Thumbnail Image

Theses

Browse

20192
Reset filters
Subject: Bioinformatics × End date: 2019 × Start date: 2019 × Thesis Type: M.Sc ×
Reset filters

Search Results

Now showing 1 - 2 of 2
  • Thumbnail Image
    ThesisItemOpen Access
    In-silico Prediction of microRNAs and their targets in Wheat (Triticum aestivum L.)
    (CCSHAU, 2019) Bishnoi, Stela; Sudhir Kumar
    Wheat (Triticum aestivum L.), a staple crop which constitutes major part of human diet, belongs to family Poaceae or Gramineae family. As a major constituent of human diet it is therefore one of the most widely cultivated food grain in not only India but the world as well. In India it is the grain with second largest consumption after rice. The miRNAs play a major biological role by modifying the expression levels of a diverse repertoire of genes in a sequence in a dependent manner which is attained at either transcriptional or post-transcriptional level. The Nucleic acids sequences of the 21- chromosomes of Triticum aestivum were downloaded from the International Wheat Genome Sequences Consortium. After downloading wheat genome sequence from IWGSC, the DNA sequence is transcribed into RNA sequence and later split through split.pl which gave an output of 138 fragments. Then after finding out palindromes of fragments using palindrome finding perl script (palindrome.pl). The fragments with at most four mismatches were stored in a file. Secondary structure was predicted using RNAfold server. The sequences are sorted out which have MFE of secondary structure less than -40kcal, and considered as putative miRNAs. From BLAST there identified 699 new miRNAs having 111175 targets. These target genes have regulatory function in certain biological processes.
  • Thumbnail Image
    ThesisItemOpen Access
    Structural and Molecular Dynamics Studies of UDP Glucose Pyrophosphorylase Dimerization in Rice (Oryza sativa L.)
    (CCSHAU, 2019) Mamatha Y S; Sudhir Kumar
    UDP-Glucose pyrophosphorylase (UGPase) (EC 2.7.7.9) belongs to family Glycosyltransferace clan (PF01702) which is present in plants as well as animals. UGPase is involved in sucrose synthesis as a catalyzing agent in the reaction, Mg+2-UTP + Glu-1-P PPi + UDP-Glu. It catalyzes both forward and reverse reaction depending on the metabolic status of the tissue. Crystal structure of UGPase shows that it have three domains with N-terminal domain at one end, catalytic domain which have nucleotide binding loop present at the center and the C-terminal domain include insertion loop at another end. C-terminal group is involved in dimer formation and stabilization of protein. Monomer is the active form in most of the parasitic and a plant UGPase. Modelling and dynamic study can uncover the interaction forces involved in UGPase activity. A 469 amino acids long rice UGPase was retrieved from NCBI and further aligned using BLAST program to identify templates for comparative structure prediction. Modelling of UGPase peptide by Modeller9.20, Swiss-model server and I-TASSER server predicted Model1, Model2 and Model3 respectively. All models were subjected to energy minimization using GROMOS96 force field and structure assessment by QMEAN. All models were further verified, validated and evaluated using WHATIF and SAVES server. The RMSD of models on superimposition with template was found to be less than 1.0 Å. Models were further refined using GROMACS-2019, a molecular dynamic (MD) code designed for highperformance simulation of large biomolecular systems. Dimers were generated by using protein-protein docking tools with predicted models. These generated dimers were further evaluated and analyzed. Dimer analysis provides the information about the hydrogen bonding in between the peptides of protein. Solvent accessible area calculated for the residues, which are present in ligand binding site. Solvent accessible area in dimer found to be less compared to monomer. The study showed that protein losses its activity due to dimerization.