Team:Paris Bettencourt/Achievements
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• Adapting existing safety assessment tools for synthetic | • Adapting existing safety assessment tools for synthetic | ||
• Proposing new methods to assess safety in synthetic biology. | • Proposing new methods to assess safety in synthetic biology. | ||
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Revision as of 23:56, 26 October 2012
Semantic containment
Aims
System
Achievements :
Both part were well characterized and works well. For the second parts, we show that as expected, one mutation is quite leaky, although it works qualitatively, but one mutation is not enough if we want to release such parts in nature. Other reasons emphasize this observation, notably the weakness of being at one mutation to recover the protein functionality.
Achievements :
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Suicide system
Aims : Implement a kill-switch that features population-level suicide and complete genome degradation. System : A synthetic toxin-anti-toxin system based on the wild type Colicin E2 operon. Achievements : We showed that Colicin E2 cells induce cell death in sensitive populations, and that these sensitive populations can be protected by providing them with our engineered immunity protein.
Part K914001 is well characterized and provides immunity to sensitive cells against the Colicin E2 activity protein, but is leaky. Part K914002 is promoterless and allows users to easily plug in the appropriate promoter for their desired purpose.
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Restriction Enzyme System
Aim: To design a plasmid self-digestion system. Experimental System: We are testing different combinations of promoters and restriction enzymes. We have to characterize both the promoters (by measuring the expression of RFP) and the restriction enzymes (by measuring killed cells). Achievements :
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Delay System
Aim : A programmed delay will allow the cell to perform its intended function before our DNA-degrading suicide machinery is expressed. Experimental system: We used two different approaches to create this delay. The first one is based on the gradual dilution of a regulatory transcription factor. The second one makes use of a stationary-phase specific promoter. Both systems eventually result in the expression of the restriction enzyme I-SceI. In the final design, I-SceI cleaves the antitoxin gene, ultimately dooming the cell. Each step in this causal sequence contributes to the overall delay in the system.
Achievements :
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MAGE
Aims : Removal of four FseI restriction sites from E. coli MG1655 genome. Experimental System: Using multiplex automated genome engineering (MAGE) - a technique capable of editing the genome by making small changes in existing genomic sequences. Achievements: Proof of concept by introducing a stop codon in the middle of the lacZ gene |
Synthetic Import Domain
Creation of a novel protein import mechanism in bacteria.
Exploit the natural Colicin import domain fused to any protein at will, dubbed here: "Synthetic Import Domain". Achievements:
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Encapsulation
Aim: Harness bacteria-containing gel beads to assure cell containment and complement activity of genetic safety systems. Experimental system: Bacterial cells are encapsulated in alginate beads. We used a cell containment assay based on plating to assess the release of cells from alginate beads. In addition, we aimed at improving the entrapment of cells through stabilization by polyethyleneimine and covalent cross-linkage by glutaraldehyde. Achievements:
Achievements :
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Aims
Safety is an important issue in synthetic biology, especially for environmentally related projects. We started to answer the question, “how safe is safe enough?” by involving experts, the public and our fellow scientists, and also by building biosafety devices. However, to really answer the question, we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about the adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks in many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology.
Objectives
• Adapting existing safety assessment tools for synthetic • Proposing new methods to assess safety in synthetic biology.
Human Practice
Aims
Human concerns arose organically during the construction of the bWARE containment system, and human practices were intrinsic to every stage of our project. In designing and building our best genetic containment system, we often encountered limits on the ability of science alone to measure our performance. When is a biosafety system safe enough? The answer to this question is partially scientific, to the extent that horizontal gene transfer events can be observed and modeled. But the answer is also social, because ultimately the public will decide if a biosafety system works well enough to use. The only way for us to know if bWARE is a success is in conversation with experts and the community. We propose and implement new ways for iGEM to organize and present biosafety information, both for scientists and the public. We believe our reforms to the BioBrick registry will help synthetic biologists to find the best biosafety tools for their application. We also imagine the beginnings of a quantitative, context-specific biosafety database serving citizen scientists. Practical safety data will feed an informed public forum.
You can find the full list of conclusions here Main Proposals
You can find the full list of proposals here Achievements :
During this summer, all of us gained knowledge in synthetic biology and learned lab skills, but that wasn't all. From the beginning of our brainstorming sessions, safety questions came up in our discussions. Our mutual interest in this topic lead us to center our project on safeguard systems and human practices related to public awareness and risk assesssment. This meant that we had to work hard not only on our wet lab project, but also on human practices. To our delight, this effort resulted not only in community outreach, but also changed our own opinion on biosafety in the context of synthetic biology. We feel that our Human Practice project changed each and every one of us.Here are our personal perceptions. |