Team:ETH Zurich/Achievements

From 2011.igem.org

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=SmoColi - Achievements =
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= SmoColi - Achievements =
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It has been long four and a half months since we started working on our SmoColi project. During that time, we worked hard and learned a lot of new stuff. Bellow we summarize shortly what we did and what we managed to achieve so far. If you want to read more about them, click on the respective links.
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'''It has been a long four and a half months since we started working on our SmoColi project. During that time, we worked hard and learned a lot of new stuff. Below we summarize shortly what we did and what we have achieved so far. If you would like to read more about a particular achievement, click on the respective link.'''
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=Modeling=
=Modeling=
* We made a [[Team:ETH_Zurich/Modeling/Microfluidics|'''reaction-diffusion model''']] for the toxic molecule gradient formation in a channel and got a feeling about the feasibility of our ideas and channel dimensions.
* We made a [[Team:ETH_Zurich/Modeling/Microfluidics|'''reaction-diffusion model''']] for the toxic molecule gradient formation in a channel and got a feeling about the feasibility of our ideas and channel dimensions.
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* We approximated the '''[[Team:ETH_Zurich/Modeling/Analytical_Approximation#Analytical_Solution|gradient analytically]]''' and checked that it coincides with the '''[[Team:ETH_Zurich/Modeling/Analytical_Approximation#Analytical_Solution|numerically]]''' obtained one. Additionally, we gave an [[Team:ETH_Zurich/Modeling/Analytical_Approximation#4._GFP_Band_Existence|analytical criterion for the existence of the GFP band]].
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* We approximated the '''[[Team:ETH_Zurich/Modeling/Analytical_Approximation#Analytical_Solution|gradient analytically]]''' and checked that it coincides with the '''[[Team:ETH_Zurich/Modeling/Analytical_Approximation#Analytical_Solution|numerically]]''' obtained one. Additionally, we gave an [[Team:ETH_Zurich/Modeling/Analytical_Approximation#4._GFP_Band_Existence|'''analytical criterion for the existence of the GFP band''']].
* We made a [[Team:ETH_Zurich/Modeling/SingleCell|'''single cell model''']] describing our circuit and verified its operation.
* We made a [[Team:ETH_Zurich/Modeling/SingleCell|'''single cell model''']] describing our circuit and verified its operation.
* We performed a [[Team:ETH_Zurich/Modeling/Analysis|'''robustness analysis''']] of our system to see how the band behaves upon parameter variations and concluded that it is robust and monostable.
* We performed a [[Team:ETH_Zurich/Modeling/Analysis|'''robustness analysis''']] of our system to see how the band behaves upon parameter variations and concluded that it is robust and monostable.
* We performed [[Team:ETH_Zurich/Modeling/Stochastic|'''stochastic analysis''']] to see how the GFP band reacts upon noise and confirmed one more time its robustness
* We performed [[Team:ETH_Zurich/Modeling/Stochastic|'''stochastic analysis''']] to see how the GFP band reacts upon noise and confirmed one more time its robustness
* We integrated the single cell model and the reaction-diffusion model in a [[Team:ETH_Zurich/Modeling/Combined|'''combined 3D spatiotemporal reaction-diffusion model''']], simulated for various channel dimensions to get a feeling how the GFP band will move and how the alarm is activated
* We integrated the single cell model and the reaction-diffusion model in a [[Team:ETH_Zurich/Modeling/Combined|'''combined 3D spatiotemporal reaction-diffusion model''']], simulated for various channel dimensions to get a feeling how the GFP band will move and how the alarm is activated
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* We extracted some information about the channel dimensions from the model and [[Team:ETH Zurich/Process/Microfluidics|used this information in the actual channel design]].
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* We extracted some information about the channel dimensions from the model and [[Team:ETH Zurich/Process/Microfluidics|'''used this information in the actual channel design''']].
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* We improved the pSB6A1 Plasmid to standard 5: [http://partsregistry.org/Part:BBa_K625005 '''pSB6A5''']
* We improved the pSB6A1 Plasmid to standard 5: [http://partsregistry.org/Part:BBa_K625005 '''pSB6A5''']
* We created the [http://partsregistry.org/Part:BBa_K625000 BioBrick '''LacI<sub>M1</sub>'''] which is a codon modified LacI for multiplasmid operations
* We created the [http://partsregistry.org/Part:BBa_K625000 BioBrick '''LacI<sub>M1</sub>'''] which is a codon modified LacI for multiplasmid operations
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* We created [https://2011.igem.org/Team:ETH_Zurich/Biology/Validation#XylR_-_the_xylene_sensor two improved version of the '''P<sub>U</sub>''' BioBrick], characterized the P<sub>U</sub> promoter and fitted a dose response curve to the data
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* We created [https://2011.igem.org/Team:ETH_Zurich/Biology/Validation#XylR_-_the_xylene_sensor two improved versions of the '''P<sub>U</sub>''' BioBrick], characterized the P<sub>U</sub> promoter and fitted a dose response curve to the data
* We characterized the [[Team:ETH_Zurich/Biology/Validation#AraC_-_the_arabinose_sensor|'''P<sub>BAD</sub>''']] dose response for homogenous expression of the P<sub>BAD</sub> in BW27783
* We characterized the [[Team:ETH_Zurich/Biology/Validation#AraC_-_the_arabinose_sensor|'''P<sub>BAD</sub>''']] dose response for homogenous expression of the P<sub>BAD</sub> in BW27783
* We successfully tested the '''channel''' in terms of '''cell viability and GFP synthesis'''
* We successfully tested the '''channel''' in terms of '''cell viability and GFP synthesis'''
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* We could established a '''gradient of a small molecule''' (IPTG and arabinose) in a tube and also in the microfluidic channel
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* We could establish a '''gradient of a small molecule''' (IPTG and arabinose) in a tube and also in the microfluidic channel
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=Microfluidics=
=Microfluidics=
* We [[Team:ETH_Zurich/Process/Validation|systematically came up with the current channel design]] through a [[Team:ETH_Zurich/Process/Microfluidics|process of developing and refining chain of ideas for different designs]].
* We [[Team:ETH_Zurich/Process/Validation|systematically came up with the current channel design]] through a [[Team:ETH_Zurich/Process/Microfluidics|process of developing and refining chain of ideas for different designs]].
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* Modeling help to improved the channel design
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* Modeling helped to improve the channel design
* We participated in the [[Team:ETH_Zurich/Process/Validation#Final Channel Construction|PDMS channel construction]].
* We participated in the [[Team:ETH_Zurich/Process/Validation#Final Channel Construction|PDMS channel construction]].
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* We also made a [[Team:ETH Zurich/Team/Human practices#Survey|'''survey''']] with critical questions related to Synthetic Biology and iGEM, asked people to fill it out and analyzed the results.
* We also made a [[Team:ETH Zurich/Team/Human practices#Survey|'''survey''']] with critical questions related to Synthetic Biology and iGEM, asked people to fill it out and analyzed the results.
* '''ETH GLOBE''' and '''NZZ''' (Neue Zeitung Zürich) will write about our participation at iGEM World Championship Jamboree
* '''ETH GLOBE''' and '''NZZ''' (Neue Zeitung Zürich) will write about our participation at iGEM World Championship Jamboree
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* We helped the [[Team:Edinburgh/Collaboration#Thanks_to_ETH_Zurich|'''Edinburgh 2011 iGEM team''']] with '''debugging their [[Team:Edinburgh/Cellulases_(MATLAB_model)|MATLAB cellulase model]]'''.
 
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=Collaboration=
=Collaboration=
* We helped the [[Team:Edinburgh/Collaboration#Thanks_to_ETH_Zurich|'''Edinburgh 2011 iGEM team''']] with '''debugging their [[Team:Edinburgh/Cellulases_(MATLAB_model)|MATLAB cellulase model]]'''
* We helped the [[Team:Edinburgh/Collaboration#Thanks_to_ETH_Zurich|'''Edinburgh 2011 iGEM team''']] with '''debugging their [[Team:Edinburgh/Cellulases_(MATLAB_model)|MATLAB cellulase model]]'''

Latest revision as of 03:16, 29 October 2011

Can you feel the smoke tonight?
 

Contents

SmoColi - Achievements

It has been a long four and a half months since we started working on our SmoColi project. During that time, we worked hard and learned a lot of new stuff. Below we summarize shortly what we did and what we have achieved so far. If you would like to read more about a particular achievement, click on the respective link.


Modeling


Biology

  • After severe cloning difficulties (due to unexpected lethality of active CI and LacI), the final system was completely established.
  • We improved the pSB6A1 Plasmid to standard 5: [http://partsregistry.org/Part:BBa_K625005 pSB6A5]
  • We created the [http://partsregistry.org/Part:BBa_K625000 BioBrick LacIM1] which is a codon modified LacI for multiplasmid operations
  • We created two improved versions of the PU BioBrick, characterized the PU promoter and fitted a dose response curve to the data
  • We characterized the PBAD dose response for homogenous expression of the PBAD in BW27783
  • We successfully tested the channel in terms of cell viability and GFP synthesis
  • We could establish a gradient of a small molecule (IPTG and arabinose) in a tube and also in the microfluidic channel


Microfluidics


Human Practices

  • We presented Synthetic Biology and iGEM to our fellow students in the CBB get together afternoon.
  • We presented iGEM and our project to the general public on the BSSE Open House Day through a poster and a slide show.
  • We also made a survey with critical questions related to Synthetic Biology and iGEM, asked people to fill it out and analyzed the results.
  • ETH GLOBE and NZZ (Neue Zeitung Zürich) will write about our participation at iGEM World Championship Jamboree


Collaboration


Personal achievements

  • xx managed to move the Dropbox folder to another location, thus making it look empty for the others.
  • xx accidentally modified an other teams wiki for 1 min
  • xx and xy slept the whole boat trip in Amsterdam
  • xy found a mistake in the PowerPoint in the morning before the presentation ("And the channel turns read")
  • xy managed to sleep at two chairs in the lab
  • We had fun!


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