Jeff Tabor/UCSF Synthetic Biology Team Challenge
*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
- 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)
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.
- Elowitz and Leibler, Nature. 2000
- Gardner et al., Nature 2000
- Guet et al., Science 2002
- Yokobayashi et al., PNAS 2002
- Kobayashi et al., PNAS 2004
- Basu et al., PNAS 2004
- Isaacs et al., Nat. Biotechnol. 2004
- Endy, Nature 2005
- Basu et al., Nature 2005
- Chan et al., Nature/EMBO MSB 2005
- Levskaya et al., Nature 2005
- Anderson et al., JMB 2005
- Bayer and Smolke, Nat. Biotechnol. 2005
- Rackham and Chin, Nat. Chem. Biol., 2005
- Posfai et al., Science 2006.