From genes to genomes : Concepts and applications of DNA technology / Jeremy W. Dale, Malcolm von Schantz and Nick Plant. — 3rd ed. — Chichester, West Sussex, England ; Hoboken, NJ : John Wiley & Sons, c2012. – (58.21/D139/3rd ed.)

Contents

    CONTENTS
    
    Preface
    1 From Genes to Genomes
    1.1 Introduction
    1.2 Basic molecular biology
    1.3 What is a gene?
    1.4 Information flow: gene expression
    1.5 Gene structure and organisation
    1.6 Refinements of the model
    2 How to Clone a Gene
    2.1 What is cloning?
    2.2 Overview of the procedures
    2.3 Extraction and purification of nucleic acids
    2.4 Detection and quantitation of nucleic acids
    2.5 Gel electrophoresis
    2.6 Restriction endonucleases
    2.7 Ligation
    2.8 Modification of restriction fragment ends
    2.9 PLasmid vectors
    2.10 Vectors based on the Lambda bacteriophage
    2.11 Cosmids
    2.12 Supervectors: YACs and BACs
    2.13 Summary
    3 Genomic and cDNA Libraries
    3.1 Genomic libraries
    3.2 Growing and storing libraries
    3.3 cDNA Libraries
    3.4 Screening libraries with gene probes
    3.5 Screening expression Libraries with antibodies
    3.6 Characterization of plasmid clones
    4 Potymerase Chain Reaction (PCR)
    4.1 The PCR reaction
    4.2 PCR in practice
    4.3 Cloning PCR products
    4.4 Long-range PCR
    4.5 Reverse-transcription PCR
    4.6 Quantitative and real-time PCR
    4.7 Applications of PCR
    5 Sequencing a Cloned Gene
    5.1 DNA sequencing
    5.2 Databank entries and annotation
    5.3 Sequence analysis
    5.4 Sequence comparisons
    5.5 Protein structure
    5.6 Confirming gene function
    6 Analysis of Gene Expression
    6.1 Analysing transcription
    6.2 Methods for studying the promoter
    6.3 Regulatory elements and DNA-binding proteins
    6.4 Translational analysis
    7 Products from Native and Manipulated Cloned Genes
    7.1 Factors affecting expression of cloned genes
    7.2 Expression of cloned genes in bacteria
    7.3 Yeast systems
    7.4 Expression in insect cells: baculovirus systems
    7.5 Mammalian cells
    7.6 Adding tags and signals
    7.7 In vitro mutagenesis
    7.8 Vaccines
    8 Genomic Analysis
    8.1 Overview of genome sequencing
    8.2 Next generation sequencing (NGS)
    8.3 De novo sequence assembly
    8.4 Analysis and annotation
    8.5 Comparing genomes
    8.6 Genome browsers
    8.7 Relating genes and functions: genetic and physical maps
    8.8 Transposon mutagenesis and other screening techniques
    8.9 Gene knockouts， gene knockdowns and gene silencing
    8.10 Metagenomics
    8.11 Conclusion
    9 Analysis of Genetic Variation
    9.1 Single nucleotide polymorphisms
    9.2 Larger scale variations
    9.3 Other methods for studying variation
    9.4 Human genetic variation: relating phenotype to genotype
    9.5 Molecular phylogeny
    10 Post-Genomic Analysis
    10.1 Analysing transcription: transcriptomes
    10.2 Array-based methods
    10.3 Transcriptome sequencing
    10.4 Translational analysis: proteomics
    10.5 Post-translational analysis: protein interactions
    10.6 Epigenetics
    10.7 Integrative studies: systems biology
    11 Modifying Organisms: Transgenics
    11.1 Transgenesis and cloning
    11.2 Animal transgenesis
    11.3 Applications of transgenic animals
    11.4 Disease prevention and treatment
    11.5 Transgenic plants and their applications
    11.6 Transgenics: a coda
    Glossary
    Bibliography
    Index