Team:Kent/Attributions
Attributions
Project design
Our entire team together with the instructors and advisors decided on the project that we are carrying out at the beginning of the summer. The team met up once every week to share project ideas and discuss the direction of the project during the summer. The project that we have designed is to create nanowire from amyloid produced by E.coli creating a more biocompatible and cheaper alternative to current materials used as nanowire. We were inspired by the pioneering work carried out by Ann Hochschild and Viknesh Sivanathan [1] which provided us with information on how to utilise the curli export system of E.coli strain VS45 to form our nanowires. Also the work of Frederick et al. 2014[2] and Glover et al. 1997[3] which helped us understand the formation of amyloid and the self-assembling ability of Sup35-NM. The amyloid fusion protein that we have produced has been made using Sup35-NM fused to a cytochrome. More on the description of our project can be found here.
Modelling and software
We wanted to develop tools to predict the growth and production of amyloid nanowires, and to find a way to visually represent the amyloid production of the E.coli bacteria in 3D. This was accomplished by the modeling team consisting of James, Moyra and Raneem. The team developed a new software implementing Brownian dynamics[4] and the Monte Carlo method[5] written in Matlab. Our model and software is available to view here.
Policy and Practice
The main Policy and Practice issues identified by the team is centered on policy and public opinion on the use of bio-nano material. Finding out what the general public and members of parliament thought of our idea was therefore carried out in order to develop a wider understanding of how our product would be received in the real world. A Policy and Practice team consisting of Moyra, Raneem, Alice and Anna was formed to allow us to communicate with other iGEM teams as well as the general public and political figures to gather their opinions and tell them more about our project. More information on our Policy and Practice can be found here.
Wet lab
The wet lab work was naturally given to the bioscientists within the team, including Katarina, Richard, Alice, Natalie, Suparna, Jonathan, Anna and Rob who have carried out a vast range of experiments including but not exclusively AFM (Atomic Force Microscopy) imaging, Gibson Assembly, Ligation and PCR (Polymerase Chain Reaction). This was vital to the success of our project and was our main focus throughout the competition. More of our protocols, experiments and results can be found here.
Writing
Throughout the course of iGEM the whole team have been carrying out research and reading papers related to our project to allow us all to contribute to writing up our final project. We have weekly meetings where we talk to one another about what has been done during the week which we record in our notebook which you can find here. We have designed and written posters, presentations and in depth explanations into our project that the whole team have helped produce. The wiki was organised and coded by our wiki team consisting of James, Natalie and Raneem.
Team members
Raneem AlJaghoub
Raneem was part of the Policy and Practice team. She interviewed international politicians and developed a questionnaire on synthetic biology. Raneem also contributed in the improvement of the wiki as well as constructing the parameters list for the modelling and designing the project. Raneem is one of the presenters at the Boston Jamboree.
James Aston
James developed the model of our system. He went the extra mile and rendered the equations into a new software tool and afterwards rendered 3D animations of our system. James also created the code for the wiki pages. He also helped the UNITN iGEM team by helping to create a model for their system. James is one of the presenters at the Boston Jamboree.
Anna Beltrami
Anna was part of the wet lab team. She performed transformations, produced competent cells and helped capture pictures of the control samples with the Atomic Force Microscope. Anna ran the organisational infrastructure of the team. She also managed the social network channels and the overall communications with other teams, and liaised the collaborations with the UNITN iGEM team. Anna is one of the presenters at the Boston Jamboree.
Moyra Chikomo
Moyra was part of the Policy and Practice team. She wrote our POST note and helped in the creation of a questionnaire on synthetic biology sent to politicians and the general public. She designed and created a GUI (Graphical User Interface) for our projects as well as designing our banner.
Richard Crane
Richard was part of the wet lab team and took part in most of the lab work. His main contribution lies specifically in the validation of our fusion protein by carrying out AFM imaging, Congo red and heme plating. He is also a contender for the team member that has made most agarose gels within the team.
Rob Middlewick
Rob was involved in lab work where he did mostly transformations as well as helping other members of the team with various protocol. He has played a key part in the scientific writing of our project, which included the project description and the description of our BioBricks.
Katarina Pisani
Kat being part of the main lab team was involved in all the wet lab aspects of our project. She has carried out ligations, PCR reactions and run diagnostic restriction digest gels as well as much more. She has also been involved in our outreach events and has contributed to the scientific writing.
Jonathan Pope
Jonathan was also responsible for creating our posters and Envirowire logo. He has presented at our outreach events and has also managed the social networking of the team. He has designed our presentations and helped with the scientific and wiki writing. He has also held the main wet lab team in carrying out diagnostic Congo red plating and transformations. Jonathan is also one of the presenters at the Boston Jamboree.
Natalie Sloan
Natalie took part in designing and writing the wiki and creating the Kent iGEM logo. She is also part of the main wet lab team where she has carried out mini-preps, Gibson assembly, ligations and transformations as well as producing competent cells. Natalie has also contributed to scientific writing for the biobrick parts.
Suparna Thakali
Suparna contributed mainly to the wet lab team where she took part in carrying out restriction DNA digestion, Gibson assembly and ligation reactions. She contributed in identifying and designing biobrick parts to improve, and in results writing. She has also been involved in our outreach events.
Alice Tomlinson
Alice was involved in the Policies and Practise aspect of our project such as gathering MPs opinion on synthetic biology and its possible applications in our society as well as aiding in the design of our questionnaire. She also conducted interviews and presented our project to other teams at our meet-ups. The majority of her time has been spent in the lab carrying out Gibson assembly and diagnostics tests, as well as validating the conductivity of our fusion protein.
Supervisors
Advisors
We would like to thank the following for their support:
References
[1] Sivanathan, V. and Hochschild, A. (2012). Generating extracellular amyloid aggregates using E. coli cells. Genes & Development, 26(23), pp.2659-2667[2] Frederick, K., Debelouchina, G., Kayatekin, C., Dorminy, T., Jacavone, A., Griffin, R. and Lindquist, S. (2014). Distinct Prion Strains Are Defined by Amyloid Core Structure and Chaperone Binding Site Dynamics. Chemistry & Biology, 21(2), pp.295-305.
[3] Glover, J., Kowal, A., Schirmer, E., Patino, M., Liu, J. and Lindquist, S. (1997). Self-Seeded Fibers Formed by Sup35, the Protein Determinant of [PSI+], a Heritable Prion-like Factor of S. cerevisiae. Cell, 89(5), pp.811-819.
[4] Philipse, A. P. (2011). Notes on Brownian Motion. Utrecht University, Debye Institute, Van’t Hoff Laboratory.
[5] Barlett, V. R., Hoyuelos, M., & Mártin, H. O. (2013). Monte Carlo simulation with fixed steplength for diffusion processes in nonhomogeneous media. Journal of Computational Physics, 239, 51-56.