IGEM:Harvard/2006/Cyanobacteria: Difference between revisions
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* '''What is the specific goal of the project?''' | * '''What is the specific goal of the project?''' | ||
**Populate Biobricks | |||
**Biobrick KaiABC oscillator (for use in either cyanobacteria AND/OR e. coli) | **Biobrick KaiABC oscillator (for use in either cyanobacteria AND/OR e. coli) | ||
***[http://www.kazusa.or.jp/cyano/WH8102/cgi-bin/orfinfo.cgi?title=Chr&name=SYNW0548&iden=1] Shows the location of kaiA,BC in WH8102 strain. 2.866kb for kaiABC + non-coding region. | ***[http://www.kazusa.or.jp/cyano/WH8102/cgi-bin/orfinfo.cgi?title=Chr&name=SYNW0548&iden=1] Shows the location of kaiA,BC in WH8102 strain. 2.866kb for kaiABC + non-coding region. | ||
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**Last resort: Just create a cyanobacteria "nightlight" if all E. coli steps fail | **Last resort: Just create a cyanobacteria "nightlight" if all E. coli steps fail | ||
* '''Risk''' | * '''Risk''' | ||
** How many untested things have to work for the project to succeed? | ** '''How many untested things have to work for the project to succeed?''' | ||
** How will you test whether those things work or not? | ***Should work unless something in E. coli causes it not to | ||
** How will you adjust your plan when one of these things fails to work? | ****Reporter gene should have no problem | ||
** How will you minimize the time/effort/resources lost to a failed design? | ****Codon bias may be a problem | ||
*** Can your time/effort/resources apply to more than one design simultaneously? | ***If more proteins are involved than KaiABC | ||
* Reward | ****It worked in vitro however... | ||
** How cool, fun, exciting is the project for you? | ***Transcription regulation of the kaiABC proteins | ||
** What if any is the usefulness or societal benefit of the project? | ****We know that KaiA mRNA constant as KaiC fluctuates (Wang et. al 2005) | ||
** What is going to impress the judges in November? | ** '''How will you test whether those things work or not?''' | ||
* Timeline | ***If we don't get results / alternative methods such as synthesis | ||
** What are the project milestones? (design, construction, testing) | ** '''How will you adjust your plan when one of these things fails to work?''' | ||
** What is the estimated time required for each? (always overestimate) | ***We have backup plans, such as only implementing a "nightlight" in cyanobacteria | ||
** If you can't reach your ultimate goal by August, is there a satisfying intermediate goal? | ** '''How will you minimize the time/effort/resources lost to a failed design?''' | ||
** What is the immediate next step in pursuing the project? | *** '''Can your time/effort/resources apply to more than one design simultaneously?''' | ||
*** If DNA synthesis will be required, how soon will you have the sequence designed? | * '''Reward''' | ||
** '''How cool, fun, exciting is the project for you?''' | |||
** '''What if any is the usefulness or societal benefit of the project?''' | |||
***Clock oscillator | |||
****Can experimentally vary it from 14h to 40h (Kondo et. al 2000) based on point mutations | |||
****Can further discretise by half | |||
***A bacterial "timer" | |||
***Unlikely, but a computer syncronization method (but too slow...) | |||
***Metal detector | |||
***Stun gun | |||
***nightlight | |||
** '''What is going to impress the judges in November?''' | |||
*** Biobricks part! | |||
* '''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 | *Nakajima et. al: in vitro, the proteins oscillate abeit not with as large of an amplitude |
Revision as of 17:25, 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?
- Populate Biobricks
- 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)
- 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?
- Should work unless something in E. coli causes it not to
- Reporter gene should have no problem
- Codon bias may be a problem
- If more proteins are involved than KaiABC
- It worked in vitro however...
- Transcription regulation of the kaiABC proteins
- We know that KaiA mRNA constant as KaiC fluctuates (Wang et. al 2005)
- Should work unless something in E. coli causes it not to
- How will you test whether those things work or not?
- If we don't get results / alternative methods such as synthesis
- How will you adjust your plan when one of these things fails to work?
- We have backup plans, such as only implementing a "nightlight" in cyanobacteria
- 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?
- How many untested things have to work for the project to succeed?
- Reward
- How cool, fun, exciting is the project for you?
- What if any is the usefulness or societal benefit of the project?
- Clock oscillator
- Can experimentally vary it from 14h to 40h (Kondo et. al 2000) based on point mutations
- Can further discretise by half
- A bacterial "timer"
- Unlikely, but a computer syncronization method (but too slow...)
- Metal detector
- Stun gun
- nightlight
- Clock oscillator
- What is going to impress the judges in November?
- Biobricks part!
- 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