APPENDIX - A

BIF303 Version No. Course Prerequisites Objectives: Genomics and Proteomics LTPC: 3 0 2 4 1.1.0 Biochemistry, Cell Biology and Genetics To equip the students with the basics and applications of genomics and proteomics. Expected Outcome: To realize the importance of genomic and proteomic studies 2. To understand the techniques involved in the analysis of genomics and proteomics 3. To utilize the genomic and proteomic patterns in industrial and medicinal diagnostics and treatment Unit No. 1 Number of hours: 9 Gene structure and sequencing Sequence complexity introns and exons genome structure in viruses and prokaryotes organelle genomes and nuclear DNA in eukaryotes chain terminator sequencing automated DNA sequencing high throughput sequencing alternate DNA sequencing methods. Unit No. 2 Number of hours: 9 Comparative genomics and Global expression profiling Protein evolution by exon shuffling comparative genomics of prokaryotes and eukaryotes horizontal and lateral gene transfer Traditional approaches to expression profiling- global analysis of RNA expression: spotted DNA arrays, printed oligonucleotide chips data acquisition and analysis serial analysis of gene expression massively parallel signature sequencing. Unit No. 3 Number of hours: 9 Functional and structural genomics Functional genomics by systematic gene knockout genome wide random mutagenesis use of chemical mutagens and phenocopy libraries Determining gene function by sequence comparison X-ray crystallography and NMR in high throughput structure determination structure prediction methods domain fusion method for functional annotation. Unit No. 4 Number of hours: 8 Proteome mining and Protein sequencing Gel electrophoresis (1DE and 2DE), liquid chromatography and mass spectrometers for protein and peptide analysis routes in proteome analysis - protein digestion techniques - protein identification by mass finger printing sequence analysis by tandem mass spectrometry data bases and algorithms in protein identification Unit No. 5 Protein Expression analysis, interaction Number of hours: 10 network and modifications Comparative proteomics use of isotope tags yeast two hybrid systems immunoprecipitation and western blot analysis short gun identification of multiprotein complex bait and reverse bait analysis protein-protein and protein-DNA interactions protein interaction network sample enrichment for detecting protein modifications integration of different algorithms to map protein modification- glycoprotein analysis protein arrays. Text Books 1. Principles of genome analysis and genomics SB Primrose and RM Twyman, 3rd edition, Blackwell publishing, 2003. 2. Introduction to proteomics: tools for the new biology Daniel C Liebler, Humana Press, 2002. References Discovering genomics, proteomics and bioinformatics, A Malcolm Campbell and Laurie J Heyer, Cold Spring Harbour Laboratory Press, 2002. Mode of Evaluation Announced / Unannounced Quiz / tests, Assignments and Written Examination List of Experiments 1. Proteomics [Aldente (PMF), Popitam (MS/MS), Phenyx (MS/MS), FindMod, PeptideMass, .] 2. DNA -> Protein [Translate] 3. Similarity searches [BLAST] 4. Pattern and profile searches [ScanProsite] 5. Post-translational modification and topology prediction 6. Primary structure analysis [ProtParam, pI/MW, ProtScale] 7. Secondary and tertiary structure prediction [SWISS-MODEL, Swiss-PdbViewer] 8. Alignment [Nomad, T-COFFEE, SIM] 9. Phylogenetic analysis 10. Biological text analysis 11. 2D gel database analysis