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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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                        <h2>Model</h2>
 +
                    </div>
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<div class="column full_size">
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<h1> Modeling</h1>
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            <div class="row">
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                <div class="col-md-12 wow fadeInDown" data-wow-delay=".3s" data-wow-duration="500ms">
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                    <p>
 +
                        According to the functional analysis results, we knew that the fluorescence expression of oxy1 and oxy4 were different.Compared with oxy1, through T7RNA polymerase and T7  promoter, oxy4 will amplify the signal(figure 1).But just how much the signal is amplified, and what is the relationship between it and the dissolved oxygen concentraion, we still don't know. So we explored the model of the correlation between fluorescence expression and oxygen concentration. In modeling, we need to use a lot of knowledge of advanced mathematics. As a senior high school student, we can't use it very well, so we only have a very simple model.But we've really worked very hard. The results are as follows.
 +
                    </p>
 +
                    <p style="text-align:center;" align="center">
 +
                        <img src="https://static.igem.org/mediawiki/2017/3/39/T-worldshaper-XSHS-s0001.png" alt="" width="419" height="249" />
 +
                    </p>
 +
                    <p style="text-align:center;" align="center">figure1. The working mechanism of Oxy4</p>
 +
                    <p> <b>Oxy1</b>
 +
                    </p>
 +
                    <p>
 +
                        <b><span style="font-weight:bold;font-size:11.0000pt;">Oxy1-sealed, 475 nm exciting light</span></b>
 +
                    </p>
 +
                    <p>
 +
                        We studied the relationship between Oxy1 bacterial fluorescence expressi0n and oxygen concentration under the condition of sealing, and did the function fitting.
 +
                    </p>
 +
                    <p>
 +
                        To make the data comparable,we standardized the fluorescence intensity and OD600 of each group.?Firstly, we subtracted the initial fluorescence intensity and the initial OD600 from the fluorescence intensity and the OD600. Then we divided the fluorescence intensity by the OD600.We had the function fitting for the obtained values, and we got the following functions and images(figure2):
 +
                    </p>
 +
                    <p>
 +
                        <span style="font-size:10.5000pt;">Equation: &nbsp;</span>
 +
                        <span style="font-size:10.5000pt;">&nbsp;r</span> <sup><span style="font-size:10.5000pt;vertical-align:super;">2</span></sup>
 +
                        <span style="font-size:10.5000pt;">=0.87,</span>
 +
                        <span>
 +
                            <img src="https://static.igem.org/mediawiki/2017/5/5e/T-worldshaper-XSHS-s0011.png" alt="" width="" height="" />
 +
                        </span>
 +
                    </p>
 +
                    <p style="text-align:center;" align="center">
 +
                        <img src="https://static.igem.org/mediawiki/2017/7/77/T-worldshaper-XSHS-s0002.png" alt="" width="540" height="234" />
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        figure2. the relationship between Oxy1 bacterial fluorescence expressi0n and oxygen concentration
 +
                    </p>
 +
                    <p>
 +
                        <span style="font-size:10.5000pt;">
 +
                            <b> When we averaged the values of each group, we got better fitting functions and images(figure3).</b>
 +
                        </span>
 +
                    </p>
 +
                    <p>
 +
                        <span style="font-size:10.5000pt;">Equation: &nbsp;</span>
 +
                        <span style="font-size:10.5000pt;">&nbsp;r</span> <sup><span style="font-size:10.5000pt;vertical-align:super;">2</span></sup>
 +
                        <span style="font-size:10.5000pt;">=0.87,</span>
 +
                        <span>
 +
                            <img src="https://static.igem.org/mediawiki/2017/f/fe/T-worldshaper-XSHS-s0012.png" alt="" width="" height="" />
 +
                        </span>
 +
                    </p>
 +
                    <p style="text-align:center;" align="center">
 +
                        <img src="https://static.igem.org/mediawiki/2017/f/f2/T-worldshaper-XSHS-s0003.png" alt="" width="536" height="226" />
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        figure3. the relationship between Oxy1 bacterial fluorescence expression and oxygen concentration
 +
                    </p>
 +
                    <p>
 +
                        <b><span style="font-weight:bold;font-size:11.0000pt;">Oxy1-sealed, 395 nm exciting light</span></b>
 +
                    </p>
 +
                    <p>
 +
                        For the fluorescence intensity of the excitation light of 395nm, we processed the data in the same way. Here are the functions and images(figure4):
 +
                    </p>
 +
                    <p>
 +
                        <span style="font-size:10.5000pt;">Equation: &nbsp;</span>
 +
                        <span style="font-size:10.5000pt;">r</span>
 +
                        <sup>
 +
                            <span style="font-size:10.5000pt;vertical-align:super;">2</span>
 +
                        </sup>
 +
                        <span style="font-size:10.5000pt;">=0.99,</span>
 +
                        <span>
 +
                            <img src="https://static.igem.org/mediawiki/2017/d/db/T-worldshaper-XSHS-s0013.png" alt="" width="" height="" />
 +
                        </span>
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        <img src="https://static.igem.org/mediawiki/2017/d/d7/T-worldshaper-XSHS-s0004.png" alt="" width="532" height="230" />
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        <span >
 +
                            figure4. the relationship between Oxy1 bacterial fluorescence expressi0n and oxygen concentration
 +
                        </span>
 +
                    </p>
 +
                    <p>
 +
                        <b>
 +
                            <span style="font-weight:bold;font-size:14.0000pt;">Oxy4</span>
 +
                        </b>
 +
                    </p>
 +
                    <p >
 +
                        <span style="font-size:10.5000pt;">
 +
                            We also studied the relationship between Oxy4 bacterial fluorescence expressi0n and oxygen concentration under different conditions, and did the function fitting. Data processing was the same as before.
 +
                        </span>
 +
                    </p>
 +
                    <p ></p>
 +
                    <p >
 +
                        <b>
 +
                            <span style="font-weight:bold;font-size:11.0000pt;">Oxy4-sealed, 475 nm exciting light</span>
 +
                        </b>
 +
                    </p>
 +
                    <p >
 +
                        <span style="font-size:10.5000pt;">Equation: &nbsp;</span>
 +
                        <span style="font-size:10.5000pt;">r</span>
 +
                        <sup>
 +
                            <span style="font-size:10.5000pt;vertical-align:super;">2</span>
 +
                        </sup>
 +
                        <span style="font-size:10.5000pt;">=0.91,</span>
 +
                        <span>
 +
                            <img src="https://static.igem.org/mediawiki/2017/0/01/T-worldshaper-XSHS-s0014.png" alt="" width="" height="" />
 +
                        </span>
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        <img src="https://static.igem.org/mediawiki/2017/a/a3/T-worldshaper-XSHS-s0005.png" alt="" width="528" height="222" />
 +
                    </p>
  
−
<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>
+
                    <p style="text-align:center;" align="center">
 +
                        figure5. the relationship between Oxy4 bacterial fluorescence expressi0n and oxygen concentration
 +
                    </p>
 +
                    <p >
 +
                        <b>
 +
                            <span style="font-weight:bold;font-size:11.0000pt;">Oxy4-sealed, 395 nm exciting light</span>
 +
                        </b>
 +
                    </p>
 +
                    <p >
 +
                        <span style="font-size:10.5000pt;">Equation: &nbsp;</span>
 +
                        <span style="font-size:10.5000pt;">r</span>
 +
                        <sup>
 +
                            <span style="font-size:10.5000pt;vertical-align:super;">2</span>
 +
                        </sup>
 +
                        <span style="font-size:10.5000pt;">=0.88,</span>
 +
                        <span>
 +
                            <img src="https://static.igem.org/mediawiki/2017/5/58/T-worldshaper-XSHS-s0015.png" alt="" width="" height="" />
 +
                        </span>
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        <img src="https://static.igem.org/mediawiki/2017/b/b4/T-worldshaper-XSHS-s0006.png" alt="" width="556" height="235" />
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        figure6. the relationship between Oxy4 bacterial fluorescence expressi0n and oxygen concentration
 +
                    </p>
  
−
</div>
+
                    <p>
−
<div class="clear"></div>
+
                        <b>
 +
                            <span style="font-weight:bold;font-size:11.0000pt;">Oxy4-unsealed, 475 nm exciting light</span>
 +
                        </b>
 +
                    </p>
 +
                    <p >
 +
                        <span style="font-size:10.5000pt;">Equation: &nbsp;</span>
 +
                        <span style="font-size:10.5000pt;">r</span>
 +
                        <sup>
 +
                            <span style="font-size:10.5000pt;vertical-align:super;">2</span>
 +
                        </sup>
 +
                        <span style="font-size:10.5000pt;">=0.94,</span>
 +
                        <span>
 +
                            <img src="https://static.igem.org/mediawiki/2017/a/a4/T-worldshaper-XSHS-s0016.png" alt="" width="" height="" />
 +
                        </span>
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        <img src="https://static.igem.org/mediawiki/2017/6/62/T-worldshaper-XSHS-s0007.png" alt="" width="575" height="237" />
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        figure7. the relationship between Oxy4 bacterial fluorescence expressi0n and oxygen concentration
 +
                    </p>
 +
                    <p >
 +
                        <b>
 +
                            <span style="font-weight:bold;font-size:11.0000pt;">Oxy4-unsealed, 395 nm exciting light</span>
 +
                        </b>
 +
                    </p>
 +
                    <p >
 +
                        <span style="font-size:10.5000pt;">Equation: &nbsp;</span>
 +
                        <span style="font-size:10.5000pt;">r</span>
 +
                        <sup>
 +
                            <span style="font-size:10.5000pt;vertical-align:super;">2</span>
 +
                        </sup>
 +
                        <span style="font-size:10.5000pt;">=0.84,</span>
 +
                        <span>
 +
                            <img src="https://static.igem.org/mediawiki/2017/3/37/T-worldshaper-XSHS-s0017.png" alt="" width="" height="" />
 +
                        </span>
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        <img src="https://static.igem.org/mediawiki/2017/f/f9/T-worldshaper-XSHS-s0008.png" alt="" width="599" height="254" />
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        figure8. the relationship between Oxy4 bacterial fluorescence expressi0n and oxygen concentration
 +
                    </p>
  
−
<div class="column half_size">
+
                    <p >
−
<h3> Gold Medal Criterion #3</h3>
+
                        <b>
−
<p>
+
                            <span style="font-weight:bold;font-size:14.0000pt;">The result of integration</span>
−
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.  
+
                        </b>
−
</p>
+
                    </p>
 +
                    <p >
 +
                        <span  >
 +
                            We integrated the expressi0n models of the two strains.It can be seen that, c
 +
                        </span>
 +
                        <span style="font-size:10.5000pt;">
 +
                            ompared with the Oxy1 strain, the fluorescence intensity of the Oxy4 strain was stronger in low oxygen condition, which suggested that the Oxy4 is more suitable for oxygen detection.
 +
                        </span>
 +
                    </p>
 +
                    <p >
 +
                        <b>
 +
                            <span style="font-weight:bold;font-size:11.0000pt;">&nbsp;</span>
 +
                        </b>
 +
                    </p>
 +
                    <p >
 +
                        <b>
 +
                            <span style="font-weight:bold;font-size:11.0000pt;">integrared, 475 nm exciting light</span>
 +
                        </b>
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        <img src="https://static.igem.org/mediawiki/2017/d/d2/T-worldshaper-XSHS-s0009.png" alt="" width="601" height="304" />
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        figure9. the integrated result of the relationship between fluorescence expressi0n and oxygen concentration
 +
                    </p>
 +
                    <p>
 +
                        <b>
 +
                            <span style="font-weight:bold;font-size:11.0000pt;">integrared, 395 nm exciting light</span>
 +
                        </b>
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        <img src="https://static.igem.org/mediawiki/2017/7/71/T-worldshaper-XSHS-s0010.png" alt="" width="553" height="280" />
 +
                    </p>
 +
                    <p  style="text-align:center;" align="center">
 +
                        <span >figure10. the integrated result of</span>
 +
                        <span >
 +
                            the relationship between fluorescence expressi0n and oxygen concentration
 +
                        </span>
 +
                    </p>
 +
                </div>
 +
            </div>
 +
        </div>
 +
    </section>
  
−
<p>
+
    <footer>
−
Please see the <a href="https://2017.igem.org/Judging/Medals"> 2017 Medals Page</a> for more information.
+
        <div class="container">
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</p>
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            <div class="foot-box">
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                    <li class="foot-box-c1">
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                        <img src="https://static.igem.org/mediawiki/2017/7/71/T-worldshaper-XSHS-logoxshs.jpeg" alt="" />
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<h3>Best Model Special Prize</h3>
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                    </li>
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                    <li class="foot-box-c2">
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<p>
+
                        <img src="https://static.igem.org/mediawiki/2017/c/ce/T-worldshaper-igemlogo.jpeg" alt="" />
−
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.
+
                    </li>
−
<br><br>
+
                    <li class="foot-box-c3">
−
You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
+
                        <p>Worldshaper-XSHS, Xiaoshan High School</p>
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</p>
+
                        <p>
−
 
+
                            Adress: No.538,Gongxiu Road,Xiaoshan District,Hangzhou,Zhejiang Province,China
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</div>
+
                        </p>
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<div class="clear"></div>
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                    <li class="foot-box-c4">
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<div class="column full_size">
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                        <img src="https://static.igem.org/mediawiki/2017/3/32/T-Worldshaper-XSHS-weixin.jpeg" alt="" />
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<h5> Inspiration </h5>
+
                    </li>
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<p>
+
                </ul>
−
Here are a few examples from previous teams:
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            </div>
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</p>
+
        </div>
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<ul>
+
    </footer>
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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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</ul>
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</div>
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</html>

Latest revision as of 12:31, 29 October 2017

Model

According to the functional analysis results, we knew that the fluorescence expression of oxy1 and oxy4 were different.Compared with oxy1, through T7RNA polymerase and T7 promoter, oxy4 will amplify the signal(figure 1).But just how much the signal is amplified, and what is the relationship between it and the dissolved oxygen concentraion, we still don't know. So we explored the model of the correlation between fluorescence expression and oxygen concentration. In modeling, we need to use a lot of knowledge of advanced mathematics. As a senior high school student, we can't use it very well, so we only have a very simple model.But we've really worked very hard. The results are as follows.

figure1. The working mechanism of Oxy4

Oxy1

Oxy1-sealed, 475 nm exciting light

We studied the relationship between Oxy1 bacterial fluorescence expressi0n and oxygen concentration under the condition of sealing, and did the function fitting.

To make the data comparable,we standardized the fluorescence intensity and OD600 of each group.?Firstly, we subtracted the initial fluorescence intensity and the initial OD600 from the fluorescence intensity and the OD600. Then we divided the fluorescence intensity by the OD600.We had the function fitting for the obtained values, and we got the following functions and images(figure2):

Equation:    r 2 =0.87,

figure2. the relationship between Oxy1 bacterial fluorescence expressi0n and oxygen concentration

When we averaged the values of each group, we got better fitting functions and images(figure3).

Equation:    r 2 =0.87,

figure3. the relationship between Oxy1 bacterial fluorescence expression and oxygen concentration

Oxy1-sealed, 395 nm exciting light

For the fluorescence intensity of the excitation light of 395nm, we processed the data in the same way. Here are the functions and images(figure4):

Equation:   r 2 =0.99,

figure4. the relationship between Oxy1 bacterial fluorescence expressi0n and oxygen concentration

Oxy4

We also studied the relationship between Oxy4 bacterial fluorescence expressi0n and oxygen concentration under different conditions, and did the function fitting. Data processing was the same as before.

Oxy4-sealed, 475 nm exciting light

Equation:   r 2 =0.91,

figure5. the relationship between Oxy4 bacterial fluorescence expressi0n and oxygen concentration

Oxy4-sealed, 395 nm exciting light

Equation:   r 2 =0.88,

figure6. the relationship between Oxy4 bacterial fluorescence expressi0n and oxygen concentration

Oxy4-unsealed, 475 nm exciting light

Equation:   r 2 =0.94,

figure7. the relationship between Oxy4 bacterial fluorescence expressi0n and oxygen concentration

Oxy4-unsealed, 395 nm exciting light

Equation:   r 2 =0.84,

figure8. the relationship between Oxy4 bacterial fluorescence expressi0n and oxygen concentration

The result of integration

We integrated the expressi0n models of the two strains.It can be seen that, c ompared with the Oxy1 strain, the fluorescence intensity of the Oxy4 strain was stronger in low oxygen condition, which suggested that the Oxy4 is more suitable for oxygen detection.

 

integrared, 475 nm exciting light

figure9. the integrated result of the relationship between fluorescence expressi0n and oxygen concentration

integrared, 395 nm exciting light

figure10. the integrated result of the relationship between fluorescence expressi0n and oxygen concentration

  • Worldshaper-XSHS, Xiaoshan High School

    Adress: No.538,Gongxiu Road,Xiaoshan District,Hangzhou,Zhejiang Province,China