Team:ETH Zurich/Achievements

From 2011.igem.org

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=SmoColi - Achievements =
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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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==General==
 
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* We came up with the idea of a bacterio-quantifier of smoke.
 
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* We worked hard and presented our work during the Regional Jamboree in Amsterdam.
 
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* We received Gold Medal and were invited to advance to the World Championship in Cambridge, USA.
 
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* We documented everything we did in our Wiki Website.
 
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==Modeling Achievements==
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=Modeling=
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* 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 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 gradient analytically and checked that it almost coincides with the numerically obtained one.
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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 made a [[Team:ETH_Zurich/Modeling/SingleCell|single cell model]] describing our circuit and verified its operation.
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* We made a [[Team:ETH_Zurich/Modeling/SingleCell|'''single cell model''']] describing our circuit and verified its operation.
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* 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.
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* 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.
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* 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
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* 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
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* 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 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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==Biology==
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=Biology=
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* We improved the pSB6A1 Plasmid to standard 5  
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* After severe cloning difficulties (due to unexpected lethality of active CI and LacI), the '''final system''' was completely established.
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* We created the BioBrick LacI<sub>M1</sub> which is a codon modified LacI for multiplasmid operations
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* We improved the pSB6A1 Plasmid to standard 5: [http://partsregistry.org/Part:BBa_K625005 '''pSB6A5''']
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* We created two improved version of the P<sub>U</sub> BioBrick
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* 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 successfully tested the channel in terms of cell viability and GFP synthesis
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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
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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 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
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* We successfully tested the '''channel''' in terms of '''cell viability and GFP synthesis'''
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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==
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* We [[Team:ETH_Zurich/Process/Validation|sistematically 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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=Microfluidics=
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* Modeling help to improved the channel design
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* 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 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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==Human Practices==
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=Human Practices=
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* We presented Synthetic Biology and iGEM to our fellow students in the [[Team:ETH Zurich/Team/Human practices#7.10.11 CBB Get together afternoon|CBB get together afternoon]].
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* We presented Synthetic Biology and iGEM to our fellow students in the [[Team:ETH Zurich/Team/Human practices#7.10.11 CBB Get together afternoon|'''CBB get together afternoon''']].
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* We presented iGEM and our project to the general public on the [[Team:ETH Zurich/Team/Human practices#22.10.11 D-BSSE Open house|BSSE Open House Day]] through a poster and a slide show.
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* We presented iGEM and our project to the general public on the [[Team:ETH Zurich/Team/Human practices#22.10.11 D-BSSE Open house|'''BSSE Open House Day''']] through a poster and a slide show.
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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.
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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.
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* ETH GLOBE and the NZZ (Neue Zeitung Zürich) will write about our participation at ????
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* '''ETH GLOBE''' and '''NZZ''' (Neue Zeitung Zürich) will write about our participation at iGEM World Championship Jamboree
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=Collaboration=
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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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==Personal achievements==
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=Personal achievements=
* xx managed to move the Dropbox folder to another location, thus making it look empty for the others.
* 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 accidentally modified an other teams wiki for 1 min
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* xx slept the whole boat trip in Amsterdam
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* xx and xy slept the whole boat trip in Amsterdam
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* xx found a mistake in the PowerPoint in the morning before the presentation ("And the channel turns read")  
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* xy found a mistake in the PowerPoint in the morning before the presentation ("And the channel turns read")
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* xy managed to sleep at two chairs in the lab
* We had fun!
* We had fun!
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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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