MBB 601 Advances in Plant Molecular Biology 3+ ... - TNAU Genomics

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Suggested text books1. Chittaranjan K. 2007. Genome Mapping and Molecular Breeding in Plants. Vols. I-VII.Springer.2. Klug WS & Cummings MR. 2003 Concepts of Genetics. Peterson Education3. Lewin B. 2008. Genes IX. Jones & Bartlett Publ.4. Newbury HJ. 2003. Plant Molecular Breeding. Blackwell Publ.5. Weising K, Nybom H, Wolff K & Kahl G. 2005. DNA Fingerprinting in Plants: Principles,Methods and Applications. Taylor & Francis.Suggested Web sites:1. http://linkage.rockefeller.edu/soft/2. http://www.gramene.org/3. http://www.stat.wisc.edu/~yandell/statgen/software/biosci/linkage.html4. http://www.mapmanager.org/qtsoftware.html5. http://www.bioinformatics.org/mqtl/wiki/MBB 605 ADVANCES IN FUNCTIONAL GENOMICS AND PROTEOMICS 2+0ObjectiveTo discuss recent advances and applications of functional genomics and proteomics in agriculture,medicine and industry.TheoryUNIT IGenomics – Structural and Functional Genomics; Genome sequencing – methods, assembly andannotation; Human, animal, plant, bacterial and yeast genome projects; Genome annotation; abinitio gene discovery; functional annotation and gene family clusters; etc.UNIT IIFunctional genomics; Functional analysis of genes; RNA-mediated interference; gene knockouts;Gene traps/ T-DNA insertion lines; yeast-two hybrid screening; homologous recombination; geneexpression and transcript profiling; EST contigs; microarray profiling; SAGE; SNPs/variation; Eco-TILLING; allele/gene mining; synteny and comparative genomics; Genome evolution, speciationand domestication etc., Functional genomics projects in Rice, ArabidopsisUNIT IIProteomics: Protein annotation; protein separation and 2D PAGE; mass spectroscopy; Proteomedatabases; Protein microarrays; Protein interactive maps; Structural Proteomics: Protein structuredetermination, prediction and threading, software and data analysis/ management, etc.UNIT IVApplications of functional genomics in Agriculture; Applications of Proteomics in designing novelagrochemicals; Discussion on selected papers on functional genomics, proteomics, integrativegenomics etc.9
Theory ScheduleL.No1. Genomics – Introduction to Genomics; Structural and Functional Genomics;2. Genome sequencing – methods and advances3. Sequence assembly and annotation;4. Human and Animal genome projects;5. Plant, Bacterial and Yeast genome projects6. ab initio gene discovery; functional annotation and gene family clusters7. Functional genomics; Functional analysis of genes; Forward genetics, Reverse genetics approaches8. Over Expression mutants; Gene knockouts; RNA-mediated interference;9. Gene traps/ T-DNA insertion lines;10. Yeast-two hybrid screening; Homologous recombination;11. Gene expression and transcript profiling; methods, advantages and disadvantages12. EST contigs; microarray profiling; SAGE;13. SNPs/variation; Eco-TILLING; allele/gene mining;14. Synteny and Comparative genomics;15. Genome evolution, speciation and domestication etc.16. Functional genomics projects in Rice, Arabidopsis17. Mid semester exam18. Proteomics – Introduction, Need for Proteomics, types and advantages:19. Protein annotation;20. Protein separation and 2D PAGE;21. Mass spectroscopy;22. Proteome databases;23. Protein microarrays; Protein interactive maps;24. Structural Proteomics – Primary, Secondary and Tertiary structure25. Protein structure determination, prediction and threading,26. Softwares for modeling; Data analysis/ management, etc.27. Applications of functional genomics in Agriculture;28. Applications of Proteomics in designing novel agrochemicals;29. Discussion on selected papers on functional genomics,30. Discussion on selected papers on functional genomics,31. Discussion on selected papers on Proteomics,32. Discussion on selected papers on Proteomics,33. Discussion on selected papers on comparative and integrative genomics34. Discussion on selected papers on comparative and integrative genomicsSuggested Text BooksStephen P. Hunt, Rick Livesey. 2009. Functional Genomics: A Practical Approach.Christopher A. Cullis. 2005. Plant Genomics and Proteomics.Primrose. S. B. and Twyman. R. 2004. Principles of Genome Analysis and Genomics. Third editionUniversity of York.Blalock. E.M (Ed). 2003. A Beginner’s Guide to Microarrays. Kluwer Academic Publishers.Genomics and Proteomics. 2000. Functional and computational aspects. Ed. Sandor Suhai,Heidelberg, GermanyBranden and Tooze. 1999. Introduction to protein structure. Garland.10
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MBB 601 Advances in Plant Molecular Biology 3+ ... - TNAU Genomics

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