IGEM:Harvard/2006/Cyanobacteria: Difference between revisions
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***Also can measure KaiC activity; create a chimeric protein w/GFP | ***Also can measure KaiC activity; create a chimeric protein w/GFP | ||
**Synthesis of ~3kb KaiABC w/ codon replacement of Ala of Leu to use in E. coli | **Synthesis of ~3kb KaiABC w/ codon replacement of Ala of Leu to use in E. coli | ||
***.11/bp w/o error correction; $2/bp with error correction (Tian et. al 2004) | |||
****But the Church lab has a better way of doing this? | |||
***Provides backup in case direct movement of KaiABC into E. coli fails | ***Provides backup in case direct movement of KaiABC into E. coli fails | ||
***Codon bias problem with 2 amino acids (can't find source but I found it the other day): then, we can synthetically modify the codons for these 2 aa's to be compatiable in e. coli | ***Codon bias problem with 2 amino acids (can't find source but I found it the other day): then, we can synthetically modify the codons for these 2 aa's to be compatiable in e. coli |
Revision as of 17:16, 17 June 2006
Organization Suggestions
3000bp, 11cents/base. --> synthetic
Think about these questions when preparing your project proposals for the group meeting.
For each project idea:
- What is the specific goal of the project?
- Biobrick KaiABC oscillator (for use in either cyanobacteria AND/OR e. coli)
- [1] Shows the location of kaiA,BC in WH8102 strain. 2.866kb for kaiABC + non-coding region.
- Research shows that KaiABC show oscillation independently (Nakajima et al. 2005)
- Test the oscillator in E. coli to create a "nightlight"
- Use a luciferase gene reporter, which was done in (Kondo et al. 2000)
- Also can measure KaiC activity; create a chimeric protein w/GFP
- Synthesis of ~3kb KaiABC w/ codon replacement of Ala of Leu to use in E. coli
- .11/bp w/o error correction; $2/bp with error correction (Tian et. al 2004)
- But the Church lab has a better way of doing this?
- Provides backup in case direct movement of KaiABC into E. coli fails
- Codon bias problem with 2 amino acids (can't find source but I found it the other day): then, we can synthetically modify the codons for these 2 aa's to be compatiable in e. coli
- .11/bp w/o error correction; $2/bp with error correction (Tian et. al 2004)
- Alternate phrasing, courtesy of Kit Parker - what is the "deliverable?" The thing you will point to and say "this is our project?"
- Our deliverable is a (multiple?) BioBrick part(s)
- Biobrick KaiABC oscillator (for use in either cyanobacteria AND/OR e. coli)
- What are two or three possible means of implementing the idea?
- Biobricks the cyanobacteria KaiABC
- Implement directly into E. coli to create a "nightlight"
- Synthesis of a E. coli compatible KaiABC and implement in E. coli
- Create a circuit with other BioBricks
- Last resort: Just create a cyanobacteria "nightlight" if all E. coli steps fail
- Risk
- How many untested things have to work for the project to succeed?
- How will you test whether those things work or not?
- How will you adjust your plan when one of these things fails to work?
- How will you minimize the time/effort/resources lost to a failed design?
- Can your time/effort/resources apply to more than one design simultaneously?
- Reward
- How cool, fun, exciting is the project for you?
- What if any is the usefulness or societal benefit of the project?
- What is going to impress the judges in November?
- Timeline
- What are the project milestones? (design, construction, testing)
- What is the estimated time required for each? (always overestimate)
- If you can't reach your ultimate goal by August, is there a satisfying intermediate goal?
- What is the immediate next step in pursuing the project?
- If DNA synthesis will be required, how soon will you have the sequence designed?
- Nakajima et. al: in vitro, the proteins oscillate abeit not with as large of an amplitude