GENOME ORGANIZATION AND GENE EXPRESSION
Introduction, genetic elements that control gene expression, constitutive and inducible gene expression, correlation between mRNA and protein abundance, functional genomic analysis using forward genetics and reverse genetics. COMPARATIVE GENOMICS: Orthologs and paralogs, Comparative genomics of bacteria and horizontal gene transfer, Comparative genomics of mitochondrial genomes and eukaryotes, applications of comparative genomics.
TRANSCRIPTOME ANALYSIS:
mRNA as a subject of gene expression studies, traditional approaches for analysis of gene expression –transcriptional run off assays, RT-PCR, DNase protection assay, differential display PCR, Genome wide measurement of gene expression – SAGE, Massively Parallel Signature Sequencing, Microarrays, interpretation of RNA analyses, relationship of DNA and mRNA levels.
PROTEOME ANALYSIS:
Introduction, protein databases,2D gel electrophoresis, MALDI-TOF analysis, MASCOT analysis, Mass spectroscopy, peptide mass fingerprinting, peptide sequence analysis by tandem mass spectrometry, SELDI protein chip technology, proteomic analysis of post translational modifications experimental approaches for protein-protein interaction mapping, differential and quantitative proteomics
Introduction, applications of genomics:
in understanding basis of polygenic disorders, pharmacogenomics, Medical proteomics-biomarker discovery and its importance, Pharmaceutical proteomics-role of proteomics in drug development, applications of proteomics for the analysis of genetically modified plants
Bioinformatics & Biological Databases:
Introduction to Bioinformatics, Goals, Scope, Applications in biological science and medicine. Biological databases –Sequence, structure, Genome, Microarray, Metabolic pathway, motif, and domain databases. Mapping databases –genome wide maps. Chromosome specific human maps.SequenceAlignment: Introduction, Types of sequence alignments-Pairwise and Multiple sequence alignment, Alignment algorithms (Needleman &Wunch, Smith &Waterman and Progressive global alignment). Database Similarity Searching-Scoring matrices–BLOSSUM and PAM, Basic Local Alignment Search Tool (BLAST), and FASTA. Next Generation Sequencing –Alignment and Assembly. Molecular Phylogenetics: Introduction, Terminology, Forms of Tree Representation. Phylogenetic Tree Construction Methods -Distance-Based & Character-Based Methods and Phylogenetic Tree evaluation.
Course outcomes:
At the end of the course the student will be able to:
1. To understand and apply the techniques of genomics and proteomics to study gene and protein expression respectively. Understand the Architecture and Schema of online databases including structure of records in these databases.
2. To apply the techniques to study differential gene expression
3. To perform a correlation between gene expression and its corresponding protein profile.
4. Apply the principles of Bioinformatics and Programming to the problems related to process simulation and process engineering in Biological system
Question paper pattern:
The SEE question paper will be set for 100 marks and the marks scored will be proportionately reduced to 60.
Textbook/ Textbooks
1 Bioinformatics and Functional Genomics Jonathan Pevsner WileyBlackwell 2015
2 Introduction to Proteomics Daniel CLiebler Humana Press 2002
Reference Books
1 Principles of Gene Manipulation and Genomics Primrose S.B, Twayman .R.M Blackwell publishing 2006
2 Principles of Proteomics Twayman.R.M Taylor and Francis 2004