Concepts and Techniques in Genomics and Proteomics

Dr Nachimuthu Saraswathy is currently Associate Professor at the Department of Biotechnology, Kumaraguru College of Technology. She teaches courses on Molecular Biology, Genetic Engineering, and Plant Biotechnology, as well as Genomics and Proteomics. Dr Saraswathy gained her Ph.D. in Molecular Biology from the National Centre for Plant Biotechnology, New Delhi. She has published several articles in journals of biotechnology and biochemistry. Mr Ponnusamy Ramalingam is Associate Professor at the Department of Biotechnology, Kumaraguru College of Technology. He received his M.Sc. In Biochemistry from Gulbarga University and Mtech in Biotechnology from Anna University. He has also taught and researched in institutions such as Kongu Engineering College and PNC&KR College, and has contributed several published journal articles.

• List of figuresList of tablesPrefaceAcknowledgementsList of abbreviationsAbout the authorsChapter 1: Introduction to genes and genomesAbstract:1.1 Introduction1.2 The cell1.3 Mendel’s contributions1.4 The chromosomal theory of inheritance1.5 The chemical nature of genetic material1.6 Composition and structure of DNA1.7 The central dogma of life1.8 Genomes of prokaryotes and eukaryotes1.9 The molecular structure of the gene1.10 ConclusionReview questions and answersWeb addressesChapter 2: The human genome projectAbstract:2.1 The history of the HGP2.2 The budget for the HGP2.3 Goals of the HGP2.4 Laboratories and investigators involved in the HGP2.5 The Human Genome Organization (HUGO)2.6 Salient findings of the HGP2.7 Potential applications of the HGP2.8 Post-HGP challenges2.9 Ethical, legal, social issues (ELSI) related to the HGP2.10 The international HapMap ProjectReview questions and answersWeb addressesChapter 3: Genomes of model organismsAbstract:3.1 Introduction3.2 The viral genome3.3 Bacterial genomes3.4 Fungal genomes3.5 Worm genome: Caenorhabditis elegans3.6 Fruit fly: Drosophila melanogaster3.7 Plant genome3.8 Animal genome3.9 The Microbial Genome ProjectChapter 4: High capacity vectorsAbstract:4.1 Introduction4.2 Cosmid vectors4.3 Fosmid vectors4.4 Bacteriophage P1 derived vector4.5 P1 derived artificial chromosome (PAC)4.6 Bacterial artificial chromosomes (BAC)4.7 Yeast artificial chromosome (YAC)Review questions and answersWeb addressChapter 5: DNA sequencing methodsAbstract:Key concepts5.1 The history of DNA sequencing5.2 Steps in DNA sequencing5.3 Chemical degradation method of DNA sequencing5.4 The chain termination method of DNA sequencing5.5 Advances in DNA sequencing methods5.6 New sequencing methods5.7 Next generation sequencing methodsWeb addressesChapter 6: Genome mappingAbstract:Key concepts6.1 Introduction6.2 Importance of genome mapping in the context of genome sequencing6.3 Genetic mapping6.4 Genetic mapping in humans6.5 Physical mapping methodsChapter 7: Genome sequencing methodsAbstract:7.1 Introduction7.2 The clone-by-clone genome sequencing method7.3 The whole genome shotgun sequencing method7.4 Error control in genome sequencingChapter 8: Genome sequence assembly and annotationAbstract:8.1 Introduction8.2 Clone contig assembly8.3 Genome assembly program8.4 Gaps and gap closing methods8.5 Draft and finished genome sequences8.6 Genome annotation8.7 Comparative genomicsChapter 9: Functional genomicsAbstract:Key concepts9.1 Introduction9.2 Northern blotting9.3 Subtractive hybridization9.4 Differential Display Reverse Transcription PCR (DDRT-PCR)9.5 Representational Difference Analysis (RDA)9.6 Serial Analysis Gene Expression (SAGE)9.7 Microarray technologyWeb addressesChapter 10: Introduction to proteomicsAbstract:Key concepts10.1 Introduction10.2 Traditional route of protein study10.3 Protein isolation methods10.4 Branches of proteomics10.5 Characteristics of proteomicsChapter 11: Two-dimensional gel electrophoresis of proteinsAbstract:11.1 Introduction11.2 Principles of 2D-PAGE11.3 2D-PAGE apparatus11.4 Sample preparation11.5 First-dimensional separation by isoelectric focusing11.6 Equilibration11.7 Second-dimensional separation by SDS-PAGE11.8 Detection of proteins on 2D-PAGE gels11.9 Image analysis11.10 Application of 2D-PAGE in proteomicsChapter 12: Mass spectrometry for proteomicsAbstract:12.1 Introduction12.2 History of the mass spectrometer12.3 Mass spectrometer12.4 Protein sample preparation for MS analysis12.5 Applications of MS proteomicsChapter 13: Protein Identification by Peptide Mass Fingerprinting (PMF)Abstract:Key concepts13.1 Introduction13.2 Principles of peptide mass fingerprinting13.3 Protein preparation for PMF13.4 Mass spectrometric analysis of peptide fragments13.4 Data analysis and identification of proteinWeb addressChapter 14: Protein sequencing techniquesAbstract:14.1 Introduction14.2 Preparation of protein sample for sequencing14.3 Steps in protein sequencing14.4 Protein sequencing by Edman degradation14.5 De novo protein sequencing by mass spectrometryReview questions and answersChapter 15: PhosphoproteomicsAbstract:15.1 Post-translational modifications of proteins15.2 Phosphoproteomics15.3 Phosphoprotein enrichment methods15.4 Mass spectrometry for phosphoprotein identificationReview questions and answersChapter 16: GlycoproteomicsAbstract:16.1 Glycoproteins16.2 Glycoprotein enrichment methods16.3 Mass spectrometric analysis of glycoproteins16.4 Importance of glycoproteins in human diseasesReview questions and answersConclusionGlossaryIndex