Once upon a time in 2016, many decided to answer the call of what seemed to be the proposal of a great scientific and human venture. After a strict selection remained only nine immaculate souls; so the mystical core of the iGEM EPFL 2017 team was formed. As soon as the members had obtained confirmation of their acceptation, brainstorming sessions were organised (as early as of February 2017) for several months in order to find a collectively acclaimed project. These meetings, coupled to extensive research on many cell-free papers, led us to focus on the usage of toehold switches and aptamers in cell lysates. From then on, the team quickly agreed to work on a biosensing device; thus our project Aptasense arose from the ashes. The iGEM EPFL 2017 team members interacted during the whole competition with many people affiliated to different scientific fields that contributed to shape the project into its final form.
The whole team took part in either wet or dry lab sessions from February until the end of the competition. In order to optimize our work, several teams were formed:
Malek, Lena, Lisa and Elia performed all research relative to cell lysates and toehold switches and were helped by Natalija in their investigation of toeholds.
Malek and Lisa performed the trigger modularity experiments in PURE and cell lysates and tested the software output in vivo.
Software and wiki
Everyone in the team participated in the writing of the texts for the wiki page of the team. The design of the logo was imagined by Felix and improved with the help of the rest of the team.
Lena and Tim provided the MATLAB graphs sustaining capital information about our research. Matteo provided the R graphs for the binding saturation curves of the aptamers.
Matteo and Lena facilitated the comprehension of the theory behind our manipulations by drawing complementary schemes.
Natalija focused on building a solid foundation for our wiki page and on displaying all of our data on it; in addition to that, she managed to nearly single-handedly encode the toehold design program of the team and compute a novel toehold later proven functional. We thank Prof. Dr. Alexander Green for his feedback on the designed software.
Human practices & Scientific outreach
Many members of the team participated in several conventions and contributed to make the knowledge they acquired during the competition accessible to as many people as possible:
Malek and Lisa joined a summer school in Davos, Switzerland, proposed by EPFL in which they presented the scientific investigation pursued in the lab.
Jonathan and Tim represented iGEM EPFL 2017 in the iGEM European Meet-Up held in Delft, Netherlands.
Lena, Lisa and Felix flew to Cambridge, Great Britain, in order to attend the Open Plant convention.
Elia prepared the mini-kit, guaranteed its biological safety, its user-friendly facet, and wrote the associated protocols.
Jonathan reached out to professors and administrators of distribution platforms in order to review and ensure the proper distribution of the kit after the end of the competition.
Elia and Tim made contact with Medisupport in order to have inputs from the industry of diagnostics.
Lena was responsible for the numerous collaborations of the team with other iGEM teamslocated at different places across the world.
Prof. Dr. Sebastian Maerkl and Dr. Barbara Grisoni, our two supervisors, stood by our side throughout the whole competition. They helped us with valuable advice, questioned and corrected our protocols and experiment designs when we didn't know what to do anymore. Sebastian Maerkl allowed the team to use all the equipment of the Laboratory of Biological Network characterization (LBNC) located at EPFL, which was crucial for our daily routine.
A huge thanks to our PhD advisors from Maerkl's lab, Ekaterina Petrova for all her advices on how to perform microfluidic assays, data analysis and on how to present our scientific data, Zoe Swank for helping us plot the graphs, providing counsel on MATLAB scripts and helping us manufacture the wafers we used for microfluidics assays, Ivan Istomin for his teaching of scientific rigorousness and how to make MITOMI chips, Barbora Lavickova for her vaste knowledge on cell-free expression systems, and Gregoire Michielin for all the help he provided on beads assays. They helped us with the countless problems we had in the lab along with a big support during the Wiki Freeze.
We'd also like to thank the TAs for their generosity since we ended up using so much of their personal stashes that they have probably spent the last nine months eating plain pasta and 1 potato on special occasions.
The iGEM EPFL 2017 team members interacted during the whole competition with many people affiliated to different scientific fields that contributed to shape the project into its final form.
Thank you to Pierre-Etienne Bourban and Josiane Smith-Clerc for letting us use their new interdisciplinary laboratory. Furthermore, Sebastian Maerkl let us use his laboratory including many indispensable machinery.
Marie-France Radigois helped us organise our travels and solve financial and organisational issues.
The experiments of the Educational Cell-Free Minikit (ECFK) were reviewed by several professors in order to hit the bullseye of an interactive yet educational lab practise; we thus would like to thank Alexandra Suter De Iaco and Bertrand Emery, professors at College Calvin in Geneva, François Lombard, professor at College Calvin and at the University of Geneva in Geneva, Jean-Luc Zanasco, professor at Ecole Moser in Geneva, and Karl Perron, professor at the University of Geneva and manager of the platform specialized in the distribution of lab material for high schools in the Canton of Geneva was also contacted to ensure the proper distribution of the ECFK after the end of the competition.
We would like to acknowledge the help of our sponsors EPFL, IDT, Nikon, Novartis, Roche and Snapgene, without whom the project would have proven itself impossible.