MSC Genetics Syllabus
MSC Genetics Syllabus
MSC Genetics Syllabus
M.Sc GENETICS
The program provides a strong theoretical and practical knowledge of key areas of Genetics and its applications. There is a
research module to help students to survey literature, analyze data and make critical assessments of scientific reports, papers
or research proposals, and to plan their own research program.
Theoretical Papers
18 Papers (Marks = 1800)
Total Credit = 54
3 credit (Theory) means 4 lecture hours per week or 42 lectures per semester per paper
2 credit (Lab.) means at least 40 hours of lab work per semester per paper
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FIRST SEMESTER
Paper (Theoretical) : 5 Papers = 500 Marks
SECOND SEMESTER
Paper (Theoretical) : 5 Papers = 500 Marks
THIRD SEMESTER
Paper (Theoretical) : 5 Papers = 500 Marks
FOURTH SEMESTER
FIRST SEMESTER
2. Cells & Chromosomes - Basic cell types – structure & evolutionary relationships, Overview of Prokaryotic &
Eukaryotic cells, Cellular environment, Chromosomes – where genes are located.
3. Basic principles of Heredity – Segregation of a single gene, the principle & verification of segregation,
segregation of two or more genes, test cross with unlinked genes.
4. Patterns of Inheritance – Autosomal inheritance, Sex chromosomes & Sex-linked inheritance, Cytoplasmic
inheritance.
5. Mendelian principles of Inheritance – The Big experiment of Mendel, principle of independent assortment.
6. Extensions & Modifications of Mendelian principles – Complete & Incomplete dominance, Epistasis.
7. Linkage, Recombination & Crossing Over – Recombination is the basis of Gene mapping, Linkage mapping,
Tetrad analysis, Gene mapping in absence of Meiosis, Genetic Fine structure mapping.
8. Genetic Variation – Genes & gene products, interaction between the alleles of one gene, interacting genes &
proteins, applications of chi-square test to gene interaction ratios.
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9. Alleles & Gene Interactions – Variations in Allele, Multiple alleles, Gene interactions, Alleles of different
genes, Modifier genes, Pleiotropic effects, Partial penetrance & variable expressivity, Lethal alleles, Phenotypes
produced by Conditional alleles.
10. Quantitative Traits & Polygenic Inheritance – Inheritance of Quantitative traits, Genetic analysis of
Quantitative traits using Statistics, Usefulness of Heritability in predicting the phenotypes of offsprings.
11. Extra-nuclear Inheritance – Chromosomes of some cytoplasmic organelles, Maternal inheritance, Paternal
inheritance, Effect of Maternal genes in the phenotype of offspring, Infectious inheritance.
12. Pedigree analysis & Applications – Study of Human Genetic Characteristics, Pedigree analysis, Molecular
markers in Human Pedigrees, Twin studies, Adoption studies, Genetic Counseling, Genetic Testing (Pre-natal &
Post-natal).
13. Testing of Genetic hypothesis – Probability in the prediction of progeny distributions using Binomial
distribution, Testing Goodness of Fit to a Genetic hypothesis, Chi-square method, Genetic analysis of quantitative
traits using Statistics (Mean, Variance, Standard deviation, Correlation, Regression, Distributions), Heritability is
useful in predicting the phenotypes of offspring.
References :
(1) Daniel L. Hartl & Elizabeth W. Jones : Genetics – analysis of Genes & Genomes
(2) Alan G. Atherly, Jack R. Girton & John F. McDonald : The Science of Genetics
(3) Benjamin A. Pierce : genetics – a conceptual approach
(4) D. Peter Snustad & Michael J. Simmons : Principles of Genetics
(5) Griffiths, Wessler, Lewontin, Gelbart, Suzuki & Miller : Introduction to Genetic analysis
2. Cell-Cell Interaction - Cell adhesion molecules; Cellular junctions;Extracellular matrix; Signal transduction:
Intracellular receptor and cell surface receptors; Signalling via G-protein linked receptors (PKA, PKC, CaM kinase);
Enzyme linked receptor signaling pathways; Network and cross-talk between different signal mechanisms;
Programmed cell death
Cyto-Genetics
1. Chromatin structure - Histones, DNA, Nucleosome and higher level organization; Chromosome organization:
Metaphase chromosome: centromere, kinetochore, telomere and its maintenance; Holocentric chromosomes and
supernumerary chromosomes; Chromosomal domains (matrix, loop domains) and their functional significance;
Heterochromatin and euchromatin; Position effect; Variegation; Boundary elements; Chromosome bandings;
Functional states of chromatin and alterations in chromatin organization; Structural and functional organization of
interphase nucleus.
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2. Giant chromosomes - Polytene chromosomes, Lampbrush chromosomes; Mitosis: Mitotic spindle and
arrangement of chromosomes on equator; Regulation of exit from metaphase; Chromosome movement at
anaphase; Meiosis: Overview of the process; Meiosis specific cellular changes; Genetic control of meiosis (example:
yeast).
Texts/References:
1. Alberts et al, Molecular Biology of The Cell, 2nd. Edition, Garland, 2007.
2. Cooper, The Cell: A Molecular Approach, 4th Edition, Washington, D.C: ASM Press, 2007.
3. Gilbert, Developmental Biology, Eighth Edition, Sinauer, 2006
4. Hennig, Structure & Function of Eukaryotic Chromosomes, 1st Edition, Springer, 1987.
5. Jeremy et al, Biochemistry, 6th edition, Freeman, 2002.
6. Karp, Cell and Molecular Biology, 4th edition, John Wiley, 2005.
7. Lewin, Genes IX. Pearson, Higher Education, 2007
8. Lodish H., Berk A., Zipursky S. L., Matsudaira P., Baltimore D. and James Darnell J., Molecular Cell Biology , Freeman,
5th Edition, 2003
9. G. Obe; A. T. Natarajan, Chromosome aberrations - Basic and Applied Aspects, Springer, 1990.
10. Pollard & Earnshaw, Cell Biology, Third Edition, Saunders, 2002.
2. DNA Structure; Replication; Repair & Recombination - Structure of DNA - A-,B-, Z- and triplex DNA;
Measurement of properties-Spectrophotometric, CD, AFM and Electron microscope analysis of DNA structure;
Replication initiation, elongation and termination in prokaryotes and eukaryotes; Enzymes and accessory proteins;
Fidelity; Replication of single stranded circular DNA; Gene stability and DNA repair- enzymes; Photo-reactivation;
Nucleotide excision repair; Mismatch correction; SOS repair; Recombination: Homologous and non-homologous;
Site specific recombination; Chi sequences in prokaryotes; Gene targeting; Gene disruption; FLP/FRT and Cre/Lox
recombination.
4. Post Transcriptional Modifications - Processing of hnRNA, tRNA, rRNA; 5'-Cap formation; 3'-end processing
and polyadenylation; Splicing; RNA editing; Nuclear export of mRNA; mRNA stability; Catalytic RNA.
5. Translation & Transport - Translation machinery; Ribosomes; Composition and assembly; Universal genetic
code; Degeneracy of codons; Termination codons; Isoaccepting tRNA; Wobble hypothesis; Mechanism of initiation,
elongation and termination; Co- and post-translational modifications; Genetic code in mitochondria; Transport of
proteins and molecular chaperones; Protein stability; Protein turnover and Degradation.
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6. Mutations; Oncogenes and Tumor suppressor genes - Nonsense, missense and point mutations; Intragenic
and Intergenic suppression; Frameshift mutations; Physical, chemical elements in prokaryotes and eukaryotes;
Mechanisms of transposition; Role of transposons in mutation; Viral and cellular oncogenes; Tumor suppressor
genes from humans; Structure, function and mechanism of action of pRB and p53 tumor suppressor proteins;
Activation of oncogenes and dominant negative effect; Suppression of tumor suppressor genes; Oncogenes as
transcriptional activators and biological mutagens; Transposition - Transposable genetic
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.
MSGEN-104 : Biophysics and Biochemistry
Topics : Biophysics
1. Molecular Modeling & Molecular Dynamics – Modeling of Macromolecules, different types of interaction
energy, molecular potential, bonding potential, non-bonding potential, potential due to angle, torsional strain,
electrostatic interaction, molecular structure of protein, lipid, nucleic acid, carbohydrate, energy minimization (SD,
ABNR), molecular dynamics simulation for simple molecules (GROMACS software)
2. Method of determination of size & shape of macromolecules – Molecular electron microscopy, measuring
electron diffraction of a solid with Electron Microscope, determination of molecular structure in Electron
Microscope, minimizing drying & shrinking artifacts, using symmetry to enhance the Electron Microscope image,
High Resolution Autoradiography, X-Ray diffraction
5. NMR Spectroscopy – Proton magnetic resonance spectra of proteins, 13C NMR spectra of proteins, 31P NMR
studies, NMR spectra of nucleic acids, Fourier transform of NMR spectroscopy, Relaxation (ID spectra)
Text/References :
Topics : Biochemistry
1. Biomolecules – structure, function & metabolism – Organization & Composition of Eukaryotic Cells;
Integration & Control of Cellular functions, Structural components of Nucleic acids, higher order DNA structure,
DNA sequence & function, functional roles of Proteins in Human, Amino acid composition of Proteins, higher levels
of Protein organization, dynamic aspects of Protein structure & Protein stability, Methods for characterization,
purification & study of Protein structure & organization, Bioenergetics & Oxidative metabolism.
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2. Mechanism of Enzyme action – Introduction to Enzymes, How Enzymes work, Enzymes are highly powerful
specific catalysts, Michaelis-Menten Model, Enzyme Kinetics as an approach to understanding mechanism,
Enzymatic reactions, Regulatory Enzymes
3. Metabolism, Pathways & Regulation – Carbohydrate metabolism – major metabolic pathways & their
control, special pathways & Glycoconjugates, Lipid metabolism – utilization & storage of energy in lipid form,
metabolic pathways of special lipids, Amino acid metabolism, Purine & Pyrimidine nucleotide metabolism,
metabolic interrelationships
4. Physiological Processes – Biochemistry of Polypeptide & Steroid Hormones, Hormones & their receptors,
Regulatory cascades, Insulin & related Growth-regulating hormones
5. Expression & Transmission of Genetic information – Genetic control of Enzyme synthesis, Control of Gene
expression, Gene expression in Prokaryotes & Eukaryotes, Response to environmental changes – Sensory systems
& Immune systems
6. Biochemical Genetics, In born Errors of Metabolism & Gene Therapy – Metabolic pathways, Overview of
the metabolic basis of inherited diseases
Text/References :
1. Jeremy M. Berg, John L. Tymoczko & Lubert Stryer : Biochemistry
2. Lehninger – David L. Nelson & Michael M. Cox : Principles of Biochemistry
3. David E Metzler : Biochemistry – The Chemical Reactions of Living Cells
4. Thomas M. Devlin : Biochemistry with Clinical Correlations
5. Charles Rascriver, Arthur L. Beaudet, William S. Sly & David Valle : The Metabolic basis of inherited diseases
3. Evolutionary Origin of Organelles – Origin & evolution of Mitochondria & Chloroplasts, Eukaryotic organelles
as Endosymbionts,
5. Patterns of Extranuclear inheritance – Uniparental inheritance, Maternal inheritance & Maternal effects,
Maternal effect in Snail Shell coiling, Heteroplasmy, Paternal inheritance.
6. Biology of Mitochondria & Chloroplasts – Biology of Mitochondria & Chloroplasts, Mitochondrial DNA,
Chloroplast DNA.
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7. Mitochondrial Genome – Origin of Mitochondrial Genome - Yeast & Human mtDNA, Mitochondrial genes;
Replication, Transcription & Translation of mtDNA, Unique Human Mitochondrial Genetic Code; Comparison of
Mitochondrial Genome with Nuclear Genome; Mitochondrial DNA phylogenies; Evolution of Mitochondrial genome.
8. Chloroplast Genome – Chloroplast biogenesis, Structure & Organization of Chloroplast cpDNA, Replication,
Transcription & Translation of cpDNA, Evolution of cpDNA, Genome comparisons.
10. Mitochondrial DNA & Aging in Human – Mechanism of age-related increase in mtDNA damage, Decline of
Oxydative phosphorylation capacity with age, Late onset degenerative diseases.
11. Tracing Human History through Mitochondrial DNA – To study Human evolution using mtDNA.
12. Human Mitochondrial Mapping – Human Mitochondrial genome, mtDNA & Human disease, non-universal
codons in mtDNA.
References :
1) Daniel L. Hartl & Elizabeth W. Jones : Genetics – analysis of Genes & Genomes
2) Benjamin A. Pierce : genetics – a conceptual approach
3) D. Peter Snustad & Michael J. Simmons : Principles of Genetics
4) Tom Strachan & Andrew P. Read : Human Molecular Genetics
PRACTICALS
MSGEN-106 : Lab on Microscopy & Instrumentation
1. Microscopy & Imaging
2. Principles & Operation of General Equipment usually used in Research laboratories
Text/References :
(1) Barch M J et al; The AGT Cytogenetics Laboratory Manual; 3 rd Ed, 1997; Lippincott- Raven; New York
(2) Celis Julio; Cell Biology – a laboratory manual; AP; 2nd Ed, 1998.
MSGEN-107 : Lab on Basic Cyto-Genetics & Cell Culture Techniques (Plant &
Animal) Techniques
Cyto-Genetics Techniques
(1) Basic principles of Cyto-Genetics procedures
(2) Setting up Laboratory
(3) Peripheral Blood Cyto-Genetics Methods
(4) Chromosome staining
(5) Microscopy & Imaging
(6) Chromosome analysis & Karyotype reporting
(7) Interpretation & Recommendations in Abnormal Chromosome study
(8) Chromosomal syndromes identification & Karyotyping
Text/References :
(1) Barch M J et al; The AGT Cytogenetics Laboratory Manual; 3 rd Ed,
1997; Lippincott-Raven; New York
(2) Purandare Hema & Chakravarty Amit : Human Cyto-Genetics Techniques & Clinical Applications; 2000; Bhalani
Publishing House; Mumbai
(3) Celis Julio; Cell Biology – a laboratory manual; AP; 2nd Ed, 1998.
(4) Culture of Animal Cells – a manual of basic techniques : R Ian Freshney (Wiley Publication)
Text/References :
Text/References :
a. Cantor & Schimmel : Biophysical Chemistry (Part I, II & III)
b. Jeremy M. Berg, John L. Tymoczko & Lubert Stryer : Biochemistry
c. David E Metzler : Biochemistry – The Chemical Reactions of Living Cells
The seminars represent only a small and somewhat arbitrary selection of topics. They are not
intended to cover an entire subject. Their aims are to:
(a) introduction about a special area
(b) tune the students to the area
(c) cover recent advances
(d) give students practice in the art of oral presentation
Journal Club
The journal clubs are on an article belonging to a topic scheduled for the semester. The article is presented by an
M.Sc./Ph.D. student or senior demonstrator, and moderated by a faculty member.
The aims of journal clubs are to:
(a) highlight recent advances
(b) discuss classical papers
(c) inculcate the faculty of critical appreciation of a research article
(d) give students and senior demonstrators practice in the art of oral presentation
(e) Faculty presentations are usually on:
Research methodology and an area of research in which the faculty member is involved
SECOND SEMESTER
MSGEN-201 : Genetics of Model Organisms
1. The content of our genome: Eukaryotic genomes contain both non repetitive and repetitive DNA sequences,
Human genome has fewer genes than expected Genomes can be mapped by linkage, restriction cleavage or DNA
sequence, RFLPs and SNPs for genetic mapping.
2. Genomes - types of genomes, genomes & genetic variation, comparison of different genomes, genome evolution.
3. Genomics – about the genomics, history, comparative genomics, comparative genomic hybridization, functional
genomics.
4. Human Genome Project (HGP) – an overview of the project, goals of the project, major scientific strategies &
approaches used in HGP, expected scientific & medical benefits of this project, about the organizations behind this
project, an overview of projects of other model organisms of Human Genome Project.
5. HGP & its impact – impact of Human Genome project in Plant, Animal & Human.
6. Biology & Life cycles – study of biology & life cycles of model organisms (E. coli, Yeast, Arabidopsis thaliana, C.
elegans, Drosophila melanogaster, laboratory mouse, Zebra fish & Human).
7. Genomics of selected Genomes – about genomics of model organisms (E. coli, Yeast, Arabidopsis thaliana, C.
elegans, Drosophila melanogaster, laboratory mouse, Zebra fish, Human).
8. How Human genome was mapped – physical mapping, genetic mapping, gene ontology, gene annotation.
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9. Technologies used in HGP – RFLP, microsatellite markers, STS, EST, DNA sequencing, DNA
microarray.
2. Hypothesis testing - Definition; Statistical & Scientific hypothesis; The null and alternative hypothesis;
Procedure (steps) for Hypothesis testing; Brief idea about various software used in biostatistics;
3. Population genetics and clinical data analysis - (SPSS, Analyse IT, POPGENE, Sigma Plot, Phylip, Popstar,
Arlequin, BLAST search & FASTA) ANOVA: General idea of one way & two way analysis; General idea of Correlation
Analysis; General idea of Regression Analysis; Test of significance: Student’s t-test, Chi-square tests, F-tests, Test of
proportion; Methods of statistical inference: Parametric and Non Parametric Methods; Methods of Sampling and
Cluster Analysis; Sample size calculation.
Population Genetics
1. Mendelian Genetics in Population-I - The Hardy- Weinberg Equilibrium for more than two alleles; A
simulation; A numerical calculation: Genotype and allele frequencies; Use of HW principle; Odds ratio and Relative
risk.
2. Mendelian Genetics in Population-II - Migration; Genetic Drift; Nonrandom Mating; General analysis of
inbreeding: coefficient of inbreeding; Inbreeding depression.
3. Mendelian Genetics in Population III - Factors affecting changes in allele and genotype frequencies; Selection;
Statistical analysis of allele and genotype frequencies using Chi-square test; Mutation, rate of mutation; Mutation
and Selection.
4. Multiple Loci - Linkage equilibrium and Linkage disequilibrium (LD); Sexual Reproduction, random mating and
LD; Quantitative Traits and QTLs; Identifying QTLs: Mapping; Heritability: Measurement, Narrow sense and Broad
Sense heritability; Monogenic traits: Bayesian calculations
5. Genetic variability in natura1 populations - Chromosomal and allozyme po1ymorphism; Adaptive genetic
polymorphism; DNA polymorphism; Genetic co-adaptation & Linkage disequilibrium Balanced genetic
polymorphism; Heterosis & heterozygous superiority
Texts/References:
1. Scott Freeman, John C. Hendon, Evolutionary Analysis, Fourth Edition, Pearson Education.
2. Hoelzel, Molecular Genetic Analysis of Populations, 2nd Edition, Oxford University, 1998.
3. Hartl and Jones, Genetics -Principles and Analysis, 5th edition Jones and Barlet.[2001]
4. SK Gupta, Statistical Methods, S Chand Company.
5. B. K. Mahajan, Methods in Biostatistics, 6th Edition Jaypee Publication.
6. P W Hedrick, Genetics of Populations, 22nd Edition, Jones & Bartlett 2000
7. Hartl & Clark, Principles of Population Genetics, Third Edition, Sinauer Associates, Inc. 1997
8. M Strickberger, Evolution, 3rd Edition, Jones & Bartlett, 2000
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3. Drosophila early development - Fertilization, cleavage and gastrulation; Pattern Formation; Primary axis
formation during oogenesis; Dorsal ventral patterning; Segmentation and anterior and posterior patterning;
Segmentation genes; Homeotic select orgenes; Homeobox and its evolutionary significance.
4. Central Nervous System in vertebrates - Neural tube formation; Tissue architecture of CNS.
5. Limb development in vertebrates - Formation of Limb Bud; Proximal Distal axis of the limb; Cell death and
formation of digits and joints.
6. Regeneration and Senescence - Epimorphic, morphallactic and compensatory regeneration; Ageing: causes
and regulation; Pleuropotency of Stem cells: Embryonic and adult stem cells, organization, characteristics and
therapeutic applications.
7. Understanding Human Birth defects through Model Organism - Developmental malformation; Teratogen
Induced Reproductive Problems; Gene-Teratogen Interaction; Environmental Factors and Genetic Susceptibility;
8. Genomic imprinting - Parent-of-origin effect; Gene silencing; Prader-Willi syndrome, Angelman syndromes and
Beckwith-Wiedemann Syndrome;
10. Molecular regulations of human development and defects I – Human Hox genes and genetic defects due to
mutation in Hox genes; Somite differentiation and homeobox genes (anterior-posterior patterning); Limb
development & limb defects.
11. Molecular regulations of human development and defect II - Eye development and eye defects;
Development of spinal cord and neural tube defects; Brain development and cranial defects.
12. Molecular regulations of human development and defect III – Cardiac development and heart defects;
Facial development and facial cleft defects; Muscle development; Kidney development and kidney.
13. Genetic defects due to abnormalities in human developmental processes : I - Abnormal gametes and
infertility; Abnormal implantation- contribution of maternal and paternal genes; Teratogenesis and tumors
associated with gastrulation; Birth defects - erythroblastosis fetalis, fetal hydrops and twin defects.
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14. Genetic defects due to abnormalities in human developmental processes : II - Craniofacial and skeletal
dysplasias; Defects in sex differentiation; Neural crest and craniofacial
defects; Vertebral defects: spina bifidia and scoliosis; Spontaneous abortions and stillbirth (etiology, pathogenesis,
genetic and other causes like immunological basis of pregnancy, clinical notes, diagnosis and management),
Reproductive failure: Infertility and Assisted reproduction (ART).
Texts/References:
1. SA Moody, Principles of Developmental Genetics, Academic Press. 2007.
2. S. P. Gilbert, Developmental Biology, 8th Edition, Sinauer Wolpert, Principles of Development, 2nd Edition, Oxford
University press, 2002.
3. T. W. Sadler, Langman’s Medical Embryology, 9th Edition, Lippincott Williams & Wilkins, 2004
4. K. L. Jones, Smith’s recognizable Patterns of Human Malformation, 6th edition, Elsevier Saunders, 2006
MSGEN-204 : Immuno-Genetics
1. Introduction to immune system - Innate and adaptive immunity; Cells and organs of the immune system;
Primary and secondary immune responses; Antigens; Antibodies and T cell receptors: Antigens, Structure and
function of immunoglobulins, Monoclonal antibodies, B and T cell receptors and coreceptors, Antigen-antibody
interactions
2. Immunoglobulin and T-cell receptor genes - Organization of Ig gene loci; Molecular mechanisms of
generation of antibody diversity; Expression of Ig genes; Regulation of Ig gene transcription; Antibody engineering;
Organization of TCR gene loci; Generation of TCR diversity
3. The HLA complex - Organization of HLA complex; Structure of class I and II HLA molecules; Expression of HLA
genes; HLA polymorphism
4. Generation and regulation of immune responses - Antigen processing and presentation; MHC-restriction;
Cytokines; T Cell Maturation, activation and differentiation; B Cell Generation, activation and differentiation; Clonal
selection and immunological memory; Complement system; Leukocyte activation and migration; Cell mediated
cytotoxic responses; Regulation of immune responses; Immunological tolerance
5. Disorders of Human Immune System - Primary and secondary immunodeficiencies; Autoimmune disorders;
Hypersensitive reactions; Cytokine-related diseases
6. Immune system in human health - Immune response to infectious diseases and malignancy; Concept of
immunotherapy; Vaccines; Transplantation immunology
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, 6 th Edition, 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.
6. Abbas et al., Cellular and Molecular Immunology., 5th Edition Saunders, 2007.
7. Benjamin et al., Immunology – A Short Course, 5th Edition, Wiley- Liss, 2003.
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2. Global patterns of Biodiversity – measuring biodiversity, Cataloging and Discovering Species, Geographical
Patterns of Species Richness, Biogeography, Importance of Distribution Patterns (Local Endemics, Sparsely
Distributed Species, Migratory Species), GAP Analysis.
3. Biodiversity & Conservation – Overexploitation threatening living species, International Trade, Animals
threatened by International trade, Problems in Controlling International Trade (Enforcement, Reservations, Illegal
Trade), Free Trade & the Environment, Free Trade & Conservation, Common patterns of Overexploitation.
4. Exotic Species – Plants, Invertebrates, Fishes, Amphibians, Reptiles, Birds, Mammals, Detrimental Effects of
Exotic Species.
5. Endangered Species Conservation – The US Endangered Species Act, State Endangered Species Acts
Successes and Failures of the Endangered Species Act Role of ESA in Habitat Protection, Critical Habitat, Problems
with the Endangered Species Act, Habitat Conservation Plans.
6. Ethics of Conservation – Values of Biodiversity, Biopiracy, Hybridized plants, GM crops (benefits & criticism),
Economic Value of Biodiversity & Legal, Ethical and Conservation issues related to uses of biodiversity, Global
Conservation Issues.
7. Human Population Growth – Carrying capacity of the Earth, Primary productivity of the Earth, Regional
Differences in Population Problems, Regional Differences in Population Density and Growth Rate, Age Structures
and the Demographic Transition, Effects of Uneven Income Distribution.
8. Basic concept of Taxonomy – Names and Naming: Essentials of Nomenclature, Classification, Construction of
Phylogenetic tree, Systematics, Cladistics, Cladograms, Phenetics.
9. Molecular phylogenies – Immunological techniques, Amino acid sequences, Quantitative DNA measurements,
Repetitive DNA sequences, Nucleic acid phylogenies based on: DNA-DNA hybridizations, Restriction Enzyme sites
& Nucleotide sequence comparisons and homologies, Combined Nucleic acid-Amino acid phylogenies, rates of
Molecular change: Evolutionary Clocks, Regulatory genes & some Evolutionary consequences.
10. Taxonomy in relation to Chromosomal morphology & Evolution – Chromosomal evolution, why location of
genes matter, evolutionary oddities about chromosomes, evolutionary effect of rearrangements of chromosomes,
karyotypic orthoselection, chromosomal evolution & speciation.
11. Molecular Taxonomy in relation to DNA characteristics & Protein sequences – modes of molecular
evolution, Neutral theory of Molecular evolution, genetic markers for taxonomic purposes, comparing total genome
by DNA-DNA hybridization, comparing DNA sequences, Cladistics, biological identification through DNA barcodes,
chromosome painting, establishing molecular homology using protein sequences.
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PRACTICALS
1. Introduction to Windows.
2. Microsoft Windows: Windows Fundamentals, File Managing Systems, Printing in Windows, Windows
Accessories.
3. Microsoft Word: MS Word Basics, Typing and Editing, Formatting Text, Page Design Layout, Mail- Marge,
Document Management.
4. Microsoft Excel: Introduction, Formatting Worksheet, Customize Workplace, Calculations, Charts, Database
Power of Excel.
5. Microsoft PowerPoint: Presentations, Graphics, Creating a Presentation, Customize a Slide Show, Editing and
Saving a presentation.
6. Image Editing Through Graphic Software and Transferring Into a Slide Presentation.
7. Microsoft Access: Concept of DBMS.
8. Application of Graphics Editing Software- Photoshop.
9. Introduction to Flash and HTML.
10. Programming : C
Data types, operators and expressions, Hierarchy of operators, control statements including decision (if, if-else),
loops (while, do-while, for), branching (switch, break, continue), functions, arrays (1D, 2D- all matrix operations
including inverse of a matrix), strings, file handling, data structures etc.
MSGEN-208 : Lab on Developmental Genetics & Genetic Toxicity Testing
Developmental Genetics
Models, specimens of early human development and slides of chick and pig embryos to correlate avian and
mammalian early development with human development. Specimens of congenital malformations.
3. in vitro / in vivo test with Cyto-genetic evaluation of chromosomal damage (Chromosomal Aberration Test)
using mammalian (Lab. Mouse) cells
4. Ames test
The seminars represent only a small and somewhat arbitrary selection of topics. They are not
intended to cover an entire subject. Their aims are to:
(a) introduction about a special area
(b) tune the students to the area
(c) cover recent advances
(d) give students practice in the art of oral presentation
Journal Club
The journal clubs are on an article belonging to a topic scheduled for the semester. The article is presented by an
M.Sc./Ph.D. student or senior demonstrator, and moderated by a faculty member.
The aims of journal clubs are to:
(a) highlight recent advances
(b) discuss classical papers
(c) inculcate the faculty of critical appreciation of a research article
(d) give students and senior demonstrators practice in the art of oral presentation
(e) Faculty presentations are usually on:
Research methodology and an area of research in which the faculty member is involved
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THIRD SEMESTER
MSGEN-301 : Microbial Genetics
1. Microbial Genomes - Physical organization of microbial genomes (Structure of the bacterial nucleoid,
Eukaryotic microbial genome and Genome of Archaea).
2. Plasmids – What is plasmid, Naming of plasmids, Functions encoded by plasmids, Structure of Plasmid ,
Plasmid replication, Origin of replication and replication proteins, Plasmid replication control mechanism,
Partitioning of plasmids at cell division, Mechanism to prevent curing of plasmid, Par system of plasmids,
Regulation of plasmid copy number and amplification, Incompatibility, Episomes, Plasmid attracting pheromones,
Shuttle plasmids.
3. Transposition - Overview of Transposition, Structure of Bacterial transposons, transposons and target-sites,
Types of Bacterial transposons, Assays of transposition, Mechanism of transposition Genetic requirements and
mechanisms of transposition by Tn3, Tn5, Tn10, Y, S, Transposition of Tn3 and Mu transposase-mediated
rearrangements, Regulation of transposition, Target immunity, Use of transposons as portable regions of
homology, Local mutagenesis, Chromosomal rearrangements, in vivo cloning, Transposons and evolution. Use of
transposons to isolate mutations in genes.
4. Bacteriophage Genetics – Infection of cells, What is transducing phages, Recombination and complementation
test with phages, Plaque Formation and Phage Mutants, Genetic experiments with the rII genes of phage T4,
Constructing the genetic linkage map of a phage, RNA phage genetics, Phage display, Genetic recombination and
concept of recon, muton, cistron.
5. Microbial Genomics - Genome sequencing of some examples of microbial genome sequencing projects,
Analysis of genome sequences - tools and resources at the NCBI, Predicting metabolism from DNA sequences –
WIT, DNA chips - studying gene expression using DNA microarrays.
4. Trisomics and tetrasomics (Hyperploids) [Classification (primary, secondary and tertiary trisomics),
methods of production, identification, meiotic pairing, breeding behavior of trisomics, trisomic and tetrasomic
ratios, utility in chromosome mapping].
6. Gene structure, expression, and regulation in plants - an overview of nuclear and organelle gene structure,
function, and expression, with emphasis on aspects that are unique to plant genes.
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7. Molecular Biology of Plant Reproduction - Molecular genetic basis of plant reproduction, Emphasis on
understanding developmentally regulated gene expression as it relates to the major changes that occur during
plant reproduction and on the genetic control of flowering.
8. Principles & Techniques of Plant Breeding – The principles, methods and applications of plant breeding and
genetics to the improvement of crop plants, Principles involved in breeding and maintaining economic crops;
factors affecting the choice of breeding methods; alternative approaches through hybridization and selection.
9. Analysis of Plant Genome with Molecular Markers – Plant Genome structure, Evolutionary relatedness,
Comparative Genome mapping, Physical & Genetic distances, Linkage Drag.
10. Analysis of Plant Gene expression with Transgenic plants – Agrobacterium-mediated transformation,
introduction of foreign genes via Agrobacterium-mediated transformation, analyzing gene expression with
Transgenic plants.
11. Plant Genetic Engineering – Plant transformation, map-based cloning of Plant genes, molecular pharming,
plantibodies, Reversible male sterility in plants, antisense RNA, Agricultural applications in developing countries.
12. Genetic modification in Agriculture – transgenic plants, genetically modified foods, application, future
applications, ecological impact of transgenic plants.
13. Genetic modification in Food industry – Genetically modified foods (organic foods, types of organic foods,
identifying organic foods, organic food & preservatives), background, history, controversies over risks, application,
future applications.
14. Methods of estimation and their application in plant breeding - Genotypic and phenotypic correlations and
path coefficient analysis in relation to crop improvement, Hybrid seed production and role of the hybrids in
enhancing crop productivity in India,
15. Principles and Practices of Seed Production - General aspects of seeds production technology, Seed
production methods, Seed production of GM crops, Production of high quality seeds.
2. Mammalian genetics - Mouse as a model mammalian genome; establishment of inbred strains; mouse genome
database. Parental Behavior and fosB Mutant Mice. Genes and environment coming together to shape animal
behavior ~ chimpanzee as a model. Environment, Genetics and Cognitive Development.
3. C. elegans Genetics: Isolation, complementation and mapping of mutants of C. elegans with special reference to
screening for suppressor/enhancer mutations. Genes affecting nervous system function and behavior.
4. Drosophila Genetics: Drosophila karyotype and genome: wild type and mutants, Genetic crosses. Mendelian
inheritance in Drosophila: Autosomal linkage & Sex-linked inheritance In Drosophila. Neurogenetics of courtship
and mating in Drosophila. Concept of gene - experiments on lozenge locus in Drosophila. Practical applications of
rearrangements: Balancers, Ring chromosomes, Attached X-chromosome in Drosophila, Aneuploidy in Drosophila.
Chromosomal and Molecular basis of sex determination in Drosophila Molecular basis of dosage compensation in
Drosophila.
21
5. Cell culture technology and its applications: Introduction to animal cell culture technology; Primary and
established cell line cultures; Biology and characterization of the cultured cells; Stem cell culture, embryonic stem
cells and their applications; Cell culture based vaccines; Organ and histotypic cultures; Measurement of cell death:
Apoptosis.
6. Genetic engineering of animals: in vitro gamete maturation. In vitro fertilization (IVF) and embryo transfer
(ET), Sex determination or sex specific makers, sexing of sperm and embryos, Assisted reproductive technology
(ART). Somatic cloning of animals; Creation of transgenic animals: microinjection technology; Improvements of
animal production and quality using transgenic approach with specific examples. Animals as bioreactors.
7. Genetically engineered animals for research: Knock-out animals. Conditional knock outs using cre-loxP
recombination; tissue specific promoters.
Texts/References:
1. S.R. Maloy, J.E. Cronan, D. Friefelder, Microbial Genetics, 2nd Edition, Jones and Bartlett Publishers, 1994.
2. N. Trun and J. Trempy, Fundamental Bacterial Genetics, Blackwell publishing, 2004.
3. Strachan T and Read A P, Human molecular genetics, 3rd Edition Wiley Bios, 2006.
4. Mange E J and Mange A. P., Human genetics, 2nd Edition, Sinauer Associates publications, 1999.
5. Hartl L D and Jones B, Analysis of genes and genomes, 3rd Edition, Jones and Bartlett Publishers, 1994.
6. S.B. Primrose, R.M. Twyman and R.W.Old; Principles of Gene Manipulation. 6th Edition, S.B.University
Press, 2001.
7. J. Sambrook and D.W. Russel; Molecular Cloning: A Laboratory Manual, Vols 1-3,
CSHL, 2001.
8. Brown TA, Genomes, 3rd ed. Garland Science 2006
9. Selected papers from scientific journals.
10. Technical Literature from Stratagene, Promega, Novagen, NewEngland Biolab etc
2. Mendelian modes of inheritance in Human Genetic diseases - single gene disorders, multifactorial traits,
chromosomal abnormalities, mitochondrial inheritance, diseases of unknown etiology "run in families",
3. Single gene disorders in human - Autosomal Dominant inheritance (Heterozygous affected phenotype,
pedigree, Variable Expressivity, Late Onset, High Recurrent, Mutation Rate, Incomplete Penetrance), Autosomal
Recessive inheritance (Carrier probabilities in a pedigree, effects of consanguinity), X-linked Dominant
inheritance (pedigree, lethality in males), X-linked Recessive inheritance (pedigree, Bayesian probability, new
mutations in genetic lethals), Sex-limited inheritance, Mitochondrial inheritance, imprinting.
5. Sex chromosome abnormalities in human – Lyon’s hypothesis, Barr bodies, Turner syndrome, Klinefelter
syndrome, XXX and XYY syndromes.
6. Non-Meiotic chromosomal abnormalities in human – Inversions, Ring chromosomes, non-Robertsonian
translocation, uniparental disomy.
8. Human Genome Mapping – Physical mapping of the human genome, Low resolution mapping, Cell hybrids,
mini- and microcells, synteny of genes, Radiation hybrid mapping; Human genome mapping: Assembly of clone
contigs and identifying genes in cloned DNA. Integration of cytogenetic, genetic and physical maps; DNA testing;
Direct and indirect testing (gene tracking) in individuals; DNA tests for identity and relationships including
forensic applications.
9. Population screening - ethics, organization and advantages Identifying human disease genes: Principles and
strategies; Position-independent and positional cloning; Candidate gene approaches; Confirming a candidate gene,
mutation screening, testing in animal models; Molecular pathology: Nomenclature of mutations and their
databases; Loss of function and gain of function mutations in diseases.
10. Cancer Genetics - Differentiation between genetic and environmental factors in cancer, Oncogenes, Tumor
suppressor genes, Genetics of common cancer, Genetic counseling in familial cancers.
11. Pharmacogenetics : Definition, Drug metabolism, Genetic variations revealed solely by the effect of drugs,
Hereditary disorders with altered drug response, Evolutionary origins of variation in drug response, pharmaco-
genetics, Eco-genetics.
12. Reproductive Genetics - Infertility and Sub-fertility, Assisted Reproductive Technologies, Extra embryos,
Cryo-preservation of Sperms, Oocytes & Embryos.
13. Genetic Counseling : Definition, Establishing the diagnosis, Calculation and Risk estimation, Discussion
options, communication and support, Counseling – directive or non-directive, outcome of genetic counseling,
special problem in genetic counseling.
14. New Approaches to treating disease and Gene therapy – Treating Genetic Disease, Therapeutic application
of recombinant DNA technology, Regulatory requirements of gene therapy, technical aspects, methods of gene
therapy, disease suitable for treatment using gene therapy
2. Reproductive Genetics - Male and female reproductive systems, Gonads and differentiation of sexual
characters, Hormonal regulation of sexual differentiation, Reproductive disorders, Disorders of gonads, Gonadal
mosaicism, genital tracts and genitalia, Pseudo-hermaphroditism, True-hermaphroditism, Gonadal dysgenesis,
Anomalies of genital ducts, Infertility, cryptorchidism, endometriosis and polycystic ovarian syndrome, Genetic
basis of male infertility, Genetic basis of female infertility, Recurrent pregnancy loss, Molecular Genetics of Human
Reproductive Failure, Sex chromosome Genetics (X and Y), genetics of Sex determination, Genetic variability in
syndromes like Turner and Klinefelter.
4. Neuro-Genetics – Major regions of Human Brain, Cellular components of nervous tissue, Subcellular
organization of the nervous system, Learning & Memory, Neuro-genetic disorders (Spino-muscular atrophy,
syndromes due to triplet nucleotide expansion, Alzheimers disease, Parkinson’s disease), Nature-nurture &
behavior (Genetic experiments to investigate animal behavior – selection studies, inbred strain studies),
Identifying genes for controlling behavior (induced mutations, quantitative trait loci, synteny/orthology),
Investigating the genetics of human behavior (Twin adoption study designs, interpreting heritability, Linkage
association studies, Environmental influence – shared and non-shared environment), Psychopathology
(Schizophrenia, Mood disorders, disorders of childhood).
3. Inheritance in bacteria - The luria and the Delbruck experiment, The newcombe experiment, the lederberg’s
experiment.
4. Genetic analysis of protein transport in Escherichia coli - Use of the mal genes to study protein transport,
signal sequences, sec and SRP The tat secretion pathway, Genetic analysis of transmembrane.domains of inner
membrame proteins in gram negative bacteria, Identification of genes for transported proteins by random phoA
fusions, Protein secretion in gram negative bacteria.
6. Catabolite-sensitive operons – cAMP and the cAMP binding proteins, Genetic analysis of catabolite regulation
in E.coli , Uses of cAMP in other organisms, A bacterial two Hybrid system based on the adenylate cyclase.
7. Regulation of nitrogen assimilation - Coordination of catabolite repression,the Ntr system and the regulation
of Amino-Acid-Degradative Operons
8. Stress responses in bacteria - Heat Shock regualtion,general stress response in gram negative bacteria,
Extracytoplasmic(envelope) stress responses, Regulation of porin synthesis,regulation of the envelope stress
response by CpxA-CpxR:a two component sensor kinase response regulator system
9. Iron regulation in Escherichia coli - The fur regulon,the RhyB RNA, the aconiatse translational repressor
24
2. Transition to Flowering - Control of flowering through the actions of transgenes, Molecular genetics and the
ABC Model for flower development, Cadasteral functions of Homeotic genes, Molecular function of MADSBox genes.
3. The Control of Flowering – Photoperiodism, Genes that Control Flowering Time, The Different Effects of Two
Different Gibberellins on Flowering (Spike Length) and Elongation (Stem Length), The Influence of Cytokinins and
Polyamines on Flowering, The Contrasting Effects of Phytochromes A and B on Flowering, A Gene That Regulates
the Floral Stimulus in Maize.
4. Molecular Approaches for Potential Crop Improvement - Introduction of basic concepts of plant molecular
biology and molecular techniques in current use, Organization and regulation of plant genes, gene cloning and
analysis, transformation systems for plants, and molecular techniques for crop improvement.
5. Plant genes Genetic transformation - promoters, intron splicing, vectors, codon optimization, gene mapping
and cloning of plant genes.Vector construction, Protoplast system (electroporation and PEG), Agrobacterium
system, en-planta transformation and Biolistic system; Screenable and selectable markers and their use;
Chloroplast transformation; Marker-free methodologies; Gene stability, Inheritance and Differential expression of
transgenes in plants (5periods)
6. Plant tissue culture - Organogenesis, Embryogenesis, in vitro fertilization, Apomixix and application of haploidy
and DH populations in transgenic breeding and crop improvement; Molecular and Biochemical markers of in vitro
regenerability of plants.
7. Molecular breeding for abiotic stress tolerance - (stress regulated genes expression, osmotic stress
signalling, application in salt, cold and drought tolerance in plants)
8. Molecular breeding for Biotic stress tolerance: Fungal resistance, Bacterial resistance, Virus resistance,
Transgenes pyramiding and Integrated Pest Management (IPM)
9. Biofortified crops (improvement of micronutrients in food crops; e.g. Iron and pro-vitaminA enriched rice,
Vitamin E-maize, Protein improvement in rice and potato etc.)
10. Gene silencing in plants - Post transcriptional and transcriptional gene silencing, mutants of gene silencing,
RNA virus in plants, virus induced gene silencing and its application
11. Plants as Biofactories – Concept of bio-pharming; Renewable Bio-fuel production in plants
12. Plant disease resistance - Types of pathogen and their mode of action, Plant defense system, Constitutive and
inducible defense, Genetic basis of plant pathogen interaction, R genes and R gene mediated resistance,
Biochemistry and Molecular biology of defense reactions, Systemic acquired resistance, Control of plant pathogen
by genetic engineering, Role of Salicylic acid Jasmonic acid and ethylene in plant defense
13. Improvement of crop yield and quality - Role of Ethylene in fruit ripening, Mutants in fruit ripening, Genetic
manipulation of fruit ripening, Molecular Farming & Plantibodies, Reversible male sterility in plants, Antisense
RNA, Agricultural applications in developing countries.
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MSGEN(AMG)-305 : Animal Molecular Genetics
1. Conservation of Animal Genetic resources - Domestic Animal Diversity in India, its origin, history and
utilization, Present status and flow of Animal Genetic Resources and its contribution to livelihood security,
Methodology for genotypic characterization of livestock and poultry breeds through systematic surveys. Concept of
conservation, In-situ and ex-situ (invivo and invitro); models of conservation; prioritization of breeds for
conservation, National and International strategies for conservation of Animal Genetic Resources.
2. Small Farm Animal Breeding - History of dairy cattle and buffalo breeding, Breeds of cattle and buffallo and
their characterization, Inheritance of important Economic traits, Methods of cross breeding, Plans for developing
new breeds of dairy cattle,
3. Poultry Breeding - Origin and history of poultry species : Chicken, turkey, duck and quail –
Important qualitative traits in poultry – Economic traits of egg-type chicken and their standardization
4. Selection criteria and selection indices – Response to selection – Genetic controls – Genotype and
environment interaction – Inbreeding, and its effects on production traits in egg and meat-type chickens – Inbred
lines – Strain development – Crossing : strain and line crosses
5. Laboratory Animal Genetics – Breeding colonies of mice, rats, hamstersand guinea pigs, Selection and mating
methods/systems – monogamous, polygamous and others, Development of genetically controlled laboratory
animals.
6. Transgenic animals their benefits in livestock production - somatic cell nuclear transfer, transgenic animals
in biomedical research, ethical consideration of transgenic animals; gene therapy and transgenic animal
production. Pharming of Pharmaceutical.
7. Utilization of non-additive genetic variance in farm animals - recent advances in estimation of non-additive
genetic variation and possible use in developing synthetic population of livestock and poultry.
Text/References:
1. Indian journal of veterinary research.
2. Indian journal of poultry research.
3. Poultry Science
PRACTICALS
MSGEN-306 : Lab on Genetic Engineering Tools
1. Transformation in E. coli DH5
2. Bacterial conjugation
3. Phage Titration
4. Plasmid preparation
6. Ligation
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2. Culture of Plant – Tissue culture (Callus culture, Cell suspension), Organ Micro-culture (Shoot tip, excised
root, Leaf culture), Plant micro-propagation (micro-culture of plants),
3. Isolation and Quantification of DNA and RNA in plant tissues by spectrophotometer method
5. DNA fingerprinting,
7. Southern analyses
5. Isolation and Quantification of DNA and RNA from animal tissues (Drosophila / Zebra fish / Mice) by
spectrophotometer method
6. DNA fingerprinting
2. Organization of a genetic screening program - Neonatal screening, Prenatal screening, Population screening
for carriers of any one genetic disorder, Family screening
3. Genetic Epidemiology study (Describe basic terminology in the field of human genetics, Explain basic
statistical methods in the field of genetic epidemiology, Describe various exposures, or markers, used in genetic
epidemiology studies, Conduct Hardy-Weinberg Equilibrium test and calculate allele and genotype frequencies,
Calculate simple statistics, such as odds ratios and LOD scores, Explain the difference between linkage and
association studies, Explain the difference between family-based and population-based studies, Interpret results of
a linkage study, Interpret results of an association study, Describe HapMap and explain Tag SNPs, Explain
interaction in association studies, Explain genome-wide association study based on hypothesis of common-disease
common-variant)
4. Cancer Epidemiology study (To provide an overview of the descriptive epidemiology of cancer - current
data and trends in incidence, mortality, and survival within India and worldwide, To describe the major
known risk factors for several common cancer sites, and to evaluate trends in the prevalence of important
etiologic factors, To describe current modalities in chemoprevention and screening, and evaluate the
effectiveness of various strategies for reducing cancer burden, To critically evaluate the literature and
examine current controversies related to cancer prevention, diagnosis, treatment, and the relative
contributions of various etiologic factors)
5. Reproductive Epidemiology study (Describe the key reproductive health indicators, both morbidity and
mortality, Discuss key epidemiologic study design and measurement issues in reproductive health, Describe the
sources of data used in reproductive epidemiology and the strengths and weaknesses of the different data sources,
Describe different methodologies used to collect data and conduct analysis on reproductive epidemiology topics,
Discuss with key study design and measurement issues in topics such as infertility, birth defects and early
reproductive loss, pregnancy-induced hypertension, and low birth weight, Describe relationships between lifestyle,
occupational factors and reproductive outcomes, Describe the key variables for the evaluation of prenatal care,
Describe the common pregnancy-induced disorders (e.g., anemia, pregnancy-induced hypertension, gestational
diabetes mellitus) and their prevalence, risk factors, maternal and infant outcomes, Describe the epidemiology of
preterm birth and understand key differences in the conducting and interpretation of results of studies of preterm
birth, intrauterine growth restriction and low birth weight, Describe the epidemiology of stillbirth/fetal death,
early neonatal death, infant mortality, perinatal mortality and maternal mortality, Discuss key evidence-based
medicine approaches in reproductive health, Discuss key evidence-based global health issues in reproductive
health, especially in developing countries, Discuss the concept and public health significance of possible fetal
origins of some health problems in later life (e.g., obesity, hypertension, type II diabetes, and cardiovascular
disease), Discuss the public health significance of major reproductive and perinatal problems and the importance
of epidemiologic studies in developing prevention strategies).
28
MSGEN(MMG)-310 : Lab on Microbial Molecular Genetics
1. Ampicilin selection of auxotrophs
2. Agents employed for the induction of various ploidy levels, identification of different polyploidy level in plants
3. Learning the precautions on handling of mutagens; Dosimetry - Studies of different mutagenic agents, Treating
the plant propagules at different doses of chemical mutagens
4. Callus induction and plant regeneration -; Standardizing the protocols for regeneration; Hardening of
regenerated plants
5. Estimation of antioxidants and antioxidant enzymes - Ascorbate, Superoxide dismutase, Catalase, and Peroxidase
7. Methods to measure various physiological processes (photosynthesis, transpiration, gas exchange, Chlorophyll
estimation, cell membrane stability) in plants
9. Estimation of Total Phenol, Total Flavonoid and screening of Phytocomponents from plants/ herbal products
2. Extraction and purification of genomic DNA, Gel electrophoresis, Restriction enzyme digestion of DNA and
analysis, PCR, PCR-RFLP, PCR-SSCP, Bioinformatics tool for DNA sequence analysis, Design of primer, Isolation of
RNA, cDNA synthesis, Statistical methods for analyzing molecular genetic data.
3. To study mutagenic and cytogenic effects of pesticides and agro-chemicals on the genome of
domestic animals
5. Optimization of breeding strategies for genetic improvement of indigenous livestock and poultry based on field
data
FOURTH SEMESTER
2. 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, Large scale genome sequencing strategies, Genome assembly and annotation,
Prediction of Genes, Promoters, Splice sites, Gene networks.
4. Pharmaco-genetics - High throughput screening in genome for drug discovery identification of gene targets,
Pharmaco-genetics and drug development
5. Structural (SG) & Functional Genomics (FG) - the need for SG, basic principles, approaches for target
selection, application of sequence based and structure-based approaches to assignment of gene functions, e.g.
sequence comparison, structure analysis (especially active sites, binding sites) and comparison,
pattern identification, etc., Use of various derived databases in function assignment.
6. Proteomics - Protein arrays : basic principles; Bioinformatics-based tools for analysis of proteomics data (Tools
available at ExPASy Proteomics server); databases (such as InterPro) and analysis tools. Protein-
protein interactions: databases such as DIP, PPI server and tools for analysis of protein-protein interactions,
Identification of disease genes: basic concepts, need for identification of disease genes, Role of Bioinformatics -
30
OMIM database, reference genome sequence, integrated genomic maps, gene expression profiling; Identification
of SNPs, SNPs databases (DbSNP), Metabolic pathways: databases such as KEGG, EMP.
9. Structural Bioinformatics - Protein structures, Ramchandran plot, protein folding structure function
relationship, conformational energy calculations, protein structure predictions, secondary and tertiary, protein
structure classification-SCOP, CATH, Immuno-informatics-epitope prediction
10. Bioinformatics: The Business of Research - Research methodology (focusing on computer-based research);
Case studies of areas of current bioinformatics research; Routes to research funding (academic and commercial);
Bioinformatics business models
11. Introduction to following DATABASEs & Tools – GenBank, Entrez, Introduction to NCBI Protein and
Nucleotide Database, OMIM, PubMed, Expasy server search tools and Databases, PIR, Swissprot, TrEmble,
PROSITE, PDB, NDB, KEGG, Complex Carbohydrate Structure Database (CCSD), Molecular visualizing tool (Rasmol,
Molmol), Gromacs.
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.
2. Agreements and Treaties - History of GATT & TRIPS Agreement; Madrid Agreement; Hague Agreement; WIPO
Treaties; Budapest Treaty; PCT; Indian Patent
Act 1970 & recent amendments
3. 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.)
31
4. 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
5. Intellectual property rights and Social-legal Aspects of Biotechnology - A commercial view of Biotechnology
and its application in Industry, Patenting Biological material, Opposition to patents in Biotechnology, Special issues
(Public opinions against the technologies), Legal Issues (legal guide lines of different countries), Ethical issues
(against the technologies).
BIOSAFETY
1. Introduction - Historical Background; Introduction to Biological Safety Cabinets; Primary Containment for
Biohazards;
2. Biosafety Levels - Biosafety Levels of Specific Microorganisms; Recommended Biosafety Levels for Infectious
Agents and Infected Animals;
3. Biosafety guidelines – in 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.
4. Regulating Recombinant DNA Technology - Approaching the biohazard problem, Environmental and
Regulatory Aspects of Using Genetically Modified plants, Relevance of multiple Environment Testing,
Environmental and Regulatory aspects of using GMMS,
5. Biosafety protocol – International protocols, International Activities in Biosafety Capacity Building, Biosafety
Regulations in India, Biological Weapons, Biosafety and Ethical Issues.
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. Ltd., 2007
A.Genomic imprinting and uniparental disomy; Spontaneous mutations; Mosaicism and chimerism; Male lethality;
X-inactivation; Consanguinity and its effects in the pedigree pattern; Allele frequency in population;
B.Complex traits-polygenic and multifactorial: Approaches to analysis of complex traits- 'Nature vs nurture'; Role
of family and shared environment; Monozygotic and dizygotic twins and adoption studies;
32
C.Polygenic inheritance of continuous (quantitative) traits, normal growth charts, Dysmorphology; Polygenic
inheritance of discontinuous (dichotomous) traits - threshold model, liability and recurrence risk; Genetic
susceptibility in complex traits; Alcoholism, cardiovascular disease, diabetes mellitus, obesity & epilepsy.
6. Population screening –
A. Ethics, organization and advantages Identifying human disease genes:
B.Principles and strategies; Position-independent and positional cloning; Candidate gene approaches; Confirming a
candidate gene,
C. Mutation screening, testing in animal models; Molecular pathology:
D.Nomenclature of mutations and their databases; Loss of function and gain of function mutations in diseases.
7. Molecular pathology –
A Instability of the human genome and diseases,
B.pathogenicity associated with repeated sequences;
C Slipped strand mispairing; Unequal crossover and unequal sister chromatid exchange;
D.Gene conversion; Retrotransposition; Illegitimate recombination.
8. Chromosomal Disorders
A Incidence of chromosomal disorders, Disorders of sex chromosomes,
B. Chromosome disorders and behavioural phenotype,
C. Chromosomal breakage syndromes,
D. Indications for chromosomal analysis
12. Pharmacogenetics
A. Definition, Drug metabolism, Genetic variations revealed solely by the effect of drugs,
B. Hereditary disorders with altered drug response,
C. Evolutionary origins of variation in drug response, pharmaco-genetics, Eco-genetics.
1. Plant genomics- Model plants, Benefits, Plant Genome Databases. Applications. Genomics of selected
Genomes –, Arabidopsis thaliana, Rice
4. Micropropagation - Methods and stages of clonal propagation, Strategies for Virus-free plant production.
:- Commercial micropropagation, Acclimatization of tissue cultured plants, Photoautotrophic
Micropropagation
6. Production of secondary metabolites by cell and organ cultures- Strategies for improvement of
metabolite production, Biotransformation using plant cell cultures, transformed cell and root cultures for
production of secondary metabolites.
34
9. Molecular approach for abiotic stress tolerance (stress regulated genes expression, osmotic stress
signalling, application in salt, cold and drought tolerance in plants)
10. Molecular approach for Biotic stress tolerance: Fungal resistance, Bacterial resistance, Virus resistance
11. Biofortified crops (improvement of micronutrients in food crops; e.g. Iron and pro-vitaminA enriched rice,
Vitamin E-maize, Protein improvement in rice and potato etc.)
12. Plants used as renewable resources;- Potato starch for industry, Soybean oil for industrial use
Gene Expression
4. Determinants of Gene Expression in Mycobacteria, Pseudomonas aeruginosa, Candida albicans
Leishmania donovani , Adenovirus, HIV
5. Gene Expression and Reporter Technologies
6. Transcription Regulation in Mycobacteria, Pseudomonas aeruginosa, Candida albicans, Leishmania
donovani , Adenovirus, HIV Metabolism
7. DNA Replication in Mycobacteria, Pseudomonas aeruginosa, Candida albicans, Leishmania donovani ,
Adenovirus, HIV
8. Genetics of Cell Wall Biosynthesis , Protein Secretion in Mycobacteria, Pseudomonas aeruginosa, Candida
albicans, Leishmania donovani .
Genetic Strategies
9. Genetics of Virulent Mycobacteria, Pseudomonas aeruginosa, Candida albicans, Leishmania donovani ,
Adenovirus, HIV.
10. Mutants and Mutagenesis in Drug Resistance Mycobacteria, Pseudomonas aeruginosa, Candida albicans,
Leishmania donovani , Adenovirus, HIV
11. Genetic Strategies for Vaccine Development and approaches to Drug Development for Mycobacteria,
Pseudomonas aeruginosa, Candida albicans, Leishmania donovani , Adenovirus, HIV.
35
MSGEN(AMG)-403 : Animal Molecular Genetics
1. Molecular Genetics in Animal Breeding : Genesis and importance of molecular techniques; Genome
organization – physical and genetic map, ; Molecular markers and their application; RFLP, RAPD, Microsatellite/
Minisatellite markers, SNP marker, DNA fingerprinting.
2. Gene transfer methods in Animals – Microinjection, Embryonic Stem cell gene transfer, Retrovirus & Gene
transfer.
5. Xenotransplantation in Human
Choosing donors; Barriers of xenotransplantation; techniques of xenotransplantation
7. Animal Reproductive biotechnology -basic anatomy of cattle reproduction, the estrus cycle, factors affecting
cattle reproduction
10. Artificial insemination (AI) in farm animals ( processing of semen, the technical details of AI, Timing of
insemination for maximum conception, benefits of AI.
11. The embryo transfer technology-in vitro maturation of sperm and ovum in vitro fertilization, transfer of
embryo to recipient, cryopreservation of embryo, micromanipulation of embryo splitting
Each student will undertake an experimental project under supervision of one of the teachers during Semester 4
and submit TWO copies of the dissertation which will include: a) Review of the relevant literature, b) Objectives of
the study, c) Materials and Methods, d) Results/Observations (supported by figures/tables etc as required), e)
Discussion of the Results/Observations, f) Summary and g) References.