 09 ISOLATED FROM BOVINE MASTITIS(Orissa Univesrity of Agriculture and Technology; Bhubaneswar, 2012) Priyadarshini, Subhashree; Pradhan, Sukanta Kumar"Mastitis refers to an inflammatory reaction of udder tissue to bacterial , chemical, thermal or mechanical injury and is caused by microbial organisms or non infectious resulting from physical injury to the gland. Mastitis among bovines is a common disease, infiicting enormous financial bet backs on farmars.Mastitis remains the most common and the most expensive disease of dairy indus try throughout the world .. Bacteria that are known to cause mastitis include Pseudomas aeruginose, mycoplasm, Staphylococcus aureus, Escherichia coli .. The attempt was made to isolate pure E.coli culture from bovine mastitis infected cow and isolate the genomic DNA.Than the amplification of genomic DNA was done using the universal primer.The amplified 16S r-RNA E.coli 09 was sequenced by ABI instrument and 16S r-RNA of E.coli was submitted to Genbank with the Accession no. JX 122856. The 16S r-RNA of E.coli09 was used to find out relationship close homologs using blast N.Than divergence of those homologs were studied using MEGA .."ThesisItem Open Access COMPUTER AIDED DRUG DESIGNiNG: MOLECULAR DOCKING OF ACETYLCHOLINESTERASE INHIBITORS ON SELECTED DRUG TARGETS OF AD TO REVEAL NEW INSIGHTS IN ITS TREATMENT(Orissa Univesrity of Agriculture and Technology; Bhubaneswar, 2012) Rath, Madhuparn; Pradhan, Sukanta Kumar"Alzheimer's disease is the most common fonn of dementia among elderly people characterised by progressive and degenerative disorrler of brain. An imp0l1ant characteristic of AD is the deposition of amyloid fibrils and neurofibrillary tangles in the brain of affected individuals mainly composed of f3-amyloid protein and phosphorylated tauproteins respectively. There is also a loss of the presynaptic markers of the cholinergic system, such as acetylcholine. The important genes now targeted for treatment of early onset of AD arc pAmyloid Protein Precursor (APP), Apolipoprotein E (APOE) and Presenilin I (PS I). In our in silica study facilitated by molecular docking studies of four acetylcholinesterase inhibitors Tacrine, Donepezil, Rivastigmine and Galantamine on these three proteins revealed some important H-bond interaction with residues located in the active site pockets. This residue infonnation can be used for further high throughput screening of large scale ligands, QSAR (2d and 3D), pharmacophore modeling and structure based drug designing."ThesisItem Open Access Computational Identification of Micro-RNAs and Their targets in Sweetpotato(Ipomoea batatas L.) Expressed Sequency Tags (ESTs).(Orissa Univesrity of Agriculture and Technology; Bhubaneswar, 2012) Nayak, Akash; Balabantaray, Sucharita"With the advent of high-throughput molecular biology techniques complemented along with Bioinformatics tools, plant biology in recent years has moved a step ahead in the process of discovery of small functional noncoding microRNAs (miRNAs) which are key molecules in regulating gene expression. These endogenous 19-23 bp nucleotide miRNAs, plays a pivotal regulatory role in animals and plants by targeting transcripts for cleavage or translational repression. Computational identification of microRNAs from expressed sequenced tags (ESTs) is considered as one of the vital resources to understand the biology of miRNAs. In the present study, we used previously known miRNAs from Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.) against a total of 23, 982 ESTs of sweetpotato (Ipomoea batatas L.) to search for potential miRNAs and their putative targets in sweetpotato. A total of 13 otential microRNAs along and 74 target genes were predicted for this species. The Pfi dings from this study revealed that sweetpotato miRNAs targets genes as well as In d . anscription factors involve In plant growth and development, post-transcriptional trene silencing and tolerance against abiotic and biotic stresses. The miRNA is g nSI'ble for the plant growth, action against fungal pathogens and in various respo developments of plants. The present study may accelerate the pace of miRNA discovery in sweetpotato leading to an improved understanding of miRNA function and biological significance."ThesisItem Open Access "RISK FACTORS OF GESTATIONAL DIABETES IN INDIAN CONTEXT"(Orissa Univesrity of Agriculture and Technology; Bhubaneswar, 2012) Dalai, Mausumee; Pradhan, Sukanta Kumar"The prevalence of Gestational Diabetes Mellitus (GDM) in India varied from 3.8 to 21% in different parts of the country, depending on the geographical location and diagnostic methods used. GDM has been found to be more prevalent in urban areas than in rural areas. The project seeks to find out various risk factors of gestational diabetes and to create awareness among the public - in particular women's groups - on gestational diabetes mellitus (GDM) and to build capacity in the health care system to prevent, manage and control the problem in Indian context. I take 31 articles with key words GDM, Risk factors, India to find out variant risk factors associated with ODM. During my study I notice that there is no significant difference between OOCT and OOTT. SO the pregnant women no need of fasting for Screening before going to the hospital for test. I also observed that less physical activity is one of the causes of obesity found majority both in young and adult women of urban. Effect of lifestyle and Child birth after 25 ages are also risk factors associated with GDM. I found that the prevalence of gestational diabetes was more in urban area than semi u, r ban area and rural area. It is noticed during study that Vitamin B 12 deficiency in women is associated with high BMI, increased adiposity, insulin resistance and GDM. Early marriage is one of the preventive pathways for GDM, as more maternal age is a risk for GDM. In more cases the GDM is treated by only diet control and exercise, no much need of insulin. We can confidently prevent the, GDM and the future Diabetes. It only Possible by create some awareness among people."ThesisItem Open Access Orissa Medicinal Plants Digital Library .(Orissa Univesrity of Agriculture and Technology; Bhubaneswar, 2006) Parida, Bikram Kumar; Panda, P. K.