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M. Tech. Genetic Engineering (Full Time) Curriculum & Syllabus (2009-2010) Faculty of Engineering & Technology SRM University, Kattankulathur, Chennai Tamil Nadu, India 603 203

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Page 1: M. Tech. Genetic Engineering (Full Time) Curriculum & … · M. Tech. Genetic Engineering (Full Time) Curriculum & Syllabus (2009-2010) Faculty of Engineering & Technology SRM University,

M. Tech. Genetic Engineering (Full Time) Curriculum & Syllabus (2009-2010)

Faculty of Engineering & Technology SRM University, Kattankulathur, Chennai

Tamil Nadu, India 603 203

Page 2: M. Tech. Genetic Engineering (Full Time) Curriculum & … · M. Tech. Genetic Engineering (Full Time) Curriculum & Syllabus (2009-2010) Faculty of Engineering & Technology SRM University,

SRM UNIVERSITY M.Tech. GENETIC ENGINEERING (FULL TIME)

CURRICULUM & SYLLABUS (2009-2010) SEMESTER- I Code Category Course L T P C GN0501 C Molecular Genetics 3 0 3 4 GN0503 C Biological Chemistry 3 0 3 4 GN0505 C Immunobiology 3 0 3 4 GN0507 S Statistical Genetics 3 0 0 3 E-1 E Elective 1 3 0 0 3

Total 15 0 9 18 SEMESTER-II Code Category Course L T P C GN0502 C Recombinant DNA Technology 3 0 3 4 GN0504 C Genomics and Proteomics 3 0 3 4 GN0506 C Regulation of Gene Expression 3 0 3 4 GN0508 S Sequence Analysis & Structure Prediction 2 0 3 3 E-2 E Elective 2 3 0 0 3

Total 14 0 12 18 SEMESTER- III Code Category Course L T P C E-3 E Elective-3 3 0 0 3 E-4 E Elective-4 3 0 0 3 E-5 E Elective-5 3/2 0 0/3 3 GN0621 C Seminar 1 0 0 1 GN0623 C Project-Phase 1 0 0 12 6

Total 10/9 0 12/15 16 SEMESTER-IV Code Category Course L T P C GN0602 C Project-Phase 2 0 0 36 18

Total 0 0 36 18 TOTAL CREDITS TO BE EARNED FOR THE AWARD OF THE DEGREE

70

LIST OF CORE ELECTIVES *

CODE CATEGORY TITLE L T P C MODULE 1: HUMAN GENETICS

GN0601 E Human Physiology 3 0 0 3 GN0603 E Human Genetics 3 0 0 3 GN0605 E Pharmacogenomics 3 0 0 3 MODULE 2: PLANT GENETICS

GN0607 E Plant Physiology and Development 3 0 0 3 GN0609 E Classical and Molecular Plant Breeding 3 0 0 3 GN0611 E Genetic Engineering of Plants 2 0 3 3 MODULE 3: MEDICAL GENETICS

BT0613 E Stem Cell Technology 3 0 0 3 BT0615 E Cancer Biology 3 0 0 3 BT0617 E Molecular Mechanisms of Infectious Disease 3 0 0 3 *Students must choose any one module only

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CREDIT HOUR SUMMARY TABLE SEMESTER I II III IV TOTAL %

C 12 12 7 18 49 70 S 3 3 0 0 6 9 E 3 3 9 0 15 21

TOTAL 18 18 16 18 70 100 CONTACT HOURS SUMMARY TABLE CATEGORY CONTACT HOURS PERCENTAGE THEORY 38 35 % PRACTICAL 72 65 % TOTAL 110 100 %

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SEMESTER I

CODE TITLE L T P C GN0501 MOLECULAR GENETICS 3 0 3 4 Purpose: To learn the fundamentals molecular genetics and its application in biology. Instructional Objectives:

• Understand the relationship between classic • al genetics and its genotype. • Understand the central dogma of life. • Understand the molecular genetics of model organisms and its application.

THEORY

FUNDAMENTALS OF GENENTICS Mendelian inheritance: Mendel’s laws - Gene interactions: intra and inter allelic, pleiotropy, multiple alleles and multiple genes - Chromosomes and heredity: linkage and linkage groups - Gene: gene concept, unit of function, replication, recombination and mutation – Fine structure of gene: bar locus, complex loci, rII locus and complementation analysis - Gene function: inborn errors of metabolism, one gene/one enzyme hypothesis, pathways of gene action. GENOME ORGANIZATION Genome organisation in prokaryotes and eukaryotes - DNA content and C-value paradox - methods to measure DNA content variation - Various types of DNA sequences – simple sequences, repetitive sequences, nonsense sequences, tandem gene clusters, satellites Variety of DNA structures: double helix, Z-DNA, B-DNA, Mechanism of DNA replication: prokaryotes and eukaryotes. MECHANISM OF TRANSCRIPTION Mechanism of transcription: prokaryotes and eukaryotes - Operon and operon concept - Eukaryotic gene structure and expression - Mechanism of translation: prokaryotes and eukaryotes, Control of gene expression - RNA processing and editing, transcriptional, post transcriptional, translational and post transnational controls, Gene mutation: point mutation and transposable elements - DNA repair and recombination. MOLECULAR GENETICS OF PHAGE AND YEAST Phage molecular genetics: genetic organisation - lytic and lysogenic cycle, regulation of genes - foundations of phage genetics – T-odd coliphages – ss DNA phages – RNA phage. Yeast molecular genetics: genome - mutants and genetic screens – genetic redundancy – cell type determination – cell cycle regulation of mitotic events – genetic interaction: two hybrid systems – gal pathway, gene regulation. MOLECULAR GENETICS OF DROSOPHILA Drosophila molecular genetics: genome - development genetics – mutants and genetic screens – P element biology – directed expression in drosophila – construction and use of genetic mosaics. Mouse molecular genetics: genome - directed gene expression – X inactivation and imprinting – gene dosage compensation – gene replacement and knockout.

LABORATORY EXPERIMENTS 1. Analysis of genetic markers in bacteria 2. Measurement of growth rate; One step growth curve using a even phage 3. Induced mutagenesis and isolation of antibiotic resistant and auxotrophic mutants 4. Enrichment for antibiotic resistant and auxotrophic mutants 5. Genetic mapping by P1 transduction 6. Genetic mapping by conjugation 7. Isolation of specialized transducing phage 8. Transposon mutagenesis

TEXT BOOKS:

1. Molecular Genetics of Bacteria, Third Edition (2007) L. Snyder, Blackwell Publishing Company,

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CODE TITLE L T P C GN0503 BIOLOGICAL CHEMISTRY 3 0 3 4 Purpose: To learn the chemical basis of biological system. Instructional Objectives:

• To teach chemistry of biomolecules • To teach the structure and metabolism of biomolecules • To teach principles of biological techniques used for analysis of biomolecules

THEORY

CHEMISTRY OF BIOMOLECULES Weak interaction in aqueous system, Ionization of water, weak acids, and weak bases. Buffering against pH changes in Biological system. Henderson-Hasselbalch equation. First and second law of thermodynamics, Free energy change, enthalpy, entropy. CARBOHYDRATES AND LIPIDS Introduction to carbohydrates and glycoconjugates–proteoglycans, glycoproteins, and glycolipids. Metabolism of carbohydrates – glycolysis, TCA cycle, gluconeogenesis, glycogen metabolism. Classification of lipids, storage lipids, structural lipids in membranes, lipids as signals, cofactors, and pigments. Metabolism of lipids. Oxidative phosphorylation -Electron transport chain, oxidative phosphyrylation. PROTEINS AND ENZYMES Amino acids and peptide bond. Structure of protein. Biosynthesis and degradation of aminoacids. Enzyme activity, specificity, Mechanism of enzyme activity – lock and key model, induced fit theory, Factors affecting enzymes activity, Enzyme kinetics. NUCLEIC ACIDS Structure of DNA. Forms of DNA- A, B, Z Structure and classification of RNA’s. Biosynthesis and catabolism of purines and pyrimidines. Dissociation and reassociation kinetics.

ANALYTICAL TECHNIQUES UV, Visible, IR and Mass Spectroscopy, NMR, X-Ray crystallography, ion exchange chromatography, affinity chromatography, gel filtration techniques, HPLC,GC, GC-MS, MS-MS, MALDI-ToF.

LABORATORY EXPERIMENTS

1. Determination of pKa of amino acid 2. Isoelectric focusing of proteins 3. Analysis of monomeric and multimeric forms of proteins

Oxford, UK. 2. Molecular Genetics of Yeast - A Practical Approach, First Edition (1994) J.R. Johnston, Oxford

University Press, UK. 3. Principles of Genome Analysis and Genomics, Third Edition (2003) S.B. Primrose and R.M. Twyman,

Blackwell Publishing Company, Oxford, UK. 4. Mouse genetics: Concepts and Applications, First Edition (1995) L M. Silver, Oxford University Press.

REFERENCES: 1. Molecular Cell Biology, Third edition (1995) W.H.H. Lodish, A.Berk, and C.A. Kaiser, Freeman & Co

Ltd. 2. Molecular Biology of the Gene, Fifth Edition (2004) J.D. Watson, T.A. Baker, S. P. Bell, A. Gann, M.

Levine, R. Losick, Pearson Education Inc. MANUALS:

1. Molecular Cloning. A Laboratory Manual. Volume 1-3. Third Edition (2001) A. Sambrook, and D.W. Russel, Cold Spring Harbor Laboratory Press, New York, USA.

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4. Enzyme kinetics 5. Enzyme inhibition kinetics 6. Protein purification using FPLC 7. HPLC 8. GC 9. TLC 10. Paper chromatography

TEXT BOOKS:

1. Principles of Biochemistry, Fifth Edition (2008) A.L. Lehninger, D.L. Nelson, and M.M. Cox, W. H. Freeman Publications

REFERENCES:

1. Fundamentals of Biochemistry. Second Edition (2005) D. Voet and J.G. Voet, Wiley Publishers MANUALS: Laboratory Manual

CODE TITLE L T P C GN0505 IMMUNOBIOLOGY 3 0 3 4 Purpose: To introduce the science of immunology and detailed study of various types of immune systems and methods used in immunology. Instructional Objectives:

• To understand the basic concepts of immunology • To know about transplantation immunology and auto immunity. • To learn the methods used in immunology (immunotechniques)

THEORY

CONCEPTS OF IMMUNOLOGY General principles of immune system, molecules, cells and tissues of immune system, primary and secondary lymphoid organs (thymus, bursa of fabricius, lymph nodes, spleen), B and T lymphocyte and their functions, lymphocyte cell mediated cytotoxicity. ANTIGENS AND ANTIBODIES Concepts of antigen, antigenic determinant, antigenicity, immunogen and immunogenicity, factors affecting antigenicity, hapten, carrier effect, cross reactivity, adjuvtants, Freund’s adjuvants and its significance, immunoglobulin, structure of immunoglobulin, types and properties of immunoglobulin, theories of antibody formation, clonal selection, Ig genes, immunoglobulin synthesis and metabolism, and antibody diversity. HUMORAL AND CELL MEDIATED IMMUNITY

MHC, MHC antigen- Class I, Class II, Class III, antigen presentation, MHC restriction, immune response gene, immune response, humoral and cell mediated immune response, BCR, TCR & generation of biodiversity, lymphocytes, T cells regulation, graft rejection. ANTIGEN- ANTIBODY REACTION

Physico-chemical basis of Ag-Ab interaction, avidity, strength of binding between Ag and Ab and its measurement, detection of Ag-Ab interaction, precipitation, agglutination and complement fixation, complement system, and cytokines.

IMMUNOTECHNIQUES One and two dimensional, single radial immuno diffusion, Ouchterlony immno diffusion, rocket immunoelectrophoresis, CIE, Graber and William technique, direct and indirect agglutination, ELISA, Direct, indirect and Sandwich immunofluorescence, hybridoma technology and monoclonal antibodies, Abezyme technique, Antiserum production, immuno histocompatibility, location of cells in tissues, immunoblotting, flow cytometry.

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LABORATORY EXPERIMENTS

1. Antibody production 2. ELISA 3. Western blotting 4. Flowcytometry. 5. Single Radial Immuno Diffusion 6. Double diffusion. 7. Rocket Immunoelectrophoresis. 8. Counter- Current Immunoelectrophoresis. 9. Characterization of Immunoglobulins by SDS-PAGE

TEXT BOOKS: 1. Essential Immunology, Eleventh Edition (2006) P. Delves, S. Martin, D. Burton and I. Roitt,

Wiley-Blackwell Publishers, UK. 2. Immunology, Third Edition (1997) J. Kuby, W H Freeman & Co Publishers. 3. Practical immunology, Fourth Edition (2002) F.C. Hay and O.M.R. Westwood, Wiley-

Blackwell Publishers. REFERENCES:

1. Immunology - A Short Course, Third Edition (1996) E. Benjamin, G. Sunshine, and S. Leskowitz, Wiley-Liss Publishers, New York.

2. Basic and Clinical Immunology, Fourth Edition (1982) D.P. Stites, J.D. Stobo and J.V. Wells, Appleton & Lange Publishers.

MANUALS: 1. Laboratory Manual

CODE TITLE L T P C GN0507 STATISTICAL GENETICS 3 0 0 3 Purpose: To learn physiology and microanatomy of human body Instructional Objectives:

• To learn basic genetics in crosses • To learn statistical techniques for genetic testing of simple crosses • To learn statistical techniques for genetic testing of populations

THEORY

PATTERN OF INHERITANCE Meaning of phenotype, genotype (homozygous, pure line, heterozygous, hybrid), dominant and recessive alleles. Mendel’s law of inheritance (Law of segregation and law of independent assortment) ALLELIC RELATIONSHIPS Single gene crosses (monohybrid cross, test cross, back cross), multi-gene crosses involving two or more genes, variations in allelic relationships, condiment alleles in complete dominance, lethal alleles. STATISTICAL GENETICS OF SIMPLE CROSSES

Probability concepts, statistical distributions, normal distribution, binomial distribution, multinomial distribution, testing genetic ratios, chi-square test. QUANTITATIVE GENETICS Qualitative versus quantitative traits, normal distribution, average measurements of variability, standard deviation, coefficient of variation, variance, variance method of estimations the number of genes, types of

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gene action STATISTICAL GENETICS OF POPULATIONS

Heritability, meaning of variance components, genetic similarity of relatives (depression analysis, correlation analysis), mendelian population, Hardy-Weinberg equilibrium, calculating gene frequencies: Autosomal loci with two alleles, autosomal loci with multiple alleles, testing a locus for equilibrium.

TEXT BOOKS:

1. Genetics, Fourth Edition (2009) L.E. Susan, W.D. Stansfield and G. Bhowmik, Tata McGraw Hill Publishing Company Limited, New Delhi.

REFERENCES:

1. An Introduction to Genetic Statistics, Revised Edition (1969) O. Kempthorne, Jhon Wiley & Sons, New York.

2. Introduction to Quantitative Genetics, Fourth Edition (1996) D.S. Falconer and T.F.C. Mackay, Benjamin Cummings Publishers.

SEMESTER II CODE TITLE L T P C

GN0502 RECOMBINANT DNA TECHNOLOGY 3 0 3 4 Purpose: To learn the molecular techniques that is required to be a successful genetic engineer of plants, animals and microorganisms. Instructional Objectives:

• To learn the gene cloning methods in theory and practice • To learn genetic engineering of living organism for human benefit

THEORY

GENETIC ENGINEERING TOOLS History of genetic engineering, restriction, modifying and polymerase enzymes used in genetic engineering, vectors used in genetic engineering of microbes, plants and animals. Bacterial and yeast hosts used in cloning and expression. PCR, optimization of PCR, gene specific and degenerate primer design, automated DNA sequencing, pyrosequencing, high throughput sequencing. CONSTRUCTION OF GENE LIBRARIES

Construction of cDNA library, PCR based cDNA library, subtractive cDNA library, normalized cDNA library, genomic DNA library, BAC library and YAC library. GENE & PROMOTER ISOLATION Screening the library by using probes, cloning of genes by PCR (gene specific and degenerate primers), nested PCR, 5’ and 3’ RACE-PCR, inverse PCR, hybrid PCR, TAIL PCR, differential display, positional cloning, promoter identification, promoter isolation by screening, promoter isolation by PCR, promoter deletion studies. GENE CLONING AND MODIFICATION

Cloning methods using restriction and modifying enzymes, cloning in expression vector, cloning of PCR products, site directed mutagenesis. GENETIC ENGINEERING OF LIVING ORGANISMS Expression and purification of recombinant proteins in E.coli, yeast, insect cells, animal

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cell lines, transgenic plants and transgenic animals.

LABORATORY EXPERIMENTS

1. Cloning using restriction enzymes

2. Cloning of PCR products

3. Cloning in expression vector

4. Induction of expression of recombinant protein

5. Purification of recombinant proteins using His Tag

6. Automated DNA sequencing

TEXT BOOKS: 1. Principles of Gene Manipulation and Genomics, Third Edition (2006) S.B. Primrose, S.B. and

R.M. Twyman, Blackwell Publishing Company, Oxford, UK. 2. Gene Cloning and DNA Analysis: An Introduction. Fifth Edition (2006) T.A. Brown, Wiley-

Blackwell, UK.

REFERENCES: 1. PCR Protocols: A Guide to Methods and Applications, First Edition (1990) M. Innis, T. White

and J.J. Sninsky, Academic Press. 2. Generation of cDNA Libraries: Methods and Protocols, First Edition (2003) S. Ying, Humana

Press

MANUALS: 1. Molecular Cloning. A Laboratory Manual. Volume 1-3. Third Edition (2001) A. Sambrook and

D.W. Russell, Cold Spring Harbor Laboratory Press, New York, USA. 2. Current Protocols in Molecular Biology, First Edition (1987) F.M. Ausubel, R. Brent, R.E.

Kingston and D.D. Moore, John Wiley & Sons, Inc., Brooklyn, New York. CODE TITLE L T P C

GN0504 GENOMICS AND PROTEOMICS 3 0 3 4 Purpose: To learn the structure and functions of the genomes together with the approaches to analyze the genomes and proteome. Instructional Objectives:

• To know the computational approaches to analyze the genomes and proteome • To understand genome maps and types • To learn the basics of protein-protein interactions

THEORY

ORGANIZATION OF THE PROKARYOTIC AND EUKARYOTIC GENOMES Genome maps and types; current sequencing technologies; partial sequencing; gene identification; gene prediction rules and software’s; Genome databases; Annotation of genome. Genome diversity: taxonomy and significance of genomes – bacteria, yeast, Caenorhabditis, Homo sapiens, Arabidopsis, etc. MICROARRAY

Gene Expression, methods for gene expression analysis; DNA array for global expression profile; Types of DNA array, Array databases; Applications of DNA microarray – analysis of gene expression, differential gene expression under different conditions and during development of organisms. HUMAN GENOME Mapping of Human Genome; Construction of physical maps; Basics of radiation hybrid maps; Sequencing

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of the entire human genome, annotation and analysis of genome sequences: sequence repeats, transposable elements, gene structure, pseudogenes; Gene analysis; gene order; chromosome rearrangement; compositional analysis; clustering of genes; composite genes. Implications of the Human Genome Project; Basics of Single Nucleotide Polymorphisms, detection and its implications. THE PROTEOME AND PROTEOME TECHNOLOGY

Introduction, Expression proteomics (express profile); Cell map proteomics; Protein separation technology - 2D-Gel Electrophoresis, liquid chromotagraphy, affinity chromatography (for cell map proteomics); mass spectroscopy and its uses in protein identification; Forward and Reverse Proteomics PROTEIN-PROTEIN INTERACTIONS

Yeast two hybrid, Co-Precipitation, Phage Display, Phylogenetic Profile, Domain fusion, Gene Neighborhood, Gene Cluster, Mirror Tree, Analysis of genome wide Protein-Protein Interactions in yeast, Genome wide yeast two hybrid analysis of other organisms, Protein fragment complementation assays.

LABORATORY EXPERIMENTS

1. 2D-Gel Electrophoresis of protein 2. Liquid chromatographic separation of protein 3. Affinity chromatography method 4. Detection of SNPs 5. DNA sequencing 6. Purification of protein using FPLC 7. Physical mapping of the genome 8. Gene structure and function prediction (Using Genscan,GenMark) 9. 3D and 2D database searching

TEXT BOOKS:

1. Principles of Genome Analysis and Genomics, Third Edition (2003) S.B. Primrose and R.M. Twyman, Blackwell Publishing Company, Oxford, UK.

2. Introduction to proteomics – Tools For The New Biology, First Edition (2002) D.C. Liebler, Humana Press Inc, New Jersey, USA.

3. Bioinformatics: Sequence and Genome Analysis, Second Edition (2004) D. Mount, Cold Spring Harbor Laboratory Press, New York.

REFERENCES:

1. Bioinformatics – A Practical Guide to the Analysis of Genes and Proteins, First Edition (1998) A.D. Baxevanis and B.F. Francis Ouellellette, John Wiley & Sons, UK.

MANUALS:

1. Laboratory Manual CODE TITLE L T P C GN0506 REGULATION OF GENE EXPRESSION 3 0 3 4 Purpose: To understand the mechanisms of control of gene expression. Instructional Objectives:

• To learn basics of gene expression • To learn transcriptional, translational, post-transcriptional and post-translational regulation of gene

expression

THEORY INTRODUCTION TO GENE EXPRESSION

Fine structure of gene, transcription and translation in prokaryotes and eukaryotes. Epigenetic regulation- histone modifications – histones and 5srRNA gene – histones and class II genes – nucleosome positioning -

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chromatin folding – remodeling – DNA methylation and imprinting. TRANSCRIPTIONAL CONTROL OF GENE EXPRESSION

DNA sequence elements: Short sequence elements – enhancers – locus control regions, DNA protein interactions: zinc fingers – leucine zipper – basic helix loop helix – helix turn helix – homeodomain, transcriptional factor: categories of activators and activation mechanism – repressors and repression mechanism – DNA binding motifs of activators – interaction among activators – non coding RNA - nuclear receptors TRANSLATIONAL CONTROL OF GENE EXPRESSION

mRNA cap and poly(A) tail interaction – upstream ORF control – regulation of ribosomal recruitment in eukaryotes – regulation of initiator met – tRNA –frame shifting, hoping and readthrough – control of elongation phase– internal ribosome entry site elements - context sequence of translation initiation codon in plants – translational control during heat shock – ferritin synthesis – translation and cancer POST-TRANSCRIPTIONAL CONTROL OF GENE EXPRESSION

mRNA stability - RNA editing - RNA export - mRNA decay in plants – Antisense – cosupression – RNAi - micro RNA – virus induced gene silencing.

POST TRANSLATIONAL GENE REGULATION

Modification of amino acid side chains – phosphorylation – GTPase switch proteins – ligand or co-factor binding – interaction with other proteins – protein targeting : nuclear localization and nuclear export signal – protein stability and degradation

LABORATORY EXPERIMENTS

1. Assay for gene induction 2. Assay for gene repression 3. RNA isolation 4. Northern analysis 5. RT PCR 6. Real time PCR 7. S1 nuclease mapping 8. Restriction mapping 9. Primer extension assay 10. C. elegans model for RNAi

TEXT BOOKS: 1. Transcriptional Regulation in Eukaryotes: Concepts, Strategies and Techniques, Second

Edition (2001) M. Carey and S.T. Smale, Cold Spring Harbor Laboratory Press. 2. Chromatin and Gene Regulation: Molecular Mechanisms in Epigenetics, First Edition (2002)

B. M. Turner, Wiley-Blackwell Publications. 3. Gene Regulation: A Eukaryotic Perspective, Second Edition (2008) D. S. Latchman, Springer

Publication. 4. Gene Expression and Regulation, First Edition (2006) J.Ma, Springer Publication.

REFERENCES:

1. Molecular Cell Biology, Third edition (1995) W.H.H. Lodish, A.Berk, and C.A. Kaiser, Freeman & Co Ltd.

2. Molecular Biology of the Gene, Fifth Edition (2004) J.D. Watson, T.A. Baker, S. P. Bell, A. Gann, M. Levine, R. Losick, Pearson Education Inc.

MANUALS:

1. Molecular Cloning. A Laboratory Manual. Volume 1-3. Third Edition (2001) A. Sambrook, and D.W. Russel, Cold Spring Harbor Laboratory Press, New York, USA.

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CODE TITLE L T P C

GN0508 SEQUENCE ANALYSIS AND STRUCTURE PREDICTION 2 0 3 3 Purpose: Aims at providing an knowledge of various bioinformatics methods involved in sequence analysis and structure prediction Instructional Objectives:

• To learn methods of sequence alignment • Tolearn the methods of protein structure prediction and interaction analysis

THEORY SEQUENCE ANALYSIS

Methods of sequence alignment: graphic similarity comparison; Dot plots; Hash tables; Scoring matrices – identify matrix, genetic code matrices (GCM); Substitution matrices, Mutation Data Matrices (MDM), Percentage accepted Mutation (PAM). Block Substitution Matrices (BLOSUM), mutation probability matrices; Sequence similarity searches and alignment tools – dynamic programming algorithms; Needlman-Wunch and Smith Waterman, Optimal global alignment and optimal local alignment; SEQUENCE ALIGNMENT Concept ; Programmes (Dot matrix, Dot plot, Dynamic programming) ; Similarity Searches ; Sequence repeats and inversion; Database searching(BLAST and FASTA.Multiple Sequence alignment (MSA) – significance; softwares (PIMA, Clustal, Pileup, ClustalW, Meme, MACAW) PHYLOGENETIC ANALYSIS Phylogenetics, cladistics and ontology; Phylogenetic representations – graphs, trees and cladograms; Steps in phylogenetic analysis; Methods of phylogenetic analysis – similarity and distance tables, distance matrix method; Method of calculation of distance matrix (UPGMA, WPGMA); The Neighbour Joining Method; The Fitch/Margoliash method; Character-based Methods – maximum parsimony, maximum likelihood; Phylogenetic softwares – PAUP, PHYLIP, MacClade. PROTEIN STRUCTURE PREDICTION

Prediction of protein secondary structure from the amino acid sequence –Chou-Fasman methods,Neural network models ,Mearest neighbor methods ,Hidden markov model. PROTEIN-PROTEIN INTERACTIONS

Prediction of three dimensional protein structure-comparative modeling, threading and ab initio method, Homology modelling

LABORATORY EXPERIMENTS

1. Sequence Analysis Packages – EMBOSS, NCBI ToolKit 2. Dynamic programming. 3. Analysis of Biological Sequences: Basic Blast and Specialized Blast 4. FASTA 5. Multiple sequence alignment 6. MEME/MAST, eMotif, InterproScan, ProSite, ProDom, Pfam 7. Phylogenetic analysis – PAUP, PHYLIP, MacClade 8. Advanced Visualization Software and 3D representations. 9. Coordinate generations and inter-conversions. 10. Secondary Structure Prediction: Fold Recognition, ab initio (Rosetta Server), Homology based

comparative protein modeling, Energy minimizations, Validation of models (WHATIF, PROSA, PROCHECK, VERIFY 3D), Protein Structure Alignment.

TEXT BOOKS:

1. Bioinformatics: Sequence and Genome Analysis, Second Edition (2004) D. Mount, Cold Spring Harbor Laboratory Press, New York.

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REFERENCES:

1. Bioinformatics – A Practical Guide to the Analysis of Genes and Proteins, Second Edition (1998) A.D. Baxevanis and B.F. Francis Ouellellette, John Wiley & Sons, UK.

MANUALS:

1. Laboratory Manual

SEMESTER III ELECTIVES- MODULE 1: HUMAN GENETICS

CODE TITLE L T P C GN0601 HUMAN PHYSIOLOGY 3 0 0 3 Purpose: To learn physiology and microanatomy of human body Instructional Objectives:

• An appreciation of normal functioning and the structure of tissues and organs • To learn the major elements and concepts that constitutes human physiology. • To learn to correlate cell and organ system physiology with ultra structure

THEORY

INTRODUCTION AND PHYSIOLOGY OF CELLS Foundations of Physiology – Functional Organization of the cell – Physiology of Membranes – Signal Transduction – Regulation of Gene Expression – Electrophysiology of the Cell Membrane – Electrical Excitability and Action Potentials – Synaptic Transmission and the Neuromuscular Junction – Cellular Physiology of Skeletal, Cardiac and Smooth Muscle. NERVOUS SYSTEM Organization – Physiology – Synaptic junction – sensory transduction – Circuits of Central Nervous System – Autonomic Nervous System – Microenvironment CARDIOVASCULAR AND RESPIRATORY SYSTEMS Organization of Respiratory system – Arteries Veins and Microcirculation – Heart pump – regulation of arterial pressure and cardiac output - Organization of Respiratory system – Transport of Oxygen and Carbon dioxide in the Blood – Gas Exchange in the Lungs – Ventilation and Perfusion of the lungs URINARY AND GASTROINTESTINAL SYSTEMS Organization of Urinary System – Glomerular filtration and Renal Blood flow – Transport of salts, organic solutes and acids and bases – Urine Concentration and Dilution – Organisation of Gastrointestinal system – Gastric function – Pacreatic and salivary glands – Nutrient digestion and Absorption. ENDOCRINE AND REPRODUCTIVE SYSTEMS Organization of Endocrine control – Endocrine regulation and growth – Thyroid, Adrenal, Pancreas and Parathyroid glands – Sexual differentiation – Male and Female Reproductive systems – Fertilization – Pregnancy and Lactation TEXT BOOKS:

1. Medical Physiology, Updated Edition (2005), W.F. Boron and E.L. Boulpaep, Saunders Publications.

REFERENCES:

1. Medical Physiology, Eleventh Edition (2005), A.C. Guyton and J.E. Hall, Saunders Publications.

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CODE TITLE L T P C GN0603 HUMAN GENETICS 3 0 0 3 Purpose: To learn about our system, what we inherit and how our system responds to disease and disorders. Instructional Objectives:

• To learn the inheritance pattern in human • To lean about the genome and its instability • To learn the strategies of genome mapping • To have an understanding of human pathology

THEORY

PEDIGREES AND ORGANIZATION OF THE HUMAN GENOME Mendelian pedigree patterns - Complications to the basic pedigree patterns - Factors affecting gene frequencies - Nonmendelian characters - General organization of the human genome - Organization and distribution of human genes - Human multigene families and repetitive coding DNA - Extragenic repeated DNA sequences and transposable elements. GENE EXPRESSION IN HUMANS

An overview of gene expression in human cells - Control of gene expression by binding of trans-acting protein factors to cis-acting regulatory sequences in DNA and RNA - Alternative transcription and processing of individual genes - differential gene expression and DNA methylation - Long-range control of gene expression and imprinting - unique organization and expression of Ig and TCR genes

MUTATION AND DNA REPAIR

An overview of mutation, polymorphism, and DNA repair - Simple mutations - Genetic mechanisms which result in sequence exchanges between repeats- Pathogenic mutations - The pathogenic potential of repeated sequences - DNA repair. GENOME MAPPING Physical and transcript mapping - Genetic mapping of mendelian characters - Genetic mapping of complex characters – Human Genome projects - Identifying human disease genes MOLECULAR PATHOLOGY Mutations - Molecular pathology: from gene to disease - Molecular pathology: from disease to gene - Molecular pathology of chromosomal disorders - Gene tracking - Population screening - Cancer genetics - Complex diseases: theory and results. TEXT BOOKS:

1.1. Human Molecular Genetics, Third Edition (2003) T. Strachan and A.P. Read, Garland Science Publication. www.ncbi.nlm.nih.gov/books

REFERENCES:

1. Molecular Cell Biology, Sixth Edition (2007) H. Lodish, A. Berk, and C.A. Kaiser, W. H. Freeman & Co Ltd.

2. Molecular Biology of the Gene, Sixth Edition (2007) J.D. Watson, T.A. Baker, S.P. Bell, A. Gann, M. Levine, R. Losick, Benjamin Cummings Publication.

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CODE TITLE L T P C GN0605 PHARMACOGENOMICS 3 0 0 3 Purpose: To learn about pharmacogenomics principles, methods and applications Instructional Objectives:

• To study about impact of polymorphism in human genome and applications. • To know about functional analysis of gene variation and genotyping techniques • To study about the pharmacogenomics application in diseases • To learn how to manage the pharmacogenomic information

THEORY INTRODUCTION TO PHARMACOGENOMICS Pharmacogenomics: Historical perspectives and current status, Human Genome and Genomic Applications, Genetic Polymorphism of Metabolic Reactions, SNPs, Association Studies in Pharmacogenomics, Study on industries developing pharmacogenomic research. FUNCTIONAL ANALYSIS OF GENE VARIATION Transfection Assays With Allele-Specific Constructs: Functional Analysis of UDP-Glucuronosyltransferase Variants, CYP 2D6, CYP2C19 in drug metabolism, Snapshot of the Allele-Specific Variation in Human Gene Expression, Genome-Wide Analysis of Allele-Specific Gene Expression Using Oligo Microarrays, Roche Ampli Chip, HaploChIP: An In Vivo Assay. GENOTYPING TECHNIQUES Aspects Influencing Genotyping Method Selection, Denaturing HPLC for Mutation Detection and Genotyping, Pyrosequencing of Clinically Relevant Polymorphisms, Kinetic Fluorescence-Quenching Detection Assay for Allele Frequency Estimation, MALDI–TOF Mass Spectrometry, Fluorescence-Based Fragment Size Analysis, SNP Genotyping in DNA Pools, Genotyping of InDel Polymorphisms PHARMACOGENOMICS IN PERSONALIZED MEDICINE Pharmacogenomics of Cardiovascular Diseases, Pharmacogenomics of Cancer treatment, Pharmacogenomics of Neurodegenerative Diseases, Pharmacogenomics in Depression, Pharmacogenomics and Respiratory diseases, Pharmacogenoomics in AIDS, Pharmacogenomics in Antibiotics. MANAGEMENT OF PHARMACOGENOMIC INFORMATION The Pharmacogenetics and Pharmacogenomics knowledge Base, Systems for the Management of Pharmacogenomic Information TEXT BOOKS:

1. Pharmacogenomics: Methods and Protocols (Methods in Molecular Biology) First Edition (2005) Federico Innocenti, Humana Press Inc, New Jersey, USA.

2. Pharmacogenomics and Personalized Medicine (Methods in Pharmacology and Toxicology) First Edition (2005) Nadine Cohen, Humana Press Inc, New Jersey, USA

REFERENCES:

1. An A-Z Guide to Pharmacogenomics, First Edition (2006) M.C. Catania, Published by American Association for Clinical Chemistry

2. Pharmacogenomics: Social, Ethical, and Clinical Dimensions, First Edition (2003) Mark A. Rothstein, Wiley-Liss Publications

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ELECTIVES- MODULE 2: PLANT GENETICS CODE TITLE L T P C GN0607 PLANT PHYSIOLOGY AND DEVELOPMENT 3 0 0 3 Purpose: The goal of this course is to know and understand what it is to be a plant. Instructional Objectives:

• Study anatomy and embryology of plants • Study photosyntheisis and respiration • Study growth and development of plants • Study the hormonal regulation of plant growth

THEORY

PLANT ANATOMY Meristems and meristematic growth – anatomy of root, stem, leaf, flower, fruit and seed PLANT EMBRYOLOGY

Stamen and Androecium - Pollen Development - Carpel and Gynoecium - Ovule and Embryo Sac - Pollination and Pollen-Stigma Interaction – Pollen tube germination, growth and Fertilization - Endosperm - Embryo. PLANTS, WATER, AND MINERALS

Whole Plant Water Relations - Plants and Inorganic Nutrients - Roots, Soils, and Nutrient Uptake - Transporter Systems - Translocation in the Phloem PHOTOSYNTHESIS AND RESPIRATION The Light Reactions - Mode of Action of Some Herbicides - Dark Reactions - Oxidative Photosynthetic Carbon Cycle – C2, C3, C4, and CAM cycle – Respiration -Utilization of Oil Reserves in Cotyledons. LIGHT AND HORMONAL CONTROL OF PLANT GROWTH

Photoperiodism - Phytochrome Regulation of Gene Expression - Blue-Light Responses - Guard Cell Osmoregulation – Auxin - Growth Hormone – Gibberellins - Regulators of Plant Height – Cytokinins - Regulators of Cell Division – Ethylene - Gaseous Hormone - Abscisic Acid - A Seed Maturation and Antistress Signal - Circadian Rhythms. REFERENCES:

1. Plant Physiology, Fourth Edition (1991) F. Salisbury and C. Ross, Brooks Cole Publisher. 2. Plant Physiology, Fourth Edition (2006) L. Taiz and E. Zeiger, Sinauer Associates Inc.

CODE TITLE L T P C GN0609 CLASSICAL AND MOLECULAR PLANT BREEDING 3 0 0 3 Purpose: To learn the principles and methods of conventional breeding and molecular breeding for crop improvement. Instructional Objectives:

• To learn genes and genotypes as individual and n populations • To learn the principles and methods of conventional plant breeding methods • To learn about molecular markers and their use in molecular breeding

THEORY INTRODUCTION History of domestication and plant breeding. Current status of crop production and scope of crop

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improvement by plant breeding. Structure of reproductive organs, reproduction by self pollination, cross pollination, apomixis and vegetative propagation. Phenotype, genotype, micro and macro environment, genotype environment interaction. Qualitative and quantitative traits. POPULATION GENETICS Genetic constitution of a population: Hardy-Weinberg equilibrium, factors affecting change in gene and genotypic frequency; Effects of mating systems, mutation, migration and selection. Continuous variation: Components of means: Additive and dominance components, non-allelic interactions, genotype x environmental interactions; Components of variance: Genetic and environmental components of variance. PLANT BREEDING METHODS Breeding methods in self-pollinated crops. Breeding methods in cross-pollinated crops. Heterosis breeding- production of hybrids using male sterile systems. Mutation Breeding. MOLECULAR MARKERS AND MAPPING Plant Genome-nuclear, chloroplast and mitochondrial genomes. Phenotypic versus molecular markers, different kinds of DNA markers for genome analysis (RFLP, RAPD, STS, SSR, AFLP, SNPs). Development of mapping population – RILs, NILs and DH lines- choice of mapping population. Molecular mapping. MOLECULAR BREEDING Marker-Assisted-Selection (MAS). Marker-Assisted Backcrossing (MABC). Case studies of MAS and MABC in rice. TEXT BOOKS:

1. Fundamentals of Plant Breeding and Hybrid Seed Production, First Edition (1998) R.L. Agarwal, Oxford & IBH Book Publishing Co Pvt Ltd, New Delhi.

2. Principles of Plant Breeding, Second Edition (1999) A.W. Allard, Science Publishers, USA.

REFERENCES: 1. Guimaraes et al (2007) Marker-Assisted Selection: Current status and future perspectives in crops,

livestock, forestry and fish. FAO Publication. 2. Collard et al (2008) Rice Molecular Breeding Laboratories in the Genomics Era: Current Status

and Future Considerations. Int J Plant Genomics. 2008:524847 CODE TITLE L T P C GN0611 GENETIC ENGINEERING OF PLANTS 2 0 3 3 Purpose: To learn the principles and practices of in vitro plant tissue culture and transformation to produced genetically modified plants Instructional Objectives:

• To understand the biology of tissue culture, regeneration and transformation • To practice different in vitro culture techniques and plant transformation • To know the bisafety, ethics and regulatory systems related to transgenic plants

THEORY

BASICS OF TISSUE CULTURE History of plant tissue culture and transformation; plant tissue culture: general techniques –sterilization techniques-tissue culture media–plant hormones and their functions in tissue culture. CELL, TISSUE AND ORGAN CULTURE Cell, callus and organ cultures establishment. In vitro Morphogenesis– organogenesis and embryogenesis and factors affecting morphogenesis in vitro.

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IN VITRO CULTURE METHODS AND APPLICATIONS Meristem culture, anther and pollen culture, ovary and ovule culture, embryo and endosperm culture, protoplast isolation, culture and fusion PLANT TRANSFORMATION Vector, constitutive and tissue specific promoters, reporter genes, selections markers and terminators for plant transformation. Biology of Agrobacterium mediated gene transfer. Biolistic method of transformation. Alternative methods of plant transformation-in planta floral dip method, silicon carbide, pollen tube pathway etc. Concerns with genetically modified plants (antibiotic marker, frankenstein food, super weeds, etc) and probable solutions. Indian regulatory systems for laboratory testing, field trail and commercial release of transgenic plants. Bioconfinement strategies for cultivated crops. Biosafety and ethics in generating genetically modified plants. Potential benefits of genetically modified plants

LABORATORY EXPERIMENTS 1. Stock and media preparation and sterilization 2. Callus culture 3. Suspension cell culture 4. Somatic embryogenesis 5. Protoplast culture 6. Transformation of Agrobacterium 7. Agrobacterium-mediated transformation of tobacco 8. Agrobacterium-mediated transformation of Arabidopsis 9. Biolistic transformation (transient) 10. Molecular and histochemical analysis of transgenic events

TEXT BOOKS:

1. Plant Tissue Culture Concepts and Laboratory Exercises, Second Edition (1999) R.N. Trigiano and D.J. Gray, CRC Press.

REFERENCES:

1. Plant Culture Media, Volume 1& 2, First Edition (1987) Formulations and Uses E.F. George, D.J.M. Puttock and H.J. George, Exegetics Ltd, UK.

2. Gelvin, S.B. (2003) Agrobacterium-mediated plant transformation: the biology behind the "gene-jockeying" tool. Microbiol Mol Biol Rev 67(1) 16-37.

MANUALS:

1. Plant Cell and Tissue Culture: A Laboratory Manual, Second Edition (1982) J. Reinert and M.M. Yoeman, Springer-Verlag.

2. Laboratory Manual

ELECTIVES- MODULE 3: MEDICAL GENETICS

CODE TITLE L T P C BT0613 STEM CELL TECHNOLOGY 3 0 0 3 Stem Cells: Definition, classification and sources, Blastocyst culture, Xeno-free derivation and Cryopreservation, Properties and application of Embryonic stem cells. Characterization of Human Embryonic stem cells. Stem cells and their Developmental Potential, subcloning and controlled differentiation of human embryonic stem cells. in vitro and in vivo differentiation of human embryonic stem cells. Feeder free culture of human embryonic stem cells Therapeutic cloning: Derivation and propagation of human embryonic stem cells by somatic cell nuclear transfer, Hurdles to improving the efficiency of Therapeutic cloning, Stem cells and translational medicine ethics.

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Haematopoietic Stem Cells: Basic science to Clinical applications, Growth factors and the regulation of haematopoietic stem cells, Haematopoietic stem cells for gene therapy, Haematopoietic cells for leukaemia Skeletal muscle stem cells, Liver stem cells, Tumour stem cells, Stem cell therapies in animal models: Their outcome and possible benefits in humans TEXT BOOKS:

1. Stem Cells: From Bench to Bedside-Ariff Bongso, Eng Hin Lee 2. Stem Cells-C S Potten

REFERENCES:

1. Nagy A, Gertenstein M,Vintersten K,Behringer R(2003).Manipulating the Mouse Embryo ,New York:Cold Spring Harbor Press.

2. Gilbert SF.(2000) Developmental biology,6th edition Sunderland,MA:Sinauer Associates,Inc. CODE TITLE L T P C BT0615 CANCER BIOLOGY 3 0 0 3 PURPOSE To provide knowledge about biological aspects of cancer INSTRUCTIONAL OBJECTIVES To impart basic concepts of cancer biology, various stages in carcinogenesis, molecular cell biology of cancer, cancer metastasis, and cancer therapy. Regulation of Cell cycle, Mutations that cause changes in signal molecules, effects on receptor, signal switches, tumour suppressor genes, Modulation of cell cycle-in cancer, Different forms of cancers, Diet and cancer. Chemical Carcinogenesis, Metabolism of Carcinogenesis, Natural History of Carcinogenesis, Targets of Chemical Carcinogenesis, Principles of Physical Carcinogenesis, X-Ray radiation – Mechanism of radiation Carcinogenesis. Oncogenes, Identification of Oncogenes, Retroviruses and Oncogenes, detection of Oncogenes, Growth factor and Growth factor receptors that are Oncogenes. Oncogenes / Proto Oncogenes activity. Growth factors related to transformations. Clinical significances of invasion, heterogeneity of metastatic phenotype, Metastatic cascade, Basement membrane disruption, Three step theory of invasion, Proteinases and tumour cell invasion. Different forms of therapy, Chemotherapy, Radiation Therapy, Detection of Cancers, Prediction of aggressiveness of Cancer, Advances in Cancer detection. TEXT BOOKS :

1. King R.J.B., Cancer Biology, Addision Wesley Longmann Ltd, U.K., 1996. 2. Ruddon.R.W., Cancer Biology, Oxford University Press, Oxford, 1995.

REFERENCES :

1. Maly B.W.J., Virology a practical approach, IRL press, Oxford, 1987. 2. Dunmock.N.J and Primrose S.B., Introduction to modern Virology, Blackwell Scientific Publications, Oxford, 1988.

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CODE TITLE L T P C BT0617 MOLECULAR MECHANISM OF INFECTIOUS DISEASES 3 0 0 3

PURPOSE To develop the skills of the students in the area of Molecular Pathogenesis INSTRUCTIONAL OBJECTIVES: At the end of the course, the students would have learnt about Host Parasite interactions, Host defense mechanisms and molecular mechanisms involved in Pathogenesis of diseases caused by E.Coli and Vibrio Cholerae. Historical perspective - discovery of microscope, Louis Pasteur's contributions, Robert Koch's postulates, early discoveries of microbial toxins, toxic assays, vaccines, antibiotics and birth of molecular genetics and modern molecular pathogenesis studies, Various pathogen types and modes of entry. Attributes & components of microbial pathogenesis, Host defense: skin, mucosa, cilia, secretions, physical movements, limitation of free iron, antimicrobial compounds, mechanism of killing by humoral and cellular defense mechanisms, complements, inflammation process, general disease symptoms, Pathogenic adaptations to overcome the above defenses. Virulence, virulence factors, virulence-associated factors and virulence lifestyle factors. Molecular genetics and gene regulation in virulence of pathogens like Vibrio Cholerae, E.coli, Shigella, Plasmodium, Influenza virus. Virulence assays: adherence, invasion, cytopathic, cytotoxic effects. Criteria & tests in identifying virulence factors, attenuated mutants, molecular characterization of virulence factors, signal transduction & host responses Classical approaches based on serotyping. Modern diagnosis based on highly conserved virulence factors, immuno & DNA-based techniques. New therapeutic strategies based on recent findings on molecular pathogenesis of a variety of pathogens, Vaccines - DNA, subunit and cocktail vaccines. TEXT BOOKS

1. Iglewski B.H and Clark V.L "Molecular basis of Bacterial Pathogenesis", Academic Press, 1990. 2. Peter Williams, Julian Ketley & George Salmond, "Methods in Microbiology: Bacterial Pathogenesis,

Vol. 27", Academic Press, 1998. REFERENCES

1. Recent reviews in Infect. Immun., Mol. Microbiol, Biochem. J., EMBO etc. 2. Nester, Anderson, Roberts, Pearsall, Nester, "Microbiology: A Human Perspective", McGraw-Hill, 3rd

Edition, 2001. 3. Eduardo A. Groisman, Principles of Bacterial Pathogenesis, Academic Press, 2001