Difference between revisions of "Team:Tianjin/Model"

 
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             <li>
 
             <li>
 
                 <a href="https://2018.igem.org/Team:Tianjin/Judging">
 
                 <a href="https://2018.igem.org/Team:Tianjin/Judging">
                     JUDGING FORM                
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                     FOR JUDGES                
 
                 </a>
 
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                                 </div>
 
                                 </div>
 
                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
                                     <p>The score of every fluorescent protein can be obtained shown as Figure1.</p>
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                                     <p>The score of every fluorescent protein can be obtained shown as <a href="#1">Figure1</a>.</p>
 
                                 </div>
 
                                 </div>
  
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/c/ce/T--Tianjin--tuu1.png" height="450"></div>  
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                                <p id="1"></p>
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                                    <p id="8">
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                                <div class="col-xs-8 picture">
                                      Figure1 Selection of report genes<br>
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                                    <img src="https://static.igem.org/mediawiki/2018/c/ce/T--Tianjin--tuu1.png">
                                    </p>
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                                      <p>  Figure1 Selection of report genes<br> </p>
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                                </div>
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                                 </div>
 
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                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
                                     Because the fluorescent protein we wanted to choose had to be optimized in yeast and had to be given by parts, the following fluorescent proteins in Figure2 were all what we could choose from.
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                                     Because the fluorescent protein we wanted to choose had to be optimized in yeast and had to be given by parts, the following fluorescent proteins in <a href="#2">Figure2</a> were all what we could choose from.
 
                                 </div>
 
                                 </div>
  
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                                <p id="2"></p>
<div align="center"><img src="https://static.igem.org/mediawiki/2018/1/1a/T--Tianjin--tuu2.png" height="400"></div>  
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                                    <p id="8">
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                                <img src="https://static.igem.org/mediawiki/2018/1/1a/T--Tianjin--tuu2.png">
                                        Figure2 Fluorescent proteins could be chose from<br>
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                                <p> Figure2 Fluorescent proteins could be chose from<br> </p>
                                    </p>
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                                 </div>
 
                                 </div>
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                                     </p>
 
                                     </p>
 
                                 </div>
 
                                 </div>
                                 <div class="col-xs-6 picture">
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                                 <div class="col-md-6 col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/1/12/T--Tianjin--tutu3.png">
 
                                     <img src="https://static.igem.org/mediawiki/2018/1/12/T--Tianjin--tutu3.png">
 
                                     <p>Figure3 EYFP Degradation Curve</p>
 
                                     <p>Figure3 EYFP Degradation Curve</p>
 
                                 </div>
 
                                 </div>
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                                     <img src="https://static.igem.org/mediawiki/2018/0/00/T--Tianjin--tutu4.png">
 
                                     <img src="https://static.igem.org/mediawiki/2018/0/00/T--Tianjin--tutu4.png">
 
                                     <p>Figure4 mCherry Degradation Curve</p>
 
                                     <p>Figure4 mCherry Degradation Curve</p>
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                                         a = 133, b =-0.005066, c =-44.38, d =-0.02168
 
                                         a = 133, b =-0.005066, c =-44.38, d =-0.02168
 
                                     </p>
 
                                     </p>
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                                      <p>  Figure5 Fitted EYFP Degradation Curve</p> </p>
 
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                                    <img src="https://static.igem.org/mediawiki/2018/7/7a/T--Tianjin--tu5.jpg">
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                                    <p id="5">Figure5 Fitted EYFP Degradation Curve</p>
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                                     <p style="text-align: center;">a = 613.8, b = -0.0003886, c = 0.0003207, d =0.06852</p>
 
                                     <p style="text-align: center;">a = 613.8, b = -0.0003886, c = 0.0003207, d =0.06852</p>
 
                                 </div>
 
                                 </div>
                                 <div class="col-xs-12 picture">
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                                <p id="6"></p>
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                                 <div class="col-xs-8 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/4/42/T--Tianjin--tu6.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/4/42/T--Tianjin--tu6.jpg">
                                    <p id="6">Figure6 Fitted mCherry Degradation Curve</p>
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                                      <p> Figure6 Fitted mCherry Degradation Curve </p>
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                                </div>
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                                 </div>
 
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                                     <p>Coefficients (with 95% confidence bounds):<br></p>
 
                                     <p>Coefficients (with 95% confidence bounds):<br></p>
 
                                     <p>$$ p_1 = -0.2287 , p_2 = 613.6$$</p>
 
                                     <p>$$ p_1 = -0.2287 , p_2 = 613.6$$</p>
 +
 
                                 </div>
 
                                 </div>
                                 <div class="col-xs-12 picture">
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                                <p id="7"></p>
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                                     <img src="https://static.igem.org/mediawiki/2018/3/35/T--Tianjin--tu7.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/3/35/T--Tianjin--tu7.jpg">
                                    <p id="7">Figure7 Linear mCherry Degradation Curve</p>
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                                      <p> Figure7 Linear mCherry Degradation Curve </p>
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                                 <div class="col-xs-12 text">
 
                                     <p>
 
                                     <p>
                                       For the OD<sub>600</sub>&nbsp;values we got, we did some processing and modeling work. And here are our steps and results.<br>
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                                       For the OD<sub>600</sub> values we got, we did some processing and modeling work. And here are our steps and results.<br>
 
                                     </p>
 
                                     </p>
 
                                 </div>
 
                                 </div>
 
                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
 
                                     <p>
 
                                     <p>
                                         There were three groups in our experiment. They were blank control group, partial control group and experimental group. After getting all the data, first, we drew a histogram and a scattergram of time and maximum OD<sub>600</sub>&nbsp; values (Figure8, 9). These results were very instructive to experiments that these results told us the best measuring point and the best measuring interval.
+
                                         There were three groups in our experiment. They were blank control group, partial control group and experimental group. After getting all the data, first, we drew a histogram and a scattergram of time and maximum OD<sub>600</sub> values (<a href="#8">Figure8, 9</a>). These results were very instructive to experiments that these results told us the best measuring point and the best measuring interval.
 
                                     </p>
 
                                     </p>
                                </div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/0/0e/T--Tianjin--tu8.png" height="550"></div>  
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<div class="col-xs-12 picture">
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                                <p id="8"></p>
                                    <p id="8">
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                                <div class="col-xs-1"></div>
                                        Figure8 histogram of Time-Maximum OD Value<br>
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                                <div class="col-xs-10 picture">
                                    </p>
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                                    <img src="https://static.igem.org/mediawiki/2018/0/0e/T--Tianjin--tu8.png">
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                                      <p> Figure8 histogram of Time-Maximum OD Value<br> </p>
 
                                 </div>
 
                                 </div>
 
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/0/0d/T--Tianjin--tu9.png" height="550"></div>  
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<div class="col-xs-12 picture">
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                                    <p id="9">
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                                <p id="9"></p>
                                        Figure9 Scatter gram of Time-Maximum OD Value
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                                <div class="col-xs-2"></div>
                                    </p>
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                                    <img src="https://static.igem.org/mediawiki/2018/0/0d/T--Tianjin--tu9.png">
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                                      <p>Figure9 Scatter gram of Time-Maximum OD Value<br></p>
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                                </div>
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                                 </div>
 
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                                 <div class="col-xs-12 text">
 
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                                     <p>
 
                                     <p>
                                         From the beginning to the maximum OD<sub>600</sub>&nbsp;value, it fits the&nbsp;logistic model. The block effect of resource and environment for the growth of yeasts is reflected in the growth rate <em>r</em>, which makes <em>r</em>&nbsp;decrease with the increase in the number of yeasts <em>x</em>. Express <em>r</em>&nbsp;as a function<em>&nbsp;</em>r(<em>x</em>) of <em>x</em>, and take a simple and convenient linear reduction function r(<em>x</em>)<em>=</em>a+b<em>x.</em>&nbsp;In order to give a real meaning to the coefficients a and b in the growth rate function, we introduced two parameters:<br>
+
                                         From the beginning to the maximum OD<sub>600</sub> value, it fits the logistic model. The block effect of resource and environment for the growth of yeasts is reflected in the growth rate <em>r</em>, which makes <em>r</em> decrease with the increase in the number of yeasts <em>x</em>. Express <em>r</em> as a function<em> </em>r(<em>x</em>) of <em>x</em>, and take a simple and convenient linear reduction function r(<em>x</em>)<em>=</em>a+b<em>x.</em> In order to give a real meaning to the coefficients a and b in the growth rate function, we introduced two parameters:<br>
 
                                         (1)<strong>Intrinsic growth rate </strong><strong><em>r</em> : </strong><em> r</em> is the growth rate when <em>x</em>=0 (in theory);<br>
 
                                         (1)<strong>Intrinsic growth rate </strong><strong><em>r</em> : </strong><em> r</em> is the growth rate when <em>x</em>=0 (in theory);<br>
                                         (2)<strong>P</strong><strong>opulation capacity </strong><strong><em>x</em></strong><strong><em><sub>m</sub></em> : </strong><em> x</em><em><sub>m</sub></em><em>&nbsp;</em> is the largest yeast amount that can be accommodated by resources and the When <em>x=x</em><em><sub>m</sub></em>, the quantity of yeasts is no longer increasing, that is r(<em>x</em><em><sub>m</sub></em>)<em>=</em>r+b<em>x</em><em><sub>m</sub></em>=0, then b=-<em>r/x</em><em><sub>m</sub></em><em>.</em><br>
+
                                         (2)<strong>P</strong><strong>opulation capacity </strong><strong><em>x</em></strong><strong><em><sub>m</sub></em> : </strong><em> x</em><em><sub>m</sub></em><em> </em> is the largest yeast amount that can be accommodated by resources and the When <em>x=x</em><em><sub>m</sub></em>, the quantity of yeasts is no longer increasing, that is r(<em>x</em><em><sub>m</sub></em>)<em>=</em>r+b<em>x</em><em><sub>m</sub></em>=0, then b=-<em>r/x</em><em><sub>m</sub></em><em>.</em><br>
                                         <em><em>r</em></em>&nbsp;and <em><em>x</em></em><em><sub><em>m</em></sub></em>&nbsp;values in our experiments are shown in the chart below.
+
                                         <em><em>r</em></em> and <em><em>x</em></em><em><sub><em>m</em></sub></em> values in our experiments are shown in the chart below.
 
                                     </p>
 
                                     </p>
 
                                     <table class="table table-bordered table-bashed">
 
                                     <table class="table table-bordered table-bashed">
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                                     </p>
 
                                     </p>
 
                                     <p>
 
                                     <p>
                                         Take <em>x</em> as the horizontal axis and <em>dx/dt</em> as the vertical axis, we obtained a parabola (<a href="#1">Figure 10</a>), when <em>x = x<sub>m</sub>/2</em>, <em>dx/dt</em> reaches the maximum. As shown in <a href="#10">Figure 10</a>, <em>dx/dt</em> changes with the increasing x, and we can do the following analysis to the curve <em>x</em>(<em>t</em>).<br>
+
                                         Take <em>x</em> as the horizontal axis and <em>dx/dt</em> as the vertical axis, we obtained a parabola (<a href="#10">Figure 10</a>), when <em>x = x<sub>m</sub>/2</em>, <em>dx/dt</em> reaches the maximum. As shown in <a href="#10">Figure 10</a>, <em>dx/dt</em> changes with the increasing x, and we can do the following analysis to the curve <em>x</em>(<em>t</em>).<br>
 
                                     </p>
 
                                     </p>
 
                                     <p>
 
                                     <p>
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                                     <p>$$x(t) = {x_m \over {1+({x_m \over x_0}-1)e^{-rt}}}          (4) $$</p>
 
                                     <p>$$x(t) = {x_m \over {1+({x_m \over x_0}-1)e^{-rt}}}          (4) $$</p>
 
                                 </div>
 
                                 </div>
                                 <div class="col-xs-6 picture">
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                                    <p id="10"></p>
 +
                                 <div class="col-md-6 col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/f/fe/T--Tianjin--tu1010.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/f/fe/T--Tianjin--tu1010.jpg">
                                     <p id="10">Figure10  example <em>x-dx/dt</em> curve</p>
+
                                     <p>Figure10  example <em>x-dx/dt</em> curve</p>
 
                                 </div>
 
                                 </div>
                                 <div class="col-xs-6 picture">
+
                                    <p id="11"></p>
 +
                                 <div class="col-md-6 col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/0/00/T--Tianjin--tu11.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/0/00/T--Tianjin--tu11.jpg">
                                     <p id="11">Figure11  example <em>t-x</em> curve</p>
+
                                     <p>Figure11  example <em>t-x</em> curve</p>
 
                                 </div>
 
                                 </div>
 
                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
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                                     <img src="">
 
                                     <img src="">
 
                                 </div>
 
                                 </div>
 +
                                <p id="12"></p>
 
                                 <div class="col-xs-12 picture">
 
                                 <div class="col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/4/46/T--Tianjin--tu12.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/4/46/T--Tianjin--tu12.jpg">
                                     <p id="12">Figure12 <em>t-x</em> curve</p>
+
                                     <p>Figure12 <em>t-x</em> curve</p>
 
                                 </div>
 
                                 </div>
 
                                 <div class="col-xs-12 picture">
 
                                 <div class="col-xs-12 picture">
 
                                     <img src="">
 
                                     <img src="">
 
                                 </div>
 
                                 </div>
 +
                                  <p id="13"></p>
 
                                 <div class="col-xs-12 picture">
 
                                 <div class="col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/1/15/T--Tianjin--tu13.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/1/15/T--Tianjin--tu13.jpg">
                                     <p id="13">Figure13  <em>x-dx/dt</em> curve</p>
+
                                     <p>Figure13  <em>x-dx/dt</em> curve</p>
 
                                 </div>
 
                                 </div>
 
                             </div>
 
                             </div>
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                         <div class="panel-title">
 
                         <div class="panel-title">
 
                             <a href="#collapseFour" role="button" data-toggle="collapse" data-parent="#accordion4" style="text-decoration: none;">
 
                             <a href="#collapseFour" role="button" data-toggle="collapse" data-parent="#accordion4" style="text-decoration: none;">
                                 Mars Model
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                                 Mars Model*
 
                             </a>
 
                             </a>
 
                         </div>
 
                         </div>
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                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
 
                                     <p>
 
                                     <p>
                                         Oscillation in KaiC phosphorylation is the best-observed parameter in this system and represents a key state variable for the clock in vivo. Thus we have sought to closely mimic this output in our project. Nakajima et al. <sup><a href="#re6">[6]</a></sup> suggest, given the dual function of KaiC and ‘‘cooperation between KaiA and KaiB,’’ that autonomous oscillation of KaiC phosphorylation might be achieved. We established a model based on known biological and biochemical observations and our experiments that did not involve transcription or translation. In Figure14, we summarized the key steps of three Kai proteins oscillation when ATP is provided in excess. It was well established that we used three circles to represent all possible combinations of three Kai proteins, just like Mars and its two satellites. This was also why we call it Mars Model.
+
                                         Oscillation in KaiC phosphorylation is the best-observed parameter in this system and represents a key state variable for the clock in vivo. Thus we have sought to closely mimic this output in our project. Nakajima et al. <sup><a href="#re6">[6]</a></sup> suggest, given the dual function of KaiC and ‘‘cooperation between KaiA and KaiB,’’ that autonomous oscillation of KaiC phosphorylation might be achieved. We established a model based on known biological and biochemical observations and our experiments that did not involve transcription or translation. In <a href="#14">Figure14</a>, we summarized the key steps of three Kai proteins oscillation when ATP is provided in excess. It was well established that we used three circles to represent all possible combinations of three Kai proteins, just like Mars and its two satellites. This was also why we call it <b>Mars Model</b>.
 
                                     </p>
 
                                     </p>
 
                                 </div>
 
                                 </div>
 
                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
 
                                     <p>
 
                                     <p>
                                         The model (Figure 14) contained twelve processes (R1-R12) describing all the protein-protein interactions and phosphorylation-dephosphorylation between the Kai proteins. KaiXY represents KaiX and KaiY compound and KaiC* represents fully phosphorylated KaiC. Process R1, R2 and R3 are six aggregations of KaiC protein, two aggregations of KaiA protein and four aggregations of KaiB protein respectively. In process R4, KaiC<sub>6</sub> binds KaiA<sub>2</sub>, forming KaiA<sub>2</sub>C<sub>6</sub> compound. Since KaiA<sub>2</sub> facilitates the autokinase activity of KaiC<sub>6</sub>, KaiA<sub>2</sub>C<sub>6</sub> first converts to partial phosphorylated form, KaiA<sub>2</sub>C<sub>6</sub>C<sub>6</sub>*, by process R5, and then rapidly converts to fully phosphorylated form, KaiA<sub>2</sub>C<sub>6</sub>*, by process R10. Then, fully phosphorylated protein KaiA<sub>2</sub>C<sub>6</sub>* combines with KaiB<sub>4</sub>, forming KaiA<sub>2</sub>B<sub>4</sub>C<sub>6</sub>*, by process R6. In process R7, KaiA<sub>2</sub> is displaced from KaiA<sub>2</sub>B<sub>4</sub>C<sub>6</sub>*. When KaiA<sub>2</sub> no longer exists in KaiA<sub>2</sub>B<sub>4</sub>C<sub>6</sub>*, KaiB<sub>4</sub> dissociates from KaiB<sub>4</sub>C<sub>6</sub>*, by process R8. Process R9, R11, and R12 are depolymerization of KaiC<sub>6</sub>, KaiA<sub>2</sub> and KaiB<sub>4</sub> protein, respectively<sup><a href="#re7">[7]</a></sup>.
+
                                         The model (<a href="#14">Figure 14</a>) contained twelve processes (R1-R12) describing all the protein-protein interactions and phosphorylation-dephosphorylation between the Kai proteins. KaiXY represents KaiX and KaiY compound and KaiC* represents fully phosphorylated KaiC. Process R1, R2 and R3 are six aggregations of KaiC protein, two aggregations of KaiA protein and four aggregations of KaiB protein respectively. In process R4, KaiC<sub>6</sub> binds KaiA<sub>2</sub>, forming KaiA<sub>2</sub>C<sub>6</sub> compound. Since KaiA<sub>2</sub> facilitates the autokinase activity of KaiC<sub>6</sub>, KaiA<sub>2</sub>C<sub>6</sub> first converts to partial phosphorylated form, KaiA<sub>2</sub>C<sub>6</sub>C<sub>6</sub>*, by process R5, and then rapidly converts to fully phosphorylated form, KaiA<sub>2</sub>C<sub>6</sub>*, by process R10. Then, fully phosphorylated protein KaiA<sub>2</sub>C<sub>6</sub>* combines with KaiB<sub>4</sub>, forming KaiA<sub>2</sub>B<sub>4</sub>C<sub>6</sub>*, by process R6. In process R7, KaiA<sub>2</sub> is displaced from KaiA<sub>2</sub>B<sub>4</sub>C<sub>6</sub>*. When KaiA<sub>2</sub> no longer exists in KaiA<sub>2</sub>B<sub>4</sub>C<sub>6</sub>*, KaiB<sub>4</sub> dissociates from KaiB<sub>4</sub>C<sub>6</sub>*, by process R8. Process R9, R11, and R12 are depolymerization of KaiC<sub>6</sub>, KaiA<sub>2</sub> and KaiB<sub>4</sub> protein, respectively<sup><a href="#re7">[7]</a></sup>.
 
                                     </p>
 
                                     </p>
 
                                 </div>
 
                                 </div>
  
 +
<p id="14"></p>
 +
<div class="col-xs-2"></div>
  
 
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                                <div class="col-xs-8 picture">
 
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                                    <img src="https://static.igem.org/mediawiki/2018/e/e1/T--Tianjin--tutu14.png">
<div align="center"><img src="https://static.igem.org/mediawiki/2018/e/e1/T--Tianjin--tutu14.png" width="450"></div>  
+
                                      <p>Figure14 A dynamic model of KaiABC proteins oscillation.See text for description
<div class="col-xs-12 picture">                             
+
                                    </p>
                                    <p id="14">Figure14 A dynamic model of KaiABC proteins oscillation.See text for description</p>
+
 
                                 </div>
 
                                 </div>
 +
<div class="col-xs-2 picture">
  
 
+
</div>
  
  
  
 
                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
                                     We established rate equation to every process (<a href="15">Figure 15</a>) and the corresponding reaction rate constants are <em>k<sub>1</sub>-k<sub>12</sub></em>.
+
                                     We established rate equation to every process (<a href="#15">Figure 15</a>) and the corresponding reaction rate constants are <em>k<sub>1</sub>-k<sub>12</sub></em>.
                                 </div>
+
                                </div>
                                 <div class="col-xs-12 picture">
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                                 <p id="15"></p>
 +
                                <div class="col-xs-2"></div>
 +
                                 <div class="col-xs-8 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/b/bd/T--Tianjin--tu15.png">
 
                                     <img src="https://static.igem.org/mediawiki/2018/b/bd/T--Tianjin--tu15.png">
                                    <p id="15">Figure15 Rate equations of every reaction</p>
+
                                      <p>Figure15 Rate equations of every reaction</p>
 
                                 </div>
 
                                 </div>
 +
                              <div class="col-xs-2 picture">
 +
                                </div>
 
                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
                                     Input reaction rate constants <em>k<sub>1</sub>-k<sub>12</sub></em> and initial concentration of every protein, oscillatory curve of every protein could be obtained as shown in Figure16.
+
                                     Input reaction rate constants <em>k<sub>1</sub>-k<sub>12</sub></em> and initial concentration of every protein, oscillatory curve of every protein could be obtained as shown in <a href="#16">Figure16</a>.
                                 </div>
+
 
                                 <div class="col-xs-12 picture">
+
                                </div>
 +
                                 <p id="16"></p>
 +
                                <div class="col-xs-2"></div>
 +
                                 <div class="col-xs-8 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/6/64/T--Tianjin--tu16.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/6/64/T--Tianjin--tu16.jpg">
                                    <p id="16">Figure16 Oscillatory curve of every protein</p>
+
                                      <p>Figure16 Oscillatory curve of every protein</p>
 
                                 </div>
 
                                 </div>
 +
                              <div class="col-xs-2 picture">
 +
                                </div>
 
                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
                                     From Figure16 it was known that although the peak time of each protein varies, the oscillation period of every protein is the same. Therefore, in the following analysis, we take KaiC as an example to show the change of periods.
+
                                     From <a href="#16">Figure16</a> it was known that although the peak time of each protein varies, the oscillation period of every protein is the same. Therefore, in the following analysis, we take KaiC as an example to show the change of periods.
 
                                 </div>
 
                                 </div>
 
                             </div>
 
                             </div>
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                                 </div>
 
                                 </div>
 
                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
                                     (1)Assume the reaction rate constants change proportionally with temperature changing, the period of protein oscillation shortens as shown in Figure17.<br>
+
                                     (1)Assume the reaction rate constants change proportionally with temperature changing, the period of protein oscillation shortens as shown in <a href="#17">Figure17</a>.<br>
 
                                     (<em>Note: All the blue curves represent the initial data and red curves represent the revised data.</em>)
 
                                     (<em>Note: All the blue curves represent the initial data and red curves represent the revised data.</em>)
 
                                 </div>
 
                                 </div>
                                 <div class="col-xs-6 picture">
+
                                  <p id="17"></p>
 +
                                 <div class="col-md-6 col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/ec/20181016152035%21T--Tianjin--tu17a.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/ec/20181016152035%21T--Tianjin--tu17a.jpg">
 
                                     <p>(a)Period shortens with temperature rising temperature falling</p>
 
                                     <p>(a)Period shortens with temperature rising temperature falling</p>
 
                                 </div>
 
                                 </div>
                                 <div class="col-xs-6 picture">
+
                                 <div class="col-md-6 col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/ec/20181016152054%21T--Tianjin--tu17a.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/ec/20181016152054%21T--Tianjin--tu17a.jpg">
 
                                     <p>(b) Period prolongs with </p>
 
                                     <p>(b) Period prolongs with </p>
 
                                 </div>
 
                                 </div>
 
                                 <div class="col-xs-12 picture">
 
                                 <div class="col-xs-12 picture">
                                     <p id="17">
+
                                     <p>
 
                                         Figure17  Period changes with temperature changing(<em>k</em> changes proportionally)
 
                                         Figure17  Period changes with temperature changing(<em>k</em> changes proportionally)
 
                                     </p>
 
                                     </p>
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                                     (2)Assume the reaction rate constants change slightly and equally with temperature changing, the period also shortens with the temperature rising and prolongs with the temperature falling as shown in <a href="#18">Figure18</a>.  
 
                                     (2)Assume the reaction rate constants change slightly and equally with temperature changing, the period also shortens with the temperature rising and prolongs with the temperature falling as shown in <a href="#18">Figure18</a>.  
 
                                 </div>
 
                                 </div>
                                 <div class="col-xs-6 picture">
+
                                      <p id="18"></p>
 +
                                 <div class="col-md-6 col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/ec/20181016152108%21T--Tianjin--tu17a.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/ec/20181016152108%21T--Tianjin--tu17a.jpg">
 
                                     <p>(a) Period shortens with temperature rising temperature falling</p>
 
                                     <p>(a) Period shortens with temperature rising temperature falling</p>
 
                                 </div>
 
                                 </div>
                                 <div class="col-xs-6 picture">
+
                                 <div class="col-md-6 col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/ec/20181016152124%21T--Tianjin--tu17a.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/ec/20181016152124%21T--Tianjin--tu17a.jpg">
 
                                     <p>(b) Period prolongs with</p>
 
                                     <p>(b) Period prolongs with</p>
 
                                 </div>
 
                                 </div>
 
                                 <div class="col-xs-12 picture">
 
                                 <div class="col-xs-12 picture">
                                     <p id="18">
+
                                      
                                        Figure18  Period changes with temperature change(<em>k</em> changes slightly)
+
                                        <p>Figure18  Period changes with temperature change(<em>k</em> changes slightly)
 
                                     </p>
 
                                     </p>
 
                                 </div>
 
                                 </div>
 
                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
 
                                     <p>
 
                                     <p>
                                         When the reaction rate constants change slightly with temperature changing, the period shortens while amplitude shortens too. Therefore, if <em>k</em> changes disproportionately, when the temperature increases, the cycle is shortened and the oscillation is unsteady. The curve tends to be gentle with time, which means the oscillation disappears shown as <a href="#18">Figure 18</a>.
+
                                         When the reaction rate constants change slightly with temperature changing, the period shortens while amplitude shortens too. Therefore, if <em>k</em> changes disproportionately, when the temperature increases, the cycle is shortened and the oscillation is unsteady. The curve tends to be gentle with time, which means the oscillation disappears shown as<a href="#19">Figure 19</a>.
 
                                     </p>
 
                                     </p>
                                 </div>
+
                             
                                 <div class="col-xs-12 picture">
+
 
 +
                                </div>
 +
                                 <p id="19"></p>
 +
                                <div class="col-xs-2"></div>
 +
                                 <div class="col-xs-8 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/e/ec/T--Tianjin--tu17a.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/e/ec/T--Tianjin--tu17a.jpg">
                                    <p id="19">Figure19  The disappearance of oscillation with temperature changing</p>
+
                                      <p>Figure19  The disappearance of oscillation with temperature changing</p>
 
                                 </div>
 
                                 </div>
 +
                              <div class="col-xs-2 picture">
 +
                                </div>
 
                             </div>
 
                             </div>
 
                             <div class="row">
 
                             <div class="row">
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                                         Phosphorylase in yeasts may have promoting effect to the phosphorylation of protein and yeasts offer enough ATP/ADP in vivo, which increase the rate of phosphorylation. Therefore, <em>k<sub>4</sub></em>may increases in yeasts, which makes oscillation cycle shortens shown as <a href="#20">Figure20</a>.
 
                                         Phosphorylase in yeasts may have promoting effect to the phosphorylation of protein and yeasts offer enough ATP/ADP in vivo, which increase the rate of phosphorylation. Therefore, <em>k<sub>4</sub></em>may increases in yeasts, which makes oscillation cycle shortens shown as <a href="#20">Figure20</a>.
 
                                     </p>
 
                                     </p>
                                 </div>
+
                                                                </div>
                                 <div class="col-xs-12 picture">
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                                 <p id="20"></p>
 +
                                <div class="col-xs-2"></div>
 +
                                 <div class="col-xs-8 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/e2/20181016152023%21T--Tianjin--tu20.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/e2/20181016152023%21T--Tianjin--tu20.jpg">
                                    <p id="20">Figure20 Period changes with phosphorylation rate changing</p>
+
                                      <p>Figure20 Period changes with phosphorylation rate changing</p>
 
                                 </div>
 
                                 </div>
 +
                              <div class="col-xs-2 picture">
 +
                                </div>
 
                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
 
                                     When the oscillation system is transplanted into yeasts, the supply rate of KaiA , KaiB and KaiC may increase and the relating reaction rate constants are <em>k<sub>2</sub></em>, <em>k<sub>3</sub></em> and <em>k<sub>1</sub></em>. They will increase with the supply rate of three Kai proteins increasing and the result is shown as <a href="#21">Figure21</a>.
 
                                     When the oscillation system is transplanted into yeasts, the supply rate of KaiA , KaiB and KaiC may increase and the relating reaction rate constants are <em>k<sub>2</sub></em>, <em>k<sub>3</sub></em> and <em>k<sub>1</sub></em>. They will increase with the supply rate of three Kai proteins increasing and the result is shown as <a href="#21">Figure21</a>.
 
                                 </div>
 
                                 </div>
                                 <div class="col-xs-4 picture">
+
                                <p id="21"></p>
 +
                                 <div class="col-md-4 col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/e2/20181016152034%21T--Tianjin--tu20.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/e2/20181016152034%21T--Tianjin--tu20.jpg">
 
                                     <p>(a)Period change with the supply rate of KaiA increasing</p>
 
                                     <p>(a)Period change with the supply rate of KaiA increasing</p>
 
                                 </div>
 
                                 </div>
                                 <div class="col-xs-4 picture">
+
                                 <div class="col-md-4 col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/e2/20181016152046%21T--Tianjin--tu20.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/e2/20181016152046%21T--Tianjin--tu20.jpg">
 
                                     <p>(b)Period change with the supply rate of KaiB increasing</p>
 
                                     <p>(b)Period change with the supply rate of KaiB increasing</p>
 
                                 </div>
 
                                 </div>
                                 <div class="col-xs-4 picture">
+
                                 <div class="col-md-4 col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/e2/20181016152105%21T--Tianjin--tu20.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/e2/20181016152105%21T--Tianjin--tu20.jpg">
 
                                     <p>(c)Period change with the supply rate of KaiC increasing</p>
 
                                     <p>(c)Period change with the supply rate of KaiC increasing</p>
 
                                 </div>
 
                                 </div>
 
                                 <div class="col-xs-12 picture">
 
                                 <div class="col-xs-12 picture">
                                    <p id="21">Figure21 Period changes with oscillation environment changing</p>
+
                                  <p> Figure21 Period changes with oscillation environment changing</p>
 
                                 </div>
 
                                 </div>
 
                             </div>
 
                             </div>
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                                 <div class="col-xs-12 text">
 
                                 <div class="col-xs-12 text">
 
                                     <p>
 
                                     <p>
                                         In the following table, we list the impact of <em>k<sub>5</sub></em>-<em>k<sub>12</sub></em> changing to the oscillation. It can be seen in Figure22 that <em>k<sub>5</sub></em> and <em>k<sub>6</sub></em> have great influence on the disappearance of the oscillation. The impact of <em>k<sub>5</sub></em>-<em>k<sub>8</sub></em> may relates to phosphorylation and temperature changing as well as other factors. Therefore, figuring out biological factors related to these reaction rate constants is one of our future work.
+
                                         In the following table, we list the impact of <em>k<sub>5</sub></em>-<em>k<sub>12</sub></em> changing to the oscillation. It can be seen in <a href="#22">Figure22</a> that <em>k<sub>5</sub></em> and <em>k<sub>6</sub></em> have great influence on the disappearance of the oscillation. The impact of <em>k<sub>5</sub></em>-<em>k<sub>8</sub></em> may relates to phosphorylation and temperature changing as well as other factors. Therefore, figuring out biological factors related to these reaction rate constants is one of our future work.
 
                                     </p>
 
                                     </p>
 
                                 </div>
 
                                 </div>
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                                     </table>
 
                                     </table>
 
                                 </div>
 
                                 </div>
 +
                                    <p id="22"></p>
 
                                 <div class="col-xs-12 picture">
 
                                 <div class="col-xs-12 picture">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/e2/20181016152116%21T--Tianjin--tu20.jpg">
 
                                     <img src="https://static.igem.org/mediawiki/2018/archive/e/e2/20181016152116%21T--Tianjin--tu20.jpg">
                                     <p id="22">Figure22 Period changes with <em>k<sub>5</sub></em> -<em>k<sub>10</sub></em> changing</p>
+
                                     <p>Figure22 Period changes with <em>k<sub>5</sub></em> -<em>k<sub>10</sub></em> changing</p>
 
                                 </div>
 
                                 </div>
 +
                                    <p id="23"></p>
 
                                 <div class="col-xs-12 picture">
 
                                 <div class="col-xs-12 picture">
                                     <img src="https://static.igem.org/mediawiki/2018/e/e2/T--Tianjin--tu20.jpg">
+
                                     <p><img src="https://static.igem.org/mediawiki/2018/e/e2/T--Tianjin--tu20.jpg">
                                     <p id="23">Figure23 Period changes with <em>k<sub>11</sub></em> and <em>k<sub>12</sub></em> changing</p>
+
                                     Figure23 Period changes with <em>k<sub>11</sub></em> and <em>k<sub>12</sub></em> changing</p>
 
                                 </div>
 
                                 </div>
 
                             </div>
 
                             </div>
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                     <h1>References</h1>
 
                     <h1>References</h1>
 
                     <p class="reftext" id="re1">
 
                     <p class="reftext" id="re1">
                         <a>[1]Ester M, Kriegel H P, Sander J et al. A density-based algorithm for discovering clusters in large spatial databases. In: Simondis E, Han J W, Fayyad U M eds. Proceedings of the 2<sup>nd</sup>&nbsp;International Conference on Data Mining (KDD-96). Portland: Oregon, 1996. 226~231</a>
+
                         <a>[1]Ester M, Kriegel H P, Sander J et al. A density-based algorithm for discovering clusters in large spatial databases. In: Simondis E, Han J W, Fayyad U M eds. Proceedings of the 2<sup>nd</sup> International Conference on Data Mining (KDD-96). Portland: Oregon, 1996. 226~231</a>
 
                         <br>
 
                         <br>
 
                     </p>
 
                     </p>

Latest revision as of 13:01, 6 December 2018

<!DOCTYPE html> Team:Tianjin - 2018.igem.org

MODEL

Overview

The models we built included four parts. First, we established a fluorescent protein model to screen out the most suitable fluorescent protein, the main modeling method here is grayscale analysis. Then, for the large amount of measured OD values, we drew the growth curve of yeasts and it fitted logistic model. It described the growth situation of the yeasts after plasmid introduction, and we compare it with yeasts without any foreign plasmid. The growth curve also offers the best measuring point and the best measuring interval. What’s more, we drew the degradation curve of the fluorescent protein, which helps us know different characteristics of the two chosen fluorescent proteins better. Finally, we constructed a model to illustrate the oscillation of KaiA, KaiB and KaiC protein called Mars Model, it explained the reason why the cycle reduced in yeasts nicely. Modeling work integrated with experiments tightly made our project complete and convincing.