Bioinformatics Section

India

Bioinformatics Section

India
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Jain S.,Bioinformatics Section | Dhillon R.,CCS Haryana Agricultural University
Journal of Plant Biochemistry and Biotechnology | Year: 2010

A collection of male and female plants of ten Jojoba [Simmondsia chinensis (Link) Schneider] genotypes was analyzed with 50 RAPD and 55 ISSR markers to compare the efficiency and utility of these techniques for detecting genetic polymorphism. RAPD and ISSR analysis yielded 442 and 566 scorable amplified products, respectively, of which 60.7 and 69.3% were polymorphic. ISSRs revealed efficiency over RAPDs due to high EMR (effective multiplex ratio), DI (diversity index, mean PIC per primer) and MI (marker index) values. Jaccard similarity matrices among male plants, among female plants and between male and female plants of the ten jojoba genotypes varied between 0.705-0.784. Dendrograms generated by cluster analysis (UPGMA, NTSYS-pc) supported by bootstrap values using RAPD and ISSR datasets led to grouping of most of male and females genotypes in separate clusters. While pattern of clustering remained more or less same, the two dendrograms did differ with respect to the grouping of a few male and female genotypes. The value of the Mantel test shows poor correlation (r = 0.41) between ISSR and RAPD marker datasets.


Pirona R.,Plant Genomics Section | Vecchietti A.,Plant Genomics Section | Lazzari B.,Bioinformatics Section | Caprera A.,Bioinformatics Section | And 8 more authors.
Plant Biology | Year: 2013

The expression profile of flavour-related genes during ripening was investigated in two peach genotypes, Bolero and OroA, which have been selected for their contrasting aroma/ripening behaviour. A new peach microarray containing 4776 oligonucleotide probes corresponding to a set of ESTs specifically enriched in secondary metabolism (μPEACH2.0) was designed to investigate transcriptome changes during three fruit ripening stages, revealing 1807 transcripts differentially expressed within and between the two genotypes. Differences in the expression of genes involved in the biosynthesis of aroma compounds were detected during the ripening process within and between the two genotypes. In particular, a subset of 12 transcripts involved in metabolism of esters, norisoprenoids, phenylpropanoids and lactones, varied in expression during ripening and between Bolero and OroA. © Parco Technologico Padona S.r.l. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.


Kumar R.,Bioinformatics Section | Kumar S.,Sewar | Sangwan S.,Chaudhary Devi Lal University | Yadav I.S.,Bioinformatics Section | Yadav R.,Guru Jambheshwar University of Science and Technology
Journal of Molecular Graphics and Modelling | Year: 2011

Myrosinase, the only known S-glycosidase, occurs particularly in Cruciferae family. It is responsible for the hydrolysis of glucosinolates and serves as a vital element of plant defense system. The biological and chemical properties of myrosinase catalyzed products of glucosinolates are well characterized. The myrosinase-protein-sequence of Brassica juncea was retrieved from NCBI database and its 3-D model was generated on the basis of crystal structure of 1MYR-A, 1E4M-M and 1DWA-M chains of myrosinase from Sinapis alba by employing Modeller9v7 program. Homolog templates from S. alba exhibited 72% identity with target sequence. The model was optimized by using molecular dynamics (MD) approach together with simulated annealing (SA) methods in the same Modeller program, and eventually verified and validated on SAVES (Structure Analysis and Verification Server) and PROCHECK programs, respectively. Ramachandran plot obtained through PROCHECK program depicted that 99.8% of total residues were confined to the allowed region while only one residue (Thr92) was restrained to the disallowed region. Additionally, B. juncea myrosinase contains three disulphide bridges which were found to be conserved in S. alba homologs as well. Further, overlapping of B. juncea myrosinase with that of template protein 1MYR-A from S. alba stipulates the amino acid residues Arg115, Gln207, Thr210, Asn350, Tyr352 and Glu429 that constitute active site of the enzyme. Active site analysis also speculates the presence of a hydrophobic pocket in addition to seven N-glycosylation sites. Docking studies of enzyme and substrate illuminate the interactions of various active site residues with diverse groups of sinigrin. Therefore, the present study furnishes the first significant, in silico insight into the 3-D structure, active site machinery, and enzyme-substrate interactions of B. juncea myrosinase. © 2010 Elsevier Inc.


He S.,Bioinformatics Section | Zhang H.,Southern Medical University | Liu H.,Bioinformatics Section | Zhu H.,Bioinformatics Section
Bioinformatics | Year: 2015

Motivation: In mammalian cells, many genes are silenced by genome methylation. DNA methyltransferases and polycomb repressive complexes, which both lack sequence-specific DNA-binding motifs, are recruited by long non-coding RNA (lncRNA) to specific genomic sites to methylate DNA and chromatin. Increasing evidence indicates that many lncRNAs contain DNA-binding motifs that can bind to DNA by forming RNA:DNA triplexes. The identification of lncRNA DNAbinding motifs and binding sites is essential for deciphering lncRNA functions and correct and erroneous genome methylation; however, such identification is challenging because lncRNAs may contain thousands of nucleotides. No computational analysis of typical lncRNAs has been reported. Here, we report a computational method and program (LongTarget) to predict lncRNA DNA-binding motifs and binding sites. We used this program to analyse multiple antisense lncRNAs, including those that control well-known imprinting clusters, and obtained results agreeing with experimental observations and epigenetic marks. These results suggest that it is feasible to predict many lncRNA DNA-binding motifs and binding sites genome-wide. © The Author 2014. Published by Oxford University Press. All rights reserved.


PubMed | Bioinformatics Section
Type: Journal Article | Journal: Journal of molecular graphics & modelling | Year: 2011

Myrosinase, the only known S-glycosidase, occurs particularly in Cruciferae family. It is responsible for the hydrolysis of glucosinolates and serves as a vital element of plant defense system. The biological and chemical properties of myrosinase catalyzed products of glucosinolates are well characterized. The myrosinase-protein-sequence of Brassica juncea was retrieved from NCBI database and its 3-D model was generated on the basis of crystal structure of 1MYR-A, 1E4M-M and 1DWA-M chains of myrosinase from Sinapis alba by employing Modeller9v7 program. Homolog templates from S. alba exhibited 72% identity with target sequence. The model was optimized by using molecular dynamics (MD) approach together with simulated annealing (SA) methods in the same Modeller program, and eventually verified and validated on SAVES (Structure Analysis and Verification Server) and PROCHECK programs, respectively. Ramachandran plot obtained through PROCHECK program depicted that 99.8% of total residues were confined to the allowed region while only one residue (Thr92) was restrained to the disallowed region. Additionally, B. juncea myrosinase contains three disulphide bridges which were found to be conserved in S. alba homologs as well. Further, overlapping of B. juncea myrosinase with that of template protein 1MYR-A from S. alba stipulates the amino acid residues Arg115, Gln207, Thr210, Asn350, Tyr352 and Glu429 that constitute active site of the enzyme. Active site analysis also speculates the presence of a hydrophobic pocket in addition to seven N-glycosylation sites. Docking studies of enzyme and substrate illuminate the interactions of various active site residues with diverse groups of sinigrin. Therefore, the present study furnishes the first significant, in silico insight into the 3-D structure, active site machinery, and enzyme-substrate interactions of B. juncea myrosinase.


Grant
Agency: Narcis | Branch: Project | Program: Completed | Phase: Physics, Chemistry and Medicine | Award Amount: | Year: 2007

None


Grant
Agency: Narcis | Branch: Project | Program: Completed | Phase: Physics, Chemistry and Medicine | Award Amount: | Year: 2007

None

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