Collaboration with Savitribai Phule Pune University and Symbiosys International University on Identification of signatures for positive selection in pigmentation genes in South Asians
Skin pigmentation is a polygenic trait showing wide phenotypic variations among global populations. To decode the genetic architecture involved in adaptation to ultraviolet radiation in South Asian populations, Phase 3 of the 1000 genomes project focusing on two South Asian populations – GIH (Gujarati Indian from Houston, Texas) and ITU (Indian Telugu from UK) were analysed. Statistical tests pertaining to identification of deviations of Site Frequency Spectrum from neutral expectations, high-frequency haplotypes with extended linkage disequilibrium and genetic differentiation between populations were performed. Genetic diversity of MC1R gene in West Maharashtra population is also being profiled.
Collaboration with Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University on de novo assembly and annotation of Yarrowia genome
Yarrowia spp. are industrially important yeast due to their role in degradation of hydrophobic substrates. Fastq data pertaining to Yarrowia spp was generated using Illumina paired end sequencing by the collaborators. de novo assembly followed by reference mapping of the contigs was carried out using tools viz., SPAdes and Chromosomer. Gene prediction and annotation were performed using GeneMark-ES and BLAST2GO. Genome assembly and annotation aid in the identification of novel lipases in Yarrowia spp.
Collaboration with Pirbright Institute, UK on SNP analysis of chicken cell lines that are susceptible and resistant to Marek's disease and Lymphoid leukemia
The Pirbright Institute and Bioinformatics Group of C-DAC have been awarded BBSRC funded Indo-UK Partenring award titled “India-United Kingdom Bioinformatics Network” for the duration Summer 2013-2017. Under this project, single nucleotide polymorphism analysis of seven in-bred chicken lines would be carried out to understand genetic resistance to avian diseases such as Marek’s disease (MD) and lymphoid leukosis (LL). Pipelines would be developed for NGS data analysis and the predicted SNPs would be mapped to dbSNP where possible.
Collaboration with NCL, Differential gene expression of Chickpea plant
Differential gene expression analysis of chickpea plant during Fusarium infection using SAGE-seq is being carried out in collaboration with Dr. Narendra Kadu and Dr. Gayatri Gurjar, Biochemical Division, NCL. The main aim of the project is to study the differential expression patterns between Fusarium-resistance chickpea and Fusarium-susceptible chickpea plants. The gene expression data has been generated by using SAGE-seq protocol at NCL. The Role of CDAC, Pune is to analyze this sequence data using bioinformatics protocol.
Development of recombinant BCG vaccine and complementary diagnostics for TB control in cattle, a joint collaboration with TANUVAS, Chennai and University of Surrey, UK
Bovine tuberculosis remains a major problem in both the developed and developing world, as well as being a cause of huge economic loss in livestock farming. Mycobacterium bovis infection can be spread to humans from infected cattle by aerosol or by consumption of contaminated dairy products to cause zoonotic tuberculosis. Control of bovine TB is by detection and elimination of infected animals. Case-finding is primarily based on the tuberculin skin test (PPD) in which a preparation of crude denatured antigen from the tubercle bacillus (tuberculin) is injected, which in infected animals provokes a measurable reaction. BCG vaccination is not used to control bovine tuberculosis, despite its proven efficacy in cattle, as vaccination interferes with the PPD test.
This project aims to generate a synergistic vaccine and diagnostic approach which would allow the vaccination of cows without interfering with the surveillance of bovine TB. By generating a modified BCG vaccination with specific antigens deleted, these antigens could then be incorporated into currently available diagnostic tests in order to enhance sensitivity and specificity. Vaccinations of cows with modified diagnostic compatible BCG will provide a cheap and effective vaccine strategy to protect cattle from TB and the diagnostic test will allow effective control strategies to be maintained. This approach would have an enormous impact on the world-wide incidence of bovine TB.
Collaboration with IASRI, Developent of an algorithm based on causal reasoning for modeling the genes involved in abiotic stress response in rice
Rice is a major staple food crops in Asia and grown all over the world. Abiotic stresses are the major causes for lower productivity in rice and it account for 50% yield loss. In India, Salinity and high temperature stress are two important abiotic stresses which need immediate attention as both are increasing at alarming rate during past decades. The project aims to identify of genes andgene system responsible for abiotic stresses in rice.