Bacterial Genetics and Genomics

  1. Mechanisms of Genetic Variation and Adaptation
    1. Mutation
      1. Types of Mutations
        1. Point Mutations
          1. Base Substitutions
            1. Transitions
              1. Transversions
              2. Functional Effects
                1. Silent Mutations
                  1. Missense Mutations
                    1. Nonsense Mutations
                  2. Insertion and Deletion Mutations
                    1. Small Indels
                      1. Frameshift Effects
                        1. Reading Frame Restoration
                        2. Large-Scale Chromosomal Changes
                          1. Inversions
                            1. Paracentric Inversions
                              1. Pericentric Inversions
                              2. Duplications
                                1. Tandem Duplications
                                  1. Dispersed Duplications
                                  2. Deletions
                                    1. Small Deletions
                                      1. Large Deletions
                                      2. Translocations
                                    2. Mutation Origins
                                      1. Spontaneous Mutations
                                        1. DNA Replication Errors
                                          1. Polymerase Slippage
                                            1. Proofreading Failures
                                            2. Spontaneous DNA Damage
                                              1. Depurination
                                                1. Deamination
                                                  1. Tautomeric Shifts
                                                2. Induced Mutations
                                                  1. Chemical Mutagens
                                                    1. Base Analogs
                                                      1. 5-Bromouracil
                                                        1. 2-Aminopurine
                                                        2. Alkylating Agents
                                                          1. Methyl Methanesulfonate
                                                            1. Ethyl Methanesulfonate
                                                            2. Intercalating Agents
                                                              1. Acridine Derivatives
                                                                1. Ethidium Bromide
                                                              2. Physical Mutagens
                                                                1. UV Radiation
                                                                  1. Pyrimidine Dimer Formation
                                                                    1. DNA Crosslinking
                                                                    2. Ionizing Radiation
                                                                      1. Free Radical Formation
                                                                        1. DNA Strand Breaks
                                                                  2. DNA Repair Systems
                                                                    1. Direct Repair
                                                                      1. Photoreactivation
                                                                        1. Photolyase Enzyme
                                                                          1. Light-Dependent Repair
                                                                          2. Alkyl Transfer Repair
                                                                            1. Ada Protein Function
                                                                          3. Excision Repair
                                                                            1. Base Excision Repair
                                                                              1. DNA Glycosylases
                                                                                1. AP Endonucleases
                                                                                  1. DNA Polymerase I
                                                                                    1. DNA Ligase
                                                                                    2. Nucleotide Excision Repair
                                                                                      1. UvrABC Excinuclease
                                                                                        1. Damage Recognition
                                                                                          1. Excision and Repair Synthesis
                                                                                        2. Mismatch Repair
                                                                                          1. MutS Protein Function
                                                                                            1. MutL Protein Function
                                                                                              1. MutH Endonuclease
                                                                                                1. Dam Methylation Role
                                                                                                2. Recombinational Repair
                                                                                                  1. Homologous Recombination
                                                                                                    1. RecA Protein Function
                                                                                                      1. Holiday Junction Resolution
                                                                                                      2. SOS Response
                                                                                                        1. LexA Repressor
                                                                                                          1. RecA Coprotease Activity
                                                                                                            1. Error-Prone Repair
                                                                                                              1. Translesion Synthesis Polymerases
                                                                                                          2. Horizontal Gene Transfer
                                                                                                            1. Transformation
                                                                                                              1. Natural Competence
                                                                                                                1. Competence Development
                                                                                                                  1. Competence Factors
                                                                                                                    1. Environmental Triggers
                                                                                                                      1. Species Variation
                                                                                                                      2. DNA Uptake Mechanisms
                                                                                                                        1. DNA Binding Proteins
                                                                                                                          1. Transport Machinery
                                                                                                                            1. Membrane Channels
                                                                                                                              1. DNA Processing
                                                                                                                              2. DNA Integration
                                                                                                                                1. Homologous Recombination
                                                                                                                                  1. Illegitimate Recombination
                                                                                                                                    1. Recombination Frequency
                                                                                                                                    2. Artificial Transformation
                                                                                                                                      1. Chemical Methods
                                                                                                                                        1. Calcium Chloride Treatment
                                                                                                                                          1. Competent Cell Preparation
                                                                                                                                          2. Physical Methods
                                                                                                                                            1. Electroporation
                                                                                                                                              1. Microinjection
                                                                                                                                          3. Conjugation
                                                                                                                                            1. F Plasmid System
                                                                                                                                              1. F Plasmid Structure
                                                                                                                                                1. tra Gene Organization
                                                                                                                                                  1. Pilus Structure and Function
                                                                                                                                                    1. DNA Transfer Process
                                                                                                                                                    2. Mating Types
                                                                                                                                                      1. F+ Cells
                                                                                                                                                        1. F- Cells
                                                                                                                                                          1. Hfr Cells
                                                                                                                                                            1. F Plasmid Integration
                                                                                                                                                              1. Chromosomal Transfer
                                                                                                                                                                1. Mapping by Interrupted Mating
                                                                                                                                                                2. F' Cells
                                                                                                                                                                  1. F' Plasmid Formation
                                                                                                                                                                    1. Merodiploid Creation
                                                                                                                                                                  2. Conjugation Process
                                                                                                                                                                    1. Cell Contact
                                                                                                                                                                      1. Pilus Retraction
                                                                                                                                                                        1. DNA Nicking and Transfer
                                                                                                                                                                          1. Complementary Strand Synthesis
                                                                                                                                                                          2. Gram-Positive Conjugation
                                                                                                                                                                            1. Pheromone Systems
                                                                                                                                                                              1. Aggregation Substances
                                                                                                                                                                                1. Plasmid Transfer Mechanisms
                                                                                                                                                                              2. Transduction
                                                                                                                                                                                1. Bacteriophage Biology
                                                                                                                                                                                  1. Phage Structure
                                                                                                                                                                                    1. Host Range Determination
                                                                                                                                                                                      1. Infection Process
                                                                                                                                                                                      2. Lytic Cycle
                                                                                                                                                                                        1. Phage Attachment
                                                                                                                                                                                          1. DNA Injection
                                                                                                                                                                                            1. Replication and Transcription
                                                                                                                                                                                              1. Lysis and Release
                                                                                                                                                                                              2. Lysogenic Cycle
                                                                                                                                                                                                1. Prophage Integration
                                                                                                                                                                                                  1. Lysogenic Conversion
                                                                                                                                                                                                    1. Prophage Induction
                                                                                                                                                                                                    2. Generalized Transduction
                                                                                                                                                                                                      1. Random DNA Packaging
                                                                                                                                                                                                        1. Pac Site Recognition
                                                                                                                                                                                                          1. Transducing Particle Formation
                                                                                                                                                                                                            1. Recipient Cell Infection
                                                                                                                                                                                                            2. Specialized Transduction
                                                                                                                                                                                                              1. Site-Specific Integration
                                                                                                                                                                                                                1. Imprecise Excision
                                                                                                                                                                                                                  1. Adjacent Gene Transfer
                                                                                                                                                                                                                    1. Lambda Phage System
                                                                                                                                                                                                                2. Mobile Genetic Elements
                                                                                                                                                                                                                  1. Insertion Sequences
                                                                                                                                                                                                                    1. IS Element Structure
                                                                                                                                                                                                                      1. Terminal Inverted Repeats
                                                                                                                                                                                                                        1. Transposase Gene
                                                                                                                                                                                                                          1. Target Site Duplication
                                                                                                                                                                                                                          2. Transposition Mechanisms
                                                                                                                                                                                                                            1. Conservative Transposition
                                                                                                                                                                                                                              1. Replicative Transposition
                                                                                                                                                                                                                                1. Target Site Selection
                                                                                                                                                                                                                                2. IS Element Families
                                                                                                                                                                                                                                  1. IS1 Family
                                                                                                                                                                                                                                    1. IS3 Family
                                                                                                                                                                                                                                      1. IS5 Family
                                                                                                                                                                                                                                        1. IS21 Family
                                                                                                                                                                                                                                      2. Transposons
                                                                                                                                                                                                                                        1. Composite Transposons
                                                                                                                                                                                                                                          1. Structure Organization
                                                                                                                                                                                                                                            1. Flanking IS Elements
                                                                                                                                                                                                                                              1. Central Region Genes
                                                                                                                                                                                                                                                1. Antibiotic Resistance Carriage
                                                                                                                                                                                                                                                2. Complex Transposons
                                                                                                                                                                                                                                                  1. Tn3 Family
                                                                                                                                                                                                                                                    1. Transposition Mechanism
                                                                                                                                                                                                                                                      1. Resolution Process
                                                                                                                                                                                                                                                        1. Cointegrate Formation
                                                                                                                                                                                                                                                        2. Conjugative Transposons
                                                                                                                                                                                                                                                          1. Self-Transfer Ability
                                                                                                                                                                                                                                                            1. Integration Mechanisms
                                                                                                                                                                                                                                                              1. Excision and Circularization
                                                                                                                                                                                                                                                            2. Integrons
                                                                                                                                                                                                                                                              1. Integron Structure
                                                                                                                                                                                                                                                                1. Integrase Gene
                                                                                                                                                                                                                                                                  1. Attachment Sites
                                                                                                                                                                                                                                                                    1. Promoter Elements
                                                                                                                                                                                                                                                                    2. Gene Cassettes
                                                                                                                                                                                                                                                                      1. Cassette Structure
                                                                                                                                                                                                                                                                        1. Site-Specific Recombination
                                                                                                                                                                                                                                                                          1. Cassette Arrays
                                                                                                                                                                                                                                                                          2. Role in Antibiotic Resistance
                                                                                                                                                                                                                                                                            1. Resistance Gene Capture
                                                                                                                                                                                                                                                                              1. Expression from Common Promoter
                                                                                                                                                                                                                                                                            2. Genomic Islands
                                                                                                                                                                                                                                                                              1. Pathogenicity Islands
                                                                                                                                                                                                                                                                                1. Virulence Gene Clusters
                                                                                                                                                                                                                                                                                  1. Horizontal Acquisition
                                                                                                                                                                                                                                                                                    1. Integration Sites
                                                                                                                                                                                                                                                                                      1. Mobility Elements
                                                                                                                                                                                                                                                                                      2. Symbiosis Islands
                                                                                                                                                                                                                                                                                        1. Nitrogen Fixation Genes
                                                                                                                                                                                                                                                                                          1. Host Interaction Genes
                                                                                                                                                                                                                                                                                          2. Metabolic Islands
                                                                                                                                                                                                                                                                                            1. Catabolic Pathways
                                                                                                                                                                                                                                                                                              1. Environmental Adaptation

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                                                                                                                                                                                                                                                                                        4. Bacterial Genomics and Bioinformatics