Jeff Tabor/UCSF Synthetic Biology Team Challenge

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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

References

  • 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.