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Introduction | |
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The Biological Universe | |
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What Is Genetics? | |
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Bacterial Genetics | |
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Phage Genetics | |
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A Brief History of Bacterial Molecular Genetics | |
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What's Ahead | |
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The Bacterial Chromosome: DNA Structure, Replication, and Segregation | |
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DNA Structure | |
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The Mechanism of DNA Replication | |
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Replication Errors | |
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Replication of the Bacterial Chromosome and Cell Division | |
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The Bacterial Nucleoid | |
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The Bacterial Genome | |
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Antibiotics That Affect Replication and DNA Structure | |
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Molecular Biology Manipulations with DNA | |
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Linear Chromosomes in Bacteria | |
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Restarting Replication Forks | |
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The Bacterial Cytoskeleton and Bacterial Cell Biology | |
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Features of Bacterial Genomes | |
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Bacterial Genome Sequencing | |
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Bacterial Gene Expression: Transcription, Translation, and Protein Folding | |
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Overview | |
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The Structure and Function of RNA | |
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Transcription | |
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Proteins | |
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Protein Folding | |
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Membrane Proteins and Protein Export | |
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Introns and Inteins | |
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Useful Concepts | |
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Antibiotics That Block Transcription and Translation | |
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Molecular Phylogeny | |
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Mimicry in Translation | |
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Exceptions to the Code | |
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Traffic Jams on mRNA: Removing Stalled Ribosomes with tmRNA | |
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Stability and Degradation of mRNA | |
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Selfish DNAs: RNA Introns and Protein Inteins | |
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Annotation and Comparative Genomics | |
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Bacterial Genetic Analysis: Forward and Reverse | |
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Definitions | |
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Useful Phenotypes in Bacterial Genetics | |
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Inheritance in Bacteria | |
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Mutation Rates | |
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Types of Mutations | |
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Reversion versus Suppression | |
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Genetic Analysis in Bacteria | |
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Gene Replacements and Reverse Genetics | |
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Isolation of Tandem Duplications of the his Operon in Salmonella enterica Serovar Typhimurium | |
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Statistical Analysis of the Number of Mutants per Culture | |
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Inversions and the Genetic Map | |
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Plasmids | |
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What Is a Plasmid? | |
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Properties of Plasmids | |
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Constructing a Plasmid Cloning Vector | |
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Plasmids and Bacterial Pathogenesis | |
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Linear Plasmids | |
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An Incompatibility Group of One's Own | |
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Plasmid Addiction | |
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Conjugation | |
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Overview | |
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Mechanism of DNA Transfer during Conjugation in Gram-Negative Bacteria | |
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Chromosome Transfer by Plasmids | |
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Transfer Systems of Gram-Positive Bacteria | |
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Other Types of Transmissible Elements | |
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Gene Exchange between Kingdoms | |
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Conjugation and Type IV Protein Secretion Systems | |
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Conjugation in Streptomycetes | |
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Conjugative Transposons (Integrating Conjugative Elements) | |
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Transformation | |
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Natural Transformation | |
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Importance of Natural Transformation for Forward and Reverse Genetics | |
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Artificially Induced Competence | |
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Antigenic Variation in Neisseria gonorrhoeae | |
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Lytic Bacteriophages: Development, Genetics, and Generalized Transduction | |
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The Bacteriophage Lytic Development Cycle | |
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Phage DNA Replication | |
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Phage Lysis | |
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Genetic Analysis of Phages | |
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Generalized Transduction | |
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RNA Phages | |
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Phage Display | |
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Protein Priming | |
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Lysogeny: the ? Paradigm and the Role of Lysogenic Conversion in Bacterial Pathogenesis | |
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Phage ? | |
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Replication of ? DNA | |
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Lysogeny | |
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Specialized Transduction | |
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Other Lysogen-Forming Phages | |
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Lysogenic Conversion and Bacterial Pathogenesis | |
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Genetic Experiments with Phage ? | |
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Effects of Prophage Integration on the Host | |
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Retroregulation | |
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How a Pathogenicity Island Gets Around | |
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Transposition, Site-Specific Recombination, and Families of Recombinases | |
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Transposition | |
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Mechanisms of Transposition | |
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Details of Transposition by the DDE Transposons | |
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Rolling-Circle Transposons | |
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Y and S Transposons | |
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General Properties of Transposons | |
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Transposon Mutagenesis | |
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Site-Specific Recombination | |
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Y and S Recombinases | |
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Importance of Transposition and Site-Specific Recombination in Bacterial Adaptation | |
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Phage Mu: a Transposon Masquerading as a Phage | |
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Transposon Mutagenesis In Vitro | |
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Molecular Mechanisms of Homologous Recombination | |
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Overview of Recombination | |
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Molecular Models of Recombination | |
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The Molecular Basis for Recombination in E. coli | |
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Phage Recombination Pathways | |
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Genetic Analysis of Recombination in Bacteria | |
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Breaking and Entering: Introns and Inteins Move by Double-Strand Break Repair or Retrohoming | |
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The Three R's: Recombination, Replication, and Repair | |
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Recombineering: Gene Replacements in E. coli with Phage ? Recombination Functions | |
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DNA Repair and Mutagenesis | |
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Evidence for DNA Repair | |
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Specific Repair Pathways | |
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General Repair Mechanisms | |
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DNA Damage Tolerance Mechanisms | |
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Summary of Repair Pathways in E. coli | |
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Bacteriophage Repair Pathways | |
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Oxygen: the Enemy Within | |
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Cancer and Mismatch Repair | |
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Transcription-Repair Coupling | |
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Translesion Synthesis and Cancer | |
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The Ames Test | |
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Regulation of Gene Expression: Operons | |
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Transcriptional Regulation in Bacteria | |
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Negative Transcriptional Regulation | |
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Positive Regulation | |
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Regulation by Attenuation of Transcription | |
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Posttranslational Regulation: Feedback Inhibition | |
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Operon Analysis for Sequenced Genomes | |
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The Helix-Turn-Helix Motif of DNA-Binding Proteins | |
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Families of Regulators | |
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Global Regulation: Regulons and Stimulons | |
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Catabolite-Sensitive Operons | |
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Regulation of Nitrogen Assimilation | |
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Stress Responses in Bacteria | |
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Extracytoplasmic (Envelope) Stress Responses | |
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Iron Regulation in E. coli | |
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Regulation of Virulence Genes in Pathogenic Bacteria | |
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Regulation of Ribosome and tRNA Synthesis | |
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Microarray and Proteomic Analysis of Regulatory Networks | |
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cAMP-Independent Catabolite Repression | |
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Nitrogen Fixation | |
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Sigma Factors | |
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Signal Transduction Systems in Bacteria | |
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Regulatory RNAs | |
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Bacterial Cell Compartmentalization and Sporulation | |
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Analysis of Protein Transport in Escherichia coli | |
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Genetic Analysis of Transmembrane Domains of Inner Membrane Proteins in Gram-Negative Bacteria | |
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Protein Secretion | |
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Genetic Analysis of Sporulation in Bacillus subtilis | |
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Secretion Systems and Motility | |
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Phosphorelay Activation of the Transcription Factor Spo0A | |
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Answers to Questions for Thought and Problems | |
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Glossary | |
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Figure and Table Credits | |
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Index | |