Research Facilities

InstrumentationAnimal House FacilityBioinformatics Facility
Instrumentation

Several sophisticated equipments including minor equipments needed for day-to-day research work. Institute is also planning to procure many other major and minor equipments in the current year. List of some of the important equipments is given below.

  1. ATOMIC ABSORPTION SPECTROPHOTOMETER (AAS)
  2. AUTOMATED DNA SEQUENCER, EIGHT CAPILLARY
  3. BINOCULAR/TRINOCULAR INVERTED MICROSCOPES WITH DIGITAL CAMERA
  4. CHEF MAPPER-XA CHILLER SYSTEM (PFGE)
  5. 2-D ELECTROPHORESIS SYSTEM
  6. ELISA READER AND WASHER
  7. FAST PROTEIN LIQUID CHROMATOGRAPHY (FPLC)
  8. FLUORESCENCE ACTIVATED CELL SORTER (FACS)
  9. FRENCH PRESSURE CELL
  10. -20OC, -80OC FREEZERS, AND WALK-IN COLD ROOM
  11. GAS CHROMATOGRAPHY (GC)
  12. GEL DOCUMENTATION SYSTEM
  13. GENE PULSER X CELL
  14. HIGH PERFORMANCE LIQUID CHROMATOGRAPHY (HPLC)
  15. HYBRIDIZATION OVEN
  16. LASER SCANNING CONFOCAL MICROSCOPE (LSCM)
  17. LIQUID NITROGEN PLANT
  18. LIQUID SCINTILLATION COUNTER
  19. LYOPHOLIZER
  20. MILLI-Q-WATER PURIFICATION SYSTEM
  21. PHOSPHOR/ FLUORO-IMAGING SYSTEM
  22. PLANT EFFICIENCY ANALYZER
  23. PORTABLE PHOTOSYNTHESIS SYSTEM
  24. REAL-TIME DNA ENGINE/ THERMAL CYCLER
  25. SONICATOR
  26. STOPPED FLOW SPECTROPHOTOMETER
  27. ULTRA CENTRIFUGES WITH ROTORS
  28. VACUUM CONCENTRATOR
Animal House Facility

Animal facility provides animal care, breeding and maintenance of experimental animals e.g. Rats, Mice, hamster for ongoing research projects of the institute. The facility works under the guidance of Institutional Animal Ethics Committee to ensure excellent animal care, humane handling & treatment and in complete compliance with the CPCSEA guidelines.

The facility has been registered (No. 76/GO/ReBi/S/1999/CPCSEA) for breeding of and experiments on animals under the Committee for the purpose of Control and Supervision of Experiments on Animals (CPCSEA), Ministry of Environment & Forests & Climate Change (Animal Welfare Division), Government of India.

The Experimental Animal Facility is located in an exclusive and specially designed building with three floors. The first and second floor is occupied with the rooms for mice, experimental rooms and health monitoring lab, which are maintained under dark & light cycles and controlled conditions for temperature, humidity, air pressure as per the regulatory requirements with the help of HVAC system. The ground floor houses the rat, hamster and service areas (washing, autoclaving and animal feed, bedding etc.)

Animal use is regulated by the IAEC, as per Government of India guidelines where the committee examines the Form B, submitted by the faculty viz. protocol, number of animal species required, etc. before experiments begins. Usually user need to inform consultant veterinarian/ scientist in-charge about animal use plans, such as animal order and breeding experiments well in advance. Breeding is normally handled by Animal house facility to supply animals to the research group. Only authorized personnel were allowed to access animal facility to minimize risk of microbial contamination to housed animals. The detail record keeping of breeding, maintenance, experimentation and health is mandatory and is kept in animal facility.

The Animal Facility regularly organizes workshops to keep abreast of the latest developments, evolve regulations and disseminate the knowledge and skills to the laboratory animal professionals within the country.

Institutional Animal Ethics Committee (IAEC)

Dr. Ajay Parida, Chairman,

Dr. Saurabh Chawla, CPCSEA Main Nominee

Mr.Subhendu Sekhar Mishra, CPCSEA Link Nominee

Mr. N.R.Mansingh, Socially Aware Nominee

Dr.N.K.Parida,Scientist from Outside the Institute

Dr. Rupesh Dash, Scientist, ILS, Bhubaneswar

Dr.Shantibhusan Senapati, Scientist, ILS, Bhubaneswar

Dr.Arun Nagaraj, Scientist, ILS, Bhubaneswar

Dr. Sarita Jena, Scientist, ILS, Member Secy. IAEC, ILS

Reconstitution of IAEC,ILS is done once in every 5 year or as & when required.

Currently, the following animal strains are maintained in the Facility

A. Mice

BALB/c, C57BL/6, C3H/OuJ, C3H/HeJ, CBA/N, CBA/CaJ, IL-4 KO, IL-10 Ko,  FVB , FVB AT-ATX KO,B6-GFP Tg,DBA/1,B6SJL,B6 MARCO-/-,B6 SRA-/-,MARCO.SRA-/-,Nude

B. Rat

Copenhagen

C. Hamster

Syrian Golden Hamster

Scientist In-charge: Dr. Sarita Jena

 

Bioinformatics Facility

Bioinformatics Centre at ILS was started in May 2002, as a part of National Bioinformatics network under the programme, Biotechnology Information System (BTIS) established by Department of Biotechnology, Government of India. This facility is providing bioinformatics support pertaining to the different research activity going on at ILS particularly functional genomics and proteomics. Institute also planning for the structure based research towards infectious disease biology. Apart from this, the total net working, web site management, mail server etc are fully depends on this facility.

Main Thrust Area

Functional Genomics & Proteomics
Sequence Analysis, Molecular Modeling and Simulation
Database and Software development in biotechnology

Softwares The centre has a good collection of commercial and public domain softwares covering a wide range of applications like sequence and structure analysis, molecular modeling and simulations, structure prediction and drug design. The software’s available are:

Accelrys DS Modeling

Accelrys DS Gene

BioMed Catchy

SPSS

STATISTICA

GOLD for Docking Studies

Redhat Enterprise 5

Windows 2008 Server Enterprise Edition

Other programming and application softwares

Training and Workshop: The DISC is conducting workshop & training programmes every

year as an integral part of the centre

Team Members

Dr. Subrat K. Das, Scientist – D, Coordinator, DISC

Mr. Satya Sidhartha  Mohanty, Lab. Technician

Mr. Kinshuk Chandra Nayak, Lab. Technician

Publications/Posters from DISC

  1. Gaurav Sablok*, Ting-Wen Chen, Chi-Ching Lee, Chi Yang, Ruei-Chi Gan, Claudio Varotto ,Kinshuk C. Nayak, Po-Jung Huang, Jill Wgerzyn, Petrus Tang (2016) ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications. DNA Research (doi: 10.1093/dnares/dsw044 )
  2. Kinshuk Chandra Nayak *(2013). Comparative genome sequence analysis of Sulfolobus acidocaldarius and 9 other isolates of its genus for factors influencing codon and amino acid usage.Gene (Elsevier), 513, (1) 163-173.
  3. Gaurav Sablok , XianMing Wu, Jimmy Kuo, Kinshuk Chandra Nayak, Vesselin Baev, Claudio Varotto, Fenfeng Zhou (2013). Combinational effect of mutational bias and translational selection for translation efficiency in tomato (Solanum lycopersicum) cv. Micro-Tom. Genomics, (Elsevier) (http://dx.doi.org/10.1016/j.bbr.2011.03.031)
  4. Gaurav Sablok*, K.C. Nayak, E. Potenza, G. Emiliani, N. La Porta (2013). Multivariate analysis revealed translational selection and mutational bias in Heterobasidion irregularedestructive fungal pathogen of conifers in the Boreal hemisphere. Genomics and Plant-Pathogen Interactions, XIII Conference Root and ButRot of Forest Trees IUFRO Working Party 7.02.01 ISBN 978-88-6655-352-6 (print), ISBN 978-88-6655-353-3 (online) © 2013 Firenze University Press
  5. Kinshuk Chandra Nayak *(2012). Comparative study on factors influencing the codon and amino acid usage in Lactobacillus sakei 23K and 13 other lactobacilli. Molecular Biology Reports,Mol. Biol. Rep. (Springer), 39, (1) 535-545.
  6. Bijay Misra, Chittaranjan Panda, Haribhakti Seba Das, Kinshuk Chandra Nayak, Shivaram Prasad Singh. Study (2011) Awareness about Hepatitis B Viran Infection in Coastal Eastern India . Hepatitis B Annual .6:19-28..(DOI:10.4103/0972- 9747.76902)
  7. Gaurav Sablok*, Kinshuk Chandra Nayak, Franck Vazquez, Tatiana V.Tatarinova. Synonymous codon usage, GC3 and Evolutionary patterns across plastomes of three pooid model species – Emerging grass genome models for monocots (2011).Molecular Biotechnology.DOI 10.1007/s12033-011-9383-9
  8. MHU Turabe Fazil, Sunil Kumar, Rohit Farmer, HP Pandey and DV Singh (2010). Binding efficiencies of carbohydrate ligands with different genotypes of cholera toxin B: Molecular Modeling, dynamics and Docking Simulation studies. Journal of Molecular Modeling (In Press, Springer publication).
  9. Kinshuk C. Nayak*, Mutational bias and Gene expression level shape codon usage in Thermobifidafusca YX. In Silico Biology(2010), 9 : 1-17.
  10. Biswaranjan Paital, Sunil Kumar*, Rohit Farmer, Niraj Kanti Tripathy, Gagan Bihari Nityananda Chainy (2010) In silico prediction and characterization of 3D structure and binding properties of catalase from the commercially important crab, Scylla serrata. Interdisciplinary Sciences: Computational Life Sciences (Accepted, Springer publication).*corresponding author.
  11. Chinmayee Mohapatra, Hirak Kumar Barman, Rudra Prasanna Panda, Sunil Kumar, Varsha Das, Ramya Mohanta, Shibani Mohapatra, Pallipuram Jayasankar (2010) Cloning of cDNA and prediction of peptide structure of plzf expressed in the spermatogonial cells of Labeo rohita, Mar. Genomics, doi: 10.1016/j.margen.2010.09.002. (Elsevier publication).
  12. Babu A. Manjasetty, Sunil Kumar, Andrew P. Turnbull, Niraj Kanti Tripathy (2009).Homology Modeling and Analysis of Human Proteins related to Disease:Structural Investigations into Shwachman-Bodian-Diamond Syndrome (SBDS) using a Bioinformatics Approach,.InterJRI Science and Technology, Vol. 1, Issue 2,97-104.
  13. MHU Turabe Fazil*, Sunil Kumar*, N Subbarao, H P Pandey and Durg V. Singh (2009) Homology Modeling of a Sensor Histidine Kinase from Aeromonas hydrophila. Journal of Molecular Modeling DOI 10.1007/s00894-009-0602-2. * Equal contribution.
  14. Sunil Kumar, B B Sahu, N K Tripathy, B P Shaw (2009) In Silico Identification of Putative Proton Binding Sites of a Plasma Membrane H+-ATPase Isoform of Arabidopsis Thaliana, AHA1. J Proteomics Bioinform 2: 349-359. doi:10.4172/jpb.1000095
  15. Sunil Kumar, N. Subbarao , Sushmita Sahu, Mamata Ray, Priyanka Das, Prosenjit Mondal, Surendra Chandra Sabat (2009). In silico Modeling of Rice CatalaseA and Docking studies with Sucrose. Poster presented at International conference on Bioinformatics (InCoB), Singapore during 7-11 Sept., 2009.
  16. Fazil MHU Turabe, Kumar Sunil , Singh DV (2009). In Silico Structural Analysis Of Vibrio Cholerae Luxp: Modelling, Docking And Molecular Dynamics Simulations Studies. Indo-US Conference on Infectious Disease, TIFR Mumbai, 5-8 January, 2010.
  17. Sunil Kumar, Priya R Debata, Prakash C Supakar (2008) Prediction of 3-dimensional structure of cathepsin L protein of Rattus norvegicus. J Proteomics Bioinform 1: 307-314.
  18. Sunil kumar, Binod Bihari Sahu and B P Shaw (2007). Comparative modeling of protein of Plasma membrane H+ ATPase of Sesuvium portulacastrum. Poster presented at International Conference on New Horizons in Biotechnology (NHBT -2007), NIIST, Trivendrum, India from November 26-29, 2007, Poster No. FAB-059.
  19. Sunil kumar (2006). A computational Identification of novel Cathepsin L like proteins in Drosophila melanogaster genome. Poster presented at 6th International conference in Bioinformatics (InCoB 2006) organized by DBT, JNU and IIT Delhi at Hotel Ashoka New Delhi from December 18-20, 2006, Poster No. 64.
  20. Vikash kumar and Sunil kumar (2004), A Rapid peptide based Alignment -free method to construct Genome trees Independent of sequence annotation. Poster presented at The 15th International Conference on Genome Informatics. “Posters and Software Demonstrations” (GIW 2004) organized by Japanese Society for Bioinformatics, Yokohama, Japan December 13-15, Pos. No. 152.
  21. Sunil kumar, Swati Nayak, Snehasish Parhi and P.C.Supakar (2003), Comparative Protein Structure Modeling. Bioinformatics India. 1(3). 11-16.
  22. Pagadala Nataraj Sekhar, Polavarapu B. Kavi Kishor, Lakkireddy Ananda Reddy, Prosenjit Mondal, Ardhendu K. Dash, Manoranjan Kar, Satya S. Mohanty and Surendra C. Sabat In silico modeling and hydrogen peroxide binding study of rice catalase.(2006) In Silico Biology ; 6: 0041.
  23. Shachindra K. Pandey, Kunwar Digvijay Narayan, Saumya Bandyopadhyay, Kinshuk C. Nayak and Subrata K. Das*(2009). Thiosulfate oxidation by Comamonas sp. S23 isolated from a sulfur spring. Curr Microbiol. 58(5):516-21.
  24. Sujogya K. Panda, V. Jyoti, Bhaskar Bhadra, Kinshuk C. Nayak, Sisinthy Shivaji, Fred A. Rainey and Subrata K. Das*(2009). Thiomonas bhubaneswarensis sp. nov., a novel obligately mixotrophic, moderately thermophilic, thiosulfate oxidizing bacterium. International Journal of Systematic and Evolutionary Microiology. 59: 2171-2175

Book Chapter

  1. Sunil Kumar. Solvent Accessibility of proteins. In Bioinformatics and Statistics in Fishries Research, 2006, Vol-III P 42-49 Published by Central Institute of Fishries and Aquaculture, Kausalyanagar, Bhubaneswar.
  2. Sunil Kumar. Basics in Bioinformatics. In Bioinformatics and Statistics in Fishries Research, 2005, Vol-II P 10-21 Published by Central Institute of Fishries and Aquaculture, Kausalyanagar, Bhubaneswar.

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