1

SYLLABUS

for

M.SC. COURSE IN

BIOTECHNOLOGY

FAKIR MOHAN UNIVERSITY Nuapadhi Campus

BALASORE-756020

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2

Course No. Title Credit Hours

FIRST SEMESTER

BT. 411 Cell Biology 4 BT. 412 Computer Application and Biostatistics 4 BT. 413 Microbial Physiology & Genetics 4 BT. 414 Biomolecules and Instrumental Techniques 4 BT. 415 Laboratory I 6 22CH

SECOND SEMESTER BT. 421 Molecular Biology 4 BT. 422 Macromolecules and Basic Enzymology 4 BT. 423 Immunology 4 BT. 424 Biophysical Chemistry 4 BT. 425 Elective paper 2 BT. 426 Laboratory II 6

24CH .

THIRD SEMESTER

BT. 531 Animal Biotechnology 4 BT. 532 Genetic Engineering 4 BT. 533 Plant Biotechnology 4 BT. 534 Student seminar 2 BT. 535 Project 8 22CH

FOURTH SEMESTER BT. 541 Bioprocess Engineering & Technology 4 BT. 542 Medical Biotechnology 4 BT. 543 Genomics, Proteomics, and Bioinformatics 4 BT. 544 Elective Paper 2 BT. 545 Project 8

22 CH

(Total 90CH)

3 Elective Paper Each student will opt for a comprehensive, interactive course with one of the faculty members. The topic of specialization and course contents will be determined by the supervisor. Project The project will be based upon the research and actual bench work. It will begin from from the third 3rd semester and will continue through the fourth one. The project report will be submitted at the end of the fourth semester and evaluated. Students Seminar Each student under the supervision of a faculty member will deliver a comprehensive seminar, which will be evaluated. The topic normally will be from an emerging area of Modern Biology, Bio-medical, Biotechnology or its applications. Laboratory I, II Independent practical may be held under each course. However, for examination purposes a single comprehensive 2-3 days practical be held for each semester, covering different courses offered during that semester. It is recommended that practical training be organized as an exercise rather than a simple demonstration. The student must actually perform the experiments. Assignments Regular assignments must be given to each student during whole semester in each course. Assignments should be relevant to the course contents. All assignments must be evaluated as internal assessment. Invited lectures from eminent researchers, industrialists and others on recent issues related to biodiversity, ethics, biosafety, intellectual property rights, patent issues, and good laboratory and manufacturing practices will be organized. It is also proposed to include the following areas as parts of �student seminar�, �elective paper� and �assignments�.

1. Proteomics, functional genomics and therapeutic genomics. 2. Topics on human genetics, genetic dissections of heritable diseases, and detection of

associated mutations, and diagnostics based on PCR.

3. Technologies being adopted for future applications like cloning of animals with a capacity to produce human macromolecules.

4

FIRST SEMESTER

BT-411 CELL BIOLOGY 4CH

Theory Unit I:

1. Diversity of cell sizes & shapes,

2. Cell theory,

3. Structure of prokaryotic and eukaryotic cells � isolation and growth of cells.

4. Microscopic techniques for study of cells � light, phase contrast, fluorescence, scanning and transmission electron microscopy.

Unit II:

5. Sub cellular fractionation and criteria of functional integrity.

6. Cellular organelles - Structural organization and function of plasma membrane, cell wall.

7. Transport of nutrients, ions and macromolecules across membranes

Unit III:

8. Cellular energy transactions � role of mitochondria and chloroplasts.

. 9. Cell cycle-molecular events and model systems.

10. Cellular responses to environmental signals in plants and animals � mechanism of signal transduction.

11. Cell motility � cilia, flagella of eukaryotes and prokaryotes.

Unit IV:

12. Biology of cancer.

13. Metabolite pathways and their regulation.

14. Biosynthesis of proteins in eukaryotic cell, co and post translational modification, intracellular protein traffic.

Unit V:

15. Cellular basis of differentiation and development � mitosis, gametogenesis and fertilization. Development in Drosophila and Arabidopsis; spatial and temporal regulation of gene expression.

16. Brief introduction to the life cycle and molecular biology of some important pathogens of AIDS, Malaria, Hepatitis, Tuberculosis, Filaria, and Kalazar.

5 17. Protein localization: synthesis of secretory and membrane protein, import into

nucleus, mitochondria, chloroplast and peroxysomes, receptor mediated endocytosis.

Practicals

1. Microscopy: bright field, phase contrast and fluorescence microscopy.

2. Microtomy.

3. Instrumental methods for cell biology.

4. Subcellular fractionation and marker enzymes.

5. Histochemical techniques.

6. Mitosis and meiosis.

Books

1. Cell Biology by De-Robertis Saunders, Singapore.

2. Reproduction in eukaryotic cells, Prescott DM, Academic Press.

3. Developmental Biology, Gilbert SF, Sinauer Assoc. Inc.

4. Cell in Development and Inheritance, Wilson EB, McMillan, New York.

5. Molecular Biology of Cells, Alberts B et al.

6. Molecular Cell Biology, Lodisch et al.

7. The Coiled Spring, Ethan Bier, Cold Spring Harbour Press.

8. Fertilisation, Longo FT, Chapman Hall, London.

9. Molecular Biology of steroid and Nuclear Hormone Receptor, Freedman LP, Birkhauser, Basel.

BT- 412 COMPUTER APPLICATIONS AND BIOSTATISTICS 4CH

Theory Unit I:

1. Brief description and tabulation of data and its graphical representation.

2. Measure of central tendency and dispersion; mean, median, mode, range, standard deviation, variance. Idea of two types of errors and level of significance, tests of significance (F- and t-test); chi-square tests.

3. Simple linear regression and correlation.

6 Unit II :

4. Introduction of digital computers; organizations; low-level and high level languages, the binary number system.

5. Flow charts and programming techniques.

Unit III

6. Introduction to programming in Q basic and C.

7. Introduction to data structures and database concepts, introduction to internet and its applications.

Unit IV

8. Introduction to MS-Office software, covering word processing, spreadsheets and presentation software.

9. Introduction to Harvard graphics / Sigma plotter.

Unit V

10. Computer � oriented statistical techniques; Frequency table of single discrete variable. Bubble sort, computation of mean, variance and standard deviation; t-test, correlation coefficient.

10. Bio-informatics and bio-technology.

Practical

BT-413 MICROBIAL PHYSIOLOGY AND GENETICS 4 CH Theory

Unit-I:

1. The beginning of Microbiology : The discovery of Microbial world by Antony van Leeuwenhoek; The controversy over spontaneous generation, role of micro-organisms in transformation of organic matter and in the causation of diseases; development of pure culture methods; the enrichment culture methods and development of microbiology in the twentieth century.

2. Methods in microbiology: Pure culture techniques; the theory and practice of sterilization; principles of microbial nutrition; construction of culture media; enrichment culture techniques for isolation and chemo-autotrophs, chemohetero-trophs, and photosynthetic micro-microorganisms.

3. Microbial evolution, systematics and taxonomy : The evolution of earth and the earliest life form; primitive organisms and their metabolic strategies; and molecular coding; new approaches to bacterial taxonomic classification, including ribotyping,

7 ribosomal RNA sequencing; characteristics of primary domains; taxonomic nomenclature and Bergen�s manual.

Unit-II:

4. Microbial growth : the definition of growth; the mathematical expression of growth, growth curve, the measurement of growth and growth yields; synchronous growth; continuous culture; growth as affected by environmental factors like temperature, acidity, alkalinity, water availability and oxygen, culture collection and mentainance of cultures.

5. Overview of basic metabolism and microbial nutrition.

6. Metabolic diversity among micro-organisms, photosynthesis in micro-organisms, role of chlorophylls, carotenoids and phycobnilins, Calvin cycle, chemolithotrophy, hydrogen - iron � nitrite - oxidizing bacteria; nitrate and sulphate reduction, methanogenesis and acetogenesis, fermentations- diversity synrophy, role of anoxic decompositions, nitrogen metabolism, nitrogen fixation, hydro-carbon fixation.

Unit-III:

7. Prokaryotic diversity:

Bacteria: Purple and green bacteria, cyano bacteria, homo-aceto-genic bacteria, gliding and sheathed bacteria; pseudomonades, lactic and propionic acid bacteria, endospores forming rods and cocci, mycobacteria; rickettsias, chlamydias, mycoplasma.

Archea: Archea as the earliest life forms, halophiles, methanogenes, hyperthermophillic archea, thermoplasma.

Eukarya: Algae, fungi, slime molds and protozoa.

Virus: Bacterial, plant, animal and tumer viruses,The discovery, classification and structure of viruses; lysogeny; DNA viruses positive strand and double stranded RNA viruses; replication; examples of herpese, pox, adeno viruses, retro viruses, viroids, prions.

8. Microbial Diseases: Disease reservoirs; epidemiological infections caused by bacteria and viruses; ogenic fungi, emerging and resurgent infecticious diseases. 9. Host-parasite relationship: Normal microflora of skin; oral cavity; gastrointestinal tract; entry of pathogens into the host;genesis.

Unit-IV:

10. Prokaryotic cells: Structure- function: cell walls of eubacteria (peptido glycan) and related molecules, outer membrane of gram negative bacteria, cell wall and cell membrane synthesis; flagella and motility; cell inclusions like endospores, gas vescicles.

8 11. Chemotherapy / Antibiotics: Antimicrobial agents, sulfa drugs, antibiotics, penicillins, and cephlosporins, broad spectrum antibiotics, antibiotics from prokaryotes; antifungal antibiobiotics, mode of action, resistance to antibiotics.

Unit-V:

12. Genes, mutation and mutagenesis: UV and chemical mutagen, types of mutations, Ames test; methods of genetic analysis.

13. Bacterial genetic system, transformation, conjugation, transduction, recombi-nation, plasmids and transposing, bacterial genetics map with reference to E. coli.

14. Viruses and their genetic system: Phage and its life cycle, RNA phages, RNA viruses, retro-viruses.

15. Genetic systems of yeast and Neurospora.

16. Extrachromosomal inheritance.

Practicals

1. Preparation of liquid and solid media for the growth of micro-organisms.

2. Isolation and mentainance of organisims by plating, streaking, and serial dilution methods, slants and stab cultures, storage of microorganisms.

3. Isolation of pure cultures from soil and water.

4. Growth; growth curve, measurement of bacterial populations by turbidometry and serial dilution methods. Effects of temperature,pH, carbon and nitrogen sources on growth.

5. Microscopic examination of bacteria, yeast and moulds and study of organisms by gram stain, acid fast stain and staining for spores.

6. Study of mutations by Ames test.

7. Assay of antibiotics and demonstration of antibiotic resistance.

8. Bacterial transformation.

9. Biochemical characterization of selected microbes.

10. Transduction.

11. One step growth curve of coliphage.

Books

1. General Microbiology, Stainer, R.Y., Ingraham, J.L., Wheelis, M.L., and Painter, P.R. The McMillan Press Lte.

2. Brock Biology of Microorganisms, Madigan, M.T., Martinko, J.M. and Parker, J.Prentice-Hall.

3. Microbiology, Pelczar, M.J., Jr. Chan, E.C.S., and Kreig, N.R., Tata-McGraw-Hill.

9 4. Microbial Genetics, Maloy, S.R., Cronan, J.E.Jr., and Friefelder, D. Jones and Bartlett

Publishers.

5. Microbiology, A Laboratory Manual, Cappuccion, J.G., and Sherman, N., Addison Wesley.

6. Microbiological Applications (A Laboratory Manual in General Microbiology), Benson, H.J., W.C.B., Wim C. Brown Publishers.

BT- 414 BIOMOLECULES AND INSTRUMENTAL TECHNIQUES 4CH

Theory Unit-I :

1. Chemical foundations of Biology : pH and pK, acids, bases, buffers, weak bonds and co-valent bonds.

2. Principles of thermodynamics. Unit-II :

3. Classes oif organic compounds and functional groups � atomic and molecular dimensions, space filling and ball and stick models.

4. Amino acids and peptides � classification, chemical reactions and physical properties.

5. Sugars � classificatin and reactions. Unit-III :

6. Heterocylcic compounds and secondary metabolites in living systems � nucleotides, pigments and isoprenoids.

7. Separation techniques for different bio-molecules. Unit-IV :

8. Lipids � classification, structure and functions. 9. Proteins � classification and separation, purification and criteria of homogeneity,

end group analysis, hierarchy in structure and Ramchandran map. Unit �V:

10. Polysachharides � types, structural features, methods for compositional analysis. 11. Analytical techniques in biophysics and biochemistry for small moleculaes and

macromolecules for quantification. Practicals

1. Titration of amino acids.

2. Colorimetric determination of pK.

3. Model building using space, filling/ ball and stick models.

4. Reactions of aminoacids, sugars and lipids including diagnostic tests.

5. Isolation, purity determination and quantification of cholesterol, DNA and RNA.

6. Quantification of proteins and sugars.

7. Analysis of oils � iodine number, saponification value and acid number.

8. UV, Visible, fluorescence and IR spectroscopy and absorption spectra.

10 9. Separation techniques � centrifugation, chromatography (gel permeation, ion exchange,

TLC etc.) and electrophoresis (PAGE-SDS and AGAROSE).

10. Cleavage of DNA with restriction enzymes and electrophoresis of fragments.

11. Labelling of DNA/ RNA, plasmid isolation.

Books

1. Biochemical Calculatio, Seagel I.H., John Wiley and Sns Inc.

2. General Chemistry, Pauling L. W.H.Freeman and Company.

3. Organic Chemistry, Cram D.J. and Hammond G.S., Mc Graw Hill.

4. Biochemistry, Voet D and Voet J.G., Wiely and Sons.

5. Physical Biochemistry, Freifilder D., W.H.Freeman and Company.

6. Laboratory Techniques in Biochemistry and Molecular Biology, Work and Work.

7. Understanding Chemistry, Rao CNR, University Press, Hyderabad, 1999.

8. A Biologist�s Guide to Principles and Techniques of Practical Biochemistry,Wilson K and Goulding KH, ELBS Edition,

9. Tools of Biochemistry by Cooper TG

10. Lehninger�s BIOCHEMISTRY

BT- 415 LABORATORY 6CH

11

SECOND SEMESTER

BT-421 MOLECULAR BIOLOGY 4 CH Theory Unit-I:

1. Introduction to Molecular Biology and Genetics

2. DNA Replication: Prokaryotic and Eukaryotic DNA replication,

3. DNA repair and recombination

Unit II

4. Transcription: Prokaryotic transcription, Eukaryotic transcription, RNA polymerase. General and specific transcription factors, regulatory elements and mechanisms of transcription regulations, transcriptional and post-transcriptional gene silencing.

5. Modifications in RNA: 5�-Cp formation, transcription termination, 3�-end processing and polyadenylation, splicing, editing, nuclear export of mRNA, mRNA stability.

Unit III

6. Translation: Prokaryotic and Eukaryotic translation, the translation machinery, mechanisms of initiation, elongation and termination, regulation of translation, co-and post-translation modifications of proteins.

7. Oncogenes and Tumour Suppressor Genes: Viral and cellular oncognes, tumour suppressor genes humans, structure, function and mechanism of action of pRB and p53 tumour suppressor proteins.

Unit IV

8. Antisense and Ribozyme Technology: Milecular mechanism of antisense molecules, inhibition of splicing, polyadenylation and translation, disruption of RNA structure and capping, biochemistry of ribozyme; hammerhead, hairpin and other ribozymes, strategies for designing ribozymes, applications of antisense and ribozyme technology.

9. Homologous Recombination: Holiday junction, gene targeting, gene disruption, FLP / FRT and Cre/Lox combination, RecA and other recombinases.

Unit V

10. Mapping of Genome : Genetic and physical maps, physical mapping and map-based cloning, choice of mapping population, simple sequence repeat loci,

12 southern and fluorescence in situ hybridization for genome analysis, chromosome microdissection and microcloning, molecular marketers in genome analysis : RFLP, RAPD and AFLP analysis, molecular markers linked to disease resistance genes : Application of RFLP in forensic, disease prognosis, genetic counseling, pedigree, varietal etc. Animal trafficking and poaching : germplasm maintenance, taxonomy and biodiversity.

11. Genome Sequencing : Genome sizes, organelle genomes, genomic libraries, YAC, BAC libraries, strategies for sequencing genome, packaging, transactions and recovery of clones, application of sequence information for identification of defective genes.

Practicals

1. Isolation of genomic DNA

2. Southern blotting

3. RFLP analysis

4. Isolation of RNA

5. Isolation of polyA+RNA

6. Nothern blotting

7. Preparation of probes

8. In vitro transaction

9. In vitro translation

10. Metabolic labeling of proteins and immunoprecipitation

Books

1. Molecular Cloning : A Laboratory Manual, J. Sambrook, E.F., Fritsch and T. Maniatis, Cold Spring Harbor Laboratory Press, New York, 2000.

2. Introduction to Practical Molecular Biology, P.D. Dabre, John Wiley and Sons Ltd., New York, 1998.

3. Molecular Biology LabFax, T.A. Brown (ed), Bios Scientific Publishers Ltd., Oxford, 1991.

4. Molecular Biology of the Gene (4th edition), J.D. Watson, N.H. Hopkins, J.W.Roberts, J.A. Steitz and A.M. Weiner, the Benjamin / Cummings Pub. Co. Inc., California, 1987.

5. Molecular Cell Biology (2nd Edition), J. Darnell, H. Lodish and D. Baltimore, Scientific American Books Inc USA 1994.

6. Molecular Biology of the Cell (2nd edition), B. Alberts, D. Bray, J. Lewis, M. Raff. K. Roberts, and J.D. Watson, Garland Publishing Inc., New York, 1994.

7. Gene VI (6th edition), Benjamin Lewin, Oxford University Press, U.K., 1988.

13 8. Molecular Biology and Biotechnology, A Comprehensive Desk Reference, R.A. Meyeres

(ed.), VCH Publishers Inc., New York, 1995.

9. Genomes, T.S. Brown.

BT-422 MACROMOLECULAES AND BASIC ENZYMOLOGY 4CH Theory Unit-I:

1. Macromolecules and supra molecular assemblies � Types of macromolecules in biological systems, molecular assemblies like membranes, ribosomes, extracellular matrix.

2. Physical techniques in protein, nucleic acids and polysaccharide structural analysis (UV, IR, NMR, LASER, Raman spectroscopy, MASS spectroscopy, fluorescence spectroscopy). Differential calorimetry, X-ray crystallography, ultra centrifugation. Electron Cryo microscopy; scanning tunneling microscopy.

Unit II

3. Sequencing of proteins and nucleic acids.

4. Protein-protein and protein-ligand interactions, physical and chemical methods for study.

5. Conformational properties of polynucleotides and polysaccharides � secondary and tertiary structural features and their analysis � theoretical and experimental; protein folding � biophysical and cellular aspects.

Unit III

6. Protein and nucleic acid data bases: structural comparison at secondary and tertiary levels.

7. Enzyme catalysis in solution � kinetics and thermodynamic analysis, effects of organic solvents on enzyme catalysis and structural consequencies.

8. Physical and chemical methods for immobilization of small and macromolecules.

Unit IV

9. Glyco and lipoprotein � structure and function.

10. Organization of macromolecular complexes � chromatin and ribosomes; protein denaturation.

11. Nucleic acid hybridization � structural analysis and biological studies.

Unit V

12. Ribozymes and Catalytic antibodies � Functional proteins � structure and drug targets (enzymes and receptors).

14 13. Computer Aided drug designing, computational techniques in structural

analysis; nanoparticles.

14. Allosteric enzymes, mnemonical enzymes, kinetics of enzyme inhibitors.

Practicals

1. Electrophoresis of proteins � native and under-denaturing conditions.

2. N- and C- terminal analysis of proteins.

3. Peptide mapping.

4. Separation techniques (HPLC, GPC, FPLC), ion exchange, gel filtration, affinity chromatography.

5. Chemical modification of proteins.

6. Enzyme : purification and kinetic analysis.

7. Hydrodynamic properties � measurement and applications.

8. Methods for immobilization of enzymes.

9. Techniques for analysis of secondary, tertiary and quaternary structures of proteins.

10. Electrophoresis of DNA � linear, circular and super coiled.

11. Protein � DNA interactions.

12. Nucleic acid hybridization.

13. Determination of Tm of nucleic acid.

14. Enzyme isolation from various tissues, precipitation methods for purification and enzyme proteins.

Books 1. Essentials of Molecular Biology, David Friefilder, Jones and Bartlett Publications.

2. Proteins � Structure and Molecular Properties, TE Creighton, WH Freeman and Company.

3. Genes VH, B. Lewin, Oxford University Press.

4. Introduction to Protein Structure, C. Branden and J. Tooze, Garland Publishing, New York.

5. Encyclopedia of Molecular Biology, J. Kendrew, Blackwell Scientific Publications, Oxford.

6. Physical Chemistry of Macromolecules, Tanford, C., John Wiley and Sons.

7. Introduction to Biophysical Chemistry, R.B. Martin, McGraw Hill, New York.

8. Biophysical Chemistry, Cantor, W.H. Freeman.

9. Protein Structure, Max Peruz.

15 BT- 423 IMMUNOLOGY 4CH Theory Unit-I

1. Introduction - Phylogeny of immune system

- Innate and acquired immunity

- Clonal nature of immune response

2. Organization and structure of lymphoid organs.

3. Nature and biology of antigens and superantigens.

4. Antibody structure and function.

Unit II

5. Antigen-antibody interactions.

6. Major histocompatibility complex.

7. BCR and TCR generation of diversity.

8. Complement system.

Unit III

9. Cells of the immune system : Hematopoiesis and differentiation, lymphocyte trafficking, B-lymphocytes, T-lymphocytes, macrophages, dendritic cells, natural killer and lymphokine activated killer cells, eosinophil, neutrophils and mast cells.

10. Regulation of immune response.

- Antigen processing and presentation, generation of humoral and cell mediated immune responses.

- Activation of B and T � lymphocytes.

- Cytokines and their role in immune regulation

- T-cell regulation, MHC restriction

- Immunological tolerance

Unit IV

11. Cell � mediated cytotoxicity : Mechnism of T cell and NK cell Mediated lysis, antibody-dependent cell-mediated cytotoxicity, macrophage mediated cytotoxicity.

12. Hypersensitivity.

16 13. Autoimmunity

Unit V

14. Transplantation

15. Immunity to infectious agents (intracellular parasites, helminthes and viruses).

16. Tumour immunology.

17. AIDS and other immunodeficiencies

18. Hybridoma technology and monoclonal antibodies.

Practicals

1. Blood film preparation and identification of cells. 2. Lymphoid organs and their microscopic organization. 3. Immunization, collection of serum. 4. Double diffusion and immuno-electrophoresis. 5. Radial immuno diffusion 6. Purification of IgG from serum. 7. Separation of mononuclear cells by Ficoll-Hypaque. 8. Con-A induced proliferation of thymocytes (by MIT method) 9. Western-blotting 10. ELISA 11. Hapten conjugation and quantization. 12. Immunodiagnostics (demonstration using commercial kits).

Books

1. Kuby Immunology, 4th edition, R.A. Goldsby, Thomas J. Kindt, Barbara A. Osborne (Freeman).

2. Immunology, A Short Course, 4th Edition, Eli Benjamin, Rcchard Coico, Geoffrey Sunshine (Wiley-Liss).

3. Fundamentals of Immunology, William Paul.

4. Immunology by Roist and others.

17 BT- 424 BIOPYSICAL CHEMISTRY 4CH

Theory

Unit I:

A. Interactions in Biological Systems.

1. Intra and inter-molecular forces, electrostatic interactions and hydrogen bonding interactions.

2. Vander Waals and Hydrophobic interactions.

3. Disulphide brides.

4. Role of Water and weak interactions.

Unit II

B. Structure of Proteins

1. Confromational properties of polypeptides.

2. Primary and secondary structure a-helix, b-sheet structure etc.

3. Tertiary and quaternary structure

Unit III

4. Structural features of membrane proteins.

5. Conjugated and metal-binding proteins.

6. Secondary and tertiary structure prediction of protein conformation.

Unit IV

C. Multiple Equilibrium

1. Titration of proteins to evaluate net and total charge.

2. Scatchard and hill plots.

3. Folding-unfolding equilibrium and denaturation of proteins.

4. Effect of temperature and solvent condition on the thermodynamics of proteins folding-unfolding equilibrium.

5. Kinetics of protein folding.

18 Unit V

D. Techniques for the study of Macromolecular Structure

1. Ultracentrifugation : Sedimentation velocity and equilibrium, determination of molecular weights.

2. Viscosity.

3. Microcalorimeter

4. Circular Dichroism spectroscopy.

5. UV, visible and fluorescence spectroscopy.

6. X-Ray diffraction.

7. Nuclear magnetic resonance (NMR).

Practicals BT-425 ELECTIVE PAPER 2CH BT-426 LABORATORY II 6CH

19

THIRD SEMESTER BT-531 ANIMAL BIOTECHNOLOGY 4CH

Theory

Unit-I: 1. Structure and organization of Animal Cell.

2. Equipments and materials for animal cell culture technology.

3. Primary and established cell line cultures.

Unit-II: 4. Introduction to the balanced salt solutions and simple growth medium. A brief

discussion on the chemical, physical and metabolic functions of different constituents of culture medium. Role of carbon dioxide, Role of serum and supplements.

5. Serum and protein-free defined media and their applications.

6. Measurement of viability and cytotoxicity.

7. Biology and characterization of cultured cells, measuring parameters of growth.

Unit-III: 8. Basic techniques of mammalian cell culture in vitro; disaggregation of tissue and

primary culture; maintenance of cell culture; cell separation.

9. Scaling-up of animal cell culture.

10. Cell synchronization.

11. Cell cloning and micromanipulation.

12. Cell transformation.

Unit-IV: 13. Application of animal cell culture.

14. Stem cell cultures, embryonic stem cells and their applications.

15. Cell culture based vaccines.

Unit-V: 16. Somatic cell genetics.

17. Organ and histotypic cultures.

18. Measurement of cell death.

19. Apoptosis

20 20. Three dimensional culture and tissue engineering.

Practicals

1. Preparation of tissue culture medium and membrane filtration.

2. Preparation of single cell suspension from spleen and thymus.

3. Cell counting and cell viability.

4. Macrophage monolayer from PEC, and measurement of phagocytic activity.

5. Trypsinization of monolayer and subculturing.

6. Cryopreservation and thawing.

7. Measurement of doubling time.

8. Role of serum in cell culture.

9. Preparation of metaphage chromosomes from cultured cells.

10. Isolation of DNA and demonstration of apoptosis of DNA laddering.

11. MTT assay for cell viability and growth.

12. Cell fusion with PEG.

Books

1. Culture of Animals Cells 3rd Edition, R. Ian Freshney, Wiley-Liss.

2. Animal Cell Culture � Practical approach, ed., John, R.W. Masters, Oxford.

3. Cell growth and Division : A Practical Approach, ed., R. Basega, IRL, Press.

4. Cell Culture Lab Fax, eds., M. Butler and M. Dawson, Bios Scientific Publications Ltd., Oxford.

5. Animal Cell Culture Techniques, eds, Martin Clynes, Springer.

5. Methods in Cell Biology, Vol.57, Animal Cell Culture Methods, eds., Jenni P. Mather and David Barnes, Academic Press.

21

BT � 532 GENETIC ENGINEERINGY 4CH Theory Unit- I :

1. Scope of Genetic Engineering.

2. Milestones in genetic engineering : Isolation of enzymes, DNA sequencing, synthesis and mutation, detection and separation, cloning, gene expression, cloning and patenting of life forms, genetic engineering guidelines.

3. Molecular tools and their applications : Restriction enzymes, modification enzymes. DNA and RNA markers.

Unit-II: 4. Nucleic acid purification, yield analysis.

5. Nucleic acid amplification and its applications.

6. Gene-cloning vectors : Plasmids, bacteriophages, phagemids, cosmids, artificial chromosomes.

7. Restriction mapping of DNA fragments and map construction, nucleic acid sequencing.

8. cDNA synthesis and cloning : mRNA enrichment, reverse transcription, DNA primers, linkers, adaptors and their chemical synthesis, library construction and screening.

9. Alternative strategies of gene cloning : Cloning interaction genes � two � and �three hybrid systems, cloning differentially expressed genes. Nucleic acid microarray arrays.

Unit-III:

10. Site-directed mutagenesis and protein engineering.

11. How to study gene regulation? DNA transactions, northern blot, primer extension, S1 mapping, Rnase protection assay, Reporter assay.

12. Expression strategies for heterologous genes : Vector engineering and codon optimization, host engineering, in vitro transcription and translation, expression in bacteria, expression in yeast, expression in plants.

Unit-IV:

13. Processing of recombinant proteins : Purification and refolding, characterization of recombinant proteins, stabilization of proteins.

22 14. Phage display.

15. T-DNA and Transposon tagging : Role of gene tagging in gene analysis, T-DNA and transposon tagging, identification and isolation of genes through T-DNA or transposon.

Unit-V: 16. Transgenic and gene knockout technologies : Targeted gene replacement,

chromosome engineering.

17. Gene therapy : Vector engineering, Strategies of gene delivery, gene replacement / augmentation, gene correction, gene editing, gene regulation and silencing.

18. Isolation of plasmids.

Practicals

1. Bacterial culture and antibiotic selection media. Preparation of competent cells.

2. Isolation of plasmid DNA.

3. Quantization of nucleic acids.

4. Agarose gel electrophoresis and restriction mapping of DNA.

5. Construction of restriction map of plasmic DNA.

6. Cloning in plasmid/phagemid vectors.

7. Preparation of single stringed DNA template.

8. DNA sequencing.

9. Gene expression of E. coli and analysis of gene product.

10. PCR

11. Reporter gene assay (Gus/CAT/-GAL)

Books

1. Molecular Cloning : A Laboratory Manual, J. Sambrook, E.F., Fritsch and T. Maniatis. Cold Spring Harbor Laboratory Press, New York, 2000.

2. DNA Cloning : A Practical Approach, D.M. Glover and B.D. Hames, IRL Press, Oxford, 1995.

3. Molecular and Cellular Methods in Biology and Medicine, P.B. Kaufman, W.Wu.D. Kim and L.J. Cseke, CRC Press, Florida, 1995.

4. Methods in Enzymology, Guide to Molecular Cloning Techniques, Vol.152, S.L. Berger and A.R. Kimmel, Academic Press Inc., San Diego, 1996.

23 5. Methods in Enzymology, Vol.185. Gene Expression Technology. D.V. Goeddel,

Academic Press Inc. San Diego, 1990.

6. DNA Science : A First Course in Recombinant Technology, D.A. Mickloss and G.A. Freyer, Cold Spring Harbor Laboratory Pres, New York, 1990.

7. Molecular Biotechnology, 2nd edition, S.B. Primrose, Blackwell Scientific Publishers, Oxford, 1994.

8. Milestones in Biotechnology, Classic Papers on Genetic Engineering, J.A. Davies and W.S. Reznikoff, Butterworth-Heinemann, Boston, 1992.

9. Route Maps in Gene Technology, M.R. Walker and R. Rapley, Blackwell Science Ltd., Oxford, 1997.

10. Genetic Engineering : An Introduction to Gene Analysis and Exploitation in Eukaryotes, S.M. Kingsman and A.J. Kingsman, Blackwell Scientific Publications, Oxford, 1998.

12. Molecular Biotechnology-Glick.

BT-533 PLANT BIOTECHNOLOGY 4CH

Theory

Unit I:

1. Conventional plant breeding.

2. Introduction to cell and tissue culture, tissue culture as a technique to produce novel plants and hybrids.

3. Tissue culture media (composition and preparation)

4. Initiation and maintenance of callus and suspension culture; single cell clones.

Unit-II:

5. Organogenesis; somatic embryogenesis; transfer and establishment of whole plants in soil.

6. Shoot-tip culture; Rapid clonal propagation and production of virus-free plants.

7. Embyro culture and embryo rescue.

8. Protoplast isolation, culture and fusion; selection of hybrid cells and regeneration

of hybrid plants; symmetric and asymmetric hybrids, hybrids Biotransformation.

9. Anther, pollen and ovary culture for production of haploid plants and homozygous lines.

10. Cryopreservation, slow growth and DNA banking for germ plasm conservation.

24 Unit-III:

11. Plant Transformation technology : The basis of tumour formation, hairy root, features of T1 and R1 plasmids, mechanisms of DNA transfer, role of virulence genes, use of T1 and R1 as vectors, binary vectors,use of 35S and other promoters, genetic markers, use of reporter genes, reporter gene with introns, use of scaffold attachment regions, methods of nuclear transformation, viral vector and their applications, multiple gene transfer, vectorless or direct DNA transfer, particle bombardment, electroporation, microinjection transformation of monocots. Transgene stability and gene silencing. In planta transformation.

12. Application of plant transformation for productivity and performance promoter trapping, activation tagging. Herbicide resistance, phosphoinothricin, glyphosate, sufonyl urea, atrazine, isect resistance, Bt. Genes, non-Bt like protease inhibitors, alpha amylase inhibitor, virus resistance, coat protein mediated, nucleocapsid gene, disease resistance, chitinase, 1-3 beta glucanase, RIP antifungal proteins, thionines, PR proteins, nematode resistence abiotic stress post-harvest losses, long shelf life of fruits and flowers, use of ACC synthase, poly-galactrunase, ACC oxidase, male sterile lines, bar and barnase systems, carbohydrate composition and storage, ADP glucose pyrophosphatase, terminator gene technology.

13. chloroplast transformation : Advantages, vectors, success with tobacco and potato.

Unit-V: 14. Metabolic engineering and industrial products : Plant secondary metabolities,

control mechanisms and manipulation of phenylpropanoid pathway, shikimate pathway; alkaloids, industrial enzymes, biodegradable plastics, polyhydroxybutyrate, therapeutic proteins, lysosomal enzymes, antibodies, edible vaccines, purification strate-gies, oleosin partitioning technology.

15. Molecular marker-aided breeding : RFLP maps, linkage analysis, RAPD markers, STS, microsatellites, SCAR (sequencie characterized amplified regions), SSCP (single strand conformational polymorphism), AFLP, QTL, map-based cloning, molecular marker-assisted selection.

16. Arid and semi-arid plant biotechnology.

17. Green house and Green-home technology.

Practicals

1. Preparation of media 2. Surface sterilization 3. Organ culture 4. Callus propagation, organogenesis, transfer of plants to soil. 5. Protoplast isolation and culture.

25 6. Anther culture, production of haploids. 7. Cytological examination of regenerated plants. 8. Agrobacterium culture, selection of transformants, reporter gene (GUS) assays. 9. Developing RFLP and RAPD maps.

Books

1. J. Hammound, P. McGarvey and V. Yusibov, eds, Plant Biotechnology; Springer Verlag, 2000.

2. T-J Fu, G. Singh, and W.R. Curtis, eds., Plant Cell and Tissue Culture for the Production of Food Ingredients, Kluwer Academic/Plenum Press, 1999.

3. H.S. Chawla, Biotechnology in Crop Improvement, International Book Distributing Company, 1998.

4. R.J. Henry, Practical Application of Plant Molecular Biology, Chanman and Hall, 1997.

5. P.K. Gupta, Elements of Biotechnology, Rastogi and Co., Meerut, 1996.

BT-534 STUDENTS SEMINAR 2CH

BT-535 PROJECT 8CH

26

FOURTH SEMESTER

BT-541 BIOPROCESS ENGINEERING AND TECHNOLOGY 4CH

Theory

Unit-I: 1. Introduction to bioprocess engineering.

2. Bioreactors

3. Isolation, preservation and maintenance of industrial microorganisms.

4. Kinetic of microbial growth and death.

Unit-II: 5. Media for industrial fermentation.

6. Air and media sterilization

7. Types of fermentation processes : Analysis of batch, fed-batch and continuous bioreactions, biotransformation, stability of microbial reactors, analysis of mixed microbial populations, specialized bioreactors (pulsed, fluidized, photobioreactors etc.).

8. Measurement and control of bioprocess parameters.

Unit-III: 9. Downstream processing : Introduction removal of microbial cells and solid

matter, foam separation, precipitation, filtration, centrifugation, cell disruptions, liquid-liquid extraction, chromatography, membrane process, drying and crystallization, effluent treatment: DOC and COD treatments and disposal of effluents.

10. Enzyme and whole cell immobilization and their industrial applications.

Unit-IV: 11. Industrial production of chemicals. Alcohol (ethanol), acids (citric, acetic and

gluconic), solvents (glycerol, acetone, butanol), antibiotics (Penicillin, streptomycin, tetracycline), aminoacids (lysine, glutamic acid), single cell protein.

12. Use of microbes in mineral beneficiation and oil recovery.

Unit-V: 13. Introduction of food technology.

- Elementary idea of canning and packing.

- Sterilization and pasteurization of food products.

27 - Technology of typical food/food products (bread, cheese, idli)

- Food preservation

Practicals

1. Isolation of industrially important microorganisms for microbial processes.

2. Determination of thermal death point (TDP) and thermal death time (TDT) of microorgaism for design of a sterilizer.

3. (a) Determination of growth curve of a supplied microorganism and also to determine substrate degradation profile

(b) Computer Specific growth rate (), growth yield (Yx/s), specific product formation rate (QP) and specific substrate consumption rate (Qs).

4. Comparative studies of ethanol production using different substrates.

5. Microbial production of citric acid using Aspergillus niger.

6. Microbial production of antibiotics (penicillin).

7. Production and estimation of alkaline protease.

8. Sauer Krant fermentation.

9. Use of alginate for cell immobilization.

10. Study of rheology of viscous polymers and microbial cultures.

11. Determination of oxygen transfer rate and Kla.

12. Determination of mixing time in bioreactors.

Books

1. Biochemical Engineering, Aiba, S., Humphrey, A.E. and Millis, N.F., University of Tokyo Press, Tokyo.

2. Biochemical Reactors, Atkinson, B., Pion Ltd., London.

3. Biochemical Engineering Fundamentals, Baily, J.E. and Ollis, D.F., McGraw-Hill Book Co., New York.

4. Bioprocess Technology : Fundamentals and Applications, KTH, Stockholm.

5. Process Engineering in Biotechnology, Jackson, A.T., Prentice Hall, Engelwood Cliffs.

6. Bioprocess Engineering : Basic Concepts, Shuler,M.L., and Kargi, F., Prentice Hall, Englewood Cliffs.

7. Principles of Fermentation Technology, Stanbury, P.F., Whitaker, A., Pergamon Press, Oxford.

8. Bioreaction Engineering Principles, Nielson, J. and Villadsen, J., Plenum Press.

28 9. Chemical Engineering Problems in Biotechnology, Schuler, M.L. (ed.) AICHE.

10. Biochemical Engineering, Lee, J.M., Prentice Hall Inc.

10. Bioprocess Engineering-Kinetics, Mass Transport, Reactors and Gene Expression, Vieth, W.F. John Wiley and Sons Inc.

BT � 542 MEDICAL BIOTECHNOLOGY 4CH Theory Unit- I : Blood products, Hemophilia A & B, Production of clotting factors, anticoagulants, t- PA-Based products, Vaccine technology, recombinant vaccines, Hepatitis B based vaccines, Approaches to vaccine design, Vaccines for AIDS & cancer.

Unit � II : Poly clonal antibody preparation, monoclonal antibody synthesis, Hybridoma technology, Therapeutic antibodies & their application in cancer diagnosis, Therapeutic enzymes, Protein engineering & recombinant enzymes. Unit � III: Hormones & growth factors, Insulin, glucagon, gonadotrophins, production of recombinant hormones & growth factors, productin of interferons, interleukins & other regulatory factors.

Unit- IV: Immobilized enzymes as diagnostic reagents, Biosensors & their application, antibodies as analytical reagents.

Unit � V: Application of animal cell cultures, stem cell cultures, stem cells & embryonic stem cells cultures and their applications, cell culture based vaccines, Apoptosis & cell death.

Books Proteins Biochemistry & Biotechnology by Walsh

BT-543 GENOMICS AND FUNCTIONAL GENOMICS 4CH

Unit-I: Whole genome analysis : Preparation of ordered cosmid libraries, bacterial artificial chromosome libraries, shotgun libraries and sequencing. Conventional sequencing (Sanger, Maxam and Gilbert methods), automated sequencing.

Unit-II: DNA Microarray : Printing of oligonucleotides and PCR products on glass slides, nitrocellulose paper. Genome analysis for global patterns of gene expression using fluorescent-labelled cDNA or end-labelled RNA probes. Analysis of single nucleotide polymorphism using DNA chips.

29 Unit-III:

Proteome analysis : Two dimensional separation of total cellular proteins, isolation and sequence analysis of individual protein spots by mass spectroscopy. Protein microarrays. Advantage and disadvantage of DNA and protein microarrays.

Unit IV:

Mass spectrometry for proteins & peptide analysis. MS data with specific protein sequences. Application of proteomics---mining, protein expression, mapping & protein modification.

Unit V:

Bioinformatics :- World Wide Web- database sequence searching in databases-PSI- Blast, Fasta format for sequence alignment, application of Bioinformatics in phylogenetic relationships, protein structure prediction & engineering.

Books

1. Bioinformatics by Lesk

2. Analysis of genes and genomes by Reece

References

1. Recent articles in journals.

2. The Internet and New Biology : Tools for Genomic and Molecular Research by Peruski, Jr. and Peruski (ASM) 1997.

3. Functional Genomics : A Practical Approach Stephen P. Hunt and Rick Livesey, eds., Oxford University Press, 2000.

4. DNA Microarrays : A Practical Approach, Mark Schlena, ed., Oxford University Press.

BT-544 ELECTIVE PAPER 2CH

BT-545 PROJECT 8CH