Team:Paris Bettencourt/Newsletter1

OUR TEAM

ETH Zürich is taking part to iGEM since it was opened to the European universities (for the second edition).

The team has known several successes in the Information Processing track of the competition. This year, we are seven highly motivated students from different backgrounds, aiming to rock the Information Processing track once again. The interaction between wet lab and dry lab is crucial for our team.

OUR PROJECT
Make a Sierpinski triangle pattern appear in a grid Conjugate quorum sensing and logic gates in bacterial colonies Implement an XOR gate in an E. coli Characterize integrases (retrieve missing parameters) Study quorum sensing mechanism aiming to lower the leakiness Be able to predict accurately the system’s behavior.

Questions it raises :
How can a complex pattern emerge from a simple logic rule?

How can leakiness, noise and lack of robustness in biological systems be handled?

Emergence of complex patterns in nature is a fascinating phenomenon, which is not fully understood yet. Some sea snail shells indeed present natural mosaics, made out of only two colors seemingly following a simple rule to form a pattern.

Our project Mosaicoli aims to implement a similar complex behavior. It challenges the high noise and the low robustness shown by biological systems. This cellular automaton consists of a regular grid of E. coli colonies. Either in an ON or OFF state, each colony interacts with its neighbours according to a fixed logic rule. Mosaicoli exploits quorum sensing, integrase logic gates and microfluidics to generate the Sierpinski triangle pattern. Communication between colonies is achieved by AHL molecules and subsequent updates in a cell state are determined by a discrete XOR integrase gate. The final state is read out via fluorescence, which collectively depicts a complex pattern. Mosaicoli deals with the leakiness of biological subunits to create a reliable complex entity, which can be considered as a first step towards the biological computer.

OUR TEAM

University of Göttingen, Germany.

We come from different countries: Germany, China, Iran, Lebanon, India and Mexico. The group formed when the team of 2013 gave a presentation of their work and how they did in the Jamboree (they won the award for the best presentation in the overgrad division at the World Championship).

OUR PROJECT

Questions it raises :
Is it possible to select a short peptide with affinity towards fungal surface proteins out of a short peptide library?

We intend to develop a fast screening technique for different invasive fungi, such as Aspergillus fumigatus, Candida albicans and Aspergillus nidulans.

The idea is to tag the invasive fungal cells with a special protein marker that allows an easy detection of fungi. By modifying the protein marker with a proper signal molecule, we will be able to accomplish a fast and direct elimination of invasive fungi.

We want to prove the principle that it’s possible to obtain short peptides with affinity towards a protein of interest through a highthroughput screening method. The proteins of interest in our project are fungal surface proteins, but they can be any other protein, such as tumor markers or other pathogenic microorganism surface proteins.

We also want to develop a diagnostic tool with those peptides. Here, our methodology is straightforward and it is mainly a proofof- principle: we will tag a GFP marker and check for fluorescence. However, if this is successful, in the long term and after other sorts of chemical modifications, these peptides can be further applied as diagnostic and even therapeutic tools.

We are running for the Health and Medicine track.

OUR TEAM

The Gothenburg team is currently working in the Systems and Synthetic Biology group, in the Department of Chemical and Biological Engineering at Chalmers.

Our team reflects the diversity of Chalmers and the iGEM competition; from the total of 10 team members, 5 of us are not Swedish, with different nationalities such as Brazilian and Indian. We are all students at Chalmers, mostly at undergraduate level, and with different backgrounds. Being the second Chalmers iGEM team is both challenging and rewarding. We are excited and inspired by the experience of the iGEM competition and having fun while learning!

OUR PROJECT

Our team goal with the iGEM project is to construct a yeast generation counter. The idea is that each time the cell divides a different florescent protein is produced. Therefore by examining the cell under a microscope or in a flow cytometer one can determine how many times the cell has divided.

Nowadays the determination of replicative age of yeast cells is done by counting the budding scars of each cell in a microscope, a process time consuming and not effective.

Our goal would be achieved by constructing a logical AND gate in the cell where the input signals consist of a cyclin activated dCas9- VP64 and a guide RNA (gRNA) signal from the previous cell cycle. The output response consist of a different fluorescent protein and a new gRNA molecule.

dCas9-VP64 is an engineered turntable transcription factor only active when dimerized with an interchangeable gRNA molecule. The gRNA also determines the specificity of the transcription factor which enables the dCas9-VP64 to activate different genes depending on the sequence of the gRNA molecule and the promoter. gRNA consists of two parts, a scaffold and a 20 bp Specificity Determinant Sequence (SDS) on the 5’ end. The scaffold constitutes the majority of the gRNA molecule and gives it its structure whereas the SDS binds to the target site in the gene promoter. Cyclins are proteins that are involved in the progression of the cell cycle, therefore activated at specific times [5]. To mimic the specific production pattern of cyclins the dCas9- VP64 gene is placed under the control of a yeast cyclin promoter. Therefore the Cas9 will be produced in the G1 phase. When the Cas9 and gRNA dimerize and the transcription factor is activated, it in turn activates the transcription of a new fluorescent protein and a new gRNA molecule to act as a memory for the next cycle. Once this age counter is implemented, it would be possible to sort cells according to their replicative age automatically with a flow cytometer device.