Difference between revisions of "Team:Exeter/Integrated Practices/lab"
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<p id="pp">One of the main factors driving our decision to focus on the use of kill switches in synthetic biology was the nature of their use in iGEM. It seemed that they were often employed as an afterthought and the dedicated kill switch section of the biosafety page on the registry had parts named "oh my god" and "test". We decided that providing better quantitative data on kill switches would be valuable. We asked individuals from industry and academia about kill switches and how they thought they might be most effectively implemented, we used their input to inform our work inside and outside the lab.<brr><br></p> | <p id="pp">One of the main factors driving our decision to focus on the use of kill switches in synthetic biology was the nature of their use in iGEM. It seemed that they were often employed as an afterthought and the dedicated kill switch section of the biosafety page on the registry had parts named "oh my god" and "test". We decided that providing better quantitative data on kill switches would be valuable. We asked individuals from industry and academia about kill switches and how they thought they might be most effectively implemented, we used their input to inform our work inside and outside the lab.<brr><br></p> | ||
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<p id="pp"> We contacted Dr Markus Gershater, the chief scientific officer at <i>Synthace Ltd</i>, to ask him what the application of kill switches might be in an industrial setting and what evidence would be satisfactory for their use. Dr Gershater gave the view that kill switches would not be as effective or economical as the physical and chemical bio-containment methods that Synthace currently employ. One of his concerns was that increasing the complexity of an industrial strain makes reproducibility and scalability more difficult. Any mis-control of the switch would incur cost as the run of that culture would die. For these reasons Dr Gershater thought that if increased containment is needed, investment in better physical containment is more effective and economical than biological methods. We decided to test how a kill switch might behave in an industrial setting by performing a continuous culture in a ministat (see <a href="https://2016.igem.org/Team:Exeter/Project#culture">here</a> for details). In this way we could test how viable a containment strategy kill switches are when used in industry.<br><br> | <p id="pp"> We contacted Dr Markus Gershater, the chief scientific officer at <i>Synthace Ltd</i>, to ask him what the application of kill switches might be in an industrial setting and what evidence would be satisfactory for their use. Dr Gershater gave the view that kill switches would not be as effective or economical as the physical and chemical bio-containment methods that Synthace currently employ. One of his concerns was that increasing the complexity of an industrial strain makes reproducibility and scalability more difficult. Any mis-control of the switch would incur cost as the run of that culture would die. For these reasons Dr Gershater thought that if increased containment is needed, investment in better physical containment is more effective and economical than biological methods. We decided to test how a kill switch might behave in an industrial setting by performing a continuous culture in a ministat (see <a href="https://2016.igem.org/Team:Exeter/Project#culture">here</a> for details). In this way we could test how viable a containment strategy kill switches are when used in industry.<br><br> | ||
| − | We then contacted Dr Tom Ellis who leads research in synthetic biology and synthetic genome engineering at Imperial College London. His view was that kill switches are not necessarily inherently flawed, but they are a lot more prone to breaking by mutation than other possible mechanisms (e.g. | + | We then contacted Dr Tom Ellis who leads research in synthetic biology and synthetic genome engineering at Imperial College London. His view was that kill switches are not necessarily inherently flawed, but they are a lot more prone to breaking by mutation than other possible mechanisms (e.g. auxotrophs). He suggested that multiple mechanisms could be combined that each have less than 1 in a billion escape rates. This would could give an escape rate of 1 in 10<sup>20</sup>. As a result of this and our own ideas we designed a system that would incorporate both KillerRed, a kill switch already in the registry and KillerOrange, a new part. Both could work together to provide a more effective kill switch and provide the increased efficiency that Dr Ellis talked about. This influenced the design of the CRISPR based kill switch we had hoped to develop as we intended to test the effect of targeting multiple essential genes within the host genome instead of just one.<br><br> |
We spoke to Prof. Robert Beardmore EPSRC Leadership Fellow in the Mathematical Biosciences at Exeter University. Much of his research has been into antibiotic resistance. We discussed how high selection pressure is applied by prolonged use of antibiotics and how kill switches may be analogous to this. It is clear that cells which develop a mutation that inactivates the kill switch would be strongly selected for. It was estimated that functional loss of the kill switch would occur in a short amount of time as a result, and if this was the case, could have strong implications for kill switch longevity. Because of this discussion we decided to test the effectiveness of kill switches over time in the ministat. We measured the efficiency of KillerRed and KillerOrange over time in a continuous culture and found that within a week the efficiency of the kill switch was reduced to the level of the control. (see <a href="https://2016.igem.org/Team:Exeter/Project#MSE">results</a>).<br><br> | We spoke to Prof. Robert Beardmore EPSRC Leadership Fellow in the Mathematical Biosciences at Exeter University. Much of his research has been into antibiotic resistance. We discussed how high selection pressure is applied by prolonged use of antibiotics and how kill switches may be analogous to this. It is clear that cells which develop a mutation that inactivates the kill switch would be strongly selected for. It was estimated that functional loss of the kill switch would occur in a short amount of time as a result, and if this was the case, could have strong implications for kill switch longevity. Because of this discussion we decided to test the effectiveness of kill switches over time in the ministat. We measured the efficiency of KillerRed and KillerOrange over time in a continuous culture and found that within a week the efficiency of the kill switch was reduced to the level of the control. (see <a href="https://2016.igem.org/Team:Exeter/Project#MSE">results</a>).<br><br> | ||
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| + | <a href="https://2016.igem.org/Team:Exeter/Integrated_Practices">Return to Integrated Practices</a> | ||
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Latest revision as of 03:13, 20 October 2016
