18BT54 Genomics & Proteomics syllabus for BT

INTRODUCTION:

Genes and Proteins, Polymorphisms – types of polymorphism, genome sequences and database subscriptions, discovery of new genes and their function. Early sequencing efforts. Extraction of DNA, Methods of preparing genomic DNA for sequencing, DNA sequence analysis methods-Maxam & Gilbert Method, Sanger Di-deoxy method, Fluorescence method, shot-gun approach. NGS – different methods and principles

GENOMICS:

Inheritance pattern in eukaryotes, Mutations, Gene variation and Single Nucleotide Polymorphisms (SNPs), Expressed sequenced tags (ESTs), Gene-disease association, diagnostic genes and drug targets, genotyping tools - DNA Chips, diagnostic assays, diagnostic services. Functional genomic studies with model systems such as Drosophila, Yeast or C. elegans. Genome projects on E.coli., Arabidopsis and rice; Human genome project and the genetic map.

GENOME MANAGEMENT :

Cell differentiation and gene regulation. C-Values of genomes. General architecture of prokaryotic and eukaryotic genome. Organization of eukaryotic genome within the nucleus, chloroplast and mitochondria. Regulation of transcription, transcription factors and the co-ordination of gene expression. Interference RNA, RNA silencing, SiRNA: Applications in Functional genomics, Medicine and Gene Knockdown. Gene Editing - Crispr Cas9

GENOME ANALYSIS :

Genetic and physical maps: Breeding requirements for mapping. Molecular markers - RFLP, RAPD, AFLP, SCAR, CAPS, microsatellites and SNPs. Methods of molecular mapping, Marker assisted selection. Map-based cloning, T-DNA and transposon tagging. Differential display via RT-PCR. Micro-array in functional genomics. Bioinformatics analysis – clustering methods. FISH - DNA amplification markers; Telomerase as molecular markers. STS mapping.

PROTEOMICS :

Introduction to proteins, Large scale preparation of proteins and peptides, Merrifield Synthesis of peptides, use of peptides as probes. proteins as drugs; two hybrid interaction screens. Mass-spec based analysis of protein expression. "Protein Chip" - interactions and detection techniques. Two dimensional PAGE for proteome analysis, Detection of proteins on SDS gels, Protein cleavage, Edman protein microsequencing, Automation in proteomics, Applications of proteome analysis to drug development and toxicology, Phage antibodies as tools for proteomics.

Course outcomes:

At the end of the course the student will be able to:

• Define structural, comparative and functional genomics and proteomics and its uses in various research fields
• Describe various methods and techniques of Genomics, high throughput DNA sequencing technology, expression profiling, proteome analysis, and its applications.

Question paper pattern:

• The question paper will have ten full questions carrying equal marks.
• Each full question will be for 20 marks.
• There will be two full questions (with a maximum of four sub- questions) from each module.
• Each full question will have sub- question covering all the topics under a module.
• The students will have to answer five full questions, selecting one full question from each module.

Textbook/s

1 Introduction to Genomics Arthur M Lesk Oxford University Press 2007

2 Discovering Genomics, Proteomics & Bioinformatics A M Campbell & L J Heyer Pearson Education, 2007

3 Proteins and Proteomics Richard J Simpson IK International 2003

Reference Books

1 Genomics & Proteomics Sabesan Ane Books 2007

2 Purifying Proteins for Proteomics Richard J Simpson IK International 2004