To provide knowledge about acids, bases and buffers. It also provides the information about structure and function of various biomolecules such as carbohydrate, protein (including their role as biocatalysts) and nucleic acids. The course also includes the introduction to types of reactions and various metabolic pathways in living systems.
UNIT-I Chemical basis of life; Composition of living matter; Water – properties; pH; ionization and hydrophobicity; Emergent properties of biomolecules in water; Biomolecular hierarchy; Macromolecules; Molecular assemblies; Structure-function relationships Amino acids – structure and functional group properties; Peptides and covalent structure of proteins; Elucidation of primary and higher order structures; Evolution of protein structure; Structure-function relationships in model proteins like ribonuclease A; myoglobin; hemoglobin; chymotrypsin etc.; Tools to characterize expressed proteins.
Learning Outcomes
Students should be able to understand the properties of water, acids, bases and buffers. Also, the students would gain knowledge about the structure and functions of various biomolecules.
UNIT-II Enzyme catalysis – general principles of catalysis; Quantitation of enzyme activity and efficiency; Enzyme characterization and Michaelis-Menten kinetics; Relevance of enzymes in metabolic regulation; activation; inhibition and covalent modification; Single substrate enzymes.
Learning Outcomes
Students should be able to understand the properties of biocatalysts (enzymes), their mechanism of catalysis, and the kinetics of enzyme reaction and inhibition.
UNIT-III Sugars; mono- di- and poly-saccharides; Suitability in the context of their different functions- cellular structure; energy storage; signaling; Glycosylation of other biomolecules - glycoproteins and glycolipids; Lipids - structure and properties of important members of storage and membrane lipids; lipoproteins.
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Learning Outcomes
Students should be able to understand the biological roles, reactions, and properties of carbohydrates and lipids. They will also gain the knowledge about the complex biomolecules formed by the interaction of lipids, carbohydrates and proteins.
UNIT-IV Biomembrane organization - sidedness and function; Membrane bound proteins - structure; properties and function; Transport phenomena; Nucleosides; nucleotides; nucleic acids - structure; diversity and function; Brief overview of central dogma. Learning Outcomes
Students should be able to learn about structure and function of phospholipids, and gather knowledge about structure, function of plasma membrane, and understand the mechanisms of regulation of various signal transduction pathways.
UNIT-V Bioenergetics-basic principles; Equilibria and concept of free energy; Coupled processes; Glycolytic pathway; Krebs’ cycle; Oxidative phosphorylation; Photosynthesis; Elucidation of metabolic pathways; Logic and integration of central metabolism; entry / exit of various biomolecules from central pathways; Principles of metabolic regulation; Regulatory steps.
Learning Outcomes
Students should be able to gather knowledge about some central metabolic pathways such as Glycolysis, TCA cycle, Electron transport chain, etc., and learn the significance of photosynthesis as the major carbon fixing pathway. Texts / References
1. V. Voet and J.G. Voet; Biochemistry; 3rd edition; John Wiley; New York; 2004. 2. A.L. Lehninger; Principles of Biochemistry; 5th edition; W.H Freeman and Company; 2004. 3. L. Stryer; Biochemistry; 5th edition; W.H. Freeman and Company; 2002.
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Course Code: BYM1002
Course Title: Analytical Techniques
Credits: 04 __________________________________________________________________________ Course Objective To educate students about the properties and preparation of buffers, and various basic analytical techniques like dialysis, filtration, spectroscopy, fluorescence techniques, chromatographic techniques, centrifugation techniques and their applications in industrial and research fields. The course is also meant to familiarize the students with radioactivity and the applications of radioisotopes in research. Also to familiarize students to some more advanced techniques used in biological research.
UNIT-I Basic Techniques: Buffers; Methods of cell disintegration; Enzyme assays and controls; Detergents and membrane proteins; Dialysis; Ultrafiltration and other membrane techniques Spectroscopy Techniques: UV; Visible and Raman Spectroscopy; Theory and application of Circular Dichroism; Fluorescence; NMR; PMR; ESR and Plasma Emission spectroscopy. Learning Outcomes
Students should be able to gather knowledge about the preparation, types, and uses of buffers used in biochemical studies. They will be able to learn about the significance and applications of each of these techniques in biotechnology-based industries and research labs.
UNIT-II Chromatography Techniques TLC and Paper chromatography; Chromatographic methods for macromolecule separation -Gel permeation; Ion exchange; Hydrophobic; Reverse-phase and Affinity chromatography; HPLC and FPLC; Criteria of protein purity Electrophoretic techniques: Theory and application of Polyacrylamide and Agarose gel electrophoresis; Capillary electrophoresis; 2D Electrophoresis; Disc gel electrophoresis; Gradient electrophoresis; Pulsed field gel electrophoresis.
Learning Outcomes
Students should be able to know the principle, working and instrumentation of various chromatographic techniques in details. They will also be able to understand the details of principle, working and instrumentation of various electrophoretic techniques.
UNIT-III Centrifugation Basic principles; Mathematics & theory (RCF; Sedimentation coefficient etc); Types of centrifuge - Microcentrifuge; High speed & Ultracentrifuges; Preparative centrifugation; Differential & density gradient centrifugation; Applications (Isolation of cell components); Analytical centrifugation; Determination of molecular weight by sedimentation velocity & sedimentation equilibrium methods.
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Learning Outcomes
Students should be able to understand the theory and principle of centrifugation. They will be able to differentiate between different types of centrifuges. Also they will be able to enumerate various applications of centrifugation techniques in research.
UNIT-IV Radioactivity Radioactive & stable isotopes; Pattern and rate of radioactive decay; Units of radioactivity; Measurement of radioactivity; Geiger-Muller counter; Solid & Liquid scintillation counters (Basic principle; instrumentation & technique); Brief idea of radiation dosimetry; Autoradiography; Measurement of stable isotopes; Falling drop method; Applications of isotopes in biochemistry; Radiotracer techniques; Distribution studies; Isotope dilution technique; Metabolic studies; Clinical application; Radioimmunoassay. Learning Outcomes
Students should be able to understand the different types of radiation emitted by radioisotopes and their measurement. They will know the applications of radioisotopes in biological research, medicine and diagnosis. Also they will understand the research significance and measurement of less abundant non-radioactive isotopes.
UNIT-V Advanced Techniques: Protein crystallization; Theory and methods; API-electrospray and MADI-TOF; Mass spectrometry; DNA & Peptide Synthesis. Learning Outcomes
Students should be able to understand the principle, methods and applications of protein crystallization. They will learn the theory, types, instrumentation and applications of mass spectrometry. They will further have a clear concept of methods DNA and peptide synthesis. Texts / References
1. Freifelder D.; Physical Biochemistry; Application to Biochemistry and Molecular Biology; 2nd Edition; W.H. Freeman & Company; San Fransisco; 1982.
2. Keith Wilson and John Walker; Principles and Techniques of Practical Biochemistry; 5th Edition; Cambridge University Press; 2000.
3. D. Holme& H. Peck; Analytical Biochemistry; 3rd Edition; Longman; 1998. 4. R. Scopes; Protein Purification - Principles& Practices; 3rd Edition; Springer Verlag; 1994. 5. Selected readings from Methods in Enzymology; Academic Press.
To introduce students to the basic concepts of statistics, probability and probability distributions. To teach them the different sampling distributions and their application in the statistical analysis and to familiarize them with the practical applications of various statistical tools. To introduce the students to the fundamentals of C programming language and its application to solve the problems related to biostatistics.
UNIT-I Descriptive Statistics: Measure of central tendency; Measure of dispersion; Exploratory data analysis and statistical inference. Basic Concepts of Probability: Events and their types; Definition of probability; Probability Calculations. Probability Distribution: Random variable; Discrete and continuous probability distributions; Expectation and variance; Binomial and Poison distribution; Normal distribution, student’s t-distribution, chi-square distribution, and F-distribution.
Learning Outcomes
Students should be able to gain knowledge of basics statistics and probability theory. They will develop an understanding of discrete and continuous probability distribution.
UNIT-II Sampling Distribution: Sampling distribution of mean, difference of mean of two populations, variance, and ratio of variance of two populations; Central limit theorem. Estimation and Hypothesis Testing: Estimation of mean and variance of a single population and difference of means and ratio of variances of two populations; Type-I and type-II error in hypothesis testing; power of test; Testing of mean, variance, equality of means and variances of two populations with known and unknown variances. Learning Outcomes
Students should be able to acquire knowledge of sampling distribution of a population. They will know the application of sampling distribution in statistical inference through estimation and hypothesis testing.
UNIT-III Data Regression Analysis: Simple and multiple regression and correlation; Design of experiments; two and three level factorial design.
Learning Outcomes
Students should be able to understand different regression analysis techniques. They will be able to gain knowledge of linear and nonlinear regression. They will know application of data regression in experiment design.
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UNIT-IV Fundamental of C Programming Language: Identifiers and keywords; Operations and expressions; Library functions; Data input and output; Control structures, branching and looping; Functions; Arrays and pointers; File handling. Learning Outcomes
Students should be able to learn the basics of C programming; data types, identifiers, keywords, operations and expressions, input and output. They will have the knowledge of control structures and functions in C. Also they will have the ability to write C programs to solve the problem related to bio-statistics.
UNIT-V Practicals: Introduction to MSEXCEL-Use of worksheet to enter data; edit data; copy data; move data. Use of in-built statistical functions for computations of Mean; S.D.; Correlation; regression coefficients etc. Use of bar diagram; histogram; scatter plots; etc. graphical tools in EXCEL for presentation of data. Introduction to statistical sofware. Learning Outcomes
Students should be able to perform various statistical operations. They will have the practical knowledge of various available software. Texts / References
Books for Biostatics;
1. Wayne W. Daniel; Biostatistics: A Foundation For Analysis In The Health Sciences, 9th
Edition; John Wiley & Sons, Inc.; 2009.
2. Satguru Prasad; Fundamentals of Biostatistics (Biometry); Emkay Publications, Delhi.
3. Prem S. Mann; Introductory Statistics; 6th Edition; Wiley; 2006.
4. John A. Rice; Mathematical Statistics and Data Analysis; 3rd Edition; John A. Rice; Duxbury
To broaden the knowledge of the students about the structure and function of prokaryotic and eukaryotic cells, as whole entities and in terms of their subcellular organelles/processes. To familiarize students with the techniques used in cell biology research. To familiarize about membrane transport, and the various phases of the cell cycle and cell death, and their regulation. Further to learn cancer biology and cell signaling. Also to make the students understand the synthesis, structure, and function of nucleic acids in prokaryotes and eukaryotes, DNA repair and recombination, and to make the students gain fundamental knowledge of transcription and translation processes.
UNIT-I Cell diversity: Chemical equilibrium and energetics; Cell theory; Cell organelles- endo-membrane systems; Golgi apparatus; lysosomes; endoplasmic reticulum; nucleus and chromatin organization; Extracellular matrix - basal lamina; connective and other tissues; Cell-cell junctions; Cell wall- structural organization and functions; Cellular energy transactions- Role of mitochondria and chloroplast; Co- and post-translational modification of Proteins; Intracellular protein trafficking; Quality control in ER and Golgi; secretary pathway and vesicular trafficking; Import into mitochondria; chloroplast; peroxisome; lysosomes; Receptor-mediated endocytosis; Cytoskeleton- actin; myosin; microfilaments; microtubules and their dynamics; Intermediate filaments; Cell motility; Cilia and flagella; Motor proteins- kinesin and dynein; Differentiation of specialized cells- stem cells differentiation; blood cell formation. Learning Outcomes
Students should be able to understand the structure of prokaryotic and eukaryotic cell. They will be able to gain deep knowledge of structure and function of cells and their organelles.
UNIT-II Basic techniques of cell biology; Light and electron microscopy; Confocal microscopy; atomic force microscopy; Sub-cellular fractionation; Culturing of metazoan cells; Protein-DNA Interactions; Foot-printing and gel-shift assays; Yeast two hybrid and Phage display; Structure determination: cryoelectron microscopy; RNA interference; Hybridization techniques; Membrane transport: Passive and active transport; diffusion and osmosis; ion channels (gated & non-gated); Symport and Antiport; Uniport and Co-transport; Trans-epithelial transport; Transport of proteins and molecular chaperones. Learning Outcomes
Students should be able to get familiar with the basic cell biology techniques. They will be able to understand about cell membrane transport.
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UNIT-III Cell cycle and cancer biology; Mitosis- role of cyclins; CDK; MPF and control of mitosis; Nuclear decondensation; Control of S-phase; Cell cycle control in mammalian cells; Check points and restriction points; Meiosis- asymmetric cell division; Gametogenesis and fertilization; Cell death and its regulation; Tumor cells and onset of cancer; Oncogenes; proto-oncogenes; Viral and cellular oncogenes; tumor suppressor genes from humans; Structure; function and mechanism of action of pRb and p53 tumor suppressor proteins; Types of cancer and metastasis; Genetic basis of cancer; Mutations as cause of cancer; Nonsense; missense and point mutations; Intragenic and Intergenic suppression; Frameshift mutations; Physical; chemical and biological mutagens; Carcinogens; Viruses and cancer; Cell signaling- surface receptors; Signal transduction; Role of GPCR; Cytokine receptors; Receptor tyrosine kinase; MAPK pathways; Secondary messengers; Gene activation by cell surface receptors. Learning Outcomes
Students should be able to understand cell division, cell death, and abnormal cell division (cancer). They will get familiar with cell signaling and signal transduction.
UNIT-IV Heterochromatin and euchromatin; DNA reassociation kinetics (Cot curve analysis); Repetitive and unique sequences; Satellite DNA; DNA melting and buoyant density; Nucleosome phasing; DNase I hypersensitive regions; DNA methylation & Imprinting; Overlapping genes; Split genes; Eukaryotic Gene structure; mobile genetic elements (transposons and retroposons) in Prokaryotes and Eukaryotes; Organelle DNAs; Organization and morphology of chromosomes; DNA replication- mechanism; enzymes and accessory proteins involved; control; Replication of single stranded circular DNA; gene stability and DNA repair enzymes; Photoreactivation; Nucleotide excision repair; mismatch correction; SOS repair; Homologous and non-homologous recombination; Site specific recombination; Chi sequences in prokaryotes; Gene targeting; Gene disruption; FLP/FRT and Cre/Lox recombination.
Learning Outcomes
Students should be able to understand chromosomes and DNA. They will be able to learn about DNA replication, repair and recombination processes.
UNIT-V Prokaryotic and Eukaryotic transcription; RNA polymerases; General and specific transcription factors; Regulatory elements- TATA box and TATA binding proteins; activators; repressors; Mechanisms of transcription regulation at initiation; elongation and Termination (Rho dependent and rho dependent); Attenuation and anti-termination; Regulation of transcription factor activity; Chromatin remodeling and histone modification; Regulation of transcription in eukaryotes- regulatory sequences (Promoters and enhancers); Gene expression in bacteria; Operon Concept (lac; trp; ara; his operons); Transcriptional control in lambda phage; Pre mRNA Modifications- 5’- cap formation; 3’- end processing and polyadenylation; splicing; mRNA stability; Processing of hnRNA; RNA editing; Nuclear export of mRNA and its regulation; tRNA modification; cytoplasmic mechanism of post transcriptional control; Genetic code- degeneracy of codons; Wobble hypothesis; Genetic code in mitochondria; Translation- Prokaryotic and eukaryotic translation; the translation machinery; Mechanism of initiation; elongation and Termination; regulation of translation; Oncogenes as transcriptional activators. Learning Outcomes
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Students should be able to understand RNA synthesis, splicing, editing and transport. They will be able to understand the genetic code. They will get knowledge of protein synthesis in prokaryotes and eukaryotes. Texts / References
1. Benjamin Lewin; Gene IX; 9th Edition; Jones and Barlett Publishers; 2007. 2. J.D. Watson; N.H. Hopkins; J.W Roberts; J. A. Seitz & A.M. Weiner; Molecular Biology of the
Gene; 6th Edition; Benjamin Cummings Publishing Company Inc; 2007. 3. Alberts et al; Molecular Biology of the Cell; 4th edition; Garland; 2002. 4. Lodish et al.; Molecular cell Biology; 4th Edition; W.H. Freeman & Company; 2000. 5. Smith & Wood; Cell Biology; 2nd Edition; Chapman & Hall; London;1996. 6. B. M. Turner; Chromatin & Gene regulation; 1st Edition; Wiley-Blackwell; 2002. 7. Watson et al.; Molecular Biology of the gene; 5th Edition; Pearson Prentice Hall. USA; 2003.
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Course Code: BYM1071
Course Title: Lab I: Biochemistry and Analytical Techniques
The objective of this practical course is to provide students with hand-on experience in biochemistry experimentation and analytical techniques. We will cover the basic experiments in biochemistry.
EXERCISES 1. Preparation of various Buffer systems and validation of the Henderson-Hasselbach
equation.
2. Determination of protein concentration in unknown solution/biological sample, plotting a standard graph of BSA using UV-Vis Spectrophotometer and validating the Beer- Lambert’s Law.
3. pH meter titration of amino acids and separation of aliphatic, aromatic and polar amino acids by TLC.
4. An enzyme purification theme (such as E. coli alkaline phosphatase or any other enzyme.
(a) Preparation of cell-free lysates.
(b) Ammonium sulfate precipitation.
(c) Ion-exchange chromatography.
(d) Gel filtration.
(e) Affinity chromatography.
(f) Generating a purification table.
(g) Assessing purity by SDS-PAGE gel electrophoresis.
(h) Assessing purity of given protein sample by PAGE.
Students should be able to make various types of buffers both by the titration and Henderson-Hasselbach equation methods. They will be able to determine proteins concentration using UV-Vis Spectrophotometer and do pH titration and TLC of amino acids. Further they will be able to perform the purification and kinetic assay of an enzyme. Also they will learn some biophysical methods like UV, fluorescence and CD spectroscopy.
The objective of this practical course is to provide students with hand-on experience in molecular biology. We will cover the basic experiments in molecular biology.
EXERCISES 1. Plasmid DNA isolation and DNA quantitation: Plasmid minipreps.
2. Restriction digestion.
3. RFLP analysis of the PCR product.
4. Preparation of competent cells.
5. Agarose gel electrophoresis.
6. Transformation of E. coli with standard plasmids, calculation of transformation efficiency.
7. Polymerase chain reaction (PCR), using standard eubacterial 16S rRNA.
8. Transformation in Bacteria.
Learning Outcomes
Students should be able to isolate plasmid and do restriction digestion, and perform RFLP analysis and Agarose gel electrophoresis. Further they will be able to prepare competent cells and do transformation experiments, and perform PCR.
The objective of this curriculum is to make students aware with recent scientific developments and techniques and to develop their communication skills by presenting their assigned topic in front of audience. In addition, the quiz based on assigned topic keeps the students in the audience to concentrate on the presented topic.
Presentation of Seminar Topics by the students assigned to them before the evaluation committee. Learning Outcomes
Students should be able to develop ability to read and understand the recent advances in science and technology. This course will improve their communication skills. They will be asked questions from the topics presented and will understand and answer the questions based on the assigned topic.
The students will get a wide knowledge of the anatomy of the immune system, and components and functioning of humoral and cell mediated immune responses. To introduce the students to various detection systems and to the development of monoclonal antibody and hybridoma technology in general. To broaden the knowledge of students about vaccinology and tumour immunology. Further to make them understand antibody genes and antibody engineering. Also to broaden the knowledge of students about intricacies of the host system in sub/optimum/hyper immune responses. Further to make them understand the role of immune system in hypersensitivity and autoimmune complications.
UNIT-I Immunology-fundamental concepts and anatomy of the immune system Components of innate and acquired immunity; Phagocytosis; Complement and Inflammatory responses; Hematopoiesis; Organs and cells of the immune system- primary and secondary Lymphoid organs; Lymphatic system; Lymphocyte circulation; Lymphocyte homing; Mucosal and Cutaneous associated Lymphoid tissue.(MALT&CALT); Mucosal Immunity; Antigens - immunogens; haptens; Major Histocompatibility Complex - MHC genes; MHC and immune responsiveness and disease susceptibility. Learning Outcomes
Students should be able to learn about the components of innate and acquired immunity. They will get wide knowledge of the organs of the immune system, and know the complement system and the MHC complex.
UNIT-II Immune responses generated by B and T lymphocytes Immunoglobulins-basic structure; classes & subclasses of immunoglobulins; antigenic determinants; Multigene organization of immunoglobulin genes; B-cell receptor; Immunoglobulin superfamily; Principles of cell signaling; Basis of self- non self- discrimination; Kinetics of immune response; memory; B cell maturation; activation and differentiation; Generation of antibody diversity; T-cell maturation; activation and differentiation and T- cell receptors; Functional T Cell Subsets; Cell-mediated immune responses; ADCC; Cytokines-properties; receptors and therapeutic uses; Antigen processing and presentation- endogenous antigens; exogenous antigens; non-peptide bacterial antigens and super-antigens. Learning Outcomes
Students should be able to know the immune responses generated by B and T lymphocytes. They will learn about immunoglobulin superfamily and how antibody diversity is generated. Also they will get knowledge of antigen processing and presentation.
Students should be able to learn about the components of antibody antigen interaction. They will get wide knowledge of the immunosensor system. They will know the application of Ag-Ab interaction in immune detection/biosensor system.
UNIT-IV Vaccinology Active and passive immunization; Live; killed; attenuated; sub unit vaccines; Vaccine technology- Role and properties of adjuvants; recombinant DNA and protein based vaccines; plant-based vaccines; reverse vaccinology; Peptide vaccines; conjugate vaccines; Antibody genes and antibody engineering- chimeric and hybrid monoclonal antibodies; Catalytic antibodies and generation of immunoglobulin gene libraries. Tumor immunology – Tumor antigens; Immune response to tumors and tumor evasion of the immune system; Cancer immunotherapy; Immunodeficiency-Primary immunodeficiencies; Acquired or secondary immunodeficiencies. Learning Outcomes
Students should be able to get deep knowledge about the various types of vaccines. They will learn about antibody genes and antibody engineering. Further they will understand the immune responses against tumours and immunotherapy.
UNIT-V Clinical Immunology Immunity to Infection: Bacteria; viral; fungal and parasitic infections (with examples from each group); Hypersensitivity – Type I-IV; Autoimmunity; Types of autoimmune diseases; Mechanism and role of CD4+ T cells; MHC and TCR in autoimmunity; Treatment of autoimmune diseases; Transplantation – Immunological basis of graft rejection; Clinical transplantation and immunosuppressive therapy. Learning Outcomes Students should be able to get deep knowledge about the various types of immune components involved in autoimmunity. They will learn about component of immune system involved in hyper immune responses. Further, they will understand the immune responses against transplantation and employed immunotherapy. Texts / References
1. Kuby; RA Goldsby; Thomas J. Kindt; Barbara; A. Osborne Immunology; 6th Edition; Freeman; 2002.
2. Brostoff J; Seaddin JK; Male D; Roitt IM.; Clinical Immunology; 6th Ed.; Gower Medical Publishing; 2002.
3. Janeway et al.; Immunobiology; 4th Edition; Current Biology publications.; 1999. 4. Paul; Fundamental of Immunology; 4th edition; Lippencott Raven; 1999. 5. Goding; Monoclonal antibodies; Academic Press. 1985.
To introduce students to the diversity of microbial world, classification of microorganisms (MOs), and various molecular biology techniques useful in characterizing and classifying MOs. To teach the students about the physiology, structure, nutrition, and growth kinetics of different MOs and the methods for culturing bacteria and different types of bacterial cultures with their characteristic growth kinetics. To teach about the various aspects, including microbial pathogenesis, the ecological roles of MOs, and various symbiotic associations of MOs with other organisms. The types and formulation of media, sterilization systems, and optimization of bioprocesses will be taught. The adjustment of conditions to suit the production of primary and secondary metabolites, and the downstream processing of products is also included.
UNIT-I Microbial Diversity & Systematics Classical and modern methods and concepts; Domain and Kingdom concepts in classification of microorganisms; Criteria for classification; Classification of Bacteria according to Bergey’s manual; Molecular methods such as Denaturing Gradient Gel Electrophoresis (DGGE); Temperature Gradient Gel Electrophoresis (TGGE); Amplified rDNA Restriction Analysis and Terminal Restriction Fragment Length Polymorphism (T-RFLP) in assessing microbial diversity; 16S rRNA sequencing and Ribosomal Database Project. Learning Outcomes
Students should be able to understand the concepts of Systematics and Taxonomy. They will have the knowledge of molecular techniques used in classification of MOs. They will have the idea of differences in the outcomes of classification of MOs using classical and modern methods.
UNIT-II Microbial growth: Growth cycle of bacteria; synchronous growth. Culture and its characteristics; pure culture, mixed culture; media and its types; Batch culture; fed-batch; continuous kinetics. Methods of growth estimation; direct microscopic count; electronic enumeration method, viable count through CFU method; membrane filter count; turbidimetric method; selection of procedure to measure growth; significance of quantitative measurement. Microbial physiology: Physiological adoption and life style of Prokaryotes; Unicellular Eukaryotes and the Extremophiles (with classical example from each group). Ultrastructure of Archaea (Methanococcus); Eubacteria (E. coli); Unicellular Eukaryotes (Yeast) and viruses (Bacterial; Plant; Animal and Tumor viruses).
Learning Outcomes
Students should be able to understand the structural details of eukaryotic MOs, eubacteria, archaebacteria and viruses. They will have a clear idea of nutritional requirements and culture methods of different types of MOs. They will be able to describe various methods used in the measurement of microbial growth. They will have the knowledge of the unusual requirements and characteristics of extremophiles.
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UNIT-III
Microbial Interactions and Infection; Host–Pathogen interactions; pathogenicity and virulence; Microbial adherence; type of microbial penetration. Microbial virulence factors; exotoxins and endotoxins; Microbes infecting humans; veterinary animals; Pathogenicity islands and their role in bacterial virulence.
Learning Outcomes
Students should be able to have the knowledge of the mechanisms used by pathogens to infect, invade and cause disease in host and various factors controlling the virulence and pathogenicity. Further they will be able to differentiate between the types and effects of microbial toxins.
UNIT-IV
Microbes and Environment Role of microorganisms in natural system and artificial system; Influence of Microbes on the Earth's Environment and Inhabitants; Ecological impacts of microbes; Symbiosis (Nitrogen fixation and ruminant symbiosis); Microbes and Nutrient cycles; Microbial communication system; Quorum sensing; Microbial fuel cells; Prebiotics and Probiotics; Vaccines.
Learning Outcomes
Students should be able to appreciate the role played by MOs in nutrient cycles. They will understand the significance of MOs as major photosynthetic, and the only nitrogen-fixing organisms. They will know about some of the ecologically important MO-MO, MO-plant, and MO-animal associations.
UNIT-V
Industrial Applications Basic principles in bioprocess technology; Media Formulation; Sterilization; Thermal death kinetics; Batch and continuous sterilization systems; Primary and secondary metabolites; Extracellular enzymes; Biotechnologically important intracellular products; exopolymers; Bioprocess control and monitoring variables such as temperature; agitation; pressure; pH Microbial processes-production; optimization; screening; strain improvement; factors affecting downstream processing and recovery; Representative examples of ethanol; organic acids; antibiotics etc. Enzyme Technology-production; recovery; stability and formulation of bacterial and fungal enzymes-amylase; protease; penicillin acylase; glucose isomerase; Immobilized Enzyme and Cell based biotransformations-steroids; antibiotics; alkaloids; enzyme/cell electrodes.
Learning Outcomes
Students should be able to differentiate between types growth kinetics of different culture systems. They will learn about primary and secondary metabolites, and growth conditions suitable for the production these metabolites. Further they will understand the strategies used for product recovery.
Texts / References
1. Pelczar MJ Jr.; Chan ECS and KreigNR.; Microbiology; 5th Edition; Tata McGraw Hill; 1993. 2. Maloy SR; Cronan JE Jr.; and Freifelder D; Microbial Genetics; Jones Bartlett Publishers;
Sudbury; Massachusetts; 2006. 3. Crueger and ACrueger; (English Ed.; TDW Brock); Biotechnology: A textbook of Industrial
Microbiology; Sinaeur Associates; 1990. 4. G Reed; Prescott and Dunn’s; Industrial Microbiology; 4th Edition; CBS Publishers; 1987. 5. M.T. Madigan and J.M. Martinko; Biology of Microorganisms; 11th Edition; Pearson Prentice
To explain the structural organization of DNA, DNA-protein interactions and steps involved in recombinant DNA technology. To educate students about various cloning and expression vectors, methodology to remove inclusion bodies, cloning methodologies, gene expression, genetic analysis etc. To introduce the students to PCR and its variants and their applications, and some other useful molecular biology techniques such as nucleic acid and protein sequencing, gene targeting, gene replacement, etc. To elaborate upon the bacterial genetics and the horizontal gene transfer in bacteria. To introduce students to types & causes of mutations, and mutant detection / selection systems. To provide information about various common genetic disorders in humans and the concept of mitochondrial inheritance.
UNIT-I Basics Concepts: DNA Structure and properties; Restriction Enzymes; DNA ligase; Klenow enzyme; T4 DNA polymerase; Polynucleotide kinase; Alkaline phosphatase; Cohesive and blunt end ligation; Linkers; Adaptors; Homopolymeric tailing; Labeling of DNA: Nick translation; Random priming; Radioactive and non-radioactive probes; Hybridization techniques: Northern; Southern and Colony hybridization; Fluorescence in situ hybridization; Chromatin Immunoprecipitation; DNA-Protein Interactions-Electromobility shift assay; DNase I footprinting; Comparative Genomic Hybridization (CGH). Learning Outcomes
Students should be able to enhance their knowledge about functional and structural organization of nucleic acids and will gain knowledge of various techniques in recombinant DNA technology. They will understand applications of genetic engineering techniques in basic and applied experimental biology.
UNIT-II Cloning Vectors and methodology: Plasmids; Bacteriophages; M13 mp vectors; PUC19 and Bluescript vectors; Phagemids; Lambda vectors; Cosmids; Artificial chromosome vectors (YACs; BACs); Animal Virus derived vectors-SV-40; Expression vectors; pMal; GST; pET-based vectors; Protein purification; His-tag; GST-tag; MBP-tag etc.; Intein-based vectors; Inclusion bodies; Methodologies to reduce formation of inclusion bodies; Plant based vectors; Ti and Ri as vectors; Yeast vectors; Shuttle vectors. Cloning Methodologies Insertion of Foreign DNA into Host Cells; Transformation; Construction of libraries; Isolation of mRNA and total RNA; cDNA and genomic libraries; Expression cloning; Jumping and hopping libraries; Southwestern and Far-western cloning; Protein-protein interactive cloning and Phage display; Principles in maximizing gene expression; Plasmid biology - copy number and its control; Incompatibility; Plasmid survival strategies; Antibiotic resistance markers on plasmids (mechanism of action and resistance); Genetic analysis using phage and plasmid. Learning Outcomes
Students should be able to learn the methods of cloning and expressing genes using various cloning and expression vectors. They will understand genetic engineering and genetic manipulation.
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UNIT-III PCR and sequencing: Primer design; Fidelity of thermostable enzymes; DNA polymerases; Types of PCR – multiplex; nested; reverse transcriptase; real time PCR; touchdown PCR; hot start PCR; colony PCR; cloning of PCR products; Proof reading enzymes; PCR in gene recombination; Deletion; addition; Overlap extension; Site specific mutagenesis; PCR in molecular diagnostics; Viral and bacterial detection; PCR based mutagenesis; Mutation detection; Assay of mutagenic agents (Ames test); Sequencing methods: Enzymatic DNA sequencing, Chemical sequencing of DNA, Automated DNA sequencing, RNA sequencing; Chemical Synthesis of oligonucleotides; Transfection techniques; Gene silencing techniques; Introduction to siRNA; Micro RNA; Construction of siRNA vectors; Principle and application of gene silencing; Gene knockouts, Transgenics and Gene Therapy; Suicide gene therapy; Gene replacement; Gene targeting; Differential gene expression. Student Learning Outcomes
Students should be able to understand various aspects of PCR and its numerous modifications. They will get the knowledge of various sequencing methods for nucleic acid and proteins. They will get information about gene silencing and the role of siRNA and miRNA in regulation of gene expression.
UNIT-IV Gene transfer: Bacterial-history; Transduction and Transformation; Merodiploid generation; Transposable genetic elements; General genetic variations: errors in cell division; Non disjunction; Structural and numerical chromosomal abnormalities; Mutations: kinds of mutation; agents of mutation; mutation selection; genome polymorphism; uses of polymorphism; Phenotype; Genotype; Gene frequency; Hardy Weinberg concepts; Mutation selection; Migration; Gene flow; Genetic drift; Human genetic diversity; Origin of major human groups. Learning Outcomes
Students should be able to know the mechanisms of gene transfer in bacteria; conjugation, transformation and transduction. They will learn about mutations, and types of chromosomal abnormalities. They will understand factors leading to genome polymorphism and genetic diversity.
UNIT-V Mendelian and Non Mendelian Genetics: Introduction to human genetics; Background and history; Types of genetic diseases; Role of genetics in medicine; Human pedigrees; Patterns of single gene inheritance-autosomal recessive; Autosomal dominant; X linked inheritance; Hemoglobinopathies - Genetic disorders of hemoglobin and their diseases. Non Mendelian patterns: Mitochondrial inheritance; Genomic imprinting; Lyon hypothesis; isodisomy; Complex inheritance-genetic and environmental variation; Heritability; Twin studies; Behavioral traits; Genes in early development; Maternal effect genes; Homeotic genes.
Learning Outcomes
Students should be able to differentiate among the different types of inheritance. They will learn some important disorders in humans that are caused due to genetic mutations and chromosomal abnormalities. Further they will get information about the different theories and studies aimed at understanding the effect of different genes in determining heritability.
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Texts / References
1. S.B. Primrose; R.M. Twyman and R.W.Old; Principles of Gene Manipulation. 6th Edition;
S.B.University Press; 2001.
2. J. Sambrook and D.W. Russel; Molecular Cloning: A Laboratory Manual; Vols 1-3; CSHL;
2001.
3. Brown TA; Genomes; 3rd ed. Garland Science 2006
4. Selected papers from scientific journals.
5. Technical Literature from Stratagene; Promega; Novagen; New England Biolab etc.
6. S.R. Maloy; J.E. Cronan; D. Friefelder; Microbial Genetics; 2nd Ed.; Jones and Bartlett
Publishers; 1994.
7. N. Trun and J. Trempy; Fundamental Bacterial Genetics; Blackwell publishing; 2004.
8. Strachan T and Read A P; Human molecular genetics; 3rd Edition Wiley Bios; 2006.
9. Mange E J and Mange A. P.; Human genetics; 2nd Edition; Sinauer Associates publications;
To impart deep knowledge of protein structure, and approaches towards the determination of protein structure. To familiarize students with protein function. The course shall be able to impart deep knowledge of protein-ligand interactions. Further to provide detailed knowledge to students of protein denaturation and folding. To broaden the knowledge of enzymes and their action and to expose the students to artificial enzymes and non-aqueous enzymology.
UNIT-I Peptides & proteins- Peptide bond conformation; dihedral angles; Ionization behavior of peptides; Peptide diversity in terms of size and composition; Peptides with biological activities; Primary: secondary and tertiary structure of proteins; Ramachandran plot; Fibrous and globular proteins; Forces stabilizing native protein conformation; Super-secondary structure: quaternary structure; Prediction of secondary structure; Chemical modification of Proteins.
Learning Outcomes
Students should be able to understand the structure of proteins and how it is stabilized by various forces. They will learn about secondary structure prediction and chemical modifications of proteins.
UNIT-II Determination of protein structure- Sequence determination of proteins; N- and C-terminal amino acid analysis; Edman’s degradation: classical and automated procedures; Use of mass spectrometry in primary structure determination.
Learning Outcomes
Students should be able to learn how to determine the primary, secondary and tertiary structure of a protein. They will understand the techniques used in protein structure determination.
UNIT-III Protein function- Protein ligand interactions; Qualitative and quantitative studies on cooperative and non-cooperative (Sigmoidal) binding of ligands; Hill equation; Sequential and concerted model for cooperative binding. Learning Outcomes
Students should be able to learn about protein-ligand interactions. Further they will understand cooperative binding of ligands to proteins and its significance.
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UNIT-IV Protein denaturation and folding; Models of protein folding and association of proteins; Anfinsen’s experiment: Thermodynamics of protein folding- Leventhal Paradox; Role of chaperons in folding; Protein misfolding disorders: Amlyloid fiber formation; Protein evolution.
Learning Outcomes
Students should be able to know how protein folding occurs in vitro and in vivo. They will learn about protein misfolding disorders with special emphasis on amyloid fiber formation. Further they will understand protein evolution.
UNIT-V Enzymes- History; Features of enzyme catalyzed reaction; Properties and study of enzyme active sites; Kinetics of single and multi-substrate reactions; Enzyme inhibition- irreversible and reversible (competitive: noncompetitive and uncompetitive inhibition); Allosteric enzymes (sequential and concerted model). Artificial enzymes- Synthetic and semi-synthetic enzymes: Catalytic antibodies; Molecular imprinting: Non-aqueous enzymology- Behavior of enzymes in non-aqueous media: application in synthesis and industry.
Learning Outcomes
Students should be able to get knowledge of enzyme kinetics and various methods of enzyme inhibition. They will learn about allosteric enzymes and artificial enzymes. Also they will learn about behavior of enzymes in organic solvents. Texts / References
1. M.M. Cox and D.L.Nelson, Lehninger; Principles of Biochemistry;(2008) 5th edition; W.H
Freeman and Company;
2. J.M. Berg, J.L. Tymoczko and L. Stryer; Biochemistry; 5th edition; (2007) W.H. Freeman and
Company.
3. H.W. Blank & D.S, Clark; Applied Biocatalysis, Vol I (1991) Marcel Dekkar Inc. N.Y.
4. D. Whitford; Proteins, Structure and Function (2001) John Wiley & Sons Ltd.
5. R. Guerois and Lopez de la Paz; Protein Design Methods and Applicatios (2006) Humana
The objective of this practical course is to provide students with hand-on experience in immunological techniques.
EXERCISES
1. Antibody titer by ELISA.
2. Double diffusion, immuno-electrophoresis and radial Immunodiffusion.
3. Complement fixation test.
4. Isolation and purification of IgG from serum or IgY from chicken egg.
5. SDS-PAGE, Immunoblotting, Dot blot assays
6. Blood smear identification of leucocytes by Giemsa stain
7. Separation of leucocytes by Dextran density gradient method
8. Separation of mononuclear cells by Ficoll-Hypaque.An enzyme purification theme (such as E. coli alkaline phosphatase or any other enzyme.
Learning Outcomes
Students should be able to perform the immunization of animals. They will get experience of doing ELISA, immuno-diffusion and immune-electrophoresis. They will do complement fixation test, and Isolate and purify IgG and do SDS-PAGE and do blotting assays with it. Further students will be able to identify leucocytes by giemsa stain and separate them by density gradient method. They will also do separation of mononuclear cells by Ficoll-Hypaque.
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Course Code: BYM2072
Course Title: Lab II: Microbiology and Industrial Applications
The objective of this practical course is to provide students with hand-on experience in microbiology and industrial applications.
EXERCISES
1. Sterilization, disinfection and safety in microbiological laboratory.
2. Preparation of media for growth of various microorganisms.
3. Identification and culturing of various microorganisms.
4. Staining and enumeration of microorganisms.
5. Growth curve, measure of bacterial population by turbidometry and studying the effects of temperature, pH, carbon and nitrogen.
6. Plasmid Isolation.
7. Assay of antibiotics production and demonstration of antibiotic resistance.
8. Isolation and screening of industrially important microorganisms.
9. Determination of thermal death point and thermal death time of microorganisms.
Learning Outcomes
Students should be able to learn how sterilization, disinfection and safety is maintained in a microbiological laboratory. They will be able to prepare media for growth of various microorganisms, and identify and culture them. They will learn to do the staining and enumeration of microorganisms. They will do experiments for getting the bacterial growth curves under different conditions. Further, students will learn to isolate plasmid and also to assay antibiotic production and resistance. They will be able to isolate and screen industrially useful microorganisms. They will be able to determine thermal death point and thermal death time of microorganisms.
The objective of this curriculum is to make students aware with recent scientific developments and techniques and to develop their communication skills by presenting their assigned topic in front of audience. In addition, the quiz based on assigned topic keeps the students in the audience to concentrate on the presented topic.
Presentation of Seminar Topics by the students assigned to them before the evaluation committee. Learning Outcomes
Students should be able to develop ability to read and understand the recent advances in science and technology. This course will improve their communication skills. They will be asked questions from the topics presented, and they will be able to understand and answer the questions based on the assigned topic.
To teach the students about the basic organization of genome in prokaryotes and eukaryotes along with various genomic analysis methodologies and methods to sequence DNA. In addition, it is aimed to impart knowledge of pharmacogenetics, and to create an understanding in the students of functional genomics and proteomics.
UNIT-I Introduction Structural organization of genome in Prokaryotes and Eukaryotes; Organelle DNA-mitochondrial; chloroplast; DNA sequencing-principles and translation to large scale projects; Recognition of coding and non-coding sequences and gene annotation; Tools for genome analysis-RFLP; DNA fingerprinting; RAPD; PCR; Linkage and Pedigree analysis-physical and genetic mapping. Learning Outcomes
Students should be able to understand the overall organization of genomes in prokaryotes and eukaryotes, and learn the basics of genomics and proteomics and tools for genomic analysis.
UNIT-II Genome sequencing projects Microbes; plants and animals; Accessing and retrieving genome project information from web; Comparative genomics; Identification and classification using molecular markers-16S rRNA typing/sequencing; EST’s and SNP’s.
Learning Outcomes
Students should be able to learn how to access genome project information from the web, and understand comparative genomics and about classification using molecular markers.
UNIT-III Proteomics Protein analysis (includes measurement of concentration; amino-acid composition; N-terminal sequencing); 2-D electrophoresis of proteins; Microscale solution isoelectric focusing; Peptide fingerprinting; LC/MS-MS for identification of proteins and modified proteins; MALDI-TOF; SAGE and Differential display proteomics; Protein-protein interactions; Yeast two hybrid system. Learning Outcomes
Students should be able to develop the basic concepts of proteomics and gain an idea of how to study protein-protein interactions. They should also be able to learn how to analyse protein sequences using various techniques such as 2-D and isoelectric focusing electrophoresis and mass spectrometry.
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UNIT-IV Pharmacogenetics High throughput screening in genome for drug discovery- identification of gene targets; Pharmacogenetics and drug development. Learning Outcomes
Students should be able to get acquainted with pharmacogenetics and understand how high throughput screening of the genome is done for drug discovery.
UNIT-V Functional genomics and proteomics Analysis of microarray data; Protein and peptide microarray-based technology; PCR-directed protein in situ arrays; Structural proteomics.
Learning Outcomes
Students should be able to understand functional genomics and proteomics, and understand DNA and Protein microarrays. Texts / References
To introduce the students to the fundamental concepts of immunology and the detailed structure of immunoglobulins, antibody diversity etc. The other objective is to make students familiar with the viruses and sub-viral agents and their detection methods besides the introduction to gene silencing and viral mechanisms that suppress gene silencing. In addition, it is aimed to introduce the students to advanced instrument and techniques.
UNIT-I
Introduction to Immunotechnology Kinetics of immune response: memory; Principles of Immunization; Techniques for analysis of Immune response ; Antibody Related Techniques Immuno-chemistry of Antigens - immunogenicity: Antigenicity: haptens: Toxins-Toxoids: Hapten-carrier system; Genetic basis of immune response; Role and properties of adjuvants: Immune modulators; B cell epitopes; Hybridoma Rabbit: human; Antigen – Antibody interaction: affinity: cross reactivity: specificity: epitope mapping; Immunoassays: RIA: ELISA: Western blotting: ELISPOT assay: immunofluorescence: Surface plasma resonance: Biosensor assays for assessing ligand –receptor interaction. New Generation Antibodies Multigene organization of immunoglobulin genes: Ab diversity; Antibody engineering; Phage display libraries; Antibodies as in vitro and in vivo probes.
Learning Outcomes
Students should be able to learn about the components of antibody antigen interaction and the application of Ag-Ab interaction in immune detection/biosensor system.
UNIT-II
CMI and Imaging techniques CD nomenclature: Identification of immune Cells; Principle of Immunofluorescence Microscopy: Fluorochromes; Staining techniques for live cell imaging and fixed cells; Flow cytometry: Instrumentation: Applications; Cell Functional Assays –lymphoproliferation: Cell Cytotoxicity: Mixed Lymphocyte Reaction: Apoptosis: Cytokine expression; Cell cloning: Reporter Assays: In–situ gene expression techniques; Cell imaging Techniques- In vitro and In vivo; Immuno-electron microscopy; In vivo cell tracking techniques; Microarrays; Transgenic mice: gene knock-outs.
Learning Outcomes
Students should be able to know the immune responses generated by B and T lymphocytes, and learn about antigen antibody interaction and its application in biosensor development. Students will also be introduced to the immunoglobulin gene structure and regulation.
UNIT-III
Classification of animal and plant viruses; Satellite viruses; Viroids; Virusoids etc.; Diseases causes by animal viruses and plant viruses; Economic loss due to important viruses: Genome
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organization of animal viruses; Replication of RNA viruses; Replication of DNA viruses; Structure of animal viruses and plant viruses; Genome organization of DNA and RNA plant viruses; Replication of DNA and RNA plant viruses.
Learning Outcomes
Students should be able to understand the basic properties, structure, classification, and genome organization and replication mechanisms of viruses, and sub-viral agents. It is also aimed to impart knowledge of the economic loss caused due to viral diseases of plants and livestock.
UNIT-IV Methods to diagnose animal virus infections: Electron microscopy: Tissue culture growth of viruses: Virus quantitation assays: Viral serology: ELISA: neutralization assays; Molecular methods: hybridization: PCR: real time PCR: sequencing: microarray: gene silencing and antiviral assays. Learning Outcomes
Students should be able to explain and compare the principle and method of various viral assays, and know about various techniques used in detection of viruses and/or virus components. In addition, they shall also learn about the mechanisms of inhibition of viruses naturally or by use of anti-viral agents.
UNIT-V Methods to study plant viruses; Infectivity assays – Sap transmission: insect vector transmission: agroinfection (using Agrobacterium); serological methods: immunelectrophoresis in gels: direct double-antibody sandwich method: Dot ELISA: Immunosorbent electron microscopy (ISEM): Decoration technique: Gene silencing: PTGS & TGS: viral suppressors of gene silencing.
Learning Outcomes
Students should be able to know the principle and applications of advanced immunological techniques. They should also understand the methods used in assay of plant viruses and introduction of foreign genes with the help of Agrobacterium. Besides this, they shall gather the knowledge about the significance, types and mechanism of gene silencing and the mechanisms through which viruses break the gene silencing circuit. Texts / References
To provide detailed knowledge of tissue culture of various plant parts and their applications, organogenesis, somatic embryogenesis and germplasm conservation. The course shall also impart detailed knowledge of plant transformation technology, plant metabolic engineering, arid plant biotechnology and green house technology. Besides this, it is aimed to sensitize students and make them realize the need for plant conservation.
UNIT-I
Conventional plant breeding.Introduction to cell and tissue culture; tissue culture as a technique to produce novel plant and hybrids.Tissue culture media (composition and preparation). Initiation and maintenance of callus and suspension culture; single cell clones. Organogenesis; somatic embryogenesis; transfer and establishmentof whole plants in soil.
Learning Outcomes
Students should be able to understand the principles, practices and applications of plant tissue culture in detail. Students will also learn about organogenesis, somatic embryogenesis, and about the methods of transfer and establishment of whole plants.
UNIT-II
Shoot-tip culture: Rapid clonal propagation. Embryo culture and embryo rescue. Protoplast isolation; culture and fusion; selection of hybrids cells and regeneration of hybrid plants; symmetric and asymmetric hybrids; hybrid biotransformation.Anther; pollen; and ovary culture for production of haploid plants and homozygous lines.Cryopreservation; slow growth and DNA banking for germplasm conservation.
Learning Outcomes
Students should be able to understand the principles, practices and applications of plant tissue culture of various plant parts in details. They should also be able to know the methods for production of haploid plants homozygous lines and learn about germplasm conservation.
UNIT-III
Transgenic Plants: Basis Introduction; T1 and R1 plasmids; molecular basis of Agrobacterium infection; Mechanisms of DNA transfer; Organization of T-DNA; organization of vir region and its role; transfer of T-DNA; integration of T-DNA into plant genome; Disarming; co-integrate vector; binary vector; plant virus vector; use of 35S and other promoters; genetic markers. Viral vectors and their applications. Vector Transformation techniques; co-culture with tissue explants, in planta transformation, agroinfection. Vector less or direct DNA transfer; chemical methods; particle bombardment, electroporation; microinjection transformation of monocots; lipofection; fiber mediated DNA delivery; laser induced DNA delivery; pollen transformation. Insect resistance; Bt. Genes; non-Bt like protease inhibitors; alpha amylase inhibitor.Herbicide resistance; phosphoinothricin; glyphosate; sulfonyl urea; atrazine. Virus resistance; coat protein mediated resistance; nucleocaspid gene; cDNA of satellite RNA; defective Viral approach; antisense RNA approach; Ribozyme mediated protection. Disease resistance;
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chitinase; 1 – 3 beta glucanase; RIP antifungal proteins; thionines; PR proteins; long shelf life of fruits and flowers; use of ACC synthase; poly- galactrunase; ACC oxidase; male sterile lines; bar and barnase systems. Biochemical production; Hirudin; phytase; polyhydroxybutyrate.Terminator gene technology.
Learning Outcomes
Students should be able to gain knowledge of how transgenic plants can be formed and about various methods of DNA transformation.
UNIT-IV
An introduction to plant conservation biotechnology, Molecular approaches to assessing plant diversity; molecular marker system; molecular markers in germ plasm characterization; population genetics; biodiversity characterization, plant germplasm acquisition; plant genetic resource conservation; acquisition procedures; planning methods involved, Phytosanitary aspects of plant germplasm conservation; safe movement of germplasm; quarantine; virus detection; production of pathogen free plants, Cryopreservation; principle; preparation and pretreatment, cryoprotection procedure, Stability assessment; natural variation; techniques; morphological variation; cytological, biochemical and molecular analysis, biotechnological advances in conservation of root and tuber crops; economical important plants; endangered plants; rain forest conservation.
Learning Outcomes
Students should be able to get an understanding of biodiversity and plant conservation biotechnology, and learn how plant germplasm is acquired.
UNIT-V
Metabolic engineering and industrial products: Plant secondary metabolites; control mechanisms and manipulation of phenylpropanoid pathway; alkaloids; industrial enzymes; biodegradable plastics; therapeutic proteins; lysosomal enzymes; antibodies; edible vaccines; purification strategies; oleosin partitioning technology. Molecular marker-aided breeding: RFLP maps; linkage analysis; RAPD markers; STS; microsatellites; SCAR (sequence characterized amplified regions); SSCP (single strand conformational polymorphism); AFLP; QTL; map-based cloning. Molecular marker-assisted selection.Arid and semi-arid plant biotechnology; Green house and Green-home technology.
Learning Outcomes
Students should be able to learn about plant secondary metabolites and other plant based industrial products, and understand molecular marker aided plant breeding. Students should also be able to know about arid plant biotechnology and green house technology.
Texts / References
1. Plant cell & tissue culture Ed: Pollard JW & Walker JM. (1990) Humana Press.
To introduce the students to the concept of nanotechnology and its applications in biological sciences and industry. To teach the students basic techniques used to characterize nanoparticles and to give a detailed insight into the structure and synthesis of different types of nanostructures and their utility in as biosensors and diagnostics. Students will also be introduced to the potential of nanoparticles to be used for drug delivery and targeting a particular tissue/organ.
UNIT-I Introduction to Nano-Biotechnology; Nanotechnology definition and concepts; Cellular Nanostructures; Nanopores; Biomolecular motors; Criteria for suitability of nanostructures for biological applications.
Learning Outcomes
Students should be able to understand the basic concept of nanobiotechnology, and learn about the suitability and applications of different nanomaterials in biological research.
UNIT-II Basic characterization techniques; Electron microscopy; Atomic force microscopy; Photon correlation spectroscopy. Learning Outcomes
Students should be able to learn the different techniques that will be required to characterize the nanoparticles after their preparation.
Students should be able to understand the basic properties of various nanostructures such as films, nanocolloids, nanospheres, nanocapsules and nanovesicles.
UNIT-IV Nanostructures for drug delivery, concepts, targeting, routes of delivery and advantages.
Learning Outcomes
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Students should be able to understand the basic concepts of drug delivery and drug targeting and appreciate the potential of nanoparticles for these purposes.
UNIT-V Nanostructures for diagnostics and biosensors; Nanoparticles for diagnostics and imaging; Nanodevices for sensor development.
Learning Outcomes
Students should be able to have the idea of different types of nanostructures. Students should be able to learn about the applications of nanomaterials as biosensors and understand how these biosensors may be extremely useful in diagnosis of diseases at very early stage and screening for multiple diseases from a single sample. Texts / References
1. Multilayer Thin Films, Editor(s): GeroDecher, Joseph B. Schlenoff Publisher: Wiley-VCH
Verlag GmbH & Co. KGaA ISBN: 3527304401.
2. Bionanotechnology: Lessons from Nature Author: David S. Goodsell Publisher: Wiley-Liss
The objective of this curriculum is to develop research skills in the students. Students are asked to develop a research proposal on which they work during their 4th semester. The objective is to encourage students to come up with their research idea and prepare a plan of research work based on that idea.
Proposal of the Project Work to be streamlined consulting the concerned Supervisor and to make a presentation of the same.
Learning Outcomes
Students should be able develop independent research thinking. They will also be made to learn how to prepare the research proposal and to chalk out the plan of work based on the proposal.
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Course Code: BYM3072
Course Title: Lab I: Genetic Engineering and Immunology
The objective of this practical course is to acquaint students with techniques used in genetic engineering. The other part of this lab course is aimed to teach additional immunological techniques that are not covered in previous semester.
EXERCISES
1. Isolation of genomic DNA from E. coli genome.
2. PCR amplification of available gene and its analysis by agarose gel electrophoresis
3. Preparation of plasmid, from E. coli DH5α and gel analysis.
4. Restriction digestion of vector (gel analysis) and insert using restriction enzymes
(a) Vector and Insert ligation
(b) Transformation in E. coli DH5a.
5. Plasmid isolation and confirmation of recombinants by PCR and RE digestion.
6. Transformation of recombinant plasmid.
7. Induction of protein with IPTG and analysis on SDS-PAGE
8. Purification of protein on Ni-NTA column and analysis of purification by SDS-PAGE
9. Antibody titre against model antigen by Sandwich Elisa method
10. Antibody isotype determination
11. SDS-PAGE profile of IgG, IgM and IgA class of antibodies
12. Western blotting using anti-sera from Candida albicans infected animals.
Learning Outcomes
Students should be able to isolate genomic DNA from bacteria, prepare plasmid vectors and transform bacterial cells and isolate plasmid and confirm recombination. The students should also be able to carry out protein purification (on Ni-NTA column), determine antibody titer by Sandwich ELISA, determine antibody isotypes, and perform SDS-PAGE and Western blotting.
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Course Code: BYM3073
Course Title: Lab II: Bioprocess Engineering and Technology
The objective of this practical course is to acquaint students with bioprocesses at lab scale and give practical training about the production and downstream processes used in industry.
EXERCISES
1. Culture optimization of yeast with various nutrients.
2. Comparative studies of ethanol production using different substrates. Determination of ethanol concentration using the alcohol dehydrogenase activity assay.
3. Various immobilization techniques of enzymes. Comparative studies of soluble and immobilized enzymes.
4. Partial purification of an enzyme by salt fractionation.
5. Purification of an enzyme by column chromatography.
Learning Outcomes
Students should be able to learn the culture optimization strategies, have practical knowledge of how to produce metabolites from microbes at flask level, and have practical knowledge of production and purification of microbial enzymes. Students should also learn production of ethanol and compare efficiency of production using different substrates. They shall also gain practical training of cell immobilization, and learn the basic strategies of protein purification.
The objective of this curriculum is to make students aware with recent scientific developments and techniques and to develop their communication skills by presenting their assigned topic in front of audience. In addition, the quiz based on assigned topic keeps the students in the audience to concentrate on the presented topic.
Presentation of Seminar Topics by the students assigned to them before the evaluation committee. Learning Outcomes
Students should be able to develop ability to read and understand the recent advances in science and technology. This course will improve their communication skills. They will be asked questions from the topics presented and will understand and answer the questions based on the assigned topic.
To explain the basic concepts of Intellectual Property (IP) Laws and familiarize them with its importance in Biotechnology and to provide an understanding about the patenting of inventions in the domain of biotechnology. It also aims at making students familiar with the system of the international IP conventions and treaties, and to impart detailed knowledge about The Patents Act, 1970, and to describe the procedures for obtaining patents and patent licensing and infringement as well as infringement of patents and remedies thereof. Another objective of this course is to introduce students with various bio safety regulations to ensure safety from the use of Genetically Modified Organisms (GMOs) and products, with an emphasis on various biosafety committees.
UNIT-I Introduction to Intellectual Property Types of IP: Patents; Trademarks; Copyright & Related Rights; Industrial Design; Traditional Knowledge; Geographical Indications; Protection of GMOs IP as a factor in R&D; IPs of relevance to Biotechnology and few Case Studies.
Learning Outcomes
Students should be able to understand the basic concepts of IPR and the laws dealing with intellectual Property, learn the various types of Intellectual Properties and the genesis for their protection and the relevance of IP to Biotechnology.
UNIT-II Agreements and Treaties History of GATT & TRIPS Agreement; Madrid Agreement; Hague Agreement; WIPO Treaties; Budapest Treaty; PCT; Indian Patent Act 1970 & recent amendments. Learning Outcomes
Students should be able to understand the various international instruments concerning IPR and in particular relating to patents. The students should also learn the international conventions governing Copyright, Patents, and Trademark etc., and understand the provisions in Patents Act concerning patenting of an invention.
UNIT-III Basics of Patents and Concept of Prior Art Introduction to Patents; Types of patent applications: Ordinary; PCT; Conventional; Divisional and Patent of Addition; Specifications: Provisional and complete; Forms and fees Invention in context of “prior art”; Patent databases; Searching International Databases; Country-wise patent searches (USPTO; esp@cenet(EPO); PATENTScope(WIPO); IPO; etc.).
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Learning Outcomes
Students should be able to know about the various forms required to be filled along with application for patent, and understand the national as well as international system of filing a patent.
UNIT-IV Patent filing procedures National & PCT filing procedure; Time frame and cost; Status of the patent applications filed; Precautions while patenting – disclosure/non-disclosure; Financial assistance for patenting introduction to existing schemes Patent licensing and agreement Patent infringement- meaning; scope; litigation; case studies. Learning Outcomes
Students should be able to understand how to draft a patent application, learn the legal aspects governing infringement, exceptions and defenses to infringement, and know about the remedies available to the patent holder in the event of infringement.
UNIT-V Biosafety Introduction; Historical background; Introduction to Biological Safety Cabinets; Primary Containment for Biohazards; Biosafety Levels; Biosafety Levels of Specific Microorganisms; Recommended Biosafety Levels for Infectious Agents and Infected Animals; Biosafety guidelines - Government of India; Definition of GMOs & LMOs; Roles of Institutional Biosafety Committee; RCGM; GEAC etc. for GMO applications in food and agriculture; Environmental release of GMOs; Risk Analysis; Risk Assessment; Risk management and communication; Overview of National Regulations and relevant International Agreements including Cartegana Protocol. Learning Outcomes
Students should be able to uderstand the recommended Bio safety Levels and guidelines and the role of institutional Bio safety committees etc. In addition, they should be able to identify the role of the Bio safety Professionals in Biomedical Research Laboratories, and understand national as well as international regulations on Bio safety. Texts / References
1. BAREACT; Indian Patent Act 1970 Acts & Rules; Universal Law Publishing Co. Pvt. Ltd.; 2007.
2. Kankanala C.; Genetic Patent Law & Strategy; 1st Edition; Manupatra Information Solution Pvt.
To introduce the students about the basics of bioprocess engineering and technology besides the knowledge of industrially important microorganisms. To teach the students about the basics of Bioreactor design and the mode and classification of fermentations, and down-stream processing. The bioconversion of cheap raw materials such as Starch, Sugar, High fructose Corn Syrup, etc. into useful products like Enzymes, Foods and beverages, and Cheese etc., will also be discussed. In addition, to apprise the students about the basics of Enzyme engineering.
UNIT-I
Basic principle of Biochemical Engineering; Isolation; screening and maintenance of industrially important microbes; Microbial growth and death kinetics (an example from each group; particularly with reference to industrially useful microorganisms); Strain improvement for increased yield and other desirable characteristics.
Learning Outcomes
Students should be able to understand the basics of bioprocess engineering, know the details of nutritional requirements and growth curve of industrial MOs and know the kinetics of growing cells and product formation.
UNIT-II
Concepts of basic mode of fermentation processes Bioreactor designs; Types of fermentation and fermenters; Concepts of basic modes of fermentation - Batch; fed batch and continuous; Conventional fermentation v/s biotransformation; Solid substrate; surface and submerged fermentation; Fermentation economics; Fermentation media; Fermenter design-mechanically agitated; Pneumatic and hydrodynamic fermenters; Large scale animal and plant cell cultivation and air sterilization; Upstream processing: Media formulation; Sterilization; Aeration and agitation in bioprocess; Measurement and control of bioprocess parameters; Scale up and scale down process.
Learning Outcomes
Students should be able to know the basics of upstream processing of a bioprocess, learn the sterilization of air and medium for aerobic and anaerobic processes, and to design the suitable configurations of Bioreactors for successful operation of industrial bioprocesses.
UNIT-III
Downstream processing; Bioseparation; filtration; centrifugation; sedimentation; flocculation; Cell disruption; Liquid-liquid extraction; Purification by chromatographic techniques; Reverse osmosis and ultra-filtration; Drying; Crystallization; Storage and packaging; Treatment of effluent and its disposal.
Learning Outcomes
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Students should be able to know the route of substrates conversion into product through metabolic pathways, compare various bioreactors and run a bioreactor, learn the bio-separation methods, and to check the suitable design, operation and monitoring of bioprocess in a given industry.
UNIT-IV
Applications of enzymes in food processing Mechanism of enzyme function and reactions in process techniques; Enzymic bioconversions e.g. starch and sugar conversion processes; High-Fructose Corn Syrup; Interesterified fat; Hydrolyzed protein etc. and their downstream processing; baking by amylases; deoxygenation and desugaring by glucoses oxidase; beer mashing and chill proofing; cheese making by proteases and various other enzyme catalytic actions in food processing. Applications of Microbes in food process operations and production Fermented foods and beverages; Food ingredients and additives prepared by fermentation and their purification; fermentation as a method of preparing and preserving foods; Microbes and their use in pickling; producing colors and flavors; alcoholic beverages and other products; Process wastes-whey; molasses; starch substrates and other food wastes for bioconversion to useful products; Bacteriocins from lactic acid bacteria – Production and applications in food preservation.
Learning Outcomes
Students should be able to learn new technology and innovative methods to improve the quality of a bio product or to develop even a better bioprocess.
UNIT-V
Enzyme kinetics; Two-substrate kinetics and pre-steady state kinetics; Allosteric enzymes; Enzyme mechanism; Enzyme inhibitors and active site determination Production; recovery and scaling up of enzymes and their role in food and other industries; Immobilization of enzymes and their industrial applications.
Learning Outcomes
Students should be able to find out parameters (to convert cheap raw materials into useful bio products and design strategies to improve the performance of a given bioprocess. Students should gain the knowledge with respect to quality and quantity of Industrial Production.
Texts / References
1. Jackson AT.; Bioprocess Engineering in Biotechnology; Prentice Hall; Engelwood Cliffs; 1991.
2. Shuler ML and Kargi F.; Bioprocess Engineering: Basic concepts; 2nd Edition; Prentice Hall;
Engelwood Cliffs; 2002.
3. Stanbury RF and Whitaker A.; Principles of Fermentation Technology; Pergamon press;
Oxford; 1997.
4. Baily JE and Ollis DF.; Biochemical Engineering fundamentals; 2nd Edition; McGraw-Hill Book
Co.; New York; 1986.
5. Aiba S; Humphrey AE and Millis NF; Biochemical Engineering; 2nd Edition; University of
Tokyo press; Tokyo; 1973.
6. Comprehensive Biotechnology: The Principles; Applications and Regulations of Biotechnology
in Industry; Agriculture and Medicine; Vol 1; 2; 3 and 4. Young M.M.; Reed Elsevier India
Private Ltd; India; 2004.
7. Mansi EMTEL; Bryle CFA. Fermentation Microbiology and Biotechnology; 2nd Edition; Taylor
To introduce the students to the different kinds of business organizations and their financial, accounting and bookkeeping aspects. To introduce the students to the product development according to the needs of the customers and its demand in the market, to provide the detail knowledge of negotiations strategies with financiers, bankers, government, law enforcement authorities and companies & Institutions. To introduce the students to Human Resource Development, and to provide the information about the development of technologies and regulation for transfer of foreign technologies.
UNIT-I Accounting and Finance
Forms of Business Organizations; Statutory and legal requirements for starting specific Organisation; Special provisions for Venture Capital Financing; Basics of accounting conventions; Difference between receipts and income; payment and expenses; Concept Profit and Loss Account; Understanding Balance Sheet related concepts; Preparation of Project for Bank Finance. Learning Outcomes
Students should be able to differentiate between the different types of business setups, and understand the Venture Capital Financing, bookkeeping and basic balance sheet related concepts.
UNIT-II Marketing
Assessment of market demand for potential product(s) of interest; Identifying needs of customers including gaps in the market; Market Segments; Prediction of market changes; packaging the product; Market linkages; branding issues; Developing distribution channels; Pricing / Policies / Competition; Promotion / Advertising; Services Marketing. Learning Outcomes
Students should be able to understand the market demand and the dynamics of the different kind of markets, and develop ability to identify the needs of the customers and potential product for it.
UNIT-III Negotiations Strategies
With financiers, bankers, government, law enforcement authorities and companies & Institutions; Technology transfer and dispute resolution skills; Changes in External
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environment; Crisis Management; Use IT for business administration and financial management; E-business setup and management.
Learning Outcomes
Students should be able to know Negotiations strategies and develop Dispute resolution skills, perform SWOT Analysis and crises management, and understand the E business setup and the ever changing landscape of IT in running a successful business.
UNIT-IV Human Resource Development (HRD)
Different types of Organizational structures; Leadership and Managerial skills; Team building, teamwork, performance appraisal, rewards system; Fundamentals of Entrepreneurship: Support mechanism for entrepreneurship in India. Learning Outcomes
Students should be able to understand the different types of Organizational structures, and the importance of relationship management, team building and team work. Students should know different types of support mechanism for entrepreneurship in India including governmental schemes.
UNIT-V Role of knowledge center and R&D
Knowledge centers like universities and research institutions; Role of technology and upgradation; Assessment of scale of development of Technology; Managing Technology Transfer; Regulations for transfer of foreign technologies; Technology transfer agencies.
Learning Outcomes
Students should be able to understand the role of different knowledge centers for improving and developing new technologies and harnessing it for innovative product development. Students should have an idea of the technology transfer and technology transfer agencies.
Case Study
1. Candidates should be made to start a ‘mock paper company’; systematically following all the procedures. (a) The market analysis developed by them will be used to choose the product or services. (b) A product or service is created in paper and positioned in the market. As a product or
services available only in paper to be sold in the market through the existing links. At this juncture; the pricing of the product or the service needs to be finalized; linking the distribution system until the product or services reaches the end consumer.
(c) Candidates who have developed such product or service could present the same as a project work to the Panel of Experts; including representatives from industry sector. If the presented product or service is found to have real potential; the candidates would be exposed to the next level of actual implementation of the project.
2. Go to any venture capital website (like sequoiacap.com) and prepare a proposal for funding from venture capital.
48
Note: Names of specific cases to be discussed in the class shall be specified from time to time. Texts / References
1. Koontz, H. and Donnel C., Essentials of Management, McGraw Hill, New Delhi.
The objective of this curriculum is to develop research skills in the students. Students work, in a comprehensive, manner on the proposed research plan, under the supervision of one of the faculties. The main objective is to make students well-acquainted with the modern research equipment and to train them for taking on research work later in Ph.D. course.
Laboratory work to be carried out on the assigned Project Topic under the supervision of the concerned teacher and the same will be evaluated by the External Examiner as well as Internal team.
Learning Outcomes
Students should be able to have the practical knowledge of using modern techniques and equipment. Besides this, the students should learn to work independently, and to solve research problems.
The objective of this curriculum is to develop skill of understanding and presenting the papers
published in high-rated journals. The aim is to train students for developing the understanding of
research methodologies which would be useful for Ph.D. course in future.
Presentation of Seminar Topics by the students assigned to them before the evaluation committee.
Learning Outcomes
Students should be able to improve upon their communication and presentation skills and develop ability to read and understand the research papers. Students should also be able to know and understand the recent techniques used in different related research fields.
Biochemistry 4 Credits Unit I Chemical basis of life; Composition of living matter; Water – properties; pH; ionization and hydrophobicity; Emergent properties of biomolecules in water; Biomolecular hierarchy; Macromolecules; Molecular assemblies; Structure-function relationships Amino acids – structure and functional group properties; Peptides and covalent structure of proteins; Elucidation of primary and higher order structures; Evolution of protein structure; Structure-function relationships in model proteins like ribonuclease A; myoglobin; hemoglobin; chymotrypsin etc.; Tools to characterize expressed proteins. Unit II Enzyme catalysis – general principles of catalysis; Quantitation of enzyme activity and efficiency; Enzyme characterization and Michaelis-Menten kinetics; Relevance of enzymes in metabolic regulation; activation; inhibition and covalent modification; Single substrate enzymes Unit III Sugars - mono; di; and polysaccharides; Suitability in the context of their different functions- cellular structure; energy storage; signaling; Glycosylation of other biomolecules - glycoproteins and glycolipids; Lipids - structure and properties of important members of storage and membrane lipids; lipoproteins Unit IV Biomembrane organization - sidedness and function; Membrane bound proteins - structure; properties and function; Transport phenomena; Nucleosides; nucleotides; nucleic acids - structure; diversity and function;; Brief overview of central dogma. Unit V Bioenergetics-basic principles; Equilibria and concept of free energy; Coupled processes; Glycolytic pathway; Kreb's cycle; Oxidative phosphorylation; Photosynthesis; Elucidation of metabolic pathways; Logic and integration of central metabolism; entry/ exit of various biomolecules from central pathways; Principles of metabolic regulation; Regulatory steps.. Texts/References: 1. V.Voet and J.G.Voet; Biochemistry; 3rd edition; John Wiley; New York; 2004. 2. A.L. Lehninger; Principles of Biochemistry; 5th edition; W.H Freeman and
Company; 2004. 3. L. Stryer; Biochemistry; 5th edition; W.H. Freeman and Company; 2002.
Analytical Techniques 4 Credits Unit I Basic Techniques: Buffers; Methods of cell disintegration; Enzyme assays and controls; Detergents and membrane proteins; Dialysis; Ultrafiltration and other membrane techniques Spectroscopy Techniques: UV; Visible and Raman Spectroscopy; Theory and application of Circular Dichroism; Fluorescence; NMR; PMR; ESR and Plasma Emission spectroscopy Unit II Chromatography Techniques TLC and Paper chromatography; Chromatographic methods for macromolecule separation -Gel permeation; Ion exchange; Hydrophobic; Reverse-phase and Affinity chromatography; HPLC and FPLC; Criteria of protein purity Electrophoretic techniques: Theory and application of Polyacrylamide and Agarose gel electrophoresis; Capillary electrophoresis; 2D Electrophoresis; Disc gel electrophoresis; Gradient electrophoresis; Pulsed field gel electrophoresis Unit III Centrifugation Basic principles; Mathematics & theory (RCF; Sedimentation coefficient etc); Types of centrifuge - Microcentrifuge; High speed & Ultracentrifuges; Preparative centrifugation; Differential & density gradient centrifugation; Applications (Isolation of cell components); Analytical centrifugation; Determination of molecular weight by sedimentation velocity & sedimentation equilibrium methods Unit IV Radioactivity Radioactive & stable isotopes; Pattern and rate of radioactive decay; Units of radioactivity; Measurement of radioactivity; Geiger-Muller counter; Solid & Liquid scintillation counters (Basic principle; instrumentation & technique); Brief idea of radiation dosimetry; Autoradiography; Measurement of stable isotopes; Falling drop method; Applications of isotopes in biochemistry; Radiotracer techniques; Distribution studies; Isotope dilution technique; Metabolic studies; Clinical application; Radioimmunoassay Unit V Advanced Techniques: Protein crystallization; Theory and methods; API-electrospray and MADI-TOF; Mass spectrometry; DNA & Peptide Synthesis. Texts/References: 1. Freifelder D.; Physical Biochemistry; Application to Biochemistry and Molecular
Biology; 2nd Edition; W.H. Freeman & Company; San Fransisco; 1982. 2. Keith Wilson and John Walker; Principles and Techniques of Practical
Biochemistry; 5th Edition; Cambridge University Press; 2000. 3. D. Holme & H. Peck; Analytical Biochemistry; 3rd Edition; Longman; 1998. 4. R. Scopes; Protein Purification - Principles & Practices; 3rd Edition; Springer
Verlag; 1994. 5. Selected readings from Methods in Enzymology; Academic Press.
Biostatistics & Computer Applications 4 Credits Unit I Fundamental concepts in applied probability; Exploratory data analysis and statistical inference; Probability and analysis of one and two way samples; discrete and continuous probability models; Expectation and variance; Central limit theorem; Inference; Hypothesis; Critical region and error probabilities; Tests for proportion; Equality of proportions; equality of means of normal populations(variance known; variance unknown); Chi-square test for independence; P-value of the statistic; Confidence limits; Introduction to one way and two-way analysis of variance; Data transformations Unit II Elements of programming language – C, Data base concept; Database management system; Database browsing and Data retrieval; Sequence database and genome database; Data Structures and Databases; Databases such as GeneBank; EMBL; DDBJ; Swissplot; PIR; MIPS; TIGR; Hovergen; TAIR; PlasmoDB; ECDC; Searching for sequence database like FASTA and Blast algorithm. Unit III Cluster analysis; Phylogenetic clustering by simple matching coefficients; Sequence Comparison; Sequence pattern; Regular expression based pattern; Theory of profiles and their use in sequence analysis; Markov models; Concept of HMMS; Baum-Welch algorithm; Use of profile HMM for protein family classification; Pattern recognition methods Unit IV Goals of a Microarray experiment; Normalization of Miroarray data; Detecting differential gene expression; Principle component analysis; Clustering of microarray data; Structure determination by X-ray crystallography; NMR spectroscopy; PDB(Protein Data Bank) and NDB(Nucleic Acid Data Bank); File formats for storage and dissemination of molecular structure. Unit V Methods for modeling; Homology modeling; Threading and protein structure prediction; Structure-structure comparison of macromolecules with reference to proteins; Force fields; Molecular energy minimization; Monte Carlo and molecular dynamics simulation Practicals: Introduction to MSEXCEL-Use of worksheet to enter data; edit data; copy data; move data. Use of in-built statistical functions for computations of Mean; S.D.; Correlation; regression coefficients etc. Use of bar diagram; histogram; scatter plots; etc. graphical tools in EXCEL for presentation of data. [Introduction to SYSTAT package. Searching PubMed ; Introduction to NCBI; NCBI data bases; BLAST BLASTn; BLASTp; PSI-BLAST; Sequence manipulation Suite; Multiple sequence alignment; Primer designing; Phylogenetic Analysis. Protein Modeling; Protein structure Analysis; Docking; Ligplot interactions.]
Texts/References: 1. Wayne W. Daniel; Biostatistics : A foundation for Analysis in the Health Sciences;
8th Edition; Wiley; 2004. 2. Prem S. Mann; Introductory Statistics; 6th Edition; Wiley; 2006. 3. John A. Rice; Mathematical Statistics and Data Analysis; 3rd Edition; John A.
Edition; Benjamin Cummings; 2002. 5. Cynthia Gibas and Per Jambeck; Developing Bioinformatics Computer Skill; 1st
Edition; O’Reilly Publication; 2001. Cellular & Molecular Biology 4 Credits Unit I Cell diversity: Chemical equilibrium and energetics; Cell theory; Cell organelles- endo-membrane systems; Golgi apparatus; lysosomes; endoplasmic reticulum; nucleus and chromatin organization; Extracellular matrix - basal lamina; connective and other tissues; Cell-cell junctions; Cell wall- structural organization and functions; Cellular energy transactions- Role of mitochondria and chloroplast; Co- and post-translational modification of Proteins; Intracellular protein trafficking; Quality control in ER and Golgi; secretary pathway and vesicular trafficking; Import into mitochondria; chloroplast; peroxisome; lysosomes; Receptor-mediated endocytosis; Cytoskeleton- actin; myosin; microfilaments; microtubules and their dynamics; Intermediate filaments; Cell motility; Cilia and flagella; Motor proteins- kinesin and dynein; Differentiation of specialized cells- stem cells differentiation; blood cell formation.
Unit II Basic techniques of cell biology; Light and electron microscopy; Confocal microscopy; atomic force microscopy; Sub-cellular fractionation; Culturing of metazoan cells; Protein-DNA Interactions; Footprinting and gel-shift asays; Yeast two hybrid and Phage display; Structure determination: cryoelectron microscopy; RNA interference; hybridization techniques; Membrane transport- Passive and active transport; diffusion and osmosis; ion channels (gated & non-gated); Symport and Antiport; Uniport and Co-transport; Trans-epithelial transport; Transport of proteins and molecular chaperones. Unit III Cell cycle and cancer biology; Mitosis- role of cyclins; CDK; MPF and control of mitosis; Nuclear decondensation; Control of S-phase; Cell cycle control in mammalian cells; Check points and restriction points; Meiosis- asymmetric cell division; Gametogenesis and fertilization; Cell death and its regulation; Tumor cells and onset of cancer; Oncogenes; proto-oncogenes; Viral and cellular oncogenes; tumour suppressor genes from humans; Structure; function and mechanism of action of pRb and p53 tumour suppressor proteins; Types of cancer and metastasis; Genetic basis of cancer; Mutations as cause of cancer; Nonsense; missense and point mutations; Intragenic and Intergenic suppression; Frameshift mutations; Physical; chemical and biological mutagens; Carcinogens; Viruses and cancer; Cell signaling- surface receptors; Signal
transduction; Role of GPCR; Cytokine receptors; Receptor tyrosine kinase; MAPK pathways; Secondary messengers; Gene activation by cell surface receptors.
Unit IV Heterochromatin and euchromatin; DNA reassociation kinetics (Cot curve analysis); Repetitive and unique sequences; Satellite DNA; DNA melting and buoyant density; Nucleosome phasing; DNase I hypersensitive regions; DNA methylation & Imprinting; Overlapping genes; Split genes; Eukaryotic Gene structure; mobile genetic elements (transposons and retroposons) in Prokaryotes and Eukaryotes; Organelle DNAs; Organization and morphology of chromosomes; DNA replication- mechanism; enzymes and accessory proteins involved; control; Replication of single stranded circular DNA; gene stability and DNA repair enzymes; Photoreactivation; Nucleotide excision repair; mismatch correction; SOS repair; Homologous and non-homologous recombinations; Site specific recombinations; Chi sequences in prokaryotes; Gene targeting; Gene disruption; FLP/FRT and Cre/Lox recombination.
Unit V Prokaryotic and Eukaryotic transcription; RNA polymerases; General and specific transcription factors; Regulatory elements- TATA box and TATA binding proteins; activators; repressors; Mechanisms of transcription regulation at initiation; elongation and Termination (Rho dependant and rho dependant); Attenuation and anti-termination; Regulation of transcription factor activity; Chromation remodelling and histone modification; Regulation of transcription in eukaryotes- regulatory sequences (Promoters and enhancers); Gene expression in bacteria; Operon Concept (lac; trp; ara; his operons); Transcriptional control in lambda phage; Pre mRNA Modifications- 5’- cap formation; 3’- end processing and polyadenylation; splicing; mRNA stability; Processing of hnRNA; RNA editing; Nuclear export of mRNA and its regulation; tRNA modification; cytoplasmic mechanism of post transcriptional control; Genetic code- degeneracy of codons; Wobble hypothesis; Genetic code in mitochondria; Translation- Procaryotic and eukaryotic translation; the translation machinery; Mechanism of initiation; elongation and Termination; regulation of translation; Oncogenes as transcriptional activators..
Text/References:
1. Benjamin Lewin; Gene IX; 9th Edition; Jones and Barlett Publishers; 2007. 2. J.D. Watson; N.H. Hopkins; J.W Roberts; J. A. Seitz & A.M. Weiner; Molecular
Biology of the Gene; 6th Edition; Benjamin Cummings Publishing Company Inc; 2007.
3. Alberts et al; Molecular Biology of the Cell; 4th edition; Garland; 2002. 4. Lodish et al.; Molecular cell Biology; 4th Edition; W.H. Freeman & Company;
2000. 5. Smith & Wood; Cell Biology; 2nd Edition; Chapman & Hall; London;1996. 6. B. M. Turner; Chromatin & Gene regulation; 1st Edition; Wiley-Blackwell; 2002. 7. Watson et al.; Molecular Biology of the gene; 5th Edition; Pearson Prentice Hall.
USA; 2003
Practicals Semester I Lab I: Biochemistry and Analytical Techniques 4 Credits
1. Preparation of variousBuffer system and validation of the Henderson-Hasselbach equation.
2. Determination of protein concentration in unknown solution/biological sample, plotting a standard graph of BSA using UV-Vis Spectrophotometer and validating the Beer- Lambert’s Law.
3. pH meter titration of amino acids and separation of aliphatic, aromatic and polar amino acids by TLC.
4. An enzyme purification theme (such as E.coli alkaline phosphatase or any other enzyme.
(a) Preparation of cell-free lysates
(b) Ammonium sulfate precipitation
(c) Ion-exchange chromatagraphy
(d) Gel filtration
(e) Affinity chromatography
(f) Generating a purification table
(g) Assessing purity by SDS-PAGE gel electrophoresis
(h) Assessing purityof given protein sample by PAGE
Semester I Lab II: Molecular Biology 4 Credits 1. Plasmid DNA isolation and DNA quantitation: Plasmid minipreps
2. Restriction digestion
3. RFLP analysis of the PCR product
4. Preparation of competent cells.
5. Agarose gel electrophoresis
6. Transformation of E.coli with standard plasmids, calculation of transformation efficiency
7. Polymerase chain reaction (PCR), using standard 16srRNA eubacterial
8. Transformation in Bacteria.
Seminar/Journal Club 4 Credits (Presentation of Seminar Topics by the students assigned to them before the evaluation committee)
SEMESTER - II Immunology 4 Credits Unit I Immunology-fundamental concepts and anatomy of the immune system Components of innate and acquired immunity; Phagocytosis; Complement and Inflammatory responses; Haematopoesis; Organs and cells of the immune system- primary and secondary Lymphoid organs; Lymphatic system; Lymphocyte circulation; Lymphocyte homing; Mucosal and Cutaneous associated Lymphoid tissue.(MALT&CALT); Mucosal Immunity; Antigens - immunogens; haptens; Major Histocompatibility Complex - MHC genes; MHC and immune responsiveness and disease susceptibility. Unit II Immune responses generated by B and T lymphocytes Immunoglobulins-basic structure; classes & subclasses of immunoglobulins; antigenic determinants; Multigene organization of immunoglobulin genes; B-cell receptor; Immunoglobulin superfamily; Principles of cell signaling;Basis of self –non-self discrimination; Kinetics of immune response; memory; B cell maturation; activation and differentiation; Generation of antibody diversity; T-cell maturation; activation and differentiation and T- cell receptors; Functional T Cell Subsets; Cell-mediated immune responses; ADCC; Cytokines-properties; receptors and therapeutic uses; Antigen processing and presentation- endogenous antigens; exogenous antigens; non-peptide bacterial antigens and super-antigens. Unit III Antigen-antibody interactions Precipitation; agglutination and complement mediated immune reactions; Advanced immunological techniques - RIA; ELISA; Western blotting; ELISPOT assay; immunofluorescence; flow cytometry and immunoelectron microscopy; Surface plasma resonance; Biosenor assays for assessing ligand –receptor interaction; CMI techniques- lymphoproliferation assay; Mixed lymphocyte reaction; Cell Cytotoxicity assays; Apoptotosis. Unit IV Vaccinology Active and passive immunization; Live; killed; attenuated; sub unit vaccines; Vaccine technology- Role and properties of adjuvants; recombinant DNA and protein based vaccines; plant-based vaccines; reverse vaccinology; Peptide vaccines; conjugate vaccines; Antibody genes and antibody engineering- chimeric and hybrid monoclonal antibodies; Catalytic antibodies and generation of immunoglobulin gene libraries. Tumor immunology – Tumor antigens; Immune response to tumors and tumor evasion of the immune system; Cancer immunotherapy; Immunodeficiency-Primary immunodeficiencies; Acquired or secondary immunodeficiencies. Unit V Clinical Immunology Immunity to Infection : Bacteria; viral; fungal and parasitic infections (with examples from each group); Hypersensitivity – Type I-IV; Autoimmunity; Types of
autoimmune diseases; Mechanism and role of CD4+ T cells; MHC and TCR in autoimmunity; Treatment of autoimmune diseases; Transplantation – Immunological basis of graft rejection; Clinical transplantation and immunosuppressive therapy. Texts/References: 1. Kuby; RA Goldsby; Thomas J. Kindt; Barbara; A. Osborne Immunology; 6th
Gower Medical Publishing; 2002. 3. Janeway et al.; Immunobiology; 4th Edition; Current Biology publications.; 1999. 4. Paul; Fundamental of Immunology; 4th edition; Lippencott Raven; 1999. 5. Goding; Monoclonal antibodies; Academic Press. 1985. Microbiology & Industrial Applications 4 Credits Unit I Microbial Diversity & Systematics Classical and modern methods and concepts; Domain and Kingdom concepts in classification of microorganisms; Criteria for classification; Classification of Bacteria according to Bergey’s manual; Molecular methods such as Denaturing Gradient Gel Electrophoresis (DGGE); Temperature Gradient Gel Electrophoresis (TGGE); Amplified rDNA Restriction Analysis and Terminal Restriction Fragment Length Polymorphism (T-RFLP) in assessing microbial diversity; 16S rDNA sequencing and Ribosomal Database Project. Unit II Microbial growth: Growth cycle of bacteria; synchronous growth. Culture and its characteristics; pure culture, mixed culture; media and its types; Batch culture ; fed-batch; continuous kinetics. Methods of growth estimation; direct microscopic count; electronic enumeration method, viable count through cfu method; membrane filter count; turbidimetric method; selection of procedure to measure growth; significance of quantitative measurement. Microbial physiology: Physiological adoption and life style of Prokaryotes; Unicellular Eukaryotes and the Extremophiles (with classical example from each group). Ultrastructure of Archaea (Methanococcus); Eubacteria (E.coli); Unicellular Eukaryotes (Yeast) and viruses (Bacterial; Plant; Animal and Tumor viruses). Unit III Microbial Interactions and Infection Host–Pathogen interactions; pathogenicity and virulence; Microbial adherence; type of microbial penetration. Microbial virulence factors; exotoxins and endotoxins; Microbes infecting humans; veterinary animals; Pathogenicity islands and their role in bacterial virulence Unit IV Microbes and Environment Role of microorganisms in natural system and artificial system; Influence of Microbes on the Earth's Environment and Inhabitants; Ecological impacts of microbes; Symbiosis (Nitrogen fixation and ruminant symbiosis); Microbes and Nutrient cycles; Microbial communication system; Quorum sensing; Microbial fuel cells; Prebiotics and Probiotics; Vaccines
Unit V Industrial Applications Basic principles in bioprocess technology; Media Formulation; Sterilization; Thermal death kinetics; Batch and continuous sterilization systems; Primary and secondary metabolites; Extracellular enzymes; Biotechnologically important intracellular products; exopolymers; Bioprocess control and monitoring variables such as temperature; agitation; pressure; pH Microbial processes-production; optimization; screening; strain improvement; factors affecting down stream processing and recovery; Representative examples of ethanol; organic acids; antibiotics etc. Enzyme Technology-production; recovery; stability and formulation of bacterial and fungal enzymes-amylase; protease; penicillin acylase; glucose isomerase; Immobilised Enzyme and Cell based biotransformations-steroids; antibiotics; alkaloids; enzyme/cell electrodes. Texts/References: 1. Pelczar MJ Jr.; Chan ECS and Kreig NR.; Microbiology; 5th Edition; Tata
McGraw Hill; 1993. 2. Maloy SR; Cronan JE Jr.; and Freifelder D; Microbial Genetics; Jones Bartlett
Publishers; Sudbury; Massachusetts; 2006. 3. Crueger and A Crueger; (English Ed.; TDW Brock); Biotechnology: A textbook of
Industrial Microbiology; Sinaeur Associates; 1990. 4. G Reed; Prescott and Dunn’s; Industrial Microbiology; 4th Edition; CBS
Publishers; 1987. 5. M.T. Madigan and J.M. Martinko; Biology of Microorganisms; 11th Edition;
Pearson Prentice Hall; USA; 2006. Genetics & Genetic Engineering 4 Credits Unit I Basics Concepts: DNA Structure and properties; Restriction Enzymes; DNA ligase; Klenow enzyme; T4 DNA polymerase; Polynucleotide kinase; Alkaline phosphatase; Cohesive and blunt end ligation; Linkers; Adaptors; Homopolymeric tailing; Labeling of DNA: Nick translation; Random priming; Radioactive and non-radioactive probes; Hybridization techniques: Northern; Southern and Colony hybridization; Fluorescence in situ hybridization; Chromatin Immunoprecipitation; DNA-Protein Interactions-Electromobility shift assay; DNaseI footprinting; Comparative Genomic Hybridization (CGH). Unit II Cloning Vectors and methodology: Plasmids; Bacteriophages; M13 mp vectors; PUC19 and Bluescript vectors; Phagemids; Lambda vectors; Cosmids; Artificial chromosome vectors (YACs; BACs); Animal Virus derived vectors-SV-40; Expression vectors; pMal; GST; pET-based vectors; Protein purification; His-tag; GST-tag; MBP-tag etc.; Intein-based vectors; Inclusion bodies; Methodologies to reduce formation of inclusion bodies; Plant based vectors; Ti and Ri as vectors; Yeast vectors; Shuttle vectors. Cloning Methodologies Insertion of Foreign DNA into Host Cells; Transformation; Construction of libraries; Isolation of mRNA and total RNA; cDNA and genomic libraries; Expression cloning; Jumping and hopping libraries; Southwestern and Far-western cloning; Protein-protein interactive cloning and Phage display; Principles in maximizing gene expression; Plasmid biology - copy number and its control; Incompatibility; Plasmid survival
strategies; Antibiotic resistance markers on plasmids (mechanism of action and resistance); Genetic analysis using phage and plasmid. Unit III PCR and sequencing: Primer design; Fidelity of thermostable enzymes; DNA polymerases; Types of PCR – multiplex; nested; reverse transcriptase; real time PCR; touchdown PCR; hot start PCR; colony PCR; cloning of PCR products; Proof reading enzymes; PCR in gene recombination; Deletion; addition; Overlap extension; Site specific mutagenesis; PCR in molecular diagnostics; Viral and bacterial detection; PCR based mutagenesis; Mutation detection; Assay of mutagenic agents (Ames test); Sequencing methods: Enzymatic DNA sequencing, Chemical sequencing of DNA, Automated DNA sequencing, RNA sequencing; Chemical Synthesis of oligonucleotides; Transfection techniques; Gene silencing techniques; Introduction to siRNA; Micro RNA; Construction of siRNA vectors; Principle and application of gene silencing; Gene knockouts, Transgenics and Gene Therapy; Suicide gene therapy; Gene replacement; Gene targeting; Differential gene expression. Unit IV Gene transfer: Bacterial-history; Transduction and Transformation; Merodiploid generation; Transposable genetic elements; General genetic variations: errors in cell division; Non disjunction; Structural and numerical chromosomal abnormalities; Mutations: kinds of mutation; agents of mutation; mutation selection; genome polymorphism; uses of polymorphism; Phenotype; Genotype; Gene frequency; Hardy Weinberg concepts; Mutation selection; Migration; Gene flow; Genetic drift; Human genetic diversity; Origin of major human groups. Unit V Mendelian and Non Mendelian Genetics: Introduction to human genetics; Background and history; Types of genetic diseases; Role of genetics in medicine; Human pedigrees; Patterns of single gene inheritance-autosomal recessive; Autosomal dominant; X linked inheritance; Hemoglobinopathies - Genetic disorders of hemoglobin and their diseases. Non Mendelian patterns: Mitochondrial inheritance; Genomic imprinting; Lyon hypothesis; isodisomy; Complex inheritance-genetic and environmental variation; Heritability; Twin studies; Behavioral traits; Genes in early development; Maternal effect genes; Homeotic genes. Text/References: 1. S.B. Primrose; R.M. Twyman and R.W.Old; Principles of Gene Manipulation. 6th
Edition; S.B.University Press; 2001. 2. J. Sambrook and D.W. Russel; Molecular Cloning: A Laboratory Manual; Vols 1-
3; CSHL; 2001. 3. Brown TA; Genomes; 3rd ed. Garland Science 2006 4. Selected papers from scientific journals. 5. Technical Literature from Stratagene; Promega; Novagen; New England Biolab etc. 6. S.R. Maloy; J.E. Cronan; D. Friefelder; Microbial Genetics; 2nd Edition; Jones
and Bartlett Publishers; 1994. 7. N. Trun and J. Trempy; Fundamental Bacterial Genetics; Blackwell publishing; 2004. 8. Strachan T and Read A P; Human molecular genetics; 3rd Edition Wiley Bios; 2006. 9. Mange E J and Mange A. P.; Human genetics; 2nd Edition; Sinauer Associates
publications; 1999.
Proteins & Enzymes 4 Credits Unit I Peptides & proteins- Peptide bond conformation; dihedral angles; Ionization behaviour of peptides; Peptide diversity in terms of size and composition; Peptides with biological activities; Primary: secondary and tertiary structure of proteins; Ramachandran plot; Fibrous and globular proteins; Forces stabilizing native protein conformation; Super-secondary structure: quaternary structure; Prediction of secondary structure; Chemical modification of Proteins. Unit II Determination of protein structure- Sequence determination of proteins; N- and C-terminal amino acid analysis; Edman’s degradation: classical and automated procedures; Use of mass spectrometry in primary structure determination. Unit III Protein function- Protein ligand interactions; Qualitative and quantitative studies on cooperative and non-cooperative (Sigmoidal) binding of ligands; Hill equation; Sequential and concerted model for cooperative binding. Unit IV Protein denaturation and folding; Models of protein folding and association of proteins; Anfinsen’s experiment: Thermodynamics of protein folding- Leventhal Paradox; Role of chaperons in folding; Protein misfolding disorders: Amlyloid fiber formation; Protein evolution. Unit V Enzymes- History; Features of enzyme catalyzed reaction; Properties and study of enzyme active sites; Kinetics of single and multi-substrate reactions; Enzyme inhibition- irreversible and reversible (competitive: noncompetitive and uncompetitive inhibition); Allosteric enzymes (sequential and concerted model). Artificial enzymes- Synthetic and semi-synthetic enzymes: Catalytic antibodies; Molecular imprinting: Non-aqueous enzymology- Behaviour of enzymes in non aqueous media: application in synthesis and industry. Texts/ References: 1. M.M. Cox and D.L.Nelson, Lehninger; Principles of Biochemistry;(2008) 5th
edition; W.H Freeman and Company; 2. J.M. Berg, J.L. Tymoczko and L. Stryer; Biochemistry; 5th edition; (2007) W.H.
Freeman and Company.. 3. H.W. Blank & D.S, Clark; Applied Biocatalysis, Vol I (1991) Marcel Dekkar Inc.
N.Y. 4. D. Whitford; Proteins, Structure and Function (2001) John Wiley & Sons Ltd. 5. R. Guerois and Lopez de la Paz; Protein Design Methods and Applicatios (2006)
Humana Press
Semester II Lab I: Immunology 4 Credits 1. Selection of animals, preparation of antigens, immunization and methods of
bleeding, serum separation, storage.
2. Antibody titre by ELISA.
3. Double diffusion, immuno-electrophoresis and radial Immuno diffusion.
4. Complement fixation test.
5. Isolation and purification of IgG from serum or IgY from chicken egg.
6. SDS-PAGE, Immunoblotting, Dot blot assays
7. Blood smear identification of leucocytes by Giemsa stain
8. Separation of leucocytes by Dextran density gradient method
9. Separation of mononuclear cells by Ficoll-Hypaque .
Semester II Lab II: Microbiology and Industrial Applications 4 Credits 1. Sterilization, disinfection and safety in microbiological laboratory.
2. Preparation of media for growth of various microorganisms.
3. Identification and culturing of various microorganisms.
4. Staining and enumeration of microorganisms.
5. Growth curve, measure of bacterial population by turbidometry and studying the effects of temperature, pH, carbon and nitrogen.
6. Plasmid Isolation.
7. Assay of antibiotics production and demonstration of antibiotic resistance.
8. Isolation and screening of industrially important microorganisms.
9. Determination of thermal death point and thermal death time of microorganisms.
Seminar/Journal Club 4 Credits (Presentation of Seminar Topics by the students assigned to them before the evaluation committee)
SEMESTER - III Genomics & Proteomics 2 Credits Unit I Introduction Structural organization of genome in Prokaryotes and Eukaryotes; Organelle DNA-mitochondrial; chloroplast; DNA sequencing-principles and translation to large scale projects; Recognition of coding and non-coding sequences and gene annotation; Tools for genome analysis-RFLP; DNA fingerprinting; RAPD; PCR; Linkage and Pedigree analysis-physical and genetic mapping. Unit II Genome sequencing projects Microbes; plants and animals; Accessing and retrieving genome project information from web; Comparative genomics; Identification and classification using molecular markers-16S rRNA typing/sequencing; EST’s and SNP’s. Unit III Proteomics Protein analysis (includes measurement of concentration; amino-acid composition; N-terminal sequencing); 2-D electrophoresis of proteins; Microscale solution isoelectricfocusing; Peptide fingerprinting; LC/MS-MS for identification of proteins and modified proteins; MALDI-TOF; SAGE and Differential display proteomics; Protein-protein interactions; Yeast two hybrid system. Unit IV Pharmacogenetics High throughput screening in genome for drug discovery- identification of gene targets; Pharmacogenetics and drug development Unit V Functional genomics and proteomics Analysis of microarray data; Protein and peptide microarray-based technology; PCR-directed protein in situ arrays; Structural proteomics Texts/References: 1. Voet D; Voet JG & Pratt CW; Fundamentals of Biochemistry; 2nd Edition. Wiley 2006 2. Brown TA; Genomes; 3rd Edition. Garland Science 2006 3. Campbell AM & Heyer LJ; Discovering Genomics; Proteomics and Bioinformatics; 2nd
Edition. Benjamin Cummings 2007 4. Primrose S & Twyman R; Principles of Gene Manipulation and Genomics; 7th Edition;
Immunotechnology & Molecular Virology 4 Credits Unit I Introduction to Immunotechnology Kinetics of immune response: memory; Principles of Immunization; Techniques for analysis of Immune response ; Antibody Related Techniques Immuno-chemistry of Antigens - immunogenecity: Antigenecity: haptens: Toxins-Toxoids: Hapten-carrier system; Genetic basis of immune response; Role and properties of adjuvants: Immune modulators; B cell epitopes; Hybridoma Rabbit: human; Antigen – Antibody interaction: affinity: cross reactivity: specificity: epitope mapping; Immuno assays: RIA: ELISA: Western blotting: ELISPOT assay: immunofluorescence: Surface plasma resonance: Biosensor assays for assessing ligand –receptor interaction New Generation Antibodies Multigene organization of immunoglobulin genes: Ab diversity; Antibody engineering; Phage display libraries; Antibodies as in vitro and in vivo probes Unit II CMI and Imaging techniques CD nomenclature: Identification of immune Cells; Principle of Immunofluorescence Microscopy: Flurochromes; Staining techniques for live cell imaging and fixed cells; Flow cytometry: Instrumentation: Applications; Cell Functional Assays –lymphoproliferation: Cell Cytotoxicity: Mixed Lymphocyte Reaction: Apoptotosis: Cytokine expression; Cell cloning: Reporter Assays: In–situ gene expression techniques; Cell imaging Techniques- In vitro and In vivo; Immuno-electron microscopy; In vivo cell tracking techniques; Microarrays; Transgenic mice: gene knock outs Unit III Classification of animal and plant viruses; Satellite viruses; Viroids; Virusoids etc.; Diseases causes by animal viruses and plant viruses; Economic loss due to important viruses : Genome organization of animal viruses; Replication of RNA viruses; Replication of DNA viruses ; Structure of animal viruses and plant viruses; Genome organization of DNA and RNA plant viruses; Replication of DNA and RNA plant viruses Unit IV Methods to diagnose animal virus infections: Electron microscopy: Tissue culture growth of viruses : Virus quantitation assays: Viral serology: ELISA: neutralization assays; Molecular methods: hybridization: PCR: real time PCR: sequencing: microarray : gene silencing and antiviral assays Unit V Methods to study plant viruses; Infectivity assays – Sap transmission: insect vector transmission: agroinfection (using Agrobacterium); serological methods: immunelectrophoresis in gels: direct double-antibody sandwich method: Dot ELISA: Immunosorbent electron microscopy (ISEM): Decoration technique: Gene silencing: PTGS & TGS: viral suppressors of gene silencing. Texts/References:
1. Voet D; Voet JG & Pratt CW; Fundamentals of Biochemistry; 2nd Edition. Wiley 2006 2. Brown TA; Genomes; 3rd Edition. Garland Science 2006 3. Campbell AM & Heyer LJ; Discovering Genomics; Proteomics and Bioinformatics; 2nd
Edition. Benjamin Cummings 2007 4. Primrose S & Twyman R; Principles of Gene Manipulation and Genomics; 7th Edition;
Blackwell; 2006. 5. Glick BR & Pasternak JJ; Molecular Biotechnology; 3rd Edition; ASM Press; 1998. Plant Biotechnology 4 Credits Unit I Conventional plant breeding. Introduction to cell and tissue culture; tissue culture as a technique to produce novel plant and hybrids. Tissue culture media (composition and preparation). Initiation and maintenance of callus and suspension culture; single cell clones. Organogenesis; somatic embryogenesis; transfer and establishment of whole plants in soil. Unit II Shoot-tip culture: Rapid clonal propagation. Embryo culture and embryo rescue. Protoplast isolation; culture and fusion; selection of hybrids cells and regeneration of hybrid plants; symmetric and asymmetric hybrids; hybrid biotransformation. Anther; pollen; and ovary culture for production of haploid plants and homozygous lines. Cryopreservation; slow growth and DNA banking for germ plasm conservation. Unit III Transgenic Plants: Basis Introduction; T1 and R1 plasmids; molecular basis of Agrobacterium infection; Mechanisms of DNA transfer; Organization of T-DNA; organization of vir region and its role; transfer of T-DNA; integration of T-DNA into plant genome; Disarming; co-integrate vector; binary vector; plant virus vector; use of 35S and other promoters; genetic markers. Viral vectors and their applications. Vector Transformation techniques; co-culture with tissue explants, in planta transformation, agroinfection. Vector less or direct DNA transfer; chemical methods; particle bombardment, electroporation; microinjection transformation of monocots; lipofection; fiber mediated DNA delivery; laser induced DNA delivery; pollen transformation. Insect resistance; Bt. Genes; non-Bt like protease inhibitors; alpha amylase inhibitor. Herbicide resistance; phosphoinothricin; glyphosate; sulfonyl urea; atrazine. Virus resistance; coat protein mediated resistance ; nucleocaspid gene; cDNA of satellite RNA; defective Viral approach; antisense RNA approach; Ribozyme mediated protection. Disease resistance; chitinase; 1 – 3 beta glucanase; RIP antifungal proteins; thionines; PR proteins; long shelf life of fruits and flowers; use of ACC synthase; poly- galactrunase; ACC oxidase; male sterile lines; bar and barnase systems. Biochemical production; Hirudin; phytase; polyhydroxybutyrate. Terminator gene technology. Unit IV
An introduction to plant conservation biotechnology, Molecular approaches to assessing plant diversity; molecular marker system; molecular markers in germ plasm characterization; population genetics; biodiversity characterization, plant germplasm acquisition; plant genetic resource conservation; acquisition procedures; planning methods involved, Phytosanitary aspects of plant germplasm conservation; safe movement of germplasm; quarantine; virus detection; production of pathogen free plants, Cryopreservation; principle; preparation and pretreatment, cryoprotection procedure, Stability assessment; natural variation; techniques; morphological variation; cytological, biochemical and molecular analysis, biotechnological advances in conservation of root and tuber crops; economical important plants; endangered plants; rain forest conservation. Unit V Metabolic engineering and industrial products: Plant secondary metabolites; control mechanisms and manipulation of phenylpropanoid pathway; alkaloids; industrial enzymes; biodegradable plastics; therapeutic proteins; lysosomal enzymes; antibodies; edible vaccines; purification strategies; oleosin partitioning technology. Molecular marker-aided breeding: RFLP maps; linkage analysis; RAPD markers; STS; microsatellites; SCAR (sequence characterized amplified regions); SSCP (single strand conformational polymorphism); AFLP; QTL; map-based cloning. Molecular marker-assisted selection. Arid and semi-arid plant biotechnology; Green house and Green-home technology. References:
1) Plant cell & tissue culture Ed: Pollard JW & Walker JM. (1990) Humana Press 2) Principles of Plant Biotechnology Ed: Mantell, Mckee RA, Matthews JA. (1987)
Kluwer Academic/Plenum 4) Plant Conservation Biotechnology by Benson EE (1999) CRC 5) Fundamentals of Plant Biotechnology by Amla Batra. (2006) Capital Publishing
House
Open Elective Course - Vaccines / Nanobiotechnology Vaccines 4 Credits Unit I Innate Immunity; Activation of the Innate Immunity through TLR mediated signaling; Adaptive Immunity; T and B cells in adaptive immunity; Immune response in infection; Protective immune response in bacterial; Viral and parasitic infections; Correlates of protection 43 List of Electives. Unit II
Vaccination and immune response; Appropriate and inappropriate immune response during infection: CD4+ and CD8+ memory T cells; Memory B cells; Generation and Maintenance of memory T and B cells; Dendritic cells in immune response Unit III Adjuvants in Vaccination; Induction of Th1 and Th2 responses by using appropriate adjuvants; Microbial, Liposomal and Microparticles as adjuvant; Chemokines and cytokines; Role of soluble mediators in vaccination; Oral immunization and mucosal Immunity Unit IV Conventional vaccines; Bacterial vaccines; Live attenuated and inactivated vaccine; Subunit Vaccines and Toxoids; Peptide Vaccine Unit V New Vaccine Technologies; Rationally designed Vaccines; DNA Vaccination; Mucosal vaccination; New approaches for vaccine delivery; Engineering virus vectors for vaccination; Vaccines for specific targets; Tuberculosis Vaccine; Malaria Vaccine; HIV vaccine Texts/References 1. Edited by Stefan H.E. Kaufmann, Novel Vaccination Strategies, Wiley-VCH Verlag
GmbH & Co. KgaA, 2004 or later edition. 2. Topley & Wilson’s, Microbiology and Microbial Infections Immunology Edited by
Stefan H.E. Kaufmann and Michael W Steward Holder Arnold, ASM Press, 2005 or later edition.
3. Edition Charles A Janeway. Jr, Paul Travers, Mark Walport and Mark J Shlomchik, Immuno Biology, The Immune system in health and Disease, 6th Edition, Garland Science, New York, 2005 or later edition.
4. Annual Review of Immunology : Relevant issues 5. Annual Review of Microbiology : Relevant issues OR Nanobiotechnology 4 Credits Unit I Introduction to Nano-Biotechnology; Nanotechnology definition and concepts; Cellular Nanostructures; Nanopores; Biomolecular motors; Criteria for suitability of nanostructures for biological applications Unit II Basic characterization techniques; Electron microscopy; Atomic force microscopy; Photon correlation spectroscopy 33 List of Electives Unit III Thin films; Colloidal nanostructures; Nanovesicles; Nanospheres; Nanocapsules Unit IV Nanostructures for drug delivery, concepts, targeting, routes of delivery and advantages Unit V Nanostructures for diagnostics and biosensors; Nanoparticles for diagnostics and imaging; Nanodevices for sensor development
Texts/References 1. Multilayer Thin Films, Editor(s): Gero Decher, Joseph B. Schlenoff Publisher:
Wiley-VCH Verlag GmbH & Co. KGaA ISBN: 3527304401 2. Bionanotechnology: Lessons from Nature Author: David S. Goodsell Publisher:
ISBN: 0-8247-2579-4 IPR & Biosafety : Non-Credit Course Unit I Introduction to Intellectual Property Types of IP: Patents; Trademarks; Copyright & Related Rights; Industrial Design; Traditional Knowledge; Geographical Indications; Protection of GMOs IP as a factor in R&D; IPs of relevance to Biotechnology and few Case Studies Unit II Agreements and Treaties History of GATT & TRIPS Agreement; Madrid Agreement; Hague Agreement; WIPO Treaties; Budapest Treaty; PCT; Indian Patent Act 1970 & recent amendments Unit III Basics of Patents and Concept of Prior Art Introduction to Patents; Types of patent applications: Ordinary; PCT; Conventional; Divisional and Patent of Addition; Specifications: Provisional and complete; Forms and fees Invention in context of “prior art”; Patent databases; Searching International Databases; Country-wise patent searches (USPTO; esp@cenet(EPO); PATENTScope(WIPO); IPO; etc.) Unit IV Patent filing procedures National & PCT filing procedure; Time frame and cost; Status of the patent applications filed; Precautions while patenting – disclosure/non-disclosure; Financial assistance for patenting introduction to existing schemes Patent licensing and agreement Patent infringement- meaning; scope; litigation; case studies Unit V Biosafety Introduction; Historical Backround; Introduction to Biological Safety Cabinets; Primary Containment for Biohazards; Biosafety Levels; Biosafety Levels of Specific Microorganisms; Recommended Biosafety Levels for Infectious Agents and Infected Animals; Biosafety guidelines - Government of India; Definition of GMOs & LMOs; Roles of Institutional Biosafety Committee; RCGM; GEAC etc. for GMO applications in food and agriculture; Environmental release of GMOs; Risk Analysis; Risk Assessment; Risk management and communication; Overview of National Regulations and relevant International Agreements including Cartegana Protocol. Texts/References: 1. BAREACT; Indian Patent Act 1970 Acts & Rules; Universal Law Publishing Co. Pvt. Ltd.;
2007 2. Kankanala C.; Genetic Patent Law & Strategy; 1st Edition; Manupatra Information
PRACTICALS Semester III Lab I: Genetic Engineering and Immunology 4 Credits 1. Isolation of genomic DNA from E. coli genome. 2. PCR amplification of available gene and its analysis by agarose gel
electrophoresis 3. Preparation of plasmid, from E.coli DH5α and gel analysis. 4. Restriction digestion of vector (gel analysis) and insert using restriction enzymes
(a) Vector and Insert ligation (b) Transformation in E.coli DH5a.
5. Plasmid isolation and confirmation of recombinants by PCR and RE digestion. 6. Transformation of recombinant plasmid . 7. Induction of protein with IPTG and analysis on SDS-PAGE 8. Purification of protein on Ni-NTA column and analysis of purification by SDS-
PAGE 9. Antibody titre against model antigen by Sandwich Elisa method 10. Antibody isotype determination 11. SDS-PAGE profile of IgG, IgM and IgA class of antibodies 12. Western blotting using anti-sera from Candida albicans infected animals. Semester III Lab II: Bioprocess Engineering and Technology 4 Credits 1. Production of microbial products at flask level 2. Study of the kinetics of enzymatic reaction by microorganisms. 3. Production and purification of various enzymes from microbes. 4. Comparative studies of ethanol production using different substrates. 5. Microbial production and downstream processing of an enzyme. 6. Various immobilization techniques of cells/enzymes, use of alginate for cell
immobilization. Seminar/Journal Club 4 Credits (Presentation of Seminar Topics by the students assigned to them before the evaluation committee) Project Proposal 2 Credits (Proposal of the Project Work to be streamline consulting the concerned Supervisor and to make a presentation of the same)
SEMESTER - IV Bioprocess Engineering & Technology 4 Credits Unit I Basic principle of Biochemical engineering Isolation; screening and maintenance of industrially important microbes; Microbial growth and death kinetics (an example from each group; particularly with reference to industrially useful microorganisms); Strain improvement for increased yield and other desirable characteristics. Unit II Concepts of basic mode of fermentation processes Bioreactor designs; Types of fermentation and fermenters; Concepts of basic modes of fermentation - Batch; fed batch and continuous; Conventional fermentation v/s biotransformation; Solid substrate; surface and submerged fermentation; Fermentation economics; Fermentation media; Fermenter design-mechanically agitated; Pneumatic and hydrodynamic fermenters; Large scale animal and plant cell cultivation and air sterilization; Upstream processing: Media formulation; Sterilization; Aeration and agitation in bioprocess; Measurement and control of bioprocess parameters; Scale up and scale down process. Unit III Downstream processing Bioseparation -filtration; centrifugation; sedimentation; flocculation; Cell disruption; Liquid-liquid extraction; Purification by chromatographic techniques; Reverse osmosis and ultra filtration; Drying; Crystallization; Storage and packaging; Treatment of effluent and its disposal. Unit IV Applications of enzymes in food processing Mechanism of enzyme function and reactions in process techniques; Enzymic bioconversions e.g. starch and sugar conversion processes; High-Fructose Corn Syrup; Interesterified fat; Hydrolyzed protein etc. and their downstream processing; baking by amylases; deoxygenation and desugaring by glucoses oxidase; beer mashing and chill proofing; cheese making by proteases and various other enzyme catalytic actions in food processing. Applications of Microbes in food process operations and production Fermented foods and beverages; Food ingredients and additives prepared by fermentation and their purification; fermentation as a method of preparing and preserving foods; Microbes and their use in pickling; producing colours and flavours; alcoholic beverages and other products; Process wastes-whey; molasses; starch substrates and other food wastes for bioconversion to useful products; Bacteriocins from lactic acid bacteria – Production and applications in food preservation. Unit V Enzyme kinetics; Two-substrate kinetics and pre-steady state kinetics; Allosteric enzymes; Enzyme mechanism; Enzyme inhibitors and active site determination Production; recovery and scaling up of enzymes and their role in food and other industries; Immobilization of enzymes and their industrial applications.
Texts/ References: 1. Jackson AT.; Bioprocess Engineering in Biotechnology; Prentice Hall; Engelwood Cliffs;
1991. 2. Shuler ML and Kargi F.; Bioprocess Engineering: Basic concepts; 2nd Edition; Prentice
Hall; Engelwood Cliffs; 2002. 3. Stanbury RF and Whitaker A.; Principles of Fermentation Technology; Pergamon press;
Oxford; 1997. 4. Baily JE and Ollis DF.; Biochemical Engineering fundamentals; 2nd Edition; McGraw-Hill
Book Co.; New York; 1986. 5. Aiba S; Humphrey AE and Millis NF; Biochemical Engineering; 2nd Edition; University of
Tokyo press; Tokyo; 1973. 6. Comprehensive Biotechnology: The Principles; Applications and Regulations of
Biotechnology in Industry; Agriculture and Medicine; Vol 1; 2; 3 and 4. Young M.M.; Reed Elsevier India Private Ltd; India; 2004.
7. Mansi EMTEL; Bryle CFA. Fermentation Microbiology and Biotechnology; 2nd Edition; Taylor & Francis Ltd; UK; 2007.
Bio-entrepreneurship 2 Credits Unit I: Accounting and Finance Forms of Business Organizations; Statutory and legal requirements for starting specific Organisation; Special provisions for Venture Capital Financing; Basics of accounting conventions; Difference between receipts and income; payment and expenses; Concept Profit and Loss Account; Understanding Balance Sheet related concepts; Preparation of Project for Bank Finance Unit II: Marketing Assessment of market demand for potential product(s) of interest; Identifying needs of customers including gaps in the market; Market Segments; Prediction of market changes; packaging the product; Market linkages; branding issues; Developing distribution channels; Pricing / Policies / Competition; Promotion / Advertising; Services Marketing Unit III: Negotiations Strategies With financiers, bankers, government, law enforcement authorities and companies & Institutions; Technology transfer and dispute resolution skills; Changes in External environment; Crisis Management; Use IT for business administration and financial management; E-business setup and management Unit IV: Human Resource Development (HRD): Different types of Organizational structures; Leadership and Managerial skills;Team building, teamwork, performance appraisal, rewards system; Fundamentals of Entrepreneurship: Support mechanism for entrepreneurship in India
Unit V: Role of knowledge centre and R&D: Knowledge centers like universities and research institutions; Role of technology and upgradation; Assessment of scale of development of Technology; Managing Technology Transfer; Regulations for transfer of foreign technologies; Technology transfer agencies. Case Study: 1. Candidates should be made to start a ‘mock paper company’; systematically
following all the procedures. - The market analysis developed by them will be used to choose the
product or services. - A product or service is created in paper and positioned in the market. As
a product or services available only in paper to be sold in the market through the existing links. At this juncture; the pricing of the product or the service needs to be finalized; linking the distribution system until the product or services reaches the end consumer.
- Candidates who have developed such product or service could present the same as a project work to the Panel of Experts; including representatives from industry sector. If the presented product or service is found to have real potential; the candidates would be exposed to the next level of actual implementation of the project.
2. Go to any venture capital website (like sequoiacap.com) and prepare a proposal for funding from venture capital.
Note: Names of specific cases to be discussed in the class shall be specified from time
to time Project Work 14 Credits
(Laboratory work to be completed on the assigned Project Topic under the supervision of the concerned teacher and the same will be evaluated by the External Examiner as well as Internal team)
Seminar/Journal Club 4 Credits (Presentation of Research Paper / Research Topics by the students assigned to them before the evaluation committee)
