HUMAN PRACTICES

Newspaper TEMPS interview & article

Mr Fabien Goubet, journalist for Le Temps, a local newspaper, came to EPFL to interview us and learn about our project. We discussed iGEM, synthetic biology, and our project.

Later in the day, he interviewed Mr Bent Stumpe, Danish electronic engineer, inventor of the Touchscreen at the CERN for the control room of the Super Proton Syncroton accelerator; and Mr Rolf Heuer, director of CERN, and talked to them about our project. This is what they said:

« They absolutely must persevere in their work. I am convinced that the screen of the future will combine electronics and biology. »

Bent Stumpe - Inventor of the touchscreen

« It is a fascinating project, with curious and creative students. If I were them, I would pursue this work, regardless of the outcome of the competition. Who knows what it could lead one day ? It reminds me of the early days of the touchscreen. When engineers from CERN designed it for control systems of the accelerators in the 1970s, who would have thought that years later, a similar technology would be invented and become as commonly used? »

Rolf Heuer - Director of CERN

We have translated the article to English. The original article can be downloaded here.

Bacteria in your pad

Technology : Students from Lausanne are working on a new type of touchscreen integrating organic elements.

They will present their project at the end of october at a competition organized by the prestigious MIT in Boston.

Fabien Goubet

No respite for smartphones and other pads. As soon as they invaded our pockets and our living rooms, some already think about the next step. Sakura Nussbaum and her thirteen teammates, students in Bachelor of Life Sciences at EPFL, are some of them. « We are working on the design and the fabrication of a « BioPad », a touchpad working with the help of biological compounds, in this case bacteria that emit light when a pressure is applied on the screen », summarizes the young student. Their project is only at its beginning, but is no less encouraging.

When we put bacteria under mechanical pressure, they don't stay inert but react to limit the consequences. It is the case for Escherichia coli, a very common intestinal bacteria. A pressure on its envelope makes it produce protective proteins that rigidify its structure to limit this stress. The mechanism by which it happens is still uncertain, but Sakura Nussbaum and her teammates have studied it closer. They noticed that it involves a protein named CpxR, which role is to stimulate the production of these protective proteins. In the absence of pressure, CpxR is divided in two distinct and inactive parts. These parts reassemble in case of pressure on the bacterial envelope and constitute the CpxR protein itself, active this time. The team of students based the concept of their project on this mechanism. « We have genetically modified Escherichia coli, so that it emits light when it is subjected to pressure », details Sakura Nussbaum. The luminescence is ensured by a protein coming from glow worm, the luciferase. This protein is « grafted » on the CpxR protein and emits light only when the two parts are assembled.

Thus, the students have bacteria that emit light when we touch them. To take advantage of this, they used a microfluidic chip. This is a small plate of a few centimeters long, composed of PDMS, a carbon and silicium polymere which structure is slightly malleable. The chip is made of 768 tiny cavities of a few micrometers in diameter in which are placed bacteria with a little culture medium. « Each chamber constitutes in a way one pixel », indicates Axel De Tonnac, the microfluidics specialist of the crew. The students are currently verifying that their bacteria really emit light when pressure is applied on it. Here is where their work is. Of course, they are still far away from a hypothetical « BioPad », but the project only started this summer. « We are still at the stage of proof of concept, admits Axel De Tonnac, But our objective now is to make sure that everything works as expected, and to present our work at the iGEM competition. »

The whole team is going to fly to Boston, where the competition international Genetically Engineered Machine (iGEM) will take place. Starting on the 30th of octobre and organized by the Massachusetts Institute of Technology (MIT), this competition reassembles 220 teams of students, from different specialities. It brings synthetic biology at honour, a discipline in which biologists work as engineers and build standardized biological compounds, « biobricks », which can be useful in the future for other researchers wanting to give particular function to living organisms.

Naturally, the obstacles to the realisation of a screen are numerous. How to renew the culture medium once it is used ? How to control the multiplication of the bacteria without compromising the performance of electric circuits ?

Bent Stumpe, retired from CERN and inventor of the first touchscreen in 1972, heard about the project. For him, they should not be impressed by this kind of inconvenients. « They absolutely must persevere in their work. I am convinced that the screens of the future will combine electronics and biology », assures the researcher.

High school students' visit

« I was impressed by the energy of the whole team and I hope that my students will pick up on this. They enjoyed the day and they had a taste of the "real life" of biologist and synthetic biology. »

Jean-Pierre Lardet

In september, our team invited two groups of high school students to come to EPFL, in Lausanne. The first group was a swiss German class from Bern (25 students), who came for one hour to attend a general presentation explaining the basics of synthetic biology, the iGEM competition and our project. The second group was composed of 4 classes (80 students) from our region, Canton de Vaud. They spent the whole day with us, receiving a complete theorical and practical overview of synthetic biology.

Before they came, we sent both groups a quiz (13 multiple choice questions) about synthetic biology, and also asked them about their opinion concerning GMOs. We wanted to know more precisely how much they had already learned at school about synthetic biology, and what were the important points that had to be brought up during the presentation. At the end of the presentation or at the end of the day (respectively for the Swiss-German or local students) we asked them to complete the quiz again, to compare the number of right answers.

General presentation

We did the same general presentation for both groups. The presentation had three parts. The first one was about iGEM, the modalities and principles of the competition, the number of participating teams, the contribution of each team, etc. The second part was about synthetic biology and, after talking about common lab techniques and procedures, we talked about the third part, our « BioPad » project.

This was all we did with the Swiss-German students. The local group discovered other aspects of biology through activities we had organized during the afternoon. For these, we divided the group in two; one sub-group went to our lab to participate in the workshops, and the other went to a class room to do the mini-iGEM projects.

Workshops

We organized four different activities in the lab:

Streaking colorful bacteria on agar plates

Learning how to streak bacteria on agar plates by drawing something with bacteria (E coli) expressing Calgary’s chromoproteins. Each student had a plate (chloramphenicol resistant), a choice of 5 colors (more than one could be used on the same plate), and their enless supply of imagination.

Loading agarose gels for electrophoresis of various DNA fragments

Learning what is an agarose gel, its composition, how fragments migrate with the current, how we can predict the size of a fragment with the gel and examples of moments when electrophoresis is really important for us. And finally each student loaded a gel with different DNA samples in order to observe how it migrates.

Microfluidic workshop

The students were able to learn more about the basic principles of microfluidics and why it is such a useful tool in synthetic biology. A quick look at the standard dimensions of common biological objects first allowed them to see that a microfluidic chip is perfectly sized to host bacteria and yeasts, which are the 2 types of microorganisms used in our project. The advantages of microfluidics over classical analytical methods were then discussed such as the low amount of reagents required and the high spatio-temporal resolution that allows very precise analyses. Before learning more precisely how the MITOMI chip works, they also got a quick introduction on the fabrication process of microfluidic chips and were shown masks and wafers. The presentation ended with a small demonstration of the loading of a chip using a green dye to show the size of the channels.

Signal detection and processing

Introducing the Raspberry Pi, a cheap and mini computer, demo of how it works and examples of projects made with it. We then explained the need of taking infrared images and the problem that arises from doing that (mainly the need to excite the IFP with the correct wavelength). We then did a brief introduction to programming and the new role it's taking into education, to illustrate it we did a demo of visual programming and explained how it is used to introduce children to programming languages in a fun way.

Mini-iGEM

The students participated in a game that we called « mini iGEM ». Each team of 6 to 7 students had to sit for 30 minutes and to pitch their ideas about a project they would present if they were participating in iGEM. They had a list of biobricks and they could invent their own. A different team member was helping each group of students. At the end, we had 12 mini-projects, each more imaginative than the next, which each team presented to the others. We played the role of judges and graded their ideas based on the originality, the utiliy, the feasability and the security of the project. The winners of the game had the opportunity to visit the clean rooms and the EPFL microfluidic lab (Maerkl Lab).

Quiz results BEFORE

For the Swiss-German group, the mean score obtained for the quiz was 46 %. For the local group, it was 55 %. As the students from Bern were younger, it is not suprizing that they knew less than the second group.

As for the GMOs' question, most of the students thought that GMO only concern agriculture. We asked them the question : « What do GMOs make you think of? », and these are some of the answers we received:

• « An extraordinary discovery for medicine but an agricultural poison for thousands of people and lands. »
• « For me, GMOs are an invention that aims to get money without worrying about the planet. »
• « These are plants that are more resistant to bacteria and diseases. For example, these plants can be bigger than normal ones. But it doesn't mean that it's always good for humans and animals. »
• « It is when we change the DNA of something. This word reminds me of an experiment that has been done years ago that was at the origin of the sheep « Dolly »

• « Monsanto. »
• « Modified plants »
• « Cancer »
• « Unhealthy food »

Quiz results AFTER

At the end of the day, we made them fill the same quiz as they had before coming. We compared the results before and after the day and the improvement was spectacular.

The mean score obtained for the test at the end of the day was 86 % (global improvement of 31%). We can then consider that we really had an impact on the students that came to visit us. It was a very interesting experience and a great chance for us that these students could come to see what our project was about. They were very collaborative and enthusiastic from the beginning to the end, and everyone participated to the activities with energy. Our message was delivered with success and we hope that they will keep good memories about this day with our team.

For the Swiss German class, we also made them fill the quiz after the presentation. The final score for them was 71 %, which is a final score 15 % lower and an improvement 6 % lower than the students who participated in the workshop and the mini iGEM game. These results show that the practical part was also important for the understanding of synthetic biology concepts and that a complete formation must include theory and practice.

Presentation at the Hackuarium

The Hackuarium is a local biohackerspace (DIY biology lab)

A biohackerspace is a […]

On August 21st, three founders/organizers of European biohackerspaces – Clément Epié (La Paillasse Paris), Nicolas Loubet (La Paillasse Paris and http://umaps.fr/) and Yann Heurtaux (Hackuarium Lausanne) – visited our EPFL lab. We gave them a quick introduction to our iGEM project, demonstrating our microfluidic chips, our bacteria expressing GFP and our colored agar plates. Clément, Nicolas and Yann then described the projects they are working on in their biohackerspaces. It was great fun!

The three biohackers contacted the EPFL iGEM team to build a solid link between iGEM and the biohackerspaces, as La Paillasse did with the CRI-Bettencourt team in Paris a few months ago. This new collaboration between iGEM and biohackerspaces stems from the fact that many iGEM teams give up their project once the contest is over, because they lack means and space to further pursue their goals. The Lausanne Hackuarium intends to collaborate with EPFL iGEM teams from now on to help them continue their projects by providing lab facilities and thinking spaces. Great ideas shouldn't be wasted!

We are excited at the prospect of this collaboration, and so we continue to meet occasionally with the members of Hackuarium. On the 10th of September, our team formally presented our iGEM during one of Hackuarium’s weekly open meetings. The presentation was given to about 30 collaborators from different backgrounds, including engineering, biology design and journalism. Some had never heard about iGEM, and were really enthusiastic about our project. We agreed to do a second presentation after the Jamboree to talk about the results of the project and our experience in Boston.