User:Anthony Lazzaro / SANDBOX: Difference between revisions
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*Chemical Control of Biofilm Production [taken from MIT 2006 Wiki] : | *Chemical Control of Biofilm Production [taken from MIT 2006 Wiki] : | ||
**Oxindolyl-L-alanine inhibits, in a dose-dependent manner, indole production and biofilm formation by strain S17-1 grown in Luria-Bertani (LB) medium. Supplementation with indole at physiologically relevant concentrations restores biofilm formation by strain S17-1 in the presence of oxindolyl-L-alanine and by mutant strain E. coli 3714 (S17-1 tnaA::Tn5) in LB medium | **Oxindolyl-L-alanine inhibits, in a dose-dependent manner, indole production and biofilm formation by strain S17-1 grown in Luria-Bertani (LB) medium. Supplementation with indole at physiologically relevant concentrations restores biofilm formation by strain S17-1 in the presence of oxindolyl-L-alanine and by mutant strain E. coli 3714 (S17-1 tnaA::Tn5) in LB medium[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14569285&dopt=Abstract link]. Problem with this is that we need to get this mutant e. coli 3714 strain? | ||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14569285&dopt=Abstract link]. Problem with this is that we need to get this mutant e. coli 3714 strain? | |||
*2-Component System Control: | *2-Component System Control: | ||
Apparantly biofilm production is initiated when bacteria adhese to a surface through a CPX signalling pathway the genes encoding for this pathway have been found.<cite>3</cite> | **Apparantly biofilm production is initiated when bacteria adhese to a surface through a CPX signalling pathway the genes encoding for this pathway have been found.<cite>3</cite> | ||
=====2.Technical Use===== | =====2.Technical Use===== |
Revision as of 05:00, 22 July 2007
Pictures:
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Anchoring
Citations for PubMed
Links
Internal : internal
External : ign
Time Stamp
Anthony Lazzaro 11:23, 12 July 2007 (EDT)
Google specific search
Search Term site :openwetware.org
Well Characterised Part in Registry:
Recievers:
BBa_F2620 :
- Input: 3OC6HCL
- Output: Pops
Summary of Brainstorming 18th July:
Hrp has promise as a black box feedback loop mechanism
- Application Thermoregulation
- General application to a system that needs feedback loop - duh!
Hrp has promise as a very specific switch
Other Promising Ideas:
Lucas: Bacteria that move away from a source
- Could expand to bacteria that move away or towards a chemical source & incorporate feedback loop seen in signals
- Possible conflict with chemotaxis (?) from last year need to check could reuse there parts if no conflict
Density flow receptor:
Not only detect presence of bacteria but also how much of it there is a particular location
eg.how much dust here compared to here
- Need some kind of measurement device or quorum sensing set up (so more stuff more cells more reporter)
Uses for Hrp System: (Blood testing)
Immediate blood-test results can mean the difference between life and death in medical situations such as poisonings and infectious diseases. In many cases, by the time the test results are analyzed and a diagnosis made, the patient is in critical condition or beyond treatment
Blood poisoning is an illness due to an infectious agent or its toxin spreading through the bloodstream. The presence of bacteria in the blood is called bacteremia.
Short bursts of low levels of bacteria in the blood usually do not cause problems. For example, mild bacteremia typically occurs during a dental cleaning or when brushing your teeth. Your body's immune system fights off these bacteria.
If bacteria persist in the blood, however, they may cause sepsis, a serious, life-threatening condition.
- Slovenia has already covered this what other blood test could we do ?
20th July
Further Brainstorming for new ideas:
All my ideas have been rejected so far
Avenues to explore for new ideas:
1.Pre-2006 iGEMs
- 2005:
2.Registry 3.New Parts in Papers (start with reviews)
Focus on Adhesion:
1.Easy Application
-Make Bacteria Bind to something when told to do so
- E. coli MC1061 synthesize type I pili encoded by the fim (fimbria) operon, which bind to
mammalian surface carbohydrates [2]
- We could use this to simply bind bacteria to carbohydrates when the operon is expressed
(eg. simple promoter activation)
- 'The ability of enteropathogenic Escherichia coli (EPEC) to form attaching and effacing intestinal lesions is a major characteristic of EPEC pathogenesis' a group has identified a chromosomal gene (eae, for E. coli attaching and effacing) that is necessary for this activity.[3]
- Anderson JC, Clarke EJ, Arkin AP, and Voigt CA. Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol. 2006 Jan 27;355(4):619-27. DOI:10.1016/j.jmb.2005.10.076 |
- Jerse AE, Yu J, Tall BD, and Kaper JB. A genetic locus of enteropathogenic Escherichia coli necessary for the production of attaching and effacing lesions on tissue culture cells. Proc Natl Acad Sci U S A. 1990 Oct;87(20):7839-43. DOI:10.1073/pnas.87.20.7839 |
2.Technical Use
-Determine how many bacteria are attached to target
3.Real World Application
-Determine A certain concentraion of a species on a surf
4.Modular Real World Application
Focus on Biofilm:
1.Easy Application
Secrete Biofilm when inducer given:
- Chemical Control of Biofilm Production [taken from MIT 2006 Wiki] :
- Oxindolyl-L-alanine inhibits, in a dose-dependent manner, indole production and biofilm formation by strain S17-1 grown in Luria-Bertani (LB) medium. Supplementation with indole at physiologically relevant concentrations restores biofilm formation by strain S17-1 in the presence of oxindolyl-L-alanine and by mutant strain E. coli 3714 (S17-1 tnaA::Tn5) in LB medium
- http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14569285&dopt=Abstract
- could we try to get this mutant e. coli 3714 strain?
- if you can find the strain here: http://cgsc.biology.yale.edu/cgsc.html we can easily get it.
- Here are 2 more articles on the mutant indole-negative e. coli strain 3714
- I hope that we can get mutant strain 3714 -- (or make our own mutant) -- what do you guys think about e. coli biofilm and cell-cell signaling systems/applications?? anyways, take a look...
2.Technical Use
- Apparantly biofilm production is initiated when bacteria adhese to a surface through a CPX signalling pathway the genes encoding for this pathway have been found.[2]
- Otto K and Silhavy TJ. Surface sensing and adhesion of Escherichia coli controlled by the Cpx-signaling pathway. Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2287-92. DOI:10.1073/pnas.042521699 |
3.Real World Application
4.Modular Real World Application
22nd July Last Minute Susan Time
Major Focus on Biofilm
1.Easy Application
Secrete Biofilm when inducer given:
- Chemical Control of Biofilm Production [taken from MIT 2006 Wiki] :
- Oxindolyl-L-alanine inhibits, in a dose-dependent manner, indole production and biofilm formation by strain S17-1 grown in Luria-Bertani (LB) medium. Supplementation with indole at physiologically relevant concentrations restores biofilm formation by strain S17-1 in the presence of oxindolyl-L-alanine and by mutant strain E. coli 3714 (S17-1 tnaA::Tn5) in LB mediumlink. Problem with this is that we need to get this mutant e. coli 3714 strain?
- 2-Component System Control:
- Apparantly biofilm production is initiated when bacteria adhese to a surface through a CPX signalling pathway the genes encoding for this pathway have been found.[5]
2.Technical Use
3.Real World Application
4.Modular Real World Application
Papers:
- Martino PD, Fursy R, Bret L, Sundararaju B, and Phillips RS. Indole can act as an extracellular signal to regulate biofilm formation of Escherichia coli and other indole-producing bacteria. Can J Microbiol. 2003 Jul;49(7):443-9. DOI:10.1139/w03-056 |
- Di Martino P, Merieau A, Phillips R, Orange N, and Hulen C. Isolation of an Escherichia coil strain mutant unable to form biofilm on polystyrene and to adhere to human pneumocyte cells: involvement of tryptophanase. Can J Microbiol. 2002 Feb;48(2):132-7. DOI:10.1139/w02-001 |
- Otto K and Silhavy TJ. Surface sensing and adhesion of Escherichia coli controlled by the Cpx-signaling pathway. Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2287-92. DOI:10.1073/pnas.042521699 |
Quick note on Noise reduction in iGEM
I think one way to reduce noise & cross talk in iGEM projects is to have 'comm channels'
'Channels' used by the chassis should be chara