M.SC. MICROBIOLOGY SYLLABUS SYLLABUS AT A GLANCE PAPER NO. TITLE OF THE THEORY MARKS PRACTICAL MARKS PAPER Semester I Th-I Biostatistics and Computer 50 P-I 25 Applications Th-II Bioenergetics and Molecular 50 P-II 25 Enzymology Th-III Bioinstrumentation 50 P-III 25 Th-IV Food and Dairy Microbiology 50 P-IV 25 Semester II Th-V Recent trends in Virology 50 P-V 25 Th-VI Molecular Immunology 50 P-VI 25 Th-VII Microbial Physiology 50 P-VII 25 Th-VIII Microbial diversity and 50 P-VIII 25 Extremophiles Semester III Th-IX Enzyme Technology 50 P-IX 25 Th-X Bioprocess Engineering and 50 P-X 25 Technology Th-XI Microbial Genetics 50 P-XI 25 Th-XII Environmental Microbial 50 P-XII 25 Technology Semester IV Th-XIII Recombinant DNA Technology 50 P-XIII 25 Th-XIV Fermentation Technology 50 P-XIV 25 Th-XV Bioinformatics, Microbial 50 P-XV 25 Genomics and Proteomics Th-XVI Pharmaceutical Microbiology 50 P-XVI 25 *Semester IV practical (P-XV and P –XVI) or a research project of 50 marks. M.Sc.Microbiology [Semester I] PAPER TH-I BIOSTATISTICS AND COMPUTER APPLICATIONS Marks 50 Unit –1 Introduction to Biostatistics Basic definitions and applications. Sampling: Representative sample, sample size, sampling bias and sampling techniques. Data collection and presentation: Types of data, methods of collection of primary and secondary data, methods of data presentation, graphical representation by histogram, polygon, ogive curves and pie diagram. Unit –2 Measures of central tendency Measures of central tendency: Mean, Median, Mode. Measures of variability: Standard deviation, standard error, range, mean deviation and coefficient of variation. Correlation and regression: Positive and negative correlation and calculation of Karl- Pearsons co-efficient of correlation. Linear regression and regression equation and multiple linear regression, ANOVA, one and two way classification. Calculation of an unknown variable using regression equation. Unit – 3 Tests of significance Tests of significance: Small sample test (Chi-square t test, F test), large sample test (Z test) and standard error. Introduction to probability theory and distributions, (concept without deviation) binomial, poison and normal (only definitions and problems) Computer oriented statistical techniques. Frequency table of single discrete variable, bubble spot, computation of mean, variance and standard Deviations, t test, correlation coefficient Unit- 4 Introduction to computers and computer applications Introduction to computers: Computer application, basics, organization, PC, mainframes and Super-computers, concept of hardware and software, concept of file, folders and directories, commonly used commands, flow charts and programming techniques. Introduction to Q basic and C. Introduction in MS Office software concerning Word processing, spreadsheets and presentation software. Unit - 5 net working concepts Networking fundamentals, client, server, LAN, WAN, Flp, TelNET, INTERNET, NICNET, WWW, html, e mail, intoduction to MEDLINE, CCOD and PUBMED, for accessing biological information. An introduction to bioinorganic software, C/C++, bioperl, biojava, bioXML, bioORACLE, etc. Introduction to Havard graphics and coral draw. PRACTICAL PAPER P-I BIOSTATISTICS AND COMPUTER APPLICATIONS Marks: 25 1. Representation of Statistical data by a) Histograms b) Ogive Curves c) Pie diagrams 2. Determination of Statistical averages/ central tendencies. a) Arithmetic mean b) Median c) Mode 3. Determination of measures of Dispersion a) Mean deviation b) b) Standard deviation and coefficient of variation c) Quartile deviation 4. Tests of Significance-Application of following a) Chi- Square test b) t- test c) Standard error 5. Computer operations-getting acquainted with different parts of Computers. [DOS] and basics of operating a computer. 6. Creating files, folders and directories. 7. Applications of computers in biology using MS-Office. A] MS-Word B] Excel C] Power Point 8. Creating an e-mail account, sending and receiving mails. 9. An introduction to INTERNET, search engines, websites, browsing and Downloading. References 1. Statistics in biology, Vol. 1 by Bliss, C.I.K. (1967) Mc Graw Hill, NewYork. 2. Practical Statistics for experimental biologist by Wardlaw, A.C. (1985). 3. Programming in C by E. Ballaguruswamy 4. How Computers work - 2000. By Ron White. Tech. Media 5. How the Internet Work 2000 by Preston Gralla Tech. Media. 6. Statistical Methods in Biology - 2000 by Bailey, N.T. J. English Univ. Press. 7. Biostatistics - 7th Edition by Daniel 8. Fundamental of Biostatistics by Khan 9. Biostatistical Methods by Lachin 10. Statisticsfor Biologist by CampbellR.C. (1974) Cambridge University Press, UK. 11. INTERNET – CDC publication, India. PAPER TH-II BIOENERGETICS AND MOLECULAR ENZYMOLOGY Marks 50 Unit – 1 Carbohydrate catabolic pathways and microbial growth on C1 Compounds EMP, HMP, ED, Phosphoketolase pathway, TCA cycle, methylglyoxal bypass. Anaplerotic sequences, catabolism of different carbohydrates, glycerol metabolism, regulation of carbohydrate metabolism, Pasteur effect. Substrate level phosphorylation. Microbial growth on C1 Compounds (Cyanide, Methane, Methanol, methylated amines and carbon monoxide). Unit - 2 Bacterial fermentations (biochemical aspects) and Biosynthesis Alcohol, lactate, mixed acid, butyric acid, acetone-butanol, propionic acid, succinate, methane, and acetate fermentations. Fermentation of single nitrogenous compounds [amino acids] - alanine, glutamate and glycine. Biosynthesis of Purines, Pyrimidines and fatty acids. Unit – 3 Endogenous metabolism and degradation of aliphatic and aromatic compounds. Functions of endogenous metabolism, types of reserve materials, enzymatic synthesis, degradation and regulation of reserve materials - glycogen, polyphosphates and polyhydroxybutyrate (PHB), PHB production and its futuristic applications. Microbial degradation of aliphatic hydrocarbons (microorganisms involved, mon-terminal, bi- terminal oxidation of propane, decane, etc.) and aromatic hydrocarbons and aromatic compounds (via catechol, protocatechuate, meta-cleavage of catechol and protocatechuate, dissimilation of catechol and protocatechuate, homogentisate and other related pathways). Unit – 4 Properties of Enzymes Classification of enzymes into six major groups with suitable examples. Numerical classification of enzymes. Different structural conformations of enzyme proteins. Enzymes as biocatalysts, catalytic power, activation energy, substrate specificity, active site, theories of mechanisms of enzyme action. Mechanism of action of lysozyme, chymotrypsin and ribonuclease. Monomeric, Oligomeric and multienzyme complex, isozymes and allosteric enzymes. Extremozymes - thermostable, solventogenic and non- aqueous enzymes. Ribozymes and abzymes Unit – 5 Enzyme kinetics Importance of enzyme kinetics, factors affecting rates of enzyme mediated reactions (pH, temperature, substrate concentration, enzyme concentration and reaction time). Derivation of Michaelis - Menton equation and its significance in enzyme kinetic studies. Lineweaver-Burke plot, Haldane-Briggs relationship, sigmoidal kinetics steady state kinetics and transient phases of enzyme reaction. PRACTICAL Paper P-II: BIOENERGETICS AND MOLECULAR ENZYMOLOGY Marks 25 1. Isolation and Identification of Reserve food material (Glycogen / polyphosphates, PHB) of B. megaterium and Azotobacter SP. 2. Quantitative estimation of amino acids by Rosen’s method. 3. Quantitative estimation of sugars by Summner’s method. 4. Demonstration of endogenous metabolism in B megaterium or E. coli and their survival under starvation conditions 5. Quantitative estimation of proteins by Folin-Lowry / Biuret method. 6. Production of fungal alpha amylase using solid-state fermentation/ production of protease by bacterial species and confirmation by determining the achromic point. 7. Purification of fungal alpha-amylase or bacterial protease by fractionation, chromatographic techniques and electrophoretic separation. 8. Studies on enzyme kinetics of alpha amylase/Protease [Optimization of parameters viz. Substrate, enzyme concentration, reaction temperature, reaction pH, Km, Vmax and metal ions as activators and inhibitors). References 1. Understanding Enzymes by Trevor Palmer 2. Enzyme Kinetics by Paul Engel. 1977. John Wiley and Sons. Inc., New York. 3. Enzymes by Dixon and Webb, 3 rd Edition 1979. Academic Press, New York 4. Biochemistry by Stryer 5th Edition WH Freeman 2001 5. Laboratory techniques in Biochemistry and Molecular Biology by Work and Work. 6. Principles of Enzyme Kinetics. 1976. By Athel Cornish - Bowden. Butterworth and Co. 7. Fundamentals of Enzymology. 3rd Edition by Price 8. Biochemistry by Chatwal 9.Methods in Enzymology by Drolittle 10.Biochemistry by Garrett 11. Principles of Biochemistry. 2 nd Edition by Horton 12. Biochemistry by Voet. 13. Methods of Biochemical Analysis by David Glick, John Wiley and Sons, New York. PAPER TH-III BIOINSTRUMENTATION Marks 50 Unit –1 Basic laboratory Instruments Principle and working of pH meter, Laminar-air flow. Centrifugation: Types of centrifuge machines, preparative and analytical centrifuges, differential centrifugation, sedimentation velocity, sedimentation equilibrium, density gradient methods and their applications. Unit – 2 Chromatographic techniques Theory, principles and applications of paper, thin layer, gel filtration, ion exchange, affinity, hydrophobic, gas liquid, high pressure/ performance liquid chromatography (HPLC) Unit – 3 Electrophoretic techniques Basic principles of electrophoresis, theory and application of paper, starch gel, agarose, native and denaturing PAGE, isoelectric focusing. Unit – 4 Spectroscopy Spectroscopic techniques, theory and applications of Uv, Visible, IR, NMR, Fluorescence, Atomic Absorption, CD, ORD, Mass, Raman Spectroscopy. Unit – 5 Radioisotopic techniques Use of radioisotopes in life sciences, radioactive labeling, principle and application of tracer techniques, detection and measurement of radioactivity using ionization chamber, proportional chamber, Geiger- Muller and Scintillation counters, autoradiography and its applications. Dosimetry. PRACTICAL PAPER P-III BIOINSTRUMENTATION Marks 25 1. Studies on pH titration curves of amino acids/ acetic acid and determination of pKa values and Handerson-Hasselbach equation. 2. Separation of bacterial lipids/amino acids/sugars/organic acids by TLC or Paper Chromatography. 3. Separation of serum protein by horizontal submerged gel electrophoresis. 4. Study of UV absorption spectra of macromolecules (protein, nucleic acid, bacterial pigments). 5. Quantitative estimation of hydrocarbons/pesticides/organic Solvents /methane by Gas chromatography. 6. Demonstration of PCR, DNA sequencer and Fermenter. 7. Separation of haemoglobin or blue dextran by gel filtration. 8. Paper electrophoresis. 9. Friske dosimetry. References 1. Instrumental Methods of Analysis. 6th Edition by H.H. Willard, L.L. Merritt Jr. and others. 1986. CBS Publishers and Distributors. 2. Instrumental Methods of Chemical Analysis. 1989 by Chatwal G and Anand, S. Himalaya Publishing House, Mumbai. 3. A Biologists Guide to Principles and Techniques of Practical Biochemistry. 1975 by Williams, B.L. and Wilson, K. 4. Spectroscopy. Volume 1. Edited by B.B. Straughan and S. Walker. Chapman and Hall Ltd. 5. Gel Electrophoresis of Proteins- A Practical Approach by Hanes. 6. Chromatography: Concepts and Contrasts- 1988 by James Miller. John Wiley and Sons. Inc., New York. 7. Analytical Biochemistry by Holme. 8. Introduction to High Performance Liquid Chromatography by R. J. Hamilton and P. A. Sewell. 9. Spectroscopy by B.P. Straughan and S. Walker. 10. Practical aspects of Gas Chromatography and Mass Spectrometry 1984 by Gordon M. Message, John Wiley and Sons, New York. 11. Gel Chromatography by Tibor Kremmery. Wiley Publications. 12. Isotopes and radiations in Biology by C.C. Thornburn, Butterworth and Co. Ltd., London. 13. The use of radioactive isotopes in the life sciences by J.M.Chapman and G.Ayrey, George Allen and Unwin Ltd., London. PAPER TH-IV FOOD AND DAIRY MICROBIOLOGY Marks 50 Unit – 1 Industrial Food fermentations Starter cultures their biochemical activities, production and preservation of the following fermented foods. a. Soy sauce fermentation by Moulds b. Fermented vegetables – Saurkraut c. Fermented Meat – Sausages d. Production and application of Bakers Yeast e. Application of microbial enzymes in food industry Unit – 2 Quality assurances in foods Foodborne infections and intoxications; bacterial with examples of infective and toxic types –, Clostridium, Salmonella, Shigella, Staphylococcus, Campylobacter, Listeria. Mycotoxins in food with reference to Aspergillus species. Quality assurance: Microbiological quality standards of food. Government regulatory practices and policies. FDA, EPA, HACCP, ISI. Unit –3 Food preservation methods Radiations - UV, Gamma and microwave Temperature Chemical and naturally occurring antimicrobials Biosensors in food industry. UNIT – 4 Microbiology of cheese and beverage fermentation. Microbiology of fermented milk products (acidophilus milk, yoghurt). Role of microorganisms in beverages – tea and coffee fermentations. Vinegar Fermentation Unit - 5 Advanced Food Microbiology Genetically modified foods. Biosensors in food, Applications of microbial enzymes in dairy industry [Protease, Lipases]. Utilization and disposal of dairy by-product - whey. PRACTICAL PAPER - P-IV FOOD AND DAIRY MICROBIOLOGY Marks 25 1. Production and estimation of lactic acid by Lactobacillus Sp. Or Streptococcus Sp. 2. Extraction and estimation of diacetyl. 3. Sauerkraut fermentation 4. Isolation of food poisoning bacteria from contaminated foods, Dairy products 5. Extraction and detection of afla toxin for infected foods. 6. Preservation of potato/onion by UV radiation 7. Production of fermented milk by Lactobacillus acidophilus. 8. Rapid analytical techniques in food quality control using microbial Biosensors. References 1. Food Microbiology. 2nd Edition By Adams 2. Basic Food Microbiology by Banwart George J. 3. Food Microbiology: Fundamentals and Frontiers by Dolle 4. Biotechnology: Food Fermentation Microbiology, Biochemistry and Technology. Volume 2 by Joshi. 5. Fundamentals of Dairy Microbiology by Prajapati. 6. Essentials of Food Microbiology. Edited by John Garbult. Arnold International Students Edition. 7. Microbiology of Fermented Foods. Volume II and I. By Brian J. Wood.Elsiever Applied Science Publication. 8. Microbiology of Foods by John C. Ayres. J. Orwin Mundt. William E. Sandinee. W. H. Freeman and Co. 9. Dairy Microbiology by Robinson. Volume II and I. 10. Food Microbiology: Fundamentals and Frontiers. 2nd Edition by Michaell P. Doyle, Larry R. Beuchat and Thomas I. Montville (Eds.), ASM Publications. 11. Bacterial Pathogenesis A Molecular Approach. 2 nd Edition. 2001 by Abigail A.Salyers and Dixie D. Whitt. ASM Publications. 12. Advances in Applied Microbiology by D. Pearlman, Academic Press. [ SEMESTER II ] PAPER TH-V RECENT TRENDS IN VIROLOGY Marks 50 Unit –1 Classification and Morphology of Viruses Cataloging the virus through virus classification schemes of ICTV / ICNV. Morphology and ultra-structure of viruses. Virus related agents, viroids and prions. Unit – 2 Cultivation and assay of viruses Cultivation of viruses using embryonated eggs, experimental animals and cell cultures (Cell-lines, cell strains and transgenic systems). Purification of viruses by adsorption, precipitation, enzymes, serological methods – haeme agglutination and ELISA. Assay of viruses – Physical and Chemical methods (Electron Microscopy and Protein and Nucleic acids studies.) Infectivity Assays (Plaque and end-point) Genetic analysis of viruses by classical genetic methods. Unit – 3 Viral Multiplication Mechanism of virus adsorption and entry into the host cell including genome replication and mRNA production by animal viruses, mechanism of RNA synthesis, mechanism of DNA synthesis, transcription mechanism and post transcriptional processing, translation of viral proteins, assembly, exit and maturation of progeny virions, multiplication of bacteriophages. Unit – 4 Pathogenesis of Viruses Host and virus factors involved in pathogenesis, patterns of infection, pathogenesis of animal viruses Adenovirus, Herpes virus, Hepatitis virus, Picorna virus, Poxvirus and Orthomyxovirus, pathogenesis of plant [TMV] and insect viruses [NPV]. Host cell transformation by viruses and oncogenesis of DNA and RNA viruses. Unit – 5 Control of Viruses and Emerging Viruses