Difference between revisions of "Team:Shanghai Metro Utd/Model"

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                    <a href="https://2021.igem.org/Team:Shanghai_Metro_Utd">Home</a>
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                    <a href="">Project</a>
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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 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. </p>
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                                    class="sub-nav-74">Description</a>
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<p>Please note you can compete for both the Gold Medal criterion #3 and the Best Model prize with this page. </p>
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<h3> Gold Medal Criterion #3</h3>
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Use modeling to gain insight into how your project works or should be implemented. Explain your model's assumptions, data, parameters, and results in a way that anyone could understand.
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Please see the <a href="https://2021.igem.org/Judging/Medals">2021 Medals Page</a> for more information.
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<p>Models and computer simulations provide a great way to describe the functioning and operation of BioBrick Parts and Devices. Synthetic biology is an engineering discipline and part of engineering is simulation and modeling to determine system behavior before building your design. 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 before or in conjunction with experiments in the wetlab.
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                                    class="sub-nav-74">Parts Collection</a></li>
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                            <li><a href="https://2021.igem.org/Team:Shanghai_Metro_Utd/Engineering"
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To compete for the <a href="https://2021.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://2021.igem.org/Judging/Judging_Form">judging form</a>.
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                                    class="sub-nav-74">Engineering</a></li>
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<p>You can look at what other teams did to get some inspiration! <br />
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Here are a few examples:</p>
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<li><a href="https://2018.igem.org/Team:GreatBay_China/Model">2018 GreatBay China</a></li>
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<li><a href="https://2020.igem.org/Team:Harvard/Model">2020 Harvard</a></li>
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<li><a href="https://2020.igem.org/Team:Leiden/Model">2020 Leiden</a></li>
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                    <a href="https://2021.igem.org/Team:Shanghai_Metro_Utd/Implementation">Implementation</a>
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        <div class="sub-title">MODEL</div>
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        <div class="article-content">As known from the litterateurs that Heparan sulfate Proteoglycans (HSPGs) are
 +
            needed for rANG to enter cells, it is necessary to explore the specific combination of ANG and HS
 +
            interaction. Therefore, we applied an enzyme-linked immunosorbent assay to detect the bonding strength
 +
            between rANG and HS and further analyzed the relationship by building a mathematical model.</div>
 +
        <div class="article-content">Below is the initial data. The OD<sub>450</sub> could indicate the interaction
 +
            ability between
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            heparin and angiogenin which means that the higher the OD<sub>450</sub> value, the greater the interaction
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            ability
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            between heparin and angiogenin. </div>
 +
        <div class="img-wrap">
 +
            <img src="https://static.igem.org/mediawiki/2021/d/d0/T--Shanghai_Metro_Utd--MODEL01.jpg" alt="" />
 +
        </div>
 +
        <div class="article-content">According to the scatter plots, there seemed several ups and downs during 3~8 ug/ml
 +
            which could be resulted from the lower concentration and the instrument errors, but the basic trend of the
 +
            data presents an S trend. In this case, we chose the logistic equation to fit our data:</div>
 +
        <div class="img-wrap">
 +
            <img src="https://static.igem.org/mediawiki/2021/2/23/T--Shanghai_Metro_Utd--MODEL02.jpg" alt="" />
 +
        </div>
 +
        <div class="article-content">After importing the data in MATLAB, we received the modeling results below where
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            the fitting degree is
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            0.9833.</div>
 +
        <div class="img-wrap">
 +
            <img src="https://static.igem.org/mediawiki/2021/5/5a/T--Shanghai_Metro_Utd--MODEL03.jpg" alt="" />
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            <span>Figure 1. Model result </span>
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        </div>
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        <div class="img-wrap">
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            <img src="https://static.igem.org/mediawiki/2021/1/1a/T--Shanghai_Metro_Utd--MODEL04.jpg" alt="" />
 +
            <span>Figure 2. The fitting curve of the model</span>
 +
        </div>
 +
        <div class="article-content">Based on the model result and fitting curve, it indicates that the more angiogenin
 +
            we added, the higher the
 +
            OD<sub>450</sub> value, namely the interaction ability between heparin and angiogenin. Therefore, it can be
 +
            concluded
 +
            that the interaction of heparin has dose-dependent with angiogenin and conforms to a certain quantitative
 +
            relation (Fig. 1). This model could contribute to the development of new drugs related to angiogenin.</div>
 +
        <div class="img-wrap">
 +
            <img src="https://static.igem.org/mediawiki/2021/a/a4/T--Shanghai_Metro_Utd--MODEL05.jpg" alt="" />
 +
            <span>Figure 3. Comparison graph to the PBS blank control</span>
 +
        </div>
 +
        <div class="article-content">In order to determine the least amount of angiogenin that could combine with
 +
            heparin, we introduced a blank control, PBS solution as the comparison where its OD<sub>450</sub> value’s
 +
            average
 +
            equals to 0.08847. In this case, we drew a horizontal line (Y=0.008847) into the fitting curve graph of the
 +
            model (Fig. 3) and we could find the cross point at (7, 0.08847). Therefore, it could be inferred that the
 +
            least amount of angiogenin that could combine with heparin would be 7 ug/ml. </div>
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Revision as of 16:20, 13 October 2021

Shanghai_Metro_Utd

MODEL
As known from the litterateurs that Heparan sulfate Proteoglycans (HSPGs) are needed for rANG to enter cells, it is necessary to explore the specific combination of ANG and HS interaction. Therefore, we applied an enzyme-linked immunosorbent assay to detect the bonding strength between rANG and HS and further analyzed the relationship by building a mathematical model.
Below is the initial data. The OD450 could indicate the interaction ability between heparin and angiogenin which means that the higher the OD450 value, the greater the interaction ability between heparin and angiogenin.
According to the scatter plots, there seemed several ups and downs during 3~8 ug/ml which could be resulted from the lower concentration and the instrument errors, but the basic trend of the data presents an S trend. In this case, we chose the logistic equation to fit our data:
After importing the data in MATLAB, we received the modeling results below where the fitting degree is 0.9833.
Figure 1. Model result
Figure 2. The fitting curve of the model
Based on the model result and fitting curve, it indicates that the more angiogenin we added, the higher the OD450 value, namely the interaction ability between heparin and angiogenin. Therefore, it can be concluded that the interaction of heparin has dose-dependent with angiogenin and conforms to a certain quantitative relation (Fig. 1). This model could contribute to the development of new drugs related to angiogenin.
Figure 3. Comparison graph to the PBS blank control
In order to determine the least amount of angiogenin that could combine with heparin, we introduced a blank control, PBS solution as the comparison where its OD450 value’s average equals to 0.08847. In this case, we drew a horizontal line (Y=0.008847) into the fitting curve graph of the model (Fig. 3) and we could find the cross point at (7, 0.08847). Therefore, it could be inferred that the least amount of angiogenin that could combine with heparin would be 7 ug/ml.

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