Notebook: Week 3

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Aims For This Week

This week we will be presenting our progress in all aspects of the project to our supervisors, but our key aim is to demonstrate that we have progressed sufficiently to begin construction.

Monday 25th June

Training – Wet lab Today four of us (James Rutley, Bethan Wolfenden, Bouran Sohrabi, Philipp Boeing) had a training on how to make competent cells which was organized by one of our iGEM advisers - Alex Templar. We completed one out of three training stages which was making minimal media and plating out our E.coli cells. This will lead onto the second stage (tomorrow) which involves the inoculation of colonies.

Meeting – Construction/Characterisation Today we had a construction/characterization meeting with our main supervisor Darren Nesbeth. The outcome of the meeting was the finalisation of five modules which are Aggregation, Salt Tolerance, Degradation, Buoyancy, and Containment (the receptor module was included into the aggregation module). Tac promoters were chosen for the degradation and salt tolerance module biobricks in case any toxicity is present. This meeting made our wet lab plan more solid, which will allow us to start working on our first module (aggregation) in the upcoming week. Work begins on finalising detailed construction and characterisation plans. Preliminary biobricks are added to the registry.

Tuesday 26th June

Achievement - Wet Lab! Our team is proud to announce that our first biobrick ‘Temperature regulated Gas Vesicle Polycistronic gene cluster composite’ is up on the registry and can be find at the following link: http://partsregistry.org/Part:BBa_K729000 Second piece of good news is that Prof John Ward (one of our iGEM advisors) has agreed to provide us the following organisms: Deinococcus radiodurans (required for salt tolerance module) as well as numerousRhodococcus strains. Having an access to these organisms assures that we are on our way of being fully prepared for the construction of degradation and salt tolerance modules.

Training – Wet lab Today we (Bethan Wolfenden, Aurelija Grigonyte, James Rutley, Bouran Sohrabi) continued on our training on how to make competent cells. We inoculated colonies from four different plates. After adding our colonies into LB medium we left them incubated in shaker overnight (at 37˚C). This will lead to the third and last stage of preparation of competent cells that we are going to complete tomorrow.

Meeting - Modelling. Erin and Tom met to work on modelling plastic particles in the North Pacific Gyre using MATLAB software. Outcome: They completed their first draft, which can be used as a base for the full simulation.

Meeting - Fund-raising map. Using the initial drawing for the fund-raising map, Martina suggested Carina draw up a poster for open day. This was the first incentive to develop a visual language for our team and could be the style adopted for our competition poster. In one of our branding meetings, the majority of the team were excited by the prospect of using an infographic style for our posters. By taking on this visual language Carina was able to create a poster inspired by the google maps interface that portrayed exactly what Plastic Republic was all about and at the same time with a fun aesthetic that people could interact with.

Wednesday 27th June

Meeting – Human Practice. Meeting arranged by our supervisor Darren to analyse the progress of our Human Practice plans, and especially how they will be presented on the wiki. Outcome: Targeted the need to create a timetable for the architectural rendering of our island – which will be a key feature of the wiki. We also highlighted the need to find ways of demonstrating everything we do in an appropriate way. This will require further brainstorming.

Achievement – Lush Article. An article written by Martina regarding the relevance of our project to the cosmetics industry was published on the Lush website. Lush is a company which produces and sells environmentally-friendly cosmetic products, but also makes a large effort to raise awareness about these issues. This is relevant to our project, because some of the microplastic contribution to the oceanic pollution comes from ‘run-off’ plastics – for example microplastics found in exfoliators, make-up and other products. We feel publishing this article was an important action as it put our message out to a community that is not necessarily of a scientific background, but who may be inspired by its relevance to their values. Outcome: Gain of publicity, and created an interface that will attract a new and very different audience, who may not necessarily find out about our research otherwise

Thursday 28th June

Meeting – Beacon Bursary Application. Martina arranged to meet with Hillary Jackson from UCL’s Public Engagement Unit to discuss the Beacon Bursary application to fund our DIYbio project. Outcome: A few minor changes were necessary but we felt confident in our application. This is an important application because it should help us put up a public lab with Biohackers

Wet Lab - Media and Reagents Preparation. James and Leonard prepared much of the media and reagents that will be required for starting biobrick transformation next week, and ordered what was missing

Social - BBQ

Friday 29th June

Meeting - Transnatural Conference Proposal. Rhiannon and Carina met to discuss how to represent our project in our Transnatural Proposal. As Carina in an architect, and the conference has a large focus on design and the use of new materials and resources, her input was really valuable, and a fresh look on what our island is capable of. Outcome: Previously found it difficult to relate our project to the theme of the first day of the conference - the theme of New Power. The New Power theme explores how systems/products can be self sufficient because they can not only work independently but they can also generate their own resources. Carina explained how the bacteria could realistically be used to provide energy for inhabitants, and how such a system could be built into the infrastructure of the island. Bouran, who is in charge of our biobrick design, wrote how this could be done with the materials we have.

Achievements - Registry. For a summary of our biobricks so far, check out the registry at http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2012&group=University_College_London

Reflections

We are all very encouraged, now that we have now reached the position where we can go into the lab and begin the experimental work - which has been scheduled for next week. Similarly, the modelling team have much of the information required to start the basis of their models. This means next week should be really active in terms of starting practical work.

Success of the Week: Loading our Biobricks onto the Registry

Team:University College London/Notebook/Week3

From 2012.igem.org

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