SmoColi - Achievements

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 which we achievements we have so far. If you want to read more about them, click on the respective links.

Modeling

• 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.

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 LacI_M1] which is a codon modified LacI for multiplasmid operations
• We created two improved version of the P_U BioBrick, characterized the P_U promoter and fitted a dose response curve to the data
• We characterized the P_BAD dose response for homogenous expression of the P_BAD in BW27783
• We successfully tested the channel in terms of cell viability and GFP synthesis
• We could established a gradient of a small molecule (IPTG and arabinose) in a tube and also in the microfluidic channel

Microfluidics

• We systematically came up with the current channel design through a process of developing and refining chain of ideas for different designs.
• Modeling help to improved the channel design
• We participated in the PDMS channel construction.

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
• We helped the Edinburgh 2011 iGEM team with debugging their MATLAB cellulase model.

Collaboration

• We helped the Edinburgh 2011 iGEM team with debugging their MATLAB cellulase model

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!