Download Functional Genomics - Yogi Vemana University

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, Transposonbased 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.
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References:
Protein Microarrays, edited by Mark schena, Jones and Bartlet pblisher, 2005.
Microbial Functional Genomics, Jizhong Zhou, Dorothea K. Thompson, Ying Xu, James M.
Tiedje, A John Wiley & Sons, Inc., Publication, 2004.
Microarrays for an Integratiul J. But. Kho and Atte, Published in India by Ane Books, 2003.
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.
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Reference books:
Genetics A conceptual approach by Benjamin A. Pierce (2010)
Genetics Analysis and principles by Robert J.Brooker (2009)
Genomes 3 by T.A.Brown (2007)
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 transmissionDirect host –to-host, indirect host-to-host transmission; Harmful microbial interactions with
humans: entry, colonization and growth, virulence, virulence factors and toxins (exo- and endotoxins); 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
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PCR Screening for insertional mutants
TILLING (Targeted Induced Local Lesion IN Genome)
Yeast two hybrid system
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
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Population Genetics related problems.
Problems related to molecular evolution.
Left-right asymmetry in mouse.
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
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Reverse Genetics
Gain of function
Types of Microarray
Applications of SAGE
Mention various chemical bonds involved in Protein – Ligand interactions
Use of M13 in proteomics
Limitation of Protein Microarray
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
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2.
3.
4.
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8.
Mention the genes which play role in floral development in Arabidopsis thaliana.
Mutations in homeobox genes and its effect in humans and in Drosophila
Variability
Relation between phenotype and genotype
Non-random mating
Allele and gene frequency
Genetic variation
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
5X3=15M
1.
2.
3.
4.
5.
6.
7.
8.
Distinguish between epidemic and endemic diseases
Disease transmission
Drug resistance
Anti-viral therapy
Conventional methods of bacterial detection
List out different strains of M. tuberculosis
Phage therapy
Signature Tagged Mutagenesis (STM)
Part-B
Answer all the questions
Each question carries 15 marks
Each answer should not exceed six pages
4X15=60M
9. Write about the virulence factors and toxins of pathogenic microbes.
(or)
10. Reemergence of Chikungunya disease and molecular diagnosis
11. What is ribozyme? How it is useful as a therapeutic agent for HIV/AIDS.
(or)
12. Describe the pathogenesis of HPV. Add a note on the role of microarray technology in
understanding the pathogenesis of HPV.
13. Describe the molecular basis of pathogenecity of Mycobactrium tuberculosis.
(or)
14. Describe the advanced molecular microbiological diagnostics
15. Contributions of genomic technologies to antibacterial research.
(or)
16. Describe the Men B vaccine production by reverse-vaccinology technique. Mention the
limitations in the production of MenB vaccine by conventional methods.