From genes to genomes : concepts and applications of DNA technology /

From genes to genomes : concepts and applications of DNA technology /

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Bibliographic Details
Author / Creator:Dale, Jeremy (Jeremy W.)
Edition:3rd ed.
Imprint:Chichester, West Sussex : John Wiley & Sons, 2012.
Description:xiv, 386 p. : ill. ; 26 cm.
Language:English
Subject:
Genetic engineering.
DNA
Genes.
Genomes.
Genetic Engineering.
Cloning, Molecular.
DNA, Recombinant.
Molecular cloning.
DNA, Recombinant.
Genetic engineering.
Molecular cloning.
Genomes.
DNA.
Genetic engineering.
Genes.
Format: Print Book
URL for this record:http://pi.lib.uchicago.edu/1001/cat/bib/8547101
Hidden Bibliographic Details
Other authors / contributors:Schantz, Malcolm von.
Plant, Nick.
ISBN:9780470683866 (cloth)
0470683864 (cloth)
9780470683859 (pbk.)
0470683856 (pbk.)
Notes:Includes bibliographical references and index.
Table of Contents:
  • Preface xiii
  • 1. From Genes to Genomes
  • 1.1. Introduction
  • 1.2. Basic molecular biology
  • 1.2.1. The DNA backbone
  • 1.2.2. The base pairs
  • 1.2.3. RNA structure
  • 1.2.4. Nucleic acid synthesis
  • 1.2.5. Coiling and supercoilin
  • 1.3. What is a gene?
  • 1.4. Information flow: gene expression
  • 1.4.1. Transcription
  • 1.4.2. Translation
  • 1.5. Gene structure and organisation
  • 1.5.1. Operons
  • 1.5.2. Exons and introns
  • 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
  • 2.3.1. Breaking up cells and tissues
  • 2.3.2. Alkaline denaturation
  • 2.3.3. Column purification
  • 2.4. Detection and quantitation of nucleic acids
  • 2.5. Gel electrophoresis
  • 2.5.1. Analytical gel electrophoresis
  • 2.5.2. Preparative gel electrophoresis
  • 2.6. Restriction endonucleases
  • 2.6.1. Specificity
  • 2.6.2. Sticky and blunt ends
  • 2.7. Ligation
  • 2.7.1. Optimising ligation conditions
  • 2.7.2. Preventing unwanted ligation: alkaline phosphatase and double digests
  • 2.7.3. Other ways of joining DNA fragments
  • 2.8. Modification of restriction fragment ends
  • 2.8.1. Linkers and adaptors
  • 2.8.2. Homopolymer tailing
  • 2.9. Plasmid vectors
  • 2.9.1. Plasmid replication
  • 2.9.2. Cloning sites
  • 2.9.3. Selectable markers
  • 2.9.4. Insertional inactivation
  • 2.9.5. Transformation
  • 2.10. Vectors based on the lambda bacteriophage
  • 2.10.1. Lambda biology
  • 2.10.2. In vitro packaging
  • 2.10.3. Insertion vectors
  • 2.10.4. Replacement vectors
  • 2.11. Cosmids
  • 2.12. Supervectors: YACs and BACs
  • 2.13. Summary
  • 3. Genomic and cDNA Libraries
  • 3.1. Genomic libraries
  • 3.1.1. Partial digests
  • 3.1.2. Choice of vectors
  • 3.1.3. Construction and evaluation of a genomic library
  • 3.2. Growing and storing libraries
  • 3.3. cDNA libraries
  • 3.3.1. Isolation of mRNA
  • 3.3.2. cDNA synthesis
  • 3.3.3. Bacterial cDNA
  • 3.4. Screening libraries with gene probes
  • 3.4.1. Hybridization
  • 3.4.2. Labelling probes
  • 3.4.3. Steps in a hybridization experiment
  • 3.4.4. Screening procedure
  • 3.4.5. Probe selection and generation
  • 3.5. Screening expression libraries with antibodies
  • 3.6. Characterization of plasmid clones
  • 3.6.1. Southern blots
  • 3.6.2. PCR and sequence analysis
  • 4. Polymerase Chain Reaction (PCR)
  • 4.1. The PCR reaction
  • 4.2. PCR in practice
  • 4.2.1. Optimisation of the PCR reaction
  • 4.2.2. Primer design
  • 4.2.3. Analysis of PCR products
  • 4.2.4. Contamination
  • 4.3. Cloning PCR products
  • 4.4. Long-range PCR
  • 4.5. Reverse-transcription PCR
  • 4.6. Quantitative and real-time PCR
  • 4.6.1. SYBR Green
  • 4.6.2. TaqMan
  • 4.6.3. Molecular beacons
  • 4.7. Applications of PCR
  • 4.7.1. Probes and other modified products
  • 4.7.2. PCR cloning strategies
  • 4.7.3. Analysis of recombinant clones and rare events
  • 4.7.4. Diagnostic applications
  • 5. Sequencing a Cloned Gene
  • 5.1. DNA sequencing
  • 5.1.1. Principles of DNA sequencing
  • 5.1.2. Automated sequencing
  • 5.1.3. Extending the sequence
  • 5.1.4. Shotgun sequencing; contig assembly
  • 5.2. Databank entries and annotation
  • 5.3. Sequence analysis
  • 5.3.1. Identification of coding region
  • 5.3.2. Expression signals
  • 5.4. Sequence comparisons
  • 5.4.1. DNA sequences
  • 5.4.2. Protein sequence comparisons
  • 5.4.3. Sequence alignments: Clustal
  • 5.5. Protein structure
  • 5.5.1. Structure predictions
  • 5.5.2. Protein motifs and domains
  • 5.6. Confirming gene function
  • 5.6.1. Allelic replacement and gene knockouts
  • 5.6.2. Complementation
  • 6. Analysis of Gene Expression
  • 6.1. Analysing transcription
  • 6.1.1. Northern blots
  • 6.1.2. Reverse transcription-PCR
  • 6.1.3. In situ hybridization
  • 6.2. Methods for studying the promoter
  • 6.2.1. Locating the promoter
  • 6.2.2. Reporter genes
  • 6.3. Regulatory elements and DNA-binding proteins
  • 6.3.1. Yeast one-hybrid assays
  • 6.3.2. DNase I footprinting
  • 6.3.3. Gel retardation assays
  • 6.3.4. Chromatin immunoprecipitation (ChIP)
  • 6.4. Translational analysis
  • 6.4.1. Western blots
  • 6.4.2. Immunocytochemistry and immunohistochemistry
  • 7. Products from Native and Manipulated Cloned Genes
  • 7.1. Factors affecting expression of cloned genes
  • 7.1.1. Transcription
  • 7.1.2. Translation initiation
  • 7.1.3. Codon usage
  • 7.1.4. Nature of the protein product
  • 7.2. Expression of cloned genes in bacteria
  • 7.2.1. Transcriptional fusions
  • 7.2.2. Stability: conditional expression
  • 7.2.3. Expression of lethal genes
  • 7.2.4. Translational fusions
  • 7.3. Yeast systems
  • 7.3.1. Cloning vectors for yeasts
  • 7.3.2. Yeast expression systems
  • 7.4. Expression in insect cells: baculovirus systems
  • 7.5. Mammalian cells
  • 7.5.1. Cloning vectors for mammalian cells
  • 7.5.2. Expression in mammalian cells
  • 7.6. Adding tags and signals
  • 7.6.1. Tagged proteins
  • 7.6.2. Secretion signals
  • 7.7. In vitro mutagenesis
  • 7.7.1. Site-directed mutagenesis
  • 7.7.2. Synthetic genes
  • 7.7.3. Assembly PCR
  • 7.7.4. Synthetic genomes
  • 7.7.5. Protein engineering
  • 7.8. Vaccines
  • 7.8.1. Subunit vaccines
  • 7.8.2. DNA vaccines
  • 8. Genomic Analysis
  • 8.1. Overview of genome sequencing
  • 8.1.1. Strategies
  • 8.2. Next generation sequencing (NGS)
  • 8.2.1. Pyrosequencing (454)
  • 8.2.2. SOLiD sequencing (Applied Biosystems)
  • 8.2.3. Bridge amplification sequencing (Solexa/Ilumina)
  • 8.2.4. Other technologies
  • 8.3. De novo sequence assembly
  • 8.3.1. Repetitive elements and gaps
  • 8.4. Analysis and annotation
  • 8.4.1. Identification of ORFs
  • 8.4.2. Identification of the function of genes and their products
  • 8.4.3. Other features of nucleic acid sequences
  • 8.5. Comparing genomes
  • 8.5.1. BLAST
  • 8.5.2. Synteny
  • 8.6. Genome browsers
  • 8.7. Relating genes and functions: genetic and physical maps
  • 8.7.1. Linkage analysis
  • 8.7.2. Ordered libraries and chromosome walking
  • 8.8. Transposon mutagenesis and other screening techniques
  • 8.8.1. Transposition in bacteria
  • 8.8.2. Transposition in Drosophila
  • 8.8.3. Transposition in other organisms
  • 8.8.4. Signature-tagged mutagenesis
  • 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
  • 9.1.1. Direct sequencing
  • 9.1.2. SNP arrays
  • 9.2. Larger scale variations
  • 9.2.1. Microarrays and indels
  • 9.3. Other methods for studying variation
  • 9.3.1. Genomic Southern blot analysis: restriction fragment length polymorphisms (RFLPs)
  • 9.3.2. VNTR and microsatellites
  • 9.3.3. Pulsed-field gel electrophoresis
  • 9.4. Human genetic variation: relating phenotype to genotype
  • 9.4.1. Linkage analysis
  • 9.4.2. Genome-wide association studies (GWAS)
  • 9.4.3. Database resources
  • 9.4.4. Genetic diagnosis
  • 9.5. Molecular phylogeny
  • 9.5.1. Methods for constructing trees
  • 10. Post-Genomic Analysis
  • 10.1. Analysing transcription: transcriptomes
  • 10.1.1. Differential screening
  • 10.1.2. Other methods: transposons and reporters
  • 10.2. Array-based methods
  • 10.2.1. Expressed sequence tag (EST) arrays
  • 10.2.2. PCR product arrays
  • 10.2.3. Synthetic oligonucleotide arrays
  • 10.2.4. Important factors in array hybridization
  • 10.3. Transcriptome sequencing
  • 10.4. Translational analysis: proteomics
  • 10.4.1. Two-dimensional electrophoresis
  • 10.4.2. Mass spectrometry
  • 10.5. Post-translational analysis: protein interactions
  • 10.5.1. Two-hybrid screening
  • 10.5.2. Phage display libraries
  • 10.6. Epigenetics
  • 10.7. Integrative studies: systems biology
  • 10.7.1. Metabolomic analysis
  • 10.7.2. Pathway analysis and systems biology
  • 11. Modifying Organisms: Transgenics
  • 11.1. Transgenesis and cloning
  • 11.1.1. Common species used for transgenesis
  • 11.1.2. Control of transgene expression
  • 11.2. Animal transgenesis
  • 11.2.1. Basic methods
  • 11.2.2. Direct injection
  • 11.2.3. Retroviral vectors
  • 11.2.4. Embryonic stem cell technology
  • 11.2.5. Gene knockouts
  • 11.2.6. Gene knock-down technology: RNA interference
  • 11.2.7. Gene knock-in technology
  • 11.3. Applications of transgenic animals
  • 11.4. Disease prevention and treatment
  • 11.4.1. Live vaccine production: modification of bacteria and viruses
  • 11.4.2. Gene therapy
  • 11.4.3. Viral vectors for gene therapy
  • 11.5. Transgenic plants and their applications
  • 11.5.1. Introducing foreign genes
  • 11.5.2. Gene subtraction
  • 11.5.3. Applications
  • 11.6. Transgenics: a coda 353 Glossary
  • Bibliography
  • Index
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