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.
- We made a 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 approximated the gradient analytically and checked that it coincides with the numerically obtained one. Additionally, we gave an analytical criterion for the existence of the GFP band.
- We made a single cell model describing our circuit and verified its operation.
- We performed a robustness analysis of our system to see how the band behaves upon parameter variations and concluded that it is robust and monostable.
- We performed 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 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 extracted some information about the channel dimensions from the model and used this information in the actual channel design.
- 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: pSB6A5
- We created the 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
- We systematically came up with the current channel design through a process of developing and refining chain of ideas for different designs.
- Modeling helped to improve the channel design
- We participated in the PDMS channel construction.
- 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
- 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!