iGEM EPFL 2018

Collaborations

Introduction

iGEM is all about synthetic biology and pushing the boundaries of the field to meet the needs of today with innovative solutions, and the spirit of iGEM has always been collaborative. We believe in adopting that spirit in our project.

It was important for us to collaborate with multiple research groups working on synthetic biology and cancer therapeutics during the course of our project. Our interactions with them were vital in the development of our project and we learned a lot from their input that allowed us to adapt and improve our project, shaping CAPOEIRA to meet the needs of the relevant stakeholders in the field. We have elaborated our story on our ‘Integrated Human Practices Page

Equally important to our project was collaboration with other iGEM teams. We were able to team up with teams around the globe on a variety of experiments that contributed to the mutual understanding and improvement of projects, exploring the ethical and regulatory landscape of a number of countries regarding synthetic biology as well as giving and receiving feedback where we can on the wiki, project, poster, presentation and other aspects of iGEM projects of our collaborators and of our own.

iGEM Austin LASA

We were very excited to collaborate with Austin_LASAand exchange ideas, given the similarities in our project. Both of our projects rely on Cas12a-fluorophore-based assays in order to create an assay that will allow early detection of HIV in infants (as Austin_LASA is performing) and early detection of cancer-relapse.

We have developed our Cas12a assay with the purpose of detecting point mutations and chromosomal rearrangements found in ctDNA as well as the detection of an amplicon that contains an amplified miRNA sequence to target. These processes are explained in detail on our Project Design page.

During our project, we spent a long time working with these Cas12a assays and there was a lot of effort that went into the optimization of these assays that came with many trials, in terms of Cas12a pre-incubation time, activator concentration, DNAse alert concentration, etc. We had a very insightful discussion about our experiences and shared our knowledge and advice on working with such Cas12a assays. Here are the protocols that we shared with the Austin_LASA team, hoping that it would provide useful insights for their Cas12a experiment designs.

In both of our projects, the ultimate goal was to design a “kit” and part of this kit would require an isothermal amplification step of a DNA target sequence. We learned that Austin_LASA’s team had successfully performed Loop mediated isothermal amplification (LAMP) for their project and we took this opportunity to learn about this possibility of isothermal amplification, as well as the implications of performing it successfully. It was a pleasure to exchange ideas with them.

NUS Singapore-Sci iGEM Team

We were very happy to get the change to collaborate with the NUS Singapore-Sci iGEM Team ! Our collaboration was based on ethical reflections linked to the project, in particular to the methods used and the social implications.

The NUS Singapore-Sci iGEM Team had created a survey on the myths and misconceptions associated with Synthetic Biology. After sharing this survey with us, we entered a discussion that lead to our team deciding to also create a survey that aims at capturing the general public opinion concerning our project. After investigating the nature of the components in our project, we followed two approaches: firstly to study the impact of the techniques used in the project as well as the awareness of those performing them, second to study the controversies that might occur in the future implementation of our project.

The survey was distributed in two stages, aimed at two distinct stakeholders of synthetic biology. The first stage was a formal EPFL questionnaire distributed among second year Life Sciences Engineering bachelor students during their laboratory practicals. It was included as a reflection part of an ethical course of engineers in biotechnology. The second stage was a distribution externally to the campus and country on animal experimentation, patient biological data protection, vaccination and biotechnology in general.

The questionnaire differs from that of the NUS Singapore-Sci iGEM Team in terms of content and is focused on gathering data specific to our project so that we can understand how to implement that data, however the discussion and exchange of ideas that we had allowed us to clarify our intentions in terms of the subjects we wanted to touch on for our surveys.

iGEM XMU China

We were very excited to get contacted by this year’s XMU iGEM team who are working on their own assay called the Aptamer Based Cell-free Detection system (ABCD system). They are using Cas12a in an ingenuitive way to detect proteins through the intermediary of aptamers. Indeed, aptamers have the capacity of recognizing a specific protein and by doing so will release a ssDNA that will be recognized by Cas12a. Since both of our teams are working on a Cas12a detection using fluorophore quencher it was natural for us to give them all the knowledge we had gathered over the summer about our Cas12a assay.

In addition to their detection method, XMU’s team worked on improving protein’s conservation and were kind enough to share their information on using SAHS proteins as a Cas12a protective agent. It was obvious for us that we could immensely benefit from this to bring our follow up cancer surveillance closer to the point-of-care. Unfortunately because of time restrictions we were not able to integrate their assay. This collaboration was nevertheless extremely conducive to reflect on how we would get closer to our end product and for this we are very appreciative!

iGEM Athens

The collaboration with the Athens team started early in the summer, after members of both teams identified multiple shared attributes between the two projects, namely cell free expression, and diagnostic kit development. Thus, the contact started with multiple video conferences over the summer. These conferences discussed iGEM EPFL’s experience with cell free systems optimization, especially with linear DNA expression templates. Moreover, the EPFL team benefited from Athens’ team knowledge and experience with kit design to start the kit design for our diagnostic tool. The collaboration finally materialized with Yannis from iGEM Athens visiting the EPFL team and spending some time with us in the lab. The discussion revolved mainly on continuing the projects beyond the iGEM competition, and especially the realization of a diagnostics kit. Both teams are planning on developing models for a diagnostic toolkit, as well as models for the 3D printing of their device enclosures. The two teams decided on setting a framework for the shared realization of these goals.

iGEM GreatBay China

We had the privilege of collaborating with Great Bay China, a high School team from Shenzhen. We received numerous tips and good advice about poster design, the flow that iGEM presentations should have as well as information about common pitfalls and how to avoid them. On our side, we were able to help them with identifying backup plans to perform the last step of their transformation chemically, since the enzyme performing this action is unknown to this day.

The Artistic Side of Synthetic Biology

Bring Science Out of Your Lab!

This year, the EPFL iGEM Team gave the opportunity to iGEMers from all over the world to compete on a new level… Art! We know how hard it is for iGEM teams to think about art before the Giant Jamboree, and we hoped to inspire teams to look at the artistic side of their experiments.

Indeed we are convinced that art is a domain which people from all backgrounds can appreciate. This is the reason why we organised a contest of artistic images from team’s experiments! A way for us to open the dialog with the public about our project and, more broadly, about biology.

Here are some of the entries that we had, we were very grateful to all the teams that participated in this photo contest, and we hope that more teams will start to explore the interface between biology and art in the future.