Publications

Mixture Distribution Models for differential Gene Expression Analysis

Author: Arfa Anjum

2013-14

Development of Crop Wild Relatives Resources (CWR) Database for Vigna and Phaseolus Species

Author: Md. Asif Khan

2013-14

Development of Infromation system on Buffalo Genome

Author: Amit Kairi

2011-12

In silico study of host-pathogen interaction under mutation effect on blast resistance genes in rice

Author: Priya Prabhakar

2011-12

The effect of mutation on proteins of blast resistance gene was analysed by detecting and comparing the natural variations (SNPs and InDels) present in 30 alleles of Pi-ta gene in Oryza spp. O. sativa indica. Three-dimensional structure of Pi-ta proteins were predicted through I-TASSER software. 3D refine web server (http://sysbio.rnet.missouri.edu/3Drefine/) was used to bring the initial model closer to the native structure. The stereo chemical quality of the model was checked using the ‘Protein Quality Assessment’ parameter option of Discovery Studio. Quantitative structural evaluations were performed to find out the stability and disease response of Pi-ta alleles upon mutation. Average number of nucleotide difference between two sequences was found lower in Oryza indica in comparison with the nucleotide difference surveyed from O. rufipogon. InDel diversity per site (Πi =0.00061) was found lower than nucleotide diversity per site (Π =0.00255) in the selected accessions of Pi-ta gene. More number of synonymous substitutions were observed in non-coding region. Susceptible indica cultivar C101A51 showed maximum number of InDels events in the gene. Most of the changes in secondary structure elements were observed in NBS-LRR region. More number of coils were found in LRR region in comparison to helix. The predicted in silico protein structure of the Pi-ta alleles was observed to be affected by mutation i.e. SNPs and InDels. Quantitative assessments of these structures showed differences in value of ASA, SFE and number of H-bonds. Normal mode analysis of modelled proteins showed differences in region of maximum atomic displacements between different alleles of Pi-ta gene. A total of 101 accessions of AvrPita proteins were found in NCBI from which 12 dominant effectors Avr-pita proteins and 8 recessive Avr-pita proteins were selected from 19 isolates of M.oryzae strain. All these sequences were not 100% similar. Value of SFE and number of H-bonds were less in recessive Avr proteins in comparison to dominant effector proteins. An approximate degree of flexibility for proteins was determined by secondary structure elements present in the structure. BAK40873.1 and BAK40874.1 contain more number of coils as compared to other structures which can lead to more degree of flexibility than others. CCD21951.1 contains least number of coils than others, so it is most rigid structure. In normal mode analysis, region of maximum atomic displacements was found different in recessive and dominant effector proteins. In another experiment, direct interaction between proteins of Pi-ta alleles and their corresponding Avr-pita was observed by two methods. First method is interaction in gene-for-gene manner and second is in silico mutagenesis and interaction of polymorphic sites in the LRR region of R proteins. Maximum BE was observed in complex of BAF91347.1 and BAK40873.1. It also contained maximum number of hydrogen-bonds. Least BE was observed between docking complexes of Pita proteins from susceptible Oryza cultivars and recessive Avr proteins. Mutation analysis of the polymorphic sites in the LRR region showed that mutability of these sites is different. The mean of the binding free energy change distribution over 19 mutations was found negative for 8 out of 11 sites. A very less correlation was found between mutations that increase stability and mutations that favour complex formation.

Web Application for classification of Proteins responsible for Abiotic Stress in Cereals

Author: Neeraj Budhlakoti

2012-13

Assembly Annotation, fuctional classification of transcriptomes and identification of key genes for moisture stress tolerance in Cucumis melo

Author: Supriya Purru

2012-13

Muskmelon (Cucumis melo L., Cucurbitaceae) is an important fruit crop worldwide. It is considered to be the most variable species in the genus Cucumis, and one of the most diverse among the cultivated vegetables. Moisture stress is one of the major restraining factors for musk melon production. To minimize the yield losses caused by moisture stress, there is a need to identify the genes possessing stress tolerance. The main objective of present study was to identify key genes that play a major role in moisture stress tolerance by de novo assembly and annotation of musk melon transcriptome. Transcriptomic analyses of plant responses to stress are an effective way in which genes, pathways and processes responsible for plant stress tolerance can be identified. In this study, a high-throughput, SOLiD sequencing technology was employed to characterize the de novo transcriptome of musk melon. A total of 47,035,393 and 45,152,235 high quality unique reads for cucumis melo control sample and stress sample were assembled into 12859 and 13448 transcripts, respectively using CAP3, DNA STAR and CLC de novo assembly programs. Merging of assemblies by CAP3 resulted in larger and robust transcripts instead of using a single program alone. This de novo assembly of melon transcriptome from control and stress samples provides a rich source for gene identification. These transcripts were annotated with gene ontology (GO) terms. All the GO terms were classified into 37 functional groups including biological processes, cellular component, and molecular function. Comparison of gene expression levels between control and stress transcriptomes by RNA-Seq mapping revealed that 122 stress responsive genes were commonly expressed in both the samples where as 72 genes were highly up regulated in stress sample such as kinases, DREB genes, heat shock proteins, MYB transcription factors, Zinc- finger, and AP2 / ERF domain containing transcription factors. Among these, 4 genes are involved in path ways such as plant-hormone signal transduction, protein processing in endoplasmic reticulum and Inositol phosphate metabolism. These selected genes will not only facilitate understanding of genetic basis of moisture stress response, but also accelerate genetic improvement in musk melon.

Development of Epigenetic Database in Livestock species

Author: Sayanti Guha Majumdar

2012-13

Demand for livestock products is constantly increasing with the continuous population growth. To meet such demand it is essential to understand molecular mechanisms of livestock species. With the advent of new technologies, it has become possible to understand the underlying mechanisms present in the growth and development of important traits of livestock species. Epigenetics is an emerging field which deals with the study of mitotic and meiotic (or both) heritable changes in gene function that cannot be explained by changes in DNA sequence. Broadly, three epigenetic mechanisms occur in nature and they are (i) DNA methylation (ii) Histone modification and (iii) RNA interference (RNAi). However, the information related to the said epigenetic mechanisms in livestock species is not available at one place. Moreover, analysis of epigenetic information is required for improvement in production traits and controlling diseases in livestock. Keeping this in view, the present study is taken up with the objectives (i) to parse and analyze data of different epigenetic mechanisms in livestock species, (ii) to populate a database on epigenetic mechanism and make it available through web interface. Initially, the gene and protein sequence information related to epigenetic mechanisms of livestock species has been downloaded from NCBI, UCSC and CABin. Besides, the microRNA information of cattle and sheep has been retrieved from miRBase. Subsequently, a tool known as “Sequence Manipulation Suit: CpG Islands” is used to obtain the probable methylation sites present in the 1k upstream region of 10,990 genes in cattle. The results reveal that the CpG islands are found in 8033 genes. In addition, the three dimensional structures of histone proteins of cow, sheep, goat, camel have been predicted, validated, refined and stabilized. Also, the probable genomic regions of histone proteins in buffalo were identified by using tBLASTn tool. The BLAST results were then parsed and kept in a suitable format to populate a database. In case of RNAi, the secondary and tertiary structures of microRNAs of cattle and sheep were predicted by RNAfold and RNAcomposer respectively. Since the miRNA information in buffalo species is not available, the genomic regions of the same were mapped by considering miRNAs of cattle as query sequences in BLASTn. For ready use of the parsed data by users, a web-based “Livestock Epigenetic Information System” has been developed with MySQL database as bottom layer, PHP as server side application-middle layer and HTML, CSS and JavaScript at top layer. The developed information system can be accessed at http://bioinformatics.iasri.res.in/edil/.

Integrated Omics Platform of Assembly, Annotation and Visualization of Lens Culinaris

Author: Ravi

2023-24

Development of an AI model for screening of antimicrobial peptides against the target protein

Author: Deeksha P.M.

2023-24

MACHINE LEARNING BASED APPROACH TO STUDY THE ASSOCIATION BETWEEN DNA METHYLATION AND GENE EXPRESSION IN PLANTS

Author: Subham Ghosh

2023-24

Unveiling Epigenetic Basis of Plant Organismic Interaction through Artificial Intelligence

Author: Abhik Sarkar

2023-24

Artificial Intelligence Based Model to Predict Emerging Genetic variants of plant RNA Viruses

Author: Sheetal Dagar

2023-24