Jeff Tabor/UCSF Synthetic Biology Team Challenge: Difference between revisions
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Remove all EcoRI, XbaI, SpeI and PstI sites and annotate those mutations<br> | Remove all EcoRI, XbaI, SpeI and PstI sites and annotate those mutations<br> | ||
Initiate each ORF with an ATG and terminate with 2-consecutive TAA's <br> | Initiate each ORF with an ATG and terminate with 2-consecutive TAA's <br> | ||
(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 <br> unless they're obvious | (note: ribosome binding sites tend to have 5'-AGGA(N6-11)ATG-3' sequences around the start codon). <br> you don't have to document all of these <br> unless they're obvious | ||
*Day 2 | *Day 2 | ||
Revision as of 14:46, 19 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
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
Notes/Powerpoint
Day 1 Lab: Specify an operon >5kb from the literature in the registry.
Specify each promoter, open reading frame and transcription terminator separately
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
- 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
- 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.
