BY4015 Advanced Genomics and Proteomics Syllabus:
BY4015 Advanced Genomics and Proteomics Syllabus – Anna University PG Syllabus Regulation 2021
COURSE OBJECTIVES
1 To impart knowledge on the organization and structure of genomes
2 To provide knowledge on the techniques in mapping of genome
3 To impart knowledge on sequencing strategies for genome analysis.
4 To impart knowledge on the comparative and functional genomics
5 To impart knowledge on the metagenomics, pharmacogenomics and paleogenomics
UNIT I ORGANIZATION AND STRUCTURE OF GENOMES
Introduction to genome organization, size and complexity – Bacterial genomes – Circular – E.coli, Linear – Streptomyces coelicolor and Agrobacterium tumefaciens, and multipartite – Borrelia burgdorferi. Eukaryotic organelle genomes – Chloroplast and mitochondria. Eukaryotic nuclear genomes: Plant – Arabidopsis and Rice; Animal: Human and mice; Fungi: Aspergillus nidulans and Baker’s yeast. C-value paradox, coding and Non-coding sequences, dynamic components of genomes. Genome sequencing projects.
UNIT II GENOME MAPPING
Fragmentation with restriction enzymes –separating large fragments: PFGE, Isolation of chromosomes by FACS, and chromosome microdissection. YAC, BAC and P1 phage based genomic libraries. Genetic Mapping – gene markers, DNA markers – RFLP, SSLP, SNP, Linkage analysis; genetic mapping in bacteria and mapping by pedigree analysis in humans. Physical Mapping – Restriction mapping, FISH and GISH, STS mapping – ESTs, SSLPs and random genomic sequences. Mapping reagents, Chromosome walking, mapping without cloning – Radiation hybrids, Happy mapping. Integration of mapping methods
UNIT III SEQUENCING OF GENOMES
Basic DNA sequencing – Sanger Dideoxy sequencing – Slab gel and capillary electrophoresis, Automated DNA sequencing. Sequencing strategies – Single-end sequencing, paired-end sequencing, Mate-paired sequencing. Next- generation sequencing methodologies – Sequencing by synthesis: illumina, 454-pyrosequencing, Pacific Biosciences, ion-semiconductor sequencing; Sequencing by ligation – ABI-Solid sequencing – Generation of polony array; Single molecule sequencing – Heliscope and nanopore-sequencing. Base calling and sequence accuracy, Closing sequence gaps
UNIT IV COMPARATIVE AND FUNCTIONAL GENOMICS
Comparative genomics: Orthologues, paralogues and gene displacement, comparative genomics of prokaryotes, eukaryotes and organelle genomes. Phylogenetic footprinting and other applications of comparative genomics. Functional Genomics: understanding genome function at the DNA level – Epistasis and ENCODE project. Transcriptomics: Microarrays, SAGE, MPSS and RNA-Seq; Loss-offunction techniques: mutagenesis, RNAi and gene knockout. Understanding genome function at protein level – Protein-protein interaction, AP/MS.
UNIT V METAGENOMICS, PHARMACOGENOMICS AND PALEOGENOMICS
Metagenomics: Approaches for metagenomic analysis, Functional Metagenomics; Pharmacogenomics; Genetic variability in drug response; Clinical Applications and challenges in Pharmacogenomics; Impact of Pharmacogenomics on future drug development. Paleogenomics: Ancient DNA Extraction, Genomic analysis of aDNA, Paleogenomics Applications – case studies – insights from genomes of archaic hominins – Neanderthals and Denisovans; Woolly Mammoth; Barley; Mycobacterium tuberculosis
TOTAL: 45 PERIODS
COURSE OUTCOMES:
At the end of the course, the students will be able
CO1 To differentiate the structure and organization of genomes of bacteria, plants, animals and fungi
CO2 To develop mapping and sequencing strategies for genome analysis.
CO3 To compare the various genomes and delineate the differences and similarities in them
CO4 To be able to develop strategies to determine the function of the genomes as a whole
CO5 To develop strategies for the analysis of metagenome, determine the interaction of genomes and drugs and learned the evolutionary significance of paleogenomics
REFERENCES
1. Hunt S.P., Livesey, F.L., “Functional genomics”, Oxford University Press, 2000.
2. Primrose S.B., Twyman R., “Principles of Genome Analysis and Genomics”. Blackwell Publishers, 3rd Edition, 2007.
3. T. A. Brown., Genomes, Garland Science T&F group, 2006
4. Arthur M. Lesk. Introduction to genomics, Oxford University Press, 2012.
6. Sandor S., “Genomics and Proteomics: Functional and Computational Aspects”. Springer, 1st Edition reprint