Concepts and Techniques in Genomics and Proteomics

<p>List of figures</p> <p>List of tables</p> <p>Preface</p> <p>Acknowledgements</p> <p>List of abbreviations</p> <p>About the authors</p> <p>Chapter 1: Introduction to genes and genomes</p> <p>Abstract:</p> <p>1.1 Introduction</p> <p>1.2 The cell</p> <p>1.3 Mendel’s contributions</p> <p>1.4 The chromosomal theory of inheritance</p> <p>1.5 The chemical nature of genetic material</p> <p>1.6 Composition and structure of DNA</p> <p>1.7 The central dogma of life</p> <p>1.8 Genomes of prokaryotes and eukaryotes</p> <p>1.9 The molecular structure of the gene</p> <p>1.10 Conclusion</p> <p>Review questions and answers</p> <p>Web addresses</p> <p>Chapter 2: The human genome project</p> <p>Abstract:</p> <p>2.1 The history of the HGP</p> <p>2.2 The budget for the HGP</p> <p>2.3 Goals of the HGP</p> <p>2.4 Laboratories and investigators involved in the HGP</p> <p>2.5 The Human Genome Organization (HUGO)</p> <p>2.6 Salient findings of the HGP</p> <p>2.7 Potential applications of the HGP</p> <p>2.8 Post-HGP challenges</p> <p>2.9 Ethical, legal, social issues (ELSI) related to the HGP</p> <p>2.10 The international HapMap Project</p> <p>Review questions and answers</p> <p>Web addresses</p> <p>Chapter 3: Genomes of model organisms</p> <p>Abstract:</p> <p>3.1 Introduction</p> <p>3.2 The viral genome</p> <p>3.3 Bacterial genomes</p> <p>3.4 Fungal genomes</p> <p>3.5 Worm genome: Caenorhabditis elegans</p> <p>3.6 Fruit fly: Drosophila melanogaster</p> <p>3.7 Plant genome</p> <p>3.8 Animal genome</p> <p>3.9 The Microbial Genome Project</p> <p>Chapter 4: High capacity vectors</p> <p>Abstract:</p> <p>4.1 Introduction</p> <p>4.2 Cosmid vectors</p> <p>4.3 Fosmid vectors</p> <p>4.4 Bacteriophage P1 derived vector</p> <p>4.5 P1 derived artificial chromosome (PAC)</p> <p>4.6 Bacterial artificial chromosomes (BAC)</p> <p>4.7 Yeast artificial chromosome (YAC)</p> <p>Review questions and answers</p> <p>Web address</p> <p>Chapter 5: DNA sequencing methods</p> <p>Abstract:</p> <p>Key concepts</p> <p>5.1 The history of DNA sequencing</p> <p>5.2 Steps in DNA sequencing</p> <p>5.3 Chemical degradation method of DNA sequencing</p> <p>5.4 The chain termination method of DNA sequencing</p> <p>5.5 Advances in DNA sequencing methods</p> <p>5.6 New sequencing methods</p> <p>5.7 Next generation sequencing methods</p> <p>Web addresses</p> <p>Chapter 6: Genome mapping</p> <p>Abstract:</p> <p>Key concepts</p> <p>6.1 Introduction</p> <p>6.2 Importance of genome mapping in the context of genome sequencing</p> <p>6.3 Genetic mapping</p> <p>6.4 Genetic mapping in humans</p> <p>6.5 Physical mapping methods</p> <p>Chapter 7: Genome sequencing methods</p> <p>Abstract:</p> <p>7.1 Introduction</p> <p>7.2 The clone-by-clone genome sequencing method</p> <p>7.3 The whole genome shotgun sequencing method</p> <p>7.4 Error control in genome sequencing</p> <p>Chapter 8: Genome sequence assembly and annotation</p> <p>Abstract:</p> <p>8.1 Introduction</p> <p>8.2 Clone contig assembly</p> <p>8.3 Genome assembly program</p> <p>8.4 Gaps and gap closing methods</p> <p>8.5 Draft and finished genome sequences</p> <p>8.6 Genome annotation</p> <p>8.7 Comparative genomics</p> <p>Chapter 9: Functional genomics</p> <p>Abstract:</p> <p>Key concepts</p> <p>9.1 Introduction</p> <p>9.2 Northern blotting</p> <p>9.3 Subtractive hybridization</p> <p>9.4 Differential Display Reverse Transcription PCR (DDRT-PCR)</p> <p>9.5 Representational Difference Analysis (RDA)</p> <p>9.6 Serial Analysis Gene Expression (SAGE)</p> <p>9.7 Microarray technology</p> <p>Web addresses</p> <p>Chapter 10: Introduction to proteomics</p> <p>Abstract:</p> <p>Key concepts</p> <p>10.1 Introduction</p> <p>10.2 Traditional route of protein study</p> <p>10.3 Protein isolation methods</p> <p>10.4 Branches of proteomics</p> <p>10.5 Characteristics of proteomics</p> <p>Chapter 11: Two-dimensional gel electrophoresis of proteins</p> <p>Abstract:</p> <p>11.1 Introduction</p> <p>11.2 Principles of 2D-PAGE</p> <p>11.3 2D-PAGE apparatus</p> <p>11.4 Sample preparation</p> <p>11.5 First-dimensional separation by isoelectric focusing</p> <p>11.6 Equilibration</p> <p>11.7 Second-dimensional separation by SDS-PAGE</p> <p>11.8 Detection of proteins on 2D-PAGE gels</p> <p>11.9 Image analysis</p> <p>11.10 Application of 2D-PAGE in proteomics</p> <p>Chapter 12: Mass spectrometry for proteomics</p> <p>Abstract:</p> <p>12.1 Introduction</p> <p>12.2 History of the mass spectrometer</p> <p>12.3 Mass spectrometer</p> <p>12.4 Protein sample preparation for MS analysis</p> <p>12.5 Applications of MS proteomics</p> <p>Chapter 13: Protein Identification by Peptide Mass Fingerprinting (PMF)</p> <p>Abstract:</p> <p>Key concepts</p> <p>13.1 Introduction</p> <p>13.2 Principles of peptide mass fingerprinting</p> <p>13.3 Protein preparation for PMF</p> <p>13.4 Mass spectrometric analysis of peptide fragments</p> <p>13.4 Data analysis and identification of protein</p> <p>Web address</p> <p>Chapter 14: Protein sequencing techniques</p> <p>Abstract:</p> <p>14.1 Introduction</p> <p>14.2 Preparation of protein sample for sequencing</p> <p>14.3 Steps in protein sequencing</p> <p>14.4 Protein sequencing by Edman degradation</p> <p>14.5 De novo protein sequencing by mass spectrometry</p> <p>Review questions and answers</p> <p>Chapter 15: Phosphoproteomics</p> <p>Abstract:</p> <p>15.1 Post-translational modifications of proteins</p> <p>15.2 Phosphoproteomics</p> <p>15.3 Phosphoprotein enrichment methods</p> <p>15.4 Mass spectrometry for phosphoprotein identification</p> <p>Review questions and answers</p> <p>Chapter 16: Glycoproteomics</p> <p>Abstract:</p> <p>16.1 Glycoproteins</p> <p>16.2 Glycoprotein enrichment methods</p> <p>16.3 Mass spectrometric analysis of glycoproteins</p> <p>16.4 Importance of glycoproteins in human diseases</p> <p>Review questions and answers</p> <p>Conclusion</p> <p>Glossary</p> <p>Index</p>