Difference between revisions of "Team:Lethbridge HS/Model"

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<h3>★  ALERT! </h3>
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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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<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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<h3> Gold Medal Criterion #3</h3>
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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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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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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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    <h1 style=" font-size: 100px;">Model</h1>
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<br> <br> <br>
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<div class="container-fluid" style="margin-left:10%; margin-right:10%;">
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<h2>&nbsp;Ink Production</h2>
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<p class="center">The modeling portion of our project will allow us to estimate our pigment yields. The main pigment example that we are using is melanin. When designing the melA expression construct, we referenced from the Lagunas-Munoz et al., 2016 and we learned that the yields of melanin in <i>E. coli</i> are the highest at a temperature of 30 degrees Celsius and at a pH of 7.0. We will be using their experimental results as a model for what we should be expecting during our attempts to produce the melA tyrosinase and melanin in <i>E. coli</i>. As our system is modified from the system used in this paper to account for BioBrick standards and what we have available to us in the lab, we may be able to explain some differences in our production levels. We are using a different plasmid, cell strain, and will initially be using richer media.
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<p> The graphs below summarize some of the data obtained by Lagunas-Munoz et al., 2016. Firstly, they found that the cultures would reach stationary phase before melanin production would begin (or at least be detectable). Secondly, melanin would only be produced when the glucose in the media was consumed, which correlates with the culture reaching stationary phase. The group also found that melanin production was not favourable at growth temperatures of 35 degrees Celsius or higher. They found that the optimal balance between cell growth and melanin production occurred at 30 degrees. Using this information, we decided to grow our melA expressing cultures at 37 degrees until we induced expression with IPTG, then continue to grow the cultures at 30 degrees.</p>
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<p> </p>
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<p> The graphs below summarize some of the data obtained by Lagunas-Munoz et al., 2016. Firstly, they found that the cultures would reach stationary phase before melanin production would begin (or at least be detectable). Secondly, melanin would only be produced when the glucose in the media was consumed, which correlates with the culture reaching stationary phase. The group also found that melanin production was not favourable at growth temperatures of 35 degrees Celsius or higher. They found that the optimal balance between cell growth and melanin production occurred at 30 degrees. Using this information, we decided to grow our melA expressing cultures at 37 degrees until we induced expression with IPTG, then continue to grow the cultures at 30 degrees.</p>
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<p class="center"> The graphs below show the highest results from the Lagunas-Munoz and colleagues. </p>
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<img class="img-responsive" src="https://static.igem.org/mediawiki/2017/e/e4/Biomass_Graph_1_Temp.png" style="height: 500px;">
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<p class= "center"> This is a graph of the data of biomass (gDWCl¯¹) vs. time (hr) at a temperature of 30 degrees Celcius. </p>
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<img class="img-responsive" src="https://static.igem.org/mediawiki/2017/9/9b/Glucose_Graph_1_Temp_2.png" style="height: 500px;>
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<p class= "center"> This is a graph of the data of glucose levels (g l¯¹) vs. time (hr) at a temperature of 30 degrees Celcius.</p>
 
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<img class="img-responsive" src="https://static.igem.org/mediawiki/2017/9/91/Eumelanin_Graph_1_Temp.png" style="height: 500px;>
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<h5> Inspiration </h5>
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<p> <class= "center"> This is a graph of the data of eumelanin (g l¯¹) vs. time (hr) at a temperature of 30 degrees Celcius.
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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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<img class="img-responsive" src="https://static.igem.org/mediawiki/2017/f/f1/Eumelanin_Graph_2_pH_2.png" style="height: 475px;>
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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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<p> <class= "center"> This is a graph of the data of eumelanin (g l¯¹) vs. time (hr) at a temperature of 30 degrees Celcius. </p>
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<p> Reference:  
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Lagunas-Munoz, V.H., N. Cabrera-Valladares, F. Bolivar, G. Gosset, and A. Martinez. Optimum melanin production using recombinant <i>Escherichia coli</i>. Journal of Applied Microbiology, 2006. 101: 1002-1008.</p>
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Latest revision as of 03:58, 2 November 2017





 Ink Production

      

The modeling portion of our project will allow us to estimate our pigment yields. The main pigment example that we are using is melanin. When designing the melA expression construct, we referenced from the Lagunas-Munoz et al., 2016 and we learned that the yields of melanin in E. coli are the highest at a temperature of 30 degrees Celsius and at a pH of 7.0. We will be using their experimental results as a model for what we should be expecting during our attempts to produce the melA tyrosinase and melanin in E. coli. As our system is modified from the system used in this paper to account for BioBrick standards and what we have available to us in the lab, we may be able to explain some differences in our production levels. We are using a different plasmid, cell strain, and will initially be using richer media.

The graphs below summarize some of the data obtained by Lagunas-Munoz et al., 2016. Firstly, they found that the cultures would reach stationary phase before melanin production would begin (or at least be detectable). Secondly, melanin would only be produced when the glucose in the media was consumed, which correlates with the culture reaching stationary phase. The group also found that melanin production was not favourable at growth temperatures of 35 degrees Celsius or higher. They found that the optimal balance between cell growth and melanin production occurred at 30 degrees. Using this information, we decided to grow our melA expressing cultures at 37 degrees until we induced expression with IPTG, then continue to grow the cultures at 30 degrees.

The graphs below summarize some of the data obtained by Lagunas-Munoz et al., 2016. Firstly, they found that the cultures would reach stationary phase before melanin production would begin (or at least be detectable). Secondly, melanin would only be produced when the glucose in the media was consumed, which correlates with the culture reaching stationary phase. The group also found that melanin production was not favourable at growth temperatures of 35 degrees Celsius or higher. They found that the optimal balance between cell growth and melanin production occurred at 30 degrees. Using this information, we decided to grow our melA expressing cultures at 37 degrees until we induced expression with IPTG, then continue to grow the cultures at 30 degrees.




The graphs below show the highest results from the Lagunas-Munoz and colleagues.

This is a graph of the data of biomass (gDWCl¯¹) vs. time (hr) at a temperature of 30 degrees Celcius.


This is a graph of the data of glucose levels (g l¯¹) vs. time (hr) at a temperature of 30 degrees Celcius.

This is a graph of the data of eumelanin (g l¯¹) vs. time (hr) at a temperature of 30 degrees Celcius.


This is a graph of the data of eumelanin (g l¯¹) vs. time (hr) at a temperature of 30 degrees Celcius.

Reference: Lagunas-Munoz, V.H., N. Cabrera-Valladares, F. Bolivar, G. Gosset, and A. Martinez. Optimum melanin production using recombinant Escherichia coli. Journal of Applied Microbiology, 2006. 101: 1002-1008.