Department of Genetics and Genomics
Semester-IV
GG13: Functional Genomics
Unit I
Functional genomics: Concepts and applications, Forward genetics and Reverse genetics approaches, Loss of function, Gain of function.
Mutagenesis as Functional Genomics Tool: T-DNA insertional mutagenesis, Transposon-based mutagenesis (Ac/Ds and En/Spm), Activation tagging, Enhancer trapping, GAL4 mediated over expression, Floxing, Viral mediated transfection.
Genome wide mutation screening: TILLING (Targeted Induced Local Lesion IN Genome) - principle and experimental approach, ECO-TILLING; DEALING (Detecting Adducts Local Lesion IN Genome) - principle, experimental approach; Site directed Mutagenesis.
Unit II
DNA Microarray Technology: Introduction, Types of Microarrays and Advantages, Experimental design- Concepts, principles, Probe design, target preparation, Hybridization and Detection, Specificity, sensitivity, reproducibility, and Data Analysis; RNA silencing: Antisense RNA technology, RNAi and Si RNA; SAGE for transcript profiling- principle, methodology, problems associated with SAGE, modifications (Micro-SAGE, Long-SAGE, Super-SAGE) and applications, SADE; Molecular analysis of gene expression (RT-PCR).
Unit III
Functional proteomics: Gene functions through protein interactions: Identification of Protein–Ligand Interactions. Yeast Two-Hybrid Selection System: Analysis of genome-wide protein–protein interactions in organisms, Use of M13, T7 Phage to Detect Protein–Ligand Interactions, Combining yeast two-hybrid and phage display data, Detecting Interactions with Protein Fragment Complementation Assays.
Use of Mass Spectrometry for Protein–Protein Interaction Mapping: Overview, Identification of substrates for E. coli GroEL, Identification of protein complexes in Saccharomyces cerevisiae; Studying the transcriptome and proteome in Escherichia coli and Saccharomyces cerevisiae.
Unit IV
Functional protein microarrays: process overview, principle, limitations; Protein microarray- Manufacturing technology, solid supports, different formats, experimental approach and detection, peptidomics; Microarray for protein-carbohydrate interaction (phage display technology); protein domain microarray; protein biochips; Antibody microarray format; protein microarray for drug discovery.
References:
1. Protein Microarrays, edited by Mark schena, Jones and Bartlet pblisher, 2005.
2. Microbial Functional Genomics, Jizhong Zhou, Dorothea K. Thompson, Ying Xu, James M. Tiedje, A John Wiley & Sons, Inc., Publication, 2004.
3. Microarrays for an Integratiul J. But. Kho and Atte, Published in India by Ane Books, 2003.
4. Gene Cloning and DNA analysis An Introduction, Sixth Edition, T. A. Brown, Wiley-Blackwell publications, A John Wiley & Sons, Inc., Publication, 2010.
Department of Genetics and Genomics
Semester-IV
GG14: EPIGENOMICS
UNIT-I
Introduction, DNA methylation-De Novo methylation, Maintanance methylation and DNA methylation and transcriptional silencing; DNA methylation in prokaryotes and eukaryotes; Histone modifications and Histone code- Acetylation, Methylation, Phosphorylation, Ubiquitinylation and ADP-Ribosylation and Sumoylation; Non-coding RNA (ncRNA)- MicroRNA biogenesis and function, Small interfering RNA biogenesis and function and Epigenetic regulation by ncRNA.
UNIT-II
Epigenetic regulation of gene and genome expression- Heterochromatin spreading and position effect variegation, Transvection, Paramutaion, Imprinting and X-chromosome inactivation; Epigenomics in Cancer- Epigenetic features of a normal cell, DNA Hypomethylation in tumours, inactivation of tumor suppressor genes, Histone modifications of cancer cells, Epigenetic factors and miRNA epigenetics in cancer management, epigenetic therapy of cancer;
UNIT III
Epigenetics and its genetic syndromes : Introduction, Chromatin remodeling- X-Linked Thalassemia Mental Retardation syndrome, CHARGE syndrome, Cockayne syndrome (CSB), ICF syndrome, Rett syndrome, CLS syndrome and FSHD.
Epigenetics and Immunity: Introduction, Epigenetics in immune differentiation and the immune response, Epigenetics in Autoimmunity, Epigenetic changes in other Autoimmune disorders
UNIT IV
Analysis of gene-specific DNA methylation : Introduction, principles of DNA methylation analysis, characteristics of individual techniques-Southern blot hybridization, Bisulfite sequencing, Combined Bisulfite restriction analysis (COBRA), Methylation-specific PCR (MSP), Real-Time MSP, pyrosequencing and MethyLight.
Methods for Assessing genome-wide DNA methylation : Introduction, Restriction Landmark genomic scanning (RLGS), Methylation sensitive restriction finger printing (MSRF), Methylated CpG island amplification coupled microarray (MCAM)
Reference Books:
1.Epigenomics by Anne C.Ferguson Smith (2009)
2.Epigenetics and diseases by Susan M.Gasser, En Li (2011)
3.Epigenetics in Biology and Medicine by Nanel Esteller (2009)
4.Handbook of Epigenetics-The new molecular and medical genetics by Trygve Tollefsbol (2011)
5.Epigenetics in Cancer-The new England journal of medicine by Manel Esteller (2008)
6.Advanced Molecular Biology by Twyman (1999)
Department of Genetics and Genomics
Semester-IV
GG15: INTERGRATED GENETIC ANALYSIS
UNIT-I
Developmental Genetics : Development through cell determination-cloning experiments on plants and animals; Genetic control of development in Drosophila- Development of fruit fly, egg-polarity genes, determination of the dorsal-ventral axis, determination of the anterior posterior axis; Segmentation of genes, Homeotic genes in Drosophila, home box genes in other organisms; Connecting concepts : Gene control the development of flowers in plants- flower anatomy, genetic control of flower development; Programmed cell death-Apoptosis, regulation of apoptosis, apoptosis in development, apoptosis in disease.
UNIT-II
Quantitative genetics : Quantitative characteristics-variability, relation between genotype and phenotype, types of quantitative characteristics, phenotypic inheritance, determining gene number for a polygenic characteristic ; Heritability- phenotypic variance, Types of heritability, calculating heritability, limitations of heritability; Locating genes that affect quantitative characteristics- Mapping QTL, Genome wide association studies.
UNIT-III
Population genetics : Fundamental concepts, genetic structure of populations- Genotype frequencies, Allele frequencies; The Hardy-Weinberg Law- Assumption, prediction, deviation and extensions; Genetic variation- in space and time, in natural populations; Forces that changes gene frequencies in population- Mutation, genetic drift, migration; Hardy-Weinberg and natural selection.
UNIT-IV
Evolutionary genetics : Organism evolve through genetic change, Natural populations, Genetic variation- Molecular variation, protein variation, DNA sequence variation; New species through evolution of reproductive isolation- the biological species concept, reproductive isolating mechanisms, modes of speciation, genetic differentiation associated with speciation; Evolutionary history by homologous characteristics- The alignment of homologous sequences, construction of phylogenetic trees; Molecular evolution : Genome evolution- early RNA world, the first DNA genome, peptide nucleic acid; Acquisition of new genes by duplication and form other species; Noncoding DNA and genome evolution- transposable elements and genome evolution, the origin of introns; evolutionary history of human genome.
Reference books:
1. Genetics A conceptual approach by Benjamin A. Pierce (2010)
2. Genetics Analysis and principles by Robert J.Brooker (2009)
3. Genomes 3 by T.A.Brown (2007)
4. iGenetics A molecular approach, second ed. By Peter J.Russell (2006)
Department of Genetics and Genomics
Semester-IV
GG16: Pathogenomics
UNIT I
Principles and vocabulary of epidemiology, common epidemic diseases in humans ( agent, sources, reservoir and control),Stages of disease progression, infectious disease transmission-Direct host –to-host, indirect host-to-host transmission; Harmful microbial interactions with humans: entry, colonization and growth, virulence, virulence factors and toxins (exo- and endo- toxins); host risk factors in infection: age, stress and diet, compromised host. Emerging and re emerging infectious diseases- Chikungunya and Swine flu (H1N1).
UNIT II
Chipping away at HIV pathogenesis-The new and improved genetic code, overview of HIV pathogenesis-introduction, host entry, manipulation of disease, target-cell depletion and apoptosis; Bioinformatic analysis of HIV effects and future of genomics; Ribozyme as gene therapeutic agents for HIV/AIDS: Introduction, antiretroviral therapy, ribozyme design and in vitro efficacy, in vivo efficacy-animal models, gene-therapy clinical trials, drug resistance and gene therapy; Microarray analysis of HPV pathogenesis-Introduction, pathogenesis , application of microarray technology in understanding HPV pathogenesis-Tissue-culture systems for studying HP, alternation of cellular gene expression during latent infection by HPV and by viral gene products during keratinocytes differentiation.
UNIT III
Genomics of the Mycobacterium tuberculosis complex and BCG vaccines: Introduction, information from complete genome sequencing , strain-to –strain variability with M.tuberculosis spp., genomic variability between subspecies of the M.tuberculosis complex, genomic analysis of M.bovis BCG vaccines; PathoGenomics-applications and new diagnostics: conventional methods for detection of bacteria; advanced molecular microbiological diagnostics
UNIT IV
Search for new antibiotics; Need for novel antibiotics, the past-present antibiotics and future directions, contributions of genomic technologies to antibacterial research: Alternative approaches in antibacterial drug discovery: Targeting the resistance mechanism, extremely narrow-spectrum drugs, phage therapies and other bacteriolytic approaches, strategies for reducing virulence; Reverse vaccinology: Impact of genomics on vaccine design, MenB vaccine approach by reverse vaccinology, identification of potential vaccine candidates using different functional genomic approaches, gene expression in vivo-IVET and STM, transcriptome analysis and comparative genomics, proteomics and vaccine design.
Reference books:
1.Pathogenomics impact on human health by Kares Joy Schaw (2002)
2.Pathogenomics-Genome analysis of pathogenomic microbes by Jory Hacker, Ulrich Dobrindt(2006)
3.Encyclopedia of genetics, genomics, proteomics and bioinformatics by Lynn B.Jorde et al.,
4. Brock biology of Microorganisms. Pearson International Edition. By Madigan, Martinko, Dunlap and Clark.
Department of Genetics and Genomics
Semester-IV
Practical Paper I: Functional Genomics and Epigenomics
1. PCR Screening for insertional mutants
2. TILLING (Targeted Induced Local Lesion IN Genome)
3. Yeast two hybrid system
4. Isolation and assay of extracellular enzymes such as Protease and Amylase from Aspergillus sps
5. Purification and characterization of proteins/ enzymes
6. Determination of molecular weight of enzymes by activity staining on Native PAGE
7. Prediction of 3D structure of proteins/ enzymes by Bioinformatics
8. Protein and ligand interactions
9. DNA Microarray
10. Discrimination of methylated and non-methylated DNA by using restriction enzymes
11. Methylation specific PCR analysis of DNA
12. COBRA- Combined bisulfate restriction analysis of DNA
13. Over-expression of recombinant proteins in E. coli system
14. Purification and confirmation of recombinant proteins
Department of Genetics and Genomics
Semester-IV
Practical Paper II: Integrated genetic analysis and Pathogenomics
1. Population Genetics related problems.
2. Problems related to molecular evolution.
3. Left-right asymmetry in mouse.
4. Genetic analysis of flower development in Arabidopsis thaliana. The ABC model of organ identity determination.
5. Symptoms based identification of various pathogens on field crops.
6. Polymerase Chain Reaction based identification of virus.
7. Identification of bacteria by Polymerase Chain Reaction.
8. Identification of fungi by Polymerase Chain Reaction.
9. Detection of virus by Southern Blotting.
10. Detection of virus by Northern Blotting.
Model Question Paper
M.Sc. Degree examinations, April-2016
Fourth Semester
Genetics and Genomics
GG 13: Functional Genomics
Time: 3 hours Max Marks: 75
Part-A
Answer any five of the following
Each Question carries three marks
Each answer should not exceed one page
5x 3 = 15 marks
1. Reverse Genetics
2. Gain of function
3. Types of Microarray
4. Applications of SAGE
5. Mention various chemical bonds involved in Protein – Ligand interactions
6. Use of M13 in proteomics
7. Limitation of Protein Microarray
8. Peptidomics
Part-B
Answer all the questions
Each question carries fifteen marks
Each answer should not exceed six pages
4 x 15 = 60 Marks
9. Write in details of the principle, experimental approach and applications of the DEALING technology
(or)
10. How transposon insertional mutagenesis help to identify gene function? Explain with diagrammatic presentation?
11. Discuss in detail the DNA microarray technology
(or)
12. Write about the RNAi technology and its applications
13. How is Yeast two hybrid system useful for analysis of protein-ligand interaction
(or)
14. Transcriptome and Proteome analysis in E. coli
15. Discuss the protein microarray technology with application
(or)
16. How to identify the protein- carbohydrate interactions using phage display method
Model Question Paper
M.Sc Degree Examinations, April, 2016
Fourth Semester
Genetics and Genomics
GG 14: Epigenomics
Time: 3 Hours Max.Marks:75
Part-A
Answer any five questions
Each question carries 3 marks
Each answer should not exceed one page
5X3=15M
1. Distinguish between de novo Methylation and maintenance of Methylation of DNA.
2. Write how the bacteria acquired immunity against exogenous phage genes?
3. List out the major distinguishing characteristics between euchromatin and heterochromatin
4. Transvection
5. Define syndrome and write characteristics of CBS
6. DNA demethylation and autoimmunity
7. Why bisulfate DNA modification has mount importance in epigenomics?
8. Histone code
Part-B
Answer all the questions
Each question carries 15 marks
Each answer should not exceed six pages
4X15=60M
9. Write how Acetylation, Methylation and Phosphorylation of histone proteins influence the genome expression and regulation?
(or)
10. Describe siRNA biogenesis and function in epigenetic regulation
11. Write the molecular basis of imprinting and X-chromosome inactivation
(or)
12. Discuss about DNA hypermethylation and their consequences in cancer biology
13. Discuss in detail about X-Linked Thalassemia Mental Retardation syndrome.
(or)
14. Write briefly about epigenetics in immune differentiation and immune response.
15. Write principle, methodology and applications of COBRA and MSP
(or)
16. List out various methods use for assessing genome-wide DNA Methylation and write in
detail about one of them.
Model Question Paper
M.Sc Degree Examinations, April, 2016
Fourth Semester
Genetics and Genomics
GG 15: Integrated Genetic Analysis
Time: 3 Hours Max.Marks:75
Part-A
Answer any five questions
Each question carries 3 marks
Each answer should not exceed one page
5X3=15M
1. Mention the genes which play role in floral development in Arabidopsis thaliana.
2. Mutations in homeobox genes and its effect in humans and in Drosophila
3. Variability
4. Relation between phenotype and genotype
5. Non-random mating
6. Allele and gene frequency
7. Genetic variation
8. write the importance of constructing phylogenetic trees
Part-B
Answer all the questions
Each question carries 15 marks
Each answer should not exceed six pages
4X15=60M
9. Write about the genes involved in the development of Drosophila.
(or)
10. What is programmed cell death? Mention its role in the developmental process of an organism and in diseased condition.
11. Describe the variance, calculation and limitations of variability.
(or)
12. QTL Mapping.
13. Describe the Hardy Weinberg law. Mention its assumptions, deviations and extensions.
(or)
14. How the genetic variation occurs over space and time.
15. Describe various modes of Speciation
(or)
16. Write an essay on Molecular evolution.
Model Question Paper
M.Sc., Degree Examinations, April, 2016
Fourth Semester
Genetics and Genomics
GG 16: Pathogenomics
Time: 3 Hours Max.Marks:75
Part-A
Answer any five questions
Each question carries 3 marks
Each answer should not exceed one page