Difference between revisions of "Team:Shanghai HS ID/Model"

 
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                     <div class="sub-nav">
 
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                         <ul>
 
                         <ul>
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                             <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Collection" class="sub-nav-74">Parts
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                             <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Parts" class="sub-nav-74">Parts
 
                                     Collection</a></li>
 
                                     Collection</a></li>
 
                             <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Engineering"
 
                             <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Engineering"
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     <div class="sub-content">
 
     <div class="sub-content">
 
         <div class="sub-title">MODEL</div>
 
         <div class="sub-title">MODEL</div>
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         <div class="article-content">In order to scientifically determine the transformation efficiency of our modified
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         <div class="article-content">To determine the increase in transformation efficiency of our modified L. casei
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            L. casei (KO) and the wild L. casei (Wild), we collected the colony cultured which were pre-spread plates
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            (KO) compared to the wild L. casei (Wild), we spread our Petri dishes by differing volumes of bacteria
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            with different volumes of bacteria solutions and measured their OD<sub>600</sub> after cultured for the same
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            solutions and cultured them under identical conditions. At the end of our experiment, we measured their
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            hours. In
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            OD<sub>600</sub>. <br />
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             the meantime, we also aimed to explore the optimal condition for our modified L. casei’ growth by applying
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             Additionally, we investigated the optimal conditions for the growth of our modified L. casei using varying
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             different amounts of the bacteria seed solution.</div>
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             volumes of bacteria seed solutions
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        </div>
 
         <div class="img-wrap no-margin">
 
         <div class="img-wrap no-margin">
 
             <span>Table 1. OD<sub>600</sub> of cultured L. casei</span>
 
             <span>Table 1. OD<sub>600</sub> of cultured L. casei</span>
 
             <img src="https://static.igem.org/mediawiki/2021/f/f0/T--Shanghai_HS_ID--model01.png" alt="" />
 
             <img src="https://static.igem.org/mediawiki/2021/f/f0/T--Shanghai_HS_ID--model01.png" alt="" />
 
         </div>
 
         </div>
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         <div class="article-content">According to the scatter plots, we chose to use the quadratic polynomial equation
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         <div class="article-content">Based on our scatter plots, we utilized a quadratic polynomial equation to
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             to build the model :
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             construct our model :
 
         </div>
 
         </div>
 
         <div class="img-wrap no-margin">
 
         <div class="img-wrap no-margin">
 
             <img src="https://static.igem.org/mediawiki/2021/b/bd/T--Shanghai_HS_ID--model02.png" alt="" />
 
             <img src="https://static.igem.org/mediawiki/2021/b/bd/T--Shanghai_HS_ID--model02.png" alt="" />
 
         </div>
 
         </div>
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         <div class="article-content">The coding we used is given below:</div>
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         <div class="article-content">Our coding is given below:</div>
 
         <div class="article-content">
 
         <div class="article-content">
 
             <b>
 
             <b>
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             </b>
 
             </b>
 
         </div>
 
         </div>
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         <div class="article-content">After calculation, below are the constants of the solved quadratic polynomial
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         <div class="article-content">Our calculations revealed the constants of the solved quadratic polynomial
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             equations of the KO group and
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             equations for the KO group and Wild group, respectively.</div>
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            Wild group, respectively.</div>
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         <div class="img-wrap no-margin">
 
         <div class="img-wrap no-margin">
 
             <span style="margin-bottom: 20px;">Table 2. Model results</span>
 
             <span style="margin-bottom: 20px;">Table 2. Model results</span>
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             <img src="https://static.igem.org/mediawiki/2021/0/06/T--Shanghai_HS_ID--model03.png" alt="" />
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             <img src="https://static.igem.org/mediawiki/2021/4/4e/T--Shanghai_HS_ID--chgt3.jpg" alt="" />
 
             <span>Figure 1. Comparison between two fitting curves of KO group(red) and Wild group(blue)</span>
 
             <span>Figure 1. Comparison between two fitting curves of KO group(red) and Wild group(blue)</span>
 
         </div>
 
         </div>
 
         <div class="article-title">Conclusion</div>
 
         <div class="article-title">Conclusion</div>
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         <div class="article-content">In figure 1, we can clearly see that the modified L. casei shows much higher
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         <div class="article-content">We can see in figure 1 that our modified L. casei displays a significantly higher
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             transformation efficiency than the wild L. casei especially when the volume of the initial bacteria seed
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             transformation efficiency than the wild L. casei, especially with less than 100 ul of initial bacteria seed
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             solution is used less than 100 uL when the difference between them is remarkable.</div>
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             solution.</div>
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        <div class="article-title">Solution</div>
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         <div class="article-content">The equation model visualizing the transformation rate of the modified L. casei
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         <div class="article-content">We constructed a plasmid equipped with a CRISPR-Cas9 complex that cuts and removes
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             (shown below) can be used to analyze the relationship between the volume of the bacteria seed solution used
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            a selected segment of the L. casei DNA. Our target gene is LSEI-2094. This gene is involved in the synthesis
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             and the final OD<sub>600</sub> of the cultures. The data model can also assist future expression efficiency
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            of an enzyme that is essential in the restriction-modification system [5]. The cell's efforts to repair its
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             tests<br />
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            DNA induces mutations, which help to inactivate the gene and prevent the production of the enzyme. After
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            With a more elaborate model, we would also be able to manipulate the variables and adjust the volume of the
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            this modification foreign DNAs could enter and express themselves much more efficiently in L.Casei.With a
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             bacteria seed solution for other cultures.
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            strain of bacteria ready to be tailored to our needs, the benefits are immeasurable. The benefits of L.
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        </div>
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            caseicould come to fruition if the technology is applied to popular and impactful industries such as
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            pharmaceuticals and food. </div>
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        <div class="article-content">Besides, the equation model we built for the modified L. casei as showing below,
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             could be used to analyze the relationship between the volume of the bacteria seed solution and its
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             OD<sub>600</sub>, it
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            could be used as a reference when we conduct the expression efficiency tests in the future. If we could
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             further build the relationship between the expression level and OD<sub>600</sub>, we could adjust the volume
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            of the
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             bacteria seed solution for culturing accordingly.</div>
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         <div class="article-content" style="text-align: center;"><b>Model for the modified L. casei: </b>f(x) =
 
         <div class="article-content" style="text-align: center;"><b>Model for the modified L. casei: </b>f(x) =
 
             0.0003x<sup>3</sup> -
 
             0.0003x<sup>3</sup> -

Latest revision as of 17:59, 19 October 2021

Shanghai_HS_ID

MODEL
To determine the increase in transformation efficiency of our modified L. casei (KO) compared to the wild L. casei (Wild), we spread our Petri dishes by differing volumes of bacteria solutions and cultured them under identical conditions. At the end of our experiment, we measured their OD600.
Additionally, we investigated the optimal conditions for the growth of our modified L. casei using varying volumes of bacteria seed solutions
Table 1. OD600 of cultured L. casei
Based on our scatter plots, we utilized a quadratic polynomial equation to construct our model :
Our coding is given below:
“
clear;clc;
v0=[50 100 150];
od10=[0.035 0.289 3.84];
od20=[0.255 1.984 5.21];
p1=polyfit(v0,od10,2)
p2=polyfit(v0,od20,2)
v=[50:150];
od1=polyval(p1,v);
od2=polyval(p2,v);
plot(v,od1,'b','LineWidth',2)
hold on
plot(v,od2,'r','LineWidth',2)
plot(v0,od10,'k*','LineWidth',2)
plot(v0,od20,'g*','LineWidth',2)
hold off
”
Our calculations revealed the constants of the solved quadratic polynomial equations for the KO group and Wild group, respectively.
Table 2. Model results
Sample p1 p2 p3
KO 0.0007 -0.0938 3.0780
Wild 0.0003 -0.0103 0.0230
Figure 1. Comparison between two fitting curves of KO group(red) and Wild group(blue)
Conclusion
We can see in figure 1 that our modified L. casei displays a significantly higher transformation efficiency than the wild L. casei, especially with less than 100 ul of initial bacteria seed solution.
The equation model visualizing the transformation rate of the modified L. casei (shown below) can be used to analyze the relationship between the volume of the bacteria seed solution used and the final OD600 of the cultures. The data model can also assist future expression efficiency tests
With a more elaborate model, we would also be able to manipulate the variables and adjust the volume of the bacteria seed solution for other cultures.
Model for the modified L. casei: f(x) = 0.0003x3 - 0.0103x2 + 0.0230
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