"
Team:Cambridge/turingpatterns
From 2010.igem.org
(Difference between revisions)
| (6 intermediate revisions not shown) | |||
| Line 1: | Line 1: | ||
| + | {{:Team:Cambridge/Templates/headerMinimalprototype}} | ||
| + | |||
| + | {{:Team:Cambridge/Templates/headerbar|colour=#96d446|title=Rough notes: Turing patterns}} | ||
| + | |||
| + | |||
==Research of the previous Team's work== | ==Research of the previous Team's work== | ||
| Line 8: | Line 13: | ||
* Apparently 11 out of 12 ligations were successful - they would have been able to test the system had the final ligation occurred. | * Apparently 11 out of 12 ligations were successful - they would have been able to test the system had the final ligation occurred. | ||
* The only experimental results were those demonstrating that AHL was initiating it's own transcription via the expression of GFP. | * The only experimental results were those demonstrating that AHL was initiating it's own transcription via the expression of GFP. | ||
| + | * Seemed to have done quite a lot of good modelling work. So will be difficult to go much further on this aspect of the project | ||
iGEM 2008 Cambridge team - iBrain | iGEM 2008 Cambridge team - iBrain | ||
* Planned to use similar quorum sensing mechanisms with the lux operon to detect activity. However, the lux operon would not work in a gram positive organism such as Bacillus therefore only E.coli could work. | * Planned to use similar quorum sensing mechanisms with the lux operon to detect activity. However, the lux operon would not work in a gram positive organism such as Bacillus therefore only E.coli could work. | ||
| - | {{:Team:Cambridge/Templates/ | + | ==Own Research== |
| + | |||
| + | Papers on Turing Patterns | ||
| + | * Original paper from Alan Turing: http://www.dna.caltech.edu/courses/cs191/paperscs191/turing.pdf | ||
| + | |||
| + | Further information | ||
| + | *Different signalling mechanisms have a large amount of cross-talk in bacteria | ||
| + | *The ACL Transcription factor is very specific initially but when bound becomes very non-specific, therefore cannot use two distinct systems in the same bacteria expressing different outputs in the same bacteria, instead 2 different strains would have to be used. This was the reason why a predator-prey model worked in a previous study. | ||
| + | * In the proposed system, there would be an activator and an inhibitor, with different diffusion rates due to the chain length of the molecules. The activator would be a short chain molecule and the inhibitor a long chain molecule so that the inhibitor diffuses slowly. | ||
| + | *One suggestion is that metabolites could be used as the morphogens in this system, for example metabolites that release or free another signalling molecule from the media, e.g. Arabinose - http://en.wikipedia.org/wiki/Arabinose. | ||
| + | * Another suggestion was peptide signalling, which uses an AGR-like system. There are 4 proteins, a pre-peptide, a processing, secreting and supporting peptide, and 2 sensing peptides. | ||
| + | |||
| + | Advantages of the Turing Project | ||
| + | * A new quorum sensing molecular system could be added to the registry which if a proven system could be easily applied to other systems. This would stand alone as an achievement no matter what the other successes or failures. | ||
| + | |||
| + | ==Conclusion== | ||
| + | |||
| + | * Turing patterns have been well described theoretically | ||
| + | * Mexico 2009 modelled the problem extensively | ||
| + | * Our project WILL have to reach the implementation stage to go a step further | ||
| + | * Some Biobricks exist. A lot of the project will have to do with fine tuning of the system | ||
| + | * Combine with one of the other projects? Bioluminescence? | ||
| + | |||
| + | |||
| + | {{:Team:Cambridge/Templates/footerMinimal}} | ||
Latest revision as of 23:44, 10 August 2010
Rough notes: Turing patterns
Research of the previous Team's work
iGEM Mexico 2007
- Project Failed
- Admitted were underfunded, no results shown
iGEM Mexico 2009
- Apparently 11 out of 12 ligations were successful - they would have been able to test the system had the final ligation occurred.
- The only experimental results were those demonstrating that AHL was initiating it's own transcription via the expression of GFP.
- Seemed to have done quite a lot of good modelling work. So will be difficult to go much further on this aspect of the project
iGEM 2008 Cambridge team - iBrain
- Planned to use similar quorum sensing mechanisms with the lux operon to detect activity. However, the lux operon would not work in a gram positive organism such as Bacillus therefore only E.coli could work.
Own Research
Papers on Turing Patterns
- Original paper from Alan Turing: http://www.dna.caltech.edu/courses/cs191/paperscs191/turing.pdf
Further information
- Different signalling mechanisms have a large amount of cross-talk in bacteria
- The ACL Transcription factor is very specific initially but when bound becomes very non-specific, therefore cannot use two distinct systems in the same bacteria expressing different outputs in the same bacteria, instead 2 different strains would have to be used. This was the reason why a predator-prey model worked in a previous study.
- In the proposed system, there would be an activator and an inhibitor, with different diffusion rates due to the chain length of the molecules. The activator would be a short chain molecule and the inhibitor a long chain molecule so that the inhibitor diffuses slowly.
- One suggestion is that metabolites could be used as the morphogens in this system, for example metabolites that release or free another signalling molecule from the media, e.g. Arabinose - http://en.wikipedia.org/wiki/Arabinose.
- Another suggestion was peptide signalling, which uses an AGR-like system. There are 4 proteins, a pre-peptide, a processing, secreting and supporting peptide, and 2 sensing peptides.
Advantages of the Turing Project
- A new quorum sensing molecular system could be added to the registry which if a proven system could be easily applied to other systems. This would stand alone as an achievement no matter what the other successes or failures.
Conclusion
- Turing patterns have been well described theoretically
- Mexico 2009 modelled the problem extensively
- Our project WILL have to reach the implementation stage to go a step further
- Some Biobricks exist. A lot of the project will have to do with fine tuning of the system
- Combine with one of the other projects? Bioluminescence?
