Concepts and techniques in genomics and proteomics / by Nachimuthu Saraswathy and Ponnusamy Ramalingam. -- Oxford : Woodhead Publishing, c2011 .—(58.1483/S243)

Contents

List of figures

List of tables

Preface

Acknowledgements

List of abbreviations

About the authors

1  Introduction to genes and genomes

1.1  Introduction

1.2  The cell

1.3  Mendel's contributions

1.4  The chromosomal theory of inheritance

1.5  The chemical nature of genetic material

1.6  Composition and structure of DNA

1.7  The central dogma of life

1.8  Genomes of prokaryotes and eukaryotes

1.9  The molecular structure of the gene

1.10  Conclusion

Review questions and answers

Recommended reading

2  The human genome project

2.1  The history of the HGP

2.2  The budget for the HGP

2.3  Goals of the HGP

2.4  Laboratories and investigators involved in the HGP

2.5  The Human Genome Organization (HUGO)

2.6  Salient findings of the HGP

2.7  Potential applications of the HGP

2.8  Post-HGP challenges

2.9  Ethical, legal, social issues (ELSI) related to the HGP

2.10  The international HapMap Project

Review questions and answers

Recommended reading

3  Genomes of model organisms

3.1  Introduction

3.2  The viral genome

3.3  Bacterial genomes

3.4  Fungal genomes

3.5  Worm genome: Caenorhabditis elegans

3.6  Fruit fly: Drosophila melanogaster

3.7  Plant genome

3.8  Animal genome

3.9  The Microbial Genome Project

Review questions and answers

Recommended reading

4  High capacity vectors

4.1  Introduction

4.2  Cosmid vectors

4.3  Fosmid vectors

4.4  Bacteriophage P1 derived vector

4.5  P1 derived artificial chromosome (PAC)

4.6  Bacterial artificial chromosomes (BAC)

4.7  Yeast artificial chromosome (YAC)

Review questions and answers

Recommended reading

5  DNA sequencing methods

5.1  The history of DNA sequencing

5.2  Steps in DNA sequencing

5.3  Chemical degradation method of DNA sequencing

5.4  The chain termination method of DNA sequencing

5.5  Advances in DNA sequencing methods

5.6  New sequencing methods

5.7  Next generation sequencing methods

Review questions and answers

Recommended reading

6  Genome mapping

6.1  introduction

6.2  Importance of genome mapping in the context of genome sequencing

6.3  Genetic mapping

6.4  Genetic mapping in humans

6.5  Physical mapping methods

Review questions and answers

Recommended reading

7  Genome sequencing methods

7.1  Introduction

7.2  The clone-by-clone genome sequencing method

7.3  The whole genome shotgun sequencing method

7.4  Error control in genome sequencing

Review questions and answers

Recommended reading

8  Genome sequence assembly and annotation

8.1  Introduction

8.2  Clone contig assembly

8.3  Genome assembly program

8.4  Gaps and gap closing methods

8.5  Draft and finished genome sequences

8.6  Genome annotation

8.7  Comparative genomics

Review questions and answers

Recommended reading

9  Functional genomics

9.1  Introduction

9.2  Northern blotting

9.3  Subtractive hybridization

9.4  Differential Display Reverse Transcription PCR (DDRT-PCR)

9.5  Representational Difference Analysis (RDA)

9.6  Serial Analysis Gene Expression (SAGE)

9.7  Microarray technology

Review questions and answers

Recommended reading

10  Introduction to proteomics

10.1  Introduction

10.2  Traditional route of protein study

10.3  Protein isolation methods

10.4  Branches of proteomics

10.5  Characteristics of proteomics

Review questions and answers

Recommended reading

11 Two-dimensional gel electrophoresis of proteins

11.1  introduction

11.2  Principles of 2D-PAGE

11.3  2D-PAGE apparatus

11.4  Sample preparation

11.5  First-dimensional separation by isoelectric focusing

11.6  Equilibration

11.7  Second-dimensional separation by SDS-PAGE

11.8  Detection of proteins on 2D-PAGE gels

11.9  Image analysis

11.10  Application of 2D-PAGE in proteomics

Review questions and answers

Recommended reading

12 Mass spectrometry for proteomics

12.1  Introduction

12.2  History of the mass spectrometer

12.3  Mass spectrometer

12.4  Protein sample preparation for MS analysis

12.5  Applications of MS proteomics

Review questions and answers

Recommended reading

13 Protein Identification by Peptide Mass Fingerprinting (PMF)

13.1  Introduction

13.2  Principles of peptide mass fingerprinting

13.3  Protein preparation for PMF

13.4  Mass spectrometric analysis of peptide fragments

13.5  Data analysis and identification of protein

Review question and answer

Recommended reading

14  Protein sequencing techniques

14.1  Introduction

14.2  Preparation of protein sample for sequencing

14.3  Steps in protein sequencing

14.4  Protein sequencing by Edman degradation

14.5  De novo protein sequencing by mass spectrometry

Review questions and answers

Recommended reading

15  Phosphoproteomics

15.1  Post-translational modifications of proteins

15.2  Phosphoproteomics

15.3  Phosphoproteins enrichment methods

15.4  Mass spectrometry for phosphoprotein identification

Review questions and answers

Recommended reading

16  Glycoproteomics

16.1  Glycoproteins

16.2  Glycoprotein enrichment methods

16.3  Mass spectrometric analysis of glycoproteins

16.4  Importance of glycoproteins in human diseases

Review questions and answers

Recommended reading

Conclusion

Glossary

Index