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Theses (M.Sc.)
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ThesisItem Open Access IDENTIFICATION AND FUNCTIONAL ANALYSIS OF SNPS IN TOLL LIKE RECEPTORS 2 AND 4 ACROSS INDIAN NATIVE CATTLE BREEDS THROUGH INSILICO MODELLING(ICAR-NDRI, KARNAL, 2020) Krishna, D. Mohan; SODHI, MONIKAToll like receptors (TLRs) are integral component of host immune response and pattern recognition molecules of pathogens. Out of 10 TLRs, TLR2 and TLR4 genes play critical roles in initiation of innate and adaptive immune response by recognizing gram positive bacteria and lipopolysaccharide of gram-negative bacteria respectively. Till date, several studies have shown functional importance of these receptors. However, not much information is available on the sequence characteristics and polymorphism in Indian native cattle breeds. Considering their importance in initiating immune response, an effort was made to sequence characterize TLR2 and TLR4 genes in diverse Indian native cattle breeds adapted to different agro climatic region of the country. A total of approximately 2000kb combined sequence data for TLR2 and TLR4 genes was generated in more than 250 animals of 11 native cattle breeds. Additionally, genomic DNA samples from 20 animals of cross-bred (Karan Fries) and exotic (Holstein Friesian) cattle were also used to generate sequence data for comparison and SNPs identification. The comparative sequence analysis of TLR2 and TLR4 genes in native (Bos indicus), cross bred and exotic (Bos taurus) identified a total of 36 variations in coding region. Out of these, 19 SNPs were non synonymous and located within predicted functional domains. The 5’ and 3’ UTRs of TLR2 and TLR4 were completely conserved and showed no variation across different cattle types. All the native breeds showed sufficient genetic diversity in TLR2 and TLR4 genes. Comparatively, the SNP density per kb (6.36 vs3.50) and percentage of non-synonymous SNPs (56.52vs 47.15) was more in TLR2 compared to TLR4. Of the 36 variations detected, 13 (36%) SNPs (11 in TLR2 and 2 in TLR4) were specific for Indian native cattle whereas no unique variations were observed in crossbred or taurine cattle. The number of haplotypes corresponding to the observed variations was 26 And 25 in TLR2 and TLR4 respectively. The LD between the different haploblocks was low to moderate. Further, bioinformatics approach was adopted to predict the consequences of nonsynonymous coding SNPs in TLR2 and TLR4. The functional and structural consequences were predicted by computational tools including SIFT, PolyPhen, PROVEAN and I-Mutant. Structural visualization of wild type and mutant amino acids was performed using the project HOPE while evolutionary conservation was studied using ConSurf server. In TLR2 and TLR4 genes 3 and 6 ns-SNPs respectively were found to have possibly damaging consequences as predicted by some of these computational tools. To the SNPs for interaction studies, FOLDX algorithm was used. Based on the FOLDX data 2 SNPs (T405M, T605M) and corresponding haplotype (H10, H22) in TLR2; 2 SNPs (L601S, L601W) and corresponding haplotype (H18,H 20) haplotypes in TLR4 having comparatively higher stabilization impact was selected for docking for respective ligand. The docking complex stability values and energy minimization values indicated more stable interactions of the ligand with variant TLRs compared to wild type TLRs. These variations leading to comparatively stable interactions with respective ligand might explain the better resistance potential of Indian native cattle breeds. Overall, the present findings provide useful information about the diversity in TLR2 and 4 across the Indian native, crossbred and exotic breeds, which can serve as a future resource to facilitate the selection of TLR variants for functional and/or association studies.ThesisItem Open Access Expression purification and characterization of recombinant proline aminopeptidase from lactobacillus brevis in E coli(NDRI, Karnal, 2016) Kumar, Vibhanshu; Kaushik, J KThesisItem Open Access Isothermal DNA amplification based identification of cattle and buffalo DNA(NDRI, Karnal, 2016) Kumar, Sonu; De, SachinandanThesisItem Open Access Effect of ascorbic acid on oxidative stress and its thermoprotectant role on in Vitro embryonic development of buffalo (Bubalus Bubalis) embryos(NDRI, Karnal, 2016) Roshan, Mayank; Chauhan, M SThesisItem Open Access Expression Analysis of Important Genes Regulating DNA Methyltransferases in Buffalo Embryos Produced by Hand-Guided Cloning and in Vitro Fertilization(NDRI, Karnal, 2016) Ashok, Disha; Singla, S kThesisItem Open Access Methylation Status of Imprinted Gene IGF2/H19 in Goat Embryos Produced Through Parthenogenesis and in Vitro Fertilization(NDRI, Karnal, 2016) Tiwari, Manish; Singh, Singh, M KThesisItem Open Access EFFECT OF SELECTION OF OOCYTES BY BRILLIANT CRESYL BLUE STAINING ON DEVELOPMENTAL COMPETENCE, HEALTH AND NUCLEAR REPROGRAMMING OF BUFFALO EMBRYOS PRODUCED BY HAND-GUIDED CLONING(NDRI, Karnal, 2013) Rao, Venkata Subba; Palta, P.ThesisItem Open Access Cell cycle synchronization of buffalo fibroblasts and effect of reprogramming times on developmental competence of intra and inter species hand made cloned embryos.(NDRI, Karnal, 2009) Naresh Lalaji, Selokar; Singla, S.K