Team:Paris Bettencourt/Newsletter4

Hi, all the iGEMers.

Last time when I wrote on this page of the newsletter, it was our first issue. Now, the summer is coming to the end and this is our fourth issue of the newsletter, also our last regular issue. Afterwards, we will replace it by special issues and review sessions, as i mentioned before. A couple schools have asked me about the timeline. I understand that school is starting and life is getting crazy. The student review of the judge question would be done by October and the peer review session would be in the first or second week of October. I will send out one more email with details and the rubrics in the coming three days.

I can’t thank you enough for being part of this community. I hope this newsletter has been and will continue to be a valuable resource for your team. In the process, we started with 8 teams and have had over 25 different teams from all over the world involved.

Again, thank you so much for all the cooperation. One thing I would like to emphasize and encourage you to do is to reach out to other teams on your own, ask for advise, talk about ideas, or just have a casual conversation. One thing I personally love about synthetic biology is how young, ambitious and creative everyone is.

Good luck with the rest of your project and journey to Boston! Watch out for the emails about the following special issues and let us know if you have specific things you would like to read or learn about!

OUR TEAM

We are the team from Zurich in Switzerland. 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.

PROJECT UPDATE

Questions to other teams:

For XMU China: Which mathematical principles do you think govern cell differentiation? Which kind of logic circuitry do you have in mind to relate chemotaxis to patterns?

Futher Plan:

We will be further characterizing the different modules of our design.

Advertisement&Plz help:

There is only one week left to complete our survey on complexity and try to win the collaboration badges (only 20 answers are needed to get the first badge). You can find our survey on our Facebook page, on our wiki and on our twitter. Thanks a lot for your help!

Our project is based on the conjugation of quorum sensing, integrasebased logic gates and diffusion. We have been investigating quorum sensing for the past few weeks. We want to find two orthogonal quorum sensing systems. Our system has two inputs, which correspond to two different homoserine lactones (HSL) concentrations. Each sensing system should be sensitive to only one HSL and should not react if the other HSL is added. We want to avoid a phenomenon called cross-talk.

We investigated three different systems: the Lux system, the Las system and the Rhl system. For each system, we built one plasmid consisting of the promoter, which can be induced by a specific signaling molecule, and of a gene coding for fast folding green fluorescent protein (GFP). Each colony was induced by different concentrations of its native HSL and also by different concentrations of HSL of the two other systems, in order to investigate cross-talk. The read-out is green fluorescence.

From the gathered experimental data, we can observe steady state, as well as the dynamic behavior of the inducing process, thanks to the fast folding property of GFP. We modeled the steady state as a Hill function of the native HSL + a constant modeling the leakiness + other Hill functions depending on other HSLs, if cross-talk was observed. The model allows a quantification of leakiness and cross-talk.

PROJECT UPDATE

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 for other teams:

We want to ask all the team how is their structure to work. Does everybody do everything? Do you have leader for each task?

We have three main groups: Lab, Model and HP. Each of the has their leader and students

At the lab we have very exiting news ☺ !! The part circled in red of the circuit is almost done. We are beginning to think about experiments to prove that the biobrick works.

We told you we had problems with the parameters in the mathematical model, but fortunately the parts of our system have been well studied and we were abled to solve the problem. Right now we are evaluating different variations of the circuit (Feed back, no feed back, different reporter…) in order to give the lab the best circuit possible.

Because we were working really hard on the lab last weeks we did not get the chance to participate in the third issue. But we still want you to meet one member of our group: his name is Skerlock coli.

Sherlock coli is a private investigator specialized in finding pathogenic bacteria. In this project he is helping us to find the bad guy Vibrio cholerae. For this purpose, Sherlock is using quorum-sensing molecules as his first lead and as soon he finds V. cholera he will give us a colorful announce.

Right now we are trying to give Sherlock the right tools to find V. cholerae. We have almost finished the circuit and we need to connect it with the phosphorylation cascade made by Peking 2011 Team.

NEXT STEP

The next steps are to prove the circuit and see what improvements can be done. In the Mathematical model the next step is the stochastic simulation.

OUR TEAM

University of Göttingen, Germany.
We come from different countries: Germany, China, Iran, Lebanon, India and Mexico.

PROJECT UPDATE

We’ve had some issues with the transformation efficiency kit. The efficiency with the provided reagents seems to be almost null. After a series of tests using control plasmids, different competent batches and different bacterial strains, we came to the conclusion that the shipping of the kit may have affected it. We’d like to let other teams be aware of that in case they are having the same issues.

We have also been working to generate 3D structures by homology modeling for some of the peptides that showed affinity towards fungal proteins. However, they still need to be assessed more thoroughly.

Predicted structure of one of our selected peptides. The portion in blue shows the scaffold (B1 domain of protein G) and the red portion is our inserted peptide. We’re using Modeller to generate the structures by homology modeling (https://salilab.org/modeller/).

OUR TEAM

Paris-Bettencourt iGEM team is part of the Center for Research and Interdisciplinarity (CRI) in Paris.

PROJECT UPDATE

Treating strong body odor using probiotics, producing a low cost perfume produced by bacteria and setting up a database of microbiome correlated to body odor

Questions it raises :
Are you more likely to use a product whose ingredients you are familiar with and can even make on your own? Is the formulation of a cream like the one we’ve described above something that you would put on your skin?

One of our sub-projects has to do with the development of the formulation that our probiotic will be given in. We wanted to make a cream that used components of daily life in order to create something that consumers can make at home and with products they can trust. One such formulation we are looking at is the development of a cream that is an emulsion of beeswax, jojoba oil, and the medium that our bacteria are grown in. We conducted an experiment of such an emulsion with fluorescent E. coli and viewed this cream under a microscope and recorded the images in a time-lapse video (which can be viewed here: http://youtu.be/4IgNmKaGdbU).

GFP E.coli under microscope.

NEXT STEP

Since our final probiotic will be with a C. striatum strain, we want to see if this bacteria can also be grown in medium which is easily found in grocery stores or something that one interacts with in their daily life. It turns out that C. striatum can actually grow very well on soymilk. Therefore, our next steps are to determine if soymilk needs to be supplemented with other nutrients or if we need to have other steps (such as boiling or filtration) in order to create the media to grow our final C. striatum strain which can then be emulsified with the beeswax and jojoba oil for our final formulation of our probiotic cream.