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M.Sc. Microbiology (Effective from June 2013) Semester I (25 credits): Course work- 17 credits, laboratory- 8 credits MBY 2101: General Microbiology and Microbial Systematics (3 credits) Microbiological techniques : Enrichment, pure culture, identification, Cultivation, preservation of microorganisms Control of microorganisms : Sterilization methods, disinfection, sterility testing of substances Ultrastructure of bacteria : Endospore, cell wall, flagella, cell membrane, pili, Capsule Bacterial nutrition : Major and minor bioelements, nutritional diversity, oxygenic & anoxygenic, photosynthesis, respiration, fermentations, chemolithotrophy, syntrophy Microbial systematics, evolution and biodiversity : Classification of bacteria : GC content analysis and nucleic acid hybridization, 16S rRNA sequence based phylogeny. Archaebacteria. Origin of life: universal ancestor, origin of eukaryotic cells MBY 2102: Medical Microbiology and Introductory Immunology- I (3 credits) Host-Parasite relationship : Nonspecific host defenses, virulence factors, normal flora and gnotobiology Epidemiology : Infectious diseases, disease cycle, epidemiological methods, diagnostic principles, control, prevention, antimicrobial therapy. Bacterial diseases : Pathogenesis, diagnosis, prevention and treatment of diseases caused by Staphylococcus, Streptococcus, Neisseria, Shigella, Salmonella, Mycobacteria, Treponema Immunology: History, cells and organs of the immune system. Antigens types and properties. Antibody structure & function Antigen-antibody interactions. Immunological techniques. Organization and expression of immunoglobulin genes. MBY 2103: Biochemistry- I(4 credits) Protein structure : amino acids, peptide bond, primary, secondary, tertiary and quarternary structure, determination of sequence, N-terminal & C-terminal analysis. Concepts of pH and buffer, chemical bonds. Principles of Bioenergetics: Anabolism, catabolism, free energy, Laws of thermodynamics, Biological oxidation-reduction, high energy compounds. Carbohydrate chemistry : structure, properties and classification, stereo chemistry, function of carbohydrates, storage polysaccharides etc. Urea cycle Lipid Chemistry & Metabolism Vitamins: Fat soluble, water soluble and coenzyme form : biosynthesis, functions, reaction Introduction to enzymes: classification, enzyme assays, purification. MBY 2104: Introductory Molecular Biology & Genetic Engineering (4 credits) Classical genetics : Mendel’s Laws, Linkage & Complementation, Genetic Mapping Gene expression in bacteria: Operon Concept, regulation of lac, ara, trp & gal operons. Genetic engineering : Enzymes in DNA manipulation- Restriction-modification enzymes, ligases, polymerases etc. Vectors : plasmid, phage, cosmids, expression etc. Basic techniques in Molecular biology and genetic engineering : Southern & Northern hybridization & preparation of labelled probes, DNA sequencing, PCR & Applications. Cloning strategies-Library construction & screening of recombinant clones. MBY 2105: Biophysics & Environmental Microbiology (3 credits) History of Microbiology Microbiology of air and monitoring air pollution. Microbiology of water: Microbiological examination of water, indicator microorganisms, disinfection, purification processes. Waste-water treatment : Characterisation of wastewater, self purification, conventional sewage treatment process, Microbiology of treatment plants, low cost plants and advances in treatment plants. Pollutants and microbial interactions : Origin and dispersal of pollutants, types of pollutantspesticides, hydrocarbons, surfactants, synthetic polymers, metals, monitoring pollutants. Biodegradation of representative pollutants and xenobiotic compounds. Bioremediation Technology : bioremediation of soils and ground water, bioventing of petroleum hydrocarbons, bioremediation of oil spills. Environmental impact assessment Microbial technology: Bioleaching, Biopesticides Study of techniques used for Biomolecules, UV, visible absorption spectroscopy, Fluorescence spectroscopy, circular dichroism. Semester II (25 credits) Course work- 16 credits, laboratory-6 credits, seminar-1credit, Dissertation-2 credit MBY 2201: Microbial diversity and techniques (3 credits) Microscopy : General principles and optics of bright field, phase contrast, dark field, fluorescence, differential interference, microscopes etc. Electron microscope & advanced microscopes (confocal laser scanning microscope, environmental scanning electron microscope) Bacterial growth kinetics & measurements : methods of estimation, growth curve, factors affecting growth, batch, continuous and fed batch growth, synchronous growth, Microbial physiology of diverse Groups thermophiles, psychrophiles, halophiles Physiology and Biochemistry of nitrogen fixing bacteria. Cyanobacteria, General characteristics of actinomycetes fungi and yeasts : classification , life cycle and cell structure. MBY 2202: Medical Microbiology and Introductory Immunology II (3 credits) Mycoses : Superficial, Subcutaneous and systemic mycosis Rickettsia, mycoplasma and chlamydia: general characteristics, pathogenesis, diagnosis, prevention and treatment of their disease Viral diseases : General characters, pathogenesis, diagnosis, prevention and treatment of diseases caused by Polio virus, Hepatitis, Rabies, Mumps, Influenza, Herpes, HIV Protozoan diseases: Representative examples Immunology: MHC complex. Antigen processing & presentation Cell mediated immunity. Immune effector mechanisms: cytokines, Complement system. Hypersensitivity. Immune response to infectious diseases. Vaccines and Monoclonal antibodies. MBY 2203: Biochemistry- II (3 credits) Principles and applications of basic techniques : Electrophoresis, Centrifugation, and ultracentrifugation, Chromatographic techniques, Radioisotopes, X-ray crystallography. Carbohydrate Metabolism: Glycolysis, gluconeogenesis, TCA cycle, ED pathway, HMP shunt - History, reactions, enzymes involved, regulation, distribution and energetics Amino acids chemistry and metabolism : classification and properties Elucidation of biosynthetic pathways, biosynthesis & catabolism of aromatic amino acids, branched amino acids, aspartate family, glycine, serine. Purine-pyrimidine metabolism MBY 2204: Introductory Genetics & Molecular Biology (4 credits) Introduction to yeast genetics. Drosophila , p elements DNA structure and properties Genetic code. Gene expression in bacteria: Transcription, promoters and RNA polymerases Introduction to bacteriophages : General characteristics and physiology of single stranded DNA phages and RNA phages, life cycles of T series phages Lambda phage- Regulation of lytic and lysogenic cycles. MBY 2215: Microbial ecology and Biostatistics (3 credits) Microbial Ecology : microbial interactions, community structure and activity. Aquatic Microbiology : Habitats and microbial communities, biofilms Methods: nucleic acid probes, radioisotopes, microelectrodes, community fingerprinting, microbial activity measurements. Microbial diversity indices. Geochemical cycling: C, N, S, P, Fe cycles. Plant pathology and plant defense Biofertilisers Dairy microbiology : microbiology of milk and milk products, cheese making. Food microbiology : enumeration of microorganisms in food, preservation and spoilage, fermented foods, food borne, Infections, food intoxications. Food flavors, Genetically modified foods. Biostatistics : Distributions - normal, binomial and Poisson, mean variance, standard deviation and standard error. Coordination and regression; Test of significance; Analysis of variance Semester III (25 credits) Course work- 16 credits, laboratory-6 credits, seminar-1 credit, dissertation-2 credits MBY 2301: Molecular Biology - 1 ( 4 credits) Genome organization in eukaryotes: chromosome structure and chromatin. Mutations : Types of mutations, inheritance in bacteria, adaptive mutations, molecular basis of spontaneous lesions and mutations, suppressor mutations, reversions, site directed mutagenesis, mutations and disease Eukaryotic Transcription : General features, enzymes & proteins in transcription machinery & regulation Transposable genetic elements : prokaryotes classification, IS elements, composite transposons, TnA family, mechanism of transposition MBY 2302: Biochemical Engineering & Industrial Microbiology -II ( 3 credits) Fermentation principles : Different types of fermentative approaches, economics of fermentation, raw materials, design of mechanically & non-mechanically agitated fermenters, animal and plant cell cultivation. Fermentation process : Screening of organisms and strain improvement. Downstream processes for fermentation product Typical fermentations : Kinetics and fermentative production of antibiotics (penicillin, streptomycin), organic acids (citric acid), amino acids (glutamic acid, lysine), vitamins (B12), solvents (ethanol), recombinant DNA products MBY 2303: Cell Biology & Enzymology -I ( 3 credits) Oxidative phosphorylation : Electron transport system in bacteria, mitochondria and chloroplast. Uncouplers and inhibitors, Theories of oxidative phosphorylation, ATPase – structure function Photosynthesis in bacteria and plants : Organization, apparatus, electron donors and acceptors, energetics. Organellar cell biology : Structure, and biogenesis of chloroplast and mitochondria, lysosomes, Protein translocation in eukaryotes: cytoskeleton, motor proteins Eukaryotic cell division cycle: Mitosis, Meiosis, Cyclins, regulation of cell cycle Enzyme kinetics : steady state kinetics, MichaelisMenten equation, significance of kinetic constants, plots, single substrate kinetics, enzyme inhibition kinetics, two substrate kinetics, presteady state kinetics. Immunology TCR, Thymic selection, T cell activation and differentiation, T cells generation and function MBY 2304: Microbial genetics and genomics (3 credits) Transduction : Generalized, restricted , linkage and mapping. Transformation : Discovery, competence development, molecular mechanism of DNA uptake, mapping. Conjugation : History, mechanism, Hfr transfer, linkage, mapping, F-plasmid and conjugative plasmids structure and function Strain construction & problems in genetics. Microbial genomics : Physical mapping, genome sequencing & annotation, functional genomics, transcriptome & proteome analysis, positional cloning, comparative genomics. Techniques : RAPD, RFLP mapping, pulse field gel electrophoresis, FISH, microarrays, Mass spectrometry. Bacterial vectors : Plasmids : Introduction, classification, incompatibility, copy number control & plasmids vector. Phage lambda as vector MBY 2305: Microbial Physiology and Biophysics (3 credits) Microbial adaptation to stress : temperature, salt and oxidative stress. Transport in prokaryotes : Types, methods of study, transport of sugars, amino acids, organic acids, iron. Secretion systems in bacteria Antibiotics : Biosynthesis, mode of action, regulation, genetics, hybrid antibiotics. Protein folding and stability Semester IV (25 credits) Course work - 15 credits, Practical-2 credits, Dissertation-6 credits, Viva-2 credits MBY 2401: Molecular Biology –II (3 credits) DNA replication : General features, replication in prokaryotes- E. coli and phages, replication in eukaryotes – animal viruses, yeast and higher eukaryotes. DNA repair : methods and mechanisms DNA recombination : models and mechanisms Eukaryotic Transcription & RNA processing :Post transcriptional modification, splicing, RNA editing, ribozymes. Translation in prokaryotes & eukaryotes : Components of translational machinery, ribosome synthesis, functions of tRNA & rRNA, Initiation, elongation, termination of translation, posttranslational modifications. Non-coding RNA, RNA silencing MBY 2402: Biochemical Engineering & Industrial Microbiology II ( 3 credits) Fermentation process : Air sterilization, Media sterilization, aeration and mixing in bioreactors, approaches for production at larger scale, instrumentation, control. Biotransformation of steroids Microbial production of enzymes : amylases, proteases, glucose isomerases, penicillin acylases. Immobilization of enzymes and cells : techniques and processes. Biosensors. MBY 2403: Cell Biology & Enzymology - II (3 credits) Membrane biology : Structure, function, membrane protein transport in eukaryotes Cell biology :cell junction and cell adhesion, extracellular matrix composition, diversity Signal transduction in eukaryotes : MAP kinase pathway, G-proteins, protein kinases, Phosphoinositides Immunology: Immune tolerance and autoimmunity, Leukocyte trafficking, Chemokines and receptors Enzyme kinetics : Mechanism of enzyme action : transition state theory, active site mapping. Case studies of chymotrypsin, lysozyme Allostery. Hill, Adair, MWC, KNF models. Case studies of aspartate transcarbamylase, hemoglobin. MBY 2419: Bioinformatics and Microbial differentiation (3 credits) Phage genetics : Mutations & recombination in phages. Microbial differentiation and regulation: Yeast mating types switching mechanismand regulation. Genetics of bacterial cell division. Genetics of sporulation in Bacillus. Genetics of nod and nif regulation in nitrogen fixation. Bioinformatics : Introduction to internet resources & databases, analysis of biological data: sequence analysis, similarity search -BLAST, multiple sequence alignment- CLUSTAL W, phylogenetic analysis, protein structure analysis. Yeast genetic engineering : vectors and cloning, yeast two hybrid system. MBY 2420: Microbial physiology and molecular pathogenesis (3 credits) Physiology of autotrophs & anaerobic respiration : autotrophic CO2 fixation, hydrogen bacteria, nitrifying bacteria, sulphur bacteria, iron bacteria, methanogens. Signal transduction prokaryotes : two component systems, chemotaxis, receptor structure & function. Quorum sensing (bioluminescence) Molecular pathogenesis : Horizontal gene transfer; pathogenicity islands, type three secretory system, regulation of virulence genes, evolution of pathogen. Molecular pathogenesis of Shigella. Cancer: characterization, retroviruses, oncogen, angiogenesis, therapy. Advances in pathogenesis: malarial research & prions IPR, patents Practicals 1. 2. 3. 4. 5. 6. SEMESTER I & II 7. 8. 9. 10. 11. 12. 13. 14. 15. Methods of sterilisation Laboratory equipments (autoclave, incubator) Preparation of media Aseptic technique Pure culture techniques Observation of bacteria : i) Staining : a) Simple techniques b) Differential techniques c) Special techniques ii) Demonstration of motility iii) Measurement of bacterial size Bacteria growth : Growth curve Relationship between cell number and turbidity Enumeration of bacteria (viable count) : Pour plate technique and spread plate method Phage titre and One step growth curve of E. coli phage Microbial control : Phenol coefficient Cultivation and morphology of common moulds auxotrophs and complementation studies sporulation and segregation of markers 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. Medical Microbiology : Identification of Gm- and Gm+ (medically important) bacteria according to Bergey's manual. Antibiotic sensitivity test 8) Immunology and Serology : Single radial diffusion Ouchterlony and immunoelectrophoresis Widal 9) Hematology : Blood grouping TLC, DLC Concept of pH, buffers, measurements and preparation Beer-Lamberts law Concept of molarity, normality etc. analytical problems 13. Separation methods : i) Paper chromatography 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. 28. 29. 30. - a) amino acid b) sugars ii) PAGE-proteins Biochemical estimations : Different methods of sugar estimations - Cole's, Hanes, Nelson-Somogii, DNSA Amino acids : methionine, proline, tryptophan Vitamins : ascorbic acid, dehydroascorbic acid Antibiotics : penicillin, streptomycin Proteins : Lowry's and Bradford's method Isolation and estimation of protein from milk Phosphatase assay Phosphate estimation : Fiske, Subbarow method Isolation of chromosomal DNA and RNA : Characterization by agarose gel electrophoresis, quantitation Isolation of microorganisms from various habitats e.g. soil, water, air, skin, root, nodules, sewage. Soil Microbiology : i) Winogradsky's column preparation : a) Isolation of anaerobes, denitrifiers by sloppy agar method ii) Enrichment culture technique for amylase producing bacteria nitrogen fixers phosphate solubilisers Wastewater Microbiology : Enrichment and enumeration of bacteriophages from sewage 31. COD determination 32. BOD determination 33. Water Microbiology : i) MPN technique 34. Food and Milk Microbiology : 35. Methylene blue reduction test 36. Phosphatase 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. 28. 29. 30. 31. 32. 33. 34. 35. 36. 37. 38. SEMESTER III & IV Effect of UV radiation on bacteria Isolation, enrichment and identification of mutants by UV and chemical mutagenesis : auxotrophic mutants pigmentless mutants repair deficient mutants mutants in carbohydrate metabolism Study of Tn5 transposition and isolation of transposon induced mutants Plasmid isolation by -alkaline lysis method SDS-boiling method Minipreps and large scale preparation Restriction enzyme digestion and agarose gel electrophoresis Recovery of DNA from agarose gels by various methods Cloning of genomic DNA and screening by insertional inactivation and blue/white assay PCR amplification of 16s rRNA gene Fermentative production of alcohol and determination of production efficiency Determination of kLa by dynamic method Immobilisation of enzymes Immobilization of microbial cells and application for conversion of sucrose to reducing sugars Determination of oxygen transfer rate by sulfite oxidation method Assay of enzymes : a) amylase; b) invertase; c) peroxidase; d) -galactosidase; e) protease etc., Immobilization of yeast invertase & inversion of sucrose using fluidized bed column. Enzyme kinetics : Determination of Km and Vmax Inhibition kinetics Effect of pH Determination of t½ at different temperatures and factors influencing temperature stability Use of inhibitors for active site amino acid determination SDS-PAGE analysis of proteins Native PAGE and activity staining of enzymes Immunology a) Isolation of lymphocytes, separation of macrophages b) Purification of antibodies c) Cell culture handling d) Fluorescent antibody test using macrophages Preparation of competent cells Plasmid transformation Effect of DNA concentration on transformation efficiency Conjugation in E. coli : Hfr mediation gene transfer Mapping of chromosomal DNA by interrupted mating Zygotic induction Transduction : a) P1 transduction; b) determination of linkage of chromosomal markers by b) cotransduction frequency 39. Bioinformatics : a) Sequence alignment : BLAST b) Multiple alignment and phylogeny c) Discovering motifs in sequences – MEME d) Searching for motifs in database – MAST e) Predicting protein structure PSI – BLAST