Team:ETH Zurich/modeling/diffmodel

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The background in our experimental setup is very high and this is high we see actual fluorescence appear only after 11 hours. In order to account for this, we also set up a background in the simulated pattern by adjusting the scale.  
The background in our experimental setup is very high and this is high we see actual fluorescence appear only after 11 hours. In order to account for this, we also set up a background in the simulated pattern by adjusting the scale.  
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{|class="wikitable" style="background-color: white; text-align:center; width:auto; margin: auto; font-size:10pt;"
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|colspan="2" style='font-size:10pt';text-align:left|{{:Team:ETH_Zurich/Templates/Video|width=1080px|id=video3|ratio=1920/720|srcMP4=<html>https://static.igem.org/mediawiki/2014/b/b1/ETH_Zurich_2014_signal_propagation_with_simulation.mp4</html>|poster=<html>https://static.igem.org/mediawiki/2014/6/69/ETH_Zurich_2014_signal_propagation_with_simulation_preview.png</html>}}
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|colspan="2" style='font-size:10pt';text-align:left|'''Video 1''' '''Row wise, self-propagating [https://2014.igem.org/Team:ETH_Zurich/project/background/biotools#Quorum_Sensing cell-to-cell communication] of ''E. coli'' cells confined in [https://2014.igem.org/Team:ETH_Zurich/lab/bead alginate beads] (d=3 mm, initially 10<sup>7</sup> cells/bead) on a [https://2014.igem.org/Team:ETH_Zurich/lab/chip custom-made millifluidic PDMS chip].'''
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|style="width:50%"|All fluorescent cells contained [https://2014.igem.org/Team:ETH_Zurich/expresults/rr#Riboregulators riboregulated] sfGFP followed by [http://parts.igem.org/Part:BBa_C0161 LuxI (BBa_C0161)] together under the control of the [http://parts.igem.org/Part:BBa_R0062 pLux promoter (BBa_R0062)], and [http://parts.igem.org/Part:BBa_J23100 constitutively (BBa_J23100)] expressed [http://parts.igem.org/Part:BBa_C0062 LuxR (BBa_C0062)]. LuxI catalyzes the production of the autoinducer 3OC6-HSL, which is then diffusing from cell to cell. For initialization, the cells in one bead of the top row were induced with 3OC6-HSL before encapsulation. Imaging was implemented with a [https://2014.igem.org/Team:ETH_Zurich/lab/protocols#Biostep_Dark-Hood_DH-50.E2.84.A2__and_the_Argus-X1.E2.84.A2_software Biostep Dark-Hood DH-50 (Argus X1 software)] fitted with a Canon EOS 500D DSLR camera and a fluorescence filter (545 nm filter). Pictures were usually taken every 2 min at an excitation wavelength of 470 nm with the standard Canon EOS Utility software. Time-lapse movies were created with Adobe After Effects CC software. 1950x faster than real-time, the video shown starts 10 h after the initiation of the experiment (however the time scale shown corresponds to minutes after loading of the chip). For precise experimental setup, check the [https://2014.igem.org/Team:ETH_Zurich/expresults#Diffusion Results] page.
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||Simulation of the propagation of the pattern in the millifluidic chip. [http://www.comsol.com/comsol-multiphysics Comsol Multiphysics Simulation software] was used in order to simulate a detailed diffusion model including quorum sensing steps in colonies and cell growth. Overall GFP concentration in beads has been scaled in order to account for the high background of the experimental setup. Green Fluorescence Protein is produced earlier in the wells, but can be seen only above a certain threshold.<br>Accurate prediction of experimental data by the model has been achieved, with parameters from our own fittings or from the literature. Experimental observation combined with simulation enables to show that a pattern is able to develop in the millifluidic chip in a reasonable time scale.
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=== Dynamics by row ===
=== Dynamics by row ===
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[[File:ETHZ AHL-regulators-pattern.png|center]]
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[[File:ETHZ AHL-regulators-pattern.png|center|900px|thumb|'''Figure 6''']]
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[[File:ETHZ GFP in beads.png|600px|center]]
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[[File:ETHZ GFP in beads.png|600px|center|thumb|'''Figure 7''' GFP in beads ]]
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[[File:ETHZ GFP in single cell.png|600px|center]]
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[[File:ETHZ GFP in single cell.png|600px|center|thumb|'''Figure 8''' GFP in single cell]]

Latest revision as of 01:13, 18 October 2014

iGEM ETH Zurich 2014