Jeff Tabor/UCSF Synthetic Biology Team Challenge

General Information
*Dates: March 19 - March 23, 2007. *Final presentations: March 26, 1:30-3:00PM GH114

*Location: M-W, F: 9AM-12PM BH 211 TH: 9AM-12PM BH 212 M-F: 9AM-5PM N114

*Breakfast/coffee @845AM every day. *Lunch @~12:30 in N114 every day.

*Contact Jeff Tabor: jeff DOT tabor AT gmail DOT com Howard Salis: howard DOT salis AT gmail DOT com

Schedule
Schedule

Groups

 * 1. Charles, Laura, Sheel (part #'s: J64700-J64799)
 * 2. David, Sai, Rebeca, Jeremy (part #'s: J64800-J64899)
 * 3. Maya, Ryan, Reid, Kris(part #'s: J64900-J64999)

Background Material
A Short Introduction to Modeling Gene Networks

Links
MIT's registry of biological parts EcoCyc E.coli encyclopedia KEGG DAS organism annotation database Colibri E.coli genome browser regulondb

Notes/Powerpoint
Day 1 Lab: Specify an operon >5kb from the literature in the registry. Parts:Specify each promoter, rbs, open reading frame and transcription terminator as a separate part Document the function of each part Document any subfeatures (i.e. -35, -10 sequence, operator sites, etc.) Remove all EcoRI, XbaI, SpeI and PstI sites and annotate those mutations Initiate each ORF with an ATG and terminate with 2-consecutive TAA's (note: ribosome binding sites tend to have 5'-AGGA(N6-11)ATG-3' sequences around the start codon). you don't have to document all of these unless they're obvious Jeff's day 1 slides

Day 2 Lab: Design a synthetic gene expression system with XOR logic. Use parts already in the registry or design your own Specify the system in the registry. Checkpoint @ ~4PM. Teams will chalkboard nascent ideas and get feedback from instructors, other teams. Jeff's day 2 slides Howard's day 2 slides

Day 3 Lab: Begin developing a model of your proposed synthetic gene network. Use the provided Matlab files as a starting point. SigmaFactors.m: Explore how changing the amounts of available sigma factor affect active RNA polymerase (Holoenzyme) numbers. BasalExpression.m: Determine the effects of the number of active sigma factors and genome competition on basal gene expression. Gene_Basal.m: A template of a function describing the basal expression of a gene. Gene_Repression.m: A template of a function describing the repressed expression of a gene (with two overlapping, repressor-binding operators with possible cooperativity). BistableSwitch.m: A template of a system of ordinary differential equations describing the bistable toggle switch (a system of two genes, each producing a repressor that represses the other gene.)

Day 4 12:30: Lunch GH 114 1:30: Checkpoint. Teams chalkboard project status and receive feedback from instructors/other students.

Day 5 12:30: Lunch GH 114 1:30: Checkpoint. Teams chalkboard project status and receive feedback from instructors/other students.

Final Presentation/Rubric
Powerpoint guideline for final presentation