m.sc course genetics - welcome to institute of genetic ... · m.sc course in genetics (modified ......

1

Syllabus for two-year MSc Course in

Genetics

(Modified syllabus of MSc in Molecular and Human Genetics proposed by Biotechnology consortium India Limited- Dept of Biotechnology Govt of India)

DURATION Four Semesters (Two Years) Total Marks = 3600

MSc GENETICS

ABOUT THE COURSE

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

The course in total is worth 90 credit points in 4 semesters TARGET GROUPS The main target group is that of Graduates (BSc) in the Biological Sciences who wish to pursue a career in Genetics either in industry or academia The program may also be suitable for those with backgrounds in BSc in Botany Zoology Physiology Anthropology Food Science amp Nutrition Biochemistry Biotechnology Molecular Biology Genetics and associated all Biological Sciences who have a strong interest in Genetics

Theoretical Papers 18 Papers (Marks = 1800)

Total Credit = 54

Practical Project Papers Total Marks = 1800)

Total Credit = 36

Total Credit in 4 Semesters = 54 + 36 = 90

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

2

FIRST SEMESTER Paper (Theoretical) 5 Papers = 500 Marks

Paper Code Name of the Paper Marks Credit hrs Classes Semester

MSGEN-101 Mendelian amp Classical Genetics 100 3 42

MSGEN-102 Cell Biology amp Cyto-Genetics 100 3 42

MSGEN-103 Molecular Biology 100 3 42

MSGEN-104 Biophysics and Biochemistry 100 3 42

MSGEN-105 Genetics of Organelles 100 3 42

Paper (Practical) 5 Papers = 500 Marks

MSGEN-106 Lab on Microscopy amp Instrumentation 100 2 40 hrs

MSGEN-107 Lab on Basic Cyto-Genetics amp Cell Culture Techniques (Plant amp Animal)

100 2 40 hrs

MSGEN-108 Lab on Molecular Biology ndash Basic Techniques

100 2 40 hrs

MSGEN-109 Lab on Biophysical amp Biochemical Techniques

100 2 40 hrs

MSGEN-110 Seminar Journal Club 100 2 40 hrs

Total Credits = 25

SECOND SEMESTER Paper (Theoretical) 5 Papers = 500 Marks


MSGEN-201 Genetics of Model Organisms 100 3 42

MSGEN-202 Bio-Statistics amp Population Genetics 100 3 42

MSGEN-203 Developmental Genetics 100 3 42

MSGEN-204 Immuno-Genetics 100 3 42

MSGEN-205 Genetic Biodiversity and Taxonomy 100 3 42


MSGEN-206 Lab on Life Cycle Studies (Model

organisms) 100 2 40 hrs

MSGEN-207 Lab on Computer Application 100 2 40 hrs

MSGEN-208 Lab on Developmental Genetics amp Genetic Toxicity Testing

100 2 40 hrs

MSGEN-209 Lab on Immunological Techniques 100 2 40 hrs


3

Total Credits = 25

THIRD SEMESTER

Paper (Theoretical) 5 Papers = 500 Marks


MSGEN-301 Microbial Genetics 100 3 42

MSGEN-302 Plant Genetics 100 3 42

MSGEN-303 Animal Genetics 100 3 42

MSGEN-304 Human Genetics 100 3 42

MSGEN(HMG)-305 MSGEN(MMG)-305 MSGEN(PMG)-305 MSGEN(AMG)-305

Elective Paper ndash I Human Molecular Genetics Microbial Molecular Genetics Plant Molecular Genetics Animal Molecular Genetics

100 3 42


MSGEN-306 Lab on Genetic Engineering Tools 100 2 40 hrs

MSGEN-307 Lab on Plant Genetics 100 2 40 hrs

MSGEN-308 Lab on Animal Genetics 100 2 40 hrs

MSGEN-309 Lab on Human Genetics 100 2 40 hrs


Lab on Elective Paper Human Molecular Genetics Microbial Molecular Genetics Plant Molecular Genetics Animal Molecular Genetics

100 2 40 hrs

Total Credits = 25

4

FOURTH SEMESTER Paper (Theoretical) 4 Papers = 400 Marks

Paper Code Name of the Paper Marks Credit hrs

Classes Semester

MSGEN-401 Genomics Proteomics and Bioinformatics

100 3 42

MSGEN-402 IPR amp Biosafety 100 3 42


Elective Paper ndash II Human Molecular Genetics Microbial Molecular Genetics Plant Molecular Genetics Animal Molecular Genetics

100 3 42

Paper (Practical) Total = 300 Marks

MSGEN-404 MSGEN-405 MSGEN-406

Comprehensive Viva-voce Project work based on Bioinformatics application Dissertation (Independent Project Work based on Spl Paper)

100

100

100

2

2

2

40

40

40

Total Credits = 15

List of Suggested Electives 1 Human Molecular Genetics 2 Microbial Molecular Genetics

5 3 Plant Molecular Genetics 4 Animal Molecular Genetics

^Any two 15 credit courses can be taken up to make one 3 credit course Kindly visit the link - ldquoElectivesrdquo on the main page for the contents of electives

FIRST SEMESTER

MSGEN-101 Mendelian amp Classical Genetics

1 Introduction to Genetics ndash Great milestones in Genetics levels of Genetic analysis (Classical Molecular amp Population Genetics) Genetics in Agriculture Medicine amp Society 2 Cells amp Chromosomes - Basic cell types ndash structure amp evolutionary relationships Overview of Prokaryotic amp Eukaryotic cells Cellular environment Chromosomes ndash where genes are located 3 Basic principles of Heredity ndash Segregation of a single gene the principle amp verification of segregation segregation of two or more genes test cross with unlinked genes 4 Patterns of Inheritance ndash Autosomal inheritance Sex chromosomes amp Sex-linked inheritance Cytoplasmic inheritance 5 Mendelian principles of Inheritance ndash The Big experiment of Mendel principle of independent assortment 6 Extensions amp Modifications of Mendelian principles ndash Complete amp Incomplete dominance Epistasis 7 Linkage Recombination amp Crossing Over ndash Recombination is the basis of Gene mapping Linkage mapping Tetrad analysis Gene mapping in absence of Meiosis Genetic Fine structure mapping 8 Genetic Variation ndash Genes amp gene products interaction between the alleles of one gene interacting genes amp proteins applications of chi-square test to gene interaction ratios

6 9 Alleles amp Gene Interactions ndash Variations in Allele Multiple alleles Gene interactions Alleles of different genes Modifier genes Pleiotropic effects Partial penetrance amp variable expressivity Lethal alleles Phenotypes produced by Conditional alleles 10 Quantitative Traits amp Polygenic Inheritance ndash Inheritance of Quantitative traits Genetic analysis of Quantitative traits using Statistics Usefulness of Heritability in predicting the phenotypes of offsprings 11 Extra-nuclear Inheritance ndash Chromosomes of some cytoplasmic organelles Maternal inheritance Paternal inheritance Effect of Maternal genes in the phenotype of offspring Infectious inheritance 12 Pedigree analysis amp Applications ndash Study of Human Genetic Characteristics Pedigree analysis Molecular markers in Human Pedigrees Twin studies Adoption studies Genetic Counseling Genetic Testing (Pre-natal amp Post-natal)

13 Testing of Genetic hypothesis ndash 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 amp Elizabeth W Jones Genetics ndash analysis of Genes amp Genomes (2) Alan G Atherly Jack R Girton amp John F McDonald The Science of Genetics (3) Benjamin A Pierce genetics ndash a conceptual approach (4) D Peter Snustad amp Michael J Simmons Principles of Genetics (5) Griffiths Wessler Lewontin Gelbart Suzuki amp Miller Introduction to Genetic analysis

MSGEN-102 Cell Biology amp Cyto-Genetics

Cell Biology 1 Plasma Membrane - Organization and dynamics of transport across membrane Mechanism of endocytosis and exocytosis Cytoskeleton Microfilaments Structural organization cell motilityand cell shape Microtubule Structural and functional organization Cilia flagella centriole Intermediate filaments Mitochondria Ultrastructure Chemiosmotic theory and respiratory chain complexes Structure and function ofperoxisome Nucleolus and biosynthesis of ribosome 2 Cell-Cell Interaction - Cell adhesion molecules Cellular junctionsExtracellular 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

7 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) 3 Chromosomal anomalies - Numerical Structural Meiosis in inversion and translocation heterozygotes Breakage Fusion-bridge cycles Induced chromosomal aberrations in somatic cells Sister chromatid exchanges and somatic crossing over Dosage compensation in Caenorhabditis Drosophila and mammals TextsReferences 1 Alberts et al Molecular Biology of The Cell 2nd Edition Garland 2007 2 Cooper The Cell A Molecular Approach 4th Edition Washington DC ASM Press 2007 3 Gilbert Developmental Biology Eighth Edition Sinauer 2006 4 Hennig Structure amp 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 amp Earnshaw Cell Biology Third Edition Saunders 2002

MSGEN-103 Molecular Biology

1 Genome organization - Organization of bacterial genome Structure of eukaryotic chromosomes Role of nuclear matrix in chromosome organization and function Matrix binding proteins Heterochromatin and Euchromatin DNA re-association kinetics(Cot curve analysis) Repetitive and unique sequences Satellite DNA DNA melting and buoyant density Nucleosome phasing DNase I hypersensitive regions DNA methylation amp Imprinting 2 DNA Structure Replication Repair amp 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 FLPFRT and CreLox recombination 3 Prokaryotic amp Eukaryotic Transcription - Prokaryotic Transcription Transcription unit Promoters - Constitutive and Inducible Operators Regulatory elements Initiation Attenuation Termination-Rho-dependent and independent Anti-termination Transcriptional regulation ndash Positive and negative Operon concept-lac trp ara his and gal operons Transcriptional control in lambda phage Transcript processing Processing of tRNA and rRNA Eucaryotic transcription and regulation RNA polymerase structure and assembly RNA polymerase I II III Eukaryotic promoters and enhancers General Transcription factors TATA binding proteins (TBP) and TBP associated factors (TAF) Activators and repressors Transcriptional and post-transcriptional gene silencing 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 amp 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

8 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 TextReferences 1 Benjamin Lewin Gene IX 9th Edition Jones and Barlett Publishers 2007 2 JD Watson NH Hopkins JW Roberts J A Seitz amp AM 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 amp Molecular Dynamics ndash 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 amp shape of macromolecules ndash Molecular electron microscopy measuring electron diffraction of a solid with Electron Microscope determination of molecular structure in Electron Microscope minimizing drying amp shrinking artifacts using symmetry to enhance the Electron Microscope image High Resolution Autoradiography X-Ray diffraction 3 Absorption Spectroscopy ndash Absorption spectroscopy of electronic states Extinction co-efficient Spectral properties of a simple molecule (Formaldehyde) Peptide group domination of far UV absorption for proteins Aromatic amino acid domination of near UV absorption for proteins estimation of protein concentration from UV absorbance nucleic acid absorption dominated by bases 4 Infrared Spectroscopy ndash Principles of IR spectroscopy vibrational spectra of biopolymers Fourier transform of Infra Red spectroscopy Instrumentation factors influencing vibrational frequency (Vibronic coupling H-bond electronic factors bond angles etc) 5 NMR Spectroscopy ndash 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) 6 X-Ray Crystallography ndash Instrumentation Fourier transformation Application

TextReferences

(1) Cantor amp Schimmel Biophysical Chemistry (Part I II amp III) (2) A Lehninger Principles of Biochemistry

Topics Biochemistry 1 Biomolecules ndash structure function amp metabolism ndash Organization amp Composition of Eukaryotic Cells Integration amp Control of Cellular functions Structural components of Nucleic acids higher order DNA structure DNA sequence amp function functional roles of Proteins in Human Amino acid composition of Proteins higher levels of Protein organization dynamic aspects of Protein structure amp Protein stability Methods for characterization purification amp study of Protein structure amp organization Bioenergetics amp Oxidative metabolism

9 2 Mechanism of Enzyme action ndash 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 amp Regulation ndash Carbohydrate metabolism ndash major metabolic pathways amp their control special pathways amp Glycoconjugates Lipid metabolism ndash utilization amp storage of energy in lipid form metabolic pathways of special lipids Amino acid metabolism Purine amp Pyrimidine nucleotide metabolism metabolic interrelationships 4 Physiological Processes ndash Biochemistry of Polypeptide amp Steroid Hormones Hormones amp their receptors Regulatory cascades Insulin amp related Growth-regulating hormones 5 Expression amp Transmission of Genetic information ndash Genetic control of Enzyme synthesis Control of Gene expression Gene expression in Prokaryotes amp Eukaryotes Response to environmental changes ndash Sensory systems amp Immune systems 6 Biochemical Genetics In born Errors of Metabolism amp Gene Therapy ndash Metabolic pathways Overview of the metabolic basis of inherited diseases 7 Signal Transduction pathways ndash Molecular circuits Seven transmembrane-Helix receptors G proteins defects in signaling pathways which lead to Cancer amp other diseases TextReferences

1 Jeremy M Berg John L Tymoczko amp Lubert Stryer Biochemistry 2 Lehninger ndash David L Nelson amp Michael M Cox Principles of Biochemistry 3 David E Metzler Biochemistry ndash The Chemical Reactions of Living Cells 4 Thomas M Devlin Biochemistry with Clinical Correlations 5 Charles Rascriver Arthur L Beaudet William S Sly amp David Valle The Metabolic basis of inherited diseases

MSGEN-105 Genetics of Organelles

1 Organelle Chromosome ndash Genetic material of organelle Leaf variegation in plants Antibiotic Resistance in Chlamydomonas Metabolic defects in Yeast 2 Organelle Heredity ndash Endosymbiont Theory Genetic codes of Organelles Respiration-defective Mitochondrial mutants Cytoplasmic Male sterility in Plants Cytoplasmic transmission of Symbionts 3 Evolutionary Origin of Organelles ndash Origin amp evolution of Mitochondria amp Chloroplasts Eukaryotic organelles as Endosymbionts 4 Genetics of Cytoplasmic Transmission ndash Expression of Mitochondrial genes Interplay between Mitochondrial amp Nuclear gene products 5 Patterns of Extranuclear inheritance ndash Uniparental inheritance Maternal inheritance amp Maternal effects Maternal effect in Snail Shell coiling Heteroplasmy Paternal inheritance 6 Biology of Mitochondria amp Chloroplasts ndash Biology of Mitochondria amp Chloroplasts Mitochondrial DNA Chloroplast DNA

10 7 Mitochondrial Genome ndash Origin of Mitochondrial Genome - Yeast amp Human mtDNA Mitochondrial genes Replication Transcription amp 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 ndash Chloroplast biogenesis Structure amp Organization of Chloroplast cpDNA Replication Transcription amp Translation of cpDNA Evolution of cpDNA Genome comparisons 9 Intergenomic exchange of Genetic Information ndash Comparison of nuclear Eukaryotic Eubacterial Mitochondrial amp Chloroplast genomes Promiscuous DNA 10 Mitochondrial DNA amp Aging in Human ndash 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 ndash To study Human evolution using mtDNA 12 Human Mitochondrial Mapping ndash Human Mitochondrial genome mtDNA amp Human disease non-universal codons in mtDNA

References 1) Daniel L Hartl amp Elizabeth W Jones Genetics ndash analysis of Genes amp Genomes 2) Benjamin A Pierce genetics ndash a conceptual approach 3) D Peter Snustad amp Michael J Simmons Principles of Genetics 4) Tom Strachan amp Andrew P Read Human Molecular Genetics

PRACTICALS

MSGEN-106 Lab on Microscopy amp Instrumentation

1 Microscopy amp Imaging 2 Principles amp Operation of General Equipment usually used in Research laboratories TextReferences (1) Barch M J et al The AGT Cytogenetics Laboratory Manual 3rd Ed 1997 Lippincott- Raven New York (2) Celis Julio Cell Biology ndash a laboratory manual AP 2nd Ed 1998

MSGEN-107 Lab on Basic Cyto-Genetics amp Cell Culture Techniques (Plant amp

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 amp Imaging (6) Chromosome analysis amp Karyotype reporting (7) Interpretation amp Recommendations in Abnormal Chromosome study (8) Chromosomal syndromes identification amp Karyotyping

Cell Culture Techniques (Plant amp Animal) Techniques

11 1 General procedure for Tissue culture 2 Primary Cultures from Embryonic Tissue 3 Culture of specific Cell types 4 Cell separation techniques 5 Cytotoxic amp Cell Growth Assays

TextReferences (1) Barch M J et al The AGT Cytogenetics Laboratory Manual 3rd Ed 1997 Lippincott-Raven New York (2) Purandare Hema amp Chakravarty Amit Human Cyto-Genetics Techniques amp Clinical Applications 2000 Bhalani Publishing House Mumbai (3) Celis Julio Cell Biology ndash a laboratory manual AP 2nd Ed 1998 (4) Culture of Animal Cells ndash a manual of basic techniques R Ian Freshney (Wiley Publication)

MSGEN-108 Lab on Molecular Biology ndash Basic Techniques 1 Plasmid DNA isolation and DNA quantitation Plasmid minipreps 2 Restriction digestion 3 Preparation of competent cells 4 Agarose gel electrophoresis 3 Restriction Enzyme digestion of DNA 4 Purification of DNA from an agarose gel 5 DNA Ligation 6 Transformation of Ecoli with standard plasmids Calculation of transformation efficiency 7 Cloning of genomic DNA in standard plasmid vectors 8 Confirmation of the insert Miniprep of recombinant plasmid DNA Restriction mapping 9 Polymerase Chain reaction using standard primers 10 RFLP analysis of the PCR product 11 Transformation of yeast Saccharomyces cerevisiae TextReferences Sambrook amp Russell Molecular Cloning 3rd Ed 2001

MSGEN-109 Lab on Biophysical amp Biochemical Techniques 1 Determination of pH of unknown solution 2 Verification of Lambert-Beerrsquos Law 3 Determination of Molecular weight of Protein by Column chromatography 4 Iso-electric focusing 5 Determination of Surface Tension by Stalagmometer 6 Determination of Viscosity by Oswaldrsquos Viscometer TextReferences

a Cantor amp Schimmel Biophysical Chemistry (Part I II amp III) b Jeremy M Berg John L Tymoczko amp Lubert Stryer Biochemistry c David E Metzler Biochemistry ndash The Chemical Reactions of Living Cells

MSGEN-110 Seminar Journal Club

Seminar

12 The seminars are on a topic scheduled for the semester The topic is presented in depth appropriate for postgraduates by one of the MSc students and moderated by a faculty member 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 MScPhD 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 amp genetic variation comparison of different genomes genome evolution 3 Genomics ndash about the genomics history comparative genomics comparative genomic hybridization functional genomics 4 Human Genome Project (HGP) ndash an overview of the project goals of the project major scientific strategies amp approaches used in HGP expected scientific amp 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 amp its impact ndash impact of Human Genome project in Plant Animal amp Human 6 Biology amp Life cycles ndash study of biology amp life cycles of model organisms (E coli Yeast Arabidopsis thaliana C elegans Drosophila melanogaster laboratory mouse Zebra fish amp Human) 7 Genomics of selected Genomes ndash 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 ndash physical mapping genetic mapping gene ontology gene annotation

13 9 Technologies used in HGP ndash RFLP microsatellite markers STS EST DNA sequencing DNA microarray

MSGEN-202 Biostatistics amp Population Genetics

Biostatistics 1 Overview - Measures of central tendency Mean Median Mode Measures of dispersion Standard deviation standard error Variance Coefficient of variation Various methods of presentation and interpretation of data 2 Hypothesis testing - Definition Statistical amp 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 amp FASTA) ANOVA General idea of one way amp two way analysis General idea of Correlation Analysis General idea of Regression Analysis Test of significance Studentrsquos 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 amp Linkage disequilibrium Balanced genetic polymorphism Heterosis amp heterozygous superiority TextsReferences 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 amp Bartlett 2000 7 Hartl amp Clark Principles of Population Genetics Third Edition Sinauer Associates Inc 1997 8 M Strickberger Evolution 3rd Edition Jones amp Bartlett 2000

14

MSGEN-203 Developmental Genetics 1 Fertilization of Vertebrates (including human) - Germ cell determination and differentiation spermatogenesis oogenesis maturation of germ cells ovulation and implantation External fertilization eg Sea Urchin Internal Fertilization in mammals Polyspermy 2 Elements of Early Development in vertebrates (including human) - Fertilization to Cleavage Pattern of Cleavage Gastrulation Cell specification and axis formation 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 9 Human embryonic development - Brief account of embryonic development Blastulation Gastrulation formation of notochord and establishment of bodyaxis Organogenesis Formation of embryonic germ layers and their derivatives Fetal development and placentation (development structure and function) Fetal membrane in twins 10 Molecular regulations of human development and defects I ndash Human Hox genes and genetic defects due to mutation in Hox genes Somite differentiation and homeobox genes (anterior-posterior patterning) Limb development amp 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 ndash 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

15 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) TextsReferences 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 Langmanrsquos Medical Embryology 9th Edition Lippincott Williams amp Wilkins 2004 4 K L Jones Smithrsquos 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 TextsReferences 1 Kuby RA Goldsby Thomas J Kindt Barbara A Osborne Immunology 6th Edition Freeman 2002 2 Brostoff J Seaddin JK Male D Roitt IM Clinical Immunology 6th 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 ndash A Short Course 5th Edition Wiley- Liss 2003

16

MSGEN-205 Genetic Biodiversity and Taxonomy 1 Basic concept of Biodiversity ndash What is Biodiversity Why should we conserve it Elements of Biodiversity - Ecosystem Diversity Genetic Diversity Species Abundance amp Diversity Patterns of Species Diversity 2 Global patterns of Biodiversity ndash 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 amp Conservation ndash Overexploitation threatening living species International Trade Animals threatened by International trade Problems in Controlling International Trade (Enforcement Reservations Illegal Trade) Free Trade amp the Environment Free Trade amp Conservation Common patterns of Overexploitation 4 Exotic Species ndash Plants Invertebrates Fishes Amphibians Reptiles Birds Mammals Detrimental Effects of Exotic Species 5 Endangered Species Conservation ndash 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 ndash Values of Biodiversity Biopiracy Hybridized plants GM crops (benefits amp criticism) Economic Value of Biodiversity amp Legal Ethical and Conservation issues related to uses of biodiversity Global Conservation Issues 7 Human Population Growth ndash 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 ndash Names and Naming Essentials of Nomenclature Classification Construction of Phylogenetic tree Systematics Cladistics Cladograms Phenetics 9 Molecular phylogenies ndash Immunological techniques Amino acid sequences Quantitative DNA measurements Repetitive DNA sequences Nucleic acid phylogenies based on DNA-DNA hybridizations Restriction Enzyme sites amp Nucleotide sequence comparisons and homologies Combined Nucleic acid-Amino acid phylogenies rates of Molecular change Evolutionary Clocks Regulatory genes amp some Evolutionary consequences 10 Taxonomy in relation to Chromosomal morphology amp Evolution ndash Chromosomal evolution why location of genes matter evolutionary oddities about chromosomes evolutionary effect of rearrangements of chromosomes karyotypic orthoselection chromosomal evolution amp speciation 11 Molecular Taxonomy in relation to DNA characteristics amp Protein sequences ndash 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

17

PRACTICALS

MSGEN-206 Lab on Life Cycle Studies (Model organisms) 1 E coli - Life cycle study isolation amp identification of mutants 2 Yeast ndash Life cycle study isolation amp identification of mutants 3 Drosophila - Life cycle study isolation amp identification of mutants 4 Zebra fish - Life cycle study isolation amp identification of mutants 5 Laboratory Mouse - Life cycle study isolation amp identification of mutants

MSGEN-207 Lab on Computer Application

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

a Concepts of flowcharting algorithm development pseudo codes etc b Computer assignments based on the following topics in lsquoCrsquo programming

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 amp 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 Genetic Toxicity Testing

18 1 Short-Term Biochemical Tests for Genetic Toxicity 2 Test for gene mutations in bacteria - Bacterial Reverse Mutation Test 3 in vitro in vivo test with Cyto-genetic evaluation of chromosomal damage (Chromosomal Aberration Test) using mammalian (Lab Mouse) cells 4 Ames test

MSGEN-209 Lab on Immunological Techniques 1 Antigen-Antibody reactions ndash Agglutination (Blood grouping testing) 2 Antibody titration (Ouchterlony Double Diffusion) 3 Antigen-Antibody reactions ndash Immuno-electrophoresis Rocket immuno-electrophoresis 4 Antigen-Antibody reactions ndash Coombrsquos test 5 Antigen-Antibody reactions ndash ELISA


Seminar The seminars are on a topic scheduled for the semester The topic is presented in depth appropriate for postgraduates by one of the MSc students and moderated by a faculty member 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 MScPhD 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


19

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 ndash 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 ndash 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 ndash

WIT DNA chips - studying gene expression using DNA microarrays

MSGEN-302 Plant Genetics

1 Unique genetic features of plants - Ability to photosynthesize Totipotency of plant cells Hermaphroditism and ability to reproduce both sexually and asexually Double fertilization Polyploidy Alternation of generations Mitosis in haploid state 2 Plant Cytogenetics ndash Haploidy [Classification (monoploids polyhaploids and aneuhaploids) methods of production (anther culture and chromosome elimination) identification androgenic and gynogenetic and parthenogenic haploids meiotic pairing utility (hybrid sorting and DH breeding)]

3 Polyploidy [Classification (autopolyploids allopolyploids) methods of production cytological and genetic methods for identification polyploid genetics (chromosome and chromatid segregation) meiotic pairing (autosyndesis and allosyndesis) diploidizing system (Ph1 locus) and role in evolution utility in crop improvement segmental poluploidy synthetic polyploids brief idea of ancient polyploidy]

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]

5 Monosomics and nullisomics (Hypoploids) [Methods of production (particularly in wheat) identification meiotic behavior breeding behavior of monosomics monosomic analysis (monogenic characters only) alien additionsubstitution lines] 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

20

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 amp Techniques of Plant Breeding ndash 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 ndash Plant Genome structure Evolutionary relatedness Comparative Genome mapping Physical amp Genetic distances Linkage Drag

10 Analysis of Plant Gene expression with Transgenic plants ndash Agrobacterium-mediated transformation introduction of foreign genes via Agrobacterium-mediated transformation analyzing gene expression with Transgenic plants 11 Plant Genetic Engineering ndash 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 ndash transgenic plants genetically modified foods application future applications ecological impact of transgenic plants 13 Genetic modification in Food industry ndash Genetically modified foods (organic foods types of organic foods identifying organic foods organic food amp 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

MSGEN-303 Animal Genetics 1 Introduction to Animal Genetics - Roles of animals in society (food production draught live capital social (eg company recreation sport) ecology (eg nature development) Genetics (plant animal molecular population genetics) 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 suppressorenhancer 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 amp 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 TextsReferences 1 SR Maloy JE 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 SB Primrose RM Twyman and RWOld Principles of Gene Manipulation 6th Edition SBUniversity Press 2001 7 J Sambrook and DW 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

MSGEN-304 Human Genetics

1 History of Human Genetics ndash Pedigrees - gathering family history Pedigree symbols Construction of pedigrees Presentation of molecular genetic data in pedigrees Pedigree analysis of monogenic traits Autosomal inheritance-dominant recessive Sex-linked inheritance- X-linked recessive dominant Yndashlinked Sex-limited and sex-influenced traits Mitochondrial inheritance MIM number 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

4 Chromosomal inheritance in human ndash importance karyotype chromosome replication autosomal abnormalities Meiotic non-disjunction Mitotic non-disjunction (Mosaic) Robertsonian translocation isochrome formation

5 Sex chromosome abnormalities in human ndash Lyonrsquos hypothesis Barr bodies Turner syndrome Klinefelter syndrome XXX and XYY syndromes 6 Non-Meiotic chromosomal abnormalities in human ndash Inversions Ring chromosomes non-Robertsonian translocation uniparental disomy 7 Multifactorial inheritance in human ndash polygenic inheritance recurrence risks

22 8 Human Genome Mapping ndash 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 amp Embryos 13 Genetic Counseling Definition Establishing the diagnosis Calculation and Risk estimation Discussion options communication and support Counseling ndash directive or non-directive outcome of genetic counseling special problem in genetic counseling 14 New Approaches to treating disease and Gene therapy ndash 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

MSGEN(HMG)-305 Human Molecular Genetics

1 Cancer Genetics ndash Genetic basis of Cancer The Cancer gene theory What are cancer genes and how are they acquired Genetic variation and cancer genes Environmental mutagens mutations and cancer Oncogenes The discovery of transmissible cancer genes Viral oncogenes Proto-oncogene activation by gene amplification Proto-oncogene activation by chromosomal translocation Multiple modes of proto-oncogene activation Proto-oncogene activation and tumorigenesis Tumor suppressor genes Tumor suppressor gene inactivation Functional inactivation of p53 Tumor suppressor genes and oncogenes interact Cancer predisposition allelic penetrance relative risk and odds ratios Breast cancer susceptibility BRCA1 and BRCA2 overview of genetic instability in cancer 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 3 Haemoglobinopathy Genetics - Types of haemoglobinopathies Classification (Genetic amp Clinical) Structure (Oxygenation and deoxygenation) amp Functions (Cooperativity Oxygen affinity and Nitric oxide transport) of

23 Human Haemoglobins like HbA HbF HbA2 HbA1C Structure amp Functions of Embryonic Haemoglobins Alpha Globin Locus beta Globin Locus Non-globin locus mutations (GATA-1 mutation amp beta thalassaemia ATRX mutation amp alpha thalassaemia) Transcription mRNA stability and Translation into globin protein Haemoglobin assembly deletion of the LCR large deletions within the globin gene cluster rearrangements within beta globin gene (Hb Lepore) mutations affecting pre-mRNA splicing (activation of cryptic splicing sites in HbE) failed Translation termination (Hb Constant Spring) altered mRNA Translation and stability (Dominant Thalassaemia trait due to nonsense codons in the final exon) 4 Neuro-Genetics ndash Major regions of Human Brain Cellular components of nervous tissue Subcellular organization of the nervous system Learning amp Memory Neuro-genetic disorders (Spino-muscular atrophy syndromes due to triplet nucleotide expansion Alzheimers disease Parkinsonrsquos disease) Nature-nurture amp behavior (Genetic experiments to investigate animal behavior ndash selection studies inbred strain studies) Identifying genes for controlling behavior (induced mutations quantitative trait loci syntenyorthology) Investigating the genetics of human behavior (Twin adoption study designs interpreting heritability Linkage association studies Environmental influence ndash shared and non-shared environment) Psychopathology (Schizophrenia Mood disorders disorders of childhood)

MSGEN(MMG)-305 Microbial Molecular Genetics 1 A brief history of microbial molecular genetics- Molecular mechanisms of bacterial gene transfer recombination within genes 2 Useful phenotypes in Bacterial genetics - Auxotrophic mutantsconditional lethal mutantsResistant mutantsStatistical analysis of number oif mutantsculture 3 Inheritance in bacteria - The luria and the Delbruck experiment The newcombe experiment the lederbergrsquos 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 transmembranedomains of inner membrame proteins in gram negative bacteria Identification of genes for transported proteins by random phoA fusions Protein secretion in gram negative bacteria 5 Genetic analysis of sporulation in Bacillus subtilis - Identification of genes that regulate sporulationregulation of initialation of sporulationcompartmentalized regulation of sporulation genes Analysis of the role of sigma factors in sporulation reaction Intercompartmental regulation during development Finding sporulation genesmutant huntssuppresor analysis and functional genomics 6 Catabolite-sensitive operons ndash cAMP and the cAMP binding proteins Genetic analysis of catabolite regulation in Ecoli Uses of cAMP in other organisms A bacterial two Hybrid system based on the adenylate cyclase 7 Regulation of nitrogen assimilation - Coordination of catabolite repressionthe Ntr system and the regulation of Amino-Acid-Degradative Operons 8 Stress responses in bacteria - Heat Shock regualtiongeneral stress response in gram negative bacteria Extracytoplasmic(envelope) stress responses Regulation of porin synthesisregulation of the envelope stress response by CpxA-CpxRa two component sensor kinase response regulator system 9 Iron regulation in Escherichia coli - The fur regulonthe RhyB RNA the aconiatse translational repressor

24

MSGEN(PMG)-305 Plant Molecular Genetics

1 Sex-determination amp Molecular Biology of Plant Reproduction - patterns Sex determination in Flowering plants - 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 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 ndash 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 genesVector 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 eg 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 ndash 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 amp Plantibodies Reversible male sterility in plants Antisense RNA Agricultural applications in developing countries

25

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 ndash Important qualitative traits in poultry ndash Economic traits of egg-type chicken and their standardization 4 Selection criteria and selection indices ndash Response to selection ndash Genetic controls ndash Genotype and environment interaction ndash Inbreeding and its effects on production traits in egg and meat-type chickens ndash Inbred lines ndash Strain development ndash Crossing strain and line crosses

5 Laboratory Animal Genetics ndash Breeding colonies of mice rats hamstersand guinea pigs Selection and mating methodssystems ndash 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 TextReferences 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 5 Restriction enzyme digestion 6 Ligation

26 7 DNA molecular size determination 8 Bacterial Antibiotic sensitivity 9 Bacterial gene expression (using Lac promoter system)

MSGEN-307 Lab on Plant Genetics

1 In vitro Culture amp Preparation of Culture media - Washing amp Sterilization Preparatory steps for tissue culture surface sterilization of plant material basic procedures for Aseptic tissue transfer incubation of culture Media composition Nutrition Hormones 2 Culture of Plant ndash 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 4 RAPD and microsatellite analyses for confirmation of hybridity 5 DNA fingerprinting

6 Analyses of transgenic plants (PCR RT-PCR)

7 Southern analyses

8 Chromosome preparations and physiological analyses of plants

MSGEN-308 Lab on Animal Genetics

1 Polytene chromosome preparation of Drosophila 2 Chromosome preparation from bone marrow of Mice Rat

3 Analyses of Chromosomes of Drosophila and Mice by experiments 4 Developmental Genetics studies on Drosophila Zebra fish Mice

5 Isolation and Quantification of DNA and RNA from animal tissues (Drosophila Zebra fish Mice) by

spectrophotometer method

6 DNA fingerprinting

MSGEN-309 Lab on Human Genetics

(1) PCR detection of known mutations eg globin gene in Thalassaemia patients (2) RFLP analysis of PCR amplified DNA (3) PCR Application for detection of Single Nucleotide Polymorphism (SNP) (4) DNA Fingerprinting - Using RAPD techniques Genotyping Analysis in Human

27 (5) Clinical Cytogenetics - Diagnosis and Interpretation (Metaphase analysis)

- Chromosomal Syndromes (Numerical + Structural) (6) Cancer Cytogenetics - Diagnosis and Interpretation (Metaphase analysis)

- Chromosome analysis in Leukemia (Bone marrow Blood) - Oncogene markers (Cancer screening Tumor)

MSGEN(HMG)-310 Lab on Human Molecular Genetics 1 Genetic testing in individuals and populations - Direct testing of individuals by Genetic diagnosis counseling and prediction from samples of blood buccal scrapes or mouthwashes hair semen tissues etc 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 (eg 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 stillbirthfetal 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 (eg 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 Mutagenesis in bacteria by Ames test

3 NTG mutagenesis in Ecoli

4 Bioremediation using GFP cloned Ecoli

5 Isolation of bacteriophage from sewage and determination of phage titer

6 Effect of temperature amp pH on microbial growth techniques for cultivation of anaerobic bacteria

7 Rapid isolation of Plasmid DNA by TELT

8 Western Blotting Technique

MSGEN(PMG)-310 Lab on Plant Molecular Genetics

1 Studies on the course of mitosis in onion and Aloe vera - Studies on the course of meiosis in onion and Rhoeo 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 6 Protoplast isolation viability test and culture 7 Methods to measure various physiological processes (photosynthesis transpiration gas exchange Chlorophyll estimation cell membrane stability) in plants 8 Secondary metabolite extraction and purification from microbesplants 9 Estimation of Total Phenol Total Flavonoid and screening of Phytocomponents from plants herbal products

MSGEN(AMG)-310 Lab on Animal Molecular Genetics 1 Characterization and cataloging of chromosomal profiles of different species of livestock and

29 Poultry identification of bar bodies in vitro and in vivo preparation of somatic metaphase chromosomes screening of chromosomal abnormalities microphotography and karyotyping banding procedures for comparing the chromosomal complement 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 4 Molecular characterization of milk proteins (DGATI gene) in cattle and buffalo 5 Optimization of breeding strategies for genetic improvement of indigenous livestock and poultry based on field data 6 Identification of molecular markers for economic traits

FOURTH SEMESTER

MSGEN-401 Genomics and Proteomics

1 Introduction - Structural organization of genome in Prokaryotes and Eukaryotes Organelle DNA-mitochondrial chloroplast DNA sequencing principles and translation to large scale projects Recognition of coding and non-coding sequences and gene annotation Tools for genome analysis-RFLP DNA fingerprinting RAPD PCR Linkage and Pedigree analysis-physical and genetic mapping 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 typingsequencing ESTrsquos and SNPrsquos Large scale genome sequencing strategies Genome assembly and annotation Prediction of Genes Promoters Splice sites Gene networks 3 Proteomics - Protein analysis (includes measurement of concentration aminoacid composition N-terminal sequencing) 2-D electrophoresis of proteins Microscale solution iso-electric focusing Peptide fingerprinting LCMS-MS for identification of proteins and modified proteins MALDI-TOF SAGE and Differential display proteomics Protein-protein interactions Yeast two hybrid system 4 Pharmaco-genetics - High throughput screening in genome for drug discovery identification of gene targets Pharmaco-genetics and drug development 5 Structural (SG) amp 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 eg 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 7 Bioinformatics Algorithms and Tools - Publicly available databases Visualisation of sequence data Sequence alignment Homology searching - including BLAST Gene expression informatics Introduction to gene finding 8 Molecular Modeling Drug designing and Chemo-informatics - Acquisition of chemical information - including molecular structures - from databases Visualisation of molecules Simulation of molecular interactions Introduction to industry-standard modeling software Energy Optimization techniques golden section method parabolic interpolation conjugate gradient Raphson genetic algorithm Structure based drug designing locating binding sites in protein structure SMILES- Simplified Molecular Input Line Entry System 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 amp Tools ndash 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 TextsReferences 1 Voet D Voet JG amp Pratt CW Fundamentals of Biochemistry 2nd Edition Wiley 2006 2 Brown TA Genomes 3rd Edition Garland Science 2006 3 Campbell AM amp Heyer LJ Discovering Genomics Proteomics and Bioinformatics 2nd Edition Benjamin Cummings 2007 4 Primrose S amp Twyman R Principles of Gene Manipulation and Genomics 7th Edition Blackwell 2006 5 Glick BR amp Pasternak JJ Molecular Biotechnology 3rd Edition ASM Press 1998

MSGEN-402 IPR amp Biosafety

IPR

1 Introduction to Intellectual Property - Types of IP Patents Trademarks Copyright amp Related Rights Industrial Design Traditional Knowledge Geographical Indications Protection of GMOs IP as a factor in RampD IPs of relevance to Biotechnology and few Case Studies 2 Agreements and Treaties - History of GATT amp TRIPS Agreement Madrid Agreement Hague Agreement WIPO Treaties Budapest Treaty PCT Indian Patent Act 1970 amp 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 ldquoprior artrdquo Patent databases Searching International Databases Country-wise patent searches (USPTO espcenet(EPO) PATENTScope(WIPO) IPO etc)

31 4 Patent filing procedures - National amp PCT filing procedure Time frame and cost Status of the patent applications filed Precautions while patenting ndash disclosurenon-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 ndash in Government of India Definition of GMOs amp 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 ndash International protocols International Activities in Biosafety Capacity Building Biosafety Regulations in India Biological Weapons Biosafety and Ethical Issues

TextsReferences 1 BAREACT Indian Patent Act 1970 Acts amp Rules Universal Law Publishing Co Pvt Ltd 2007 2 Kankanala C Genetic Patent Law amp Strategy 1st Edition Manupatra Information Solution Pvt Ltd 2007


1 History of Human Genetics ndash Pedigrees A Gathering family history Pedigree symbols Construction of pedigrees Presentation of molecular genetic data in

pedigrees B Pedigree analysis of monogenic traits Autosomal inheritance-dominant recessive Sex-linked inheritance- X-

linked recessive dominant Yndashlinked Sex-limited and sex-influenced traits Mitochondrial inheritance MIM number

2 Complications to the basic pedigree patterns I A Non-penetrance variable expressivity pleiotropy onset dominance problem B Anticipation Compound heterozygosity 3 Complications to the basic pedigree patterns II AGenomic 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 BComplex 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 CPolygenic 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 amp epilepsy

4 Genetic mapping of Mendelian and complex characters A Identifying recombinants and non-recombinants in pedigrees Genetic and physical map distances Genetic

markers BMapping of genetic traits Two-point mapping-LOD score analysis Multipoint mapping Homozygosity mapping CGenetic mapping of complex traits Difficulties in mapping Allele sharing methods- affected sib pair analysis

Allelic association Linkage disequilibrium mapping Transmission disequilibrium test 5 Human Genome Mapping ndash A Physical mapping of the human genome Low resolution mapping Cell hybrids mini- and microcells synteny of

genes Radiation hybrid mapping B Human genome mapping Assembly of clone contigs and identifying genes in cloned DNA Integration of

cytogenetic genetic and physical maps C DNA testing Direct and indirect testing (gene tracking) in individuals DNA tests for identity and relationships

including forensic applications 6 Population screening ndash A Ethics organization and advantages Identifying human disease genes BPrinciples and strategies Position-independent and positional cloning Candidate gene approaches Confirming a

candidate gene C Mutation screening testing in animal models Molecular pathology DNomenclature of mutations and their databases Loss of function and gain of function mutations in diseases 7 Molecular pathology ndash A Instability of the human genome and diseases Bpathogenicity associated with repeated sequences C Slipped strand mispairing Unequal crossover and unequal sister chromatid exchange DGene 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 9 Single Gene Disorders (selected disorders) A Introduction to Genetic Metabolic Disorders B Disorders of Metabolism - Amino Acids Carbohydrates Lipids Purine amp Pyrimidines Organic acid Disorders C Thalassaemia disorders Sickle cell anaemia Hemophilia D Huntington disease Myotonic Dystrophy Hereditary Motor and sensory Neuropathy Neurofibromatosis

Marfan syndrome E Cystic fibrosis Inherited Arrythmias and Cardiomyopathies Spinal Muscular Atrophies Duchenne Muscular

Dystrophy 10 Genetic Factors in Common Disorders AGenetic susceptibility in common diseases ndash B Diabetes mellitus Hypertension Coronary Artery Diseases Epilepsies CSchizophrenia Affective disorders Alzheimer Hemochromatosis Venous Thrombosis

33 11 Cancer Genetics A Differentiation between genetic and environmental factors in cancer B Oncogenes Tumor suppressor genes C Genetics of common cancer D Genetic counseling in familial cancers 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 13 Reproductive Genetics A Infertility and Sub-fertility Assisted Reproductive Technologies B Extra embryos Cryo-preservation of Sperms Oocytes amp Embryos 14 Genetic Counseling A Definition Establishing the diagnosis Calculation and Risk estimation B Discussion options communication and support Counseling ndash directive or non-directive outcome of genetic

counseling special problem in genetic counseling 15 Screening for genetic disorders and Prenatal Diagnosis A Screening of those on high risks Carrier testing for Mendelian diseases Neonatal and Adult screening B Prenatal screening and counseling Techniques used in prenatal diagnosis C Laboratory methods used in prenatal diagnosis D Prenatal diagnosis by Non-invasive methods and Future trends in prenatal diagnosis 16 New Approaches to treating disease and Gene therapy A Treating Genetic Disease Therapeutic application of recombinant DNA technology B Regulatory requirements of gene therapy CTechnical aspects methods of gene therapy disease suitable for treatment using gene therapy


1 Plant genomics- Model plants Benefits Plant Genome Databases Applications Genomics of selected Genomes ndash Arabidopsis thaliana Rice

2 Phytohormones - general action

3 Role of phytohormone in - Organogenesis Somatic embryogenesis Root culture Embryo culture Endosperm culture and triploid production Androgenesis Gynogenesis

4 Micropropagation - Methods and stages of clonal propagation Strategies for Virus-free plant production - Commercial micropropagation Acclimatization of tissue cultured plants Photoautotrophic Micropropagation

5 Germplasm conservation- concept of in situ and ex situ conservations of germplasms Cryopreservation- principle Techniques and applications

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

7 Bioreactors-concept types and use in plant tissue culture

8 Genetic manipulation in plants-aGenetic engineering of crops Commercial status of transgenic plants Herbicide resistance glyphosate sulfonyl urea phosphinothricin Pest resistance Bt toxin synthetic Bt toxin Protease inhibitor lectins α-amylase inhibitor nematode resistance Genetic engineering for male sterility-Barnase-Barstar Delay of fruit ripening polygalacturanase ACC synthase ACC oxidase Improving and altering the composition of starch and plant oils Golden rice for β-carotene accumulation Production of antibodies and pharmaceuticals in plants Bio-safety concerns of transgenic plants

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 eg 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

13 Transgenic plants for phyto-remediation

14 Global issues and biosafety of transgenic plants

MSGEN(MMG)-403 Microbial Molecular Genetics Genome and Genetic exchange

1 GenomeBiology and Evolution of the Mycobacterium tuberculosis Complex Pseudomonas aeruginosa Candida albicans Leishmania donovani Adenovirus HIV

2 Plasmids Transposons and their Applications in Mycobacteria Pseudomonas aeruginosa Candida albicans Leishmania donovani Adenovirus HIV

3 General Recombination and DNA Transfer by conjugation and transduction in Mycobacteria Pseudomonas aeruginosa 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 ndash physical and genetic map Molecular markers and their application RFLP RAPD Microsatellite Minisatellite markers SNP marker DNA fingerprinting 2 Gene transfer methods in Animals ndash Microinjection Embryonic Stem cell gene transfer Retrovirus amp Gene transfer 3 Transgenic Animals Mice Cow Pig Goat Bird Insect 4 Animal cloning Techniques benefits 5 Xenotransplantation in Human Choosing donors Barriers of xenotransplantation techniques of xenotransplantation 6 Current development in animal Biotechnology -Impacts of Genomics Agricultural application of transgenic animals Live stock cloning new vaccine technologies 7 Animal Reproductive biotechnology -basic anatomy of cattle reproduction the estrus cycle factors affecting cattle reproduction 8 Assisted reproductive Biotechnology Estrus synchronization-using prostaglandin GnRH-PGF based synchronization 9 Physiological basis of superovulation- factors influencing superovulatory responses Hormonal induction of superovulatory responses in farm animals 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 12 Embryo sexing

MGM-404 Comprehensive Viva-voce

MSGEN-405 Project work based on Bioinformatics application

MGM-406 Dissertation (Independent Project Work based on Spl Paper)

36

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) ResultsObservations (supported by figurestables etc as required) e) Discussion of the ResultsObservations f) Summary and g) References

2

FIRST SEMESTER Paper (Theoretical) 5 Papers = 500 Marks


MSGEN-101 Mendelian amp Classical Genetics 100 3 42

MSGEN-102 Cell Biology amp Cyto-Genetics 100 3 42

MSGEN-103 Molecular Biology 100 3 42

MSGEN-104 Biophysics and Biochemistry 100 3 42

MSGEN-105 Genetics of Organelles 100 3 42


MSGEN-106 Lab on Microscopy amp Instrumentation 100 2 40 hrs

MSGEN-107 Lab on Basic Cyto-Genetics amp Cell Culture Techniques (Plant amp Animal)

100 2 40 hrs

MSGEN-108 Lab on Molecular Biology ndash Basic Techniques

100 2 40 hrs

MSGEN-109 Lab on Biophysical amp Biochemical Techniques

100 2 40 hrs


Total Credits = 25

SECOND SEMESTER Paper (Theoretical) 5 Papers = 500 Marks


MSGEN-201 Genetics of Model Organisms 100 3 42

MSGEN-202 Bio-Statistics amp Population Genetics 100 3 42

MSGEN-203 Developmental Genetics 100 3 42

MSGEN-204 Immuno-Genetics 100 3 42

MSGEN-205 Genetic Biodiversity and Taxonomy 100 3 42


MSGEN-206 Lab on Life Cycle Studies (Model

organisms) 100 2 40 hrs

MSGEN-207 Lab on Computer Application 100 2 40 hrs

MSGEN-208 Lab on Developmental Genetics amp Genetic Toxicity Testing

100 2 40 hrs

MSGEN-209 Lab on Immunological Techniques 100 2 40 hrs


3

Total Credits = 25

THIRD SEMESTER









100 3 42








100 2 40 hrs

Total Credits = 25

4



Classes Semester


100 3 42




100 3 42




100

100

100

2

2

2

40

40

40

Total Credits = 15




FIRST SEMESTER















TextReferences









PRACTICALS




Animal) Techniques









Seminar



SECOND SEMESTER







14





16


17

PRACTICALS





Accessories


Document Management


Power of Excel







10 Programming C










19

THIRD SEMESTER







Shuttle plasmids



















20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36


3

Total Credits = 25

THIRD SEMESTER









100 3 42








100 2 40 hrs

Total Credits = 25

4



Classes Semester


100 3 42




100 3 42




100

100

100

2

2

2

40

40

40

Total Credits = 15




FIRST SEMESTER















TextReferences









PRACTICALS




Animal) Techniques









Seminar



SECOND SEMESTER







14





16


17

PRACTICALS





Accessories


Document Management


Power of Excel







10 Programming C










19

THIRD SEMESTER







Shuttle plasmids



















20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36


4



Classes Semester


100 3 42




100 3 42




100

100

100

2

2

2

40

40

40

Total Credits = 15




FIRST SEMESTER















TextReferences









PRACTICALS




Animal) Techniques









Seminar



SECOND SEMESTER







14





16


17

PRACTICALS





Accessories


Document Management


Power of Excel







10 Programming C










19

THIRD SEMESTER







Shuttle plasmids



















20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36




FIRST SEMESTER















TextReferences









PRACTICALS




Animal) Techniques









Seminar



SECOND SEMESTER







14





16


17

PRACTICALS





Accessories


Document Management


Power of Excel







10 Programming C










19

THIRD SEMESTER







Shuttle plasmids



















20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36














TextReferences









PRACTICALS




Animal) Techniques









Seminar



SECOND SEMESTER







14





16


17

PRACTICALS





Accessories


Document Management


Power of Excel







10 Programming C










19

THIRD SEMESTER







Shuttle plasmids



















20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36








PRACTICALS




Animal) Techniques









Seminar



SECOND SEMESTER







14





16


17

PRACTICALS





Accessories


Document Management


Power of Excel







10 Programming C










19

THIRD SEMESTER







Shuttle plasmids



















20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36








Seminar



SECOND SEMESTER







14





16


17

PRACTICALS





Accessories


Document Management


Power of Excel







10 Programming C










19

THIRD SEMESTER







Shuttle plasmids



















20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36




SECOND SEMESTER







14





16


17

PRACTICALS





Accessories


Document Management


Power of Excel







10 Programming C










19

THIRD SEMESTER







Shuttle plasmids



















20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36






14





16


17

PRACTICALS





Accessories


Document Management


Power of Excel







10 Programming C










19

THIRD SEMESTER







Shuttle plasmids



















20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36





16


17

PRACTICALS





Accessories


Document Management


Power of Excel







10 Programming C










19

THIRD SEMESTER







Shuttle plasmids



















20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36


17

PRACTICALS





Accessories


Document Management


Power of Excel







10 Programming C










19

THIRD SEMESTER







Shuttle plasmids



















20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36








19

THIRD SEMESTER







Shuttle plasmids



















20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36


20



















24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36













24



25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36


25






PRACTICALS







7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36






7 Southern analyses














28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36






28














FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36



FOURTH SEMESTER





IPR
































34


















Genetic Strategies





35





36




IPR
































34


















Genetic Strategies





35





36
































34


















Genetic Strategies





35





36


35





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