Genome

1. I know you are all familiar with genome projects in terms of their output, but lets review the typical steps in a genome project. First is the sequencing phase in which enough small random genomic clones are sequenced to cover the genome many times over. Next comes the assembly phase in which computer pattern-matching algorithms complemented with directed cloning and sequencing try to bring all the pieces of the puzzle together. Finally, the sequence is analyzed for what it can tell us about gene content, gene function, and evolution. This is known as sequence annotation. Ultimately, this annotation brings us back to the lab where we connect genes to functions. Let me give you 3 quick examples from my own work over the past 12 years of how undergrads can make a difference.I know you are all familiar with genome projects in terms of their output, but lets review the typical steps in a genome project. First is the sequencing phase in which enough small random genomic clones are sequenced to cover the genome many times over. Next comes the assembly phase in which computer pattern-matching algorithms complemented with directed cloning and sequencing try to bring all the pieces of the puzzle together. Finally, the sequence is analyzed for what it can tell us about gene content, gene function, and evolution. This is known as sequence annotation. Ultimately, this annotation brings us back to the lab where we connect genes to functions. Let me give you 3 quick examples from my own work over the past 12 years of how undergrads can make a difference.

2. I know you are all familiar with genome projects in terms of their output, but lets review the typical steps in a genome project. First is the sequencing phase in which enough small random genomic clones are sequenced to cover the genome many times over. Next comes the assembly phase in which computer pattern-matching algorithms complemented with directed cloning and sequencing try to bring all the pieces of the puzzle together. Finally, the sequence is analyzed for what it can tell us about gene content, gene function, and evolution. This is known as sequence annotation. Ultimately, this annotation brings us back to the lab where we connect genes to functions. Let me give you 3 quick examples from my own work over the past 12 years of how undergrads can make a difference.I know you are all familiar with genome projects in terms of their output, but lets review the typical steps in a genome project. First is the sequencing phase in which enough small random genomic clones are sequenced to cover the genome many times over. Next comes the assembly phase in which computer pattern-matching algorithms complemented with directed cloning and sequencing try to bring all the pieces of the puzzle together. Finally, the sequence is analyzed for what it can tell us about gene content, gene function, and evolution. This is known as sequence annotation. Ultimately, this annotation brings us back to the lab where we connect genes to functions. Let me give you 3 quick examples from my own work over the past 12 years of how undergrads can make a difference.

3. Why Functional Genomics?Students Connecting Genes to Functions We all teach glycolysis & gluconeogenesis, but how many of us have actually gone to the trouble of proving that a particular organism can carry out these processes. Our students can become just such experts through sequence annotation. For 2 of the genomes that my students and I have worked on over the past 12 years, we have been unable to find the typical fructose-1,6-bisphosphatase involved in gluconeogenesis. What to do? Send students to the literature � is there a 2nd way to do the same job? Actually, there are 6 different types of FBPase! But our two genomes have none of the 6, so there must be at least 7 different ways.We all teach glycolysis & gluconeogenesis, but how many of us have actually gone to the trouble of proving that a particular organism can carry out these processes. Our students can become just such experts through sequence annotation. For 2 of the genomes that my students and I have worked on over the past 12 years, we have been unable to find the typical fructose-1,6-bisphosphatase involved in gluconeogenesis. What to do? Send students to the literature � is there a 2nd way to do the same job? Actually, there are 6 different types of FBPase! But our two genomes have none of the 6, so there must be at least 7 different ways.

4. Forward genetics is still incredibly useful, especially when we use all the tricks of the trade at our disposal. On this slide, the teacher in each of us should see concept and skill development: mutagenesis, transposons, mutant hunts, biochemical complementation, plasmid isolation and characterization, and sequence analysis. The researcher in us all should see a great way to connect genes to functions.Forward genetics is still incredibly useful, especially when we use all the tricks of the trade at our disposal. On this slide, the teacher in each of us should see concept and skill development: mutagenesis, transposons, mutant hunts, biochemical complementation, plasmid isolation and characterization, and sequence analysis. The researcher in us all should see a great way to connect genes to functions.

5. Forward GeneticsStudents Filling in Holes in Annotation We all teach glycolysis & gluconeogenesis, but how many of us have actually gone to the trouble of proving that a particular organism can carry out these processes. Our students can become just such experts through sequence annotation. For 2 of the genomes that my students and I have worked on over the past 12 years, we have been unable to find the typical fructose-1,6-bisphosphatase involved in gluconeogenesis. What to do? Send students to the literature � is there a 2nd way to do the same job? Actually, there are 6 different types of FBPase! But our two genomes have none of the 6, so there must be at least 7 different ways.We all teach glycolysis & gluconeogenesis, but how many of us have actually gone to the trouble of proving that a particular organism can carry out these processes. Our students can become just such experts through sequence annotation. For 2 of the genomes that my students and I have worked on over the past 12 years, we have been unable to find the typical fructose-1,6-bisphosphatase involved in gluconeogenesis. What to do? Send students to the literature � is there a 2nd way to do the same job? Actually, there are 6 different types of FBPase! But our two genomes have none of the 6, so there must be at least 7 different ways.

6. Forward GeneticsStudents Filling in Holes in Annotation Have a Tn hit in gene Atu3885: - annotated as myo-inositol monophosphatase family member - mutation leads to auxotroph - now know it cannot make histidine - TIGR Fam hit to alternative histidinol-P phosphatase � now proven through experimentation We all teach glycolysis & gluconeogenesis, but how many of us have actually gone to the trouble of proving that a particular organism can carry out these processes. Our students can become just such experts through sequence annotation. For 2 of the genomes that my students and I have worked on over the past 12 years, we have been unable to find the typical fructose-1,6-bisphosphatase involved in gluconeogenesis. What to do? Send students to the literature � is there a 2nd way to do the same job? Actually, there are 6 different types of FBPase! But our two genomes have none of the 6, so there must be at least 7 different ways.We all teach glycolysis & gluconeogenesis, but how many of us have actually gone to the trouble of proving that a particular organism can carry out these processes. Our students can become just such experts through sequence annotation. For 2 of the genomes that my students and I have worked on over the past 12 years, we have been unable to find the typical fructose-1,6-bisphosphatase involved in gluconeogenesis. What to do? Send students to the literature � is there a 2nd way to do the same job? Actually, there are 6 different types of FBPase! But our two genomes have none of the 6, so there must be at least 7 different ways.

7. Getting Transposon into Host Cells

8. Getting Transposon into Host CellsTransformation

9. Getting Transposon into Host CellsTransduction

10. Getting DNA into CellsConjugation

15. Transposon Mutagenesis Cloning Out Tn Insertions