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Team:ETH Zurich/achievements
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'''We have achieved more than half of the goals we planned at the beginning of our project. These achievements are well distributed between experimental results, theoretical work and human reflection and socialisation. As a team of seven students, we all contributed to all achievements and this is why everyone of us can feel the fruitfulness of such a wide project. ''' | '''We have achieved more than half of the goals we planned at the beginning of our project. These achievements are well distributed between experimental results, theoretical work and human reflection and socialisation. As a team of seven students, we all contributed to all achievements and this is why everyone of us can feel the fruitfulness of such a wide project. ''' | ||
| + | == Lab == | ||
=== [https://2014.igem.org/Team:ETH_Zurich/expresults#Quorum Quorum sensing crosstalk full characterization] === | === [https://2014.igem.org/Team:ETH_Zurich/expresults#Quorum Quorum sensing crosstalk full characterization] === | ||
We highlighted 3 levels of crosstalk between Las, Lux and Rhl quorum sensing systems and fully quantitatively characterized all possible combinations of crosstalk at these three levels. | We highlighted 3 levels of crosstalk between Las, Lux and Rhl quorum sensing systems and fully quantitatively characterized all possible combinations of crosstalk at these three levels. | ||
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We quantitatively characterized leakiness of the three quorum sensing systems. We have designed a new biobrick for lowering leakiness of these systems and proved its efficiency on the lux system, which is the most leaky of the three. | We quantitatively characterized leakiness of the three quorum sensing systems. We have designed a new biobrick for lowering leakiness of these systems and proved its efficiency on the lux system, which is the most leaky of the three. | ||
| + | === [https://2014.igem.org/Team:ETH_Zurich/lab/chip Novel millifluidic chip construction method] === | ||
| + | We designed a rapid prototyping approach for creating millifluidic chips, which is perfectly in line with the do-it-yourself spirit of iGEM. | ||
| + | |||
| + | == Modeling == | ||
=== [https://2014.igem.org/Team:ETH_Zurich/modeling/int Integrase theoretical characterization] === | === [https://2014.igem.org/Team:ETH_Zurich/modeling/int Integrase theoretical characterization] === | ||
Basing our investigation on Bonnet et al.'s paper "Amplifying genetic logic gates" <sup>[[Team:ETH_Zurich/project/references#refEmergence|[9]]]</sup>, we used their experimenta data and a very detailed model in order to characterize integrases, and could in particular find a significant number of parameters unknown from the literature, such as binding affinity of integrases to their sites. | Basing our investigation on Bonnet et al.'s paper "Amplifying genetic logic gates" <sup>[[Team:ETH_Zurich/project/references#refEmergence|[9]]]</sup>, we used their experimenta data and a very detailed model in order to characterize integrases, and could in particular find a significant number of parameters unknown from the literature, such as binding affinity of integrases to their sites. | ||
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We have a thorough model for the whole system, which is the result of a detailed study of every module of this system, including quorum sensing, integrases, diffusion. We derived every formula from mass action kinetics and state precisely which approximations we do and why we can do them. All our steady state and some of our dynamic simulation results fit to experimental data from our own experiments or found in literature. | We have a thorough model for the whole system, which is the result of a detailed study of every module of this system, including quorum sensing, integrases, diffusion. We derived every formula from mass action kinetics and state precisely which approximations we do and why we can do them. All our steady state and some of our dynamic simulation results fit to experimental data from our own experiments or found in literature. | ||
| - | === | + | == Collaborations == |
| - | + | ||
| - | + | ||
===[https://2014.igem.org/Team:ETH_Zurich/collaborations Successful collaboration with Colombia, Helsinki and Edinburgh iGEM teams] === | ===[https://2014.igem.org/Team:ETH_Zurich/collaborations Successful collaboration with Colombia, Helsinki and Edinburgh iGEM teams] === | ||
We collaborated with Colombia and Helsinki iGEM teams by responding to Coombia team's challenge to find out low budget protocols. Our cheap PCR technique has been as successful as a standard PCR. | We collaborated with Colombia and Helsinki iGEM teams by responding to Coombia team's challenge to find out low budget protocols. Our cheap PCR technique has been as successful as a standard PCR. | ||
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We theoretically fused our project with Edinburgh's iGEM team's project on metabolic wiring. This fusion gave us a promising alternative to the cross-talk issues that happen when using quorum sensing only. | We theoretically fused our project with Edinburgh's iGEM team's project on metabolic wiring. This fusion gave us a promising alternative to the cross-talk issues that happen when using quorum sensing only. | ||
| + | == Human Practice == | ||
=== [https://2014.igem.org/Team:ETH_Zurich/human/overview Detailed investigation on the question of complexity through seven interviews of experts, a survey and our own reflection] === | === [https://2014.igem.org/Team:ETH_Zurich/human/overview Detailed investigation on the question of complexity through seven interviews of experts, a survey and our own reflection] === | ||
We conducted a deep study of complexity, how it emerges, and how we should deal with it. By [https://2014.igem.org/Team:ETH_Zurich/human/interviews interviewing experts] from different fields and by listening to the public with a [https://2014.igem.org/Team:ETH_Zurich/human/survey survey], we have broaden our views. Our own biological project also raised questions on this subject and we finally integrated everything that we learnt in [https://2014.igem.org/Team:ETH_Zurich/human/essay a reflection of our own]. | We conducted a deep study of complexity, how it emerges, and how we should deal with it. By [https://2014.igem.org/Team:ETH_Zurich/human/interviews interviewing experts] from different fields and by listening to the public with a [https://2014.igem.org/Team:ETH_Zurich/human/survey survey], we have broaden our views. Our own biological project also raised questions on this subject and we finally integrated everything that we learnt in [https://2014.igem.org/Team:ETH_Zurich/human/essay a reflection of our own]. | ||
Revision as of 11:08, 13 October 2014
Achievements
We have achieved more than half of the goals we planned at the beginning of our project. These achievements are well distributed between experimental results, theoretical work and human reflection and socialisation. As a team of seven students, we all contributed to all achievements and this is why everyone of us can feel the fruitfulness of such a wide project.
Lab
Quorum sensing crosstalk full characterization
We highlighted 3 levels of crosstalk between Las, Lux and Rhl quorum sensing systems and fully quantitatively characterized all possible combinations of crosstalk at these three levels.
Characterizing and lowering leakiness in quorum sensing systems
We quantitatively characterized leakiness of the three quorum sensing systems. We have designed a new biobrick for lowering leakiness of these systems and proved its efficiency on the lux system, which is the most leaky of the three.
Novel millifluidic chip construction method
We designed a rapid prototyping approach for creating millifluidic chips, which is perfectly in line with the do-it-yourself spirit of iGEM.
Modeling
Integrase theoretical characterization
Basing our investigation on Bonnet et al.'s paper "Amplifying genetic logic gates" [9], we used their experimenta data and a very detailed model in order to characterize integrases, and could in particular find a significant number of parameters unknown from the literature, such as binding affinity of integrases to their sites.
Predicting the whole system's behavior with a thorough, fully derived model
We have a thorough model for the whole system, which is the result of a detailed study of every module of this system, including quorum sensing, integrases, diffusion. We derived every formula from mass action kinetics and state precisely which approximations we do and why we can do them. All our steady state and some of our dynamic simulation results fit to experimental data from our own experiments or found in literature.
Collaborations
Successful collaboration with Colombia, Helsinki and Edinburgh iGEM teams
We collaborated with Colombia and Helsinki iGEM teams by responding to Coombia team's challenge to find out low budget protocols. Our cheap PCR technique has been as successful as a standard PCR.
We theoretically fused our project with Edinburgh's iGEM team's project on metabolic wiring. This fusion gave us a promising alternative to the cross-talk issues that happen when using quorum sensing only.
Human Practice
Detailed investigation on the question of complexity through seven interviews of experts, a survey and our own reflection
We conducted a deep study of complexity, how it emerges, and how we should deal with it. By interviewing experts from different fields and by listening to the public with a survey, we have broaden our views. Our own biological project also raised questions on this subject and we finally integrated everything that we learnt in a reflection of our own.
Bringing synthetic biology to the public
Last but not least, we have been communicating our enthusiasm for the field of synthetic biology during the whole project, through school visits, open house days, science slams, social media... We are commited to make our project, and synthetic biology in general, understandable and interesting for everyone. This is also why we placed some "simplify" buttons all over our wiki, each time a scientific text could be hermetic to the public.
