Team:Edinburgh/Notebook/Collaboration

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Revision as of 11:12, 27 October 2010

Collaboration

This page is a brief overview of the collaborations that we undertook with other teams during the summer. We did not keep a dated notebook of our collaborations, but the information is all held in emails between the teams.

Information and parts bridged the oceans between the Illuminati of Edinburgh and the WiFi Coli project of UNAM-Genomics Mexico. Our communications with UNAM-Genomic Mexico are available for perusal on their wiki.

We also worked with the Osaka iGEM team in the joint development of a RFC standard for the design and construction of new BioBrick parts and devices.

Our main collaborators on this project were Mexico UNAM-Genomics, who have been absolute stars this summer and supplied us with half the things this project needed to actually work in any way.

In early July it became apparent that Mexico were doing exactly the same project on bacterial light communication as we were. And when I say exactly, I mean down to each individual proposed BioBrick. Of course, we first panicked, then decided, since we were never going to complete this project ourselves, that we should contact them. This we did via an immediate email.

It turned out that Mexico had seen our project too and were also interested in collaboration. We held a Skype conference in mid July to discuss where to take the project. Both teams wanted to hold their own in the project as appearing too dependent on another team may have hurt our chances at the Jamboree. The agreement was to share DNA, some characterisation data, and any hints and tips that we picked up while working with the common parts and protocols, but to otherwise continue working as before.

The parts

By the time we had our Skype conference, Mexico had already ordered several genes from Mr. Gene. As it seemed they had a larger synthesis budget than we did, they very generously offered to send us them when they arrived. All of the genes were mutation-free and codon optimised for E. coli. These were:
YFP - the protein we were originally going to fuse with LuxAB to produce green light. We have since decided to use the natural firefly luciferase, but Mexico are still working on this fusion.
LovTAP - we were having problems with LovTAP at the time. We later discovered a frameshift mutation in the BioBrick. It cost us several weeks but luckily Mexico's copy got to us just in time.
CcaS - The PCB-containing and light-absorbing component of the green light sensor. Edinburgh and Mexico were working on different versions of the green light sensor, both of which require CcaS.
NB: Mexico sent us more than 3 tubes of DNA. They sent us the subunits and composite part for LovTAP and both original PCRs are BioBrick versions of some genes.

Mexico then requested several things from us that they had been unable to get hold of:
LuxAB and LuxCDE - we had sent them these previously but the versions we sent were those that last year's team had submitted to the Registry which turned out to be incorrect. At the time we sent the new copies, however, we still hadn't managed to create a self sufficient glow.
LumP - this had also been amongst the original genes sent to Mexico. So far as we know, it never worked for them and we are unsure as to why.
Ho1/PycA - the phycocyanobillin synthesis genes. Whilst they had CcaS, they did not have the PCB for it to work. We had a copy in order to build the red light sensor so we sent it on.
The LovTAP readout system - they had synthesised LovTAP but their copy did not have a downstream reporter. We sent them our trpR system that Marta had been working with.

The characterisation

For a while it seemed that Edinburgh was in a better position to characterise some of the BioBricks than Mexico. We had a reporter system for our LovTAP (which due to a delay at Customs they had not received) and we had successfully mutated our red luciferase.

We had agreed that we would share any significant results we achieved from the characterisation of LovTAP. Unfortunately, this never came to fruition; at the date of the wiki freeze neither LovTAP nor the red light sensor were showing any difference for us in readout in response to light. We gave Mexico what information we could but it was too late and of too little relevance to alter their own results.

The Edinburgh and Osaka teams this year wanted to use BioBricks without the NotI site so that BioBrick primers could be designed with ease and efficiency. This required the submission of a new RFC (request for comments) to replace the existing standard RFC10.

RFC54: | in pdf format (not yet uploaded to [http://biobricks.org/RFC.php | the BioBricks Foundation].