Difference between revisions of "Team:BIT-China/Model"

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{{BIT-China}}
 
 
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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://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</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://2018.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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Convince the judges that your project's design and/or implementation is based on insight you have gained from modeling. This could be either a new model you develop or the implementation of a model from a previous team. You must thoroughly document your model's contribution to your project on your team's wiki, including assumptions, relevant data, model results, and a clear explanation of your model that anyone can understand.
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<br><br>
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The model should impact your project design in a meaningful way. Modeling may include, but is not limited to, deterministic, exploratory, molecular dynamic, and stochastic models. Teams may also explore the physical modeling of a single component within a system or utilize mathematical modeling for predicting function of a more complex device.
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Please see the <a href="https://2018.igem.org/Judging/Medals"> 2018
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Medals Page</a> for more information.
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<h3>Best Model Special Prize</h3>
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<body>
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To compete for the <a href="https://2018.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://2018.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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</div>
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          <ul id="left-nav">
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        <li>
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            <a>PROJECT</a>
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            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Background">Background</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Description">Description</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Design">Idea & Design</a></li>
 +
            </ul>
 +
        </li>
  
 +
        <li>
 +
            <a>EXPERIMENTS</a>
 +
            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/ExperimentsRegulator">Regulator</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/ExperimentsFeedback">Feedback</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/ExperimentsOutput">Output</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Results">Results</a></li>
 +
            </ul>
 +
        </li>
  
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<div class="column third_size">
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        <li>
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<div class="highlight decoration_A_full">
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            <a>MODELING</a>
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<h3> Inspiration </h3>
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            <ul>
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<p>
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                <li><a href="https://2018.igem.org/Team:BIT-China/Model">Overview</a></li>
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Here are a few examples from previous teams:
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                <li><a href="https://2018.igem.org/Team:BIT-China/FluorescentProbesModel">Fluorescent Probe Model </a></li>
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</p>
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                <li><a href="https://2018.igem.org/Team:BIT-China/H2O2DecompositionModel">H<sub>2</sub>O<sub>2</sub>
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<ul>
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                        Decomposition Model</a></li>
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<li><a href="https://2016.igem.org/Team:Manchester/Model">2016 Manchester</a></li>
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−
<li><a href="https://2016.igem.org/Team:TU_Delft/Model">2016 TU Delft</li>
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                <li><a href="https://2018.igem.org/Team:BIT-China/roGFP2-Orp1MichaelisEquationModel">roGFP2-Orp1
−
<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">2014 ETH Zurich</a></li>
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                        Michaelis equation Model</a></li>
−
<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">2014 Waterloo</a></li>
+
            </ul>
−
</ul>
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        </li>
−
</div>
+
 
−
</div>
+
        <li>
 +
            <a>HUMAN PRACTICES</a>
 +
            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/HPOverview">Overview</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Human_Practices">Integrated Human Practices</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Public_Engagement">Education & Public Engagement</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Collaborations">Collaborations</a></li>
 +
            </ul>
 +
        </li>
 +
 
 +
        <li>
 +
            <a>NOTEBOOK</a>
 +
            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Notebook">Lab Book</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Protocols">Methodology / Protocols</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Equipment">Material & Equipment</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/InterLab">Measurement / InterLab</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Safety">Safety</a></li>
 +
            </ul>
 +
        </li>
 +
 
 +
        <li>
 +
            <a>ACHIEVEMENTS</a>
 +
            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/JudgingForm">Judging Form</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Parts">Parts</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Improve">Improve</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Applied_Design">Applied Design</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Demonstrate">Demonstrate</a></li>
 +
            </ul>
 +
        </li>
 +
 
 +
        <li>
 +
            <a>TEAM</a>
 +
            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Team">Members</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Attributions">Attributions</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Gallery">Gallery</a></li>
 +
            </ul>
 +
        </li>
 +
    </ul>
 +
 
 +
    <a href="https://2018.igem.org/Team:BIT-China"><img id="imgA" class="imgA-new-pos" src="https://static.igem.org/mediawiki/2018/4/46/T--BIT-China--iGEM2018-A_img.png" /></a>
 +
    <!-- end -->
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 +
    <img src="https://static.igem.org/mediawiki/2018/0/0e/T--BIT-China--iGEM2018-mod-BG2.png" style="position:fixed;height:100vh;top:0;right:0;">
 +
 
 +
    <div class="MD-white-head"></div>
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 +
    <div id="MD-content-all" class="MD-content-container" style="margin-top:calc(25vh - 30px);">
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        <div class="MD-title">
 +
            <a style="border-bottom-style: solid;text-decoration: none;color: #131313;">OVERVIEW</a>
 +
        </div>
 +
        <div id="MD1" class="MD-overview MD-margin-toTitle">
 +
 
 +
            <div class="MD-content">
 +
                <p class="MD-content-p">
 +
                    Modeling is significant for supporting and improving the meaning of our project. Generally
 +
                    speaking, we hope to use mathematics methods to verify the feasibility and validity of our project.
 +
                    In this modeling, four core variables were introduced: fluorescence intensity of DFCH-DA probe,
 +
                    fluorescence intensity of roGFP2-Orp1 protein, external H<sub>2</sub>O<sub>2</sub> concentration
 +
                    and intracellular H<sub>2</sub>O<sub>2</sub> concentration.
 +
                </p>
 +
                <p class="MD-content-p MD-margin-toP">
 +
                    roGFP2-Orp1 protein expression cassette is our core manner for detecting and measuring ROS level.
 +
                    In the further application of our device, users can calculate antioxidative ability by collecting
 +
                    roGFP2-Orp1fluoresecent intensities data. The whole modeling goes with the goal that making
 +
                    roGFP2-Orp1 realize it's proper functions.
 +
                </p>
 +
                <p class="MD-content-p MD-margin-toP">
 +
                    To verify the functions of <i>yno1/ndi1</i> genes and roGFP2-Orp1 fluorescent protein, DCFH-DA
 +
                    fluorescent
 +
                    probe was chosen as our output signal reference, which can detect and measure ROS concentration
 +
                    changes and present relative antioxidative strength. The process is indirect, so we set up <b>Fluorescent
 +
                        Probe Model</b> to normalize fluorescence intensities and H<sub>2</sub>O<sub>2</sub>
 +
                    concentration, which made them comparable to each other.
 +
                </p>
 +
                <p class="MD-content-p MD-margin-toP">
 +
                    To simulate the accumulation of intracellular H<sub>2</sub>O<sub>2</sub> and set a relationship
 +
                    with external H<sub>2</sub>O<sub>2</sub>(the external H<sub>2</sub>O<sub>2</sub> is the H<sub>2</sub>O<sub>2</sub>
 +
                    we added in media), <b>H<sub>2</sub>O<sub>2</sub> Decomposition Model</b> was induced.
 +
                </p>
 +
                <p class="MD-content-p MD-margin-toP">
 +
                    With simulating the process that how roGFP2-Orp1 generates, reacts and degrades inside cells,
 +
                    roGFP2-Orp1 Michealis equation Model described the connection between roGFP2-Orp1 and intracellular
 +
                    H<sub>2</sub>O<sub>2</sub>.
 +
                </p>
 +
                <p class="MD-content-p MD-margin-toP">
 +
                    With the three models mentioned above, we finally proved the accessibility of our roGFP2-Orp1 detecting method.
 +
                </p>
 +
 
 +
            </div>
 +
        </div>
 +
 
 +
        <div id="MD2" class="cd-section MD-margin-title2ToUp">
 +
            <div class="MD-title-1" style="border-left-style:solid;padding-left:10px;">
 +
                Fluorescent Probe Model <a href="https://2018.igem.org/Team:BIT-China/FluorescentProbesModel" style="color:#131313;text-decoration:none;font-size: 16px;">
 +
                    (Chick
 +
                    here for details)</a>
 +
            </div>
 +
 
 +
            <div class="MD-content MD-margin-toTitle1">
 +
                <p class="MD-content-p">
 +
                    The model was established based on the mechanism of the fluorescence probe and we revised it
 +
                    according to the experimental results. From this model we can realize the conversion between
 +
                    fluorescence intensity of the probe and intracellular H<sub>2</sub>O<sub>2</sub> concentration from
 +
                    overexpression of genes.
 +
                </p>
 +
            </div>
 +
        </div>
 +
 
 +
        <div id="MD3" class="cd-section MD-margin-title2ToUp">
 +
            <div class="MD-title-1 MD-margin-title1ToUp" style="border-left-style:solid;padding-left:10px;">
 +
                H<sub>2</sub>O<sub>2</sub> Decomposition Model <a href="https://2018.igem.org/Team:BIT-China/H2O2DecompositionModel"
 +
                    style="color:#131313;text-decoration:none;font-size: 16px;"> (Click
 +
                    here for details)</a>
 +
            </div>
 +
 
 +
            <div class="MD-content MD-margin-toTitle1">
 +
                <p class="MD-content-p">
 +
                    In our experiment, we found it was hard to measure the intracellular H<sub>2</sub>O<sub>2</sub> concentration, so we controlled the external H<sub>2</sub>O<sub>2</sub> concentration in culture to confirm our system's function because the H<sub>2</sub>O<sub>2</sub> can entry the cell quickly through simple diffusion. So we fitted the relationship between two kinds of H<sub>2</sub>O<sub>2</sub> concentration, through experimental data and ordinary differential equation based on the processes of H<sub>2</sub>O<sub>2</sub> diffusion and decomposition in yeast cells. In this way, the mutual translation of external and intracellular H<sub>2</sub>O<sub>2</sub> concentrations can be achieved.
 +
                </p>
 +
            </div>
 +
        </div>
 +
 
 +
        <div id="MD4" class="cd-section MD-margin-title2ToUp">
 +
            <div class="MD-title-1 MD-margin-title1ToUp" style="border-left-style:solid;padding-left:10px;">
 +
                roGFP2-Orp1 Michaelis equation model<a href="https://2018.igem.org/Team:BIT-China/roGFP2-Orp1MichaelisEquationModel"
 +
                    style="color:#131313;text-decoration:none;font-size: 16px;"> (Click
 +
                    here for details)</a>
 +
            </div>
 +
 
 +
            <div class="MD-content MD-margin-toTitle2">
 +
                <p class="MD-content-p">
 +
                    The model was established based on the mechanism of the Michealis equation to describe the
 +
                    relationship between intracellular H<sub>2</sub>O<sub>2</sub> concentrations and the roGFP2
 +
                    fluorescence intensity changing. We simplified the process of the reaction between roGFP2-Orp1 and
 +
                    intracellular H<sub>2</sub>O<sub>2</sub> as a classic Michealis equation, which helped us
 +
                    understanding this process better.
 +
                </p>
 +
            </div>
 +
        </div>
 +
 
 +
    </div>
 +
 
 +
    <!-- footer start -->
 +
    <div class="footer-all" style="margin-top:65px;">
 +
        <div class="footer-left">
 +
            <img src="https://static.igem.org/mediawiki/2018/c/ca/T--BIT-China--iGEM2018-sponsor-1.png">
 +
            <img src="https://static.igem.org/mediawiki/2018/0/07/T--BIT-China--iGEM2018-sponsor-2.png">
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        <div class="footer-right">
 +
            <p style="font-family:'kg_second_chances_solidRg';font-size:12px;margin: 0;padding: 0 0 3px;margin-top: 6px;">Contact</p>
 +
            <p style="font-size:15px;margin: 0;padding: 0;margin-top: 4px;">Institute of
 +
                Biotransformation and synthetic biosystem School of Chemistry and Chemical Engineering.
 +
            </p>
 +
            <p style="font-size:15px;margin: 0;padding: 0;margin-top: 4px;">
 +
                Beijing Institute of Technology
 +
            </p>
 +
            <p style="font-size:15px;margin: 0;padding: 0;margin-top: 4px;">
 +
                100081, Beijing
 +
            </p>
 +
            <p style="font-size:15px;margin: 0;padding: 0;margin-top: 4px;">
 +
                Email:lichun@bit.edu.cn
 +
            </p>
 +
 
 +
            <p style="font-size:15px;margin: 0;padding: 0;margin-top: 4px;color:  rgb(161, 161, 161);">
 +
                Copyright © 2018 BIT-China
 +
            </p>
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Latest revision as of 00:40, 18 October 2018

OVERVIEW

Modeling is significant for supporting and improving the meaning of our project. Generally speaking, we hope to use mathematics methods to verify the feasibility and validity of our project. In this modeling, four core variables were introduced: fluorescence intensity of DFCH-DA probe, fluorescence intensity of roGFP2-Orp1 protein, external H2O2 concentration and intracellular H2O2 concentration.

roGFP2-Orp1 protein expression cassette is our core manner for detecting and measuring ROS level. In the further application of our device, users can calculate antioxidative ability by collecting roGFP2-Orp1fluoresecent intensities data. The whole modeling goes with the goal that making roGFP2-Orp1 realize it's proper functions.

To verify the functions of yno1/ndi1 genes and roGFP2-Orp1 fluorescent protein, DCFH-DA fluorescent probe was chosen as our output signal reference, which can detect and measure ROS concentration changes and present relative antioxidative strength. The process is indirect, so we set up Fluorescent Probe Model to normalize fluorescence intensities and H2O2 concentration, which made them comparable to each other.

To simulate the accumulation of intracellular H2O2 and set a relationship with external H2O2(the external H2O2 is the H2O2 we added in media), H2O2 Decomposition Model was induced.

With simulating the process that how roGFP2-Orp1 generates, reacts and degrades inside cells, roGFP2-Orp1 Michealis equation Model described the connection between roGFP2-Orp1 and intracellular H2O2.

With the three models mentioned above, we finally proved the accessibility of our roGFP2-Orp1 detecting method.

Fluorescent Probe Model (Chick here for details)

The model was established based on the mechanism of the fluorescence probe and we revised it according to the experimental results. From this model we can realize the conversion between fluorescence intensity of the probe and intracellular H2O2 concentration from overexpression of genes.

H2O2 Decomposition Model (Click here for details)

In our experiment, we found it was hard to measure the intracellular H2O2 concentration, so we controlled the external H2O2 concentration in culture to confirm our system's function because the H2O2 can entry the cell quickly through simple diffusion. So we fitted the relationship between two kinds of H2O2 concentration, through experimental data and ordinary differential equation based on the processes of H2O2 diffusion and decomposition in yeast cells. In this way, the mutual translation of external and intracellular H2O2 concentrations can be achieved.

roGFP2-Orp1 Michaelis equation model (Click here for details)

The model was established based on the mechanism of the Michealis equation to describe the relationship between intracellular H2O2 concentrations and the roGFP2 fluorescence intensity changing. We simplified the process of the reaction between roGFP2-Orp1 and intracellular H2O2 as a classic Michealis equation, which helped us understanding this process better.

Contact

Institute of Biotransformation and synthetic biosystem School of Chemistry and Chemical Engineering.

Beijing Institute of Technology

100081, Beijing

Email:lichun@bit.edu.cn

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