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R & D in TCB
Establishment of national rice resource database

Two distinct activities have been initiated to formulate this database. The first activity is being coordinated by the NBPGR, New Delhi with participation of NRCPB, New Delhi; CRRI, Cuttack; DRR, Hyderabad; CSSRI, Karnal; IGKV, Raipur and BHU, Varanasi in multicentric mode.

This activity aims at characterisation of rice germplasm based on agronomic traits so as to form a core/mini-core germplasm.

Subsequently, the unique collection of germplasm would be characterised in detail at molecular level to generate passport data. The second activity is being carried out by University of Delhi, South campus and will aims at compiling data on whole genome sequence/proteome of rice and a huge collection of experimental data generated over several decades.

Establishment of national database on Tuberculosis

This database has been developed in a multi-centric mode. The layout of this database has been designed by NJIL&OMID, Agra in first phase of the project and it is now being implemented simultaneously at NJIL&OMD, Agra and MANIT, Bhopal.

The MANIT has created an online data warehouse for storage of biological data, developed tools for data-mining etc. and is also providing technical support to participating institutions.

The NTI, Bangalore is providing input in the areas of epidemiological, sociological issues in addition to monitoring of revised RNTCP programme.

The IOB, Bangalore has its input in the form of a TB-NET portal, web resource for proteomic, host-pathogen interaction and building up pathway resources.

JNU, New Delhi, will be giving incepts through the MGDD database and its up gradation.

The IISC, Bangalore has developed the database from system level modelling and genome profiling of MTB.

In addition, structural bioinformatics analysis and methodologies for genotype- phenotype mapping is being done by IISc. TRC, Chennai is annotating the genomes of mycobacteriophages, under study and is also developing bioinformatics tools for analysis of the database.

Indo-Japan Collaboration in Bioinformatics

The DBT, India and AIST, Japan had signed an MoU in the month of February, 2007 to work jointly in the field of biotechnology, which has recently been extended for another 5 yrs. In the first instance, it was decided to work in the area of Bioinformatics and Computational biology.

Four challenging themes viz. (1) Designing potential targets in membrane proteins, (2) Designing GPCRs Mimetics, (3) Designing FIXER for disorders, and (4) Designing cybrog lectins were identified.

The proposals were implemented in collaboration with the CBRC group of AIST, Tokyo. The project at Manonmaniam Sundaranar University, Tirunelveli focuses mainly on the carbohydrade-hemagglutinin complexes of Influenza A virus and designing cyborg lectin by mutating the important amino-acid residues.

The overall conformation and hydrogen bonding patterns of 4 biologically important sialydisaccharide have been deciphered. The binding specificity of 4 hemagglutinin lectins of influenza-A virus and 6 biologically important sialydisaccharide have been studied.

Mutation studies in the active site of wheat germ agglutinin have been carried out and a promising mutant has been identified by in-silico methods. This cyborg lectin can be used for targeted drug delivery and biological cell marker in cancer therapeutics.

The project has resulted in two high impact factor joint publications. The second project on Genome wide survey of olfactory receptors in diverse eukaryotic model organisms is being implemented at NCBS, Bangalore and Bharathidasan University.

The project has led to the development of a software to identify olfactory receptors (OR) from whole genomes of organisms. This TM-MODIF software has been published and will be distributed for academic purposes soon. Further, an exhaustive database on ORs comprising of sequences cluster analysis data, 3D structure of more 800 ORs, mutations and their effect on odour response, predicted dimer interface has been developed and would be released on public domain after publication.

The third project at University of Madras and SRM University is on identification of efflux pump inhibitors to gram-negative organism using bioinformatics tools, in vitro analyses and crystallographic studies.

In an attempt to identify efflux pump inhibitors to gram negative organism the computational structural analysis of two pumps ArcB and MexB was done. Through virtual screening and in vitro assays for validation, two promising inhibitors viz. quercetin and thionine were identified.

In-vitro testing of another 100 putative inhibitors is under progress. In fourth project on Designing cyborg lectins based on subunit-association in jacalin-type lectins at NCL, Pune attempt is being made to design cyborg (artificial) tetrameric lectins which can act as a carrier for a peptide-like drug molecule and can also recognise cells through their sugar binding capacity, a functional requirement for a carrier molecule in targeted drug delivery.

Several joint publications in indexed journals have resulted from this collaboration.

The 2nd Bilateral Indo-Japan Workshop was organised in Hyderabad in November 2008. It was agreed to evolve projects in the field of Glycoscience, Biomarker and Cell Engineering in the next phase of corporation.

Since then, four projects have been supported in the area of cell engineering focusing mainly on senescence and cell proliferation, with the aim to understand cancers and develop novel ways for intervention.

The projects employ molecular biology and system biology approach. The objective of one of the projects is to develop Ashwagandha (Withania somnifera) derived phytochemicals for differentiation-based therapy of brain cancers.

Another complementary project aims at developing mass propagation for Ashwagandha and also standardise a protocol for development of Ashwagandha transgenics to understand metabolite accumulation and transport.

R&D project supported under competitive grant scheme

The first R&D proposal in bioinformatics was received by the department in 1999. Since then the division has supported 97 projects of which 29 are ongoing and 10 are in pipeline.

Over the years the projects have been supported in various areas such as drug and inhibitor designing through molecular modelling; development of tools for genome/microarray databases/protein structure analysis; development of database of biological importance; better algorithms for imaging; tools for deciphering genes and pathways involved in diseases; tools and database for efficient disease management and agri-informatics.

Over the years a general shift in trend in bioinformatics research has been observed. In early 2000 most of the projects funded focussed on using existing tools for solving problems in Agriculture and Medical Science.

In some projects novel algorithms, tools and software were developed particularly for protein structure analysis.

However, biological validation component in these projects was non-existent. The project now being supported focus on developing novel tools with strong experimental validation component.

A number of projects funded in last 3 years aim at developing novel tools for the robust analysis of voluminous data being generated through the ‘omics’ approach.

The project at NDRI, Karnal and IASRI, New Delhi on ‘Buffalo Genome Information Resource’ focusses on designing and developing buffalo genome database and maintaining gene annotations and revealing the underlying mechanism of chromosomal evolution between cattle and buffalo.

Another proposal at IARI, New Delhi aims at development of a comprehensive genomic resource and knowledge base of two plant parasitic nematodes, Meloidogyne graminicola and Heterodera avenae, important nematode problems of rice and wheat respectively worldwide.

The joint project being implemented at Birla Institute of Technology, Mesra, Ranchi, and Chaudhary Charan Singh University, Meerut aims at discovery, annotation, validation and characterisation of SNPs in Wheat (Triticum aestivum L.) using Next-Generation Sequencing Data.