Alternative Roots/Protocols

Newcastle iGEM 2018

Medal Requirements

Medal Criteria Explanation
1 Registration and Jamboree Attendance Alternative Roots has registered and will be attending the Giant Jamboree Boston. We hope to meet you there!
2 Competition Deliverables We have completed the following tasks: #1. Our wiki (its right here!) #2. Our poster (please come visit us at our poster!) #3. Our presentation (26th October, 11.00-12.30, room 309, Session F) and finally, #4. The judging form was completed and submitted on the 12th October.
3 Attributions Our attributions can be found here.

4 Characterisation/contribution We chose option 4.1. Our team collected and deposited data for the 2018 InterLab study. The data has been accepted by iGEM and can be found here.
1 Validated Part / Validated Contribution We have submitted several new, validated parts to the registry this year. These are BBa_K2797002 - a new streptomycin resistance cassette, shown to confer streptomycin resistance to E. coli and BBa_K2797004 and BBa_K2797007 - new GFP reporter constructs with improved characteristics compared to the mutGFP in frequent use within the registry.
2 Collaboration We have undertaken three different collaborations this year. First, we have conducted wet-lab experiments for the University of Exeter iGEM team. Specifically, we have generated data on the impact of perchlorate on the growth of three bacterial species. Second, for Sorbonne University we provided graphical visualisations of their concept that they have been able to use in their outreach and engagement activities. Third, we provided water samples from the Ouseburn river for the University of Warwick. These Collaborations are detailed here.

3 Human Practices We contextualised our Human Practices, within the Newcastle City Council plan to make Newcastle into a 'Smart City.' We have proposed an additional scenario to those already outlined, one concerning sustainable agriculture; an urban farm inside the Victoria Tunnel which runs underneath the city. This conceptual design project forced us to think carefully about the safety regarding GMOs when used in contained environments. Before designing the urban farm, we spoke to: local farmers, several commercial urban farms, a social food enterprise and a research director. We used this design exercise to bring together all that we learned from our comprehensive stakeholder engagement.
1 Integrated Human Practices This design exercise outlined in the silver criteria integrates / was informed by all elements of our project: stakeholder engagement, wetware, hardware, and safety. Once we had consulted the relevant stakeholders and felt we had sufficient information we began to feed this in to the design and execution of the project. We have documented on our wiki how our project has been influenced by our Human Practices work. See our integrated Human Practices journey here.
2 Improve a Previous Part or Project We introduced an RFP device into pSB1C3 to act as an internal standard (IS) for each test device used in the InterLab study. This new plasmid part is BBa_K2797013.
3 Model Your Project We used two different mathematical modelling approaches to describe and simulate different aspects of our project. We built an agent-based model to understand the behaviour of nitrogen-fixing bacteria in response to the chemoattractant naringenin. We used Simbiotics to visualise stochastic simulations via real-time animations. These models guided experimental work and were then informed by data from our chemotaxis experiments and bacterial growth characterisation. Our model provided insight into the biofilm formation process, including biofilm thickness and number of cells of each nitrogen-fixing species present. We also built a kinetic model describing metabolic flux through the naringenin biosynthetic pathway. Our model employed mass action kinetics to describe the behaviour of reactants and products for each step in the pathway. By coupling this information with models describing the rates of production and turnover of the four naringenin biosynthetic enzymes we developed an improved genetic design for our biosynthetic devices.
4 Demonstration of Your Work We have summarised our successes on our demonstrate page found here.