(Prototype team page) |
|||
Line 1: | Line 1: | ||
− | + | <html lang="en"> | |
− | + | ||
− | <html> | + | |
+ | <head> | ||
+ | <meta charset="UTF-8"> | ||
+ | <meta http-equiv="X-UA-Compatible" content="IE=edge"> | ||
+ | <meta name="viewport" content="width=device-width, initial-scale=1.0"> | ||
+ | <title>Shanghai_HS_ID</title> | ||
+ | <link rel="stylesheet" | ||
+ | href="https://2021.igem.org/wiki/index.php?title=Template:Shanghai_HS_ID/Main_CSS&action=raw&ctype=text/css" /> | ||
+ | </head> | ||
− | + | <body> | |
− | <div class=" | + | <nav class="head-nav clearfix"> |
− | < | + | <div class="top-block"></div> |
− | < | + | <div class="top-nav-bar"> |
− | < | + | <ul class="clearfix"> |
− | < | + | <span class="small-logo"></span> |
− | + | <li> | |
− | + | <a href="https://2021.igem.org/Team:Shanghai_HS_ID">Home</a> | |
− | < | + | </li> |
− | + | <li> | |
− | + | <a href="">Project</a> | |
− | < | + | <div class="sub-nav"> |
− | < | + | <ul> |
− | + | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Description" | |
− | < | + | class="sub-nav-74">Description</a></li> |
− | + | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Experiments" | |
− | < | + | class="sub-nav-74">Experiments</a></li> |
− | + | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Results" | |
− | </div> | + | class="sub-nav-74">Results</a></li> |
− | < | + | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Proof_Of_Concept" |
− | + | class="sub-nav-52">Proof Of Concept</a></li> | |
− | <div class=" | + | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Notebook" |
− | < | + | class="sub-nav-52">Notebook</a></li> |
− | < | + | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Safety">Safety</a></li> |
− | + | </ul> | |
− | < | + | </div> |
− | + | </li> | |
− | </ | + | <li> |
− | + | <a href="">Parts</a> | |
− | </div> | + | <div class="sub-nav"> |
− | + | <ul> | |
− | <div class=" | + | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Collection" class="sub-nav-74">Parts |
− | < | + | Collection</a></li> |
− | + | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Engineering" | |
− | < | + | class="sub-nav-74">Engineering</a></li> |
− | </ | + | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Contribution" |
− | + | class="sub-nav-74">Contribution</a></li> | |
− | </ | + | </ul> |
− | + | </div> | |
− | </div> | + | </li> |
− | + | <li> | |
− | + | <a href="">Human Practices</a> | |
− | < | + | <div class="sub-nav"> |
− | < | + | <ul> |
− | < | + | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Human_Practices" |
− | < | + | class="sub-nav-74">Integrated Human Practice</a></li> |
− | + | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Communication" | |
− | <ul> | + | class="sub-nav-74">Communication</a></li> |
− | <li><a href="https:// | + | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Fundraising" |
− | <li><a href="https:// | + | class="sub-nav-74">Fundraising</a></li> |
− | <li><a href="https:// | + | </ul> |
− | <li><a href="https:// | + | </div> |
− | <li>< | + | </li> |
− | < | + | <li> |
− | < | + | <a href="https://2021.igem.org/Team:Shanghai_HS_ID/Implementation">Implementation</a> |
− | </ | + | </li> |
− | </div> | + | <li> |
− | </div> | + | <a href="https://2021.igem.org/Team:Shanghai_HS_ID/Entrepreneurship">Entrepreneurship</a> |
+ | </li> | ||
+ | <li class="active"> | ||
+ | <a href="#">Model</a> | ||
+ | </li> | ||
+ | <li> | ||
+ | <a href="">Team</a> | ||
+ | <div class="sub-nav"> | ||
+ | <ul> | ||
+ | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Members" class="sub-nav-74">Team | ||
+ | Members</a></li> | ||
+ | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Attributions" | ||
+ | class="sub-nav-74">Attributions</a></li> | ||
+ | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Collaborations" | ||
+ | class="sub-nav-74">Collaborations</a></li> | ||
+ | <li><a href="https://2021.igem.org/Team:Shanghai_HS_ID/Partnership" | ||
+ | class="sub-nav-74">Partnership</a></li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | </nav> | ||
+ | <div class="sub-banner"> | ||
+ | <img src="https://static.igem.org/mediawiki/2021/c/c3/T--Shanghai_HS_ID--banner.jpg" alt="" /> | ||
+ | </div> | ||
+ | <div class="sub-content"> | ||
+ | <div class="sub-title">MODEL</div> | ||
+ | <div class="article-content">In order to scientifically determine the transformation efficiency of our modified | ||
+ | L. casei (KO) and the wild L. casei (Wild), we collected the colony cultured which were pre-spread plates | ||
+ | with different volumes of bacteria solutions and measured their OD<sub>600</sub> after cultured for the same | ||
+ | hours. In | ||
+ | the meantime, we also aimed to explore the optimal condition for our modified L. casei’ growth by applying | ||
+ | different amounts of the bacteria seed solution.</div> | ||
+ | <div class="img-wrap no-margin"> | ||
+ | <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="" /> | ||
+ | </div> | ||
+ | <div class="article-content">According to the scatter plots, we chose to use the quadratic polynomial equation | ||
+ | to build the model : | ||
+ | </div> | ||
+ | <div class="img-wrap no-margin"> | ||
+ | <img src="https://static.igem.org/mediawiki/2021/b/bd/T--Shanghai_HS_ID--model02.png" alt="" /> | ||
+ | </div> | ||
+ | <div class="article-content">The coding we used is given below:</div> | ||
+ | <div class="article-content"> | ||
+ | <b> | ||
+ | “<br /> | ||
+ | clear;clc;<br /> | ||
+ | v0=[50 100 150];<br /> | ||
+ | od10=[0.035 0.289 3.84];<br /> | ||
+ | od20=[0.255 1.984 5.21];<br /> | ||
+ | p1=polyfit(v0,od10,2)<br /> | ||
+ | p2=polyfit(v0,od20,2)<br /> | ||
+ | v=[50:150];<br /> | ||
+ | od1=polyval(p1,v);<br /> | ||
+ | od2=polyval(p2,v);<br /> | ||
+ | plot(v,od1,'b','LineWidth',2)<br /> | ||
+ | hold on<br /> | ||
+ | plot(v,od2,'r','LineWidth',2)<br /> | ||
+ | plot(v0,od10,'k*','LineWidth',2)<br /> | ||
+ | plot(v0,od20,'g*','LineWidth',2)<br /> | ||
+ | hold off<br /> | ||
+ | ” | ||
+ | </b> | ||
+ | </div> | ||
+ | <div class="article-content">After calculation, below are the constants of the solved quadratic polynomial | ||
+ | equations of the KO group and | ||
+ | Wild group, respectively.</div> | ||
+ | <div class="img-wrap no-margin"> | ||
+ | <span style="margin-bottom: 20px;">Table 2. Model results</span> | ||
+ | <table id="sub-table" border="1" cellspacing="0" cellpadding="0"> | ||
+ | <tr> | ||
+ | <td>Sample</td> | ||
+ | <td>p1 </td> | ||
+ | <td>p2 </td> | ||
+ | <td>p3 </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>KO</td> | ||
+ | <td>0.0007 </td> | ||
+ | <td>-0.0938 </td> | ||
+ | <td>3.0780 </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Wild</td> | ||
+ | <td>0.0003 </td> | ||
+ | <td>-0.0103 </td> | ||
+ | <td>0.0230 </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <div class="img-wrap no-margin"> | ||
+ | <img src="https://static.igem.org/mediawiki/2021/0/06/T--Shanghai_HS_ID--model03.png" alt="" /> | ||
+ | <span>Figure 1. Comparison between two fitting curves of KO group(red) and Wild group(blue)</span> | ||
+ | </div> | ||
+ | <div class="article-title">Conclusion</div> | ||
+ | <div class="article-content">In figure 1, we can clearly see that the modified L. casei shows much higher | ||
+ | transformation efficiency than the wild L. casei especially when the volume of the initial bacteria seed | ||
+ | solution is used less than 100 uL when the difference between them is remarkable.</div> | ||
+ | <div class="article-title">Solution</div> | ||
+ | <div class="article-content">We constructed a plasmid equipped with a CRISPR-Cas9 complex that cuts and removes | ||
+ | a selected segment of the L. casei DNA. Our target gene is LSEI-2094. This gene is involved in the synthesis | ||
+ | of an enzyme that is essential in the restriction-modification system [5]. The cell's efforts to repair its | ||
+ | DNA induces mutations, which help to inactivate the gene and prevent the production of the enzyme. After | ||
+ | this modification foreign DNAs could enter and express themselves much more efficiently in L.Casei.With a | ||
+ | strain of bacteria ready to be tailored to our needs, the benefits are immeasurable. The benefits of L. | ||
+ | caseicould come to fruition if the technology is applied to popular and impactful industries such as | ||
+ | pharmaceuticals and food. </div> | ||
+ | <div class="article-content">Besides, the equation model we built for the modified L. casei as showing below, | ||
+ | could be used to analyze the relationship between the volume of the bacteria seed solution and its | ||
+ | OD<sub>600</sub>, it | ||
+ | could be used as a reference when we conduct the expression efficiency tests in the future. If we could | ||
+ | further build the relationship between the expression level and OD<sub>600</sub>, we could adjust the volume | ||
+ | of the | ||
+ | bacteria seed solution for culturing accordingly.</div> | ||
+ | <div class="article-content" style="text-align: center;"><b>Model for the modified L. casei: </b>f(x) = | ||
+ | 0.0003x<sup>3</sup> - | ||
+ | 0.0103x<sup>2</sup> + 0.0230</div> | ||
+ | </div> | ||
+ | <footer class="footer"> | ||
+ | <section class="footer-wrap"> | ||
+ | <div class="footer-contact">Follow us on WeChat!</div> | ||
+ | <img class="footer-qrcode" src="https://static.igem.org/mediawiki/2021/c/c3/T--Shanghai_HS_ID--qrcode.png" /> | ||
+ | <p class="margin-bottom-10"><i>WeChat Official Account: 乳酸LAB</i></p> | ||
+ | <p>Contact Email:<i>jhxchen@gmail.com</i></p> | ||
+ | </section> | ||
+ | </footer> | ||
+ | </body> | ||
+ | <script> | ||
+ | let liTags = document.querySelectorAll(".top-nav-bar > ul > li"); | ||
+ | let len = liTags.length; | ||
+ | for (let i = 0; i < len; i++) { | ||
+ | liTags[i].onclick = function (e) { | ||
+ | //先移除所有的点击样式 | ||
+ | for (let j = 0; j < len; j++) { | ||
+ | liTags[j].classList.remove("active"); | ||
+ | } | ||
+ | //再添加点击样式 | ||
+ | let li = e.currentTarget; | ||
+ | li.classList.add("active"); | ||
+ | } | ||
+ | } | ||
+ | </script> | ||
</html> | </html> |
Revision as of 15:42, 15 October 2021
MODEL
In order to scientifically determine the transformation efficiency of our modified
L. casei (KO) and the wild L. casei (Wild), we collected the colony cultured which were pre-spread plates
with different volumes of bacteria solutions and measured their OD600 after cultured for the same
hours. In
the meantime, we also aimed to explore the optimal condition for our modified L. casei’ growth by applying
different amounts of the bacteria seed solution.
Table 1. OD600 of cultured L. casei
![](https://static.igem.org/mediawiki/2021/f/f0/T--Shanghai_HS_ID--model01.png)
According to the scatter plots, we chose to use the quadratic polynomial equation
to build the model :
![](https://static.igem.org/mediawiki/2021/b/bd/T--Shanghai_HS_ID--model02.png)
The coding we used 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
”
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
”
After calculation, below are the constants of the solved quadratic polynomial
equations of 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 |
![](https://static.igem.org/mediawiki/2021/0/06/T--Shanghai_HS_ID--model03.png)
Conclusion
In figure 1, we can clearly see that the modified L. casei shows much higher
transformation efficiency than the wild L. casei especially when the volume of the initial bacteria seed
solution is used less than 100 uL when the difference between them is remarkable.
Solution
We constructed a plasmid equipped with a CRISPR-Cas9 complex that cuts and removes
a selected segment of the L. casei DNA. Our target gene is LSEI-2094. This gene is involved in the synthesis
of an enzyme that is essential in the restriction-modification system [5]. The cell's efforts to repair its
DNA induces mutations, which help to inactivate the gene and prevent the production of the enzyme. After
this modification foreign DNAs could enter and express themselves much more efficiently in L.Casei.With a
strain of bacteria ready to be tailored to our needs, the benefits are immeasurable. The benefits of L.
caseicould come to fruition if the technology is applied to popular and impactful industries such as
pharmaceuticals and food.
Besides, the equation model we built for the modified L. casei as showing below,
could be used to analyze the relationship between the volume of the bacteria seed solution and its
OD600, it
could be used as a reference when we conduct the expression efficiency tests in the future. If we could
further build the relationship between the expression level and OD600, we could adjust the volume
of the
bacteria seed solution for culturing accordingly.
Model for the modified L. casei: f(x) =
0.0003x3 -
0.0103x2 + 0.0230