EXIGENCIAS DEL BANCO CENTRAL DE CHILE EN MATERIAS DE SEGURIDAD

Coordinator: Dr. Ashok K Varma

Summary of the progress made by the centre from its inception

The Department of Biotechnology (DBT), Government of India, funded to establish the Biotechnology Information Service (BTIS)/Bioinformatics Centre at the Cancer Research Institute in 1989. Since its inception DBT is continuously funding the centre to support infrastructure and softwares. TMC-ACTREC also supports as and when required for gradual maturation of the facility. In addition to expansion of the institutional infrastructure, there is increase in number of full- time users also. In year 2012-13 we have procured one high-end workstation with 24GB RAM for NGS data analysis. Presently, the softwares available in the centre are extensively used by six Principal Investigators which comprise senior and middle level scientists, Ph. D students from ACTREC and number of project trainees from various academic institutes of India. The main theme of the centre is to provide infrastructure, training and software support to the scientists and young investigators working on Basic or translational research projects using bioinformatics based approaches to fulfil the mandate of DBT for setting up the SubDIC centre at ACTREC. BTIS at ACTREC organizes every year a two-day workshop to train faculties/Ph.D. students from various colleges/universities. We provide them training from basic knowledge of bioinformatics to modern approaches/ tools in molecular modelling & drug discovery. This helps them in teaching bioinformatics related subjects in their home institute.

Major research activities in biotechnology and its related fields:

 The major focus of the institute is basic and translational research in cancer biology.

 The detailed list of scientists working on different aspects of cancer biology and translational research are

available in http://www.actrec.gov.in/basic_main.htm.

 Activities on data-base analysis, structural bioinformatics, molecular modeling, and structure based drug design.

 Molecular profiling of oral, cervix, lung, breast, gastric and brain cancer, hematological malignancies using

genomics and proteomics technologies

 Molecular imaging for targeting cancer specific genes/proteins

 Cancer Immunology

 Basic research investigations on cell proliferation, differentiation and metastasis and aberrations in cancer are also ongoing towards identifying molecular targets.

 Structural Biology approaches towards understanding proteosomal dynamics, apoptosis and BRACA1 inter-

acting partners

 This year centre has started Macromolecular crystallography using X-ray diffraction analysis and Next-Gen-

Major achievements made during year 2012-13

 Inhibitor designing for of Gankyrin-ATPase complex.

 ATP binding site analysis in 14-3-3 zeta.

 Binding partners for Protease HtrA2.

 A data base is being made of basic research scientists working on Oral cancer in India. The database will

provide information via appropriate links of their ongoing work.

 SNPs and Indels analysis of deep sequencing data of brain tumor exomes.

 Identification of leads from marine seaweeds against human â-tubulin

 Targeting Pim1 kinase for potential drug-development using 3D-QSAR.

 Organization of two days workshop.

 Training of new JRF (batch 2011-12) of Institute registering for their Ph. D degree.

 Training of M. Sc., M. Tech., Ph.D. students of neighboring Institute so that they can use the bioinformatics

based approaches in enhancing their carrier/research work.

 Elucidation of MAPK pathways using in-silico tools.

 Checkpoint kinases and anti-cancer drug design.

Infrastructure facilities in the Bioinformatics Centre A. Computer & Communication facility:

This year one-high end graphics workstation with 24GB RAM has been added. In addition, we have very good Linux based IBM servers, purchased using DBT grant, and are used as the Internet and mail servers. Total we have six workstations for Molecular dynamics and NGS data analysis.

B. Scientific Software packages: Sybyl from Coordinator grant.

C. Databases & other information resources: Database on oral cancer genes and Histone database (See 11 below)

Details about Staff members working in the centre

All staff on DBT funding was absorbed by the institute way back in 1994. The centre has one full time Scientist D, Mr. Nikhil

Gadewal, with a post graduate degree in Biotechnology and a diploma in Bioinformatics who provides full support to users. Centre is also supported by staff from IT department of Institute and biostatistics personnel who are permanent staff of the Institute as and when required. However A support staff is needed to assist the permanent staff for bioinformatics based calculation, analyzing the data from recently started activities like proteomics, microarray, and next-generation sequence data analysis.

2. Types of services provided:

 Training from basics tools to modern approaches in bioinformatics to scientific staff/doctoral students of Institute and also neighboring institutes;

 Special emphasis is to train scientific staff, and post graduate students of basic sciences from academic insti- tutes in the state.

 Institute organizes two days open day, on this day we call most of the colleges of Mumbai and make them aware

of the latest technologies and research on Cancer.

Educational activities : Nil

Initiative to validate the outcome of bioinformatics resources:

 Each year there are about ~ 50 short- term trainees from different parts of the country who undertake their

 Good numbers of students/academic staff members from Mumbai and nearby institutes also regularly access the facility/take suggestions relevant to their work from BTIS staff.

Collaborative works/ initiatives: Nil

Databases/ Software packages developed:

The Oral cancer data-base of genes involved in oral cancer. The new markers (genes) were also identified by comparing the gene lists from published articles

 A new database was developed here and uploaded on our website. (URL-http://www.actrec.gov.in/OCDB/

index.htm).

 A new Histone database was uploaded on our website (http://www.actrec.gov.in/histome/index.php)

Papers/ published or presented in the conferences

 Pruthvi Raj Bejugam, Raja R Kuppili, Nitu Singh, Nikhil Gadewal, Lalith K. Chaganti, G. Madhavi Sastry, Kakoli Bose, Allosteric regulation of serine protease HtrA2 through a novel non canonical substrate binding pocket. PloS One. 2013 (Accepted)

 Selvaa KC, Gadewal NS, Mohammed SM. Identification of leads from marine seaweeds against human â-tubulin.

Letters in Drug Discovery, 2013, 10:67-74.

 Gadewal NS and Varma AK. Targeting Pim1 kinase for potential drug-development, Int J Comput Biol Drug Des.,

2012; 5(2):137-151.

 Badjugar DC, Sawant U, Mahadik H, Gadewal NS, Varma AK. Pathogenicity of mutations discovered in BRCA1

BRCT domains is characterized by destabilizing the hydrophobic interactions. J Cancer Sci Ther, 2012, 4(11): 386-393.

 Satyajeet P. Khare, Farhat Habib, Rahul Sharma, Nikhil Gadewal, Sanjay Gupta, and Sanjeev Galande, HIstome—

a relational knowledgebase of human histone proteins and histone modifying enzymes, Nucleic Acids Research, D337–D342, (40) 2012

 Nikhil S Gadewal & Narendra N Joshi, In silico analysis of peptide binding features of HLA-B*4006, Indian

Journal of Experimental Biology, Vol.50, January 2012,

Initiation of R&D activities in Bioinformatics

 Bioinformatics based approaches for retrieval of scientific information and further validation.

 Protein-protein interactions, protein-drug interactions, molecular modeling and structure based receptor design are an integrated approach of this centre.

 Genomics and Proteomics data analysis for oral cancer, cervical cancer, brain cancer and hematological malig- nancies using bioinformatics.

 Recently in 2011, Expertise in Next- Gen-Sequencing has been introduced.

speaker for first day was Dr. Petety Balaji from IIT Bombay, Mumbai who presented a case study for annotations of hypothetical proteins. Next day key note speaker was Dr. V. N. Balaji, Jubilant Biosys Ltd., Banglore entitled ‘Development of docking screening protocol for enzyme inhibitor hit identification and lead optimization: A case study for HIV Protease Inhibitors’. Dr. Shailza Singh from NCCS covered detailed talk on homology modeling. The other speakers were Amit Dutt, Prasanna Venkatraman, K, Bose, R Govekar from ACTREC. The morning session was for lectures and afternoon was hands –on- workshop. Hands on session covered data bases retrieval, protein structure visualization, prediction of secondary and tertiary structures, its validation, molecular modeling and dynamics.

 A special program for the Bioinformatics faculty/coordinator from North-East Region of the country was orga-

nized by the centre. Each faculty got hands- on -training on gene cloning, protein purifications and crystalliza tion. The training details will be provided separately to DBT.

~7 students were provided six months training on Database development, protein modeling and structure

activity relationship, microarray analysis, next- gen data analysis.

Impact shown by the Centre

 Papers published from the center-90, Book chapter-2 ;

 Invited lectures by the scientists of BTIS-ACTREC in neighboring Universities/colleges and other part of

country .

 There is a growing demand from many city colleges/institutes to hold the bioinformatics workshop twice in a

year for three days.

 Increasing demand from students from various part of country to undertake projects at the centre

Proposed activities for 2013-14:

 Organizing

 Workshop on Cancer Informatics workshop using NGS data analysis on 28-30 Jan 2013

 Workshop on Basics of Bioinformatics on February 21st _-22nd_{, 2013 and January 30}th _-31st_{, 2014.}

 Infrastructure and expertise development in molecular-dynamics, Microarray data analysis, Next- Gen Sequenc-

ing.

 Structural dynamics of nucleosome core particle containing homomorphous histone variants:

 National Cancer Data Base for Translational Research

 Proteomics of metastasis

Contact details:

Name of the Coordinator Dr. Ashok K Varma

Postal Address Bioinformatics Centre, Advanced Centre for Treatment, Research & Education in

Cancer (ACTREC), Kharghar, Navi Mumbai - 410 210.

Phone Number 022-2740 5112

Fax No. 022-2740 5085

Email [email protected]; [email protected]

Website www.actrec.gov.in