Difference between revisions of "Team:Newcastle/Collaborations"

Collaboration

Over the course of the summer, we collaborated with a variety of iGEM teams through links built during the UK Regional iGEM meet in Edinburgh, UK iGEM meet in London, and European iGEM meet in Paris. We also attended the International Workshop on Biodesign Automation (IWBDA) conference, where we discussed our project with researchers in the field to gather their thoughts and feedback. We have documented these collaborations below.

Exeter

Team Exeter kindly helped us by conducting thermal conductivity experiments on lysogeny broth (LB) and M9 media. These were important in allowing us to correctly model the temperature change caused by running an electric current through popular bacterial growth media. They found that the conductivity of both LB and M9 to be very similar to that of water. Water has a thermal conductivity of 598.4 mW/Km (milliwatts per metre kelvin) at room temperature. Exeter found that LB has a slightly higher thermal conductivity at 605 (± 20) mW/Km and M9 a slightly lower thermal conductivity of 570 (± 30) mW/Km.

This data was incorporated into our modelling and helped us identify which media to use in our later conductivity experiments. It also gave us some useful pointers for exploring other fluids with different specific heat capacities. Thanks Exeter!

European iGEM Meetup

This years, European iGEM Meetup was jointly hosted by iGEM EVRY and iGEM IONIS in Paris. During the morning event, our team presented both a poster and talk outlining our project to fellow iGEM teams. Subsequently, we were able to identify other groups who were working on similar projects, or who might need access to equipment we had available for collaboration.

We received lots of positive feedback on our project, particularly with regards to our poster design, which lead to a redesign for the following UK iGEM meet in Westminster. In the afternoon there were two roundtable discussions with members of the synthetic biology community. Of particular interest to us was the talk on biosecurity which contained useful information on considerations for our human practices around biosecurity and introduced us to the concept of 'dual purpose' constructs which is something we discuss further in our safety work.

National iGEM Meetup

On 17-18th August half of our team attended the UK iGEM meet at the University of Westminster. During the event, we once again had the opportunity to display our poster and present a talk.

The presentation received unanimous praise, with some good feedback suggestions. Firstly, the segregated structure of the presentation, such as microfluidics, breadboard, and human practices, was particularly well received. Feedback suggested a rendering of our breadboard design should be included as part of the talk to help people visualise how our final product will look. Our human practices section was lauded for being very integrative to our core project, a stark contrast to other teams. Finally, the chronological order of the presentation was easy for listeners to follow and understand, thus we are planning to extend this approach to other parts of our presentation in Boston.

The poster was received positively as well. However, when comparing ours with the ones of other teams we found a few areas that could be improved. First of all, our poster could have contained less text, or maybe bullet points, to increase legibility. By reducing the amount of text in the poster, we are also able to make the heading and text larger. Finally, we would like to make the sections of our final poster more segregated than before. Even though this poster had better separation than the previous one, the components description were a little bit scattered and thus harder to follow.

IWDBA 2016

While half of our team were attending the UK iGEM meet in Westminster, the other half were attending IWBDA 2016, the international workshop on biodesign automation. At IWBDA we heard talks from researchers in fields relating to synthetic biology, and we were able to explain our idea to them to get feedback on our project. We found that the feedback was positive once people fully understood our idea, but we were not explaining our end product, the 'plug n play' kit, very well. We resolved this issue by planning to make better use of props, such as the existing electronics kits for children, at future presentation opportunities. While gathering feedback on our idea we were fortunate to find someone working in the same area, but from the opposite direction. In particular, utilising electronics to sense signals from bacteria. Luis Ortiz of Boston University was using pH probes to sense the bacteria and integrate this information into a computer system. He gave us useful information on altering the pH of a growth media using bacteria. This was something we later investigated further as an alternative method of changing the resistance of our growth media in our various 'resistor' constructs. We also heard from researchers working on new microfluidics fabrication techniques involving the etching of plastics rather than moulding PDMS. We investigated this further when considering our 'environmental responsibility' from both a human practices and safety perspective.

While at IWBDA we also had the pleasure of meeting the 2016 Leiden iGEM team and to hear about their idea and discuss the progress of both our projects.

Regional iGEM Meetup

The Northern UK iGEM Meetup was held on the 29^th of July at the University of Edinburgh. It provided an opportunity for teams from Scotland and Northern England to get together and present the work they had done so far. As we had not completed a great deal of experimental work at this point, we gave a similar presentation to the one we delivered to sixth form students at our school's taster day for synthetic biology. We thought this would be a good opportunity to start our human practices work, and so covered information about our project and where we can see our research and ideas in the coming years. We also made sure to pose some important ethical issues that we had been encountering in our project to the audience in order to gauge their responses.

We also used the Northern UK iGEM meet to look for new collaboration opportunities. It was here we met the Edinburgh undergraduate (UG) iGEM team. Like us, they were working on a project interfacing bacteria and electronics, in this case on creating a modular system for storing data in DNA. Also like us, they had encountered problems explaining their work to other people and getting feedback from them. This was particularly important to them as the end-product of their technology is a system usable by consumers.

We explained to them that we were creating a computer game based ‘thought experiment’ designed to stimulate discussion about the consequences of using our technology as part of our human practices and offered to integrate their storage system into our thought experiment so that they could use it to get feedback. They thought this was an excellent idea and we invited them down to Newcastle to meet with us and discuss how they wanted their system to be presented within our 'thought experiment'.

Edinburgh (Undergraduate Team)

Following our first meeting at the Northern UK iGEM meet, the Edinburgh UG team came down to Newcastle to discuss their idea and collaboration in more detail. The problem they are tackling through their iGEM project is that much of today’s digitally generated data must be archived for significant periods of time. A practice often mandated by law.

Current digital storage systems have many limitations such as cost and low density. The Edinburgh UG team were investigating the use of a DNA storage system which has a much higher information density and lasts a longer time, thereby reducing costs. They hoped that their technology would eventually form part of consumer products. Serving large libraries and institutions with significant amounts of archived data, like the National Library of Scotland.

Well aware of the concerns of the public around the use of genetically modified organisms (GMOs) the Edinburgh UG team wanted a way to explain their technology and gather feedback on people’s perceptions of it. As part of our project, we were building a game based ‘thought experiment’ designed to stimulate discussion on the consequences of using our technology in real world scenarios. We felt this approach to human practices would also be applicable for use by the Edinburgh UG team. You can read more about why we chose this approach on our human practices background page.

After some discussion we agreed that we would aim to guide the user to consider some uses of their technology and to think through the effects of its use. The Edinburgh UG team were particularly keen for us to explore the privacy concerns around long-term data storage, so we set out to design a level of our game that would explain the notion of DNA storage and the security aspects that the Edinburgh UG team were implementing.

Through their meetings with staff from their Informatics department, Dr Kami Vaniea and Dr Aggelos Kiayias, they had found that there was already some skepticism around whether or not encryption was really necessary for their system. By providing them with a tool that showed how they encryption would work in some of their threat scenarios we hoped to make it easier to explain and justify their approach.

Consequently, we integrated an illustration of their storage and encryption scheme, implemented in a simplified form in JavaScript whilst maintaining the core principles, into our ‘thought experiment’ game which you can play here on our wiki.

Edinburgh (Overgraduate Team)

We assisted with the characterisation of their IPTG inducible promoter Sca6-2 (BBa_K1968021) using various concentrations of IPTG and compared the results to that of a simlar constitutive construct which expresses the iLOV protein (BBa_K1968016).

In return, the Edinburgh Overgraduate Team looked at our heat induced "Light Bulb" constructs BBa_K1895000 and BBa_K1895006.

The Edinburgh team took overnight cultures, grown at 37°C of our constructs and diluted them down to an OD600 of 0.05 with LB broth and 34μg/ml chloramphenicol. The cells were placed in a plate reader for 20 hours at 300 RPM. Measurements of OD, at 600nm, and fluorescence, with an excitation filter of 485nm and emission filter of 538nm, were taken every 30 minutes. There results can be seen below in Figure 5.