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Centres of excellence – Salient Achievements

The salient achievements of the “Centre of Excellence” supported so far are …

Genetics and genomics of silkmoths

Studies on silkworm-BmNPV interactions led to the identification of virus-derived microRNA (miRNAs) that have a number of interesting cellular targets involved in different antiviral host defense mechanisms in silkworms (Bombyx mori) at Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad. Genetic diversity and population structure of two wild silkmoth species, Antheraea assama and A. mylitta, have been studied using microsatellite markers developed in the laboratory. Full-length silk fibroin gene of A. assama, which is 9 kb with a short but highly conserved 5’ non-repetitious terminus of 407 bp and a shorter 3’ terminus of 252 bp, has been sequenced. Small accessory silk proteins of the domesticated silkworm (B. mori) known as seroins have been shown to act as antiviral agents against BmNPV.

Co-ordinated research on tuberculosis

Based on whole-cell screening methods, inhibitors against the intraphagosomal survival of Mycobacterium tuberculosis have been identified jointly at International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi and University of Delhi South Campus (UDSC), New Delhi. Secretory phosphatases deficient mutant of M. tuberculosis imparts protection at the primary site of infection in guinea pigs. Adjunctive chemotherapy with -crystallin based DNA vaccination reduces tuberculosis chemotherapy period in chronically infected mice.

Research on Hepatitis-C Virus

Phyllanthin and corilagin isolated from Phyllanthus amarus have been proved as potent anti-HCV therapeutic candidates based on in vivo tests at Indian Institute of Science, Bangalore. A neutralising antibody nAb-C002 (isolated from human serum) has significantly blocked HCV inhibition in cell culture. The peptides mapped from the epitope of the antibody are being tested for blocking HCV entry into human liver cells. A highly conserved beta-turn in human La protein has been found to contribute to species specificity of HCV, which raise a possibility of creating an immuno-competent HCV mouse model using human specific cell entry factors and a humanised form of La protein.

Genome Science and Predictive Medicine

Genome-Wide Association Studies (GWAS) on rheumatoid arthritis (RA) and ulcerative colitis (UC) for identification of novel genes/loci in North Indian population have been completed jointly by UDSC, New Delhi, National Institute of Immunology, New Delhi, University of Delhi, Delhi, Indian Agricultural Statistics Research Institute, New Delhi, All India Institute of Medical Sciences (AIIMS), New Delhi, Dayanand Medical College, Ludhiana and Sri Venkateshwara College, New Delhi. Cell-type specific networks in RA have been continued along with identification of potential drug targets utilising the GWAS data. Three dimensional structures of two important dopaminergic genes namely Dopamine receptor D4 and Dopamine -hydroxylase have been established for the first time with implications for rationalised drug design. DNA banks generation has become a useful resource for cross-ethnicity based fine mapping to identify disease causing variants in North Indian populations.

Stem Cell Research

A low cost method for culture and maintenance of human embryonic stem cells (hESC) using conditioned media from immortalised human feeder cells has been developed at AIIMS, New Delhi. A novel inducer for the generation of cardiomyocytes from bone marrow derived mesenchymal stem cells has been reported. New methods to generate more efficient, functionally active neurons from adult stem cells have been standardised. Multicentric trials have been completed on use of bone marrow derived mononuclear cells in degenerative diseases such as limb ischemia, myocardial infarction and stroke. Animal studies have been carried out on use of bio-composite scaffolds to transplant stem cells at the site of injury in long bone defects.

Microbial Biology Research

Multidisciplinary approaches are being employed to understand fundamental life processes in the model bacterium Escherichia coli, including replication and cell division, gene expression and its regulation, systems biology of functional protein-protein interactions, and membrane transport and energetics at CDFD, Hyderabad and Centre for Cellular and Molecular Biology (CCMB), Hyderabad. Significant achievements during the year include the formulation of models to explain the causes and consequences of transcription-associated RNA-DNA hybrids (R-loops) in bacteria and the role of Rho-mediated transcription termination there on, delineation of the mechanisms of transcription anti-termination mediated by the Psu protein of phage P4 and the N protein of phage lambda, and the identification of YciM as an essential protein that is required for regulation of lipopolysaccharide synthesis in E. coli.

High-throughput Approach

A comprehensive high-throughput whole genome microarray based transcriptome analysis as well as an extensive phenotype- and genotype-correlation analysis has been carried out on segregating populations of rice to identify the molecular components involved in the process of heterosis at UDSC, New Delhi in collaboration with Maharashtra Hybrid Seeds Company Limited, Jalna, Maharashtra. Differentially expressed genes and their signature expression profiles are being utilised for development of a prediction system for heterosis. A number of rice transformation events with genes/promoters selected for their specific expression in leaves, roots, panicles and seeds and differential expression in the MRP5401 F1 hybrid have been generated and are at various levels of characterisation.

Under a network project implemented by International Crop Research Institute for the Semi-Arid-Tropics (ICRISAT), Patancheru, Acharya NG Ranga Agricultural University (ANGRAU), Hyderabad, Indian Agricultural Research Institute (IARI), New Delhi and Indian Institute of Pulses Research (IIPR), Kanpur. SNP genotyping platform has become fully functional. Efforts have been continued to deploy marker-assisted back crossing and marker-assisted recurrent selection approaches for enhancing drought tolerance in chickpea and molecular mapping of FW and SMD in pigeonpea. A total of 22 BC3F5 lines of chick pea along with parents and two control genotypes (JG 11 and JAKI9218) have been sown at Patancheru, Nandyal and Dharward for multi-location phenotyping under rainfed and irrigated environments for yield and harvest index related traits. A set of 41 (KWR 108 × ICC 4958) and 33 polymorphic markers (DCP92-3 × ICC 4958) were obtained after screening the parental genotypes with 576 SSR markers.

Genome Mapping and Molecular Breeding

Efforts on generation of high-density linkage and saturation maps of QTL regions in Brassica juncea continued at University of Delhi South Campus, New Delhi. Transcriptome sequencing of diverse genotypes of three Brassica species namely, B. rapa, B. nigra and B. juncea has been carried out using an Illumina sequencing platform. Testing of SNP markers for saturating a QTL region has been undertaken in B. rapa. A total of 52 SNPs (34 singletons and 18 multi-copies) were synthesised from the QTL region. Transcriptome sequencing has been carried out in B. juncea using inflorescence, leaf, stem, developing pod and seedling tissues. SNP mapping was undertaken between two varieties Varuna and Heera for mapping several important traits such as erucic acid, glucosinolate, seed coat colour, white rust resistance and several yield associated traits. A total of 1058 SNPs were genotyped following KASPar technology and an SNP map of B. juncea was developed using 1026 SNP markers. Some of these markers were also used to saturate four QTL regions responsible for glucosinolate variation. Two bi-parental DH mapping populations have been generated for oil content. Linkage maps based on the two populations have been developed. The mapping populations have been phenotyped for oil content and other yield associated traits at three locations (Delhi, Alwar and Bharatpur). The Data there from is being compiled and will be subjected to QTL dissection and the maps are being further enriched by incorporating SNP markers obtained from the NGS based transcriptome studies.

Computational and System Biology Research

Protein domain superfamilies were analysed critically for structurally deviant members which are structurally and functionally distinct at National Centre for Biological Sciences (NCBS), Bangalore. Multimerisation status and interacting protein partners have been recorded for all the PASS2 domains and psuedoenergy ranges have been established using 310 protein-protein interfaces. Two computational algorithms have been devised to recognise protein-protein interaction ‘hotspots’ which would form the focus of virtual screening and design of point mutations and in vitro experiments. With an objective to identify druggable small molecules and focusing on the site of point mutation which was observed to abrogate Hedgehog-hedgehog oligomerisation earlier, virtual screening has been carried out against more than 1,00,000 small molecules. Analysis of three divergent RNA polymerase complexes indicates high conservation of the interfaces despite overall sequence divergence emphasising the importance of interface properties for overall function for these proteins.

Epigenetics Research

Genome sequencing of Hydra valgaris using multiple platforms has been completed at Indian Institute of Science Education and Research, Pune, CCMB, Hyderabad, Agharkar Research Institute, Pune, CDFD, Hyderabad and Tata Institute of Fundamental Research, Mumbai. It has been shown that hierarchical assembly is a cost-effective method for de novo assembly of complex genomes. A comprehensive Hydra transcriptomic profile using Illumina paired-end design technology has also been obtained. Transcriptome analysis provided clues towards genes important for patterning and axis formation. Phylogenetic analysis and comparative sequence analysis of hydra histones suggested the occurrence of H2AX and macro H2A homologues for the first time in phylum Cnidaria. The histone variants were differentially expressed in different body parts of hydra suggesting their specific roles.

Epilepsy Research

Video Electroencephalogram (VEEG) of 50 patients has been recorded along with collection of 110 brain samples and data of over 120 patients at AIIMS, New Delhi in collaboration with NBRC, Manesar. Magnetoencephalography (MEG) facility is at advanced stage of completion at NBRC, Manesar. The facility will be used for non-invasive localisation of epileptogenic focus. The role of neuronavigation-guided functional MRI and diffusion tensor tractography along with cortical stimulation in patients with eloquent cortex lesions has been elucidated.

Translational Research on Eye Diseases

Limbal stem cell based therapy has been provided to over 800 needy patients. Long-term follow up of 400 such autologous cultivated limbal epithelial transplantation shows 70% success. The induced pluripotent stem cells (iPSCs) have been generated from the skin cells of a retina patient and differentiated into retinal pigment epithelial cells (RPE). The ARMS2/HTRA1 genes at the 10q26 locus have been associated with risk of age-related macular degeneration (AMD), with one of the most significantly associated variants being (rs10490924), del443ins54. Screening for del443ins54 in a large cohort of ~1500 subjects from Indian and Australian two populations reveal the association of del443ins54 variant in two different ethnicities, despite differences in allele and haplotype frequencies between them.