Molecular Genetics of Bacteria 5th Edition (PDF)

Molecular Genetics  of Bacteria

Author:
Jeremy W. Dale, Simon F. Park
Release at: 2010
Pages: 403
Edition:
5th Edition
File Size: 8 MB
File Type: Pdf
Language: English



Description of Molecular Genetics of Bacteria 5th Edition (PDF)

Molecular Genetics of Bacteria 5th edition by Jeremy W. Dale, Simon F. Park is a great bacterial Genetics book available in (PDF) download. In the preface to the fourth edition (published in 2004) we referred to the revolution in bacterial genetics that was started by gene cloning and sequencing, coupled with related techniques such as the polymerase chain reaction (PCR) and microarrays, and culminated in the knowledge of genome sequences of a rapidly expanding range of bacteria. This posed a dilemma. How could we accommodate these new techniques, and the wealth of exciting new information they provided, while not losing sight of classical bacterial genetics? This dilemma has become even more acute.

True, many of the older methods are now no longer used and could be relegated to the pages of history. But there is a danger of throwing out the baby with the bathwater. Not only is there a need to maintain some sense of how the subject has got to the stage we are now at, but also a discussion of some of these methods is useful in establishing an understanding of how bacterial genetics operates in natural environments. Genetics is not just about how we find out about bacteria: it is about how bacteria have evolved, and continue to evolve and continue to adapt to changing environments. Molecular genetics, in isolation, is essentially reductionist. Even genome sequencing, and global analysis of gene expression, by themselves merely provide catalogs of genes. Ultimately, those lists have to be related to the behavior of the whole organism, and from there to how organisms interact with one another and with their environment.




Content of Molecular Genetics of Bacteria 5th Edition (PDF)


Chapter 1: Nucleic Acid Structure and Function

  • Structure of nucleic acids
  • DNA
  • RNA
  • Hydrophobic interactions
  • Different forms of the double helix
  • Supercoiling
  • Denaturation and hybridization
  • Orientation of nucleic acid strands
  • Replication of DNA
  • Unwinding and rewinding
  • Fidelity of replication; proofreading
  • Chromosome replication and cell division
  • DNA repair
  • Mismatch repair
  • Excision repair
  • Recombination (post-replication) repair
  • SOS repair
  • Gene expression
  • Transcription
  • Translation
  • Post-translational events
  • Gene organization
  • Chapter 2: Mutation and Variation

  • Variation and evolution
  • Fluctuation test
  • Replica plating
  • Directed mutation in bacteria?
  • Types of mutation
  • Point mutations
  • Conditional mutants
  • Variation due to larger-scale DNA alterations
  • Extrachromosomal agents and horizontal gene transfer
  • Recombination
  • A model of the general (homologous) recombination process
  • Enzymes involved in recombination
  • Phenotypes
  • Restoration of phenotype
  • chanisms of mutation
  • Spontaneous mutation
  • Chemical mutagens
  • Ultraviolet irradiation
  • Isolation and identification of mutants
  • Mutation and selection
  • Replica plating
  • Isolation of other mutants
  • Molecular methods
  • Chapter 3: Regulation of Gene Expression

  • Gene copy number
  • Transcriptional control
  • Promoters
  • Terminators, attenuators and anti-terminators
  • Induction and repression: regulatory proteins
  • Two-component regulatory systems
  • Global regulatory systems
  • Quorum sensing
  • Translational control
  • Ribosome binding
  • Codon usage
  • Stringent response
  • Regulatory RNA
  • Phase variation of
  • Chapter 4: Genetics of Bacteriophages

  • Bacteriophage structure
  • Single-strand DNA bacteriophages
  • φX174
  • M13
  • RNA-containing phages: MS2
  • Double-stranded DNA phages
  • Bacteriophage T4
  • Bacteriophage λ
  • Lytic and lysogenic regulation of bacteriophage λ
  • Restriction and modification
  • Bacterial resistance to phage attack
  • Complementation and recombination
  • Why are bacteriophages important?
  • Phage typing
  • Phage therapy
  • Phage display
  • Phages in the natural environment
  • Bacterial virulence and phage conversion
  • Chapter 5: Plasmids

  • Some bacterial characteristics are determined by plasmids
  • Antibiotic resistance
  • Colicins and bacteriocins
  • Virulence determinants
  • Plasmids in plant-associated bacteria
  • Metabolic activities
  • Molecular properties of plasmids
  • Plasmid replication and control
  • Partitioning
  • Host range
  • Plasmid incompatibility
  • Plasmid stability
  • Plasmid integrity
  • Partitioning
  • Differential growth rate of
  • Associating a plasmid with a phenotype
  • Chapter 6: Gene Transfer

  • Transformation
  • Conjugation
  • Mechanism of conjugation
  • The F plasmid
  • Conjugation in other bacteria
  • Transduction
  • Specialized transduction
  • Recombination
  • Consequences of recombination
  • Site-specific and non-homologous (illegitimate) recombination
  • Mosaic genes and chromosome plasticity
  • Chapter 7: Genomic Plasticity: Movable Genes and Phase Variation

  • Insertion sequences
  • Structure of insertion sequences
  • Occurrence of insertion sequences
  • Transposons
  • Structure of transposons
  • Integrons
  • ISCR elements
  • Mechanisms of transposition
  • Replicative transposition
  • Non-replicative (conservative) transposition
  • Regulation of transposition
  • Activation of genes by transposable elements
  • Mu: A transposable bacteriophage
  • Conjugative transposons
  • Phase variation of
  • Variation mediated by simple DNA inversion
  • Variation mediated by nested DNA inversion
  • Antigenic variation in the gonococcus
  • Phase variation by slipped-strand mispairing
  • Phase variation mediated by differential DNA methylation
  • Clustered regularly interspersed short palindromic repeats
  • Chapter 8: Genetic Modification: Exploiting the Potential of Bacteria

  • Strain development
  • Generation of variation
  • Selection of desired variants
  • Overproduction of primary metabolites
  • Simple pathways
  • Branched pathways
  • Overproduction of secondary metabolites
  • Gene cloning
  • Cutting and joining DNA
  • Plasmid vectors
  • Bacteriophage λ vectors
  • Cloning larger fragments
  • Bacteriophage M13 vectors
  • Gene libraries
  • Construction of genomic libraries
  • Screening a gene library
  • Cloning PCR products
  • Construction of a cDNA library
  • Products from cloned genes
  • Expression vectors
  • Making new genes
  • Other bacterial hosts
  • Novel vaccines
  • Other uses of gene technology
  • Chapter 9: Genetic Methods for Investigating Bacteria

  • Metabolic pathways
  • Complementation
  • Cross-feeding
  • Microbial physiology
  • Reporter genes
  • Chromatin immunoprecipitation
  • Cell division
  • Motility and chemotaxis
  • Cell differentiation
  • Bacterial virulence
  • Wide-range mechanisms of bacterial pathogenesis
  • Detection of virulence genes
  • Specific mutagenesis
  • Gene replacement
  • Antisense RNA
  • Taxonomy, evolution and epidemiology
  • Molecular taxonomy
  • GC content
  • 16 S rRNA
  • Denaturing-gradient gel electrophoresis and temperature-gradient gel electrophoresis
  • Diagnostic use of PCR
  • Molecular epidemiology
  • Chapter 10: Gene Mapping to Genomics and Beyond

  • Gene mapping
  • Conjugational analysis
  • Gene libraries
  • Restriction mapping and pulsed-field gel electrophoresis
  • DNA sequence determination
  • Sanger sequencing
  • Dye terminator sequencing
  • Pyrosequencing
  • Massively parallel sequencing
  • Genome sequencing
  • Genome-sequencing strategies
  • Relating sequence to function
  • Metagenomics
  • Comparative genomics
  • Microarrays
  • Analysis of gene expression
  • Transcriptional analysis
  • Translational analysis
  • Metabolomics
  • Systems biology and synthetic genomics
  • Systems biology
  • Synthetic genomics
  • Conclusion
  • Appendix A Further Reading

    Appendix B Abbreviations Used

    Appendix C Glossary

    Appendix D Enzymes and other Proteins

    Appendix E Genes

    Appendix F Standard Genetic Code

    Appendix G Bacterial Species

    Index

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