Difference between revisions of "Team:UCSC/Model"

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    <h1>Modelling</h1>
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    <h4>Estimate and optimize yield.</h4>
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    </br>
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    <div align="left">
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        <h5>Acetaminophen</h5>
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        To predict theoretical acetaminophen production, we calculated the amount of a precursor, chorismate, by quantifying its main products, the aromatic amino acids phenylalanine, tyrosine, and tryptophan.
 +
        We analyzed amino acid composition literature for similar cyanobacteria species since none were available for Synechococcus and found that between one and 13.6 percent of amino acids were aromatics by weight.
 +
        With the assumption that our enzymes would take a quarter of the chorismate precursor and the molar conversions from Equations 1 and 2 below, we got an estimate for acetaminophen concentration of between 17.5mg and 1.29 mg per gram dried biomass.
 +
        To further verify our organism’s amount of precursor, we ran both the genome and the ribosomal protein sequences through a self programmed amino acid converter-counter and got aromatic amino acid molar percentages of 9.3% and 5.14% respectively.
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        These numbers show that there is likely enough precursor and that acetaminophen production should be within a measurable range.
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    </div>
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    <h4>Biomass</h4>
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    <div id="container"></div>
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<body align="center">
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    Timescale: <button onclick="MinusDays(); MakeChart();"> < </button>
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        <var id="htmlDaysID"></var> days
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    <button onclick="PlusDays(); MakeChart();"> > </button>
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        </br>
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        Light Intensity: <button onclick="MinusOneLight();MakeChart();"> < </button>
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        <var id="htmlIntensityID"></var> µE m<sup>-2</sup> s<sup>-1</sup>
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        <button onclick="PlusOneLight(); MakeChart();"> > </button>
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        </br>
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        Temperature: <button onclick="MinusOneDegree(); MakeChart();"> < </button>
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        <var id="htmlTempID"></var> &#x2103;
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        <button onclick="PlusOneDegree(); MakeChart();"> > </button>
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        </br>
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        Starting Density: <button id="MinusDensity" onclick="MinusDensity(); MakeChart();"> < </button>
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        <var id="htmlDensityID"></var> g biomass/ L
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        <button onclick="PlusDensity(); MakeChart();">  > </button>
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        </br>
  
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        <div id="demo"></div>
  
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<div class="column full_size judges-will-not-evaluate">
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        <h3>References</h3>
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<h3>★  ALERT! </h3>
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        <a href= http://onlinelibrary.wiley.com/doi/10.1002/cjce.22154/abstract>Growth optimization of Synechococcus elongatus PCC7942 in lab flasks and a 2-D photobioreactor<a> </br>
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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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        <a href= http://ucelinks.cdlib.org:8888/sfx_local?ID=doi:10.1007%2Fs10811-011-9683-2&genre=article&atitle=Carbon%20metabolism%20and%20energy%20conversion%
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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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        >Carbon metabolism and energy conversion of Synechococcus sp. PCC 7942 under mixotrophic conditions.<a>
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    </body>
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<div class="column full_size">
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<style>
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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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<div class="column half_size">
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    function MinusDays() {
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<h3> Gold Medal Criterion #3</h3>
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        if(localStorage.jsDaysValue>1){
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<p>
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            localStorage.jsDaysValue=parseInt(localStorage.jsDaysValue)-1;
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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>
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        document.getElementById("htmlIntensityID").innerHTML=localStorage.jsIntensityValue;
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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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    }
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</p>
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</div>
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<div class="column half_size">
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    function MinusOneDegree() {
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<h3>Best Model Special Prize</h3>
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<p>
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</script>
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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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<br><br>
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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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</p>
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<script src="https://code.highcharts.com/highcharts.src.js"></script>
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<div class="clear"></div>
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<div class="column full_size">
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<script> //Charting
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<h5> Inspiration </h5>
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    function MakeChart(){
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<p>
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        var yValueArray = []
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Here are a few examples from previous teams:
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        for(var dayNum=0; dayNum<=localStorage.jsDaysValue; dayNum++){
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</p>
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            var myNum = 1/(1+(Math.pow(Math.E,((-1+(Math.abs(localStorage.jsIntensityValue-100)/250))+(Math.abs(localStorage.jsTempValue-33)/9))*dayNum+5)))
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<ul>
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            //yValueArray.push(myNum);
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<li><a href="https://2016.igem.org/Team:Manchester/Model">Manchester 2016</a></li>
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            yValueArray.push(Number(myNum.toFixed(4))+Number(localStorage.jsDensityValue));
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">TU Delft 2016  </li>
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        }   
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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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</ul>
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        //document.getElementById("demo").innerHTML = localStorage.jsDensityValue;
  
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</div>
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        Highcharts.chart('container', {
  
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            title: {
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                text: 'Biomass Production'
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            },
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            subtitle: {
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                text: 'Data Aggregated from sources below'
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            },
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            yAxis: {
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                title: {
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                    text: 'Grams Dried Biomass per Liter'
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                }
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            },
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            xAxis: {
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                title: {
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                    text: 'Days'
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                align: 'right',
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                series: {
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            },
 +
            series: [{
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                name: 'Synechococcus 7942',
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                data: yValueArray,
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            }]
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        });
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    }
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    MakeChart()
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</script>
 
</html>
 
</html>
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{{Ucscfooter}}
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{{UCSC-Footer}}

Revision as of 18:38, 19 September 2017

Modelling

Estimate and optimize yield.


Acetaminophen
To predict theoretical acetaminophen production, we calculated the amount of a precursor, chorismate, by quantifying its main products, the aromatic amino acids phenylalanine, tyrosine, and tryptophan. We analyzed amino acid composition literature for similar cyanobacteria species since none were available for Synechococcus and found that between one and 13.6 percent of amino acids were aromatics by weight. With the assumption that our enzymes would take a quarter of the chorismate precursor and the molar conversions from Equations 1 and 2 below, we got an estimate for acetaminophen concentration of between 17.5mg and 1.29 mg per gram dried biomass. To further verify our organism’s amount of precursor, we ran both the genome and the ribosomal protein sequences through a self programmed amino acid converter-counter and got aromatic amino acid molar percentages of 9.3% and 5.14% respectively. These numbers show that there is likely enough precursor and that acetaminophen production should be within a measurable range.

Biomass

Timescale: days
Light Intensity: µE m-2 s-1
Temperature: ℃
Starting Density: g biomass/ L

References

Growth optimization of Synechococcus elongatus PCC7942 in lab flasks and a 2-D photobioreactor
Carbon metabolism and energy conversion of Synechococcus sp. PCC 7942 under mixotrophic conditions.
Jack Baskin School of Engineering
University of California, Santa Cruz
1156 High Street
Santa Cruz, California, 95064
Contact Us: UCSC iGEM
S P O N S O R S
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C O N T A C T
Jack Baskin School of Engineering
University of California, Santa Cruz
1156 High Street
Santa Cruz, California, 95064