Course Syllabus and Supplemental Topics:

1. What is genetics?
   1. What you can learn from genomics
      • Physical mapping of chromosomes: Pulsed field gel electrophoresis
      • Genomic DNA sequence analysis
      • DNA chips and microarrays
   2. What you can't learn from genomics - who needs genetics in a post-genome era?

2. Chromosomes, genes, and proteins
   1. Prokaryotes vs Eukaryotes
   2. Genome size
   3. Chromosome organization
   4. DNA - RNA - Protein: A review of central dogma
      • DNA replication
      • Supercoiling
      • Transcription
      • Translation
      • Polarity

3. Mutants and mutations
   1. DNA Damage and repair: What causes mutations?
      • DNA damage mechanisms
        • Spontaneous
        • Mutagens
      • DNA repair mechanisms
        • Direct repair: photolyase and Ada
        • Mismatch repair: mutSLH
        • Recombinational repair: recA, recFOR, and recBCD
        • SOS and translesion synthesis: umuCD
      • Mutator genes
   2. Mutations
      • Types of mutations
        • Effect on the DNA sequence: point mutations, insertions, deletions, and rearrangements
        • Effect on the gene product
          • Loss of function mutants: null, leaky, and conditional mutations
          • Gain of function mutants
      • Are mutations random events or adaptive?
      • Mutation rates, probability, and target theory
   3. Mutants
      • Isolation of mutants: Selections, screens, and enrichments
      • Uses of mutants
      • Genotype vs phenotype, genetic nomenclature, wild-type and isogenic strains

4. Reversion and suppression
   1. Intragenic Reversion
      • True revertants
      • Second-site intragenic revertants of missense and frameshift mutations
      • Reversion as a test of cause and effect
      • Reversion assays to detect mutagens and carcinogens
   2. Intergenic reversion: Suppression
      • Informational suppressors
      • Interaction suppressors: allele specificity
      • Physiological suppression
      • Multicopy suppressors
      • Suppressor analysis
   3. Synthetic lethal mutations

5. Genetic analysis of mutants
   1. Complementation
      • In vitro complementation: Cross-feeding
      • In vivo complementation: dominance and cis/trans tests
   2. Genetic recombination
      • Mechanisms of recombination
      • Tests of epistasis
      • Isogenic strains

6. Genetic exchange
   1. Mechanisms of genetic exchange: transformation, conjugation, and transduction
   2. Genetic exchange in nature
   3. Genetic exchange in the lab
   4. Barriers to genetic exchange: host restriction and modification

7. Transformation
   1. Discovery of transformation
   2. Natural competence
   3. Chemical transformation
   4. Electrotransformation
   5. Genetic mapping by transformation

8. Plasmids
   1. Properties of some bacterial plasmids
   2. Plasmid replication
      • Origin of replication and replication proteins
      • Partitioning of plasmids at cell division
      • Regulation of plasmid copy number and amplification
      • Incompatibility
   3. Conjugation
      • Cell-cell contact and adhesion
      • Mobilization and transfer
      • Regulation of conjugation
      • HFR strains
        • Isolation of HFR strains
        • Interrupted mating and time-of-entry mapping
        • Chromosome transfer in other bacteria
      • Isolation of F' plasmids
   4. Suicide plasmids and allele replacement

9. Phage
   1. General properties of phages
      • Lytic growth
      • Host specificity
   2. Lysogenic phage
      • Phage Lambda
        • Lysis: Transcription, DNA replication, maturation, and assembly
        • Lysogeny
          • Discovery: zygotic induction, immunity, and clear-plaque mutants
          • Repression: cI, cII, cIII, and cro
          • Integration and excision
          • Prophage induction
          • What determines the lysis-lysogeny decision?
      • Phage P22 - Antirepressor and superinfection immunity
      • Phage P1 - Plasmid prophage
      • Lysogenic conversion
   3. Transduction
      • Specialized transduction
      • Generalized transduction: Phage P22 and P1
      • Cotransduction, linkage and multifactor crosses
      • Genetic mapping: How and why? (Why not just sequence?)

10. Transposable elements
    1. Insertion sequences, transposons, and integrons
    2. Transposition
       • Structure of transposons and target-sites
       • Replicative transposition
       • Nonreplicative transposition
       • Excision and transposase-mediated rearrangements
       • Regulation of transposition
    3. Phage Mu
    4. Use of transposons to isolate mutations in genes
       • Transposon insertions
    5. Use of transposons as portable regions of homology
       • Local mutagenesis
       • Chromosomal rearrangements
       • In vivo cloning
    6. Transposons and evolution

11. Genetic regulation
    1. Regulation of gene expression: A brief review of paradigms
       1. Repression
       2. Activation
       3. Attenuation
       4. Antisense control
    2. Genetic approaches for studying gene regulation
       • Reporter genes
         • Advantages and disadvantages of different reporter genes
         • Gene and operon fusions
       • Uses of fusions
         • Genetic regulation
         • Identification of genes regulated by particular environmental conditions (IVET, RIVET, STM, GAMBIT)
         • Protein-protein interactions
         • DNA-protein interactions: Challenge phage
         • Protein localization
    3. In vitro approaches for studying DNA-protein interactions
       • Gel shift assays
       • Footprinting assays
       • Surface plasmon resonance

12. In vitro genetics
    1. Cloning and expression vectors
    2. Purification tag vectors
    3. DNA sequence analysis: What does sequence similarity tell you?
    4. Site-directed mutagenesis
       • "Playing god" - When and why use site directed mutagenesis?
       • Constructing deletions
       • Constructing point mutations at random sites in a particular region of DNA
       • Constructing point mutations at a particular base pair
       • Reversion of site-directed mutations
    5. Polymerase chain reaction
       • Amplification
       • Mutagenesis
       • Inverse PCR

13. Genomics
    1. Genome sequencing - some examples of microbial genome sequencing projects
    2. Analysis of genome sequences - tools and resources at the NCBI
    3. Predicting metabolism from DNA sequences - WIT
    4. DNA chips - studying gene expression using DNA microarrays
    5. Proteomics

14. Genetic analysis of other bacteria
    1. Paradigm organisms
    2. Developing a genetic toolkit
    3. Surrogate genetics

Please send comments, suggestions, or questions to smaloy@sciences.sdsu.edu
Contents last modified April 6, 2006