Preface |
Nucleic Acid Structure and Function / 1: |
Structure of nucleic acids / 1.1: |
DNA / 1.1.1: |
RNA / 1.1.2: |
Hydrophobic interactions / 1.1.3: |
Different forms of the double helix / 1.1.4: |
Supercoiling / 1.1.5: |
Denaturation and hybridization / 1.1.6: |
Orientation of nucleic acid strands / 1.1.7: |
Replication of DNA / 1.2: |
Unwinding and rewinding / 1.2.1: |
Fidelity of replication; proofreading / 1.2.2: |
Chromosome replication and cell division / 1.3: |
DNA repair / 1.4: |
Mismatch repair / 1.4.1: |
Excision repair / 1.4.2: |
Recombination (post-replication) repair / 1.4.3: |
SOS repair / 1.4.4: |
Gene expression / 1.5: |
Transcription / 1.5.1: |
Translation / 1.5.2: |
Post-translational events / 1.5.3: |
Gene organization / 1.6: |
Mutation and Variation / 2: |
Variation and evolution / 2.1: |
Fluctuation test / 2.1.1: |
Replica plating / 2.1.2: |
Directed mutation in bacteria? / 2.1.3: |
Types of mutation / 2.2: |
Point mutations / 2.2.1: |
Conditional mutants / 2.2.2: |
Variation due to larger-scale DNA alterations / 2.2.3: |
Extrachromosomal agents and horizontal gene transfer / 2.2.4: |
Recombination / 2.3: |
A model of the general (homologous) recombination process / 2.3.1: |
Enzymes involved in recombination / 2.3.2: |
Phenotypes / 2.4: |
Restoration of phenotype / 2.4.1: |
Mechanisms of mutation / 2.5: |
Spontaneous mutation / 2.5.1: |
Chemical mutagens / 2.5.2: |
Ultraviolet irradiation / 2.5.3: |
Isolation and identification of mutants / 2.6: |
Mutation and selection / 2.6.1: |
Isolation of other mutants / 2.6.2: |
Molecular methods / 2.6.4: |
Regulation of Gene Expression / 3: |
Gene copy number / 3.1: |
Transcriptional control / 3.2: |
Promoters / 3.2.1: |
Terminators, attenuators and anti-terminators / 3.2.2: |
Induction and repression: regulatory proteins / 3.2.3: |
Two-component regulatory systems / 3.2.4: |
Global regulatory systems / 3.2.5: |
Quorum sensing / 3.2.6: |
Translational control / 3.3: |
Ribosome binding / 3.3.1: |
Codon usage / 3.3.2: |
Stringent response / 3.3.3: |
Regulatory RNA / 3.3.4: |
Phase variation / 3.4: |
Genetics of Bacteriophages / 4: |
Bacteriophage structure / 4.1: |
Single-strand DNA bacteriophages / 4.2: |
ΦX174 / 4.2.1: |
M13 / 4.2.2: |
RNA-containing phages: MS2 / 4.3: |
Double-stranded DNA phages / 4.4: |
Bacteriophage T4 / 4.4.1: |
Bacteriophage λ / 4.4.2: |
Lytic and lysogenic regulation of bacteriophage λ / 4.4.3: |
Restriction and modification / 4.5: |
Bacterial resistance to phage attack / 4.6: |
Complementation and recombination / 4.7: |
Why are bacteriophages important? / 4.8: |
Phage typing / 4.8.1: |
Phage therapy / 4.8.2: |
Phage display / 4.8.3: |
Phages in the natural environment / 4.8.4: |
Bacterial virulence and phage conversion / 4.8.5: |
Plasmids / 5: |
Some bacterial characteristics are determined by plasmids / 5.1: |
Antibiotic resistance / 5.1.1: |
Colicins and bacteriocins / 5.1.2: |
Virulence determinants / 5.1.3: |
Plasmids in plant-associated bacteria / 5.1.4: |
Metabolic activities / 5.1.5: |
Molecular properties of plasmids / 5.2: |
Plasmid replication and control / 5.2.1: |
Partitioning / 5.2.2: |
Host range / 5.2.3: |
Plasmid incompatibility / 5.2.4: |
Plasmid stability / 5.3: |
Plasmid integrity / 5.3.1: |
Differential growth rate / 5.3.2: |
Associating a plasmid with a phenotype / 5.4: |
Gene Transfer / 6: |
Transformation / 6.1: |
Conjugation / 6.2: |
Mechanism of conjugation / 6.2.1: |
The F plasmid / 6.2.2: |
Conjugation in other bacteria / 6.2.3: |
Transduction / 6.3: |
Specialized transduction / 6.3.1: |
Consequences of recombination / 6.4: |
Site-specific and non-homologous (illegitimate) recombination / 6.4.2: |
Mosaic genes and chromosome plasticity / 6.5: |
Genomic Plasticity: Movable Genes and Phase Variation / 7: |
Insertion sequences / 7.1: |
Structure of insertion sequences / 7.1.1: |
Occurrence of insertion sequences / 7.1.2: |
Transposons / 7.2: |
Structure of transposons / 7.2.1: |
Integrons / 7.2.2: |
ISCR elements / 7.2.3: |
Mechanisms of transposition / 7.3: |
Replicative transposition / 7.3.1: |
Non-replicative (conservative) transposition / 7.3.2: |
Regulation of transposition / 7.3.3: |
Activation of genes by transposable elements / 7.3.4: |
Mu: A transposable bacteriophage / 7.3.5: |
Conjugative transposons / 7.3.6: |
Variation mediated by simple DNA inversion / 7.4: |
Variation mediated by nested DNA inversion / 7.4.2: |
Antigenic variation in the gonococcus / 7.4.3: |
Phase variation by slipped-strand mispairing / 7.4.4: |
Phase variation mediated by differential DNA methylation / 7.4.5: |
Clustered regularly interspersed short palindromic repeats / 7.5: |
Genetic Modification: Exploiting the Potential of Bacteria / 8: |
Strain development / 8.1: |
Generation of variation / 8.1.1: |
Selection of desired variants / 8.1.2: |
Overproduction of primary metabolites / 8.2: |
Simple pathways / 8.2.1: |
Branched pathways / 8.2.2: |
Overproduction of secondary metabolites / 8.3: |
Gene cloning / 8.4: |
Cutting and joining DNA / 8.4.1: |
Plasmid vectors / 8.4.2: |
Bacteriophage λ vectors / 8.4.3: |
Cloning larger fragments / 8.4.4: |
Bacteriophage M13 vectors / 8.4.5: |
Gene libraries / 8.5: |
Construction of genomic libraries / 8.5.1: |
Screening a gene library / 8.5.2: |
Cloning PCR products / 8.5.3: |
Construction of a cDNA library / 8.5.4: |
Products from cloned genes / 8.6: |
Expression vectors / 8.6.1: |
Making new genes / 8.6.2: |
Other bacterial hosts / 8.6.3: |
Novel vaccines / 8.6.4: |
Other uses of gene technology / 8.7: |
Genetic Methods for Investigating Bacteria / 9: |
Metabolic pathways / 9.1: |
Complementation / 9.1.1: |
Cross-feeding / 9.1.2: |
Microbial physiology / 9.2: |
Reporter genes / 9.2.1: |
Chromatin immunoprecipitation / 9.2.2: |
Cell division / 9.2.3: |
Motility and chemotaxis / 9.2.4: |
Cell differentiation / 9.2.5: |
Bacterial virulence / 9.3: |
Wide-range mechanisms of bacterial pathogenesis / 9.3.1: |
Detection of virulence genes / 9.3.2: |
Specific mutagenesis / 9.4: |
Gene replacement / 9.4.1: |
Antisense RNA / 9.4.2: |
Taxonomy, evolution and epidemiology / 9.5: |
Molecular taxonomy / 9.5.1: |
GC content / 9.5.2: |
16 S rRNA / 9.5.3: |
Denaturing-gradient gel electrophoresis and temperature-gradient gel electrophoresis / 9.5.4: |
Diagnostic use of PCR / 9.5.5: |
Molecular epidemiology / 9.5.6: |
Gene Mapping to Genomics and Beyond / 10: |
Gene mapping / 10.1: |
Conjugational analysis / 10.1.1: |
Restriction mapping and pulsed-field gel electrophoresis / 10.1.2: |
DNA sequence determination / 10.2: |
Sanger sequencing / 10.2.1: |
Dye terminator sequencing / 10.2.2: |
Pyrosequencing / 10.2.3: |
Massively parallel sequencing / 10.2.4: |
Genome sequencing / 10.3: |
Genome-sequencing strategies / 10.3.1: |
Relating sequence to function / 10.3.2: |
Metagenomics / 10.3.3: |
Comparative genomics / 10.4: |
Microarrays / 10.4.1: |
Analysis of gene expression / 10.5: |
Transcriptional analysis / 10.5.1: |
Translational analysis / 10.5.2: |
Metabolomics / 10.6: |
Systems biology and synthetic genomics / 10.7: |
Systems biology / 10.7.1: |
Synthetic genomics / 10.7.2: |
Conclusion / 10.8: |
Further Reading / Appendix A: |
Abbreviations Used / Appendix B: |
Glossary / Appendix C: |
Enzymes and other Proteins / Appendix D: |
Genes / Appendix E: |
Standard Genetic Code / Appendix F: |
Bacterial Species / Appendix G: |
Index |
?X174 |
Bacteriophage ? |
Lytic and lysogenic regulation of bacteriophage ? |
Bacteriophage ? vectors |
Preface |
Nucleic Acid Structure and Function / 1: |
Structure of nucleic acids / 1.1: |
DNA / 1.1.1: |
RNA / 1.1.2: |
Hydrophobic interactions / 1.1.3: |