Team:UCSF/Auxotroph Data

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<a href="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/Kerner%202012%20PLoS%20ONE.pdf"><b>A Programmable <i>Escherichia coli</i> Consortium via Tunable Symbiosis </b> </a>. They showed some experimental analysis which were the first steps at showing that these strains could be induced at varying levels to get a range of ratios between the two strains. <br>
<a href="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/Kerner%202012%20PLoS%20ONE.pdf"><b>A Programmable <i>Escherichia coli</i> Consortium via Tunable Symbiosis </b> </a>. They showed some experimental analysis which were the first steps at showing that these strains could be induced at varying levels to get a range of ratios between the two strains. <br>
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<regulartext>Based on comments made in the discussion section of the Kerner paper, we believed that it was necessary to determine whether the population of the two strains could be determined based on an equation relating the total OD of the two strains and the YFP reading from one of the strains (Y3). For this reason we created a standard curve of YFP fluorescence versus cell density. <br> <p>
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<img align="left" style="margin-right:128px;margin-left:68px; width:555px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/yfp_std.jpg"> <br> <p>
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<regulartext> We were able to create our own version of the model presented in the Kerner 2012 paper, using parameters we found in the literature and obtained through our own data collection.
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<regulartext> We were able to create our own version of the model presented in the Kerner 2012 paper and obtain a model based on data that we collected.  
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<img align="left" style="margin-right:178px;margin-left:68px; margin-bottom:8px; width:500px;height:250px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/Surface-model.jpg"><br><p>
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<p> <regulartext>Based on this model, it seems that a wide variety of ratios of the two strains could be obtained.
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<p><br>
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<p> <regulartext>So, we performed experiments to determine the ratios of the two strains that could be collected in a variety of inducer conditions. However, based on our results from the YFP standard curve (above) we realized that the data would only be accurate in a small range of cell concentrations. The details of our experimental setup can be found on our Project Protocols page: <a href="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/Protocols/Coculturing%20of%20Auxotrophs.pdf"><b> Co-culturing of Auxotroph Strains  </b> </a>. 
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<regulartext> A 3D surface of that graph was obtained and a slice of the graph is shown here:  
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<regulartext> A 3D surface of that graph was obtained and a slice of the graph are shown below: <br> <p>
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<h3> While in some amounts of inducer concentrations, the system seems tunable, it is not nearly as robust as the model predicts. Thus, we turned to our toxin/antitoxin system as a new approach to tuning communities of cells. <br><p>
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<img align="left" style="margin-bottom:18px; width:555px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/surf-data.png">
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<img align="left" style="margin-bottom:8px; width:555px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/slice.png">
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<img align="left" style="margin-left:168px;margin-bottom:8px; width:555px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/slice.png">

Latest revision as of 03:47, 4 October 2012

Growth and Analysis of Auxotroph System in E. coli


The W3 and Y3 strains (tryptophan ad tyrosine auxotrophs) that we obtained from the Lin Lab at the University of Michigan had already been studied in a paper published earlier this year. A Programmable Escherichia coli Consortium via Tunable Symbiosis . They showed some experimental analysis which were the first steps at showing that these strains could be induced at varying levels to get a range of ratios between the two strains.


Based on comments made in the discussion section of the Kerner paper, we believed that it was necessary to determine whether the population of the two strains could be determined based on an equation relating the total OD of the two strains and the YFP reading from one of the strains (Y3). For this reason we created a standard curve of YFP fluorescence versus cell density.


We were able to create our own version of the model presented in the Kerner 2012 paper, using parameters we found in the literature and obtained through our own data collection.

Based on this model, it seems that a wide variety of ratios of the two strains could be obtained.


So, we performed experiments to determine the ratios of the two strains that could be collected in a variety of inducer conditions. However, based on our results from the YFP standard curve (above) we realized that the data would only be accurate in a small range of cell concentrations. The details of our experimental setup can be found on our Project Protocols page: Co-culturing of Auxotroph Strains .

A 3D surface of that graph was obtained and a slice of the graph are shown below:

While in some amounts of inducer concentrations, the system seems tunable, it is not nearly as robust as the model predicts. Thus, we turned to our toxin/antitoxin system as a new approach to tuning communities of cells.

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