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Chaudhary Charan Singh Haryana Agricultural University, Hisar

Chaudhary Charan Singh Haryana Agricultural University popularly known as HAU, is one of Asia's biggest agricultural universities, located at Hisar in the Indian state of Haryana. It is named after India's seventh Prime Minister, Chaudhary Charan Singh. It is a leader in agricultural research in India and contributed significantly to Green Revolution and White Revolution in India in the 1960s and 70s. It has a very large campus and has several research centres throughout the state. It won the Indian Council of Agricultural Research's Award for the Best Institute in 1997. HAU was initially a campus of Punjab Agricultural University, Ludhiana. After the formation of Haryana in 1966, it became an autonomous institution on February 2, 1970 through a Presidential Ordinance, later ratified as Haryana and Punjab Agricultural Universities Act, 1970, passed by the Lok Sabha on March 29, 1970. A. L. Fletcher, the first Vice-Chancellor of the university, was instrumental in its initial growth.

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2012 - 201812
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Subject: Bioinformatics × End date: 2018 × Type: Thesis × Thesis Type: M.Sc ×
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Now showing 1 - 9 of 12
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    ThesisItemOpen Access
    Virtual high throughput screening of sodium channel blockers as potential insecticide leads
    (CCSHAU, 2018) Naina Kumari; Sudhir Kumar
    Sodium channels are integral transmembrane proteins responsible for the initiation and propagation of action potential. Sodium channel consists of α and β subunits. α subunit is responsible for voltage dependent ion conductance whereas β subunit is responsible for membrane localization. By the use of virtual high throughput screening (molecular docking), potential inhibitors of voltage gated sodium channel were identified. vHTS is a computational method for screening in silico collection of compound libraries. Using vHTS, the binding affinity of the compounds from in silico library and target receptor was predicted. The crystal structure of insect sodium channel (5X0M) consisting of 1553 amino acids was retrieved from RCSB PDB and the active site and binding pocket were identified by CastP tool.. On the basis of substructure similarity of well-known inhibitors of sodium channel, 2,06,404 small molecules/ligands were obtained from ZINC15 database. Out of 2, 06,404 ligands, 1,65,437 were selected on the basis of Lipinski’s rule of 5. Molecular docking of the ligands with the sodium channel protein was performed using USCF DOCK6. 4,854 Docked ligands were obtained on the basis of acceptable binding energy score. The ligands were further filtered by their ADMET properties prediction through vNN-ADMET and TEST. Out of 2,06,404 ligands, 47 ligands were identified as non-toxicant and potential insect sodium channel blockers. The interaction study of the 47 accepted leads with the sodium channel protein revealed that ARG 1138, ARG 1120, GLU 1435, LEU 1224, ILE 1152, ASP 1412, GLU 1123, LEU 1224 and TYR 1430 are the key residues involved in interaction through hydrogen bonding, electrostatic interactions or vander waals forces.
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    ThesisItemOpen Access
    Computational modelling and molecular dynamic simulation of glutamate decarboxylase of wheat (Triticum aestivum L.),
    (CCSHAU, 2018) Jakhar, Ritu; Sudhir kumar
    Glutamate decarboxylase (GAD) catalyses the decarboxylation of glutamate amino acid to γ – amino butyrate (GABA) in presence of Pyridoxal phosphate cofactor. GABA build up happens after GAD activation in plants in response to various biotic and abiotic stress such as hypoxia, temperature shock, water stress, salinity stress, acidosis, virus infection and mechanical manipulation. GAD assembled into dimer and subsequently in hexamer for activation. In plants, GAD dimerisation and activation is associated with binding of CaM and C-terminal of GAD. The N-terminal residues are required for the assembly and stabilization of hexameric state of GAD. Modelling and dynamics study can uncover the interaction forces involved in GAD activity. A 500 AA long wheat GAD sequence was retrieved from UniProtKB and further aligned using BLAST program to identify templates for comparative structure prediction. Modelling of GAD peptide (monomer subunit) by Modeller9.19 and Phyre2 server provided Model1 and Model2, respectively. Model1 was generated in two fragments for N- and C- terminal with Modeller9.19 and joined using Chimera visualization tool. Both models were subjected to energy minimisation using GROMOS force field and structure assessment by GROMOS, QMEAN and ANOLEA. Both models were further verified, validated and evaluated using WHATIF and SAVES server. The RMSD of models on superimposition with the template was found to be less than 2.0 Å. Models were further refined using NAMD, a molecular dynamics (MD) code designed for high-performance simulation of large biomolecular systems. Out of two models, Model1 was predicted better model than Model2 on the basis of RMSD between initial and simulated model.
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    ThesisItemOpen Access
    Computational modeling and molecular dynamic simulation of pyrophosphatase of rice (Oryza sativa L.)
    (CCSHAU, 2018) Manisha; Sudhir Kumar
    Inorganic pyrophosphatase plays a significant role in various processes in plants. It causes chalkiness and hydrolytic breakdown of ADP-glucose in plastidal compartment. It has significance in lipid metabolism, calcium absorption, DNA synthesis and biochemical transformations. The sequence of inorganic pyrophosphatse was retrieved from NCBI and template was identified using BLASTP. With 84% query coverage and 71% identity 4LUG was selected as template. Modeller 9.19 and RaptorX were used for computational modeling. Predicted models were refined by energy minimization with GROMOS force field from Swiss-pdb Viewer. Minimum energy calculated for Modeller 9.19 and RaptorX predicted models were -2394.489KJ/mol and -7365.312KJ/mol respectively. The structures were assessed by GROMOS, ANOLEA and QMEAN graphs. More favourable region was shown by GROMOS and ANOLEA as compare to QMEAN. WHATIF server programs were used for structures optimization and validation. Bond length Z-score, bond angle Z-score, coarse packing quality and Ramachandran Z-score, were approximately 0.4, 1.2, -0.9 and 0.1 respectively. SAVES server programs score for PROVE, VERIFY3D and ERRAT were approximately 4.2%, 81% and 91% respectively. Ramachandran plot calculated by PROCHECK showed approximately 94% amino acid in core and 6% in allowed region. The models visualization showed coils were dominantly present in both the structures. RMSD for the structures was less than 0.5. Explicit solvent molecular dynamic simulation was done by VMD and NAMD software. The total energy and RMSD graphs calculated after simulation were stable for the structures. Structure superimposition with template showed significant conserved region between template and predicted structures. RMSD calculated after simulation was less than 0.5 Å against for both models template. The model predicted by RaptorX was found better as compared to Modeller 9.19 predicted model.
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    ThesisItemOpen Access
    In silico characterization of WRKY transcription factor in rice (Oryza sativa L.)
    (CCSHAU, 2017) Simerpreet; Sudhir Kumar
    Rice, being a model plant for genomic research of grass species can pave a way for characterization of WRKY transcription factors involved in DNA binding. WRKY protein is 60-70 long amino acid sequence present at N-terminal end and/or C-terminal end along with zinc finger like motif. WRKY TFs are involved in many plant processes e.g. plant growth and senescence, physiological, biological processes, regulation of transcription etc. Thus, present study aimed the in silico characterization of WRKY TF of rice from GRASSIUS database for homology search, analysis of conserved motifs and phylogenetic relatedness with WRKY family of maize, sorghum and sugarcane. Total of 369 WRKY protein sequences of rice, maize, sorghum and sugarcane were retrieved from GRASSIUS database of transcription factor. They were analyzed for the presence of WRKY domain using SMART and HMMER database. True WRKY proteins sequences after removal of partial and unwanted domains were subjected to homology search using BLAST which revealed that maize WRKY proteins have highest identity to OsWRKY proteins instead of sorghum and sugarcane WRKY proteins. Conserved residues were identified in multiple sequence alignment along with conserved WRKY motif and zinc finger motif which helps in specific binding activity. All species belong to poaceae family, their phylogenetic analysis revealed many orthologs and paralogs indicating the evolutionary significance and indicating presence of WRKY domains before divergence of species. Maximum orthologs were shown by rice and maize while in case of SbWRKY and ScWRKY, ortholgs obtained were on the basis of alignment of proteins on the basis of conserved region only. These results clearly indicates that rice is more closely related to maize than sorghum and sugarcane due to the ancient events like gene loss events which causes more divergence and gene duplication, tandem duplication which relates the genes between other species. Conserved motifs analysis using MEME tool identified conserved motifs in the sequences and provided motif distribution map. Genes having same motif distribution have a possibility of functioning in same conditions. The present study therefore, opens up possibility for further investigation of functional characterization WRKY regulatory proteins by wet lab experimentation with potential for rice improvement.
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    ThesisItemOpen Access
    Phylogeny and homology modeling of starch synthases of rice (Oryza sativa L.)
    (CCSHAU, 2017) Palak Singh; Sudhir Kumar
    The research work entitled “Phylogeny and homology modelling of starch synthase of rice (Oryza sativa L.)” was conducted keeping in mind the importance of starch in production and improvement in rice quality as well as in various food and non-food sectors, it is necessary to understand the basic proteins involved in the synthesis of starch in rice granule. The study explains the basic structural features and relationships of the Starch Synthase (SS) enzyme in rice with the other plants for the same enzyme. SS in rice consists of 11 genes grouped into five isoforms namely GBSS, SSI, SSII, SSIII and SSIV. Total of 28 GBSS and 50 SS (SSI to SSV) isoform sequences in rice as well as in other plants were retrieved from NCBI and were aligned using CLUSTALW program. The phylogenetic analysis of SSs in rice with other plants was done using MEGA7 and PHYLIP softwares and best fit tree was obtained by bootstrapped parsimony method. Phylogenetic consensus trees clearly depicted separate clusters for each isoforms and within each clusters of starch synthase isoforms (GBSS, SSI, SSII, SSIII, and SSIV) monocots and dicots were found to have two distinct clusters. Homology modelling of five isoforms was done by three softwares Modeller9.18, Swiss Model server and RaptorX server. Models obtained were then subjected to energy minimisation using Gromos force field and assessed by GROMOS and ANOLEA graph in which Swiss Model Server models were found best and hence were used for further studies. All the five selected models (GBSSII, SSI, SSII, SSIII and SSIV) of Swiss Model server were verified, validated using WHATIF server and were evaluated using SAVES server. Superimposition of target-template of each isoform showed conserved structural similarity, especially for ligand binding regions. The RMSD for all models on superimposition with the template was found to be less than 2.0 Å.
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    ThesisItemOpen Access
    Subunit-subunit interactions in the heterotetrameric structure of rice (Oryza sativa) ADP-Glucose Pyrophosphorylase
    (CCSHAU, 2012) Dawar, Chhavi; Jain, Sunita
    ADP-glucose pyrophosphorylase, a key allosteric enzyme involved in higher plant starch biosynthesis, is composed of large (LS) and small subunits (SS). Current evidence indicates that the two subunits play distinct roles in enzyme function. The LS is involved in mainly allosteric regulation through its interaction with the catalytic SS. Recently the crystal structure of the SS homotetramer from potato tuber has been solved, but no crystal structure of the native heterotetrameric enzyme is currently available for any species. In this study, homology modeling of the three-dimensional structure of the LS and SS from rice (Oryza sativa) was done using Swiss Model Server to construct the heterotetrameric assembly of the enzyme. The SS from the crystal structure of potato tuber was taken as the template. The models were evaluated using PROCHECK, VERIFY3D and ERRAT from SAVES. Further the two subunits were docked using GRAMM-X rigid docking server first to obtain the stable heterodimer orientation (LS as receptor and SS as ligand) and then the heterotetrameric orientation. The initial heterotetrameric orientation was further refined using RosettaDock Server and idealization of bond geometry and removal of unfavorable non-bonded contacts was performed by energy minimization with force field GROMOS96 from Swiss- Pdb Viewer. A minimized energy state of -69853 KJ/mol for the heterotetramer was obtained. MD simulation of the representative heterodimer and heterotetramer was performed using NAMD on an 8-node Linux cluster operating at 0.1 TFLOPS. The studies indicated that the tail-to-tail interaction of the LS and SS was more stable with -437086 kcal/mol energy as compared to the head-to-head orientation (-396097 kcal/mol) also the heterotetramer energy was minimized to -767011 kcal/mol. Following this the subunit-subunit interaction studies were carried out on the heterotetramer using NACCESS and Dimplot programs. NACCESS indicated interface residues; 57 residues for SS out of which 30 were hydrophobic and 27 were hydrophilic and 63 residues (31 hydrophobic and 32 hydrophilic residues) for LS. Dimplot plotted the hydrophobic interactions and hydrogen bonds between different chains of the heterotetramer. Lastly superimposition of the deduced heterotetramer on the template homotetramer (1YP2) was done and found to be quite similar as evident by 0.822Å RMSD.
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    ThesisItemOpen Access
    Multiple Sequence Alignment: Comparison and Evaluation
    (2012) Ritu; Jain, Sunita
    The present investigation was undertaken to compare and evaluate eleven tools of Multiple Sequence Alignment, namely Bali-phy, ClustalW, DCA, Dialign, Kalign, MAFFT, Multalin, MUSCLE, PRALINE, PROBCONS and T-COFFEE and to present a choice to the users of MSA regarding the optimal program. Nineteen sequences, each of cytochrome C and hexokinase were aligned by these tools using their default parameters. On comparing the various features of MSA tools, it was found that linux was the most favoured operating system and Fasta was the most favoured input as well as output format. PRALINE was the only web-based and Bali-phy was the only stand-alone tool, while the rest of the tools were both stand-alone as well as web-based. Various MSA programs were based on different alignment algorithms and scoring matrices. Alignments produced were used to generate phylogenetic trees. Comparison of these phylogenetic trees with the reference phylogenetic tree i.e. NCBI Taxonomy Common Tree, showed that while the tree obtained from the T-COFFEE alignment tool was nearest to the NCBI Taxonomy Common Tree, phylogenetic trees produced by none of the MSA tools were consistent. Multalin tool was found to give the highest diversity of position scores on Scorecons server for both cytochrome C and hexokinase sequences; while TCOFFEE, MUSCLE, Kalign and MAFFT programs gave low scores. The benchmark database, BAliBASE was used in the current study for cytochrome C sequences. It was found that MSA programs Praline, MAFFT, MUSCLE and PROBCONS gave high SP scores for both divergent sequences and sub-families, while T-COFFEE gave low score. Inconsistent phylogenetic trees and discrepancy between Scorecons and BAliBASE scores from various MSA tools may be attributed to the use of highly divergent sequences from bacteria to human in the current study.
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    ThesisItemOpen Access
    Prediction of codon bias in rice (Oryza sativa) genes
    (CCSHAU, 2012) Savita; Jain, Sunita
    Patterns and degrees of codon usage bias vary not only among different organisms, but also among genes in the same organism. Codon usage bias (CUB) conveys useful information about the selection on synonymous codons induced by gene expression, translation efficiency and about the distinctive evolutionary properties. In the present study, by using 28502 complete coding sequences (CDS) of rice (Oryza sativa) with full length cDNA support, a detailed analysis of the codon bias was performed by employing Automated Codon Usage Analysis (ACUA) tool. 27897 genes demonstrated codon bias as their ENc (effective number of codons) values varied from 20 to less than 61. On basis of GC3 content values, 267 biased genes were taken as high GC 3(GC3>=0.8) whereas 27630 biased genes were termed as low GC3(GC3 <0.8) genes. Quantification of genomic compositional asymmetry and dinucleotide frequency distribution analysis were further performed on selected biased genes to provide possible reasons of differences in nucleotide composition and compositional gradients along the coding regions of all the genes. GC3 gradient analysis results revealed that from the 5' end to 3' end of the open reading frame, high GC3 biased genes had a very slight positive gradient and low GC 3biased genes had strong negative gradient. CG3 skewness analysis showed that C3 preference even though higher for high GC 3genes than low GC 3genes, varied differentially as a function of distance from ATG codon. The analysis for CG3- and GC3- skewness as a function of distance from the startcodon in rice genes clearly depicted the prevailing tendency for GC 3 to decrease toward the 3' end. By dinucleotide frequencies ratio distribution analysis, 45/267 high GC 3 biased genes were detected at CG/GC dinucleotide frequencies ratio peak centered at 1.1, whereas 1729/27630 and 1762/27630 low GC3 genes with CG/GC dinucleotide frequencies ratio peaks centered at 0.5 and 1.1, respectively were observed that clearly depicted that high GC 3 genes had a significantly higher frequency of CG dinucleotides than low GC 3genes. The differential pattern of GC 3bias in rice genes shown in our study corroborate with the previous studies that plant codon usage might be affected by translational selection.
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    ThesisItemOpen Access
    Identification of microRNA in rice (Oryza sativa)
    (CCSHAU, 2012) Mamta Rani; Sudhir Kumar
    Th e pr e s e n t i n ve s t i g a t i on h a s be e n un d er t a k en t o i d e n t i f y m i c r oRNA i n Or y z a s a t i v a u s i n g c om p u t a t i on a l a p pr oa c h . Th e m i RNA p l a y s i g n i f i c a n t r ol e i n pl a n t bi ol og y a s n e g a t i ve r e g u l a t or of g e n e e x p r e s s i on a n d h a ve b e e n s h own t o r e g u l a t e d i ve r s e fu n c t i on s i n c l u di n g t r a n s c r i pt i on , c a t a l ys i s , t r a n s p or t er a c t i vi t y, s t r e s s r e s p on s e , p r ot e i n d e g r a d a t i on , n ut r i e n t m e t a bol i sm , r oot g r owt h , or g a n d e ve l op m e n t s u c h a s l e a f m or ph og e n e s i s . In p l a n t s , m os t o f t h e mi RNA bi n d t o c od i n g s e q u e n c e or op e n r e a di n g f r a m e of t h e i r m RNA t a r g e t s wi t h p er fe c t or n e a r l y p e r fe c t c om p l em e n t a r i t i e s a n d i n d u c e s t a r g e t m RNA c l e a va g e . I n t h e p r e s e n t s t u d y, 1 2 9 m i RNAs we r e i d e n t i f i e d i n r i c e g e n om e b y i d e n t i f yi n g p a l i n dr om e s e q u e n c e s a n d pr e d i c t i on of s e c on d a r y s t r u c t ur e b y R N A f o l d , t h en f i l t e r ou t t h e s e q u e n c e s wh os e MF E s e c on d a r y s t r u c t ur e wa s l e s s t h a n - 4 0 k c a l a n d f i n a l l y a l l r e p or t e d m i RNAs we r e ve r i f i e d a g a i n s t kn own s e q u e n c e s o f m i RNAs i n m i RBa s e d a t a ba s e . T wo n ew m i RN A ( Os a - MI R8 1 2 m , Os a - MI R8 1 2 o) we r e r e p or t e d on t h i r d a n d s e v e n t h c h r om os om e . Nu m b e r s o f m i RNA r e p or t e d we r e d i f f e r e n t on d i f fe r e n t ch r om o s om e s ; h i gh er m i RNA ( 1 7 ) we r e r e p or t e d on s i xt h c h r om os om e wh i l e on l y t h r e e m i RNA we r e i d e n t i f i e d on 1 2 t h c h r om os om e . Th e m os t a bu n d a n t l y e x p r e s s e d m i RNA fa m i l i e s i n r i c e s e e d l i n g s a r e MI R1 6 9 a n d MI R1 5 6 on c h r om os om e 2 n d a n d 4 t h . S om e m i RNA ( Os a - MI R4 2 6 , Os a - MI R4 1 7 , Os a MI R4 2 0 Os a - MI R4 1 6 ) we r e f ou n d t o be c on s e r v e d be t we e n r i c e a n d A r a bi d o p s i s wh i l e Os a MI R4 4 4 e , Os a - MI R1 4 2 7 , Os a - MI R1 4 3 0 , Os a - MI R1 4 3 7 , Os a - MI R1 6 7 , Os a - MI R1 4 4 0 we r e f ou n d t o be a bs e n t i n A r a b i d o p s i s bu t pr e s e n t i n c l os e l y r e l a t e d m on oc ot s . T h e mi RNA Os a MI R3 9 9 d , Os a - MI R2 1 2 3 a we r e r e p or t e d on f i r s t a n d t h i r d c h r om os om e a n d i n vol v e d i n s t r e s s r e s p on s e s . Ot h e r m i RNA l i k e Os a - MI R8 1 2 e , Os a - MI R2 8 7 3 , Os a - MI R5 4 9 1 , Os a MI R5 5 3 4 b, Os a - MI R8 1 2 g , Os a - MI R8 1 9 k a n d Os a - MI R2 1 0 2 i d e n t i f i e d on f i r s t , t h i r d a n d n i n t h ch r om os om e a n d h a ve r e g u l a t or y r ol e i n p l a n t pos t em br yog e n i c d e ve l op m e n t , p ol l en a n d s e e d d e ve l op m e n t , d i f f e r e n t r ol e s i n s u p er i or a n d i n fe r i or s p i k e l e t s of r i c e . C on s e r ve d m i RNAs - t a r g e t pa i r s we r e f ou n d t o be a s s oc i a t e d wi t h d e ve l op m e n t a l pr oc e s s e s a n d t r a n s c r i p t i on a l r e g u l a t i on , wh i l e n on - c on s e r ve d p a i r s we r e i n vol ve d i n s i gn a l t r a n s d u c t i on a n d r e s p on s e t o s t r e s s pr oc e s s e s . A n on - s i gn i f i c a n t c or r e l a t i on ( 0. 2 7 ) h a s be e n fou n d be t we e n g e n e s a n d m i RNAs p r e d i c t e d i n r i c e g e n om e .