Team:Exeter/Partnership
Partnership - University College London
We were first introduced to the team at University College London (UCL) when we attended a virtual meetup hosted by the University of St Andrews’ iGEM team, where we introduced ourselves and our project to 8 other teams from around the country.
Our partnership with the team from UCL began when we first met on the 14th July 2020 at 10am BST. In this meeting we introduced each other to our projects and considered ways in which we could collaborate. As one of our original candidate project ideas focused of PETases, we began communicating with UCL who were also focusing on this topic. Although research for our project ended up shifting to bioconcretes, we identified several ways to collaborate together. We found that we had many common interests and experiences, especially with the changing coronavirus pandemic situation in the UK. Therefore, we decided to keep in regular contact and work together to achieve each of our objectives. As such, we decided to meet almost all of the following Monday’s at 4pm BST to discuss how iGEM was going for us both and to discuss how we could help one another. On top of this we also created a live chat on the 26th of July to keep in contact between meetings.
Flux Balance Analysis of B.subtilis
UCL worked incredibly hard for several months to perform Flux Balance Analysis on our terminal B.subtilis system which aimed to provide us with more information on our enzymatic and metabolic pathways and with an accurate organism simulation. On the 17th October, we received the final copy with three 2D plots and one 3D plot as well as information on which genes to knock out to maximise carbonate production in a live script. This modelling information has given us a critical insight into our synthetic biology approaches and will prove incredibly useful for any future research into CalcifEXE technology. We are all incredibly grateful for all of the work UCL team members Anna and Dani put into modelling this for us.
Below are some of the results UCL provided us through the Flux Balance Analysis
To see more about our Flux Balance Analysis Work please vist our modelling page (link here) .
Wiki Building Workshop
On the 8th of October, Anna and Laide from the UCL team very kindly gave several members of our team a workshop to help us understand HTML so that we could help contribute to the coding for the Wiki. This mentorship was useful for those of us who had no HTML experience, but we also hope the teaching experience was beneficial to Anna and Laide by helping them to cement their own knowledge of the subject and to develop their skill set.
Sharing of Outsourced Knowledge
B. subtilis Transformation help
We met with members of the UCL team and their supervisor Dr Stefanie Frank on the 10th of September, to discuss the genetic engineering we were planning to do for the UCL team. Whilst we were discussing the issues we had faced with our Bacillus Subtilis transformation protocol from the Frank Young Lab, UCL suggested that they could help and provided us with the contact details for Dr Rebekka Biedendieck from the Technical University of Braunshweig, a Team Leader and Bacillus specialist. On the 18th of September, Dr Biedendieck sent us an improved Bacillus Subtilis transformation protocol that her Bachelor student had been successfully using. Unfortunately, due to limitations imposed by the COVID-19 pandemic we were unable to test this protocol to see if we had greater success but we are incredibly grateful to the UCL team for directing us to Dr Biedendieck.
Contact with Ashesi Ghana
Dr Biedendieck was not the only person the UCL team helped us contact who was beneficial to our project. On the 10th of August, Pedro and Stefan from the UCL team put us in contact with the iGEM team from Ashesi University, Ghana. Team Ashesi are aiming to incorporate plastic bioremediation (using PETase) and bioconcrete systems into a living coastal defence system. UCL noticed the similarities between Ashesi Univeristy’s bioconcrete synthetic biology and our microbially-induced calcium carbonate precipitation. Following this, we met with Ghana on the 24th of August and on the 23rd of September to discuss the initial design of the specialised nozzle for our 3D printer. As we had no engineers on our team and the majority of Team Ashesi had engineering experience, the critical insight they gave us proved incredibly useful in optimising our nozzle design.
Contact with PetEXE
We put the UCL team into contact with several members of Exeter’s 2019 iGEM project ‘PETEXE’. PETEXE aimed to develop a PETase-based filter that could be put into washing machines to help prevent microplastic pollution from reaching the ocean. This work has huge crossover with UCL 2020’s microbial desalination and plastic degradation cell which is fuelled by the action of the PETase enzyme.
Laboratory Work and 3D printing
As a team, Exeter iGEM 2020 were incredibly fortunate in that, unlike our partners at UCL, we had laboratory access for at least a portion of the project duration. It was decided early on that as part of our partnership we would help perform some experiments for them to help them generate some practical data. After several weeks we were informed that their protocol (answering questions including: how to run PNP assays on PETase, whether a PNP assay could be prepared on a growth media, how to detect TPA, and whether means exist to test for MHETase activity amongst others), the DNA was ordered. When it arrives, this DNA will be used to transform and express a custom biobrick in E. coli BL expression cells, allowing us to attempt to characterise the expression and function of UCL’s PETase-MHETase fusion protein construct.
Initially, we had planned for our team in Exeter to use our 3D printer to help make a prototype Acrylonitrile Butadiene Styrene reactor for UCL’s desalination process. We had set up the printer and had obtained the ABS, however, due to the coronavirus pandemic and the time restrictions it imposed, the UCL team did not have time to design their prototype and so this was decided against internally. This process did help educate the Exeter Team on how a 3D printer worked and helped inform discussions such as the need to design a specialised nozzle, and it was still of benefit to both teams.
Support Throughout COVID-19
The global development of the COVID-19 pandemic has been accompanied by heightened levels of psychological distress and mental health issues, particularly for students at university level [1]. In what was an unusual summer for all of us, it was amazing for us to be able to look forward to a weekly talk to the team at UCL, who existed outside of our limited ‘bubble’. These meetings were not only great for sharing our project progress, but also were often crucial in keeping our motivation high and our routines more productive and healthier. They also often served as a great outlet for both teams to share their experiences during the, pandemic with many students being in a similar situation. Despite the distance we bonded very closely with the UCL Collaborations team. On the 11th of August, whilst Stefan and Oliver from the UCL Team and Velizar from the Exeter iGEM Team were in Sofia, Bulgaria, they met up and spent the day together. There are now plans for the Exeter iGEM and UCL iGEM teams to meet up in London when we can, so that we can finally meet in person!
Message from UCL
Early in this year’s competition, we attended a virtual meetup hosted by the University of St. Andrews, allowing us to introduce ourselves to the 8 other teams from the UK. After taking a keen interest in Exeter’s project, we began communicating with their team very closely. Soon we came to realise that Exeter’s team would likely be afforded laboratory access despite COVID-19 restrictions in the UK, which piqued our interest even further. This complimented our project nicely, as our project was focused on computational modelling of biological processes due to COVID-19 restrictions. After multiple video meetings, we were able to arrive at two shared objectives that would be central to the success of our respective projects:
1. Attempt to characterise the expression and function of our PETase-MHETase fusion protein construct
2. Perform Flux Balance Analysis modelling on their bacterium’s metabolism to gain critical insight into synthetic biology approaches to achieve desired outcomes
- Our Partnership Story, UCL’s Wiki
Sources
[1] Grubic, N. et al., (2020). Student mental health in the midst of the COVID-19 pandemic: A call for further research and immediate solutions. International Journal of Psychiatry, 66(5), 517-518 DOI: 0020764020925108
