Team:Paris Bettencourt/Project

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Project abstract

Mankind is only beginning to grasp the complexity of living organisms. New discoveries often challenge our understanding of life. We believe that synthetic biology can be used as a powerful and reliable tool to help us comprehend and characterize the phenomena we just encountered.
As an iGEM team, we decided to work on one of the most intriguing microbiology discovery of the last decade: the existence of nanotubes in Bacillus subtilis!

Summary:
Our project is based on an article published by Dubey and Ben-Yehuda [http://bms.ucsf.edu/sites/ucsf-bms.ixm.ca/files/marjordan_06022011.pdf] in the Journal Cell. In this paper, they show an extraordinary new form of communication between Bacillus subtilis cells and even exchanges with E. coli.

The existence of the nanotube network discovered by Dubey and Ben-Yehuda is still discussed. We want to use synthetic biology to provide new evidences supporting the existence of a new cell-to-cell communication in Bacillus Subtilis and between Bacillus Subtilis and E.coli. Then, we want to characterize this communiction as best as we can using carefully tuned genetic designs. We also aim at proposing new applications combining synthetic biology and the nanotubes network.

Each step of our project corresponds to a new level of understanding of the nanotube network inner mechanisms.

Steps of the project:

Direct observation

We want first to prove de novo what the authors found. Although some microscopy images prove solidly the existence of these so-called nanotubes, we aim at using synthetic biology to get a definite proof of the existence of nanotubes. We will simply re-do the experiments done in the paper with simple observations.
Designs for direct observation step.

Characterization

Our second aim is to characterize the nanotubes: what passes through them and what are the typical diffusion times through the network. We will examine if RNA, proteins of different sizes and/or metabolites can pass through and with which ease and rate. For that purpose, we are going to engineer, thanks to synthetic biology, [http://en.wikipedia.org/wiki/BioBrick BioBricks] following this general design:

• An emitter cell that produces a messenger (RNA, protein etc.)
• This messenger passes through the nanotubes and into the receiver cell
• The emitter cell has specific promoters that activates an amplification system
• This amplification system in turn trigger a detection mechanism we can measure (fluroescence, others)

As a general outline we will first investigate the inter-species (subtilis-coli) connection to take advantage of all the existing biobricks for E .coli. We will then move on to an intra-species (subtilis to subtilis) connection and develop new parts specific to subtilis.
Designs for nanotube characterization.

Master-slave system

A very interesting system would involve a master strain and a slave strain. The master would have complete control over the state of the slave. Toggle switches seem to be an excellent idea to obtain this kind of behaviour.
Designs for a Master-Slave system.

Bi-directional communication

There are other goals that we are still working on such as use of this nanotube network to perform more complex tasks (pattern formation for instance) using more complex genetic circuits. This constructs would probably involve some sort of bi-directionnal communication, each cell reacting to the behaviour of its direct neighbours.
Designs for a bidirectional communication.

You can find out more about the different steps in the Project details section.

Real time project map

You can follow the evolution of the design using the xmind map.

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