Meetings

Wednesday 28^th May

First meeting on Coli Rulez

In the last five weeks, we have been deciding on a project for our iGEM team this year. Finally, we came up with the idea of building a cellular automaton that will follow the rules 90, 110 and maybe 30.

The rules firstly described by Wolfram correspond to a deterministic model of cellular automaton. The spatial domain is divided into a fixed lattice. Each lattice is either in the on or off state. The next state of a lattice is determined by the state of its neighbours. Here, each line of a square grid is considered to represent the system state at time t. The next line state is determined thanks to its three neighbors from above.

Some rules particularly retained our attention:

• the rule 30 whose emerging pattern seems random, without any sign of regularity.
• the rule 90, also called Sierpinski triangles, with its nested pattern.
• the rule 110, with localized structures, known to be a Turing-complete machine. The proof of this property has been made by Matthew Cook, professor at the Institue of Neuroinformatics in Zürich.

  The genetic design of the rules was discussed. For the three rules chosen, they consist of combination of logical gates. Those logical gates will be implemented using recombinases.

  As we are working with bacteria on a fixed grid, it is necessary to implement this organization with a spatial structure. This can be done with beads and a microfluidic chip. As the feasibility of such a device are not yet well-defined for the team members, we also consider to implement that on 3D agar plate grid, that could be printed by a 3D printer. The exact form of those devices is still under discussion.

  We are also searching for the molecules that could fit our problem. The family of serine recombinases offers a wide variety of site specific and unidirectional recombinases. It is, however, not well explored. Some problem may arise with riboswitches. Moreover, we have to find three orthogonal signaling molecules. Some perspectives have been opened, like looking for non-bacterial communication systems or using artificial quorum sensing system. These steps are still under discussion.

  A first draft of our schedule has also been presented.

Human Practice

Saturday 10^th May

BSSE Open House Day

On May 10th the public in Basel had the unique chance to get an insight into many different scientific laboratories and the work done there. It was the joint open house day of D-BSSE of ETH (Department of Biosystems Science and Engineering) and the Biozentrum of the University of Basel. The many different labs opened their doors to the public and many scientists were present to give interested people some details about their daily work. So did the ETH iGEM team 2014. The team was present with a poster showing the history of iGEM, the previous ETH iGEM teams with their projects and general information about synthetic biology. Additionally there was a slideshow giving a best-of photo collection of last years jamboree. The goal of this day was to inform the public about synthetic biology in general and specifically about the spirit and the many different projects of iGEM. Many people showed strong interest in truly student driven projects and are curious to follow our team wiki for the next months. Below some impressions of the day.