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Team:Newcastle University/Conclusions
From 2008.igem.org
Newcastle University
GOLD MEDAL WINNER 2008
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Conclusions
The outcome of the project is disappointing, in a way, since we didn't achieve our overall goal of evolving an ANN and implementing it in B. subtilis. However, it is also exciting, since we demonstrated that it is possible do the basic biological function on which the whole project depends – getting two-component quorum-sensing systems from one strain of Bacillus to work in another strain, and produce the right output.
The preliminary work involved identifying suitable target pathogens, the quorum communication peptides produced by them, and the amount of overlap between peptides produced by different species. This took much longer than anticipated, and involved a lot of searching the literature and online databases, but resulted in a database of species and peptides which is a good training set for the system.
Software development also took up a lot of our time, since all of the code had to be developed from scratch, and this could not be done without learning a lot of skills, including the principles of neural networks and evolutionary algorithms, advanced Java, CellML and JSim, databases and JDBC and Web services. The fact that the software works and the different parts communicate with each other is very rewarding, and the software may be a valuable resource for future iGEM teams, if they choose to work in this area.
The lab work was also a positive experience, as we managed to clone the proof of concept BioBrick into an integration vector, and get it to integrate into the chromosome of the Bacillus. Once again, this required the acquisition of a host of new skills, both at the bench and microscopy, flow cytometry and, for some of us, computing and the use of Wikis.
Overall, the 2008 Newcastle iGEM team had a lot of fun, learned a lot of skills, and made (hopefully useful) contributions to the BioBricks Repository, as well as local databases and software tools. Jamboree, here we come!
Future Work
- Integration vector is not BioBrick compatible
- Need to completely characterize subtilin Brick
- Extend to full original plan
