Bacterial Genetics and Genomics

  1. Applications and Advanced Topics
    1. Antibiotic Resistance
      1. Resistance Mechanisms
        1. Target Modification
          1. Ribosomal RNA Methylation
            1. Protein Target Alteration
              1. Enzyme Active Site Changes
              2. Drug Inactivation
                1. Beta-Lactamases
                  1. Aminoglycoside-Modifying Enzymes
                    1. Chloramphenicol Acetyltransferases
                    2. Efflux Systems
                      1. Major Facilitator Superfamily
                        1. Resistance-Nodulation-Division Family
                          1. ATP-Binding Cassette Transporters
                            1. Multidrug Efflux Pumps
                            2. Permeability Changes
                              1. Porin Mutations
                                1. Outer Membrane Modifications
                                  1. Cell Wall Alterations
                                2. Resistance Gene Dissemination
                                  1. Plasmid-Mediated Resistance
                                    1. R Plasmid Structure
                                      1. Conjugative Transfer
                                        1. Mobilization Mechanisms
                                        2. Transposon-Mediated Spread
                                          1. Composite Transposons
                                            1. Integron Systems
                                              1. Chromosomal Integration
                                              2. Clonal Spread
                                                1. Epidemic Strains
                                                  1. Clonal Complex Analysis
                                                    1. Population Structure
                                                  2. Clinical and Public Health Impact
                                                    1. Multidrug-Resistant Organisms
                                                      1. Healthcare-Associated Infections
                                                        1. Community-Acquired Resistance
                                                          1. Surveillance Systems
                                                        2. Bacterial Pathogenesis and Virulence
                                                          1. Virulence Factor Genetics
                                                            1. Virulence Gene Regulation
                                                              1. Environmental Sensing
                                                                1. Quorum Sensing Control
                                                                  1. Two-Component Systems
                                                                    1. Global Regulators
                                                                    2. Horizontal Acquisition
                                                                      1. Pathogenicity Islands
                                                                        1. Plasmid-Borne Virulence
                                                                          1. Phage-Mediated Transfer
                                                                        2. Major Virulence Factors
                                                                          1. Adhesion Factors
                                                                            1. Fimbrial Adhesins
                                                                              1. Afimbrial Adhesins
                                                                                1. Biofilm Formation
                                                                                2. Toxins
                                                                                  1. Endotoxins
                                                                                    1. Lipopolysaccharide Structure
                                                                                      1. Pyrogenic Effects
                                                                                        1. Septic Shock
                                                                                        2. Exotoxins
                                                                                          1. A-B Toxins
                                                                                            1. Membrane-Damaging Toxins
                                                                                              1. Superantigens
                                                                                            2. Secretion Systems
                                                                                              1. Type I Secretion
                                                                                                1. Type II Secretion
                                                                                                  1. Type III Secretion
                                                                                                    1. Needle Complex Structure
                                                                                                      1. Effector Proteins
                                                                                                        1. Host Cell Manipulation
                                                                                                        2. Type IV Secretion
                                                                                                          1. Conjugation-Like Systems
                                                                                                            1. DNA and Protein Transfer
                                                                                                            2. Type V Secretion
                                                                                                              1. Type VI Secretion
                                                                                                              2. Immune Evasion
                                                                                                                1. Capsule Formation
                                                                                                                  1. Antigenic Variation
                                                                                                                    1. Complement Resistance
                                                                                                                      1. Intracellular Survival
                                                                                                                  2. Biotechnology and Synthetic Biology
                                                                                                                    1. Recombinant DNA Technology
                                                                                                                      1. Cloning Vectors
                                                                                                                        1. Plasmid Vectors
                                                                                                                          1. Bacteriophage Vectors
                                                                                                                            1. Cosmid Vectors
                                                                                                                              1. BAC and YAC Systems
                                                                                                                              2. Expression Systems
                                                                                                                                1. Promoter Selection
                                                                                                                                  1. Ribosome Binding Sites
                                                                                                                                    1. Codon Optimization
                                                                                                                                      1. Protein Folding
                                                                                                                                      2. Selection and Screening
                                                                                                                                        1. Antibiotic Resistance Markers
                                                                                                                                          1. Blue-White Screening
                                                                                                                                            1. Complementation Systems
                                                                                                                                          2. Metabolic Engineering
                                                                                                                                            1. Pathway Design
                                                                                                                                              1. Enzyme Selection
                                                                                                                                                1. Pathway Optimization
                                                                                                                                                  1. Metabolic Flux Analysis
                                                                                                                                                  2. Strain Development
                                                                                                                                                    1. Knockout Strategies
                                                                                                                                                      1. Overexpression Systems
                                                                                                                                                        1. Regulatory Modifications
                                                                                                                                                        2. Bioproduction Applications
                                                                                                                                                          1. Pharmaceutical Compounds
                                                                                                                                                            1. Industrial Chemicals
                                                                                                                                                              1. Biofuels
                                                                                                                                                            2. CRISPR-Cas Systems
                                                                                                                                                              1. Natural CRISPR Function
                                                                                                                                                                1. Adaptive Immunity
                                                                                                                                                                  1. Spacer Acquisition
                                                                                                                                                                    1. Interference Mechanism
                                                                                                                                                                      1. PAM Recognition
                                                                                                                                                                      2. CRISPR as Biotechnology Tool
                                                                                                                                                                        1. Guide RNA Design
                                                                                                                                                                          1. Cas Nuclease Engineering
                                                                                                                                                                            1. Genome Editing Applications
                                                                                                                                                                              1. Base Editing
                                                                                                                                                                                1. Prime Editing
                                                                                                                                                                              2. Synthetic Biology
                                                                                                                                                                                1. BioBrick Standards
                                                                                                                                                                                  1. Genetic Circuits
                                                                                                                                                                                    1. Biosensors
                                                                                                                                                                                      1. Minimal Genomes
                                                                                                                                                                                    2. Microbial Evolution and Phylogenetics
                                                                                                                                                                                      1. Molecular Taxonomy
                                                                                                                                                                                        1. 16S rRNA Gene Analysis
                                                                                                                                                                                          1. Universal Primers
                                                                                                                                                                                            1. Phylogenetic Markers
                                                                                                                                                                                              1. Database Comparisons
                                                                                                                                                                                              2. Multilocus Sequence Analysis
                                                                                                                                                                                                1. Housekeeping Gene Selection
                                                                                                                                                                                                  1. Allelic Profiling
                                                                                                                                                                                                    1. Population Structure
                                                                                                                                                                                                    2. Whole-Genome Taxonomy
                                                                                                                                                                                                      1. Average Nucleotide Identity
                                                                                                                                                                                                        1. Digital DNA-DNA Hybridization
                                                                                                                                                                                                          1. Genome-Based Classification
                                                                                                                                                                                                        2. Evolutionary Analysis
                                                                                                                                                                                                          1. Molecular Clocks
                                                                                                                                                                                                            1. Mutation Rate Estimation
                                                                                                                                                                                                              1. Calibration Methods
                                                                                                                                                                                                                1. Divergence Time Calculation
                                                                                                                                                                                                                2. Phylogenetic Methods
                                                                                                                                                                                                                  1. Distance-Based Methods
                                                                                                                                                                                                                    1. Maximum Likelihood
                                                                                                                                                                                                                      1. Bayesian Inference
                                                                                                                                                                                                                        1. Tree Validation
                                                                                                                                                                                                                        2. Population Genetics
                                                                                                                                                                                                                          1. Genetic Diversity
                                                                                                                                                                                                                            1. Population Structure
                                                                                                                                                                                                                              1. Migration Patterns
                                                                                                                                                                                                                                1. Selection Pressures
                                                                                                                                                                                                                              2. Horizontal Gene Transfer Detection
                                                                                                                                                                                                                                1. Compositional Analysis
                                                                                                                                                                                                                                  1. Phylogenetic Incongruence
                                                                                                                                                                                                                                    1. Genomic Islands
                                                                                                                                                                                                                                      1. Transfer Quantification
                                                                                                                                                                                                                                    2. Metagenomics
                                                                                                                                                                                                                                      1. Environmental Sampling
                                                                                                                                                                                                                                        1. Sample Collection
                                                                                                                                                                                                                                          1. DNA Extraction Methods
                                                                                                                                                                                                                                            1. Quality Assessment
                                                                                                                                                                                                                                              1. Storage Considerations
                                                                                                                                                                                                                                              2. Sequencing Approaches
                                                                                                                                                                                                                                                1. Amplicon Sequencing
                                                                                                                                                                                                                                                  1. 16S rRNA Gene Amplification
                                                                                                                                                                                                                                                    1. Primer Selection
                                                                                                                                                                                                                                                      1. PCR Bias Considerations
                                                                                                                                                                                                                                                      2. Shotgun Metagenomics
                                                                                                                                                                                                                                                        1. Random Fragmentation
                                                                                                                                                                                                                                                          1. Library Preparation
                                                                                                                                                                                                                                                            1. Sequencing Depth
                                                                                                                                                                                                                                                          2. Data Analysis
                                                                                                                                                                                                                                                            1. Quality Control
                                                                                                                                                                                                                                                              1. Taxonomic Classification
                                                                                                                                                                                                                                                                1. Functional Annotation
                                                                                                                                                                                                                                                                  1. Diversity Analysis
                                                                                                                                                                                                                                                                    1. Statistical Methods
                                                                                                                                                                                                                                                                    2. Metagenome-Assembled Genomes
                                                                                                                                                                                                                                                                      1. Assembly Strategies
                                                                                                                                                                                                                                                                        1. Binning Methods
                                                                                                                                                                                                                                                                          1. Genome Completeness
                                                                                                                                                                                                                                                                            1. Contamination Assessment
                                                                                                                                                                                                                                                                            2. Applications
                                                                                                                                                                                                                                                                              1. Human Microbiome
                                                                                                                                                                                                                                                                                1. Health and Disease
                                                                                                                                                                                                                                                                                  1. Drug Metabolism
                                                                                                                                                                                                                                                                                    1. Immune System Interactions
                                                                                                                                                                                                                                                                                    2. Environmental Studies
                                                                                                                                                                                                                                                                                      1. Ecosystem Function
                                                                                                                                                                                                                                                                                        1. Biogeochemical Cycles
                                                                                                                                                                                                                                                                                          1. Climate Change Impact
                                                                                                                                                                                                                                                                                          2. Biotechnology Applications
                                                                                                                                                                                                                                                                                            1. Enzyme Discovery
                                                                                                                                                                                                                                                                                              1. Pathway Mining
                                                                                                                                                                                                                                                                                                1. Bioremediation

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                                                                                                                                                                                                                                                                                          4. Bacterial Genomics and Bioinformatics

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                                                                                                                                                                                                                                                                                          1. Foundations of Bacterial Genetics