MI 402 BIOPHYSICS & INSTRUMENTATION
MI 403 ENVIRONMENTAL MICROBIOLOGY
MI 404 COMPUTER APPLICATIONS AND BIOSTATISTICS
Laboratory MI 405 and MI 406
MI 502 MICROBIAL PHYSIOLOGY & BIOCHEMISTRY
MI 503 BIOPROCESS AND FERMENTATION TECHNOLOGY
MI 504 ENVIRONMENTAL BIOTECHNOLOGY
Laboratory MI 505 and MI 506
MI 602 IMMUNOLOGY
MI 603 MICROBIAL BIOTECHNOLOGY
MI 604 ENZYMOLOGY AND ENZYME TECHNOLOGY
Laboratory MI 605 and MI 606
¨ Evolution of cell :
Cell as a unit of living organism.
Evolution and structure of prokaryotic cell
Evolution of eukaryotic cell
¨ Major structural and functional features of eukaryotic cells :
Plasma membrane, Cell organells endoplasmic reticulum, golgi complex, lysosomes, vacuoles, peroxisomes, mitochondria, chloroplast, cytoskeleton, microtubules, nucleus, extracellular matrixes, etc.,
¨ Nucleic acids as genetic information carriers: experimental evidence. DNA structure: historical aspects and current concepts, melting of DNA. DNA replication : general principles, various modes of replication, isolation and properties of DNA polymerases, proof reading, continuous and discontinuous synthesis. Asymmetric & dimeric nature of DNA polymerase III and simultaneous synthesis of leading and lagging strands, DNA polymerase, exonuclease activity in eukaryotic DNA polymeases. Superhelicity in DNA, linking number, topological properties, mechanism of action of topoisomerases.
¨ Initiation of replication of single stranded DNA. Construction of replication fork in test tube. Retroviruses and their unique mode of DNA synthesis. Relationship between replication and cell cycle. Inhibitors of DNA replication (blocking precursor synthesis, nucleotide polymeriztion, altering DNA structure).
¨ Structural features of RNA (rRNA, tRNA and mRNA) and relation to function. Initiator and elongator class of tRNA, ribosome binding site on mRNA and corresponding site on rRNA, peptidyl transferase activity of 23S rRNA. Transcription : general principles, basic apparatus, types of RNA polymerases, steps : initiation, elongation and termination, inhibitors of RNA synthesis. Polycistronic and monocistronic RNAs. Control of transcription by interaction between RNA polymerases and promoter regions, use of alternate sigma factors, controlled termination : attenuation and antitermination.
¨ Regulation of gene expression : operon conept, catabolite repression, instability of bacterial RNA, positive and negative regulation, inducers and corepressors. Negative regulation E. coli lac operon; positive regulation E. coli ara operon; regulation by attenuation his and trp operons; antitermination N protein and nut sites in I. DNA binding proteins, enhancer sequences and control of transcription. Identification of protein binding sites on DNA. Global regulatory responses : heat shock response, stringent response and regulation by small molecules such as ppGpp and cAMP, regulation of rRNA and tRNA synthesis.
¨ Maturation and processing of RNA : methylation, cutting and trimming of rRNA; capping, polyadenylation and splicing of mRNA; cutting and modification of tRNA degradation systems. Catalytic of RNA, group I and group II intron splicing, RNase P.
¨ Basic features of the genetic code. Protein synthesis : steps, details of initiation, elongation and termination, role of various factors in the above steps, inhibitors of protein synthesis. Synthesis of exported proteins on membrane-bound ribosomes, signal hypothesis. In vitro transcription and translation systems.
Reference books :
1. Genes VII. Lewin (Oxford University Press) 2000.
2. E.coli and Salmonella, Cellular and molecular biology, 2nd edition.
3. Bookman Neidhardt et. al 1996. (ASM press).
4. Molecular cell biology (W.H.Freeman) by Lodish, Berk, Zippursky.
5. Matsudaira, Baltimore, Darnell, 4th edition, 2000.
¨ Introduction to biophysics : Molecular organization, different levels, organization of proteins primary, secondary, tertiary and quaternary structures.
¨ Conformational analysis : Nucleic acids and their organization in living cells; Interactions of nucleic acids.
¨ Methods in biophysical analysis : CD, ORD & fluorescence spectroscopy, Raman spectroscopy.
¨ Separation and characterization of biomolecules using centrifugal, electrophoretic and chromatographic techniques.
¨ Absorption and emission spectroscopy Theory, instrumentation and applications of Visible, UV, IR, AAS, NMR, ESR and MS spectroscopy.
¨ Characterization of macromolecules using X-ray diffraction analysis.
¨ Use of analytical microscopy in elucidating the structure-function relationship in prokaryotes : Electron microscopy, phase contrast and fluorescence microscopy and scanning tunneling microscopy.
¨ Radio isotope techniques : Detection and measurement of radioactivity, Geiger Muller counters, Scintillation counting, Autoradiography and RIA; Applications of isotopes in biological studies.
Reference Books :
Physical Biochemistry : David Freifelder.
Instrumental methods of analysis : Willard, Merrit, Dean and Settle.
Spectroscopy: D.R.Browning
Principles and techniques of practical Biochemistry: Wilson and Walker
Instrumental methods of analysis: D.A.Skoog
MI 403 : ENVIRONMENTAL MICROBIOLOGY
¨ Environment : Basic concepts
¨ Global Environmental Problems
Nitrogen
Phosphorous
Sulfur
¨ Biological Nitrogen Fixation in detail :
Structure, function and genetic regulation of nitrogenases.
Asymbiotic and symbiotic nitrogen fixation.
¨ Waste Pollution : Physical, Chemical, Biological and its consequences
Eutrophication and its control
¨ Biodeterioration :
Metals, Pharmaceuticals, wood, leather, textiles etc.
¨ Biodegradation of xenobiotic compounds
Aliphatic and aromatic hydrocarbons
Polydromatic and Halogenated hydrocarbons
Pesticides
Dyes etc.
Factors influencing biodegradation of xenobiotics
¨ Biodegradation of lignin and its applications
¨ Microbial Production of environmental pollutants
¨ Microbial diversity in extreme environments of pH, temperature and salts
Physiology and Molecular adaptation to stresses in halophiles, thermophiles psychrophiles etc.
Biotechnological applications / potential of extremophiles
¨ Air pollution
Reference Books :
Comprehensive Biotechnology. Murray Moo Young. Vol. - 4
Biotechnology. Rehm and Reid
Microbes in extreme environments. R. A. Hubert and G. A. Codd.
Environmental Microbiology. R. M. Maier, I. L. Pepper & G. P. Gerba.
MI 404 : COMPUTER APPLICATIONS AND BIOSTATISTICS
History, development and types of computers.
General awareness of computer systems hardware and software (CPU and other peripheral devices, computer arithmetic, computer logic, programming languages machine language, assembly language, higher level languages).
Definitions and scope of Biostatistics : Variable in biology, collection, classification and tabulation of data. Graphical and diagrammatic representation, histogram, frequency polygon, frequency curve.
Descriptive statistics : Measures of central tendency Mean (arithmetic, harmonic and geometric), Median and Mode.
Measures of dispersion Standard deviation and standard errors.
Elements of probability theory. Probability distributions binominal, Poisson and normal distribution. Correlation coefficient. Simple linear regression. Probit and logit analysis.
Basic idea of significance test. Statistical hypotheses, types of errors, level of significance, Students t, chi-square, goodness of fit and F tests.
General awareness and use of popular software package for word processing, DBMS, spread sheets, graphics, statistical packages SPSS, SAS, MINITAB, MATLAB etc.,
Bioinformatics : Introduction to bioinformatics. Use of nucleic acid and protein data banks NCBI, EMBL, DDBJ, SWISSPORT. Multiple sequence alignment. Gene prediction. Genome analysis and phylogenetic prediction.
Reference Books :
D. H. Sanders Computers Today. Mc. Graw-Hill. Book Company.
C. Gibas and P. Jamback : Developing bioinformatics computer skills. OReilly Associates.
J. Peek, G. Todino & J. Straug Learning the unix operating system. OReilly Associates.
P. Baldi & S. Brunak. Bioinformatics A machine learning approach. M. I. T. Press.
A. D. Bzxevanis and B. F. F. Onellette Bioinformatics : A Practical guide to the analysis of lienes and Proteins.
S. Misenes and S. A. Krawetz (Eds.) Methods in molecular biology Vol. 132. Bioinformatics Methods and protocols.
S. C. Gupta. Fundamentals of Statistics. Himalaya Pub. House.
J. Medhi. Statistical Methods An introductory text. New Age International (P) Ltd. Publishers.
P. S. S. Sudar Rao & J. Richard. An introduction to biostatistics. Prentice Hall of India. N. Delhi.
Laboratory MI 405 and MI 406
MI 501 : MICROBIAL GENETICS
¨ Gene as unit of mutation and recombination. Molecular nature of mutations; mutagens. Spontaneous mutations origin. DNA Damage and Repair : type of DNA damage (deamination, oxidative damage, alkylation, pyrimidine dimers) Repair pathways methyl directed mismatch repair, very short patch repair, nucleotide excision repair, base excision repair, recombination, repair, SOS system etc.
¨ Biochemical genetics
¨ Fungal genetics : Tetrad analysis and parasexual cycle.
¨ Viral genetics :
Bacteriophages T series, l - biology.
Miniphages M 13, f X 174, Mu.
Bacteriophage recombination complementation, fine structure analysis.
Plant and animal viruses.
Viroids and prions.
¨ Plasmid biology (general properties, types, replication, compatibility, control of copy number etc.,)
¨ Transposable elements.
¨ Bacterial recombination :
Molecular basis of recombination
Conjugation, transformation and transduction.
¨ The genetic basis of cancer.
The control of cell proliferation
Agents that cause cancer in animals
DNA and RNA tumor viruses.
¨ Aging (apoptoin)
Reference Books :
Microbial Genetics. Maloy et. al. 1994. Jones & Barlett Publishers.
Molecular genetics of bacteria. J. W. Dale 1994. John Wiley & Sones.
Modern microbial genetics. 1991. Streips & Yasbin. Niley. Ltd.
Reference Books :
Lehniger Principles of Biochemistry. D. L. Nelson and M.M. Cox.
Microbial Physiology : Moat and Foster
¨ Introduction to bioprocess technology
¨ Isolation, cultivation, preservation and improvement of industrially important organisms.
¨ Substrates for fermentation processes.
¨ Elements of biochemical engineering:
Bioreactor design: Laboratory, pilot and large scale reactors.
Sterilization of media and air
Mass transfer of oxygen
Inoculum development and aseptic inoculation and sampling.
Bioprocess kinetics: Kinetics of growth and substrate utilization in batch, fedbatch and continuous system.
Control of process parameters: Instrumentation for monitoring bioreactor and fermentation processes, microprocessor based control systems, data analysis, dynamic modeling of fermentation processes.
Downstream processing: Cell separation and product purification.
¨ Bioprocess economics.
Reference Books :
Principles of Fermentation Technology : Whitekar & Stanbury
Comprehensive Biotechnology : Murray Moo Young
Methods in Industrial Microbiology : Sikyta
MI 504 : ENVIRONMENTAL BIOTECHNOLOGY
¨ Waste water characterization : COD, BOD, Inorganic constituents, solids, biological compounds.
¨ Waste water management :
Principles and aims of biological waste water treatments.
Biochemistry and microbiology of inorganic phosphorous and nitrogen removal
Suspended growth technologies Activated sludge, oxidation ditches, lagoons etc.
Fixed film technologies : Trickling filters, rotating biological contactors, activated biofilters, fluidized bed etc.
Waste stabilization ponds.
Sludge treatment and disposal
Anaerobic waste water treatments RBC, UASB etc.
¨ Bioremediation oil spills, metals and other hazardous wastes
In situ and ex situ bioremediation of contaminated water and soil.
¨ Use of GMO in bioremediation
¨ Biogeotechnology : Bioleaching of metals, biobeneficiation, microbially enhanced oil recovery, desulfurization of coal.
¨ Biosufactansts and their applications
¨ Solid waste management
Utilization of wastes for food fuel and fertilizers
Biomethanation in detail
Composting
¨ Microbial insecticides
¨ Biofertilizers and Mycorrhyzae
Reference Books :
Waste water treatment for pollution control. 2nd edition. Arceivala.
Environmental Microbiology. R. M. Maier, I. L. Pepper & G. P. Gerba
Comprehensive Biotechnology Vol. 4. Murray Moo Young.
Biotechnology. Rehm and Reid.
Laboratory MI 505 and MI 506
¨ Core techniques and essential enzymes used in r-DNA technology. Restriction digestion, ligation and transformation.
¨ Cloning vectors-plasmids, phages and cosmids. Cloning strategies. Cloning and selection of individual genes, gene libraries: cDNA and genomic libraries.
¨ Specialized cloning strategies. Expression vectors, Promoter probe vectors, vectors for library construction-artificial chromosomes.
¨ PCR methods and application.
¨ Characterization of cloned DNA Restriction mapping, DNA sequencing methods; dideoxy and chemical method. Sequence assembly. Automated sequencing. Genome sequencing and physical mapping of genomes.
¨ Expression of cloned DNA
Expression in heterologus system
Studying the transcript of a clones gene
¨ Modification of cloned DNA
Site directed mutagenesis
Efficient expression of cloned gene
Secretion of cloned product
¨ Application of recombinant DNA technology
Transgenic animal
Gene therapy
Transgenic plant
Pharmaceutical products
¨ Safety of recombinant DNA technology
Restriction and regulation for the release of GMOs
¨ Vaccines (whole organism, recombinant vector and DNA vaccines)
¨ Liposome as drug delivery system.
¨ Biotechnology of artificial cells (including artificial organs in brief)
¨ Patenting
Reference Books:
Principles of gene manipulation. 1994. Old & Primrose. Blackwell Scientific Publications.
Molecular cloning. 3 volumes. Sambrose and Russell. 2000. CSH press.
Genome analysis. Four volumes. 2000. CSH Press.
MI 602 : IMMUNOLOGY
¨ Overview of the immune system: innate and adaptive immunity, cells and organs of immune system, antigens, epitopes, immunoglobulins structure and function.
¨ BCR, TCR, generation of diversity. MHC, antigen processing and presentation.
¨ Complement system.
¨ Cell mediated immune responses. Activation of T and B lymphocytes. Cytokines and their role. Hypersensitivity.
¨ Autoimmunity. Transplantation. Immunity to infectious agents. Tumour immunology. AIDS and other immunodeficiencies.
¨ Hybridoma technology and other experimental systems.
Reference Books :
Essential Immunology : Ivan Roitt.
Kuby Immunology : Goldsby, Kindt and Osborne.
Immunology : Roitt, Brostoff, Mole.
Introductory Immunology : Huw Davies.
¨ General concept of Microbial biotechnology
¨ Microbial production of:
Antibiotics: Penicillin, streptomycin
Enzymes: proteases, amylases
Organic acids: Citric acid, acetic acid
Vitamins: Vit B12, B2
Amino acids: Glutamic acid, Lysine
Ergot Alkaloids
Alcohol, Beer, wine
Exo Polysaccharides
¨ Food and dairy products:
Single cell protein
Single cell oil
Flavours
Cheese, bread and yogurt.
¨ Mushroom cultivation
¨ Plant and animal cell culture.
¨ Steroid transformation
¨ Biopolymers and Bioplastics.
Reference Books :
Biotechnology : Rehm and Reid.
Comprehensive biotechnology : Murray Moo Young.
MI - 604 : ENZYMOLOGY AND ENZYME TECHNOLOGY
¨ Introduction to enzymology and historical developments in enzymology
¨ Enzyme Structure: Primary, secondary, tertiary and quaternary structure, techniques used in determination of protein structure and molecular weight.
¨ Enzyme classification: IUB enzyme classification.
¨ Enzyme Activity: Principle and techniques of enzymatic analysis, factors affecting enzyme activity.
¨ Extraction and Purification of enzyme: Objectives and strategy, seperation techniques, test of purity.
¨ Mechanism of Enzyme Action:
Enzyme activators, co-enzymes and co-factors in enzyme catalysis
Enzyme and substrate specificity
Investigation of active Centre
Factors affecting catalytic efficiency
Experimental approaches to determine enzyme mechanisms.
Enzyme mechanisms: Lysozyme, Chymotrypsin, carboxypeptidase, ATCase.
¨ Enzyme Kinetics:
Single substrate kinetics: Equilibrium and Steady state kinetics, significance of Km, Vmax & Kcat. Pre-steady state and Relaxation kinetics.
Multisubstrate kinetics: General rate equation, compulsory order, random order and ping-pong mechanisms and their primary and secondary plots.
Enzyme inhibition and its kinetics: Reversible and irreversible inhibition, competitive, non-competitive and uncompetitive, mixed, partial, substrate and allosteric inhibition.
Thermal kinetics: Effect of temperature on reaction rate, enzyme stability, Arrhenius equation and activation energy.
¨ Isoenzymes and its physiological significance
¨ Enzyme engineering:
Chemical modification of enzymes: methods of modification of primary structure, catalytic and allosteric properties, use of group specific reagents.
¨ Enzyme technology:
Enzymes in non conventional media
Biosensors
¨ Enzymes as analytical reagents
Fundamentals of Enzymology : Nicholes C. Price and Lewis Stevens, Oxford Univ. Press.
Enzyme Structure and mechanism : Alan Fersht, Reading, USA.
Understanding Enzymes : Trevor Palmer
The chemical kinetics of enzyme action : K. J. Laider and P. S. Bunting, Oxford University Press, London.
Laboratory MI 605 and MI 606