Team:Paris Bettencourt/Overview

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1) Physical containment: Our cells will be encapsulated with Arabinose and LB in order to avoid release of DNA/cells and to permit growth

1) Physical containment: Our cells will be encapsulated with Arabinose and LB in order to avoid release of DNA/cells, while permitting their growth.

2) Semantic Containment: Our synthetic system will have an amber codon embedded in its genes. The amber suppressor system will ensure their expression in our bacteria, while preventing it in natural populations.

1) Physical containment: Our cells will be encapsulated with Arabinose and LB in order to avoid release of DNA/cells, while permitting their growth.

2) Semantic Containment: Our synthetic system will have an amber codon embedded in its genes. The amber suppressor system will ensure their expression in our bacteria, while preventing it in natural populations.

3) Delay system: In the presence of Arabinose, LacI is produced, repressing the expression of a restriction enzyme. Once Arabinose is not present any more, the LacI repressor concentration decreases with dilution and degradation. This leads to the expression of the restriction enzyme.

1) Physical containment: Our cells will be encapsulated with Arabinose and LB in order to avoid release of DNA/cells, while permitting their growth.

2) Semantic Containment: Our synthetic system will have an amber codon embedded in its genes. The amber suppressor system will ensure their expression in our bacteria, while preventing it in natural populations.

3) Delay system: In the presence of Arabinose, LacI is produced, repressing the expression of a restriction enzyme. Once Arabinose is not present any more, the LacI repressor concentration decreases with dilution and degradation. This leads to the expression of the restriction enzyme.

4) Restriction Enzyme system: The restriction enzyme destroys the plasmid carrying the synthetic circuit and the anti-toxin gene.

1) Physical containment: Our cells will be encapsulated with Arabinose and LB in order to avoid release of DNA/cells, while permitting their growth.

2) Semantic Containment: Our synthetic system will have an amber codon embedded in its genes. The amber suppressor system will ensure their expression in our bacteria, while preventing it in natural populations.

3) Delay system: In the presence of Arabinose, LacI is produced, repressing the expression of a restriction enzyme. Once Arabinose is not present any more, the LacI repressor concentration decreases with dilution and degradation. This leads to the expression of the restriction enzyme.

4) Restriction Enzyme system: The restriction enzyme destroys the plasmid carrying the synthetic circuit and the anti-toxin gene.

5) Suicide system: Once the anti-toxin concentration is below a given threshold, the toxin is no longer inhibited. It kills the cell as well as its neighbors, and eliminates extracellular DNA via its DNase activity.

An example of an application for our project

Imagine a farmer that would like to know how much fertilizer is in his field, and optimize its use. We would provide him with cells carrying a nitrate biosensor (AgrEcoli), encapsulated in beads containing arabinose. He would spray the beads in his field, wait for 12h and then check if they are glowing in response to the nitrates contained in his soil.
We want to prevent the engineered organism or its DNA from being released and potentially transferred to a soil organism. For this reason once the arabinose is completely degraded inside the beads, the delay system would trigger the degradation of any DNA, followed by the collective death of our organisms due to the activation of toxic Colicins. Moreover, the semantic containment system would ensure that even if a synthetic gene is transferred to a natural organism, it would not be translated into a functional protein. Using our mechanism, the farmer would be able to use this device without endangering the environment by the release of synthetic genes.

Objectives

Our project aims to:

• Raise the issue of biosafety, and advocate the discerning use of biosafety circuits in future iGEM projects as a requirement
• Evaluate the risk of HGT in different SynBio applications
• Develop a new, improved containment system to expand the range of environments where GEOs can be used safely.

To do so, we:

• Engaged the general public and scientific community through debate
• Raised the question about how we can regulate this practices
• Compiled a parts page of safety circuits in the registry
• Relied on three levels of containment :
  1. Physical containment with alginate capsules
  2. Semantic containment using an amber suppressor system
  3. An improved killswitch featuring delayed population-level suicide through complete genome degradation.

We strived to make our system as robust against mutations as possible.