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Team:Edinburgh/Results
From 2010.igem.org
Project Results
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Results: Genomic BRIDGEs
Characterisation of sacB:
We demonstrated that cell lines containing sacB are unable to grow in sucrose at a concentration of 10% compared to control cells which grew normally.
Characterisation of cat:
Protocol:
We managed to fine tune the protocol to our resources and particular strains.
We narrowed down the source of entry of a contamination and by using negative controls and stringent aseptic technique managed to eliminate contamination entirely.
We developed a simple titre for determining a) the level of success of the procedure and b) the level of resistance of an antibiotic resistance gene.
Unfortunately we never achieved our goal of replacing tnaA with the cat/sacB construct via recombineering, but our lab will continue to work with this protocol, possibly replacing the cat gene with a kanamycin resistance gene.
For anyone wishing to use this protocol we recommend focusing on the recombinase induction step, as this seems to be the problem area which results in the lack of recombinants.
Results: Bacterial BRIDGEs
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Results: Modelling BRIDGEs
The main result achieved by the modelling component of our project was the theoretical conclusion that, given the information available and the assumptions made, the biological systems proposed throughout our project should work. The genomic BRIDGEs model provided verification of the time course of the BRIDGE protocol. The intracellular bacterial BRIDGEs model acted to verify the idea of a light-based repressilating system, and to confirm that the responses of the various light pathways were as expected. Finally, the intercellular bacterial BRIDGEs model established the concept of light-based communication within colonies of cells, in all its complexity.
Each of the above models was extensively analysed via a variety of methods available, in an attempt to push the boundaries of understanding regarding the biological processes embodied within. Some interesting results were revealed, but overall this extensive analysis did much to reinforce the conclusion made above - that theoretically, our systems should work!
Throughout the process, Ty Thomson's framework for modelling BioBricks in Kappa was found to be an invaluable aid in organising and thoroughly describing the biological parts involved. Whether in simply ensuring that the entirety of the BioBrick's actions were described, or in making explicit the correlation between various rate parameters and their effects upon the model, the usefulness of such a structured and standardised framework in developing biological models cannot be understated.
One final result that hopefully was achieved by our modelling is the establishment and promotion of the Kappa stochastic rule-based modelling language as a BioBrick-friendly alternative to traditional methods of modelling such as differential equations. From its introduction to iGEM by last year's Edinburgh team, this year its use has spread to a handful of other teams as well... we are hopeful that this trend will continue in the near future, due to the numerous advantages that are inherent in the approach.
Results: Human BRIDGEs
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Results: In conclusion
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