Difference between revisions of "Team:BostonU/Model"

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  <p class="wide-heading-type mainwrap align-center">MODELING</p>
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<div id="panel1" class="link-slideup">
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  <p class="body-type mainwrap">Initially, there was not a defined relationship between the concentration of DNA added to the cell-free batches we made and protein expression. The maximum amount of DNA that our in-house cell free can handle was also undefined. Part of this is due to the variety in capabilities of a particular ‘batch’ of cell-free, even if the same protocol is used. Modeling this relationship allows us to maximize expression when performing experiments that use many different pieces of interacting DNA; such as in later tests where a plasmid containing a toehold switch driving a recombinase interacts with a reporter plasmid. </p>
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  <p class="body-type mainwrap">&nbsp;</p>
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<p class="body-type mainwrap">We collected data on the fluorescence from a plasmid containing constitutive deGFP. The plasmid was added to the cell free reaction at 10 nM, 20 nM, 30 nM, and 40 nM. There was also a reaction with no DNA. The resulting data can be seen in Figure 1. </p>
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  <p class="body-type mainwrap">&nbsp;</p>
  
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  <img src="https://static.igem.org/mediawiki/2017/6/60/T--BostonU--MaxDNAData.png"></img>
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  <p class="body-type"><strong>Figure 1.</strong>This figure shows fluorescence from constitutive deGFP plasmids at 10 nM, 20 nM, 30 nM, and 40 nM concentrations as well as a reaction containing no DNA. </p>
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  <p class="body-type mainwrap">&nbsp;</p>
  
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  <p class="body-type mainwrap"> Initially we planned on modeling this capacity with a single logistic curve. The results of this initial model are shown in figure 2.</p>
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<h3>★  ALERT! </h3>
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  <p class="body-type mainwrap">&nbsp;</p>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<h1> Modeling</h1>
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  <img src="https://static.igem.org/mediawiki/2017/1/12/T--BostonU--UniphasticModel.png"></img>
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  <p class="body-type"><strong>Figure 2.</strong>Model of cell free saturation from Figure 1 data based off of a single logistic curve. </p>
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
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  <p class="body-type mainwrap"> After looking at the data more closely, we determined that a more complex curve was required and fit a bell shaped dose response curve. A bell shaped dose response curve is the sum of two dose response curves. Here, low concentrations of DNA stimulate gene expression while high concentrations inhibit gene expression. </p>
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  <img src="https://static.igem.org/mediawiki/2017/9/91/BostonU_Biphasic_Model_With_Parameters.png"></img>
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  <p class="body-type"><strong>Figure 3.</strong>Adapted model of cell free saturation from Figure 1 data using a double dosage response curve. </p>
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  <p class="body-type mainwrap">&nbsp;</p>
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  <p class="body-type mainwrap">&nbsp;</p>
  
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  <p class="body-type mainwrap"> From this information, we see that the maximal levels of expression are achieved around 20 nM concentrations of DNA. In the future, when possible we aim to achieve the highest levels of expression by adding no more than 20 nM concentrations of total DNA in the system. For example, when testing plasmid toehold deGFP expression in response to a plasmid trigger, we had to ensure that we did not oversaturate our cell free system. We tuned the concentrations and volumes of these plasmids added in response to the results from this model. </p>
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<h3> Gold Medal Criterion #3</h3>
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  <p class="body-type mainwrap">&nbsp;</p>
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<p>
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To complete for the gold medal criterion #3, please describe your work on this page and fill out the description on your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>. To achieve this medal criterion, you must convince the judges that your team has gained insight into your project from modeling. You may not convince the judges if your model does not have an effect on your project design or implementation.  
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  <p class="body-type mainwrap"> We believe that the activity shown by our model may be a result of molecular activity of the cell-free machinery. This has been dubbed 'burn-out' by some researchers and it is when the amount of DNA that is added to a cell-free system is so great that it overwhelms one or more key proteins within the transcription translation pathway. There is not currently any available literature on this subject, but as the use of bacterial cell-free systems becomes more common we expected this issue to be studied in further depth. </p>
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Please see the <a href="https://2017.igem.org/Judging/Medals"> 2017 Medals Page</a> for more information.
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<h3>Best Model Special Prize</h3>
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<p>
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To compete for the <a href="https://2017.igem.org/Judging/Awards">Best Model prize</a>, please describe your work on this page  and also fill out the description on the <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>. Please note you can compete for both the gold medal criterion #3 and the best model prize with this page.  
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You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
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<h5> Inspiration </h5>
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Here are a few examples from previous teams:
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<li><a href="https://2016.igem.org/Team:Manchester/Model">Manchester 2016</a></li>
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">TU Delft 2016  </li>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
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Latest revision as of 17:09, 1 November 2017

MODELING