Notebook: Week 7
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Aims of the Week
This week, 6 of our team members of going to the CAM conference in Munich, where they will be presenting our project at the poster session. They will also meet with the LMU Munich iGEM team to discuss a collaboration. This has been a really exciting event for the team, in particular the modellers who are keen to collaborate, as we have been talking with the Munich team on skype for several weeks. Remaining in London are most of the lab team, who want to get our important biobricks transformed and commence 3A assembly. Rhiannon intends to finish updating the Research pages of the wiki; in particular she is working on the overview and design pages, as well as developing some research diagrams. Philipp also is aiming to get some wiki programming done, so we can start including some of the features we have designed. Yeping will be contacting the Southbank centre in order to discuss organising a Public Engagement event, and will continue discussing safety with London Hackspace regarding the DIYbio streetlab. Carina will be working on the physical model of our island for the Human Practice event at Southbank, where members of the public can themselves help construct the island using plastic. She also aims to have a more specified idea of the architectural side of the project after a meeting with the team on Friday.
Monday 23rd July
Wet Lab - In the lab today, Leonard transformed the TetR promoter (BBa_C0040) for Expt 7.1. Rhiannon and Yeping set up a restriction digest for K540000, I13522, K123003, and K398108 for Expt 7.2. A gel revealed that all except K123003 had been successful. Rhiannon, Yeping and Martina also continued the protocol for Expt 6.3 by picking colonies for our strong Constitutive Promoter (BBa_J23119), our Gas Vesicle Gene (BBa_I750016), our Double Terminator (BBa_B0015) and our Ribosome Binding Site (BBa_B0034).
Meeting - Human Practice. Yeping and Martina met with Mike Hughes from Gureilla Sciences. He had useful suggestions of how to make DIYbio more engaging, and had some useful contacts that may be able to help us with speed debating. He also passed on some tips on how to engage/approach people on the street for South bank project.
Meeting - Collaboration. Bouran meets with Henrik Cordes, Darmstadt, discuss potential for collaboration - agree expression of degradative component in Roseo and characteristaion.
Modelling - Talked to iGEM Bielefield, who are using the same enzyme in their degradation module, about their strategies for modelling and any limitations they are experiencing.
Human Practice - Radio Show. Bouran, Bethan and Philipp held a short interview with Eriko Takano following her presentation on 'Synthetic Biology of Antibiotic Production' for our radio program.
Tuesday 24th July
Wet Lab - Early today we checked the results from the transformation of the Tetr promoter (BBa_C0040) for Expt 7.1, which demonstrated colony formation. The aim is therefore to pick colonies for BBa_C0040 in the evening. We also checked the results from the colony picking for Expt 6.3, which demonstrated growth for only two of the picked BioBricks - the Constitutive Promoter (BBa_J23119) and the Double Terminator (BBa_B0015). These two underwent miniprep, restriction digest, gel electrophoresis and nanodrop - but demonstrated no product. This is likely because of the very low plasmid concentration found under nanodrop. As a result we set up another experiment (Expt 7.3) that re-attempted the colony picking from all four BioBricks form Expt 6.3, as well as the TetR repressor from Expt 7.1, which demonstrated colonies this morning.
We also received the good news of a potential collaboration with a research group who have a strain of bacteria we require for its Laccase gene.
Meeting - Primers - Leonard and James met with our supervisor Darren to discuss our primer design before an order is set through. This proved very useful, and they have taken the necessary steps to redesign the primers before they are sent off.
Meeting - Skype to the rest of team at Munich Conference - we caught up with the rest of the team this afternoon, and were pleased to find our project had been received very positively at the poster presentation. We also caught up on the key targets for the next few weeks, to ensure members of the Lab Team continue progress with Human Practice, while the rest of the team is away.
Meeting - Darmstadt. Discussion with Darmstadt about the modelling strategies.
Human Practice - Radio Show. Bethan, Bouran and Philipp held an interview with Brynne Stanton of the Voigt Lab, MIT.
Wednesday 25th July
Wetlab: The results from Expt 7.3 demonstrated that there have been growth for only the Ribosome Binding Site (BBa_B0034), the Double Terminator (BBa_B0015) and the Constitutive Promoter (BBa_J23119). The reasons for the failure of the TetR promoter (BBa_C0040) and the Gas Vesicle Gene (BBa_I750016) is not clear. For those that were successful we continued with the miniprep, digest, gel electrophoresis and nanodrop. This demonstrated that the Double Terminator (BBa_B0015) was a success - it produced bands of the correct size, and a useable plasmid concentration. The Ribsome Binding Site (BBa_B0034) and the Constitutive Promoter (BBa_J23119) however have inserts that are too small to detect against a 1000bp ladder. We will therefore investigate how best to demonstrate whether the transformation was a success. The plasmid backbone for each, however, is of the correct size, which is promising.
Meeting - Darmstadt. Bouran discussed a possible characterisation collaboration with Henrik from iGEM TU Darmstadt. We are considering if it would be possible to express their degradation module in Roseobacter and characterise it with our techniques to give them an alternative perspective. We will follow up after the Munich conference via Skype.
Modelling Joanne and Aurelija worked on modelling presentation for the workshop we are hosting for Munich on Thursday. They also discussed possible modelling collaboration with TU Munich, who will be present at modelling workshop on Thursday.
Human Practice - Visit to Hackspace. Yeping and Martina went to discuss our health and safety to concrete our plans for events.
Human Practice - Radio Show. Bouran, Bethan and Philipp held a short interview with Alfred Nordmann and Jay Keasling
Human Practice - Rathenau Debate. Erin has almost finished writing her paper, but needs to shorten it.
Thursday 26th July
Wetlab: Today James began Expt 7.4 - which aimed to transform the TetR Repressor (BBa_C0040) which failed in Expt 7.1, the gas vesicle cluster (BBa_I750016) which failed in Expt 6.3 and TetR repressible promoter (BBa_R0040) which failed in Expt 5.1.
Friday 27th July
Wet Lab: Today we checked the results of the transformation for EXPT 7.4, and were pleased to find growth for the Gas Vesicle Gene Cluster (BBa_I750016) but disappointed to find contamination of the negative control - and also, judging by the appearance, the Tetracycline Repressor (BBa_C0040).
Press Bethan sent some emails out to Science Magazines to the raise the profile of the events we are running over the next few weeks, including the upcoming speed debating and DIYbio.
Saturday 28th July
Island Collaborative Art: Carina and Yeping made a prototype for our island out of plaster to be used an interactive display at Southbank event this Sunday.
Sunday
Southbank EngagementMartina, Yeping and Aurelijia put up a stand at Southbank with our poster and island prototype on display to tell the public about our project. This allowed part of the wet lab team to have experiences of engaging with the public. They also gave out leaflets which invited members of public to take part in our speed debating event.
Reflections
This week was full of activity for the team. The Munich conference went smoothly, and we were all pleased our project was received very well by attendees there. We have also enjoyed the collaboration with Munich, and we are looking forward to continuing the communication. The Lab team who remained in London also managed to do a great deal of lab work, but we are still encountering various problems with transforming BioBricks. The reasons for this are not clear, and are likely to vary between experiments. However, we hope to resolve some of the issues next week in order to begin assembly. Overall, we are a little disheartened by the difficulties we continue to encounter in the lab, and the barriers that face us in setting up the ambitious DIYbio event. However, we are encouraged by the progress they both continue to make, even if it is not as quickly as we would wish.
Success of the Week - Collaboration with Munich
Fail of the Week - Buoyancy BioBricks
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