Microbial Biotechnology

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Microbial Biotechnology

  1. 1. M.Sc. Microbial Biotechnology Proposed Syllabus for Session 2009- 2010, 2010-11 SEMESTER- I P-I Microbiology and Immunology P-II Microbial Genetics P-III Microbial Biochemistry P-IV Analytical Techniques PRCTICAL PAPER – 1: PERTAINING TO THEORY PAPER PI & PII. PRACTICAL PAPER – 2: PERTAINING TO THEORY PAPER PIII & PIV. 2ND SEMESTER P-V MICROBIAL METABOLISM P-VI GENETICS AND METABOLIC ENGINEERING P-VII BIOPROCESS AND FERMENTATION ENGINEERING P-VIII ENZYMOLOGY AND ENZYME TECHNOLOGY PRCTICAL PAPER – 3: PERTAINING TO THEORY PAPER PV & PVI. PRACTICAL PAPER – 4: PERTAINING TO THEORY PAPER PVII & PVIII. 3RD SEMESTER P-IX INDUSTRIAL MICROBIOLOGY – I (HEALTH, FOOD AND METABOLITES) P-X INDUTRAIAL MICROBIOLOGY –II (ENVIRONMENTAL BIOFUELS, CHEMICALS AND BIOMASS) P-XI BIOSTATAISTICS AND COMPUTER APPLICATIONS P-XII BIOSAFETY, BIOETHICS AND INTELLECTUAL PROPERTY RIGHTS PRACTICAL – 5: PERTAINING TO THEORY PAPER, P – IX & P-X PRACTICAL – 6: PERTAINING TO THEORY PAPER, P-XI & P- XII 4TH SEMESTER P-XIII ENTERPRENEURSHIP, PROJECT MANAGEMENT AND QUALITY ASSURANCE P-XIV BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
  2. 2. PRACTICAL PAPER – 7, PERTAINING TO THEORY PAPER, P-XIII & P- XIV DISSERTATION Paper – I Microbiology & Immunology M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section - A 1. Introduction and history of Microbiology: Microscopy- light microscopy, fluorescent microscopy, electron microscopy, Phase contrast 2. Microbial groups: Prokaryotes & Eukaryotes: structure, function & classification. 3. Viruses: Bacteriophages, cyanophages, plant & animal viruses – A brief account.
  3. 3. Section – B 1. Pure culture techniques: isolation & maintenance of microbes, strain improvement & media optimization 02. Microbial Growth characteristics: growth curve, kinetics of Growth, Factors affecting growth, measurement of growth. 03. Microbial spoilage: Toxins, microbial infections, a brief account including prevention and control. Section – C 01. Introduction to immunology, Historical Background, innate immunity, adaptive immunity, cells & organ of the immune system, antigens, Antibodies, 02. Cell mediated immune response and its mechanism: Humoral response & its mechanism. Complement system. 3. Transplantation, MHC, auto immunity, Hypersensitivity. Section – D 1. Hybridoma techniques & monoclonal antibody production, Application of monoclonal antibodies. 2. Vaccine development & production and immune-potentiation. 3. Techniques of cell mediated and humoral immune response. Suggested Readings (Latest Editions) : 1. Betty Forbes, Daniel Sahm, Alice Weinfield, Bailey – Scott’s Diagnostic Microbiology, 12th Edition Mosby, 2007
  4. 4. 2. Gerald Collee J, Andrew G Fraser, Barrie P Marmion, Mackie and McCartney’s Practical Medical Microbiology , Elsevier . 2006 3. Elmer W Koneman et al., Koneman’s Color Atlas and Text Book of Diagnostic Microbiology, 6th Edition Lippincott Willams and Wilkins, 2005 4. Patrick R. Murray, Ken S. Rosenthal, Michael A Pfaller. Medical Microbiology , 5ht ed. (Philadelphia: Elsevier/ Mosby , 2005 5. Harvey, R.A., P.C. Champe, and B.D. Fisher. Microbiology 2nd Edition, LIPPINCOTTS’S ILLUSTRATED REVIEWS (Philadelphia : Lippincott. Williams & Wilkins, 2007) 6. Text Book of Bacteriology – N. C. Day & T. K. Day 7. Parasitology – K.D. Chatterjee. 8. Text Book of Microbiology – Chakarbourty. 9. Bacteriology / Mycology / Virology : 10. Microbiology – Prescott, et. al 11. Microbiology – Bernard D. Davis, et. al 12. Immunology , A. Goldsby , J, Kindt, Osborne, 4ht Edition 2000, W.H. Freeman. 13. Immunology & Immunopatholog by Stewart. 14. Cellular and Molecular Immunology by Abul K. Abbas et al. 15. Text Book of immunology by Barret. 16. Essential immunology by Roitt. Brostoff, Male, Harcourt Brace & Company (5th Edition), Mosby (6th Edition ). 17. Immunology by Kuby by Richard A Godlsby , Thomas J. Kindt. Barbara A. Osborne, Freeman & Company Mosby Publishers. 18. Molecular Biotechnology by Bernard R. Glick & Jack . J. Pasternak. 19. Immunology by Kuby.
  5. 5. P-II Microbial Genetics M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section – A 1. Genome Organization:- Types of genetic material : DNA- A, B-,Z, and triplex DNA, RNA, organization of bacteriophage genomes-PhiX174, lambda, T4, Mu, fine structure of chromatin, bacterial and eukaryotic genome organization : Role of nuclear matrix in chromosome organization and function: Matrix binding proteins. 2. Heterochromatin and Euchromatin: DNA melting an buoyant density: DNA re- association kinetics (Cot curve analysis): Repetitive and unique sequences: Satellite DNA; Nucleosome phasing: DNase I hypersensitive regions: 3. Genome Replication and Repair: - Replication initiation, elongation and termination in prokaryotes and eukaryotes; Enzymes and accessory proteins: Fidelity: Polymerase chain reaction, Replication of single stranded circular DNA: Gene stability DNA repair – enzymes: Photo reactivation: Nucleotide excision repair: Mismatch correction: SOS repair. Section – B
  6. 6. 4. Prokaryotic and Eukaryotic Transcription: Prokaryotic Transcription: Transcription Unit; RNA polymerase, Promoters, Operators, Regulatory elements, Initiation: Termination – Rho- dependent and independent : Anti – termination. Transcriptional regulation – Positive and negative: 5. Eukaryotic Transcription Process: Transcriptional RNA polymerases, transcription factors, regulatory elements, RNA polymerase structure and assembly ;RNA polymerase I, II, III; eukaryotic promoters and enhancers; General Transcription factors: Activators and repressor 6. Transcript Processing: - Processing of tRNA and rRNA; co- transcriptional and post – transcriptional modifications; 5’ Capping polyadenylation, nuclear export of mRNA, mRNA stability, Splicing; RNA editing, Catalytic RNAs. Section – C 7. Translation: - Prokaryotic and Eukaryotic Translation process: Genetic code. degeneracy of genetic code, altered genetic code- mitochondria, Termination codons; Isoaccepting tRNA; Wobble hypothesis. 8. Ribosome, tRNAs, mechanism of prokaryotic and eukaryotic translation processes; initiation, elongation and termination, the translation machinery, co- translational and post- translational modifications of proteins; Transport of proteins and molecular chaperones; Protein folding, stability; Protein turnover and degradation 9. Regulation of gene expression in prokaryotes and eukaryotes:- regulatory signal elements, hLh motifs, activators and inhibitors of protein synthesis, the operon concept, Lac, Trp Ara,, His operons, positive, negative and compound control, Attenuation, quorum sensing, spatial and temporal regulation of Gene expression in eukaryotes. DNA Methylation & Imprinting. Section – D 10. Mutations: Oncogenes and Tumor suppressor genes:- Nonsense, missense and point mutations; intragenic and Intergenic suppression; Frame shift mutations; Physical, ,chemical and biological mutagens; Transposition – Transposable genetic elements in prokaryotes and eukaryotes; Mechanisms of transposition; Role of transposons in mutation . 11. Viral and Cellular oncogenes; Tumor suppressor genes from humans; Structure, function and mechanism of action of pRB and p53 tumor suppressor proteins;
  7. 7. Activation of oncogenes and dominant negative effect; Suppression of tumor suppressor genes; Oncogenes as transcriptional activators. 12. Gene Disruption and Gene Targeting: - Homologous Recombination: Holliday junction, FLP/FRT and Cre/Lox recombination gene targeting, gene disruption Rec A and other recombinases; Antisense and Ribozyme Technology; Molecular mechanism of antisense molecules, inhibition of splicing, polyadenylation and translation, disruption of RNA structure and capping, strategies for designing ribozymes and antisense RNA, Application of Antisense and ribozyme technologies in medical science. Suggested Readings (Latest Editions) : 1. Biotechnology – Fundamentals of Microbial Genetics and Genetic Engineering (Vol. 12) by R.H. Rehm and G. Reed, Veriag Press, NY, 1992. 2. Gene Cloning by T.A. Brown, Van Nesterland and Rainold, NY, 1996. 3. Genes VII by B. Lewin, John Wiley & Sons, NY, 4. Genetic Fundamentals & Genetic Engineering by H.R. Rehm and G. Reed, Vol-12 VCH, 1993. 5. Genetics for Microbes by A. Brainbridge, Balckkis & Sons Ltd. New York, 1987 6. Molecular Biology by D. Grialder, Narosa Publishing House, New Delhi, 1989 7. Molecular Biology of the Cell by B. Alberts, D. Bray, J.Lewis , M. raft, K. Ropbertis and J. Watson, Gerland Publish ICE, 1988. 8. Molecular Cloning (Vol. 1,2, & 3) J. Sambrook, E.F. Fristsch and T. Maniatis, Cold Spring, Harbor, NY, 1989 9. Microbial Biotechnology by D. Drilder, Narosa Publishing House New Delhi, 1989 10. Molecular Biotechnology : Principles & Applications of recombinant DNA by Bernard R.Click and Jack J. Pasternak, ASM Press, Washington, D.C. 1997.
  8. 8. 11. Principles of Gene Manipulation by R.W. Old and S. B. Primrose, Blackwell Scientific Publications, 1997. 12. Principles of Genetic by Gardner and D.P. Snusted, John Wiley & Sons, NY, 1988. 13. Recombinant DNA by J.D. Watson, J. Tooz and K. Kurtz, Scientific American Books, NY, 1988 14. Recombinant DNMA Methodology by R. Wu, L. Grossman and K. Maidenme (ed.) Academic Press, San Diegd, 1989 15. Micrbial Genetics- 1997 Freifielder. 16. Molecular Genetics – T.A. Brown Van Nesteorland & Raink , New York, 1997 17. Genes to Clones – Winnacker, 1997.
  9. 9. P-III Microbial Biochemistry M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section – A 1. Chemical basis of life : Composition of living matter ; Water – properties, pH, pK, acids, bases, Buffers, weak bonds, covalent bonds, ionization and hydrophobicity; Emergent properties of biomolecules in water; Biomolecular hierarchy; Macromolecules; Molecular assemblies; atomic and molecular dimensions, space filing and ball and stick models. 2. Biological Macromolecules (Amino acids and Proteins) :- Amino acids and peptides; classification , chemical reaction and physical properties; Peptides and covalent structure of proteins. 3. Elucidation of primary and higher order structures; Evolution of protein structure, hierarchy in structure ; Structure- function relationships in model proteins like ribonuclease A, myoglobin, hemoglobin, chymotrypsin etc; Tools to characterize expressed proteins; Ramachandran map. Section –B
  10. 10. 4. Sugars:- Sugars; mono, di and polysaccharides; Suitability in the context of their different functions – cellular structure, energy storage, signaling; Glycosylation of other biomolecules- glycoproteins and gycolipids, 5. Lipids: classification, structure and properties of important members of storage and membrane lipids; lipoproteins. 6. Lipo-proteins, Glycoproteins, Glycolipids etc. Section - C 7. Biological Macromolecules (Nucleic acids and heterocyclics): Types, structural features, methods for compositional analysis of Nucleosides, nucleotides, nucleic acids; structure, diversity, and function; Heterocyclic compounds and secondary metabolites in living systems; pigments, isoprenoids 8. Vitamins: Water soluble and fat soluble vitamins. Hormones :- hormones, their structures and functions. 9. EnzymesIntroduction and scope, enzymes coenzymes, Nomenclature, Mechanism of Catalysis, Chemical and Physical properties of enzyme; general principles of catalysis; Quantitation of enzyme activity and efficiency; Enzyme characterization and Michaelis- Menten kinetics; Relevance of enzymes in metabolic regulation, activation , inhibition and covalent modification ; Single substrate enzymes; Inhibitors and activators; Multi-substrate systems; Effect of pH and temperature; Allosteric enzymes. Section-D 10. Enzymes: Introduction and scope, enzymes coenzymes, Nomenclature, Mechanism of Catalysis, Chemical and Physical properties of enzyme; general principles of catalysis; Quantitation of enzyme activity and efficiency. 11. Enzyme characterization and Michaelis- Menten kinetics; Relevance of enzymes in metabolic regulation, activation, inhibition and covalent modification; Single substrate enzymes; Inhibitors and activators; Multi-substrate systems; Effect of pH and temperature; Allosteric enzymes. 12. Organization of Biomembrane and Cell Wall:- Properties of lipid aggregates, micelles, liposome’s, structure and properties, membrane proteins and their function, fluid mosaic model, membrane mediated transport, membrane
  11. 11. equilibrium and permeability, chemical, physical composition and biosynthesis of cell wall components. Suggesting Reading (Latest Editions) : 1. Fundamentals of Enzymology. N.Price, and L. Stevens, 1999. 3rd Edition. Oxford University Press Inc. New York 2. Fundamentals of Biochemistry, 3rd Edition by D. Voet, J.G.Voet, C.W. Pratt. 2004, John Wiley and Sons, New York. 3. Principles of Biochemistry, A.L. Lehninger. D.L. Nelson and M.M. Cox, 4ht Edition. W.H. Freeman and Company, 2004 4. Biochemistry, G. Zubay, 4th Edition, 1998. Brow Dubuque, Lowa, 5. Biochemistry, L. Stryer, 5ht, Edition.2002. W.H. Freeman and Co. 6. Harper’s Biochemistry, R.K. Murray, D.K Grammer, P.A. Mayes, V.W. Rodwell, 25th Edition. 2000. Appleton and Lange. 7. Enzymes – Dixon & Webb.
  12. 12. P- IV Analytical Techniques M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section – A 1. Basic Techniques: - Buffers, Methods of Cell Disintegration: Physical chemical & biological methods, detergents and membrane proteins; Dialysis, Ultrafiltration and other membrane techniques. 2. Spectroscopy Techniques & X- ray diffraction: - UV, Visible and Raman Spectroscopy: Theory and application of Circular Dichroism, Fluorescence, NMR, PMR, ESR, Plasma Emission spectroscopy MALDI-TOF; Mass spectrometry. 3. X-ray diffraction Section – B 4. Chromatography Techniques TLC and Paper chromatography; methods for macromolecule separation – Gel permeation, Ion exchange; hydrophobic; Reverse- phase and Affinity chromatography. 5. HPLC and FPLC, Criteria of protein purity.
  13. 13. 6. Electrophoretic techniques :- Theory and application of Polyacrylamide and Agarose gel electrophoresis; Capillary electrophoresis;; Disc gel electrophoresis; Gradient electrophoresis; 2D Gel Electrophoresis Pulsed field gel electrophoresis. Section – C 7. Centrifugation : Basic Principles; Mathematics and theory (RCF, Sedimentation coefficient etc); Types of centrifuge- Microcentrifuge, High speed and Ultracentrifuges; Preparative centrifugations; Differential and density gradient centrifugation; Application (Isolation of cell components); Analytical centrifugation ; Determination of molecular weight by sedimentation velocity and sedimentation equilibrium methods. 8. Radioactivity:- Radioactive and stable isotopes; Pattern and rate of radioactive decay; Units of radioactivity; Measurement of radioactivity; Geiger- Muller counter; Solid and Liquid scintillation counters (Basic principle, instrumentation and technique); Brief idea of radiation dosimetry; Cerenkov radiation. 9. Autoradiography : Measurement of stable isotopes; Falling drop method ; Applications of isotopes in biochemistry; Radiotracer techniques; Distribution studies ; Isotope dilution technique; Metabolic studies; Clinical application ; Radioimmunoassay. Section – D 10. Techniques used in Functional Genomics;- Protein sequencing methods, Nucleic acid sequencing techniques Maxam- Gilbert and Sanger’s dideoxy method, automated sequencing PCR, Flourescent In – situ hybridization, Blotting methods; Southern, Northern, Western, Dot Blotting. 11. Advanced Techniques:- Protein crystallization, Theory and methods; API – electrospray, DNA and peptide Synthesis. 12. Enzyme and cell immobilization techniques. Suggested Readings (Latest Editions) : 1. Biotechnology – Fundamentals of Microbial Genetics and Genetic Engineering (Vol. 12) by R.H. Rehm and G. Reed Veriag Press, NY 1992 2. Genes VII by B. Lewin, John Wiley & Sons, NY, 2001
  14. 14. 3. Genetic Fundamentals & Genetic Engineering by H.R. Rehm and G.Reed , Vol 12 VCH, 1993. 4. Genetics for Microbes by A. Brainbridge, Balckkis & Sons Ltd. New York, 1987. 5. Molecular Biology by D. Grialder, Narosa Publishing House, New Delhi, 1988. 6. Molecular Biology of the Cell by B. Ablerts. D. Bray, J. Lewis, M.Raft, K. Rolbertis and J Watson, Gerland Publish ICE, 1988 7. Molecular Cloning (Vol. 1,2, & 3) Sambrook, E.F. Fristsch and T. Maniatis, Cold Spring Harbor, NY, 1989 8. Microbial Genetics by D. Drilder, Narosa Publishing House , New Delhi, 1989 9. Molecular Biotechnology: Principles & Applications of Recombinant DNA by Bernard R. Click and Jack J. Pasternak, ASM Press, Washington, D.C. 1997. 10. Principles of Genetic by Gardner and D.P. Snusted, John Wiley & Sons, NY, 1988. 11. Recombinant DNA by J.D. Watson, J. Tooz and K. Kurtz, Scientific American Books, NY, 1988 12. Microbial Genetics – 1997 Freifielder. 13. Molecular Genetic – T.A.Brown Van Nesteorland & Raink, New York, 1997 14. Molecular Biology and Biotechnology, J.M. Walker and E.B. Gingold, 3rd Edition 1993. Royal Chemistry Society. 15. Molecular Cell Biology, Lodish, Berk, Zipursky, 4th Edition. 2000. W.H. Freeman. 16. Cell and Molecular Biology, Gerald Karp, 3rd Edition, 2002, John Wiley and Sons. 17. Advanced Molecular Biology, M. Twynmen, 1999. Viva Books Pvt. Ltd. 18. Cell and Molecular Biology by De Robertis, E.D.P. De Robertis, E.M.F Latest edn., B.I. Waverly Pvt. Ltd, New Delhi. 19. Chromatin & Gene Regulation by B. M. Turner, 1st Edition , Wiley – Blackwell, 2002. 20. Freifelder D,Physical Biochemistry . Application to Biochemistry and Molecular Biology, 2nd Edition W.H, .Freeman & Company , San Fransisco, 1982. 21. Keith Wilson and John Walker, Principles and Techniques of Practical Biochemistry , 5ht Edition Cambridge University Press, 2000 22. D.Holme & H. Peck, Analytical Biochemistry , 3rd Edition , Longman,1998.
  15. 15. 23. R. Scopes. Protein Purification – Principles & Practices, 3rd Edition, Springer Verlag,1994 24. Selected readings from Methods in Enzymology, Academic Press.
  16. 16. Practical I: pertaining to Theory Paper I and II Max. Marks: 100 Practical Time: 60 hours Time: 4 hours 1. Isolation of Chromosomal DNA from E. coli 2. Isolation of Chromosomal DNA from plant cells 3. Isolation of plasmid DNA 4. Determination of Tm and % (G+C) of DNA 5. Spectrophotometric analysis of DNA/protein & RNA 6. Agarose gel electrophoresis of DNA 7. Use of basic instruments in Microbiology (Light microscope, pH meter, autoclave, Laminar Flow chamber, Deionized water purification systems, centrifuge, electronic balance, Spectrophotometer). 8. Staining of bacteria, yeast and fungi. 9. Purification of mixed cultures by streaking technique 10. Determination of viable count 11. Correlation of viable counting and optical density of cultures 12. Isolation of microbes from environment (soil, water, skin bread, milk) 13. Isolation of extremophiles from environment 14. Bacteriophage screening 15. Preparation of complex and synthetic medium 16. Sterilization of liquid and solid items 17. Storage (short & long term) of microbes 18. Collection, handling and storage of clinical samples 19. Culture identification of bacteria (E.coli, Salmonella, Shigella, Staphylococcus, Streptocossus) 20. Culture identification of fungal pathogens (Candida, Aspergilllus) 21. Identification of pathogens by PCR technology 22. Antibiotic sensitivity of clinical pathogens 23. Animal handling 24. Routes of Injections 25. Drawing blood from animals 26. TLC and DLC for blood samples. 27. Determination of cell number (viable/non-viable) 28. Ficoll density gradient separation of cell types. 29. Raising antibodies in animals. 30. Immunoassays. 31. Collection, handling and storage of clinical samples
  17. 17. Practical II: for Paper III and IV Max. Marks: 100 Practical Time: 60 hours Time: 4 hours • Qualitative and quantitative assay of sugars • Qualitative and quantitative assay of proteins • Qualitative and quantitative assay of lipids • Qualitative and quantitative assay of nucleic acids • Separation of proteins on non-denaturing gels. • Separation of proteins on denaturing gels • Gel exclusion chromatography • Ion-Exchange chromatography • Affinity chromatography • Operation of HPLC • Operation of IR • Operation of NMR • Operation of Atomic absorption spectroscopy • Demonstration of Polyacrylamide gel electrophoresis • Demonstration of 2D- gel electrophoresis
  18. 18. P- V Microbial Metabolism M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section - A 1. Carbohydrate metabolism: glycolysis, biochemistry of alcohol and lactic acid fermentation. 2. Citric acid cycle, pentose phosphate pathway, EDP pathway, 3. Disaccharide and polysaccharide metabolism, gluconeogenesis, regulation of carbohydrate metabolism. Section – B 4. Oxidative phosphorylation / respiration: electron transport chain, Photorespiration, microsomal electron transport. 5. Biochemistry of lipid metabolism; biosynthesis and catabolism of acids regulation of fatty acid metabolism. 6. Neutral lipids, phospholipids cholesterol, glycolate cycle. Section – C 7. Amino acid metabolism; biosynthetic families of amino acids, ammonia ion assimilation into amino acid by glu and gln, regulation acid synthesis.
  19. 19. 8. Degradation of amino acids ; oxidative deamination of glutamate, carbon atom degradation, amino acid is major metabolic intermediates, C3, D4,, and C5 families, amino acid degradation to succinyl CoA, Leucine , Phenyl alanine and tyrosine degradation. 9. Urea cycle, nitrogen fixation and nitrogenase complex. Section – D 10. Nucleotide metabolism; Purine and Pyrimidine nucleotide Biosynthesis, synthesis of deoxyribonucleotides, 11. Degradation of purines, regulation of nucleotide metabolism. 12. Photosynthesis: Photosynthetic pigiments, cyclic and monocyclic electron flow, oxygen evolution system, Calvin cycle, C3, C4, mode of photosynthesis. RECOMMENDED READING (Latest Editions) : 1. Biochemistry by Voet, D and J.G. Voet, John Wiley and Co. 1990 2. Lehinger Principles of Biochemistry , 3rd Edition. By David L. Nelson and Michael M. Cox Printed in India by Repubic Press Pvt. Ltd. New Dehli For Machmillen Press/Publishes 2000 3. Biochemistry by Stryer, LK, CBS Publishers and Distribution, New Delhi, 1995. 4. Catherine Desktop Molecular Modellar3, by James M.C. Carbbe, John R. Abbey and Oxford University Press. 5. Fundamentals of Nitrogen Fixation, by Postage J.R. Cambridge University Press, Oxfords, 1982.
  20. 20. P- VI Genetic and Metabolic Engineering M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section – A 1. Tools of Genetic Engineering: Scope and history of Genetic Engineering, Tools in genetic engineering, DNA modifying enzymes, restriction endonucleases, reverse transcriptase, RNaseA, RNase H, alkaline phosphatatase, Polynucleotide kinase, SI Nuclease, exonucleses; DNA polymerases, Klenow enzyme, T4 DNA polymerases. 2. DNa ligase; Cohesive and blunt end ligation, Linkers, Adaptors, Homopolymeric tailing; labeling of DNA; Nick translation, Radioactive and non- radioactive probes, Hybridization techniques ; Northern, Southern and colony hybridization, Fluorescence in situ hybridization; Chemical Synthesis of DNA. 3. Vectors used in Gene Cloning; plasmids- pBR322; Bacteriophages, lambda; M13 mp vectors; pUC19 and Bluescript vectors, phagemids; Insertion and Replacement vectors; Cosmids; Artificial chromosome vectors (YACs’ BACs) Yeast vectors, Shuttle vectors. Section – B 4. High Expression Vectors; Principles in maximizing gene expression, Properties of expression vectors; pMal; GST; pET – based vectors ; Protein purification ; His – tag; GST- tag; MBP- tag etc. inclusion bodies; Methodologies to reduce
  21. 21. formation of inclusion bodies, chimeric constructs, processing of recombinant proteins; Purification refolding and characterization of recombinant proteins 5. Cloning Methodologies; Insertion of Foreign DNA into Host Cells ; Transformation; Construction of libraries; Isolation of mRNA and total RNA; cDNA and genomic libraries; cDNA and genomic cloning; 6. Expression cloning; Jumping and hopping libraries; Southwestern and Farwestern cloning ; Protein – protein interactive cloning and Yeast two hybrid system; Phage display ; Section - C 7. PCR and its Applications ; Primer design ; Fidelity of thermostable enzymes; DNA polymerases; Types of PCR- multiplex, nested, reverse transcriptase, real time PCR, touchdown PCR, hot start PCR, colony PCR, Proof reading enzymes and SOEing; PCR in molecular diagnostics; 8. Mutagenesis and Protein engineering: PCR based mutagenesis, Site- Directed Mutagenesis and Protein Engineering. 9. Selection and Identification of Recombinant Organisms: Direct and indirect methods, methods of Recombinant screening and selection; immunological methods; Sequencing methods; Enzymatic DNA sequencing ; Chemical sequencing of DNA ; Automated DNA sequencing ; RNA sequencing; Section - D 10. Application of Genetic Engineering: Expression of industrially important products in bacteria yeast. DNA marker technology, DNA foot printing and DNA fingerprinting. 11. Generically engineered biotherapeutics and vaccines and their manufacturing, Potential risks and guidelines on R- DNA (NIH, DBT and FDA guidelines) 12. Metabolic Engineering : - Metabolism, metabolic flux analysis, strategies to increase/alter metabolite flow, metabolic control analysis; Importance of metabolic Engineering : Completion of partial pathways giving novel products (Erwinia herbicola), transfer of entire biosynthetic pathway (Trp biosynthesis to E.coli and overproduction of Trp in C glutamicum), Creating new products (indigo and melanin in E coli) , redirecting metabolite flow (Increased Thr in bacteria and Lys
  22. 22. in crops; Increased CephC production); Metabolic engineering of PHAs and Carotenoids. Suggested Reading(Latest Editions) : 11. Biotechnology – Fundamentals of Microbial Genetics and Genetic Engineering (Vol. 12) by R.H. Rehm and G. Reed, Veriag Press, NY, 1992. 12. Gene Cloning by T.A. Brown, Van Nesterland and Rainold, NY, 1996. 13. Genes VII by B. Lewin, John Wiley & Sons, NY, 14. Genetic Fundamentals & Genetic Engineering by H.R. Rehm and G. Reed, Vol-12 VCH, 1993. 15. Genetics for Microbes by A. Brainbridge, Balckkis & Sons Ltd. New York, 1987 16. Molecular Biology by D. Grialder, Narosa Publishing House, New Delhi, 1989 17. Molecular Biology of the Cell by B. Alberts, D. Bray, J.Lewis , M. raft, K. Ropbertis and J. Watson, Gerland Publish ICE, 1988. 18. Molecular Cloning (Vol. 1,2, & 3) J. Sambrook, E.F. Fristsch and T. Maniatis, Cold Spring, Harbor, NY, 1989 19. Microbial Biotechnology by D. Drilder, Narosa Publishing House New Delhi, 1989 20. Molecular Biotechnology : Principles & Applications of recombinant DNA by Bernard R.Click and Jack J. Pasternak, ASM Press, Washington, D.C. 1997. 21. Principles of Gene Manipulation by R.W. Old and S. B. Primrose, Blackwell Scientific Publications, 1997. 22. Principles of Genetic by Gardner and D.P. Snusted, John Wiley & Sons, NY, 1988. 23. Recombinant DNA by J.D. Watson, J. Tooz and K. Kurtz, Scientific American Books, NY, 1988 24. Recombinant DNMA Methodology by R. Wu, L. Grossman and K. Maidenme (ed.) Academic Press, San Diegd, 1989
  23. 23. 25. Micrbial Genetics- 1997 Freifielder. 26. Molecular Genetics – T.A. Brown Van Nesteorland & Raink , New York, 1997 27. Genes to Clones – Winnacker, 1997. 28. Metabolic Engineering by S. Y. Lee and E.P. Popoutsakis (Eds.) M. Dekekr, NY, USA. 29. Metabolic Engineering by G. N. Stephanopoulous, A.A. Aristidon, J. Neilson, Academic Press, USA.
  24. 24. Paper – VII Bioprocess and Fermentation Engineering M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section – A 1. Introduction: Fundamentals of bioprocess development. 2. Bio-reactor design, Designing criteria of a bioreactor, types of bioreactors. 3. Bioprocess control and monitoring; In line and on line Instruments / probes in process control, computer control in bioreactors. Section – B 4. Sterilization in bioreactors: kinetics of batch, continuous and fibrous filter sterilization. 5. Aeration and Agitation: Agitation is shake flask as tube rollers, factor affecting agitation as aeration in shake flasks, Fluid Rheology. 6. Transport phenomenon is bioreactors: Mass transfer co-efficient (k for gases, liquids, Determination of KLa by various methods, factors affecting kLa , heat transfer coefficient Dimensionless groups. Section – C
  25. 25. 7. Scale – UP : Scale up of bioprocess 8. Fermentation economics: cost determination in bioprocesses, capital investment and raw materials etc. 9. Mathematical modeling: mathematical modeling in bioprocesses. Section – D 10. Pilot and industrial scale bioreactors- design and development. 11. Neural networking: neural networking in bioprocesses. 12. Downstream processing in bioreactors: filtration, centrifugation, extraction, solid-liquid extraction, liquid-liquid extraction, finishing steps in bioproduct development. RECOMMENDED READING (Latest Editions) : 1. Biochemical Engineering by A. Aiba, A.E. Humphery and N.F. Mkili University of Tokyo, 1973. 2. Biotechnology Vol : 1, 2 and 7 by Moo Young, Pergamoon Press, NY, 1985. 3. Comprehensive Biotechnology Vol. 2 by Moo Young, Pergamnon Press, NY, 1985. 4. Fundamentals of Biotechnology by P. Prave, F. Eaus, W. Sitting and D.A. Sukatech, ECH Weinheim, 1987. 5. Biochemical Engienering Fundamentals by J.E. Bailley and D.F. Ollis, McGraw Hill Co., NY, 1986. 6. Methods in Industrial Microbiology by B. Sikyata, Ellis Horwood Ltd., London, 1983. 7. Principles of Fermentation Technology by P.F. Stanbury and A. Whitaker, Pergamnon Press, NY, 1984. 8. Principles of Microbial and Cell Cultivation by S.J. Pirt. Black Well Scientific Publications, London, 1983.
  26. 26. Paper – VIII Enzymology and Enzyme Technology M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section – A 1. Introduction to enzymes and how it works, Specificity of Enzyme: Basic concept and types. Physical structure of enzyme – the monomeric and oligomeric enzymes. Concept of Active Site- Ogston’s experiment, Lock and Key and Induced Fit hypotheses. 2. Kinetics of Enzyme activity- Introduction of Chemical Kinetics, Kinetics of Single substrate enzymes catalysed reactions – Wilhelmy’s and Brown’s work, Henri and Michaelis and Menten derivations, Briggs and Haldane Modification, 3. Significance of the M-M equation and Km. Modification of the M-M equation – Lineweaver – Burk, Eadie–Hofstee, Hanes and Eisenthal & Cornish Bowden; Kinetics of multi – substrate reactions. Sigmoidal Kinetics – Hill and Adair equations for co-operativity.
  27. 27. Section – B 4. Basic concept of catalysis – activation energy barrier and the transition state theory. Catalytic mechanisms in Chemistry and in Enzymes – acid – base, covalent and electrochemical reactions. 5. Factors enhancing the catalytic efficiency of enzymes proximity and orientation, oribital steering, distortion and strain. 6. Functional group involved in the catalytic mechanisms – a) Amino acid b) Cofactors – prosthetic groups, coenzymes, co- substrates, c) metal ions in enzyme function – their role, metal activated and metallo enzymes, ternary complexes. Section - C 7. Regulation of Enzyme Function: Models proposed to explain the mechanism of functioning (MWC and KNF) structural aspects of asparatate: carbamoyl transferase, role of allosteric enzymes in metabolic regulation (feedback inhibition). 8. Enzymes in organized systems and their role in control of function: Multienzyme systems – basic concepts, significance and types with examples, Structural aspects of pyruvate dehydrogenase and fatty acid synthetase. 9. Isoenzymes – basic concepts, types with examples and their significance to the cells and to the medical field. Section – D 10. Enzymes in Medical Diagnosis – Lactate dehydrogenase, malate dehydrogenase, Fructose-6-biphosphatase, acid and alkaline phosphatase, Glucose 6 phosphate dehydrogenase. 11. Enzyme therapy – cancer, Genetic disease, clotting disorders, Neonatal jaundice, surgery, toxicity, artificial cells, enzyme carriers, enzyme probe. 12. Industrial applications – catalysts in the manufacturing and other conversion processes immobilization of enzyme in bioprocess as analytical tools (enzyme electrode). Suggested Readings (Latest Editions) :
  28. 28. 1. Enzyme Nomenclature – International Union of Biochemists (IUB), Academic Press. 2. Understanding Enzymes – Trevor Palmer, Ellis Horwood Publications. 3. Fundamentals of Enzymologoy – N.C. Price and L. Stevens, Oxford University Press. 4. Enzymes - P. Boyer, Academic Press. 5. The Enzymes – M. Dixon and E.C. Webb. 6. Advances in Enzymology – Series edited by N.O. Kaplan, Academic Press. 7. Enzyme Structure and Mechanism – A. Fersht, Freeman , USA. 8. Enzyme Biotechnology – Tripathi.
  29. 29. Practical III: Pertaining to Theory papers V and VI 1. Isolation of microbes from environment (soil, water, skin bread, milk) 2. Isolation of extremophiles from environment 3. Culture identification of bacteria ( E.coli, Salmonella, Shigella, Staphylococcus, Streptocossus) 4. Antibiotic sensitivity of clinical pathogens 5. Preparation of competent cells 6. RAPD on bacterial DNA 7. Isolation and estimation of DNA from bacteria/ yeast / fungi / bacteriophage 8. Isolation and estimation of RNA / mRNA from bacteria/ yeast/ fungi 9. Restriction digestion (complete and partial) of DNA 10. Cloning and expression of a gene in E. coli 11. Amplification of DNA by PCR 12. Southern Hybridization 13. Isolation of DNA, RNA and plasmids and staining with ethidium bromide. 14. 10 Electrophoretic separation of DNA fragments and their recovery from gel slabs. 11. Performance of Southern and Northern blotting. 15. Transformation of E. coli with plasmids by chemical and electroporation. 16. Purification of mRNA by using immobilized technique. 17. Mapping of restriction sites on a plasmid. 18. Cloning using restriction enzyme generated cohesive/blunt ends. 19. Sequencing of DNA fragement with Maxam-Gillbert method. 20. Qualitative and Quantitative analysis of Proteins and Nucleic acids by U.V. Spectrophotometer. 21. Determination of protein in pressence of nucleic acid by spectrophotometer method.
  30. 30. Practical IV: Pertaining to Theory Paper VII and VIII Max. Marks: 100 Practical Time: 60 hours Time: 4 hours 12. Screening of microbes for production of industrially important enzymes. 13. Optimization of conditions for optimal production of enzyme: Media composition, Incubation temperature, Aeration, Incubation time. 14. Assay of enzymes (amylases, lipases, proteases) 15. Effect of pH and temperature on enzyme activity 16. Substrate specificity and efficiency of enzymatic catalysis 17. Enzyme/cell immobilization in different matrices 18. Protein purification by Gel exclusion chromatography 19. Protein Purification by Ion-Exchange chromatography 20. Protein Purification by Affinity chromatography 21. Introduction to laboratory scale bioreactor, its fabrication and evaluation of performance 22. Isolation of useful microorganisms from natural samples 23. Growth of microorganisms and estimation of Monod parameters 24. Batch, fed batch and continuous cultures: Estimation of Monod parameters, Pure and mixed cultures, Production of secondary metabolites in synthetic and complex industrial media 25. Determination of KLa value
  31. 31. P-IX Industrial Microbiology – 1 (Health, Food, Enzymes) M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section – A 1. Primary and Secondary metabolites of industrial importance, 2. Techniques involved in screening / detection of industrially important metabolites from microbes 3. Biosynthesis and fermentation process involve in: Role of Bioproducts as Neutraceutics : Mycoproteins, Phycoproteins, High Fructose syrups. Section – B 4. Antibiotics (Penicillin, Streptomycin, Tetracycline), Alkaloids (ergot, lysergic acid), 5. Biotransformations (Steroids, chirals), Vaccines (BCG, DPT, polio, hepatitis) 6. Therapeutic Proteins (Interferons, Insulin, Streptokinase, Erythropoietin) Bacteriophages. Section – C
  32. 32. 7. Fermentative production of Beer, wine, whisky organic acids- citric, lactic, acetic acids, vinegar. 8. Production of Cheese, Yoghurt, Probiotics, Traditional Fermented foods 9. Food Additives: lipids, vitamins, flavours. Section - D 10. Pharma and Therapeutic enzymes 11. Enzymes in detergent 12. Enzymes in textile & leather industries. Suggested Readings (Latest Editions) : 1. Publisher: American Society Microbiology, 3rd edition (J2007) ISBN – 10, 1555814077 ISBN-13:978-1555814076, Food Microbiology: Fundamentals and Frontiers by Dolye. 2. Publisher : American Society Microbiology, 1st Edition (2005) ISBN – 10 1555813089 ISBN- 13 : 978-1555813086, Food Microbiology : An Introduction by Montville 3. Publisher: Academic Press: 2nd edition (2004) ISBN – 10: 0125506562, ISBN – 13: 978 -01255016564, Environmental Microbiology: a Laboration Manual by Ian L. Pepper and Charles P. Gerba. 4. Publisher: Academic Press: 1st edition (2003) ISBN – 10: 0120164477, ISBN-13; 978-0120164479, Advances in Food & Nutrition Research by Steve Taylor. 5. Publisher: Academic Press: 1st edition (2000) ISBN – 10: 0124975704, ISBN- 13: 978 – 01254975705, Environmental Microbiology by Raina M. Maier. Ian I. Pepper and Charles P. Gerba. 6. Publisher : CRC 2nd edition (2001) ISBN – 10 : 082470536x, ISBN- 13, ; 978-0824705367, Applied Dairy Microbiology , by Elmer H. Math and James Steele.
  33. 33. P-X Industrial Microbiology – II (Environment, Biofuels, Chemicals, Biomass) M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section - A 1. Bioremediation: Types and sources of pollution – Inorganic, organic and biotic. Clinical example of air, water and land pollutions. Environmental impact of pollution and measurement methods. Composting of organic wastes, microbial bioremediation of oil spills. 2. Waste water treatment – sewage treatment and common industrial effluent treatment. Concept of bioremediation (in – situ and ex – situ); Bioremediation of toxic metal ions – bisorption and bioaccumulation principles. Concept of phytoremediation. Microbial biotransformatioln of pesticides and xenobiotics . 3. Bio-leaching: Microbial leaching of ores – direct and indirect mechanisms. Biodegradation of Polyaromatic hydrocarbons, Desulphurization of coal, Biodesulfurization of petroleum. Section – B
  34. 34. 4. Classification , Characteristics and conversion methods of bio- mass and solid wastes,Bio – mass combustion: Principles and mechanism, furnaces and their design. 5. Chemical conversion of bio – mass and agricultural waste into pulp, paper, various other products and chemicals. Conversion of agricultural wastes into energy chemicals. 6. Utilization of Milling by–products of cereals, pulses and other bearing materials for foods, feed and chemicals production, Biomass as Baker’s yeast, SCPs, Mushrooms. Section – C 7. Biomass and Bio– fuels: Plant biomass (Cellulose, starch, pectin, gum materials), Animal biomass (chitin, milk whey, Slaughter house wastes), Microbial biomass (algal blooms – in fresh and sea waters, Fungal – Mushrooms, yeasts and bacterial fermentation biomass wastes) 8. Concepts of single cell proteins, probiotics and their application. Biomass feed stocks to fermentation. 9. Microbial production of fuels; alcohols, hydrogen and methane. Microbial production of polymers (xanthan gums) Section – D 10. Biofertilizers : Biofertilizers and their importance in corp productivity . Algal and fungal (mycorrhizae) biofertilizers, Bacterial rhizobial , free living N2 fixers and phosphate solublizing bacteria, their significance and practice 11. Biopesticides: Bacterial (Bt pesticides), fungal (Trichoderma). Viral biopesticides – Baculovirus, NPV insecticides. 12. Production of biofertilizers and biopesticides for large scale application.. Suggested Readings (Latest Editions) : 1. Publisher: American Society Microbiology, 3rd edition (J2007) ISBN – 10, 1555814077 ISBN-13:978-1555814076, Food Microbiology : Fundamentals and Frontiers by Dolye. 2. Publisher : American Society Microbiology, 1st Edition (2005) ISBN – 10 1555813089 ISBN- 13 : 978-1555813086, Food Microbiology : An Introduction by Montville
  35. 35. 3. Publisher: Academic Press: 2nd edition (2004) ISBN – 10: 0125506562, ISBN – 13: 978 -01255016564, Environmental Microbiology: a Laboration Manual by Ian L. Pepper and Charles P. Gerba. 4. Publisher: Academic Press: 1st edition (2003) ISBN – 10: 0120164477, ISBN-13; 978-0120164479, Advances in Food & Nutrition Research by Steve Taylor. 5. Publisher: Academic Press: 1st edition (2000) ISBN – 10: 0124975704, ISBN- 13: 978 – 01254975705, Environmental Microbiology by Raina M. Maier. Ian I. Pepper and Charles P. Gerba. 6. Publisher: CRC 2nd edition (2001) ISBN – 10 : 082470536x, ISBN- 13, ; 978-0824705367, Applied Dairy Microbiology , by Elmer H. Math and James Steele. 7. Comprehensive Biotechnology (All volumes) Ed. Young. M.Y. Pub: Pergmon Press.
  36. 36. P – XI Biostatistics and Computer applications M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section – A 1. Fundamental concepts in Biostatistics : applied probability: exploratory data analysis and statistical inference; Probability and analysis of one two way samples : discrete and continuous probability models; 2. Expectation and variance; Central limit theorem; Inference; Hypothesis; Critical region and error probabilities. 3. Statistical Tools : Tests for proportion ; Equality of proportions; equality of means of normal populations (variance known, variance unknown); Chi – square test for independence ; P – value of the statistic; Confidence limits; Introduction to one way and two – way analysis of variance; Data transformations Section – B 4. Fundamentals of computers; Definition of computers, computer organization memory, number systems, input and output devices. 5. Types of computers, network computers, working with mainframe, personal computer 6. Computer Networking: LAN, WAN, intranet, internet, TCP/IP, http, ftp, web page, web site and World Wide Web, network securities, applications of computers in biological sciences.
  37. 37. Section - C 7. Operating Systems : Need of OS, its functions, features, functions of common OS; 8. Functions of OS: Windows 9. Functions of OS: Linux. Section - D 10. Programming Languages: Programming Language C: character set, identifiers and keywords data types, 11. Operator and expression control statements, switch break, continue statements 12. Function arrays, pointers, Suggested Readings (Latest Editions) : 1. Wayen W. Biostatistics : A foundation for Analysis in the Health Sciences, 8th Edition, Wiley 2004 2. Prem S. Mann, Introductory Statistics, 6th Edition , Wiely, 2006 3. John A. Rice: Mathematical Statistics and Data Analysis, 3rd Edition, John A. Rice Duxbury Press, 2006 4. Campbell and Heyer, Discovering Genomics, Proteomics, & Bioinformatics, 2nd Edition, Benjamin Cummings, 2002 5. Cynthia Gibas and Per Jambeck, Developing Bioinformatics Computer Skill, 1st Edition , O’Reilly Publication, 2001 6. Object Oriented Programming in C ++, by Robert Lafore, Techmedia, 2002 7. The C ++ Programming Language by Stroustrup, Addison Wesely, 2001 8. Functions of OS : Windows 9. Function of OS : Linux
  38. 38. P-XII Biosafety, Bioethics & IPR M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section – A 1. Introduction: General Introduction to IPR (Patents, Plant Breeders’ rights) Trade, Marks, Industrial design, trade secrets (or undisclosed information) integrated circuit designs. 2. Copyright and right related to copyright, Patent Claims, the legal decision – making process. 3. Ownership of Tangible and intellectual process, Basic requirements of patentability, patentable subject matter, novelty and the public Domain : Non- obviousness, Special issues in Biotechnology Patents : Disclosure requirements, Collaborative research, competitive research, Microbial biotechnology, Foreign Patents. Section – B 4. Patenting Principle, International Standards & Patent Validity (Neem and Relaxins). 5. Patent Litigation: Substantive aspects of patent litigation, Procedural aspects of patent litigation.
  39. 39. 6. Recent Development in Patent System and Patentability of Biotechnology invention IPR issues of the Indian context. Section – C 7. IPR Regime in the Digital Society; International Treaties and Conventions: Business software Patents, Domain Name Dispute and Resolution. 8. Patenting of biological processes, patenting regulations in India, USA & Europe, Buda pest treaty & convention. 9. Public Acceptance issues for biotechnology: Case studies / experiences from developing and developed countries, Section - D 10. Biotechnology and hunger: Challenges for the Indian Biotechnological research and industries. Biosafety : The Cartagena protocol on biosafety 11. Biosafety management: Key to the environmentally responsible use of biotechnology, 12. Ethical implications of biotechnological products techniques, Social and ethical implication of biological weapons Suggested Readings (Latest Editions) : 1. Asia Law House, Hyderabad, 2001, Law of Intellectual property by Myneni.S.R. 2. Butterworth’s London 2001. Intellectual property law by Davis. Jennifer 3. Universal Law Publishing, Delhi 2001, Intellectual property: Patents trade marks and allied rights by Cornish W. R. 4. Sign KC : Intellectual Property Rights on Biotechnology , BCIL, New Delhi
  40. 40. Practical V: Pertaining to theory papers Paper IX and X Max. Marks: 100 Practical Time: 60 hours Time: 4 hours 1. Yoghurt Fermentation 2. Cheese Fermentation 3. Wine fermentation 4. Purification of antimicrobial metabolites from a microbe. 5. Isolation and partial purification of industrially important enzymes 6. Fermentative production of organic acids and ethanol 7. Production of alcoholic beverages 8. Medium optimization for bacterial growth by statistical method 10. Biomass estimation by different methods 11. Isolation of Biofertilizer microbes by biological enrichment method 12. Production of microbial biofertilizers and biopesticides 13. Efficacy testing for biofertilizers (nodulation test for rhizobia) and biopesticides 14. Estimation of BOD & COD 15. Testing for microbiological quality of potable water (Coliform test) 16. Microbial degradation of organic matter 17. Testing for effect of chemical pesticides on soil microbial respiration 18. Testing for microbial biodegradation of pesticides
  41. 41. Practical VI: Pertaining to theory papers Paper XI and XII Max. Marks: 100 Practical Time: 60 hours Time: 4 hours 1. Searching of National Patent databases 2. Drafting of National Patent application 3. Searching of International Patent databases 4. Drafting of International Patent applications 5. Generating Global Technology Strategic Report (GSTR) 6. Other exercise related to theory course 7. Representation of statistical data by a) Histograms b) Ogive curves c) Pie diagrams 8. Determination of statistical averages/central tendencies a) Arithmetic mean b) Median c) Mode 9. Tests of significance-Applicaton of following a) Chi-square test b) t-test c) Standard error 10. Computer operations-getting acquainted with different parts of computer, DOS and basics of operating systems 11. Creating files, folders and directories 12. Applications of computer in biology using MS-Office a) MS word b) Excel c) Power point 13. Creating an e-mail account, sending and receiving mails.
  42. 42. P-XIII Entrepreneurship, Project Management and Quality Assurance M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section – A 1. Entrepreneurship: Need scope and philosophy, Creativity and Entrepreneurship. 2. Entrepreneurship competencies and traits, factors affecting Entrepreneurship development, Introduction to entrepreneurship. Barriers to entrepreneurship, community and entrepreneurship. 3. Functions of entrepreneurship, classification of entrepreneurship. Section – B 4. Forms of Project Organization: Project Planning, Developing a Project, Control. 5. Human aspects of project management, per – requisites for successful project implantation, project management of project network time estimation, determination of critical path. Scheduling when resources are limited. 6. PERT and CPM models network cost – system, venous techniques of market survey.
  43. 43. Section – C 7. Plant and equipment financial procedure and their significance. 8. Books of accounts. 9. Financial and fund flow analysis. Section – D 10. Introduction to quality: quality assurance and testing of products 11. Elemental knowledge of marketing and Sales Management, Marketing Strategies. 12. Packaging and advertising. Suggested Readings (Latest Editions) : 1. Enterpreneurship : Rajeev Ray (2000) Oxford University. 2. Peter F Drucker. Innovation and Entrepreneurship, Harper & Row , 1985 3. Prasanna Chandra – Projects: Preparation Appraisal and Superimplementation. Tata Mc- Graw – Hill Co. Ltd. 4. Enterpreship Development Small Business Enterpreship (2004) Purnima M. Charantimath. 5. Project Management Clofford F Gray, TATA Mc Graw Hill. 6. The Management & Control Quality James R . Erans.
  44. 44. Paper – XIV Bioinformatics and Computation Biology M. Marks: 80 Lectures to be delivered: 60 Time allowed: 3 hours Pass Marks: 35% (Theory and Practicals separately) Instructions for the paper setters The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have two questions from the respective sections of the syllabus and carry 15 marks each. Section E will consist of 10 short answer type questions which will cover the entire syllabus uniformly and will carry 20 marks in all. Instructions for the candidates 1. Candidates are required to attempt one question each from sections A, B, C and D of the question paper and the entire section E. 2. The use of scientific calculators is allowed. Section – A 1. Introduction to Bioinformatics : what is bioinformatics use of computer for biological research 2. Overview of web servers and software : NCBI, EBI, PDRB, 3. Search engines: Pubmed, ENTREZ, Expasy and SRS. Section - B 4. Biological database : Genbank, EMBL, EBI, DDBJ, PDRB, 5. Primary and secondary database of Nucleic acid: Genbank, SCOR, and Protein databases: Swiss PROT,PIR.SCOP,CAT, prosite, PDB. 6. Composite database OWL, metabolic pathway database: KEGG, Ecocyc, MetaCyc Section - C 7. Computation Biology : Analysis of Nucleic acid and protein sequences, sequence comparison algorithm scoring schemes, BLOSUM, PAM 250 8. Sequence and Genome analysis : Local alignment , global alignment, FASTA, BLAST, (Blast P, Blast N, Blast X) and similarity searching scores and their statistical interpretation. 9. Functional genomics strategies for generating EST and full length inserts, EST clustering and assembly, statistical analysis of EST data microarray. Section - D 10. Functional Proteomics: Protein family and domain databases (PROSITE) Pfam, SMART), algorithms for multiple sequence alignment (CLUSTAL x and CLUSTAL w) and comparison with sequence databases, Biological motifs (PSSMs, HMMs) , finding protein – coding regions.
  45. 45. 11. Prediction of macromolecular structure ( protein secondary and tertiary structures) and properties, software for displaying macromolecular structures (Port Param, PREDATOR ) 12. Protein modeling software: RASMOL, MOLMOL,INSIGHT, EMBOSS, and their applications. Suggested Readings (Latest Editions) : 1. Introduction to Bioinformatics By A. M. Lesk, Oxford University Press, USA, 2005 2. Bioinformatics Basics: application in biological science and medicine. By Hooman Rashidi and L. K. Buehler, CRC Press, 2005. 3. Proteins and Proteomics : a lab manual by R. J sompson , Cold Sprin Harbor, US, 2003 4. Bioinformatics : Genes , proteins and Computers by C A Orengo and J M Thornton, Taylor and Francis, US 2003 5. Bioinformatics Computing By Bryan Bergeron, Pearson Education, US 2002 6. Bioinformatics sequence and genes analysis by Mount, D.A. 2001 7. Bioinformatics methods and Protocols by Baxevanis, A. D. 2001 8. Introduction to protein Architecture; The structural biology of proteins By A M. Lesk, Oxford University Press, UK , 2000 9. Bioinformatics : A practical guide Analysis of genes and proteins 2nd ed, 10. Let Us C by Y. Kanitkar BPB Publications 11. Computer Fundamentals by P.K. Sinha
  46. 46. Practical Paper VII Pertaining to Theory Paper: XIII and XIV Max. Marks: 100 Practical Time: 60 hours Time: 4 hours 1. Retrieval of sequences using ENTREZ 2. Sequence analysis using BLAT, Align, Lalign 3. Multiple sequence alignment and Phylogenetic analyzing using Clustal, ClustalW 4. Studying 3D structure using RASMOL 5. Homology Modeling using Swiss PDB – Hb, Protease 6. Calculation of Phi and Psi angle - Hb, Protease 7. Docking: protein-protein; protein-small molecules 8. Potential energy calculation of regular structures 9. To mutate protein and energy minimization using Swiss PDB viewer 10. Gene prediction – Gene D’cefer 11. Adhesion protein prediction – Sea path 12. Comparative proteomics and genomics – Proteome calculator 13. Protein annotation – PLHost Dissertation

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