M.Sc. Biotechnology

II Year Course(Semester Pattern)

Eligibility for admission:

A first class B.Sc., degree in Biology ,Biochemistry, Botany, Chemistry, Mathematics, Microbiology, Physics,Zoology or agriculture or B.E., or M.B.B.S., or B.V.Sc., of a recognized Indian or Foreign University.

Processing of application:

Applicants will be selected on an all-India basis. Apart from the Bachelor degree marks, selected applicants should pass an entrance examination. Among the successful candidates one seat will be allotted for a qualified candidate sponsored by an industry. Total number of students per year is twenty.

COURSE STRUCTURE

Semester I

Semester

Course code

Course Title

I

SBT-0.1.3.1C

Biochemistry

I

SBT-0.1.3.2C

Microbiology

I

SBT-0.1.3.3C

Molecular Genetics

I

SBT-0.1.3.4C

Immunology

I

SBT-0.1.2.5C

Biophysics

I

SBT-0.1.2.1P

Lab in Analytical Biochemistry

I

SBT-0.1.2.2P

Lab in Molecular Genetics

Semester II

Semester

Course code

Course Title

II

SBT-0.2.3.1C

Enzymology and Enzyme Technology

II

SBT-0.2.3.2C

Molecular and Developmental Biology

II

SBT-0.2.3.3C

Plant Molecular Biology

II

SBT-0.2.3.4C

Biology of cloning vectors

II

SBT-0.2.3.5C

Bioinformatics, IPR & Biosafety

II

SBT-0.2.2.1P

Lab in Microbial Technology

II

SBT-0.2.2.2P

Lab in Immunology & animal cell culture

Semester III

Semester

Course Code

Course Title

III

SBT-0.3.3.1C

Recombinant DNA Technology

III

SBT-0.3.3.2C

Animal Biotechnology 

III

SBT-0.3.2.3C

Bioprocess Technology

III

SBT-0.3.2.1P

Lab in Recombinant DNA Technology

III

SBT-0.3.2.2P

Lab in Plant Biotechnology

Semester IV

Semester

Course Code

Course Title

IV

SBT-0.4.3.1C

Microbial Biotechnology
IV SBT-0.4.3.2C Immunotechnology

IV

SBT-0.4.6.1D

Dissertation (Project work)

SYLLABUS :

SEMESTER I

SBT-0.1.3.1C.   BIOCHEMISTRY

Principles of Bioenergetics.  Glycolysis and the catabolism of hexoses.  The citric acid cycle, Oxidation of fatty acids.  Oxidation of amino acids.  Oxidative phosphorylation, Photophosphorylation.  Carbohydrate biosynthesis.  Lipid biosynthesis.  Biosynthesis of amino acids, nucleotides and related molecules.  Integration and hormonal regulation of mammmalian metabolism.  Biological membranes and transport.  Prostaglandins, leukotrienes, thrombaxanes.  Interferons and interleukins.  Antibiotics. Alkaloids. Animal pigments. Cytoskeletal organisation.  Chemical synthesis of peptides and oligosaccharides.

Reference Books:

1.      Principles of Biochemistry by A.L.Lehninger, D.L.Nelson & M.M.Cox. (1993) Worth Publishers, New York.

2.      Biochemistry by L.Stryer (1994) Freeman & Co,  New York.

3.      Biochemistry by G. Zubay  (1988)  Macmillan Publishing Co, New York.

4.      The vital force:  A study of  Bioenergetics by  F.M.Harold  (1986)  Freeman & Co, New York.

A Biologist’s Physical Chemistry by J.G.Morris  (1968)  Edward Arnold Publishers, London.

SBT-0.1.3.2C. MICROBIOLOGY

 Ultra structure of bacteria, fungi, algae, protozoa and viruses. Classification of microbes. Molecular taxonomy. Current methods of microbial identification. Characteristic features of eubacteria, archae, fungi, algae, protozoa and viruses. Biology of Escherichia coli,  Bacillus subtilis, Rhizobium sp., Agrobacterium tumefaciens, Saccharomyces cerevisiae, and phage lambda. Dairy and food microbiology. Plant-microbe interactions. Human pathogens. Disinfectants, Antibiotics and mechanisms of antibiosis.  Environmental Microbiology.

Reference Books:

1.      Methods for general and Molecular Bacteriology by Gerhardt et al. (1994) ASM  Press.

2.      Microbiology by Pelczar, Chan and Kreig (1986) McGraw Hill.

3.      Microbiology by Presestt, Harley and Klein (1996)  William C.  Brown Press.

SBT-0.1.3.3C. MOLECULAR GENETICS

Gene as the unit of mutation and recombination. Identification of DNA as the genetic material. Mutations: molecular nature; mutagenesis by nitrous acid, hydroxylamine, alkalating agents, intercalators and UV; origin of spontaneous mutations and control. Parasexual process in bacteria; transformation, transduction and conjugal gene transfer – the phenomena, mechanisms and applications. Fine structure genetic analysis with examples. Recombination – control; models and mechanisms. Gene as the unit of expression. Colinearity of gene and polypeptide. Elucidation of nonsense, missence and frameshift mutations. Regulation of gene expression. The operon concept – positive and negative control, attenuation control, control sequences: promotor, operator, terminator and attenuator.

DNA damage and repair: DNA damage by UV, alkylating agents, cross linkers. Mechanisms of repair – photoreactivation, excision repair, recombinational repair. The SOS and adaptive responses and their regulation. Heat shock response. Extra-chromosomal heredity; Biology of plasmids – discovery, types and structure of F, RIF, col-factors and Ti. Replication and partitioning. Incompatibility and copy number control. Natural and artificial plasmid transfer and their applications. Transposable genetic elements: discovery, early experiments of McClintock in maize. Insertion sequence in prokaryotes. Complex transposons – Tn10, Tn5, Tn9 and Tn3 as examples. Mechanisms, control, consequences and applications of transposition by simple and complex elements.

Genetics of eukaryotes: Gene linkage and chromosome mapping, crossing over, three point cross, tetrad analysis. Complementation. Organisation of chromosomes, specialised chromosomes. Chromosome abnormalities, quantitative inheritance, population genetics. Developmental genetics using Drosophila as model system. Somatic cell genetics.

Reference Books:

1.      Microbial Genetics by S.R. Maloy, J.E. Cronan and D. Friefelder (1994) Jones and Bartlett Publishers.

2.      Molecular Genetics of Bacteria by J.W. Dale (1994) John Wiley & Sons.

3.      Basic Genetics by D.L. Hartl (1991) Jones & Bartlett Publishers.

SBT-0.1.3.4C.  IMMUNOLOGY

History and scope of Immunology. Types of immunity – innate, acquired, passive and active. Physiology of immue response – MI and CMI specificity and memory. Antigen-antibody reactions. Antigens – types – Hapten, immunoglobulins – structure, distribution and function. Molecular biology of Ig synthesis. Lymphoid tissues – Ontogeny and physiology of immune system – origin and development, differentiation of lymphocytes. Lymphocyte sub-populations of mouse and man. Structure and functions of classI and II molecules. Antigen distribution in population – HLA in human health and diseases. Transplantation immunity – Organ transplantation and HLA tissue typing. Effector mechanisms in immunity – macrophage activation. Cell-mediated cytotoxicity. Hypersensitivity reactions. Cellular interactions in immune response. Antigen recognition. T, B-cell receptors, MHC restriction. Lymphocyte activation, clonal proliferation, differentiation. Interleukins and their role. The complement systems – mode of activation, classical and alternate pathway, biological functions. Immunoregulation – helper and suppressor cells, specific factors, idiotype network. Immune response genes. Immunological tolerance – immunosuppression. Introduction to tumor immunology, autoimmune disorders and immunology of infectious diseases.

Reference Books:

1.      Immunology by I.M. Roitt, J.Brostoff and D.K. Male (1993) Gower Medical Publishing, London.

2.      Immunology by J. Kuby (1991) Freeman and Company.

SBT-0.1.2.5C.  BIOPHYSICS

Physics and Biology: Scope and methods of Biophysics. Levels of molecular organisation. Understanding structures of proteins at different levels – primary, secondary, tertiary and quaternary: conformational analysis and forces. Understanding structures of nucleic acids at different levels – primary, secondary, tertiary, quaternary; analysis of interactions; Protein – Nucleic acid interactions. Polysaccharides. Association of macromolecules. Lipids in Biological membranes. Protein in biological membranes. Molecular mechanics and dynamics.

Reference Books:

1.      Introduction to Protein structure by C. Branden, J. Tooze (1991) Garland Publishing Inc.

2.      Biochemistry by L. Stryer (1999) WH Freeman and Co.

3.      Biophyscial chemistry Part I & III by Cantor and Schimmel (1980) WH Freeman & Company.

4.      Nucleic acid structure by S.Neidle (ed) (1987) VCH Publishing, Weinheim.

5.      The structure and action of proteins by Dickerson and Geis (1969) Benjamin/ Cummings Publishing.

SBT-0.1.2.1P.  LAB IN ANALYTICAL BIOCHEMISTRY

Theory and applications of colorimeter, spectrophotometer, pH meter.  Preparation buffers. Methods of protein estimation (Lowry and Bradford). Thin layer chromatography. Screening and indentification of industrially important microorganisms. Production of an extracellular enzyme from bacteria/fungus and downstream processing a) Ultrafiltration, b) Ammonium sulphate precipitation, c) Dialysis, d)ion exchange chromatography, d) Gel permeation chromatography, etc. Polyacrylamide gel electrophoresis. Radioactive labelling and measurement of radioactivity. Demonstration of GLC and HPLC.

Reference Books:

1.      Principles of Instrumental analysis by D.S. Skoog (1985) H.L.Saunders.

2.      Laboratory Manual of Biochemistry by J. Jayaraman (1980) Wiely Eastern.

3.      Williamd, B.L. and Wilson, K,  Principles and techniques of practical biochemistry  (1995)  Edward Arnold.

SBT-0.1.2.2P.  LAB IN MOLECULAR GENETICS

Single colony isolation and checking for genetic markers: Measurement of growth rate; one step growth curve using aT even phage; induced mutagenesis and isolation of antibiotic resistant and auxotrophic mutants; Enrichment methods for auxotrophic and antibiotic resistant mutants; Genetic mapping by P1 transduction; Genetic mapping by conjugation; Isolation of specialised transducing phage; Transposan mutagenesis of chromosomal DNA; Transposan mutagenesis of plasmid DNA; Experiments with gene fusion.

Reference Books:

1.      A short course in Bacterial Genetics by J.H. Miller (1992) Cold Spring Harbor Laboratory.

2.      Methods for General and Molecular Bacteriology by Ed. RGF. Murray, WA. Wood and NB.Krieg (1994) American Society for Microbiology,  Washington DC.

 

SEMESTER II

SBT-0.2.3.1C.   ENZYMOLOGY AND ENZYME TECHNOLOGY

 Enzyme nomenclature and classification. General properties of enzymes like effect of pH, temperature, ions etc. Extraction, assay and purification of enzymes. Steady state kinetics. Michaelis-Menten, Lineweaver-Burke, Eadie-Hofstee and Hanes-Woolf equations and Km value. Enzyme inhibitors. Pre-steady state kinetics. Fast kinetics to elucidate the intermediates and rate limiting steps (Flow and Relaxation methods). Enzyme specificity. Evidences for enzyme substrate complex. Nucleophilic and electrophilic attack. Role of metal ions in enzyme catalysis. Mechanism of enzyme action eg. Lysozyme, chymotrypsin, DNA polymerase, RNase, etc. Zymogens and enzyme activation. Allosteric interactions and product inhibition: Complex kinetics and analysis. Membrane bound enzymes – extraction, assay, lipid-protein interaction and effect of fludity on enzyme activity. Coenzymes. Clinical and industrial applications of enzymes. Immobilisation of enzymes and their applications. Ribozymes and their applications. Enzyme engineering.

 Reference Books:

1.      Biological chemistry by H.R. Mahler and E. Cordes (1986)

2.      Enzymes by Dixon and Webb

3.      Gene VI by Benjamin Lewin (1997).

SBT-0.2.3.2C.  MOLECULAR AND DEVELOPMENTAL BIOLOGY

Cellular organelles – Structure and function. Organisation of cytoskeleton and nuclei. Chromatin structure. Molecular aspects of cell division and cell cycle. Cell fusion. Nuclear-cytoplasmic interactions. Structure of DNA and RNA melting and unwinding kinetics. DNA replication, kinetics, Repair and gene amplification. RNA transcription and processing. Protein synthesis and secretion, Transcriptional and Translational controls. Hormones and gene expression. Viruses and gene expression. Growth factors, Mitogens and oncogenes. Cellular regulation, development and differentiation.

Reference Books:

1.      The Molecular Biology of the Cell by Alberts et al. (1991)

2.      The Molecular Biology of the Gene by J. D. Watson et al. (1987) Benjamin Cummings.

3.      Gene V by B. Lewin (1994) Oxford University Press, Oxford.

4.      Molecular cell biology by Lodish et al. (1995) Scientific American press.

SBT-0.2.3.3C.    PLANT MOLECULAR BIOLOGY

Plant genome organization, structural features of a representative plant gene, gene families in plants. Organization of chloroplast genome, nucleus – encoded and chloroplast-encoded genes for chloroplast proteins, targetting of proteins to chloroplast,  Organization of mitochondrial genome, nuclear and mitochondria – encoded genes for mitochondrial proteins, RNA editing in plant mitochondria, mitochondrial genome and cytoplasmic male sterility.  Seed storate proteins.  Regulation of gene expression in plant development.  Plant hormones and phytochrome. 

Symbiotic nitrogen fixation in legumes by Rhizobia – biochemistry and molecular biology.  Agrobacterium and crown gall tumours.  Mechanism of T-DNA transfer to plants.  Ti  plasmid vectors for plant transformation.  Classification and molecular biology of plant viruses.  Molecular biology of plant stress response.

Genetic engineering in plants, selectable markers, reporter genes and promoters used in plant vectors.  Genetic engineering of plants for virus resistance, pest resistance, herbicide tolerance, cytoplasmic male-sterility, delay of fruit ripening, resistance to fungi and bacteria.  Production of antibodies, viral antigens and peptide hormones in plants.  Gene silencing in transgenic plants.   Management  aspects  of  plant genetic engineering. Molecular biology of plant pathogen interactions.

Reference Books:

1.      Plant Molecular Biology by Grierson and S.N. Covey (1988) Blackie.

2.      Plant Biochemistry and Molecular Biology by P.J.Lea and R.C.Leegood (1993) John Wiley & Sons.

3.      Plants, Genes and Agriculture by M.J. Chrispeels and D.F.Sadava (1994) Jones and Bartlett.

4.      Molecular Genetics of  Photosynthesis by B.Anderson, H.Salter and J.Barber (1996), IRL Press, Oxford.

5.      Plant Virology (3rd Edition) by R.E.E.Mathews (1991) Academic Press.

6.      Post translational control and gene expression in plants.  Plant Molecular Biology 32 (1-2) (1996).

7.      Trends in Plant Sciences-Current issues.

SBT-0.2.3.4C. BIOLOGY OF CLONING VECTORS

DNA Transactions: replication, recombination, repair and restriction. 

Plasmid biology: plasmids of Gram negative bacteria - ColE1, p15A, R1, IncPa, pSC101.  Plasmids of Gram positive bacteria - RCR plasmids, plasmids of Streptomyces.  Plasmid vectors of various types.  Biology of bacteriophages - Lambda, P1 and  Mu.  In vitro construction of Bacteriophage vectors.  Phages as in vivo vectors.  Cosmid vectors and their applications.  Biology of filamentous phages, applications of filamentous phage vectors and phagemids.  Streptomyces phage vectors.  Specialized vectors – expression vectors, promoter probe vectors, gene fusion vectors.  Biology of Yeast vectors and applications.

Reference Books:

1.      Vectors, Raymond L. Rodriguez and David T. Denhardt

            Butterworth.

2.      Lambda II

        Cold Spring Harbor

3.      Phage Mu

        Cold Spring Harbor

4.      The Bacterophages Vol II, R. Calender,

Plenum Press.

5.      Molecular Biotechnology, Bernard R. Glick and Jack J. Pasternack.

            II edition, ASM Press

 Journals:

 Molecular Microbiology.

Journal of Bacteriology

Microbiolgy and Molecular Biology Reviews.

Trends in Microbiology.

Journal of Molecular Biology.

Plasmid.

Microbiology.

Proceedings of National Academy of Science.

SBT-0.2.3.5C.   BIOINFORMATICS, IPR & BIOSAFETY

Bioinformatics:

Use of databases in biology sequence databases, structural databases,  Sequence Analysis – protein and nucleic acids, Structural comparisons, genome projects.

Information theory and biology:  Entropy, Shannon’s formula, divergences from equiprobability and independence, Markov chains, ergodic processes, redundancy,  application to DNA and protein sequences.

Intellectual Property Right:

WTO-GATT & TRIPS. Different types of intellectual property rights – Patents – Plant breeder’s rights.  Patent application – Rules governing patents.  Examples of patents in biotechnology.  Special application of patent laws in biotechnology.  Licensing  and cross licensing.   Flavr SavrTm  tomato as a model case.  

 Biosafety:

 General guidelines – Guidelines for rDNA research activity – Containment facilities and Biosafety practices – Guidelines for research in transgenic plants.

 Reference Books:

1.      Molecular databases for protein sequence and structure studies by Sillince,  JA and Sillince  M  (1991)  springer Verlag.

2.      Sequence Analysis primer by M. Gribskov, J. Devereux (1989) Stockton Press.

3.      Computational Methods in Mol.Biol./.Now Comprehensive Biochemistry Vol.32.  S.L.Seizberg,  DB Searls, S.Kasif    Elsevier  1998.

4.      Computer methods for macromolecular analysis.

Methods in Enzymology.  Vol.266 by R.F.Doolittle.  Academic Press 1996.

5.      Information theory and living systems by L.I. Garfield, (1992) Columbia University Press.

6.      Recombinant DNA safety guidelines, Department of Biotechnology, Ministry of  Science & Technology, Government of India

7.      Recombinant DNA safety guidelines & Regulation, Department of Biotechnology, Ministry of  Science & Technology, Government of India

8.      Revised guidelines for research in Transgenic plants, Department of Biotechnology, Ministry of  Science & Technology, Government of India

 SBT-0.2.2.1P.  LAB IN MICROBIAL TECHNOLOGY

Isolation of DNA from cloning vectors –  plasmids and phages.  Extraction of total DNA from plant and animal tissues.  Transformation of  bacteria (E.coli and B.subtilis) by competence and electroporation protocols.  Large-scale preparation of plasmid DNA.  Restriction  mapping.  PCR.   Immunoblot analysis.  Pulsed-field electrophoresis. Introduction to bioprocess technology parts and designs of  bioreactors;  production of biomass;  batch and continuous fed batch fermentation, scale up recovery of products.

Reference books:

 1.      Molecular cloning: A laboratory mannual vol.1-3 by Sambrook et al., (1989) Cold Spring Harbor           Laboratory.

Current Protocols in Molecular Biology Vol.1 & 2 by F.M.Asubel et al. (1987) John Wiley Publishers, New York.

SBT-0.2.2.2P.  LAB IN IMMUNOLOGY AND ANIMAL CELL CULTURE

Preparation of antigens – protocol of immunization, methods of bleeding.  Preparation of serum and complement.  Antigen- antibody reactions-Haemagglutination, Haemolysis, passive HA, precipitin ring test, immunodiffusion, immunoelectrophoresis. Complement fixation test, Enzyme-linked immunoabsorbent assay, Plaque forming cell assay, isolation of immunoglobulin, Characterization, Peripheral blood mononuclear cell separation, Lymphocyte subset identification and enumeration.  Western blotting.  Preparation of media, preparation of primary culture, maintenance of secondary culture, evaluation of culture dynamics.  Cell synchronization – preservation and revival of cells.  Hybridoma technology and monoclonal antibody production.

Reference Books:

1.      Hand book of Experimental immunology Vol.I & II by Weir, D.M. (1986) Blackwell Scienrific Publications.

2.      Practical Immunology by Hudson, L and Hay, H.C. (1980) Blackwell Scientific Publications.

3.      Techniques in clinical immunology by Thompson, R.A. (1977) Blackwell Scientific Publications.

4.      Hybridoma techniques:   A Laboratory Course by Muthukkaruppan, V.R., Baskar, S. and F. Sinigaglia (1986) Macmillan India Limited.

5.      Cell Biology Vol I to III by  V.E. Celis (1994) Academic Press.

SEMESTER III

SBT-0.3.3.1C.  RECOMBINANT DNA TECHNOLOGY

Core techniques in gene manipulation.   Cutting and joining DNA, introduction of  DNA into cells.  Cloning strategies, construction of genomic libraries and cDNA libraries.   Probe  construction,  recombinant selection and screening.   Analysis of expression.   Analysis of recombinant DNA, sequencing, mutagenesis, altered expression and engineering genes.  DNA amplification using polymerase chain reaction.  Key concepts.  Analysis of amplified products.  Applications of PCR;  Ligase chain reaction.  Expression systems and their applications.   E.coli.,  Streptomyces, Yeast, Baculovirus and animal cells as cloning hosts.

Reference Books:

1.      Principles of gene manipulation by RN.Old & SB.Primrose  (1994)  Blackwell Scientific Publications.

2.      DNA cloning I & II by DM. Glover & BD. Hames  (1995) IRL Press.

3.      PCR stratagies  by MA. Innis, DH.Gelfand & JJ. Sninskey (1995) Academic Press.

4.      Concepts in Biotechnology – Editors D.Balasubramanian  et al.  University Press,  (1996).

5.      Biotechnology, Annual Review Edited by M.R. EL-Gewelly Elsevier Publications, Amsterdam.

6.      Gene therapy-Edited by N.R.Lemoine and D.N.cooper BIOS Scienrific Publishers, Oxford.

7.      Diagnostic Molecular Microbiology.  Principles and Application Edited by David H.Persing et al. American Society for  Microbiology, Washington D.C.

8.      Methods in Molecular Biology vol.62  Edited by R.S.Tuan, Humana Press, Totowa, New Jersey.

DNA replication by A. Kornber and T.A. Baker WH Freeman and Company, New York

.

SBT-0.3.3.2C. ANIMAL BIOTECHNOLOGY

Transformation of animal cells, immortalization, cell lines.  Biology of Viral vectors – SV40, adeno virus, retro virus, vaccinia virus, herpes virus adeno associated virus, baculo virus. Construction of animal viral vectors for gene transfer into cell lines. Animal biotechnology for production of regulatory proteins, blood products, vaccines and hormones and other therapeutic proteins.  Gene therapy - prospects and problems.  Biotechnological applications for HIV diagnostics and therapy.  Oncogenes and antioncogenes.  Phage display technology.  Signal transduction. Transgenic animal production and application in expression of therapeutic proteins.   Gene knock out and mice model for human genetic disorder.  Baculovirus in biocontrol.  Baculo virus for expression of foreign genes.  Nucleic acid based detection of human disease genes.  Mapping of human genome.  Human genome project. 

Reference books:

1.      Gene Tranfer snf Rxpression Protocols. E.T. Murray (ed).

Methods in Molecular Biology, Vol.7, Humana Press.

2.      Recombinant DNA. J.D. Watson, M. Gilamn, J. Witkowski and M. Zoller.

Scientific American Books, NY.

3.      Genetic engineering in Animals. A.Puller (ed).

VCH Publishers.

4.      Molecular Biotechnology, II edition, Bernard R Glick and Jack J. Pasternack.

Asm Press.

Journa