Human Practices

To ensure that our project would stay on track to tackle real-life problems, we continuously sought input from people working ‘in the field’. This included professionals with backgrounds such as synthetic biology, computer sciences, education, academia and industry. By presenting our project at several events and always engaging in discussions, we received a lot of opinions and feedback and worked to evolve our project according to this interdisciplinary spirit.

Rapid Prototyping Workshop, EPFL

A first step in this direction was taken when one team member went to the Rapid Prototyping Workshop : “Teaching how to develop creative and practical solutions to real-life, complex, scientific and engineering problems” on June 8th 2017 to represent EPFL iGEM and gain valuable insights on problem solving, how to approach problems in general and as well as feedback on organizing the Wiki space and our web page. The workshop consisted of small groups having to solve individual problems by making use of a given ‘toolbox’. The problems included making prototypes for a project webpage, improvising an informative video describing a project, organizing the lab/office space optimally, how to improve the team performance and identifying the composition of an ideal curriculum for future (bio-)engineers. We later on implemented a lot of the feedback (for instance in teamwork) and believe it helped us for getting more efficient at organizing ourselves and meeting deadlines.

Hosting a High School Class in the Lab

The high school students in our lab

During our summer exam period we were approached by EPFL’s study promotion responsible Maya Frühauf, asking us if we could set up a wet-lab workshop for and supervise a high school class visiting EPFL in the beginning of July. Of course we were more than happy to introduce those high school students to the concepts of synthetic and cell-free biology, and hopefully pass on our motivation for the exciting field of bioengineering. The more than 25 high school students, in 9th grade and from the gymnasium Lerbermatt, Bern, would be spending half a day with us, which gave us plenty of time to let them do fun experiments with our guidance. After discussing the matter within the team, we made a list of several experiments and prepared everything for their arrival; we planned on explaining to them the working of chromoproteins and letting them perform a lysate reaction in tubes. We started with a presentation on what the iGEM competition is, placing it within its context of synthetic biology and explaining how this field is transforming the world we live in.

We then explained the workshop we had set up for them. Experiments included showing the enzyme activity of beta-galactosidase, which is closely related to our project as it is the reporter protein in our detection scheme. Another experiment was performing an E.Coli lysate reaction, where we explained how we make the lysate in the lab and what the advantages of a cell-free environment are. They would also prepare a PCR reaction, after we explained to them how the PCR machine works and that it's something we use every day in the lab, as well as prepare an agarose gel and run the electrophoresis and check the gel under the UV illuminator at the end. The last experiment would serve to explain how recombinant proteins, transformation and cloning all are connected as the students would plate E.Coli cells transformed with chromoproteins on agar plates. Beforehand a safety coordinator at EPFL had approved this workshop, and we worked with P1 equipment and components only. In the lab, we equipped every student with a lab coat, a pair of gloves and glasses to ensure safety and and divided them into groups of two. In those groups they performed the experiments, with us explaining some select biological principles at work (eg. protein expression, cell-free biology, transformation, cloning) and a paper manual we wrote to resume the course of experiments. At the end of the day and after a successfull workshop, they gave us feedback on our performance as well as the experiments we had chosen for them. We took many of their comments into account for developing the Mini-Kit, which is described in detail below.

Drawing with Chromoproteins, a high schooler's interpretation

Open Plant Forum and Workshop, Cambridge

At a later occasion, three team members went on a trip to Cambridge, UK where we followed the Open Plant Forum in July and more specifically the part of it that treated cell-free synthetic biology. We were able to get in touch with Keith Pardee, on whose paper1 we based the toehold part of our project (a toehold switch gets triggered by a complementary trigger sequence, unfolds and let's the downstream reporter gene be transcribed). Together we talked about our experimental setup, because at the time we were quite desperate as we hadn’t managed to get the toehold switch to unfold yet, so it was a relief to hear we were on the good track. We were working on a software to streamline the process of finding toehold/trigger pairs from a given input sequence, which would be the first computer program of its kind and a great tool for anyone working with toehold switches, so we also discussed our approach to the code with Pardee, namely how much weight certain parameters in our scoring function could be attributed.

By chance we met the Oxford iGEM team at that very same conference, and it was the beginning of a fruitful collaboration as they also work on a cell-free biosensor and we were able to exchange protocols and ideas on improving the E.Coli lysate reaction later on. However the highlight of this trip was definitely the one-day workshop on the integration of cell-free biology in the educational system of the UK. Named “Open Plant curriculum development working group”, this workshop was an interactive opportunity to discuss the advantages of including cell-free biology in the UK’s high school curricula and exchange ideas on the implementation thereof. Our first-hand knowledge of manipulating and making E.Coli lysate was a good starting point for many conversations, as we were closest to the target age group and were able to contribute unique points of view.

At the end of the day, we were convinced that cell-free biology will provide high schools with an amazing tool to explain certain principles of biology (eg. gene transcription, translation and regulation, transformation, cloning, energy of a system) all in a hands-on way, while at the same time developing an intuition for biology that students cannot get from books. The idea of our Mini-Kit was born: A small toolbox that would enable teachers to give a live demonstration of various biomolecular processes. An easy to handle, high-impact collection of experiments that poses no biohazard as it doesn’t contain living cells, perfect for explaining the concepts listed before to high school kids. A creative and novel way to stimulate each student’s learning process. The workshop was ideal to give us a roadmap, as a lot of technical details were discussed, and it inspired us to take this message home and implement it in our local context.

iGEM EPFL at the Curriculum Development Workshop

The Educational Cell Free Mini Kit project

Ever since the workshop in Cambridge, iGEM EPFL 2017 aimed to difuse cell-free biology as an accessible andexciting scientific field for the younger. Thus arose the idea of the Educational Cell Free Mini Kit (ECFK) that consists in a set of five experiments intended for demonstrations at local high schools. Leaving a footprint after the end of the competition was also something dear to the team, who found solace in the distribution of the minikit to several high schools in the Canton of Geneva, set in the francophone part of Switzerland. For this purpose, we reached out to several high schools located in regions nearby EPFL to ensure they had interests in our kit and that they would add it to their classes. A few days later we received many encouraging responses from high school and university professors in Geneva: François Lombard, Alexandra Suter de Iaco, Bertrand Emery and Jean-Luc Zanasco showed great interest in the implementation of such a kit in their theoretical and practical lectures and provided us with precise counselling on how to improve it in order to make it as accurate and suitable for high school classes as possible. Professor at the University of Geneva and manager of the plateform BiOutils Karl Perron also shared his enthusiastic thoughts about the project and reviewed our protocols for the minikit. As BiOutils is a platform which takes care of the production and distribution of experiments for high schools fo the whole Canton of Geneva, we transmitted him our will to bring cell-free biology into the classes and he agreed to have BiOutils ship our ECFK project !

The ECFK consists of several tubes containing different lysate reaction components, ideal to show a range of biomolecular processes. There are two kits: one freeze dried, which permits the simplicity of manipulations and storage for high schools with low budget, and one non-freeze dried, which permits for students to learn how to pipette and make more elaborated experiments. At the same time, it would be equipped with a detailed description of the experiments that could be performed with it as well as suggestions as to which topics a biology teacher could cover with them. The ECFK is a diverse toolbox suitable for demonstrating biological principles to all age groups, as the teacher is free to provide the students with an adequate background for their grade level.

We also reached out to our university’s biosafety department to make sure we were complying with national safety requirements.

Biosafety evaluation ECFK

Professional Input on Viral Contenders

When the time came to test our software in previously unchartered territory (eg. with new viruses), our first concern was finding a suitable ‘viral contender’. It had to be present in a bodily fluid, if possible with high amounts of viral RNA or DNA circulating. In order to make the best choice and detect a virus having a high impact on today’s health landscape, we contacted several professionals form different organizations and labs for their input. This included the following scientists : Jacques Fellay whose lab is working on Human Genomics of infectious diseases, virus-host interactions and translational genomics at EPFL; Samuel Cordey from the Virology lab at HUG in Geneva; Bruno Correia heading the laboratory of Protein Design and Immunoengineering at EPFL; and Didier Trono from the laboratory of Virology and Genetics at EPFL.

Their suggestions for a relevant virus that needed quick detection as well as our team brainstorming led us to single out the Hepatitis virus as a main contender, of which we then chose genomic sequence unique to Hepatitis C, genotype 1, as it is the most common of all Hepatitis C (HCV) genotypes. Today, Hepatitis C is diagnosed by taking blood and liver samples that need to be analyzed by a hospital laboratory. Our testing would dramatically reduce the amount of time needed to detect the virus and would also be more reliable, as we are directly targeting the viral genome instead of HCV antibodies secreted by the human immune system (which only get produced after several months of exposure to the antigen).

Summer School : Shaping the Future of Bioengineering, Davos

The summer school's program
Poster Session

In September, two of our team members went to Davos, Switzerland, to attend the Summer School on Shaping the Future of Bioengineering. There we presented our project as well as a first poster at a poster session and got feedback from professionals in academia and industry on key experiments and how to present our data in a more scientific manner.

At the same time we learned about and discussed related applications and expansions to our project (like what a 3D dignostics kit could look like, how to test for several diseases at the same time, who would be interested in this kits, and much more), which decidedly had a big impact on our ideas and is further explained in the Outlook section.

Group photo of participants, speakers and organisators

Computational Biology Symposium, EPFL

We also took part in the Computational Biology Symposium 2017 hosted at EPFL in October to present the software part of our project during a poster session. Three team members were present to explain what our iGEM project was about and exchange ideas on how to make our code public in the best way. At the end of the day we were happy to have found the most suitable solution to this problem and having gained absolutely inspiring insights into the world of computational biology.

1. Pardee, Keith, et al. "Rapid, low-cost detection of Zika virus using programmable biomolecular components." Cell 165.5 (2016): 1255-1266.