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UNIVERSITY OF MUMBAI
SYLLABUS FOR MSc BIOTECHNOLOGY (REVISED) PROGRAM: M.Sc COURSE: BIOTECHNOLOGY CREDIT BASED SEMESTER AND GRADING SYSTEM WITH EFFECT FROM ACADEMIC YEAR 2016-17 2016-17
MSc Part I BT 16 17 REV SYLL 1 Syllabus Mumbai University by munotes
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UNIVERSITY OF MUMBAI
SYLLABUS FOR SEM I PROGRAM: M.Sc COURSE: BIOTECHNOLOGY CREDIT BASED SEMESTER AND GRADING SYSTEM WITH EFFECT FROM ACADEMIC YEAR 2016-17
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PSBT 101 Biochemistry Total Credits: 4 (1 lecture / week) Unit I: Storage of Carbohydrates- Structure and Function: Starch and Glycogen. Cellulose, Chitin , Glycosaminoglycans- Heparin, Chondroitin sulphate, Hyaluronic acid Glycoproteins & Glycolipids, Acidic sugars – ascorbic, glucuronic Unit II: Structure-function-Physiological Significance: Opioid peptides- Enkephalins and Endorphins, Lipids- Lipoproteins, Vitamins and co-enzymes -significance in metabolism Prostaglandins Unit III: Inborn errors of metabolism and nutritional disorders: PEM (Kwashiorkar and Marasmus), Obesity, Metabolic disorders-Diabetes; Carbohydrates - glycogen storage disorders, Cori’s disease; Amino acid metabolism- PKU Lipids- e.x. Atherosclerosis; Nucleic acids- Gout, Lesch-Nyhan syndrome Unit IV: Neurobiology-neurochemistry
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Neurophysiology of thermo regulation, Nerve structure, neurotoxins Neurochemistry, Special senses: taste, vision, odor, hearing, Chemistry of thinking References: 1. Guyton, Text book of Medical Physiology, Saunders Publishers, 12th edition, 2010 2. Textbook of Biochemistry with Clinical Correlations, 7th Edition, Thomas M. Devlin, January 2010, 3. Proteins: biotechnology and biochemistry, 1stedition (2001), Gary Walsch, Wiley, USA 4. Biochemical Calculations, 2nd Ed., (1997) Segel Irvin H., Publisher: John Wiley and Sons, New York. 5. Enzymes: Biochemistry, Biotechnology & Clinical chemistry, (2001) Palmer Trevor, Publisher: Horwood Pub. Co., England. 6. Outlines of Biochemistry: 5th Edition, Erice Conn & Paul Stumpf ; John Wiley and Sons, USA 7. Fundamentals of Biochemistry. 3rd Edition (2008), Donald
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Voet & Judith Voet , John Wiley and Sons, Inc. USA 8. Lehninger, Principles of Biochemistry. 5th Edition (2008), David Nelson & Michael Cox, W.H. Freeman and company, NY. 9. Biochemistry: 7th Edition, (2012), Jeremy Berg, Lubert Stryer, W.H.Freeman and company, NY
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PSBT 102: Immunology Credits: 4 (1 lecture / week) Unit I: Advanced Immunology Antigen presentation. Secondary signaling, co-stimulation, Cell signaling in immune response. DC activation, B cells as APC, experimental models in APC. Complements-Lectin pathway Unit II: Molecular immunology Peptide epitopes, T cell B cell antigenic properties, prediction of T and B cell epitopes, Chimeric peptides, polytope vaccines, Major Histocompatibility Complex, Polymorphism transplantation Unit III: Clinical immunology Cytokines: properties, receptor, antagonists, diseases, Therapeutic use of cytokines Experimental immunology: Vaccine development (Recombinant, Combined and polyvalent vaccines), Antigen Antibody reactions in diagnostics. Cancer Immunology Unit IV: Effector mechanisms: Mucosal immunity, Peyer’s patches, gut barriers, oral immunization, Oral tolerance, Cytotoxic response, ADCC, NK cells, CTL, Th, T
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regulation, Immunoregulation, anergy, tolerance, anti idiotype, Mechanisms of antiviral innate immune response References: 1. Immunology 5th ed Janis Kuby, W.H.Freeman & Co Ltd; 5th Revised edition. 2. Fundamental Immunology 5th edition (August 2003): by William E., Md. Paul (Editor) By Lippincott Williams & Wilkins Publishers 4. Essential Immunology, Ivan M. Roit (1994)– Blackwell Scientific Pub, Oxford. 5. Cellular and Molecular Immunology, 3rd ed, Abbas, Saunders; 7 edition (11 June 2011)
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PSBT 103: Molecular Biology Credits: 4 (1 lecture / week) Unit I Chromatin structure and gene expression Transcription in prokaryotes and Eukaryotes Types of RNA polymerases, Promoters, initiation, elongation, termination and anti-termination. Initiation factor, role of transcription factors, Regulation of RNA polymerase Chromatin structure and transcription. Transcription in cell organelles Unit II: Post Transcriptional events RNA processing in eukaryotes: modifications, splicing and splicing machinery, processing of RNA. Editing and amplification Translation in Prokaryotes and Eukaryotes Codon assignments, Wobble hypothesis, initiation, elongation, and termination, Modification folding and transport protein Molecular chaperons in folding, Protein sorting and trafficking using signal proteins
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Unit III: Translation and mobile DNA elements DNA rearrangement, RNAi, regulation of translation. Post translational modification. Mobile DNA elements, Transposable elements in bacteria, Controlling elements in TnA and Tn 10 transposition. SINES and LINES, retrotransposons Unit IV Genomics and Proteomics: an overview omes and omics, Concepts and applications Genome overview at the level of Chromosome (with model organisms as example); Strategies for large scale DNA sequencing- Whole genome analysis techniques, Next generation sequencing methods; Organization, structure and mapping of genomes ( with model organisms as example)
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Reference Books: 1. Genes XI, 11th edition (2012), Benjamin Lewin, Publisher - Jones and Barlett Inc. USA 2. Molecular Biology of the Gene, 6th Edition (2008), James D. Watson, Pearson Education, Inc. and Dorling Kindersley Publishing, Inc. USA 3. Molecular Biology, 5th Edition (2011), Weaver R., McGraw Hill Science. USA 4. Fundamentals of Molecular Biology, (2009), Pal J.K. and Saroj Ghaskadbi, Oxford University Press. India 5. Molecular Biology: genes to proteins, 4th edition (2011), Burton E Tropp Jones & Bartlett Learning, USA 6. Discovering genomics, Proteomics and Bioinformatics (2006) A. Malcoln Campbell, laurie J. Heyer Benjamin Cummings; 2nd edition
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PSBT 104 Biochemical and Biophysical techniques (4 credits 1 lecture / week) Unit I Microscopic techniques : AFM, Fluorescence Microscopy, Confocal microscopy, cryotomy scanning and transmission microscopes, different fixation and staining techniques for EM, freeze-etch and freeze- fracture methods for EM, image processing methods in microscopy, single cell imaging. Environmental SEM, and its advantages Unit II: Spectroscopy Introduction, principle and analysis using UV/visible spectrophotometer, fluorescence spectroscopy, circular dichroism, NMR and ESR spectroscopy , Molecular structure determination using X-ray diffraction, X ray crystallography and NMR, Molecular analysis using light scattering, mass spectrometry and LC-MS, GC-MS, and surface plasma resonance methods, IR.
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Unit III: Chromatography and Radioisotopy Introduction, principle and analysis using HPTLC, HPLC, GLC, Affinity chromatography and its types IEF and 2 D electrophoresis. Applications of the above techniques. Radioisotopes techniques- Radio assay (nature of radioactivity, units, decay, half life, detection/measurement), scintillation counting, safety aspects and applications of radioisotopes. Unit IV: Histochemical and Immunotechniques Antibody generation, blotting techniques, Immuno - precipitation, Flow cytometry and immunofluorescence, detection of antigens in living cells, in situ localization by techniques such as FISH and GISH.
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References Books: 1. Principles and Techniques of Biochemistry and Molecular Biology,7th edition Wilson K.M., Walker J.M., Cambridge University Press, UK (2010), 2. Biochemical spectroscopy. Vol 46 of Methods in Enzymology. (1995) Kenneth Sauer. Academic Press, USA 3. Modern experimental biochemistry 3rd edition Publisher, USA.edition. (2000) Rodney Boyer. Prentice Hall 4. Analytical Biochemistry, 3 edition, (1998), David Holmes, H.Peck , Prentice Hall, UK.
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PSBT 101 Biochemistry: 2 credits 1. Isolation of starch from potato and its estimation by Anthrone method. 2. The isolation and assay of glycogen from liver and skeletal muscles of bird / mammal. 3. Estimation of Vitamin C from fruits. 4. Estimation of Creatinine in blood / urine. Estimation of urate/creatinine ratio to diagnose Lesch-Nyhan syndrome. 5. Chemistry of thinking: a. Study of different regions of brain using models. b. Stroop test and blind spot test. c. Color blindness and optical illusions
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Reference: 1. Biochemical Methods for Agricultural Sciences – Sadasivam and Manikam. Wiley Eastern Limited, 1992.. 2. Practical Clinical Biochemistry Harold Varley, CBS; 6 edition (1 December 2006) 3. An Introduction to Practical Biochemistry (3rd Edition) – David T Plummer. Tata McGraw-Hill Publishing Company Limited, 1992.
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PSBT 102 Immunology: 2 credits 1. Preparation of TAB or any other vaccine. 2. Antigen antibody reactions: one of each type : precipitation (VDRL setup in tube or gels), WIDAL. 3. Quantification of antigen using Single Radial Immuno-Diffusion. 4. Double Immuno-diffusion. 5. Immuno-diffusion and immune-electrophoresis (electrophoresis of serum and then reaction with anti-whole human serum antiserum).. 6. Serum electrophoresis. Reference: 1. Practical immunology, Frank Hay, 4th Edition , Blackwell Science 2. Medical Microbiology, Anantnarayan 3. Introduction to Practical Biochemistry, D.T. Plummer, Tata MacGraw Hill 4. A Handbook of Practical Immunology – G P Talkwar 5. Text Book of Medical Biochemistry, Praful Godkar. Bahalani Publishers.
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PSBT 103 Molecular Biology: 2 credits 1. Extraction of genomic DNA from bacteria and blood 2. Perform transformation of bacteria. 3. Expression of recombinant protein 4. Problems on RE digests / RFLP; Demonstration of ligation reaction. 5. Conjugation 6. Induction of β-Galactosidase in of E. coli (and effect of inducers). Reference: Molecular Cloning a laboratory manual. Sambrook and Russel
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PSBT 104 Biochemical and Biophysical techniques: 2 credits 1. Extraction of pigments from biological sources – plants and/or microorganisms and study of their absorption spectrum in visible light. 2. Verification of Beer lamberts law and calculation of molar extinction coefficient of a coloured chemical compound of known molecular weight. 3. Use of UV spectrophotometry to determine the concentration of protein. 4. Demonstration and interpretation of NMR, HPLC, GC read-outs. 5. Separation of sugars in coconut water using TLC 6. Use of affinity chromatography for purification of antibodies from serum. 7. Visit to a facility housing EM and other analytical tools
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References : 1. An Introduction to Practical Biochemistry (3rd Edition) – David T Plummer. Tata McGraw-Hill Publishing Company Limited, 1992. 2. Principles and techniques in biochemistry, Wilson and Walker
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UNIVERSITY OF MUMBAI
SYLLABUS FOR SEMESTER II PROGRAM: M.Sc COURSE: BIOTECHNOLOGY CREDIT BASED SEMESTER AND GRADING SYSTEM WITH EFFECT FROM ACADEMIC YEAR 2016-17
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PSBT 201 Metabolism: 4 credits (1 lecture/ week) Unit 1 Carbohydrate and lipid metabolism HMP and gamma amino butyrate shunt, glycogenesis and glycogenolysis. Role of B group Vitamins in metabolic pathways. Lipid metabolism: Structure of essential and nonessential fatty acids and FAS complex, Interrelationship between dietary lipids and cholesterol metabolism Unit II Physiological biochemistry Regulation of acid-base balance, types and functions of acid-base buffers, clinical abnormalities associated with acid-base imbalance. Water and Mineral metabolism Unit III Stress metabolism in plants Environmental stresses, salinity, water stress, heat, chilling, anaerobiosis, pathogenesis, heavy metals, radiations and their impact on plant growth and metabolism, criteria of stress tolerance Unit IV Plant and microbial metabolism
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CAM, glyoxalate pathway, photosynthetic formation of hydrogen, Nitrogen fixation and role of nitrogenase. Microbial degradation of xenobiotics and their application in bioremediation References: 1. Biochemistry, L Stryer, Freeman and Co, NY 2. Biochemistry, Zubay, Addison Wesley and Co. 3. Textbook of Physiology, Guyton 4. Physiology, Berne and Levy 5. Harper’s Biochemistry- 27th edition 6. Text book of Human Biochemistry- Ed. G. P. Talwar 8. Essentials of food and nutrition M Swaminathan Vol. II, Applied aspects (1974), Ganesh Pub, Madras 9.Human biochemistry – James Orten and Otto Neuhaus, 10th ed , CV Mosby co London 10. Human nutrition and dietetics-Davidson and Passmore 11. Plant physiology, Salisbury and Ross (2007) CBS publishers and distributors
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12. Biochemistry and Physiology of Plant Hormones, Thomas Moore, Springer Verlag New York 13. Plant Biochemistry- Hans Walter Heldt, 3rd Edition, Elesvier Academic Press 14. Introduction to Plant Biochemistry- T.W. Goodwin and E.L. Mercer 15. Plant Physiology- Devlin, CBS Publishers 16. Plant Biochemistry- Dey, Academic Press, 1999
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PSBT 202: Immunology Unit I. Immunological diseases Autoimmunity mechanisms, altered antigens, Systemic Lupus erythematosus, Graves diseases, Rheumatoid arthritis, Myasthenia Gravis, Multiple sclerosis, animal models of autoimmunity Transplantation immunology, GvH, Immunodeficiency: phagocytic, humoral, CMI, combined HLA association with disease. Unit II: Molecular immunology and animal models Animal models and transgenic animals and their use in immunological studies, Routes of Inoculation , Antibody engineering, Chimeric antibodies, Phage display Unit III: CMI and imaging Cell Cytotoxicity, mixed lymphocyte reaction, Apoptosis, Cytokine expression; Cell cloning, Reporter Assays, In–situ gene expression techniques; Cell imaging Techniques- In vitro and In vivo; Immuno-electron microscopy; In vivo cell tracking techniques; Microarrays Unit IV: Introduction to Psycho-neuro-immunology
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Connections of CNS to immune system and vise versa, Psychological modulation of immunity, stress and immunity, implication for diseases, functional significance – inflammation and acute phase response, role of glucocorticoids, stress response, energy demand and balance, References: 1. Immunology 5th ed Janis Kuby 2. Fundamental Immunology 5th edition (August 2003): by William E., Md. Paul (Editor) By Lippincott Williams & Wilkins Publishers 3. Essential Immunology, Ivan M. Roit (1994)– Blackwell Scientific Pub, Oxford. 4. Cellular and Molecular Immunology, 3rd ed, Abbas 6. Psychoneuroimmunology, Stress, and Infection, By Herman Friedman, Thomas W. Klein, Andrea L. Friedman, CRC Press, 1996
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PSBT 203: Bioprocess technology Unit I: Concepts of basic mode of fermentation processes Strain improvement for increased yield and other desirable characteristics; Upstream processing: Media formulation; Sterilization Bioreactor designs; classification of fermenters; Batch, fed batch and continuous; Conventional fermentation v/s biotransformation; Solid substrate, surface and submerged fermentation; Fermenter design- mechanically agitated; Pneumatic and hydrodynamic fermenters; Large scale animal and plant cell cultivation; Aeration and agitation in bioprocess; Measurement and control of bioprocess parameters; Unit II: Downstream processing Bio separation - filtration, centrifugation, sedimentation, flocculation; Cell disruption; Liquid-liquid extraction; Purification by chromatographic techniques; Reverse osmosis and ultra filtration; Drying; Crystallization; Storage and packaging; Treatment of effluent and its disposal. Unit III: Applications of enzymes in food processing
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Mechanism of enzyme function and reactions in process techniques; Enzymic bioconversions e.g. starch and sugar conversion processes; High-Fructose Corn Syrup; Interesterified fat; Hydrolyzed protein etc. and their downstream processing; baking by amylases, deoxygenation and desugaring by glucoses oxidase, beer mashing and chill proofing; cheese making by proteases and various other enzyme catalytic actions in food processing. Unit IV: Applications of Microbes in food process operations and production Fermented foods and beverages; Food ingredients and additives prepared by fermentation and their purification; fermentation as a method of preparing and preserving foods; Microbes and their use in pickling, producing colours and flavours, alcoholic beverages and acids; Process wastes-whey, molasses, starch substrates and other food wastes for bioconversion to useful products; Bacteriocins from lactic acid bacteria – Production and applications in food preservation.
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References 1. Jackson AT., Bioprocess Engineering in Biotechnology, Prentice Hall, Engelwood Cliffs, 1991. 2. Shuler ML and Kargi F., Bioprocess Engineering: Basic concepts, 2nd Edition, Prentice Hall, Engelwood Cliffs, 2002. 3. Stanbury RF and Whitaker A., Principles of Fermentation Technology, Pergamon press, Oxford, 1997. 4. Baily JE and Ollis DF., Biochemical Engineering fundamentals, 2nd Edition, McGraw-Hill Book Co., New York, 1986. 5. Aiba S, Humphrey AE and Millis NF, Biochemical Engineering, 2nd Edition, University of Tokyo press, Tokyo, 1973. 6. Comprehensive Biotechnology: The Principles, Applications and Regulations of Biotechnology in Industry, Agriculture and Medicine, Vol 1, 2, 3 and 4. Young M.M., Reed Elsevier India Private Ltd, India, 2004. 7. El-Mansi, Bryle CFA. Fermentation Microbiology and Biotechnology, 2nd Edition, Taylor & Francis Ltd, UK, 2007.
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PSBT 204 IPR & Biosafety 4 Credits Unit I: Introduction to Intellectual Property Patents, Trademarks, Copyright & Related Rights, Industrial Design, Traditional Knowledge, Geographical Indications, Protection of New GMOs; International framework for the protection of IP Biotechnology & the law: objective, evolution, basic structure of gene techniques, applications, commercial potential of biotech inventions, rational for IPR protection. Unit II Concept of ‘prior art’ Patenting biotech inventions: objectives, concept of novelty, concept of inventive step, microorganisms, and moral issues in patenting biotech inventions; Patent databases; Searching International Databases; Country-wise patent searches (USPTO, EPO, India etc.); Analysis and report formation
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Unit III :Patent filing and Infringement Patent application- forms and guidelines, fee structure, time frames; Types of patent applications: provisional and complete specifications; PCT and convention patent applications; International patenting-requirement, procedures and costs; Financial assistance for patenting-introduction to existing schemes; Publication of patents-gazette of India, status in Europe and US Patenting by research students, lecturers and scientists-University/organizational rules in India and abroad, credit sharing by workers, financial incentives Patent infringement- meaning, scope, litigation, case studies and examples Unit IV Biosafety Historical Backround; Introduction to Biological Safety Cabinets; Primary Containment for Biohazards; Biosafety Levels of Specific Microorganisms; Recommended Biosafety Levels for Infectious Agents and Infected Animals; Biosafety guidelines - Government of India; Definition of GMOs & LMOs; Roles of Institutional
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Biosafety Committee, RCGM, GEAC etc. for GMO applications in food and agriculture; Environmental release of GMOs; Risk Analysis; Risk Assessment; Risk management and communication; References: http://www.w3.org/IPR/ http://www.wipo.int/portal/index.html.en http://www.ipr.co.uk/IP_conventions/patent_cooperation_treaty.html www.patentoffice.nic.in www.iprlawindia.org/ - 31k - Cached - Similar page http://www.cbd.int/biosafety/background.shtml http://www.cdc.gov/OD/ohs/symp5/jyrtext.htm http://web.princeton.edu/sites/ehs/biosafety/biosafetypage/section3.html
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PSBT 201 Metabolism : 1. Estimation of Niacin by the CNBr method. 2. Isolation of cholesterol and lecithin from egg yolks. 3. Effect of different types on stresses on plant growth using an appropriate plant model system. Stresses: Salinity, water stress, temperature stress (heat / cold), heavy and metal stress. Appropriate controls to be used and data analysed using appropriate software for analysis. 4. Isolation of Rhizobia from root nodules of leguminous plants. 5. Estimation of leghaemoglobin. PSBT 202: Immunology 1. In-vitro demonstration of phagocytosis and calculating phagocytic index. 2. Demonstration of HLA typing. 3. Latex bead agglutination / precipitation test for detection of rheumatoid factor (RF). 4. Separation of lymphocytes on Ficoll-Histopaque, viability count and separation of B and T lymphocytes using Fenwall wool. 5. Assay for plaque forming cells.
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6.Video demonstration or field visit a. Raising antibodies in laboratory animals b. Cell imaging Techniques- In vitro and In vivo; Immuno-electron microscopy; In vivo cell tracking techniques; Microarrays. PSBT 203: Bioprocess technology 1. Demonstration of: Plackett-Burman design for formulation of fermentation media. 2. Pigment production and isolation from a microbial source (yeast, fungi or bacteria) 3. Physico-chemical characterization of an industrial effluents. 4. Detection of different food enzymes by simple tests (amylase, catalase, invertase, papain, pectinase, pepsin). Reference : http://www.ableweb.org/volumes/vol-6/10-miller.pdf 5. Study of pickling process (sauerkraut / pickled cucumbers) with respect to physical, chemical / biochemical and biological changes occurring during the pickling process.
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PSBT 204 IPR & Biosafety 1. Study of a patent and developing a hypothetical patent application for a hypothetical product / process. (To be submit for exam) 2. Writing of SOP for 3-4 laboratory equipment’s / instruments. 3. Use of Microsoft PowerPoint / Corel Draw to prepare a poster (ideally on a topic to be pursued for Sem IV project, otherwise to prepare a poster on a paper from peer-reviewed journal no more than 5 years old – to be brought for practical exam and if possible presented as in a poster presentation at a conference) 4. Compilation of information on recommended biosafety practices in a biotechnology laboratory (demonstration by field visit or video)