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

• 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 versions 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 establish 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 helped to improve 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

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!