1. Does gene order matter? Cis-regulatory elements, proteins, and messengers are integrated into biological circuits. Does gene location in the genome affect the circuit? Genome evolution – gene order does matter that’s why we observe synteny

2. Gene order in T7 T7 produces 59 proteins from 56 genes…only 33 have known function T7 infection is unique, first 850 bp are inserted, transcription begins, then the remainder is pulled in E. coli polymerase pulls the first 15% of genomic DNA into the cell at ~45 bp/sec through transcription at 5 promoters– what a cool molecular machine

3. Gene 1 T7 RNA polymerase Uses 17 different promoters in the remaining 85% of genome Pulls at a rate of 200 bp per second. What happens if Gene 1 is moved elsewhere on the genome?

4. In silico analysis http://model.mit.edu/cgi-bin/t7web/t7v2.5 Measured optimal time for phage-induced lysis for 72 distinct T7 genomes Some genotypes were better than others T7 is suboptimal? Where’s the data?

5. Experiments Three phage genome constructs were generated and tested at positions 1.7, 3.8 and 12 (controls had random DNA inserted at these positions or a late promoter inserted early in genome) Little agreement between predicted and experimental data

6. Systems biology Watson School of Biological Sciences at CSH “…The systems approach defines all of th eelements in a system and then studies how each behaves in relation to the others as the system is functioning. Ultimately the systems approach requires mathematical model which will both describe the nature of the system and its systems properties.”

7. “Systems Biology Superstars” Integration of multiple -omes: –Metabolomics –Proteomics –Genomics “Looking at individual silos of genomics, proteomics, or metabolomics is akin to using a laser pointer in a dark office to describe its contents…”

8. Galactose metabolism in yeast as an example Define all genes in the genome and the subset of genes, proteins and other molecules constituting the galactose pathway..build a model Perturb each pathway component using genetics or environmental challenges Utilize microarrays and ICAT to collect gene expression data Refine model

9. Functional genomics Grew wild type and deletion strains and assessed gene expression via microarrays Used Northerns as controls How reliable are microarrays?

10. Proteomics http://occawlonline.pearsoned.com/bookbin d/pubbooks/bc_mcampbell_genomics_1/me dialib/method/ICAT/ICAT.htmlhttp://occawlonline.pearsoned.com/bookbin d/pubbooks/bc_mcampbell_genomics_1/me dialib/method/ICAT/ICAT.html Measured 289 proteins using ICAT, only 30 observed differences; 15 of which showed no change in RNA levels, post- transcriptional control

11. Going system… http://depts.washington.edu/sfields/ Ideker uses Fields protein interaction data to identify 997 mRNA and 15 proteins whose expression is altered by galactose Discovery questions 7-9 in Chapter 9 I relent on the writing: “Typically, if good data conflict with your model, trust your data”