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Structure of B. Sc (Biological Sciences) program under CBCS
DISCIPLINE:: GENETICS
SEMESTER
Semester1
Semester2
Semester 3
Semester 4
Semester 5
Semester 6
Semester 7
Semester 8
PAPER
Paper I
Paper II
Paper III
Paper IV
Paper V
Paper VI
or
Paper VI
or
Paper VI
Paper VII
COMP/ELEC
Compulsory
Compulsory
Compulsory
Compulsory
Compulsory
Elective A
CODE
DSC 2 A
DSC 2 B
DSC 2 C
DSC 2 D
DSE 2 E
DSE 2 F
Elective C
Compulsory
DSE 2 G
Paper VIII
or
Paper VIII
Elective A
DSE 2 H
Elective B
Elective B
PAPER TITLE
General Genetics
Molecular Genetics
Recombinant DNA Technology
Statistical Methods in Genetics
Population Genetics
Human Genetics
or
Animal Genetics & Breeding
or
Plant Genetics & Breeding
Genome Informatics
Genetic Diagnostic Techniques
or
DNA Cloning Techniques
Semester I
DSC 2 A (Paper I): General Genetics
Unit 1: Mendelian Genetics and Extensions
1.1 Mendelian Principles of inheritance - Law of segregation, Law of independent
assortment; Chromosome theory of inheritance.
1.2 Incomplete dominance and codominance; Multiple alleles, Lethal alleles, Pleiotropy,
Penetrance and Expressivity;
1.3 Two gene interactions – Epistatic, nonepistatic interactions; Polygenic inheritance –
continuous variation, genetic variance and heritability, QTL .
1.4 Genes and environment –norm of reaction, phenocopies, developmental noise
Unit 2 Sex Linked Inheritance and Sex Determination
2.1 Sex Linked Inheritance - Sex linked inheritance in drosophila and human; Sex limited and
Sex influenced inheritance
2.2 Sex Determination - Sex determination in drosophila – genic balance theory;
2.3 Sex determination in eukaryotes –heterogametic, homogametic, haplodiploidy, role of
environmental factors, mosaics, gynandromorphs,
2.4 sex determination in melandrium; Sex determination in mammals- human Y
chromosome
Unit 3 Extrachromosomal Inheritance
3.1 Mitochondrial inheritance (petite mutations);
3.2 Chloroplast inheritance (Variegation in Four o’clock plant);
3.3 Maternal inheritance-shell coiling in snail, ephestia pigmentation;
3.4 Infective heredity- symbionts in Drosophila,Kappa particles in Paramecium.
Unit 4: Linkage, crossing over and chromosome mapping
4.1 Linkage and chromosome mapping in eukaryotes – cytological basis of crossingover;
recombination frequency, two factor and three factor crosses; interference and
coincidence; Mitotic recombination; tetrad analysis in chlamydomonas.
4.2 Linkage and chromosome mapping in prokaryotes – bacteria and bacteriophages –
transformation, transduction, conjugation; gene mapping in bacteria.
4.3 Genetic definition of gene - Complementation test, limitations of cis-trans test,
intragenic complementation,rII locus of phage T4,concept of cistron
Unit 5: Cell Division - Variation in Chromosome number and structure
5.1 Mitosis and meiosis - Mitotic and meiotic transmission of chromosomes
5.2 Specialized chromosomes - Lampbrush chromosomes. Polytene chromosomes:
Supernumerary chromosomes.
5.3 Variation in chromosome structure - Deletion, Duplication, Inversion, Translocation,
Position effect
5.4 Variation in chromosome number - Euploidy and Aneuploidy
Practicals:
1. Mendel’s laws through seed ratios & Drosophila mutants.
2. Statistical tests in genetic analysis - application of laws of probability (product rule,
sum rule, binomial probability); chi square test and its application in the analysis of
genetic data.
3. Study of linkage, recombination, chromosome mapping using test cross data.
4. Pedigree analysis for dominant and recessive autosomal and sex linked traits.
5. Study of human genetic traits: Sickle cell anemia, XerodermaPigmentosum, Albinism,
red-green Colour blindness, Widow’s peak, Rolling of tongue, Hitchhiker’s thumb and
Attached ear lobe.
6. Incomplete dominance and gene interaction through seed ratios
7. Blood Typing: ABO groups & Rh factor.
8. Study of aneuploidy: Down’s, Klinefelter’s and Turner’s syndromes.
9. Permanent Slides showing Translocation Ring, Laggards and Inversion Bridge.
10. Mitosis & Meiosis through temporary squash preparation.
11. Squash preparation of salivary glands to observe polytene chromosomes.
12.Smear technique to demonstrate sex chromatinin buccal epithelialcells.
Suggested Readings
1. Gardner, E.J., Simmons, M.J., Snustad, D.P. (1991). Principles of Genetics, John Wiley
& sons, India. 8th edition.
2. Snustad, D.P. and Simmons, M.J. (2010). Principles of Genetics, John Wiley & Sons
Inc., India. 5th edition.
3. Klug, W.S., Cummings, M.R., Spencer, C.A. (2012). Concepts of Genetics. Benjamin
Cummings, U.S.A. 10th edition.
4. Griffiths, A.J.F., Wessler, S.R., Carroll, S.B., Doebley, J. (2010). Introduction to Genetic
Analysis. W. H. Freeman and Co., U.S.A. 10th edition.
Semester - II
DSC 2 B (Paper – II): Molecular Genetics
Unit 1: Nucleic acids – Structure and Organization
1.1
DNA as carrier of genetic information Griffith’s, Hershey & Chase, Avery, McLeod & McCarty, Fraenkel-Conrat’s experiment.
1.2 Structure of DNA and RNA Genetic Material: DNA Structure - Watson and Crick model,
Salient features of double helix, Types of DNA;
1.3 RNA Structure-mRNA, tRNA and rRNA
Unit 2 Genome organization
2.1 Organization of DNA: denaturation and renaturation, cot curves;
2.2 Prokaryotes, Viruses, Eukaryotes genome organization;
2.3 Organelle DNA -mitochondria and chloroplast DNA;
2.4 Transposable elements – prokaryotic and eukaryotic.
2.5 Organization of DNA in Chromosomes - Nucleosome – Chromatin structure Euchromatin, Heterochromatin -Constitutive and Facultative heterochromatin.
Unit 3: DNA replication, Mutation, Recombination & Repair
3.1DNA replication - General principles –bidirectional, Semiconservative and semi
discontinuous replication, RNA priming;
3.2DNA replicaton - Various models of DNA replication, including rolling circle, θ (theta)
mode of replication, replication of linear ds-DNA, replication of the 5’end of linear
chromosome; Enzymes involved in DNA replication.
3.3DNA Mutation – types of mutation; molecular basis of mutations; mutagens –
physical and chemical agents; Detection of mutations – ClB method
3.4DNA Recombination & Repair: enzymes involved in recombination-Holliday model;
types of DNA repair
Unit 4: Transcription & Translation
4.1Transcription in prokaryotes; Transcription in eukaryotes
4.2Processing and modification of RNA- Split genes - spliceosome machinery, splicing
pathways; eukaryotic mRNA processing(5’ cap, 3’ poly A tail); Ribozymes, exon
shuffling; RNA editing and mRNA transport.
4.3Translation - Ribosome structure and assembly, mRNA; Charging of tRNA, aminoacyl
tRNA synthetases; genetic code - key experiments establishing Genetic code
(deciphering & salient features- wobble hypothesis); central dogma
4.4Translation - Various steps in protein synthesis, proteins involved in initiation,
elongation and termination of polypeptides; Post-translational modifications of
proteins.
Unit 5: Regulation of Gene Expression
5.1 Regulation of gene expression in prokarytoes - principles of transcriptional
regulation; Prokaryotes - Regulation of lactose metabolism and tryptophan synthesis
in E.coli.
5.2 Regulation of gene expression in eukaryotes –heterochromatin, euchromatin,
chromatin remodeling: regulation of galactose metabolism genes in yeast
5.3 DNA binding activators and co-activators, repressors, enhancers and silencers; DNA
binding domains, transcription factors, heat shock proteins, steroids and peptide
hormones; regulatory RNAs, riboswitches
5.4 Post-transcription gene silencing by RNAinterference
Practicals:
1. Preparation of LB medium and raising E. coli.
2. Isolation of genomic DNA from E. coli.
3. DNA isolation from cauliflower head.
4.Ultraviolet absorption spectrum of DNA and RNA
5.Determination of DNA and RNA concentration by A260nm
6.Determination of melting temperature and GC content of DNA.
7. DNA estimation by diphenylamine reagent.
8 Isolation of total RNA from yeast cells
9. Estimation of RNA by Orcinol method.
10. Separation of nucleotide based by chromatography.
Suggested Readings
1. Watson J.D., Baker, T.A., Bell, S.P., Gann, A., Levine, M., Losick, R. (2007). Molecular
Biology of the Gene, Pearson Benjamin Cummings, CSHL Press, New York, U.S.A. 6th
edition.
2. Snustad, D.P. and Simmons, M.J. (2010). Principles of Genetics. John Wiley and Sons
Inc., U.S.A. 5th edition.
3. Klug, W.S., Cummings, M.R., Spencer, C.A. (2009). Concepts of Genetics. Benjamin
Cummings. U.S.A. 9th edition.
4. Russell, P. J. (2010). Genetics- A Molecular Approach. Benjamin Cummings, U.S.A. 3rd
edition.
5. Griffiths, A.J.F., Wessler, S.R., Carroll, S.B., Doebley, J. (2010). Introduction to Genetic
Analysis. W. H. Freeman and Co., U.S.A. 10th edition.
Semester - III
DSC 2 C (Paper- III): Recombinant DNA Technology
Unit 1 Introduction to recombinant DNA technology
1.1 Restriction endonucleases and other enzymes used in manipulating DNA molecules
1.2 Cloning vectors for prokaryotes and eukaryotes: Plasmids and bacteriophages as
vectors for gene cloning. Cloning vectors based on E. coli plasmids, pBR322, pUC8,
pGEM3Z. Cloning vectors based on M13 and λ bacteriophage Vectors for yeast, higher
plants and animals.
1.3 Joining of DNA fragments: Ligation of DNA molecules. DNA ligase, sticky ends, blunt
ends, linkers and adapters. Synthetic oligonucleotides, synthesis and use.
1.4 Generation of genomic and cDNA libraries; DNA markers.
Unit 2 Gene transfer methods and selection for recombinants
2.1 Selection for transformed cells - Uptake of DNA by cells, preparation of competent cells.
2.2 Identification for recombinants - insertional inactivation, blue-white selection.
2.3 Introduction of phage DNA into bacterial cells. Identification of recombinant phages.
Introduction of DNA into animal cells, Introduction of DNA into plant cells
2.4 Methods for clone identification: The problem of selection, direct selection, marker
rescue. Gene libraries, identification of a clone from gene library, colony and plaque
hybridization probing, methods based on detection of the translation product of the
cloned gene.
Unit 3 PCR and DNA sequencing
3.1 Polymerase chain reaction: Fundamentals of polymerase chain reaction,
3.2 designing primers for PCR. Studying PCR products, Cloning PCR products. Real time PCR.
3.3 DNA sequencing: DNA sequencing by Sanger’s method, modifications based on Sanger’s
method. Automated DNA sequencing. Pyrosequencing.
Unit 4 Expression of Cloned genes
4.1Expression of cloned genes - Vectors for expression of foreign genes in E. coli,
4.2 cassettes and gene fusions.
4.3Challenges in producing recombinant protein in E. coli.
4.4Production of recombinant protein by eukaryotic cells. Fusion tags and their role in
purification of recombinant proteins.
4.5Site–directed mutagenesis and protein engineering.
Unit 5 Applications of genetic engineering
5.1Applications in production of recombinant pharmaceuticals - insulin, human growth
hormone, factor VIII. Recombinant vaccines.
5.2 Genomics - organization of genomes, mapping and sequencing genomes.
5.3 Analysis of transcriptome- microarrays, EST
5.4 Proteomics- structural and functional proteomics
Practicals
1. Isolation of plasmid DNA from E. coli cells.
2. Digestion of plasmid DNA with restriction enzymes.
3.Estimation of size of a DNA fragment after electrophoresis using DNA markers
4. Construction of restriction digestion maps from data provided
5. Amplification of a DNA fragment by PCR.
6. Transformation of E. coli cells with plasmid DNA.
7. Hyper expression of poly histidine-tagged recombinant protein and purification using
Ni-affinity resin.
8. Complementation of beta−galactosidase for Blue and White selection.
9. Recovery of DNA from low-melting temperature agarose gel
10. SDS gel electrophoresis of proteins
11. Southern blotting
12. Western blotting.
Suggested Readings
1. Gene Cloning and DNA Analysis (2010) 6th ed., Brown, T.A., Wiley-Blackwell
publishing(Oxford, UK), ISBN: 978-1-4051-8173-0.
2. Principles of Gene Manipulation and Genomics (2006) 7th ed., Primrose, S.B., and
Twyman, R. M., Blackwell publishing (Oxford, UK) ISBN:13: 978-1-4051-3544-3.
3. Molecular Biotechnology: Principles and Applications of Recombinant DNA (2010) 4th
ed., Glick B.R., Pasternak, J.J. and Patten, C.L., ASM Press (Washington DC), ISBN: 978-155581-498-4 (HC).
Semester - IV
DSC 2 D (Paper- IV): Statistical Methods in Genetics
Unit 1 Descriptive Statistics
1.1 Classification and tabulation of data – frequency distribution, graphical representation
of data, histogram, frequency polygon, frequency curve.
1.2 Measures of Central tendency – definition and calculation of arithmetic mean,
geometric mean, harmonic mean, median quantiles and mode in grouped and
ungrouped data
1.3Measures of Dispersion - definition and calculation of range, quartile deviation, mean
deviation, standard deviation and variance, coefficient of variation.
Unit 2 Elementary Probability
2.1 Mathematical definition of probability of an event, Use of permutations and
combinations in calculations of Probability
2.2 Conditional probability, Additive and Multiplication law of Probability, Random
Variables, Mathematical expectation and variances
2.3 Probability Distributions: Binomial, Poisson and normal distributions.
Unit 3 Correlation and Regression
3.1Correlation and Regression — Relationship between variables
3.2Covariance, Karl-Pearson's Correlation Coefficient, Spearman's rank Correlation
Coefficient,
3.3 Least square technique for regression lines,
3.4 Regression Coefficients, Relationship between Correlation analysis and Regression
Analysis.
Unit 4 Statistical Inference
4.1 Hypothesis Testing — Sample, Population, Statistics and Parameters,
4.2 Basic principles of hypothesis testing: test, critical region, type I error and type II
error, level of significance. Null Hypothesis, Level of significance,
4.3 Chi–square, ‘t’ and ‘F’ variates - Applications in testing of hypothesis.
Unit 5 Analysis of Variance
5.1 Analysis of variance for one-way classified data,
5.2 Analysis of variance for two-way classified data with one observation for cell,
analysis of variance
5.3 Analysis of variance for two-way classified data with one observation for cell,
analysis of variance for two-way classified data with multiple but equal number of
observations per cell.
Practicals
1.Frequency distribution
2.Various types of graphs
3.Mean, geometric mean, harmonic mean
4.Median, quartiles deviation, mean deviation
5.Standard deviation, variance and coefficient of varition
6.Testing of hypotheses regarding population mean
7.Testing of hypotheses about the difference between population means
8.Chi-square test
9.Testing of Correlation Coefficient
10.Fitting of simple linear regression
11.One-way ANOVA
12.Two-way ANOVA
Suggested Readings
1. Fowler, J., Cohen, L. and Jarvis, P. (1998). Practical Statistics for Field Biology. John
Wiley and Sons, 2nd ed. .
2. Bland, M. (2006). An Introduction to Medical Statistics. Oxford University Press, 3rd
ed.
3. Finney, D.J. (1980). Statistics for Biologists. Chapman and Hall Ltd.
4. Wayne, W, Daniel (1999). Biostatistics: A Foundation for Analysis in Health
Sciences. John Wiley and Sons, 7th ed.
Semester – V
DSC 2 E (Paper V): Population Genetics
Unit 1 Hardy-Weinberg Equilibrium
1.1 Allele frequencies - deriving genotypic & allelic frequencies, deriving allelic frequencies
from molecular data, changes in allele frequencies.
1.2 Polymorphism - phenotypic & genotypic polymorphisms, transient polymorphism,
balanced polymorphisms
1.3 Random & Non-random mating – positive & negative assortative mating, role in
population size & change in gene frequency.
1.4 Hardy-Weinberg method & its applications – calculating allelic frequencies, assumptions
of Hardy-Weinberg equilibrium, proof of Hardy-Weinberg equilibrium, Generation time,
testing for fit to Hardy-Weinberg equilibrium
Unit 2 Factors affecting Hardy-Weinberg Equilibrium
2.1 Inbreeding & outbreeding - inbreeding co-efficient, genotype frequencies under
inbreeding, uses & effects of inbreeding in farm animals, genetic consequences of
inbreeding, reasons for inbreeding.
2.2 Random Genetic drift – definition, its effects in small & large populations, bottlenecking
& founder effect, genetic drift simulation, genetic drift vs selection.
2.3 Genetic equilibrium – definition, conditions for its stability, deviation of it (evolution).
2.4 Selection – overview, types & subtypes, negative & positive selections, patterns of
selection (stabilizing, disruptive, directional, balancing), mechanisms of selection
(disassortative sexual selection, frequency dependent selection), overdominance,
natural selection, artificial selection, ecological selection.
Unit 3 Evolution
3.1 Models for Population Genetics – deterministic & stochastic models.
3.2 Synthetic theory of Evolution – Lamarckian evolution theory, Darwin’s theory of
evolution, Neo- Darwinism, modern synthesis theory of evolution, Macroevolution &
Microevolution.
3.3 Human and great ape genetic history – Human-Ape comparisons.
3.4 Evolution of Genetic Diversity - natural variation, sources of genetic variation:
chromosomes & crossing over, SNPs, mutation, deletion & rearrangements,
recombination, transgenic, genetic drift & gene flow.
Unit 4 Molecular evolution and phylogenetic tree
4.1 Molecular Evolution – detecting selection at molecular level, rates of molecular
evolution, Weak selection on non–coding gene features.
4.2 Evolution of eukaryotic genome structure, New genes, new functions: Gene family
evolution and phylogenetics, Gene genealogies, causes of change in allele frequency,
molecular study of phylogeny, neutral theory of molecular evolution, Gene function and
molecular evolution.
Unit 5 Speciation and Evolution tree
5.1 Genetics of Speciation - Patterns and processes of speciation.
5.2 Evolution of Mitochondrial genome & the origin of Eukaryotic cells;
5.3 Evolution of Eukaryotic Nuclear genome, genome duplication & large-scale
chromosomal alterations,
Practicals:
1. PTC testing in a population and calculation of allele and genotype frequencies
2. Calculation of change in gene frequencies.
3. Experiments on Genetic Drift: a) Population size b) Sampling Error
4. Studies on Homology Analogy
5. Estimation of gene and genotype frequencies;
6. Estimation of effect of mutation, migration and selection on equilibrium;
7. Equilibrium in sex linked genes;
8. Estimation of effective population size,
9.Estimation of rate of inbreeding, inbreeding co-efficient, path coefficient.
Suggested Readings:
1 T. A. Brown, 1999. Genomes, John Wiley & Sons (Asia) PTE Ltd.
2 Scott Freeman & Jon C. Herron, 2001. Evolutionary Analysis (2nd Edition), Prentice
Hall.
3 Falconer & Mackay, 1996. Introduction to Quantitative Genetics (IV Edition),
Longman.
4 David P. Mindell, 1997. Avian Molecular Evolution & Systematics, Academic Press.
5 Derek A. Roff, 1997. Evolutionary Quantitative Genetics, Chapman & Hall.
6 R.S.Singh & C. Krimbas, 2000. Evolutionary Genetics- From Molecules to Morphology,
Cambridge University Press.
7 Peter Donnelly & Simon Tavare, 1997. Progress in Population Genetics & Human
Evolution (Vol. 87), Springer.
8 William S. Klug & Michael R. Cummings, 2000. Concepts of Genetics (Sixth Edition),
Prentice Hall.
9. Monre W. Strickberger, 1985. Genetics (Third Edition), Prentice Hall of India.
Semester - V
DSC 2 F (Paper VI): Elective A- Human Genetics
Unit I Pattern of inheritance and pedigree analysis
1.1 Introduction to Human Genetics: growth of human genetics; levels of genetics.
1.2 Pattern of inheritance: Autosomal Dominant, Autosomal Recessive, X-linked
Dominant, X-linked Recessive, Y-linked, sex limited inheritance, sex influenced
inheritance, X inactivation, Multifactorial inheritance, mitochondrial inheritance,
imprinting
1.3 Pedigree analysis of some genetic disorders: Haemophilia, Color blindness,
Duchenne Muscular Dystrophy (DMD), achondroplasia and PKU.
Unit 2 Human chromosomes
2.1 Structure and composition of the human chromosome: basic structure of DNA;
molecular structure and organisation.
2.2 Classification of Human chromosomes: Paris nomenclature / ISCN; methods of
studying chromosomes; identification of individual chromosomes; Flow Karyotyping
(Quantification on DNA of individual chromosomes); FACS – Fluorescence activated
cell sorter).
Unit 3 Human Chromosomal abnormalities
3.1 Numerical abnormalities (somies; ploidies; mosaic; chimera; syndromes.);
3.2 Structural abnormalities: Translocations; Deletions; Duplications; Inversion;
isochromosomes; Ring chromosomes; causes for genetic abnormalities- meiotic and
mitotic nondisjunction; uniparental disomy; mutations; single gene disorders.
Unit 4 Genetics of cancer and molecular genetic techniques for diagnosis
4.1 Genetics of Cancer: introduction, characteristics of cancer cells, origin of cancer
cells, genes associated with cancer, environmental causes of cancer, human genome
datatailor diagnosis and treatment.
4.2 Molecular genetic techniques used in genetic diagnosis: Blotting techniques –
Southern, Northern and Western, PCR / RFLP, FISH, DNA sequencing & DNA
fingerprinting.
4.3 Dermatoglyphics and its application in the diagnosis of human genetic disorders
Principles of FISH, RFLP & DNA finger printing and their uses in human genetics
Unit 5 Applied Human Genetics
5.1 Reproductive technologies: infertility and subfertility, assisted reproductive
technologies (IUI, surrogate motherhood, IVF, GZIT, ZIFT), preimplantation genetic
diagnosis.
5.2 Genetics and Society : (i) Human genome project : (ii) Forensic science (iii) DNA
finger printing application (iv) Gene therapy (v) Eugenics. vi) Stem cell research.
5.3 Prenatal Diagnosis: Definition: Various procedures - Amniocentesis, Chorionic villus
sampling, Ultrasonography and Fetoscopy.
5.4 Genetic Counselling.
Practicals:
1. Sterilization techniques for leukocyte culture
2. Inoculation and Culture of human leucocytes
3. Preparation of metaphase plates and their staining and analysis
4. G- banding of metaphase plates and their analysis
5. Human karyotyping – numericals on chromosome number.
6. Barr Body analysis.
7. Micrometric analysis of chromosomes.
8. Camera-lucida drawing of chromosomes.
9. Dermatoglyphics
10. Working out of Genetic problems
11. Sister Chromatid exchange analysis from peripheral blood
Suggested Readings
1. Cummings ML, Human Genetics, CENGAGE Learning, Stamford
2. Kothari ML, Mehta LA and Roychoudhury SS, Essentials of Human Genetics, Oxford
University Press, India.
3. Hoelzel AR, Molecular Genetic Analysis of Populations ,Oxford University Press, India.
4. Gersen SL and Keagle MB, The Principles of Clinical Cytogenetics, Humana Press, Totowa,
New Jersey
5. Turnpenny P and Ellard S, Emery’s Elements of Medical Genetics, Elsevier, UK
Semester - V
DSC 2 F (Paper VI): Elective B - Animal Genetics & Breeding
Unit 1 Animal Genetics
1.1 Animal cytogenetics
1.2 Application of immunogenetics in farm animals –major histocompatiblecomplex,
genetics of variants and their applications- Ir genes and concepts of disease resistance
and its significance.
1.3 Reproductive Genetics – genetics of sex determination & sexual differentiation
1.4 Assisted Reproductive technologies - artificial insemination, cryo-preservation of oocyte,
sperm & embryo, in vitro fertilization, embryo transfer, ICSI, Sperm sexing
Unit 2 Animal Genomes and marker assisted selection
2.1 Animal genome organization
2.2 Physical and genetic maps
2.3 Genome maps of live stock
2.4 Molecular markers and their application - Candidate gene approach, Marker Assisted
Selection basics, QTL mapping and its application in animal breeding
Unit 3 Transgenic animals
3.1 Transgenesis and methods of gene transfer
3.2 Animal cloning
3.3 Applications of transgenic animals – livestock and pharming
Unit 4 Animal Breeding
4.1 Selection methods Type of selection and their genetic consequences. Response to
selection and its prediction and improvement of response to selection.
4.2 Mating Systems -Genetic aspects and consequences of various mating systems.
Application of various mating system in animal improvement. Selection for general and
specific combining ability.
4.3 Inbreeding and crossbreeding for livestock improvement-Development and uses of
inbreed lines- heterosis: genetic aspects, exploitation, crossbreeding systems.
4.4 Quantitative genetics-gene effects, population mean and variance and its
partitioning, biometric relations between relatives.
Unit 5. Conservation of Animal Genetic Resources
5.1 Methodology for molecular genetic characertization, diversity analysis and
relationship among the breeds.
5.2 Conservation of Animal Genetic Resources and their sustainable utilization –
5.3Cryopreservation and Cryoprotection and gamete banking
Practicals
1. Identification of animals: identification methods; Record keeping: Maintenance of
history sheets and other registers for recording information on various species.
2. Conversion of information from different registers and history sheets for electronic data
storage, analysis and presentation. Use of computer packages for data handling.
3. Selection of animals on the basis of individual, pedigree, progeny and other information.
Appraisal of sire summaries.
4. Rectal palpation for checking the condition of reproductive organs, heat detection and
pregnancy diagnosis.
5. Insemination of buffalo, cattle, sheep, goats and poultry.
6. Semen collection from bulls, its evaluation, dilution, preservation and storage.
7. Biochemical polymorphism analyses – blood groups, transferrins, milk proteins.
8. DNA fingerprinting – isolation, quantification and analysis of DNA from blood
9. Estimation of inbreeding and relationship
10. Laboratory animal species – mice, rat, guinea pig, rabbit, dog and monkey –breeding
methods
Suggested Reading
1. Buchanan, Clutter, Northcutt and Pomp. 1993. Animal Breeding: Principles and
Applications - 4th Edition
2. VanVleck, L.D., E.J. Pollak, E.A.B. Oltenacu. 1987. Genetics for the Animal Sciences
Semester - V
DSC 2 F (Paper VI): Elective C - Plant Genetics & Breeding
Unit 1 Plant Genetic Engineering
1.1 Plant transformation vectors -Ti-plasmid and viral vectors,
1.2 Genetic transformation - Plant transformation by Agrobacterium sp., and in planta
transformation, direct gene transfer methods;
1.3 Transgenic plants – genetic engineering approaches to drought tolerance, salt
tolerance and protein quality in field crops.
Unit 2 Plant Biotechnology – In vitro culture techniques
2.1 Callus culture, cell suspension culture
2.2 Protoplast cultures
2.3 Embryo rescue
2.4 Somaclonal variations
2.5 Micropropagation
Unit 3 Plant Breeding
3.1Reproductive systems in major crop plants.
3.2Breeding self-pollinated crops: introduction, mass selection, pure line selection;
hybridization, pedigree method, bulk method and backcross technique.
3.3Breeding cross-pollinated crops: introduction, mass selection, recurrent selection,
development and evaluation of inbred lines, development of hybrids, synthetic and
composite populations.
3.4 Application of biotechnology in plant breeding.
Unit 4 Biodiversity and Plant Genetic Resources
4.1Principles and strategies of germplasm collection,
4.2Seed banks. Mechanism of gene banking, maintenance, evaluation and conservation.
4.3Utilization of genetic resources in crop research and plant breeding.
Unit 5 Plant Genomes
5.1 Plant genome – genome size and complexity
5.2 Genome mapping and use of molecular markers in plant breeding
5.3 Strategies for mapping genes of agronomic traits in plants – mapping QTL, map
based cloning of plant genes.
Practicals:
1. Introduction to aseptic techniques, autoclaving, sterilization, use of laminar flow and
fume hoods.
2. Media preparation. Storage and weighing of chemicals, preparation of stock-solutions,
adjusting pH, making dilutions.
3. Callus formation and regeneration from plant material.
4. Descriptive study of floral biology,
5. Scientific names and chromosome number of important field crops.
6. Selfing and crossing techniques in self and cross-pollinated crops.
7. DNA fingerprinting using PCR technique
8. Micropropagation of tobacco plant by leaf disc culture.
9. Agrobacterium mediated plant transformation
10. Insertion of gene into appropriate vector.
Suggested Readings
1. Khan, M. A. and M. Ahmad. 2008. Plant Breeding. Daya Publishing House, New Delhi,
India.
2. Sleper, D. A. and J.M. Poehlman. 2006. Breeding Field Crops. 5th ed. Iowa State
University Press, Ames, USA.
3. Chahal, G.S. and S.S. Gosal. 2003. Principles and Procedures of Plant Breeding. Narosa
Publishing House New Delhi India.
4. Singh, B. D. 2003. Plant Breeding: Principles and Methods. Kalyani Publishers, New
Delhi, India.
5. Singh, P. 2003. Essentials of Plant Breeding. Kalyani Publishers, New Delhi, India.
Semester – VI
DSC 2 G (Paper VII): Genome Informatics
Unit 1 Introduction to Genome Informatics
1.1 Computer fundamentals – information networks, internet, Genome net.
1.2 Programming languages in genome informatics – introduction to linux/unix
operating systems, java, xml, bioperl script languages, DBMS, SQL
1.3 Scope of genome informatics - genomics, proteomics, genome projects, genome
analysis
Unit 2 Biological databases and data retrieval
2.1 Introduction to biological databases - primary, secondary and composite databases,
NCBI,
2.2 Nucleic acid databases (GenBank, EMBL, DDBJ, NDB);
2.3 Protein databases (PIR, Swiss-Prot,TrEMBL, PDB); protein sequence motif databases
(PFAM, PROSITE)
2.4 Metabolic pathway database (KEGG, EcoCyc, and MetaCyc),
2.5 Small molecule databases (PubChem, Drug Bank, ZINC, CSD).
Unit 3 Sequence Analysis
3.1 Sequence analysis programs – pairwise alignment, multiple sequence alignment
3.2 Database searching - FASTA, BLAST
3.3 Concept of evolutionary trees - Construction of phylogenetic tree, dendrograms.
Unit 4
Structural biology & Structural databases
4.1 nucleic acid structures – RNA folding, RNA loops, Conformational study, various
ribose ring conformations
4.2 Protien – protein interactions – protein ligand interactions, DNA binding proteins,
RNA binding proteins, Ramachandran plot
4.3 structural databases: protein data bank (PDB), nucleic acid data bank (NDB),
molecular modeling data bank (MMDB), secondary structure, three-dimensional
structure predication, protein folding and functional sites, protein folding classes.
4.4Structure viewers (Ras Mol, J mol), file formats.
Unit 5 Drug discovery and computer aided drug designing
5.1 pharmacogenetics and pharmacogenomics, SNPs
5.2 Drug design and its approaches
5.3 Quantum CAChe and project leader, ligand design methods, docking programs.
5.4 Gene structure in prokaryotes and eukaryotes, gene prediction methods and tools.
5.5 Computer aided drug design (structure based and ligand based approaches) and
Systems Biology.
Practicals
1.Sequence retrieval (protein and gene) from NCBI
2.Structure download (protein and DNA) from PDB
3. Molecular file formats - FASTA, GenBank, Genpept, GCG, CLUSTAL, Swiss-Prot, FIR.
4.Molecular viewer by visualization software
5.BLAST suite of tools for pairwise alignment.
6.Multiple sequence alignment using CLUSTALW
7.Generating phylogenetic tree using PHYLIP Gene finding tools- GenScan, GLIMMER
8.Introduction to proteomics Protparam, GOR, nnPredict, SWISSMODEL
9.Visualization Softwares - Rasmol, JMOL 3-D Protein structure visualization and
measurement of bond length, bond angle and torsion angles using RasMol.
10.Gene prediction using GENSCAN and GLIMMER
11. Molecular Docking and Drug designing by using Chimera.
Suggested Readings:
1. Introduction to Bioinformatics, Attwood, Parry- Smith, Phukan, 2007, Pearson
Education
2. Bioinformatics, CSHL Press 2001, David Mount
Semester – VI
DSC 2 H (Paper VII): Elective A - DNA Cloning Techniques
Unit 1 Basic techniques for analysis of nucleic acids & proteins
1.1Electrophoresis – general principles, agarose, polyacrylamide gel electrophoresis,
1.2 Spectophotometry analysis of nucleic acids and proteins
1.3 Centrifugation – principle and techniques
Unit 2 Genetic Engineering Techniques
2.1 Enzymes used in recombinant DNA technology -restriction enzymes, various DNA
modifying enzymes used in cloning
2.2 Cloning vectors – plasmid based vectors, lamba phage based vectors, M13 phage
based vectors;
2.3 Covalent linkage of DNA fragments to vector molecules – linkers, adapters,
conversion adapters, homopolymer tailing
Unit 3 Nucleic acid hybridization and amplifying DNA
3.1 Blotting techniques – Southern blot and factors affecting DNA transfer, Northern blot,
Western blot, colony and plaque lift, dot blot
3.2 Amplification of DNA and RNA sequences -components of the PCR, importance of
primer designing, various thermostable enzymes vs Taq polymerase.
3.3 RAPD
Unit 4 Optimization of Gene Expression In bacteria and yeast
4.1 Cloning in bacteria -Expression vectors (lac promoter, tryptophan promoter, Lambda cI
promoter, arabinose promoter based) optimization of protein expression(using
upstream and downstream signals) Fusion proteins, cell-free translation systems.
4.2 Cloning in Yeast -methods of gene transfer to yeast ,YIp, YEp, YCp, YRp, shuttle
vectors), optimization of protein expression.
Unit 5 Optimization of Gene expression in plant and animal cells
5.1 Cloning in plants -Biolistics, protoplast mediated, electroporation, Agrobacterium
mediated transfer (Ti plasmid, disarmed vectors, cointegrate vectors, binary
vectors),virusmediated transfer (CaMV), in planta transformation, signals for
optimization of protein synthesis.
5.2 Cloning in animal cells -chemical transfection, lipofection, electroporation, genegun,microinjection, transient and stable transformation, optimization of protein
synthesis, use of reporter genes.
5.3 DNA analysis -Restriction mapping, DNA sequencing (dideoxy chain termination,
chemical degradation, pyrosequencing, shotgun sequencing and contig assembly).
Practicals:
1.GTC method of mRNA isolation,
2.Agarose Gel electrophoresis, .
3.Determination of molecular weight of proteins by SDS-PAGE,
4.Gel filtration technique,
5.Bacmid vectors,
6.pET vectors in bacteria,
7.pcDNA mammalian vector – characteristic,
8.yeast vectors,
9.antibody markers using kit method.
10.Media preparation Growing of SF 31 cells
11.Expression of Fusion proteins (GST, HIS, FC –tag) in DH5α cells.
12. Growing of mammalian cells – NIH 3T3, HEK 293.
13.Western blot.
Suggested Reading
1. Primrose, SB and Twyan RM. Principles of gene manipulation and genomics. 7th
edition. Blackwell Science, 2006.
2. Watson, Myers and Caudy. Recombinant DNA: Genes and Genomes-A short course.
3rd edition. 2006. Freeman W.H. and Company.
Semester – VI
DSC 2 H (Paper VII): Elective B- Genetic Diagnostic Techniques
Unit 1 Basics of Cell Culture & Instrumentation
1.1 Techniques of cell cultures (short term lymphocyte, primary
cultures, maintenance of cell lines)
1.2 Spectrophotometer, centrifugation,
1.3 ELISA, radioactivity detection,
1.4 Mass spectrometry,
1.5High performance liquid chromatography);
and secondary cell
Unit 2 Techniques in chromosome analysis
2.1Techniques of chromosome analysis - (a) Chromosome preparation from cultured
lymphocytes, cell lines and solid tumors (b) Karyotyping, C-,G-banding and fluorescence
banding, nomenclatures of bandings (c) In-situ hybridization techniques (d) Meiotic
chromosomes in mouse testis
2.2Chromosomal anomalies and disorders - Numerical (polyploidy, aneuploidy,
autosomal, sex- chromosomal) - Structural (deletion, duplication, translocation,
inversion, isochromosome, ring chromosome) - Chromosomal abnormalities in cancer
2.3Microscopy -Metaphase chromosome preparations from bone marrow of mouse, rat,
human ,Sex chromatin (buccal mucosa, hair bud),Comet assay, Micronuclei assay,
Chromosome preparation from chorionic villi, stem cells, cell line , Sister Chromatid
Exchange (SCE)
Unit 3 Genetic disorders & Molecular techniques for disease identification
3.1 Genetic Disorders - Classification of genetic disorders, Single gene Disorders (Cystic
Fibrosis, Marfan’s syndrome), Multifactorial disorders (Diabetes, Atherosclerosis,
Schizophrenia)
3.2 Molecular Techniques PCR-RFLP , ARMS-PCR , Multiplex-PCR, SSCP, CSGE, DGGE,
DHPLC MALDI-TOF
3.3. Disease identification and Genetic tests for following disorders: (a) Thalassemia,
Fanconi , Sickle Cell anemia, Fragile-X syndrome, Alzheimer’s disease (b) Duchenne
Muscular Dystrophy/Becker’s Muscular Dystrophy, Huntington’s disease (c) Allelic
susceptibility test for multifactorial disorders (Neural Tube Defect, Cleft Lip and Palate,
Cardio Vascular Disorder, Male infertility)
Unit 4 Biochemical Genetic Diagnosis
4.1 Biochemical tests: sugar, albumin, urea, protein, globulin, vitamin ;
4.2 Biochemistry and diagnostic tests of following diseases -Duchenne Muscular
Dystrophy (DMD) (Creatine phosphokinase-CPK),Phenylketonuria-PKU
(phenylketone) ,G6PD deficiency syndrome (G6PD) ,Mucopolysaccharidosis, Endocrine
disorders related to thyroid and reproduction (TSH, T3, T4, Estradiol, Testosterone, LH,
FSH)
Unit 5 Genetic counseling & Prenatal diagnosis
5.1 causes and factors for seeking counselling
5.2Dysmorphology
5.3 Ethical and legal issues in genetic counseling
5.4 Prenatal and preimplantation diagnosis
Practicals
1.Metaphase chromosome preparations from bone marrow of mouse, rat, human
2.Chromosome preparation from lymphocyte culture
3.G-banding, C-banding , R-banding
4.Karyotyping
5.Fluorescence in-situ Hybridization (FISH)
6.Meiosis in mouse testis
7.Sex chromatin (buccal mucosa, hair bud)
8.Comet assay
9.Micronuclei assay
10.Chromosome preparation from chorionic villi, stem cells, cell line
11.Sister Chromatid Exchange (SCE)
12.Molecular markers for tumor detection
13.Bcr-abl (RT-PCR)
14.Genetic counseling (pedigree analysis in disease conditions, risk calculation)
15.Prenatal diagnosis of Thalassemia
16.Y-chromosome microdeletion
17.Biochemical tests for sugar, albumin, Creatine phosphokinase-CPK, glucose 6 phosphate
dehydrogenase-G6PD
Suggested Readings
1. Chen, Harold Atlas of Genetic Diagnosis and Counseling Springer 2012.
2. Thompson and Thompson & Thompson Genetics in Medicine, Robert L. Nussbaum,
Roderick R. McInnes, Huntington F. Willard (eds)