Technical Expertise

Technical expertise which would be imparted through this programme
(Hands on experience will be provided on the following)

LAB 1 : Genomics, proteomics, and bioinformatics

  1. DNA extraction from prokaryotes, eukaryotes and marine environmental samples
  2. DNA quantitation by UV Visible spectrophotometry
  3. Purification of DNA, agarose gel electrophoresis, Pulsed Field Gel Electrophoresis
  4. DNA restriction analysis
  5. Primer and Probe design
  6. PCR amplification of 16S, 18S rDNA and internal transcribed spacers, purification of the PCR products
  7. Ligation .
  8. Cloning of genes and expression studies
  9. Bacterial transformation, Screening of transformants by colony PCR
  10. Southern blotting
  11. Plasmid extraction, restriction digestion of the plasmid DNA
  12. Bacterial 16SrDNA and eukaryotic 18S rDNA and internal transcribed spacers sequencing
  13. DNA fingerprinting techniques - RFLP, RAPD, AFLP, microsatellite, Barcoding
  14. Denaturing Gradient Gel Electrophoresis
  15. Fluorescent In-Situ Hybridization
  16. RNA Isolation, cDNA synthesis, cDNA library construction and library screening and expression, Northern blotting
  17. Extraction and Purification of proteins
  18. Native & SDS PAGE, and Gradient Gel Electrophoresis,
  19. Western blotting, 2-Dimensional Gel electrophoresis
  20. Introduction to biological databases: Data mining- NCBI, EBI, DDBJ, Swiss-prot, Protein Data Bank (PDB), Protein Information Resource (PIR). Secondary databases- KEGG, Prosite, SCOP etc, and Data retrieval tools: Entrez, SRS etc, Literature search: Pubmed, Medline and OMIM etc.
  21. Methods in sequence analysis: pair-wise alignment -BLAST, FASTA, PSI-BLAST, flavors of BLAST (blastn, blastp,blastx, tblastx). Multiple sequence alignment-CLSUTALW, phylogenetic analysis –PHYLIP etc. Other online tools available for sequence analysis.
  22. Structure analysis and drug design: protein structure prediction tools-MODELLER, SWISS MODEL, and using other commercial softwares, structure visualization tools-Swiss PdbViewer, RASMOL, Cn3D etc. docking tools- ArgusLab, AutoDock and using other commercial packages. Online tools for ADME-Tox prediction
  23. Demonstrations
    • DNA microarray technology
    • DNA sequencing methods
    • Lipid profiling and species identification
    • Radioisotope techniques
    • NMR, MS-MS, X-ray crystallography

LAB 2 : Microbiology (Bacteriology, Virology and Mycology)

  1. Isolation, identification and characterization (phenotypic and genotypic) of marine bacteria.
  2. Hydrolytic enzyme production by the marine bacterial isolates.
  3. 16S rRNA gene sequencing and phylogenetic analysis.
  4. Marine bacterial enumeration by epifluorescency.
  5. Isolation of marine fungi and characterization.
  6. Isolation of bacteriophages and plaque assay.
  7. Microbial community structure analysis using molecular tools.

LAB 3 : Biotechnological intervention in Aquaculture

  1. Disease Diagnosis and pathogen detection
    1. Fish sampling for laboratory observation
    2. Anatomy of fish and shellfish: Dissections to study the internal organs of fishes and shellfishes.
    3. Clinical study – skin, internal organs and gill biopsy,
    4. Histological methods
    5. Microbiological methods, Isolation of aetiological agents - identification, characterization,
    6. Immunodiagnostic techniques – Agglutination, Haemagglutination, Precipitation, Latex agglutination, Immuno fluorescence, Immunofluorescence histochemistry, Radial immuno diffusion,Immuno electrophoresis, Countercurrent electrophoresis and ELISA,
    7. DNA based diagnostic techniques: Nucleic acid probes, Dot blot hybridization, In situ hybridization, Polymerase chain reaction (PCR), RT-PCR, Nested PCR, Multiplex PCR, Broad range PCR, Real time PCR, Ribotyping, Loop Mediated isothermal Amplification (LAMP),
    8. Use of cell lines in disease diagnosis, Bioassay,
    9. Electron microscopy in disease diagnosis,
  2. Disease Management protocol
    1. Prophylaxis- Environmental management,
    2. Bioremediation, application of probiotics, vaccines;
    3. Therapy – Application of antibiotics in non-edible fish
    4. Water quality analysis and management
  3. Fish and Shell fish immunology
    1. Determination of total and differential haemocyte/blood count
    2. Prophenol oxidase activity
    3. NBT reduction assay
    4. Alkaline phosphatase and Acid phosphatase
    5. Lysozyme activity
    6. Superoxide dismutase, Catalase , Glutathione peroxidase assa
    7. Haemeagglutination
    8. Detection and quantification of antibodies in serum
    9. Isolation of antimicrobial peptides from shrimp haemocytes
  4. Cell line development and maintenance : Basic techniques in animal Cell culture: Preparation of media, Developing primary cell culture, Cell line maintenance – anchor dependent and suspension cell cultures, Subculturing, enumeration of viable cells by dye up take and exclusion, Split ratio and growth cycle,  MTT assay, BrdU assay, Cytoskeleton staining, Cryo preservation,
  5. Application of cell lines : Virus isolation – plaque assay, Virus titration - TCID 50, Detection of viruses through immunohistochemistry/immunoflourescent staining and  toxicological studies – LD 50.
  6. Application of Molecular markers and Marker Assisted Selection (MAS) for broodstock developments: Molecular markers – RFLP, RAPD, AFLP, Microsatellite markers, SNP, Allozymes and isozymes, Mitochondrial DNA markers, an exercise on application of DNA markers for MAS and breeding.

LAB 4 :  Bioprospecting and bioprocess technology

  1. Collection and field identification of marine organisms
  2. Extraction of Bioactive compounds with different solvent systems
  3. Screening of extracts for bioactivity (anti-bacterial, anti viral, anti fungal and cytotoxic)
  4. Partitioning and enriching the bioactive compound by solid phase extraction (SPE) system
  5. Isolation and partial characterization of lead compound by thin layer chromatography
  6. Purification by column chromatography and HPLC
  7. Possible structure elucidation by NMR, MS-MS
  8. High throughput assays using cell culture: Cell viability assay, MTT assay, LDH assay
  9. Detection of apoptosis using DNA laddering assay and comet assay
  10. Screening of marine organisms for antagonistic properties using disc diffusion and microplate Quantitative assay
  11. Designing and optimization of culture media by Response Surface Methodology (RSM)
  12. Down stream processing for bioactive compounds and microbial cells
  13. Submerged fermentation and Solid state fermentation
  14. Determination of kinetics of fermentation