------Department of Microbiology

CURRICULUM AND SYLLABI FOR MSc MICROBIOLOGY PROGRAM

The Department of Microbiology, Central University of Tamil Nadu offers a two-year full-time MSc Degree Program in Microbiology.

Purpose: To impart knowledge and training across the different fields in Microbiology to be able to equip students for academics/industry.

Eligibility: Bachelor’s degree in Microbiology, Applied Microbiology, Human Genetics, Nutrition and Dietetics, Botany, Zoology, Biochemistry, Biotechnology, Life Sciences, Dairy Sciences, Agriculture and Horticulture, Home Science, Veterinary Sciences, Fisheries Sciences, Public Health, and Allied Health Sciences from a recognized university or equivalent. Candidates should have secured a minimum of 60% marks or 6.5 CGPA (on a 10-point scale) in the qualifying degree examination for General Category, 55% marks or 6.0 CGPA (on a 10-point scale) for OBC (non-creamy layer) and 50% aggregate marks or 5.5 CGPA (on a 10-point scale) for SC/ST/PWD candidates.

Credits: The program consists of courses with a total of 72 credits.

Core Course (CC): 60 credits Elective Course (EC): 12 credits

Number of Semesters, Course Distribution: The program comprises 4 semesters; each semester has courses equivalent of 20 credits.

Project Work & Dissertation: Compulsory, with 6 credits in Semester IV to impart research training.

MSc Microbiology: Semester 1 COURSE TYPE NUMBER OF SL. NO. COURSE NAME CODE OF COURSE CREDITS I Semester: Theory 1 General Microbiology CMB101 CC 3 2 Cell & Molecular Biology CMB102 CC 3 3 Microbial Biochemistry CMB103 CC 3 4 Immunobiology CMB104 CC 3 5 Microbial Genetics CMB105 CC 3 6 Microbial Physiology CMB106 CC 3 I Semester: Practicals 1 Practical Microbiology I PMB101 CC 2 2 Practical Microbiology II PMB102 CC 2

MSc Microbiology: Semester 2 COURSE TYPE NUMBER OF SL. NO. COURSE NAME CODE OF COURSE CREDITS II Semester: Theory 1 Bacteriology & Mycology CMB201 CC 3 2 Virology & Parasitology CMB202 CC 3 3 Food & Industrial Microbiology CMB203 CC 3 4 Agricultural Microbiology & Plant Pathology CMB204 CC 3 5 Methods in Gene Technology CM205 CC 3 6 Biosafety, Bioethics & IPR CMB206 CC 3 II Semester: Practicals 1 Practical Microbiology III PMB201 CC 2 2 Practical Microbiology IV PMB202 CC 2

MSc Microbiology: Semester 3

COURSE TYPE NUMBER OF SL. NO. COURSE NAME CODE OF COURSE CREDITS III Semester: Theory 1 Computational Biology & Biostatistics CMB301 CC 3 2 Marine Microbiology CMB302 CC 3 3 Environmental Microbiology CMB303 CC 3 4 Pharmaceutical Microbiology CMB304 CC 3 5 Medical Microbiology CMB305 CC 3 6 Microbial Technology CMB306 CC 3 III Semester: Practicals 1 Practical Microbiology V PMB301 CC 2 2 Practical Microbiology VI PMB302 CC 2

MSc Microbiology: Semester 4 COURSE TYPE NUMBER OF SL. NO. COURSE NAME CODE OF COURSE CREDITS IV Semester: Theory 1 Biomedical Techniques EMB401 EC 3 2 Diagnostic Microbiology EMB402 EC 3 3 Drug Design and Discovery EMB403 EC 3 4 Nanotechnology Applications in Microbiology EMB404 EC 3

COURSE TYPE NUMBER OF SL. NO. COURSE NAME CODE OF COURSE CREDITS IV Semester: Project Work 1 SEEC/Project/Dissertation CMB401 CC 6 Total Number of Credits 84

MSc Microbiology: Semester 1 GENERAL MICROBIOLOGY Course Code: CMB101 Total Number of Credits: 03 General Microbiology course is aimed at introducing the history and development of microbiology. The contents aims to help students understand the history, biology, and growth and control of microorganisms. Beginners of the course are rightly exposed to the foundation of microbiology, which would lead them towards progressive advancement of the subject.

Unit 1: Scope of microbiology, Ancient microbiology - Refutation of a biogenesis: Discovery of penicillin: Discovery of vaccination: One-gene one-enzyme hypothesis, Contribution of scientists – Leeuwenhoeck, Edward Jenner, Alexander Fleming, Joseph Lister, Robert Koch, Louis Pasteur, Hargobind Khorrana. Modern Microbiology: Landmark achievements in 20th century. Microbial taxonomy - Definition and systematics, Nomenclatural rules and identification. Haeckel’s three kingdom classification, Whittaker’s five kingdom approach - Woese domain system. Major characteristics used in taxonomy: Morphological, physiological and metabolic, genetic and molecular taxonomy. Bergey’s Classification of bacteria.

Unit 2: Differences between prokaryotic and eukaryotic cell. Biology of bacteria - cell structure, size, shape, arrangement membrane, cell wall, cytoplasmic inclusions, mesosomes, flagella and motility, slime, glycocalyx, capsule, pili, chemotaxis, endospore - biology of fungi, structure, physiology and classification – biology of yeast – reproduction - virus (bacteriophages) structure, life cycle (lytic and lysogenic) – biology of algae – mycoplasma – prions.

Unit 3: Microbial nutrition: Microbial nutrient requirements, macro-nutrients, micro-elements, growth factors, sources of nutrients, nutritional classification of bacteria: phototroph, chemotroph, autotroph, heterotroph, photoautotroph, photoheterotroph, chemoautotroph, chemoheterotroph – nutritional patterns of pathogens – saprophytes – auxotroph.

Unit 4: Extremophiles: Diversity of microorganisms of arctic, antarctic and hydrothermal vents – Archaeal biology - acidophile, alkaliphile, anaerobe, cryptoendolith, halophile, hyperthermophile, hypolith, lithoautotroph, metal-tolerant microbes, oligotroph, osmophile, piezophile, polyextremophile, psychrophile/cryophile, radio-resistant, thermophile, thermoacidophile, xerophile – mechanism of extremophiles.

Unit 5: Cultivation and control of microbes: Types of growth media (natural, synthetic, complex, enriched, selective- definition with examples), pure culture methods (streak plate, spread plate, pour plate, stab culture, slant culture). Anaerobic (thioglycollate, anaerobic chamber, Robertson’s media, microaerophilic), liquid shake culture of aerobic bacteria, Control of microbes - sterilisation, disinfection, antiseptic, tyndalization, pasteurization: physical - dry heat, moist heat, UV light, ionizing radiation, filtration, HEPA filter, chemical methods.

References 1. Christopher J. Woolverton, Linda Sherwood, Joanne Willey Prescott LM Harley JP and Klein DA (2016). Microbiology (10th edition) McGraw-Hill Education. 2. Schaechter M and Leaderberg J (2009). The Desk encyclopedia of Microbiology (3rd edition) Elseiver Academic press, California. 3. John Webster (January 25, 2007). Introduction to Fungi. (3rd edition). Cambridge University Press, Cambridge. 4. Nester, E.W., Roberts, C.V. and Nester, M.T. (2015). Microbiology, A human perspective.(8th Edition) McGraw-Hill Education (January 6, 2015) 5. Madigan MT Martinko. JM and Parker J Brock TD (2017). Biology of Microorganisms. (15th edition). Pearson 6. Holt, J.S., Kreig, N.R., Sneath, P.H.A and Williams, S.T. Bergey’s Manual of Determinative Bacteriology (9th Edition), Williams and Wilkins, Baltimore. 7. Mara D. and Horan N. (2013). The Handbook of Water and Waste-Water Microbiology. (3rd edition) Academic CRC Press.

MSc Microbiology: Semester 1 CELL & MOLECULAR BIOLOGY Course Code: CMB102 Total Number of Credits: 03 Cell and Molecular Biology aims to introduce the fundamentals and basic biology of life. The contents will help students understand the features and differences between a prokaryotic and eukaryotic cell. It will elaborate the central dogma of the cell i.e., gene expression viz. transcription and translation across both prokaryotes and eukaryotes.

Unit 1: The molecules of life, the architecture of cells: Cell theory, Emergence of modern cell biology, Structure of prokaryotic and eukaryotic cells- cell wall, cell membrane, cell organelles - organization and functions, Cell cycle events - Molecular cell biology - protein structure and function, Hierarchical structure of proteins - folding, modification and degradation, functional design of proteins - membrane proteins - purification, detection and characterization.

Unit 2: Biosynthesis of macromolecules - Biomembranes and subcellular organization of prokaryotic and eukaryotic cells - cell architecture - Cell signaling – types, Chemical signals and cellular receptors, G Protein-linked receptors, Protein kinase-associated receptors, Growth factors as messengers, Cell signals and Apoptosis, Cytoskeleton: microfilaments-intermediate filaments-microtubules.

Unit 3: Prokaryotic and eukaryotic DNA replication, mechanisms of DNA replication, fidelity of replication, enzymes and proteins involved in DNA replication. Types of gene mutations. Suppression, Transposable Genetic Elements, Ames’ test. DNA damage and repair mechanisms, DNA repair and aging, DNA repair modulation.

Unit 4: Prokaryotic transcription: RNA polymerase, holoenzyme and apoenzyme, sigma factors, details of initiation, elongation, termination. Eukaryotic transcription: Types of RNA polymerases. Promoter of RNA polymerase II. Enhancers. General and inducible transcription factors. Post- translational modification: mRNA processing, processing, capping, cleavage and poly- adenylation, splicing of nuclear pre-mRNA, mRNA stability.

Unit 5: Gene code: characteristics, deciphering the code. Protein biosynthesis: Prokaryotic and eukaryotic translation, the translational machinery, mechanism of initiation, elongation and termination. Regulation of expression in eukaryotes: Britten-Davidson model. DNA binding and activation domains of transcription factors. Packaging of chromosomes and its relation to transcription regulation. Regulation of translation by 3’ and 5’ UTR motifs.

References 1. Watson. J. D, Baker. T. A, Bell. S. P, Gann. A, Levine. M, Losick. R. Molecular Biology of Gene. (7th edition) Pearson 2. Weaver. R. F. Molecular Biology. 5th Ed. McGraw-Hill Education 3. Alberts Bruce (2014) Molecular Biology of Cell (6th edition), Garland Science 4. Russel Peter. Essential Genetics. 2nd Ed, Blackwell Science Publications 5. Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter. Darnell, Lodish and Baltimore. Molecular Cell Biology, 6th Ed. Garland Science 6. Benjamin Lewin. Gene VIII. Pearson Education Inc. NJ, 2004

MSc Microbiology: Semester 1 MICROBIAL BIOCHEMISTRY Course Code: CMB103 Total Number of Credits: 03 Microbial Biochemistry is an interdisciplinary course designed to introduce the essential fundamentals of biochemistry. This course focuses on the concepts of biochemistry and important microbial macromolecules and their metabolism.

Unit 1: Chemistry of Life and Special Microbial Molecules: Bonds: ionic bonding, Ion-dipole. Covalent bond, H-bonds, Van der Wall’s interaction, Hydrophobic and hydrophilic interactions. Water as a biological solvent and its role in biological processes pH, Henderson-Hasselbalch equation, concept of buffer, strength of buffer, range of buffer, important biological buffers. Structure of Microbial Molecules: Peptidoglycan, bacteriorhodopsin, biphytanyl chains and lipids in archaeal cell membranes and their significance in adaptation in extreme conditions.

Unit 2: Bioenergetics: Laws of thermodynamics, entropy, enthalpy, free energy, free energy and equilibrium constant, Gibbs free energy equation, determination of free energy of hydrolytic and biological oxidation reduction reactions, under standard and non-standard conditions, high energy compounds, coupled reactions, determination of feasibility of reactions. ATP and other different groups of high energy phosphate compounds.

Unit 3: Proteins: Structural features of amino acids & classification, peptide linkage: partial double bond nature, determination of primary structure of polypeptide, structural classification of proteins, primary, secondary, tertiary, quaternary structures of proteins. Ramchandran plot. Structure of purines, pyrimidines, nucleosides and nucleotides. Physiochemical properties of nucleic acids - Denaturation of nucleic acids. Hyperchromic effect and Tm. Chargaff's rule, Secondary structure of DNA - Watson and Crick model. Secondary structure of tRNA - clover leaf model.

Unit 4: Carbohydrates: Monosaccharides, disaccharides, oligosaccharides and polysaccharides, concepts of epimer, isomer. Lipids: Saturated and unsaturated fatty acids, fatty acid oxidation. Biosynthesis of fatty acids, triacylglycerols and phospholipids.

Unit 5: Metabolic Pathways and Fermentations: Glycolytic pathway, Pentose phosphate pathway (HMP), Entner-Doudroff pathway, Tricarboxylic acid cycle, PDH Multi-enzyme complex Amphibolic pathway, anaplerotic reactions. ETC, generation and maintenance of proton motive force PMF, chemi-osmotic theory, Q cycle, Ubiquinone, Cyt C. Substrate level and oxidative phosphorylation, inhibitors and un-couplers of electron transport chain and function of ATPase (bacterial and mitochondrial), shuttle systems. Fermentation - Lactic acid fermentation, LDH - Alcoholic fermentation ADH - Catabolism of glycogen. Amino acid catabolism- Urea cycle: deamination and transamination reactions. de novo biosynthesis of purines and pyrimidines, ribonucleotide reductase and its role in nucleic acid metabolism.

References 1. D.L. Nelson, Michael M. Cox Lehninger’s Principle of Biochemistry. 6th ed. W. H. Freeman, 2012 2. J.M. Willey, Lansing M. Prescott Microbiology. 7th Ed. McGraw-Hill Higher Education, 2008 3. Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto, Jr., Lubert Stryer Biochemistry. 8th Ed. W. H. Freeman, 2015 4. White David. Physiology and Biochemistry of Prokaryotes. 3rd Ed. Oxford University Press, New York, 2007

MSc Microbiology: Semester 1 IMMUNOBIOLOGY Course Code: CMB104 Total Number of Credits: 03 Immunology course is aimed at introducing the host defense system and host-microbial interactions. It focuses on the essential concepts of immune factors and immune system. It also elaborates emerging aspects in human immunology.

Unit 1: Introduction to Immunobiology and Innate Immunity: Principles of innate and adaptive immunity, Effector mechanisms – The first-lines of defense, Complement system, Pattern recognition, induced innate responses to infection.

Unit 2: Recognition of Antigen: Antigen recognition by B-cell and T-cell receptors, Structure of antibody molecule, the interaction of antibody molecule with specific antigen, Antigen recognition by T cells, Generation of lymphocyte antigen receptors, primary Ig rearrangement, T-cell receptor gene rearrangement, structural variation in Ig constant regions, secondary diversification of antibody repertoire, antigen presentation to T lymphocytes, generation of T-cell receptor ligands, the MHC and its functions.

Unit 3: Development of Mature Lymphocyte Receptor Repertoires: Signaling through immune- system receptors, general principles of signal transduction and propagation, antigen receptor signaling and lymphocyte activation, Other receptors and signaling pathways: cytokine and cytokine receptors, apoptosis receptors, Development of B lymphocytes and T lymphocytes, Positive and negative selection, Survival and maturation of lymphocytes in lymphoid tissues.

Unit 4: Adaptive Immune Response: T cell-mediated immunity, entry of naïve T cells and APCs into peripheral lymphoid organs, priming of naïve T cells by DCs, General properties of effector T cells and their cytokines, T cell-mediated cytotoxicity, macrophage activation by Th1 cells, Th2 cells, Th17 cells & Tregs. Humoral Immune Response: B cell activation by helper T cells, Distribution and functions of Ig classes, Destruction of antibody-coated pathogens via Fc receptors, Dynamics of adaptive immunity, The mucosal immune system and organization, Mucosal responses to infection and regulation.

Unit 5: Immune System in Health and Disease: Failures of host defense mechanisms: Evasion and subversion of immune defenses, Immunodeficiency diseases, Allergy and other hypersensitivity disorders and mechanisms, Autoimmunity and transplantation: The making and breaking of self-tolerance, autoimmune diseases and mechanisms, genetic and environmental basis of autoimmunity, responses to alloantigens, transplant rejection, manipulation of immune responses, treatment of adverse iresponses, anti-tumor responses and vaccination. Immunodiagnostics: Serological reactions: Immunoprecipitation, flocculation, agglutination, ELISA, RIA, complement fixation, western blotting, flow cytometry, cytokine arrays.

References 1. Janeway Immunobiology. 9th Edition. Publisher-Garland Science, 2016 2. Abul K Abbas, Andrew H Lichtman & Shiv Pillai, Cellular & Molecular Immunology, 8th Edition 2014, Elsevier 3. Roitt's Essential Immunology, 13th Edition, Peter J. Delves, Seamus J. Martin, Dennis R. Burton, Ivan M. Roitt 2016, Wiley-Blackwell. 4. William E. Paul. Fundamental Immunology. 7th Edition. Lippincott Williams and Wilkins, 2012.

MSc Microbiology: Semester 1 MICROBIAL GENETICS Course Code: CMB105 Total Number of Credits: 03 Microbial Genetics is an important tool in dissecting the genetic structure of an organism. The basic principles are of major importance in constructing new organisms for practical applications leading to research in genetic recombination and genetic engineering.

Unit 1: Microbial Genetics: Definition and scope of Genetics. Pre-mendelian genetic concepts – Preformationism, Epigenesis, Inheritance of acquired characters, traits, Germplasm theory. Hereditary and Environment, Genotype and Phenotype. Microbes as genetic tools for genetic studies.

Unit 2: Viral Genetics: General characteristics of viral genome, T4 virulent Phage - Structure- life cycle. Lambda temperate phage- Structure - Lytic and lysogenic cycle, Lysogenic repression. Genetic mapping of viruses, Recombination in viruses; Genetics of bacteriophage.

Unit 3: Bacterial Genetics: Organization of genetic material in bacteria, Gene transfer mechanisms: Conjugation, Transformation and Transduction. Recombination in bacteria. Natural transformation systems- Streptococcus pneumoniae and Haemophilus influenzae. Transfection and forced competence. Bacterial Conjugation- Properties of the F plasmid, F+ x F - mating, F’ x F- conjugation. Transduction- Generalized and specialized transduction, Drug resistance in bacteria.

Unit 4: Fungal Genetics: Features and consequences of heterothallism, homothallism, mating types, Vegetative incompatibility, Polyploidy and aneuploidy. Neurospora- Tetrad analysis and linkage detection - 2 point and 3 point crosses – Induction of Mutations - Mitotic recombination in Neurospora – Transposable elements - Gene conversion. Yeast plasmids, Mating type genetics of yeast.

Unit 5: Gene Regulation & Expression: Operon concept, Repression of the lac operon, Regulation of tryptophan biosynthesis operon by attenuation, catabolite repression instability of bacterial RNA, positive and negative regulation, inducers and co-repressors. Negative regulation - E. coli lac operon; Regulation of the heat-shock regulation by an alternate sigma factor, Two component regulatory systems.

References 1. Larry Snyder, Joseph E. Peters, Tina M. Henkin, Wendy Champness -Molecular Genetics of Bacteria- 4th edition; publisher: ASM Press 2013. 2. Daniel L. Hartl - Essential Genetics: A Genomics Perspective- 6th Edition; publisher: Jones & Bartlett Learning 2012. 3. Jeremy W. Dale , Simon F. Park - Molecular Genetics of Bacteria- 5th edition; publisher: Wiley 2010 4. James D. Watson , Tania A. Baker , Stephen P. Bell , Alexander Gann , Michael Levine , Richard Losick - Molecular Biology of the Gene-7th Edition; publisher: Pearson 2013

MSc Microbiology: Semester 1 MICROBIAL PHYSIOLOGY Course Code: CMB106 Total Number of Credits: 03 Microbial Physiology course will help students how microbes can grow on substrates other than glucose, their inorganic metabolism and photosynthesis and how do they respond to the changes in environment. It will elaborate the anaerobic respiration by variety of groups of microbes and non-genetic regulation at metabolic pathways.

Unit 1: Metabolic Diversity: Heterotrophic metabolism on substrates other than glucose. Hydrolysis of polymers - Starch hydrolysis, Cellulose hydrolysis, Oxidation of aliphatic hydrocarbons - Amino acid utilization: Oxidative deamination, Transamination - Oxidation of aromatic compounds - Methanotrophy; Characteristics of methanotrophs, Dissimilation of methane by methanotrophs - Carbon assimilation by methylotrophs - Energy efficiency in C1 metabolism

Unit 2: Photosynthesis & Inorganic Metabolism: Characteristics and Metabolism of Autotrophs, Photosynthetic Bacteria and Cyanobacteria Autotrophic CO2 Fixation and Mechanisms of Photosynthesis, Photosystem I and II in cyanobacteria – Methanogenesis - Nitrification: Nitrifying Bacteria, Ammonia oxidation, Nitrite oxidation, anaerobic nitrification - Sulfur bacteria and the oxidation of sulfur compounds

Unit 3: Anaerobic Respiration: Denitrification: Biochemistry of denitrification, - Regulation of denitrification - Metal reduction: Fe (III) and Mn (IV) reduction,Microbial reduction of other metals, Metal reduction and the environment - Sulfidogenesis: Biochemistry of sulfidogenesis, Reduction of sulfate and sulfur, - sulphur reducing bacteria

Unit 4: Metabolic Regulation: Regulation through modulation of enzyme activity: fine regulation, Feedback inhibition Enzyme activity modulation through structural changes, Phosphorylation Adenylylation, Acetylation, Other chemical modifications, Regulation through physical modification and dissociation/association, Allosteric regulation and Feedback control- Regulation of E. coli aspartate carbamoyltransferase

Unit 5: Adaptive & Developmental Changes: Myxobacterial developmental cycle: Life Cycle of myxobacteria, Aggregation and fruiting body formation, Intercellular signaling in myxobacteria - Caulobacter differentiation: Life cycle of Caulobacter crescentus, The stalk, the holdfast, and the flagellum: Structure, Genetics, and regulation, Regulation and checkpoints of the cell cycle of C. crescentus - Oxidative stress, heat shock response, Quorum sensing, response to changes in osmotic pressure, chemotaxis.

References 1. Alcomo, I.E. 2011. Fundamentals of Microbiology. 9th Edition, Jones and Bartlett Publishers, Sudbury. Massachusetts. 2. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Microbiology-An Introduction.11th edition Pearson, 2013 3. David White., 2007 The Physiology and Biochemistry of Prokaryotes, 3rd edn, Oxford University Press 4. Perry, J.J., Staley, J.T. and Lory, S. 2007. Microbial Life. 2nd edition Sinauer Associates, Publishers, Sunderland, Massachusetts. 5. Schaechter, M. Ingraham, J.L. and Neidhardt, F.C. 2006. Microbe. ASM Press, Washington. D.C.

MSc Microbiology: Semester 1 Laboratory Practical PRACTICAL MICROBIOLOGY - I Course Code: PMB101 Total Number of Credits: 02

PART I: Principles and methods of sterilization, Direct microscopic observations of bacterial shape – cocci, rods, chains, fungal spores, mycelium, yeast budding, Preparation of Media: Nutrient broth, Nutrient agar, plates, slants, soft agar, Pure culture technique: Streak plate, spread plate and pour plate methods, Measurement of size of microbes – micrometry, Bacterial motility by hanging drop method, Enumeration of bacterial/yeast cells-viable count (plate count) Total count (Haemocytometer), Isolation and purification of cyanobacteria, actinomycetes, fungi and protozoans, Staining methods: Simple, Negative, acid fast, Gram staining, spore, Capsule, Metachromatic granular staining, Lactophenol cotton blue staining - Fungal slide culture.

PART II: Preparation of permanent slides, Observation of prokaryotic and eukaryotic cells and cell types, Study of cell organelles adopting preparations/models, Squash preparation of giant chromosome of salivary gland of chironomous larva, Squash preparation of onion root tip, testis and anther lobes, Preparation of buccal smear, Red blood cell as osmometer, Subcellular fractionation and biochemical/enzymological analysis, Metaphase chromosome preparations and preliminary banding techniques.

MSc Microbiology: Semester 1 Laboratory Practical PRACTICAL MICROBIOLOGY - II Course Code: PMB102 Total Number of Credits: 02

PART I: Preparation of standard buffers and determination of pH of a solution, Qualitative tests for Carbohydrates- Tests for sugars: Fructose, lactose, maltose, glucose and starch, Qualitative tests for amino acids, Quantitative estimation of glucose by DNS method, Quantitative estimation of protein by Biuret method, Quantitative estimation of protein by Lowry’s method, Determination of Iodine value, Estimation of carbohydrates by anthrone method, Estimation of amino acids by ninhydrin method, Estimation of DNA/RNA.

PART II: Virtual demonstration (as per UGC guidelines) of handling of laboratory animals, Different ways of injecting antigens to mouse (IP, SC, IV, retro-orbital), Isolation of organs and tissues of immune system from mouse, Quantification of blood cells using haemocytometer, extraction of human PBMCs by Ficoll-Hypaque overlay method, flow cytometry and data analysis, WIDAL test for enteric fever, Immunoelectrophoresis, ELISA, Western blotting, VDRL test for syphilis.

MSc Microbiology: Semester 2 BACTERIOLOGY & MYCOLOGY Course Code: CMB201 Total Number of Credits: 03 Bacteriology and Mycology course is designed to have a holistic approach on bacteria and fungi. It is structured to offer comprehensive knowledge on bacterial systematics, major bacterial genera, basic principles on bacterial and fungal ultrastructure, methods to isolate, detect and enumerate growth and kinetics, and their economic importance with respect to agriculture, medicine & industry, control of bacterial and fungal diseases by chemotherapy and understanding the mode of action of drugs.

Unit 1: Bacterial classification based on Bergey’s Manual of Determinative Bacteriology - Gram negative, Gram positive, the mycoplasmas and archea; Classification based on serology, biochemistry, 16s rRNA, G+C content and molecular tools. Bacterial ultrastructure and organelles. Staining of bacteria and organelles. Fungal taxonomy – Criteria. Traditional, chemo and molecular taxonomy. Fungal ecology, distribution of yeasts and fungi. General characteristics, structure and organization of fungi – Fungal body and cell, Colony, communication and signaling. Cell differentiation and reproduction. Fungal reproduction - Vegetative, asexual and sexual.

Unit 2: Bacterial Growth: Culture conditions - bacterial culture media- chemically defined, complex, differential and selective media - for aerobes and anaerobes; Bacterial growth curve; Effect of physical and chemical factors on growth. Measuring bacterial growth- Spectrophotometric method, microscopic counting, serial dilution and viable cell count. Bacterial reproduction. Fungal nutrition and metabolism – nutritional requirement, saprophytic, parasitic, obligatory and facultative. Culture media and natural substrates of fungi. Biotrophic semi- biotrophic and necrotrophic mode of growth. Fungal-microbe interaction, fungal - plant interactions – symbiotic and antagonistic interactions.

Unit 3: Microbial Biology: Staphylococcus, streptococcus, Pneumococcus, Neisseria, Corynebacterium, Bacillus, Clostridium, Proteus, Shigella, Salmonella, Vibrio, Pseudomonas, Yersinia, Haemophilus, Bordetella, Brucella, Mycobacterium, spirochetes, mycoplasmas, rickettsiae and chlamydiae. Myxomycetes, Ascomycetes, Basidiomycetes and imperfect fungi.

Unit 4: Antibiotics and chemotherapeutics: Mode of action, Antibiotic sensitivity assays- disc method; replica plating technique; Ames test; Antibiotic resistance in bacteria- factors of development of resistance, Quorum sensing, Biofilms, anti-fungal drugs and their mode of action, anti-fungal sensitivity testing, antifungal resistance.

Unit 5: Significance of Fungi: Agricultural production and plant productivity, toxigenic fungi and mycotoxins, plant pathogens, fungi in biocontrol; Fungi in biotechnology and industrial production; Fungal metabolites and economic significance – mycotoxins, medicinal uses, food additives, alcohol, vinegar, enzymes, biopesticides. Edible fungi – mushrooms, Mushroom poisoning.

References 1. Joanne M. Willey, Linda M. Sherwood, Christopher J. Woolverton –Microbiology-10th edition; publisher: Mcgraw-Hill College 2016. 2. Jacquelyn G. Black, Laura J. Black- Microbiology: Principles and Explorations, 9th edition; Publisher: Wiley 2014 3. Gerard J. Tortora, Berdell R. Funke, Christine L. Case- Microbiology: An Introduction -12th edition: publisher: Pearson 2015. 4. Mehrotra RS and KR Aneja. An Introduction to Mycology, New Age Publishers 5. Steven L. Stephenson (2010), The Kingdom Fungi: The Biology of Mushrooms, molds and lichens. MSc Microbiology: Semester 2 VIROLOGY AND PARASITOLOGY Course Code: MBC202 Total Number of Credits: 03 Virology has been tailored to provide an insight into the history and ultra-structure, and diagnosis of viral diseases. Emerging virus and challenges have also been included for the better understanding of the latest developments in virology.

Unit 1: Definitive properties of viruses: Morphology, Ultra structure, Chemical composition - proteins, nucleic acids, and enzymes. Classification and nomenclature; Group I, Group II, Group III, Group IV, Group V, Group VI, Group VII. Sub-viral particles: Discovery, Structure, Classification, replication and diseases caused. Cellular interactions—clathrin coated pits, lipid rafts, caveolae, endocytosis and virus uncoating mechanisms. Oncogenesis: oncogenic viruses, viral transformation by activation of cellular signal transduction pathways, viral transformation via cell cycle control pathways.

Unit 2: General aspects of plant and animal viral diseases. Introduction to viral vaccines, preparation of vaccines, new vaccine technology; antiviral drugs, antiviral gene therapy, antiviral libraries, antiretrovirals—mechanism of action and drug resistance. Modern approaches for virus control: Antisense RNA, siRNA, ribozymes, in silico approaches for drug designing. T-phages, Cyanophages, Baculovirus. Mechanism of host cell damage- Host cell ‘shut off’, apoptosis, necrosis, alteration of signaling pathways. Viruses and future: Promises and problems. Emerging diseases, sources and causes. Medical technology to eliminate viral diseases. Silver lining: viruses as therapeutic agents, viruses for gene delivery, viruses to destroy other viruses, e.g. GB virus. Importance of modern virology. Zika, ebola & flu epidemics & challenges in control

Unit 3: Diagnostic Virology: Biological activity of viruses, Physical, chemical, structural components, visualization, detection and enumeration: physical, biological, immunological and molecular methods. Isolation, purification, and cultivation: Embryonated eggs, laboratory animals and cell cultures. Serological methods, PCR-based assays and immunohistochemistry. Infectivity assays for phages and plant viruses, viral products expressed in infected cells.

Unit 4: Parasitology: Basic features and nomenclature, Aerobic and anaerobic amoebae, Giardia lamblia, Trichomonas vaginalis; Trypanosomes, Leishmania, Plasmodia, coccidian parasites, Babesia microti; Balantidium coli

Unit – 5: Cestodes, schistosomes and other flukes, nematodes. Anti-parasitic drugs and treatment, Basic entomology and ectoparasites, Pharmacology of common antiparasitic drugs & drug resistance, immune responses & evasion mechanisms of parasites from host immune responses.

References 1. Fields Virology. Vol 1 and 2. B.N. Fields, D.M. Knipe, P.M. Howley, R.M. Chanock, J.L. Melnick, T.P. Monath, B. Roizman, and S.E. Straus, eds.), 3rd Edition. Lippincott-Raven, Philadelphia, PA. 2. Basic Virology. Edward K. Wagner, Martinez J. Hewlett, David C. Bloom, David Camerini. 3. Virology: Principles and Applications John Carter, Venetia Saunders. 4. Virology Methods Manual. Brian W.J. Mahy (Editor), Hillar O. Kangro (Editor). Elsevier Science & Technology Books. 5. Parasitology (Protozoology & Helminthology) K.D. Chatterjee, 13th Edition 2012, Published by CBS Publishers 6. Bailey & Scott’s Diagnostic Microbiology, 13th Edition, Patricia M. Tille, Elsevier, 2014

MSc Microbiology: Semester 2 FOOD & INDUSTRIAL MICROBIOLOGY Course Code: CMB203 Total Number of Credits: 03 Food & Industrial Microbiology is oriented towards the industrial application of microorganisms and recent microbial products. The paper elaborates the applied and industrial aspects of microbiology such as screening of microorganisms, strain improvement, microbial metabolites, fermented microbial products, microbial enzymes, Biofuels using microbes and microbial production of biopolymers. The course would also enable students to learn about the epidemiology of food and milk-borne diseases.

Unit 1: Food Microbiology & Food-Borne Pathogens: Importance and significance of microorganisms. Factors – Intrinsic and extrinsic factors affecting their growth in food. Food-borne diseases; detection and enumeration of their products in food- Culture-dependent methods- Sample collection, processing, analysis, surface testing, Direct microscopy, enumeration and isolation; Animal and cell culture models; Culture independent methods – Metagenomics, biosensor-, Immunologic- and nucleic acid-based detection – PCR, Molecular typing and differentiation; Analytical methods for detection of microbial toxins and metabolites.

Unit 2: Basics of Industrial Microbiology: Historical account of microbes in industrial microbiology; sources and characters of industrially important microbes; their isolation, purification and maintenance; Screening of useful strains; primary and secondary screening; Strain improvement through random mutation and genetic engineering; types of fermentation and fermenters. Microbial growth kinetics in batch, continuous and fed-batch fermentation. Microbial production of metabolites. Commercial production of antibiotics, steroids, alkaloids, interferon, human proteins-insulin, somatostatin, vaccines and anti-cancer agents.

Unit 3: Fermented Microbial Products: Milk, fermentation and dairy products. Food fermentations- Manufacture of fermented foods- Meat and fishery products, plant products- Sauerkraut and fermented olives, breads, beverages. Microbial cells as food- SCP, mushroom cultivation. Source and applications of microbial enzymes, antioxidants, bio-surfactants, polysaccharides, flavors and colors. Probiotics and advantages, Genetically modified foods. Microbiology and production of alcoholic beverages, organic acids, amino acids, and vitamins. Microbial Enzymes: Immobilization of microbial enzymes and whole cells; Industrial enzymes production; and their applications. Enzymes involved in microbial biocatalyst/transformations.

Unit 4: Food Spoilage & Food Preservation: Organisms involved, characteristic features, dynamics and significance of spoilage of different groups of foods - Cereal and cereal products, vegetables and fruits, meat, poultry and sea foods, milk and milk products, packed and canned foods. Spoilage and defects of fermented foods. Food preservation- use of temperatures- Significance of psychrophilic microbes in cold-stored and frozen foods, Drying, Chemical, Modified atmosphere, Radiation, other food protection methods and microbial resistance.

Unit 5: Food Safety & Quality Management Systems: General principles of food safety risk management, Recent concerns on food safety- Safe food alternatives (Organic foods), Good agricultural practices (GAP), Food indicators of water and food safety and quality- Microbiological criteria of foods and their significance. The HACCP and ISO systems for food safety. Biofuels & Biopolymers: Biofuels (ethanol and methane) from organic residues; fuels from algae; Mushroom cultivation; other microbial products - Biopolymers and EPS, Bioplastics, Biosurfactants, effluent treatment, SCP.

References 1. James M. Jay., Loessner, M. J., and Golden D. A., 2005, Modern Food Microbiology, 7th edition. 2. Arun K. Bhunia, 2008, Foodborne Microbial Pathogens- Mechanisms and Pathogenesis, Food Science text Series, Springer International, New York, USA. 3. Doyle, M. P. & Beuchat, L. R., 2007, Food Microbiology- Fundamentals and Frontiers, ASM Press. 4. Marriott, N. G. and Gravani R. B. 2006. Principles of Food Sanitation, Food Science text Series, Springer International, New York, USA. Nduka Okafor (2007). Modern Industrial Microbiology and Biotechnology. 1st Edition: Science Publishers. 5. Richard H. Baltz, Julian E. Davies, and Arnold L. Demain (2010). Manual of Industrial Microbiology and Biotechnology. 3rd Edition, ASM Press. 6. Modern Industrial Microbiology & Biotechnology by N. Okafer, Scientific Publishers, Enfield, USA, 2007.

MSc Microbiology: Semester 2 AGRICULTURAL MICROBIOLOGY & PLANT PATHOLOGY Course Code: CMB204 Total Number of Credits: 03 Agricultural Microbiology and plant pathology is designed to introduce the essential fundamentals such as soil environment, major plant diseases caused by fungi, bacteria and viruses, biopesticides & biofertilizers and plant microbe-interactions. The course also is aimed at introducing the mechanisms, features, symptoms, and control strategies against plant pathogens to improve crop productivity.

Unit 1: Soil Environment- Microorganisms, soil structure, profile, physico-chemical conditions, Microbial composition, sampling techniques, microorganisms in organic decomposition. Bio-geo chemical cycles – Carbon, sulpher, iron, phosphorus cycles & nitrogen cycles – Nitrogen fixation, nitrification, de-nitrification, Rhizospheric microorganisms, Siderophores. PGPM-Plant growth promoting microorganisms. Plant-microbe interactions. Mechanisms of plant growth promotion.

Unit 2: Major plant disease symptoms caused by fungi, bacteria and viruses. Development and stages of disease development, pathogen dissemination, Relationship between disease cycles and epidemics, pathogenicity genes, Genes controlling: Degradation of cuticle and cell wall, Production of secondary metabolites-fungal toxins; Resistance (R) genes of plants, Plant diseases – Principles, symptoms and control: Fungal – General characteristics of diseases: Myxomycetes, Chytridiomycetes, Zygomycetes, Ascomycetes, Basidiomycetes and Deuteromycetes, Bacterial – Blight of rice, citrus canker, Xanthomonas. Viral and mycoplasmal – Bud necrosis of groundnut, citrus mosaic, little leaf of brinjal, tomato leaf curl.

Unit 3: Biofertilizers – Introduction, biofertilizers using N2-fixing microbes – phosphate solubilization- Rhizobium, Azatobacter, Azospirillum, Azolla; Anabaena symbiosis, blue green algae and mycorrhizal associations – endo and ecto mycorrhizae. Cultivation, mass production and inoculation of Rhizobium, Azotobacter, Azospirillum, Azolla and cyanobacteria, Carrier- based inoculants, methods of application, QC, agronomic importance. Application methods.

Unit 4: Principles of plant disease control. Protection - Diseases of field, vegetable, orchard and plantation crops and their control; causes and classification of plant diseases; principles of biological control of diseases. Methods to exclude pathogens from host- Quarantines and Inspections, Crop certification, Evasion or avoidance of pathogen, use of pathogen-free propagating material, pathogen-free seeds and vegetative propagating materials. Plant immunization; Direct protection; Integrated control, Biopesticides – Bacillus thuringiensis, B. sphaericus, B. popilliae, Pseudomonas syringae. Biocontrol- Microbial control - Trichoderma. Biological control – Use of Baculovirus, NPV virus, protozoa & fungi in biological control. Endophytic fungi - symbiotic and opportunistic associations, co-evolution and loss of reproductive structures, Secondary metabolite production, toxins – importance, toxicity to herbivores and insects. Use of endophytic fungi as biocontrol agents against plant diseases, insect herbivores.

Unit 5: Molecular plant microbe-interactions: Cell signalling, Quorum sensing, and Biofilm formation. Invasion of plant tissue: Resistance mechanisms against attack by plant pathogens. Molecular detection of pathogens. Integrated pest management-concepts and components; host plant resistance-biological control of insect pests; Recycling of agricultural wastes - Microbiology of biogas, bioethanol and value added products. Mushroom cultivation and vermicomposting.

References 1. Dirk J, Elas V, Trevors JT, Wellington, EMH Modern Soil Microbiology, CRC Press; 2 edition (21 December 2006) 2. Microbes For Sustainable Agriculture by K.V.B.R. Tilak, K.K. Pal, Rinku Dey I K International Publishing House Pvt. Ltd (12 January 2009) 3. George N. Agrios. 2005. Plant Pathology, 5th Edition, Academic Press. 4. Schumann, G.L. 2006. Essential Plant Pathology. APS Press. 5. Sharma, P.D. 2006. Plant Pathology.

MSc Microbiology: Semester 2 METHODS IN GENE TECHNOLOGY Course Code: CMB205 Total Number of Credits: 03 Nucleic Acid Biology course aims to enable the students to understand gene cloning and strategies of rDNA technology. It provides an insight into the vectors and techniques in rDNA technology. The techniques are elaborated with PCR, hybridization, cDNA library construction and gene transfer.

Unit 1: History of nucleic acid, role of genes inside the cell, genetic code, genetic elements that control gene expression. Enzymes in recombinant DNA technology- DNA polymerase, reverse transcriptase, restriction endonucleases, polynucleotide kinase, terminal deoxynucleotidyl transferase, DNase, methylase, phosphatases, ligases RNase and their mode of action. Vectors in recombinant DNA technology Introduction to cloning vectors, biology and features of vectors, types of vector - plasmids, cosmids, phages, BAC and YAC and viruses.

Unit 2: Nucleic Acid Amplification & Hybridization Techniques: Polymerase chain reaction (PCR) and its applications, variations in PCR and applications, methods of nucleic acid detection, methods of nucleic acid hybridization, sequencing methods, probes and target sequences, Southern blotting, Northern blotting, in situ hybridization, nucleic acid mutagenesis in vivo and in vitro.

Unit 3: Construction of DNA Library: Construction of genomic and cDNA libraries, Screening libraries with gene probes, colony hybridization, plaque hybridization, screening by gain of function, immunological screening.

Unit 4: Gene Transfer Techniques: Gene transfer techniques in microbes, animals and plants - transformation, electroporation, microprojectile system, liposome-mediated gene transfer, DNA/calcium phosphate co-precipitate method, gene-gun, transfection with phage vectors etc. Agrobacterium based gene transfer in plants - Ti plasmid: structure and functions, Ti plasmid based vectors. Chloroplast transformation.

Unit 5: Applications & Legal Issues: Applications of recombinant DNA technology in Agriculture, Veterinary, Industry, Forensic science and Medicine. Gene mapping-restriction mapping, RFLP, RAPD, AFLP. Engineering microbes for the production of antibiotics, enzymes, Insulin, growth hormones, monoclonal antibodies etc. Transgenic organisms from mice to rice, Human genetic engineering and Gene therapy- methods of gene therapy, gene therapy in treatment of diseases, Stem cell therapy, Future of stem cell therapy. Science and the constitution- ethical, legal and environmental issues.

References 1. Sandy Primose (2006). Principles of Gene Manipulation and Genomics. 7th Ed., Blackwell Publishers. 2. Brown T.A. (2010). Gene Cloning and DNA analysis. 6th Edition, Wiley-Blackwell. 3. David E Newton. (2010). DNA technology. ABC-CLIO, LLC 4. Beiquan Mou and Ralph Scorza. (2011). Transgenic Horticultural Crops: Challenges and Oppurtunities. CRC press. 5. Thomas F. Budinger and Miriam D. Budinger. (2006). Ethics of Emerging Technologies: Scientific Facts and Moral Challenges. John Wiley and Sons Inc. 6. Pete Shanks. (2005). Human Genetic engineering. Avalon publishing groups.

MSc Microbiology: Semester 2 BIOSAFETY, BIOETHICS & INTELLECTUAL PROPERTY RIGHTS Course Code: CMB206 Total Number of Credits: 03 Biosafety, Bioethics & IPR aims to introduce the importance and basic procedures in biosafety and bioethics in biomedical research. It also describes the process of Universal Standard Precautions in the microbiology laboratory, including handling of infectious materials, personal hygiene, use of personal protective equipment, handling of sharp objects, and hand-washing procedures.

Unit 1: Good laboratory practices, Chemical safety, Fire safety, Electrical safety, Exposure control plan, Employee education and orientation, Disposal of hazardous waste, Standard precautions, Engineering controls: Lab environment, biosafety cabinet, personal protective equipment, post-exposure control, post-exposure control, Classification of biologic agents based on hazard, Mailing bio-hazardous material.

Unit 2: Legal, socioeconomic, public elucidation of process of biotechnology in generating new forms of life. Biosafety in general, Food and feed products containing GMOs, Risk assessment/analysis, Risk management, Ethical aspects of GMOs, policy on the storage of GMOs, Gene technology act, Precautionary principle, Potential environmental risks & benefits, Potential socio-economical risks & benefits. Recombinant DNA safety guidelines and regulations.

Unit 3: Biomedical ethics: Ethical theories, contemporary approaches to medical ethics, physician-patient relationship, confidentiality, truth telling, autonomy, paternalism & informed consent, abortion, medical experimentation, justice and health care system, the nature of bioethics, Genetic modification/research on plants and animals, therapeutic cloning, human cloning, stem cell research. Federal Laws and the roles of: The Food and Drug Administration, The Centers for Disease Control and Prevention, The United States Department of Agriculture, The Environmental Protection Agency, State and Local Agencies.

Unit 4: Introduction to IPR: IPR, forms of IPR and Intellectual property protection. Concept of property with respect to intellectual creativity, Tangible and Intangible property. WTO: agency controlling trade among nations, WTO with reference to biotechnological affairs, TRIPs. WIPO, EPO.

Unit 5: Concept related to patents novelty, non-obviousness, utility, anticipation, prior art etc. Type of patents. Indian patent act and foreign patents. Patentability, Patent application, Revocation of patent, Infringement and Litigation with case studies on patent, Commercialization and Licensing.

References 1. Biological Safety: Principles And Practices (Biological Safety: Principles & Practices) 4th Edition by Diane O. Fleming, Debra L. Hunt, 4th Edition, ASM Press, 2007 2. Bioethics and Biosafety by M.K. Sateesh, IK International Publishing, 2010 3. Biosafety in Microbiological and Biomedical Laboratories, Centers for Disease Control & Prevention, National Institutes of Health, 5th Edition. 4. Law Relating to Intellectual Property Rights, VK Ahuja, 2nd Edition, Lexis Nexis (2013) ISBN: 9788180389894. 5. Law and Strategy of biotechnological patents by Sibley. Butterworth publication. (2007) ISBN: 075069440, 9780750694445.

MSc Microbiology: Semester 2 Laboratory Practical PRACTICAL MICROBIOLOGY - III Course Code: PMB201 Total Number of Credits: 02

Part I: Introduction to good laboratory practices and preparation of different minimal, complex and differential media, Isolation of bacteria from air, water, soil, Endospore staining, Flagella staining and Capsule staining, Bacterial culture techniques-Liquid broth culture & Pure culture techniques-serial dilution technique, Pour plate, spread plate, streak plate techniques, Measurement of bacterial population by turbidimetry and colony counting by serial dilution of samples, Bacterial growth curve, Antibiotic sensitivity tests-disc method, Preservation of pure cultures: slant preparation, water stock, glycerol stock, Biochemical tests for bacterial identification, Detection of bacterial pathogens by PCR method.

Part II: Methods of isolation and identification of fungi by traditional methods, Preparation of pure culture and preservation of culture, Isolation and identification of endophytic fungi from plants, Observation and identification of mycorrhiza, Isolation and identification of fungi from seeds, Study of soil fungi from varied geographical origins, Isolation of antibacterial/ antimycotic compounds from fungi, Staining and observation of plant pathogenic fungi, Study of asexual reproduction in Saccharomyces, staining of human fungal pathogens using LPCB and culture.

MSc Microbiology: Semester 2 Laboratory Practical PRACTICAL MICROBIOLOGY - IV Course Code: PMB202 Total Number of Credits: 02

Part I: Isolation of bacteriophages from sewage, Estimation of virus yields - plaque assay, Routes of inoculations in embryonated eggs, Haemagglutination test, Hemagglutination inhibition assay, Biocontrol assay on insect larvae using NPV, ELISA test, Study of virus infected plant material, One step growth curve of bacteriophage by Burst size determination, Demonstration of identification of arthropod vectors of viral transmission. Microscopic examination of parasites of medical importance (ova, cysts, blood smear examination), stool concentration, staining and observation.

Part II: Isolation of Genomic DNA and quantification, Isolation of Plasmid and quantification, Preparation of Vector and Insert by restriction digestion, Preparation of competent cells using CaCl2, Ligation reaction of restriction digested Vector and Insert, Transformation of recombinant DNA, PCR amplification of gene of interest, Isolation of RNA and quantification, Reverse transcriptase PCR, Restriction Fragment Length Polymorphism (RFLP) analysis, RAPD and phylogenetic tree, Quantitative Real Time – PCR (Demonstration).

MSc Microbiology: Semester 3 COMPUTATIONAL BIOLOGY & BIOSTATISTICS Course Code: CMB302 Total Number of Credits: 03 This course aims to introduce the basics of computational biology and biostatistics and would enlighten students to apply the subjects to biomedical research.

Unit 1: Overview of Bioinformatics: Overview of databases in bioinformatics Biological databases: Sequence and Structure databases – Protein Sequence databases – SWISS-PROT, PIR - Nucleic Acid Sequence Databases – GenBank, EMBL, DDBJ –pattern and motif searches databases – PROSITE, BLOCKS, PRINTS, PFAM – structure databases – PDB – structural classification – SCOP, CATH , PRINTS, BLOCKS, PRINTS, PRODOM, PFAM.

Unit 2: Sequence Alignment Algorithms: Pairwise alignment - Local and Global alignment concepts –Databases searches for homologous sequences - FASTA and BLAST - Multiple sequence alignment – Progressive Alignment - Clustal W, methods for phylogenetic tree construction.

Unit 3: Qualitative and quantitative data, cross-sectional and time series data, discrete and continuous data, nominal, ordinal, ratio and interval scales; Presentation of data: Frequency distribution and cumulative frequency distribution, Measures of variability z-score and standard normal distribution, diagrammatic and graphical presentation of data, construction of bar, pie diagrams, histograms, frequency polygon, and frequency curve.

Unit 4: Introduction to the t-statistic (one sample), the independent samples t-test, the dependent (paired) samples t-test, One-way ANOVA, simple linear regression analysis, Chi-Square and other non-parametric tests, introduction to multivariate analysis

Unit 5: Software for Data Analysis: Introduction to the software, required data format, tables, descriptive measures, graphs and charts, presentation of tables/charts.

References 1. Arthur. M. Lesk, Introduction to Bioinformatics, 4th Edition, 2014, Oxford University Press. 2. K. Najarian, S.Najarian, S. Gharibzadeh, C. N. Eichelberger, Systems Biology and Bioinformatics: A Computational Approach 1st Edition, 2009, CRC Press. ISBN: 978- 1420046502 3. Gupta SC, Kapoor VK (2014). Fundamentals of Mathematical Statistics, S Chand and sons, India. 4. Gupta SP (2009). Statistical Methods, 28th edition, S Chand and Sons, India.

MSc Microbiology: Semester 3 MARINE MICROBIOLOGY Course Code: CMB302 Total Number of Credits: 03 Marine Microbiology is designed introduce the students to understand microbial processes and dynamics of marine environment.

Unit 1: Introduction to Microbial Oceanography – marine ecosystem: benthic & littoral zone, saltpan, mangroves and estuarine microbes, microbial loop - marine microbial communities - phytoplankton, protozoa, bacteria, fungi, and virus. Microbial endosymbionts – epiphytes - coral- microbial association, sponge-microbial association.

Unit 2: Dynamics of Marine Microbes - Carbon cycle: Phototrophic microbes, the oceanic carbonate system and global warming - Nitrogen cycle: Nitrogen fixers – Iron limitation – ocean fertilization - phosphorus cycle; Decomposition of organic matter; Bioleaching and biodeteroriation of natural and synthetic materials.

Unit 3: Microbial products: Microbial interaction Microbes of Biotechnological importance; Primary and secondary metabolites - enzymes, antibiotics, organic acid, toxins, biosurfactants and pigments.

Unit 4: Microbes of extreme environments – mechanism of extremophiles – halophiles – halorhodopsin – deep sea microbes – microbes of hydrothermal vents - thermophilic, alkalophilic, asmophilic and barophilic, psychrophilic microorganisms – hyperthermophiles and halophiles – importance in biotechnology.

Unit 5: Seafood microbiology - normal genera associated with fish, food spoilage, fish & human pathogens; zoonotics – Brief account on aquaculture pathogens - Vibriosis – shrimp diseases – WSSV – MBV etc. Rapid diagnosis of contamination in sea foods and aquaculture products.

References 1. Colin Munn, Marine Microbiology: Ecology & Applications 2nd Edition. Garland Science, Taylor & Francis, 2009. ISBN: 978-0815365174. 2. David L. Kirchman, Microbial Ecology of the Oceans, 2nd Edition, John WIley & Sons, 2008. ISBN: 978-0470043448 3. M.T. Madigan and J.M. Martinko, Biology of Microorganisms, 11th Edition, Pearson Prentice Hall, USA, 2006 4. Bhakuni, D.S. and Rawat, D.S. (2005). Bioactive marine natural products. Anamaya Publishers, New Delhi. 5. Joseph Selvin and A. S. Ninawe (2009). Shrimp Disease Management. ANE Publishers.

MSc Microbiology: Semester 3 ENVIRONMENTAL MICROBIOLOGY Course Code: CMB303 Total Number of Credits: 03 Environmental Microbiology is historic as well as eminently modern. The activities of the microorganisms at large in nature/ environment is considered in this paper. Microbes play far more important roles in nature than their small sizes would suggest. In order to evaluate the roles of microorganisms in ecosystems, it is essential to understand the precise natural habitats and how their activities can be explored.

Unit 1: Microbial Ecology: Interaction between abiotic and biotic factors in an ecosystem, ecological niche, limiting factor, concept of community, fluctuation and succession. Ecological pyramid, energy flow, food chain, food webs and their dynamism, stability and complexity of ecosystem. Interactions between microbes and organisms at trophic levels: commensalism, mutualism, parasitism and predation with examples. Microbial Communities: Microenvironment and niche, communities in soil, water, air. Biofilms, microbial mats and their significance.

Unit 2: Aquatic Microbiology: The aquatic environment - major environmental conditions influencing microflora. Distribution of microorganisms in the aquatic environments - freshwater environment, estuaries and marine environment. Microbiology of drinking water, water pollution, purification of water for human consumption. Assessment of microbial status in water and waste water. Wastewater characteristics, Effluent treatment processes (like trickling filter, activated sludge, oxidative pond, anaerobic digestion and chemical disinfection).

Unit 3: Plant-Microbe Interactions: Introduction, concepts and scope of agricultural microbiology, Interrelationships between plants and microorganisms, Rhizosphere and phyllosphere microorganisms and their interactions with plants. Plant pathogens (bacterial and fungal), Mechanisms of plant pathogenicity, symptoms of plant diseases, transmission of plant diseases. Signalling events in pathogenesis and resistance to pathogens. Molecular basis of plant disease control along with cultural practices, chemical and biological control. Microbial control of insects. Beneficial association between plant and microorganisms (association of plants with cyanobacteria, actinomycetes and fungus).

Unit 4: Cyanobacteriology: Origins of life and photosynthesis, Diversity of cyanobacteria, Molecular ecology and environmental genomics of cyanobacteria, comparative genomics of marine cyanobacteria, stress response-regulatory system, Molecular biology of cyanelles and chloroplast, supramolecular membrane organization; phycobilisome and phycobiliprotein structures, Use of cyanobacteria in the study of the structure and function of photosystem II and cytochrome complex; photosystem I, F-type ATPase in Cyanobacteria, Biochemistry and molecular regulation of CO2 metabolism and genetic analysis of cyanobacteria, Heterocyst metabolism and development, Differentiation of hormogonia and relationships with other biological processes.

Unit 5: Biofertilizers: Bacterial bio fertilizer: Rhizobium, Azotobacter- Azopirillum, Acetobacter diazotrophicus - phosphobacteria and Frankia. Algal fertilizer - Blue green algae, Azolla – Importance, Mass cultivation of cyanobacteria under outdoor and indoor conditions. Cyanobacteria as biofertilizer for paddy cultivation. Hydrogen production by cyanobacteria: Mechanism, progress and prospects. Fungal fertilizers - Mycorrhizae – ecto and endomycorrhiza. Principles of mass production, Quality Control and Field applications. Bioremediation: Factors affecting the bioremediation process, Bioremediation of toxic waste sites; Role of microbes; Microbial degradation of environmental pollutants- industrial solvents, pesticides, petroleum hydrocarbons, xenobiotics; bioremediation practices and technologies.

References 1. Prabhakaran, G. 2004. Introduction to Soil and Agricultural Microbiology, Himalaya Publishing House. 2. George N. Agrios. 2005. Plant Pathology. 5th Edition. Academic Press. 3. Raina M. Maier, Ian A. Pepper and Charles Gerba (2009) Environmental Microbiology (2nd edition). Academic Press. 4. Antonia Herrero & Enrique Flores. The Cyanobacteria: Molecular Biology, Genomics and Evolution, Caister Academic Press, 2008. 5. T. A. Sarma. Handbook of Cyanobacteria, CRC press, 2012. 6. Samit Ray. Cyanobacteria, New Age International Pvt. Ltd Publishers, 2006. 7. Percy M. Gault & Harris J. Marler. Handbook on Cyanobacteria: Biochemistry, Biotechnology and Applications (Bacteriology Research Developments), Nova Science Publishers, Inc. 2009.

MSc Microbiology: Semester 3 PHARMACEUTICAL MICROBIOLOGY Course Code: CMB304 Total Number of Credits: 03 Pharmaceutical Microbiology is designed introduce the students to understand the processes and mechanisms associated with anti-microbial drugs and industrial production and manufacture of pharmaceutical drugs, their quality control and testing.

Unit 1: Antibiotics and synthetic antimicrobial agents, Antibiotics and synthetic antimicrobial agents, (Aminoglycosides, β lactams, tetracyclines, ansamycins, macrolid antibiotics), Antifungal antibiotics, antitumor substances. Peptide antibiotics, Chloramphenicol, Sulphonamides and Quinolinone antimicrobial agents. Chemical disinfectants, antiseptics and preservatives.

Unit 2: Mechanism of action of antibiotics, Mechanism of action of antibiotics (inhibitors of cell wall synthesis, nucleic acid and protein synthesis), Molecular principles of drug targeting, Drug delivery system in gene therapy, Bacterial resistance to antibiotics, Mode of action of bacterial killing by quinolinones, Bacterial resistance to quionolinones, Mode of action of non – antibiotic antimicrobial agents, Penetrating defenses – How the antimicrobial agents reach the targets (cellular permeability barrier, cellular transport system and drug diffusion).

Unit 3: Microbial production and Spoilage of pharmaceutical Products Microbial contamination and spoilage of pharmaceutical products (sterile injectibles, non-injectibles, ophthalmic preparations and implants) and their sterilization. Manufacturing procedures and in process control of pharmaceuticals. Other pharmaceuticals produced by microbial fermentations (streptokinase, streptodornase). New vaccine technology, DNA vaccines, synthetic peptide vaccines, multivalent subunit vaccines. Vaccine clinical trials.

Unit 4: Regulatory practices, biosensors and applications in Pharmaceuticals Financing R&D capital and market outlook. IP, BP, USP. Government regulatory practices and policies, FDA perspective. Reimbursement of drugs and biologicals, legislative perspective. Rational drug design. Immobilization procedures for pharmaceutical applications (liposomes). Macromolecular, cellular and synthetic drug carriers. Biosensors in pharmaceuticals. Application of microbial enzymes in pharmaceuticals.

Unit 5: Quality Assurance and Validation Good Manufacturing Practices (GMP) and Good Laboratory Practices (GLP) in pharmaceutical industry. Regulatory aspects of quality control. Quality assurance and quality management in pharmaceuticals ISO, WHO and US certification. Sterilization control and sterility testing (heat sterilization, D value, z value, survival curve, Radiation, gaseous and filter sterilization) Chemical and biological indicators. Design and layout of sterile product manufacturing unit. (Designing of Microbiology laboratory) Safety in microbiology laboratory.

References 1. Pharmaceutical Microbiology – Edt. by W.B.Hugo & A.D.Russell Sixth edition. Blackwell scientific Publications. 2. Analytical Microbiology –Edt by Frederick Kavanagh Volume I & II. Academic Press New York. 3. Quinolinone antimicrobial agents – Edt. by David C. Hooper, John S.Wolfson .ASM Washington DC. 4. Quality control in the Pharmaceutical Industry - Edt. by Murray S.Cooper Vol.2. Academic Press New York. 5. Biotechnology – Edt. by H.J.Rehm & G.Reed, Vol 4. VCH Publications, Federal Republic of Germany. 6. Pharmaceutical Biotechnology by S.P.Vyas & V.K.Dixit. CBS Publishers & Distributors, New Delhi. 7. Good Manufacturing Practices for Pharmaceuticals Second Edition, by Sydney H.Willig, Murray M.Tuckerman, William S.Hitchings IV. Mercel Dekker NC New York. 8. Advances in Applied Biotechnology Series Vol 10, Biopharmaceuticals in transition. Industrial Biotechnology Association by Paine Webber. Gulf Publishing Company Houston. 9. Drug Carriers in biology & Medicine Edt. by Gregory Gregoriadis. Academic Press New York. 10. Quality Assurance in Microbiology by Rajesh Bhatia, Rattan lal Ihhpunjani. CBS Publishers & Distributors, New Delhi.

MSc Microbiology: Semester 3 MEDICAL MICROBIOLOGY Course Code: CMB305 Total Number of Credits: 03 Medical Microbiology course deals with importance of the microorganisms in human health. The basic concepts and medical terms will be explained along with information related to biosafety levels. Modes of transmission, host- pathogen interactions will be discussed in detail. Students will study important diseases by body system with reference to the etiology, pathogenesis, treatment, diagnosis and prevention of infectious diseases.

Unit 1: Basic Principles of Medical Microbiology: Bacterial morphology and bacterial structures, Commensal and pathogenic microbial flora in humans, Sterilization. Disinfection and antisepsis, Basic concepts of immune responses to infectious agents, antimicrobial vaccines, General principles of laboratory diagnosis, microscopic principles and applications, molecular diagnosis, serologic diagnosis.

Unit 2: Medical Bacteriology: Staphylococcus and related organisms, Streptococcus, Enterococcus and other Gram Positive cocci, Bacillus, Listeria and Erysipelothrix, Corynebacterium and other Gram positive rods, Nocardia and related bacteria, Mycobacterium, Neisseria and related genera, Enterobacteriaceae, Vibrio and Aeromonas, Campylobacter and Helicobacter, Pseudomonas and related organisms, Haemophilus and related bacteria, Bordetella, Brucella and Francisella, Legionella, Anaerobic spore-forming Gram positive bacilli, Anaerobic non- spore-forming Gram positive bacteria, Anaerobic Gram negative bacteria, Treponema, Borrelia and Leptospira, Mycoplasma and Ureaplasma, Rickettsia and Orientia, Ehrlichia, Anaplasma and Coxiella, Chlamydiaceae, Role of bacteria in disease.

Unit 3: Medical Virology: Mechanisms of viral pathogenesis, Antiviral agents, Laboratory diagnosis of viral diseases, Poxviruses, human herpesviruses, Adenoviruses, Papillomaviruses, Polyomaviruses, Parvoviruses, Picornaviruses, Coronaviruses and Noraviruses, Paramyxoviruses, Orthomyxoviruses, Rhabdoviruses, Filoviruses, Bornaviruses, Reoviruses, Togaviruses, Flaviviruses, Bunyaviridae, Arenaviridae, Retroviruses, hepatitis viruses, Unconventional agents and prions, Role of viruses in disease.

Unit 4: Medical Mycology: Pathogenesis of fungal diseases, antifungal agents, Laboratory diagnosis of fungal diseases, Superficial and cutaneous mycoses, Subcutaneous mycoses, Systemic mycoses caused by endemic dimorphic fungal pathogens, Opportunistic mycoses, Fungal and fungal-like infections of unusual etiology, Mycotoxins and mycotoxicoses, Role of fungi in disease.

Unit 5: Medical Parasitology: Pathogenesis of parasitic diseases, anti-parasitic agents, laboratory diagnosis of parasitic diseases, intestinal and urogenital protozoa, blood, and tissue protozoa, nematodes, trematodes, cestodes, arthropods, Role of parasites in disease.

References 1. David Greenwood, Richard Slack, John Peutherer, Mike Barer, Medical Microbiology 17th Ed., Churchill Livingstone, 2007. 2. Murray P.R., Pfaller M.A., Tenover F.C., & Yolken R.H. 2007. Clinical Microbiology, ASM Press. 3. Bauman, R.W. 2009. Microbiology: with Diseases by Body System; Benjamin Cummings 4. Sherris, John C, Medical Microbiology: An Introduction to Infectious Diseases, 2nd Edition, Elsevier. 5. David Wilks, Mark Farrington and David Rubenstein 2010. Infectious Diseases Manual: Blackwell Science. 6. George F. Brooks, Karen C. Carroll, Janet S.Butel, Stephen A. Morse. 2007. Jawetz, Melnick & Adelberg’s Medical Microbiology. 24th Ed. McGraw-Hill Professional. 7. Nester E. W., Anderson D. G. & Nester M. T. 2006. Microbiology: A Human Perspective, McGraw Hill. 8. Harvey, R.A., Champe, P.C. & Fisher, B.D. 2007. Lippincott’s Illustrated Reviews: Microbiology. Lippincott Williams and Wilkins, New Delhi/New York.

MSc Microbiology: Semester 3 MICROBIAL TECHNOLOGY Course Code: CMB306 Total Number of Credits: 03

Microbial Technology aims to help students to understand the importance of microorganisms especially with microbial production of beverages, antimicrobials, organic acids and enzymes, microbiology of wastewater and solid waste treatment, plant growth promoting rhizobacteria and renewable bioenergy using microorganisms.

Unit 1: Beverages and enzymes – Role of microorganisms in food and dairy industry. Fermented beverages-beer, wine and other alcoholic beverages. Microbial preparation of Tempeh, sauerkraut, Miso, yogurt. Probiotics. Single cell protein. Mushroom cultivation.

Unit 2: Antimicrobials, Organic acids and enzymes- microbial production of pencillin, Tetracycline and peptide antibiotics; Acetic acid; Lactic acid; Gluconic acid. Microbial production and commercial applications of Amylases, Proteases, Lipases. Biotransformation of steroids.

Unit 3: Microbiology of wastewater and solid waste treatment: - biological, aerobic, anaerobic, primary, secondary and tertiary treatments. Activated sludge and Anaerobic digestion process. Treatment of industrial effluents by microorganisms. Composting. Microbiology of degradation of xenobiotics. Bioremediation of insecticides, pesticides and heavy metals.

Unit 4: Plant Growth Promoting Rhizobacteria (PGPR). Biofertilizers- Rhizobium, Azospirillum, Azotobacter, Gluconacetobacter, Azorhizobium, phosphobacteria - mycorrhizae - Blue Green Algae and Azolla. Biopesticides - Bacillus thuringiensis, NPV, Beauveria bassiana. Mass production of biofertilizers and biopesticides.

Unit 5: Renewable bioenergy using microorganisms – Methanogenesis, Methane production by anaerobic digestion of waste organic materials. Bioethanol and Biobutanolproduction by using microorganisms. Biohydrogen Generation, Microbial Fuel. Biodiesel from algae.

References 1. W.B. Hugo & A. D. Russell, Pharmaceutical Microbiology –Wiley-Blackwell; 8th Edition (2011). Blackwell Scientific Publications. 2. Joanne M. Willey, Lansing M. Prescott Microbiology. 7th ed. McGraw-Hill Higher Education, 2008 3. Wulf Cruger and Anneliese Cruger., Biotechnoloogy, (A text book of industrial Microbiology), Panima Publishers, New Delhi, 2nd edition, 2003. 4. Waste Water Engineering - Treatment, Disposal and Re-use by Metcalf and Eddy, 3rd Edition Inc., Tata MacGraw Hill, New Delhi.

MSc Microbiology: Semester 3 Laboratory Practical PRACTICAL MICROBIOLOGY - V Course Code: PMB301 Total Number of Credits: 02

Part I: Study of normal micro-biota of mouth and skin; isolation, identification and preservation, Identification and Biochemical tests of respiratory tract bacterial pathogen (using avirulent strain of MTCC Culture of – Streptococci/Klebsiella pneumoniae. Identification and Biochemical tests of gastrointestinal bacterial infection (using avirulent strain of MTCC Culture) – Salmonella/Shigella sps. Laboratory examination and identification and biochemical tests of pus (using avirulent strain of MTCC culture) for Staphylococcus aureus, Streptococcus pyogenes and Pseudomonas aeruginosa. Laboratory examination of sputum: Collection and microbiological examination of sputum for pus cells and bacteria. Ziehl-Neelsen staining to detect Mycobacteria (using avirulent strain).

Part II: Examination of microbial load in soft drinks, ice creams, packaged and canned foods. Isolation and identification of food poisoning bacteria from contaminated foods, dairy products. Isolation and identification of food spoilage fungi from foods. Isolation, extraction and detection of aflatoxin from foods. Production and estimation of lactic acid by Lactobacillus sp./ Streptococcus sp. Role of microbes in fermented foods- Bread making, Sauerkraut. Detection of number of bacteria in milk by standard plate count (SPC). Determination of quality of milk sample by methylene blue reduction test. Assessment of water quality by multiple tube fermentation test.

MSc Microbiology: Semester 3 Laboratory Practical PRACTICAL MICROBIOLOGY - VI Course Code: PMB303 Total Number of Credits: 03

Part I: Bioassay of nicotinic acid, Production of ethanol by yeast, Isolation of amylase producing microorganisms from soil, Isolation of protease producing microorganisms from soil, Isolation of lipase producing microorganisms from soil, Production and extraction of thuricides, Laboratory production of biofertilizers, Production and quantification of citric acid, Demonstration: Reactor Studies: Batch, fed-batch, and continuous flow reactor analysis and residence time distribution, Demonstration: Down-stream processing lab, Determination of specific growth rate in submerged fermentations, Production of wine from grape juice, Preparation of fermented food: curd, cheese and alcohols, Isolation and characterization of plant growth promoting bacteria.

Part II: Isolation and identification of nitrogen-fixing bacteria from soil, Splash liberation of fungal spores from diseased tissue, Seed health testing by using Standard Blotter Method, Estimation of phenols from healthy and diseased plant tissues, Degradation of cellulose by fungi (Chaetomium), Associative and antagonistic relationships among soil microorganisms, Microbial management of organic wastes, Microbial degradation of oil, Isolation of hydrocarbon and heavy metal tolerant microorganisms, Production and analysis of Polyhydrxy butyrates (PHB).

Part III: Isolation HMW DNA, DNA cloning and expression in E. coli cells, end repairing and cloning in fosmid/BAC, restriction analysis, polymerase chain reaction-Gradient, RT-PCR (demo), 16S typing, Mega software, Entrez Human genome map viewer.

MSc Microbiology: Semester 4 BIOMEDICAL TECHNIQUES Course Code: EMB401 Total Number of Credits: 03 Biomedical Techniques course aims to introduce various biomedical research techniques and instrumentation methods required in microbiology.

Unit 1: Microscopy- Principles and applications, simple, compound, phase-contrast and fluorescent microscopes. Centrifugation Techniques: Principles, type of centrifuges, buoyant and density gradient centrifugation, ultracentrifuges.

Unit 2: Spectroscopy - Electromagnetic spectrum, Beer and Lambert’s Law. Photometry, UV/VIS Spectrophotometry, Infrared spectroscopy, Atomic absorption spectroscopy, ESR and H and C NMR spectroscopy. Mass spectroscopy (LC-MS, GC-MS). Fluorescent spectroscopy, principle, instrumentation and application of MALDI-TOF.

Unit 3: Chromatography - Introduction and types of chromatography, paper, thin layer, gas, partition, Gel permeation, ion-exchange, HP-TLC, HPLC, FPLC and affinity chromatography and instrumentation. Applications of chromatographic techniques in microbiology.

Unit 4: Electrophoresis and Blotting techniques - Paper and gel electrophoresis, PAGE (native and SDS), Agarose gel electrophoresis, PFGE, Blotting- Southern, Western and Northern blotting, Immunoblotting, Labelling and Detection methods - Nature and types of radiations, preparation of labelled biological samples. Detection and measurement of radioactivity, GM counter, Scintillation counter, Autoradiography, Flow cytometry and data analysis. Safety measures in handling radioisotopes. RIA, non-radiolabelling.

Unit 5: DNA sequencing methods - Major landmarks in DNA sequencing - Maxam-Gilbert sequencing, Chain-termination methods, Advanced methods and de novo sequencing, Shotgun sequencing, Next-generation methods, Massively Parallel Signature Sequencing (MPSS), Polony sequencing, 454 pyrosequencing, Illumina (Solexa) sequencing, SOLiD sequencing, Ion semiconductor sequencing, DNA nanoball sequencing, Heliscope single molecule sequencing, Single molecule real time (SMRT) sequencing.

References 1. Gerard J. Tortora, Berdell R. Funke, Christine L. Case. Microbiology-An Introduction.11th edition Pearson, 2013. 2. Schaechter, M. Ingraham, J.L. and Neidhardt, F.C. 2006. Microbe. ASM Press, Washington. 3. Perry, J.J., Staley, J.T. and Lory, S. 2002. Microbial Life. Sinauer Associates, Publishers, Sunderland, Massachusetts. 4. J. C. Pommerville, Alcomos Fundamentals of Microbiology. I.E. 2013. 9th Edition, Jones and Bartlett Publishers, Sudbury, Massachusetts.

MSc Microbiology: Semester 4 DIAGNOSTIC MICROBIOLOGY Course Code: EMB402 Total Number of Credits: 03 Diagnostic Microbiology aims to understand the principles, and technical advancements in the diagnosis, treatment and control of infectious diseases that continue to pose major challenges in laboratory and medical care.

Unit 1: General Principles in Clinical Microbiology: Safety and specimen management, Approaches to diagnosis of infectious diseases, Role of microscopy, Traditional cultivation and identification, nucleic acid-based analytic methods for microbial identification and characterization, Immunochemical methods used for organism detection, Serologic diagnosis of infectious diseases, Evaluation of antimicrobial activity: Principles of antimicrobial action and resistance, Laboratory methods and strategies for antimicrobial susceptibility testing.

Unit 2: Principles of Identification: Overview of bacterial identification methods and strategies, Staphylococcus and Micrococcus, Streptococcus and Enterococcus, Bacillus, Listeria, Corynebacterium, Erysipelothrix, Lactobacillus, Nocardia, Streptomyces, Rhodococcus, Enterobacteriaceae, Acinetobacter, Stenotrophomonas, Pseudomonas, Burkholderia, Vibrio, Aeromonas, Bordetella, Moraxella, HACEK, Haemophilus, Campylobacter, Helicobacter, Legionella, Brucella, Bordetella, Francicella, Neisseria, mycobacteria, Anaerobes, Obligate intracellular and non-cultivable bacteria, cell wall-deficient bacteria, spirochetes.

Unit 3: Parasitology: Laboratory methods for the diagnosis of parasitic infections, intestinal protozoa, blood and tissue protozoa, other protozoa, Intestinal nematodes, tissue nematodes, blood and tissue nematodes, intestinal cestodes, tissue cestodes, intestinal trematodes, liver and lung trematodes, blood trematodes.

Unit 4: Mycology: Laboratory methods for the diagnosis of fungal infections, Hyaline molds, Mucorales, dermatophytes, opportunistic and systemic mycoses, dematiaceious molds, Pneumocystis jiroveci, yeasts, antifungal susceptibility testing, therapy, and prevention.

Unit 5: Virology: Overview of the methods and strategies in virology, viruses in human disease, antiviral therapy, susceptibility testing and prevention.

References 1. David Greenwood, Richard Slack, John Peutherer, Mike Barer, Medical Microbiology 17th Ed., Churchill Livingstone, 2007. 2. Murray P.R., Pfaller M.A., Tenover F.C., & Yolken R.H. 2007. Clinical Microbiology, ASM Press. 3. Bauman, R.W. 2009. Microbiology: with Diseases by Body System; Benjamin Cummings 4. Sherris, John C, Medical Microbiology: An Introduction to Infectious Diseases, 2nd Edition, Elsevier. 5. David Wilks, Mark Farrington and David Rubenstein 2010. Infectious Diseases Manual: Blackwell Science. 6. George F. Brooks, Karen C. Carroll, Janet S.Butel, Stephen A. Morse. 2007. Jawetz, Melnick & Adelberg’s Medical Microbiology. 24th Ed. McGraw-Hill Professional. 7. Harvey, R.A., Champe, P.C. & Fisher, B.D. 2007. Lippincott’s Illustrated Reviews: Microbiology. Lippincott Williams and Wilkins, New Delhi/New York.

MSc Microbiology: Semester 4 DRUG DESIGN & DISCOVERY Course Code: EMB403 Total Number of Credits: 03 Pharmaceutical Microbiology & Drug Discovery course introduce the basic principles of modern drug design, discovery and development. The course deals with the different source of drug with specific focus on microbial source, drug development and manufacturing process. The course will have more focus on detection, selection, and validation of new antibacterial targets, vaccines and the use of gene technology in pharmaceutical industry.

Unit 1: Introduction: History of drug design, Current approaches and philosophies in drug design, Mechanisms of action of antibiotics, and drugs with examples. Pharmaceutical products, Pharmaceuticals of microbial origin (macrolides, ansamycin, peptide and other antibiotics).

Unit 2: Sources of Drugs: Microbial drugs, E. coli as a source of recombinant therapeutic proteins. Expression of recombinant proteins in yeasts, animal cell culture systems. Additional production systems: Fungal production systems, Transgenic animals, Transgenic plants and Insect cell-based systems. Rational drug design and Combinatorial approaches to drug discovery.

Unit 3: Drug Development Process: Impact of genomics and related technologies upon drug discovery: Gene chips, proteomics, structural genomics and pharmacogenetics. Drug manufacturing process- Guides to good manufacturing practice, production of final product - cell banking systems, Upstream processing, microbial cell fermentation, mammalian cell culture systems, downstream processing, final product formulation, freeze-drying, labelling and packing.

Unit 4: Vaccines & Adjuvants: Traditional vaccine preparations, attenuated, dead or inactivated bacteria, Attenuated and inactivated viral vaccines, Toxoids, antigen-based and other vaccine preparations. Impact of genetic engineering on vaccine technology. Peptide vaccines Vaccine vectors. Development of an AIDS vaccine, difficulties associated with vaccine development, AIDS vaccines in clinical trials, Cancer vaccines, recombinant veterinary vaccines. Adjuvant technology: Adjuvant-mode of action, mineral-based adjuvants, oil-based emulsion adjuvants Bacteria/bacterial products as adjuvants.

Unit 5: Nucleic Acids as Drugs: Gene therapy: Basic approach to gene therapy, vectors used in gene therapy -Retroviral vectors, additional viral-based vectors, manufacture of viral vectors, non-viral vectors. Gene therapy and genetic disease, cancer, gene therapy and AIDS, gene- based vaccines.

References 1. Povl Krogsgaard-Larsen, Ulf Madsen and Kristian Stromgaar. Textbook of Drug Design and Discovery, Fourth Edition, CRC press, 2009. 2. Kenneth M. Merz, Dagmar Ringe and Charles H. Reynolds. Drug Design: Structure and Ligand-Based Approaches, Cambridge University press, 2010. 3. Thomas J. Dougherty and Steven J. Projan. Microbial Genomics and Drug Discovery, Taylor and Francis, 2003. 4. Tommy Liljefors, Povl Krogsgaard-Larsen and Ulf Madsen. Textbook of Drug Design and Discovery, Third Edition, Taylor and Francis, 2002

MSc Microbiology: Semester 4 APPLICATIONS OF NANOTECHNOLOGY IN MICROBIOLOGY Course Code: EMB404 Total Number of Credits: 03 This discipline helps to indicate the merger of biological research with various fields of nanotechnology. This technical approach to biology allows scientists to imagine and create systems that can be used for biological research. The most important objectives that are frequently found in nanobiology involve applying nanotools to relevant medical/ biological problems and refining these applications. Developing new tools for the medical and biological fields is another primary objective in nanotechnology. Microbes are playing an important role in the synthesis of nanoparticles. This syllabus would enlighten the students to understand basic concepts and application of nanotechnology.

Unit 1: Introduction to Nanotechnology: Characteristic scale for quantum phenomena, nanoparticles, nano-clusters, nanocomposite, nanotubes, nanowires and emergence of bionanotechnology. Characterization of nanoparticles – UV-VIS spectroscopy, Electron Microscopy – HRTEM, SEM, AFM, EDS, XRD.

Unit 2: Microbial nanotechnology –Microbial synthesis of Nanoparticles. Synthesis of nanodrugs – metal nanoparticles and drug delivery vechicles – Nanoshells – Tectodentrimers Nanoparticle drug systems – Diagnostic applications of nanotechnology.

Unit 3: Preparation of nanobiomaterials – Polymeric scaffolds collagen, Elastins: Mucopolysaccharides, proteoglycans, cellulose and derivates, Dextrans, Alginates, Pectins, Chitin. Nanoparticles – types, functions – Silver, Gold and Titanium. Physical and chemical properties of nanoparticles.

Unit 4: Nanoscale applications in biology and medicine: Nanotechnologies for biology and medicine - Micro- and nano- fluidics - Scanning probe microscopy in biology and medicine - Selfassembly of biological molecules. Drug delivery – protein mediated and nanoparticle mediated. Hybridconjugates of gold nanoparticles – DNA oligomers – use of DNA molecules in nanomechanics and Computing. Nanoparticles as carrier for genetic material. Genetically Modified Organisms (GMO) and applications.

Unit 5: Implications of nanotechnology: Health and safety implications from nanoparticles: Health issues – Environmental issues – Need for regulation – Societal implications: Possible military applications – Potential benefits and risks for developing countries – Intellectual property issues – Criticism of Nanotechnology – Studies on the implications of Nanotechnology.

References 1. Parthasarathy, B.K. (2007). Introduction to Nanotechnology, Isha Publication. 2. Elisabeth Papazoglou and Aravind Parthasarathy (2007). Bionanotechnology. Morgan & Claypool Publishers. 3. Bernd Rehm (2006). Microbial Bionanotechnology: Biological Self-assembly Systems and Biopolymer-based Nanostructures. Horizon Scientific Press. 4. David E. Reisner, Joseph D. Bronzino (2008). Bionanotechnology: Global Prospects. CRC Press. 5. Ehud Gazit (2006). Plenty of Room for Biology at the Bottom: An Introduction to Bionanotechnology. Imperial College Press.