Jeff Tabor/UCSF Synthetic Biology Team Challenge: Difference between revisions

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  Lab: Design a synthetic gene expression system with XOR logic.  Use parts already in the registry or design your own <br>
  Lab: Design a synthetic gene expression system with XOR logic.  Use parts already in the registry or design your own <br>
  Specify the system in the registry. <br>
  Specify the system in the registry. <br>
  Checkpoint @ ~4PM.  Teams will chalkboard nascent ideas and get feedback from instructors, other teams.  
  Checkpoint @ ~4PM.  Teams will chalkboard nascent ideas and get feedback from instructors, other teams. <br>
[http://openwetware.org/wiki/Image:Jt_day_2.ppt Jeff's day 2 slides]


*Day 3
*Day 3

Revision as of 15:59, 20 March 2007

General Information

*Dates: March 19 - March 23, 2007.
*Final presentations: March 26, 11-1230AM 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 


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
  • Day 3
  • Day 4
  • Day 5

Final Presentation/Rubric

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.
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