Recepción Final

Coordinator: Dr. S.M.H. Qadri

Summary of the progress made by the center from its inception

The Bioinformatics Centre at CSRTI, Mysore was established in November, 1999 under the BTIS programme of the DBT, Govt. of India as a Sub-DIC. The website of the center is hosted from the centre’s server with the URL www.btismysore.in. The main focus of the centre is to support biotechnology research pertaining to Sericulture. So far six databases and 2 softwares related to the host plant mulberry and silkworm have been developed, updated and maintained. Infrastructure facilities and support through bioinformatics tools and techniques were provided for the scientists of the Institute for their projects and experiments.

Major research activities in biotechnology and its related fields in your institution

Presently, 4 research projects funded by DBT/ DST and 22 projects funded by Central Silk Board are being carried out. Important areas of research like Development of mulberry transgenics over expressing transcription factors associated with drought and epicuticular wax biosynthesis, DNA marker aided analysis of mulberry gene bank towards a core assembly for sustainable conservation, breeding for NPV resistance using BmNOX marker assisted selection, DNA marker assisted breeding for thermotolerance, use of silk fibroin solutions for producing silk films, application of nano-particles for control- ling silkworm diseases etc. are covered in the afore said projects.

Area of Specialization of the center

The main thrust area of this center is Seri-biotechnology and Seri-bioinformatics

Major activities of the center during the year 2012-13 Databases developed and maintained:

1. SILKPROT : An Annotated Protein database for Silkworm and Mulberry : SilkProt is a comprehensive, fully

annotated, organism specific database for silkworm proteins. SilkProt was developed with MySQL as back-end database and PHP with HTML as front-end. The database contains data about ~1000 silkworm proteins se- quences. It has user-friendly interface for accessing the data with Boolean AND based filtering of the results and with easy page navigation. The selected sequences can be viewed as FASTA format. The database has cross reference to other databases like SwissProt, Pubmed, PDB and ModBase.

2. SilkTF: Silkworm specific transcription factor database. Developed using MySQL and PHP. The database

contains 587 protein sequences of mulberry silkworm having the transcription factors.

3. Mulberry Genome Database : Extensive Molecular marker data on DNA fingerprints, binary scores, similarity,

and dissimilarity index matrices, phylogenetic relationship in terms of dendrogram and marker segregation pattern has been compiled and stored using relational database with Visual Basic Platform. The database is also made available in the form of CD and is also being updated regularly.

4. The Silk e-Lab : The silk e-lab which contains a compendium of sequence information of the silkworm genome,

Databases under development:

i. BioinfoLib

Under this Bioinformatics Library information system, one can access specialized bioinformatics centers as well as books, scientific journals, manuals, newsletters and the information on latest research & development in those institutes on bioinformatics and allied areas. This library will be accessible over Internet through the URL of the centre that can be used by all the scientists/research students and the teachers of the research institutes and universities.

ii. Database on Mulberry Pests and Diseases

It provides the information about the various pests and diseases which affects the mulberry plant such time of occurrence, symptoms etc.

iii. Database on Silkworm Pests and Diseases

It provides the information about the various pests and diseases, which affect the silkworm.

Softwares

1. Sample Web Application for Analysis of Molecular ID.

2. Construction of growth indices in popular breeds/hybrids of silkworm Bombyx mori L. in relation to nutritional conditions

Infrastructure facilities at the institute and Bioinformatics Centre

CSRTI, Mysore has well equipped research laboratories with a wide range of equipments like Electron Microscope (with SEM facilities), Spectrophotometers, High speed Ultracentrifuges, HPLC, PCR machines, Gel Doc System etc. All the sections and laboratories of the Institute are well connected through LAN with 2 Mbps Internet connectivity. The Institute has a library equipped with all the modern facilities, subscribing for 92 national and international journals of repute and having a collection of 9380 books and 200 technical reports, besides 6760 bound back volumes of scientific journals. The Bioinformatics center has 4 Pentium IV, 2 Pentium III desktop computers, 1 Lap top computer, 1 HP Compaq ML 150 Server, Canon laser colour printers, HP Office Jet 6500 printer, HP Officejet 2515, 1 Sony digital Video camera, and 5 KVA UPS. The internet access is through 2 Mbps leased line from BSNL. The scientific software packages available are, PHYLIP, SPSS, Cn3D, Clustal W, PDB – on five CDs, EMBOSS, Artimis – Genome analysis package, Pinnacle DV Studio.

Papers published or presented in the conferences with reference

1. Sumathy, R.; Gopalakrishnan, V.K. and Ashwath S.K (2012) The prediction of Protein-protein interaction in

Silkworm Bombyx mori. Karpagam University 4th _{Annual Research Congress, Coimbatore.Tamil Nadu, Novem-}

ber 29-30, pp.369.

2. Sumathy, R.; Ashwath, S.K.; Shariff, A.A and Qadri, S.M.H (2012) In silico analysis and modeling of G protein coupled receptors of silkworm, Bombyx mori. National Symposium on Bioinformatics : Challenges in the post- genomic era held at School of Biotechnology, University of Jammu, Jammu, Februvary 02, pp 57

3. Kantharaj, H.M.; Ashwath, S.K.; Avinash, C.; Shariff, A.A and Qadri, S.M.H (2012) Secondary structure analysis of GP64 protein of BmNPV. National Symposium on Bioinformatics : Challenges in the post-genomic era held at School of Biotechnology, University of Jammu, Jammu, February 02, pp 54.

4. Sumathy, R.; Avinash C.; Shariff, A.A.; Ashwath, S.K and Qadri, S.M.H (2012) Insilico Structural Analysis of

Transmembrane Proteins in Silkworm. International Interdisciplinary Science Conference (IISC- 2012) on Protein Folding and Diseases held at Jamia Milia Islamia University, NewDelhi, December 08-10, pp.23.

Papers published in the Journal

1. Sumathy, R.; Ashwath S.K.; Gopalakrishnan V.K 2012. Theoretical modeling and Docking studies of silkworm

serotonin receptor, J Proteomics Bioinform 5(9): 230-234.

2. Kantharaj H.M., Ashwath S.K.; Qadri S.M.H 2012 In silico Structural and Functional Analysis of the P74 Protein Related to the (PDV) Polyhedra Derived Virus Infection of BmNPV into the Silkworm. Adv. Bio Tech:11(9):29-32

3. M. Ismail Shareef; S. Leelavathi; Anis Ahmed Shariff. 2012. Inhibition of In Vitro TNF-a Production by Anisomeles

malabarica R.Br. Reinforces Its Anti-Rheumatic and Immunomodulatory Properties. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 1(6):1-5.

4. Kantharaj H. M.; Ashwath, S. K.; Qadri, S. M. H. (2012) Biological databases and Bioinformatics tools-Key

resources for advanced research in sericulture biotechnology: An overview. Indian J. Seric. (In Press).

Initiation of R&D activities in Bioinformatics:

The centre is involved in protein-protein prediction using computational methods, docking studies of G protein coupled receptor, developing algorithm, designing database structure and modifying the same for the development of databases on silkworm proteins and ESTs.

Details of Training/Workshop organized

32 scientists from CSRTI, Mysore & its nested units have attended the Workshop on Bioinformatics and its Applications conducted on 29-30 November 2012. So far 665 persons have been trained in Bioinformatics.

Students Visit to the centre

Students of M.Sc., Biotechnology of local colleges visited this center and lecture sessions were organized to appraise the students in the area of Bioinformatics and its applications. The databases, softwares, tools and techniques developed by the centre were demonstrated.

Impact shown by your centre on the growth of biotechnology and allied areas.

During the year a total of 263 Research papers were published by the scientists of the Institute & Nested units (International - 47; National – 35; Presented in Conferences – 128; Popular articles – 52; Books and Booklets - 01). The institute is publishing the Indian Journal of Sericulture ( Biannual), Seridoc (Biannual), Reshme Vahini (Kannada, Bimonthly), Reshme Kiran (Hindi – Half Yearly) and Pattu Vignanam (Telugu, Bimonthly). CSRTI, Mysore is has made a mark as a leading R & D institute on tropical sericulture in the country and is well recognized as centre for higher learning and advanced training on international front. As a major component of the institute mandate, training was provided to a total of 2819 persons under different programmes. Major Sericulture states were covered to impart training in different disciplines of sericulture. During the year, One patent have been filed for Poshan’ – a multi-nutrient formulation for mulberry Further technologies commer- cialized are Navinya – A bio formulation for control of root rot disease of mulberry and Azotobacter biofertilizer for mulberry plants.

Services provided

The centre is equipped with 2 Mbps BSNL MLLN Internet connectivity which provides internet facility to all the research laboratories through LAN. The centre extends the infrastructure facilities and software support to the scientists working in the field of molecular biology & seri-bioinformatics in CSRTI and its allied institutes. Guidance is offered to the students of various universities in India for their dissertation or project work in the field of Seribioinformatics.

Plan of work for the year 2012-13

ii. SilkGpcr

It provides the information about the G protein coupled receptor protein of Silkworm, Bombyx mori and classified as Rhodopsin like, Secretin like receptor, Metabotropic glutamate receptors etc.

c) Conducting of Workshop on Bioinformatics and its Application

It is proposed to hold the two workshops on Bioinformatics and its Applications to be funded by DBT.

d) Improvement and maintenance of Website of the centre

The website of the center www.btismysore.in will be updated periodically and maintained.

e) Academics:

Each year this centre is receiving a number of applications for project/dissertation works from students of M.Sc./B.Tech (biotechnology/bioinformatics) from universities/institutions all over India. It is proposed to take up two to three projects/ dissertation works especially in the area of seribioinformatics.

Contact details:

Name of the Coordinator Dr. S.M.H. Qadri

Postal Address Director and Coordinator, Central Sericultural Research & Training Institute,

Manandavadi Road, Srirampura, Mysore 570008, Karnataka.

Phone Number (0821) 2362757, 2362406, 2363440

Fax No. (0821) 2362845, 2362420

Email [email protected], [email protected]; [email protected]

Website www.btismysore.in, www.csrtimys.res.in