From Genes to Genomes - 2nd edition

Preface

1 Introduction

2 Basic molecular biology 2.1 Nucleic acid structure 2.2 What is a gene? 2.3 Information flow: gene expression 2.4 Gene structure and organization

3 How to clone a gene 3.1 What is cloning? 3.2 Overview of the procedures 3.3 Gene libraries 3.4 Hybridization 3.5 Polymerase chain reaction 3.6 Extraction and purification of nucleic acids 3.7 Detection and quantitation of nucleic acids 3.8 Gel electrophoresis

4 Cutting and joining DNA 4.1 Restriction endonucleases 4.2 Ligation 4.3 Modification of restriction fragment ends 4.4 Other ways of joining DNA molecules

5 Vectors 5.1 Plasmid vectors 5.2 Vectors based on the lambda bacteriophage 5.3 Cosmids 5.4 M13 vectors CONTENTS 5.5 Expression vectors 5.6 Vectors for cloning and expression in eukaryotic cells 5.7 Supervectors: YACs and BACs 5.8 Summary

6 Genomic and cDNA libraries 6.1 Genomic libraries 6.2 Growing and storing libraries 6.3 cDNA libraries 6.4 Random, arrayed and ordered libraries

7 Finding the right clone 7.1 Screening libraries with gene probes 7.2 Screening expression libraries with antibodies 7.3 Subcloning 7.4 Characterization of plasmid clones

8 Polymerase chain reaction 8.1 The PCR reaction 8.2 PCR in practice 8.3 Cloning PCR products 8.4 Long-range PCR 8.5 Reverse-transcription PCR 8.6 Rapid amplification of cDNA ends 8.7 Quantitative PCR 8.8 Applications of PCR

9 Characterization of a cloned gene 9.1 DNA sequencing 9.2 Databank entries and annotation 9.3 Sequence analysis 9.4 Sequence comparisons 9.5 Protein structure 9.6 Confirming gene function

10 Analysis of gene expression 10.1 Analysing transcription 10.2 Methods for studying the promoter 10.3 Regulatory elements and DNA-binding proteins 10.4 Translational analysis CONTENTS

11 Products from native and manipulated cloned genes 11.1 Factors affecting expression of cloned genes 11.2 Expression of cloned genes in bacteria 11.3 Expression in eukaryotic host cells 11.4 Adding tags and signals 11.5 In vitro mutagenesis 11.6 Vaccines

12 Genomic analysis 12.1 Genome sequencing 12.2 Analysis and annotation 12.3 Comparing genomes 12.4 Genome browsers 12.5 Relating genes and functions: genetic and physical maps 12.6 Transposon mutagenesis and other screening techniques 12.7 Conclusion

13 Analysis of genetic variation 13.1 Single nucleotide polymorphisms 13.2 Larger-scale variations 13.3 Other methods for studying variation 13.4 Human genetic diseases 13.5 Molecular phylogeny

14 Post-genomic analysis 14.1 Analysing transcription; transcriptomes 14.2 Array-based methods 14.3 Translational analysis; proteomics 3 14.4 Post-translational analysis: protein interactions 14.5 Integrative studies; systems biology

15 Modifying organisms; transgenics 15.1 Modification of bacteria and viruses: live vaccines 15.2 Transgenesis and cloning 15.3 Animal transgenesis 15.4 Applications of transgenic animals 15.5 Transgenic plants and their applications

Glossary

Bibliography

Index