Difference between revisions of "Team:Peking/Improve"

 
(30 intermediate revisions by 5 users not shown)
Line 66: Line 66:
 
             position: relative;
 
             position: relative;
 
         }
 
         }
 +
        #page-wrap a:hover {color:#6495ED;}
 
          
 
          
 
         #sidebar {
 
         #sidebar {
Line 169: Line 170:
 
          
 
          
 
         .coll p a{
 
         .coll p a{
−
             color:#5c9085 !important;
+
             color:#6495ED !important;
 
         }
 
         }
 
         .coll p a:hover{
 
         .coll p a:hover{
−
             color:#11abb0 !important;
+
             color:#6495ED!important;
 
         }
 
         }
 
         .coll {
 
         .coll {
Line 282: Line 283:
 
                 <div class="twelve columns centered text-center">
 
                 <div class="twelve columns centered text-center">
 
                     <h1>Improvement</h1>
 
                     <h1>Improvement</h1>
−
                    <p class="title1" style="text-align:center">In this section, you could see the Improvement.</p>
+
                 
 
                 </div>
 
                 </div>
 
             </div>
 
             </div>
Line 299: Line 300:
 
                             <div id="page-wrap">
 
                             <div id="page-wrap">
 
                                 <div id="sidebar" style="color:#000000">
 
                                 <div id="sidebar" style="color:#000000">
−
                                     <h4><a href="javascript:void(0);" onclick="naver('A')">Overview</a></h4>
+
                                     <h4><a href="javascript:void(0);" onclick="naver('A')">&bull;Fused&nbsp;with&nbsp;yEGFP</a></h4>
−
                                    <h4><a href="javascript:void(0);" onclick="naver('B')">Phase&nbsp;Separation</a></h4>
+
                                     <h4><a href="javascript:void(0);" onclick="naver('B')">&bull;Phase&nbsp;Separation</a></h4>
−
                                    <ul>
+
                   
−
                                        <li><a href="javascript:void(0);" onclick="naver('B1')">Spontaneous</a></li>
+
−
                                        <li><a href="javascript:void(0);" onclick="naver('B2')">The&nbsp;formation</a></li>
+
−
                                    </ul>
+
−
                                     <h4><a href="javascript:void(0);" onclick="naver('C')">Functional&nbsp;Organelles</a></h4>
+
−
                                    <h4><a href="javascript:void(0);" onclick="naver('D')">Perspective</a></h4>
+
 
                                 </div>
 
                                 </div>
 
                             </div>
 
                             </div>
Line 316: Line 312:
 
                         <div class="nine columns">
 
                         <div class="nine columns">
 
                              
 
                              
−
                             <div class="texttitle">Fuse with yEGFP
+
                             <div class="texttitle">Fused with yEGFP
 
<a id="A"></a></div>  
 
<a id="A"></a></div>  
 
                             <hr style="border:2px dashed; height:2px" color="#666666">
 
                             <hr style="border:2px dashed; height:2px" color="#666666">
Line 323: Line 319:
 
                                  
 
                                  
 
                                 <div class="content">
 
                                 <div class="content">
−
                                     <p>We fuse part <a href="http://parts.igem.org/Part:BBa_K209496">BBa_K209496</a> (Frb) and <a href="http://parts.igem.org/Part:BBa_K209496">BBa_K209023</a> (FKBP) with yEGFP, which make it visible in the yeast under fluorescent microscope. Then we got part<a href="http://parts.igem.org/Part:BBa_K2601008">BBa_K2601008(FKBP-yEGFP)</a> and <a href="http://parts.igem.org/Part:BBa_K2601007">BBa_K2601007(Frb-yEGFP).</a> </p>
+
                                     <p>We fused part Frb<a href="http://parts.igem.org/Part:BBa_K209496"> (BBa_K209496) </a> and FKBP<a href="http://parts.igem.org/Part:BBa_K209023"> (BBa_K209023) </a>with yEGFP, which made it visible in the yeast under fluorescent microscope. Then we got part Frb-yEGFP<a href="http://parts.igem.org/Part:BBa_K2601007"> (BBa_K2601007) </a> and FKBP-yEGFP<a href="http://parts.igem.org/Part:BBa_K2601008"> (BBa_K2601008) </a>.</p>
 
                                 </div>
 
                                 </div>
 
                             </div>
 
                             </div>
Line 335: Line 331:
 
                                  
 
                                  
 
                                 <div class="content">
 
                                 <div class="content">
−
                                     <p>Afterward, we drive the expression of FKBP-yEGFP and Frb-yEGFP with 4 promoters pUra3, pTet07,pTEF1 and PDH3. The expression of these promoters were measure by flow cytometry(Fig. 1). We then got prats <a href="http://parts.igem.org/Part:BBa_K2601021">BBa_K2601021 (Tet07-Frb-yEGFP)</a>, <a href="http://parts.igem.org/Part:BBa_K2601023"> K2601023 (PDH3-Frb-yEGFP)</a>, <a href="http://parts.igem.org/Part:BBa_K2601025">BBa_K2601025 (Tet07-FKBP-yEGFP)</a>, <a href="http://parts.igem.org/Part:BBa_K2601026">BBa_K2601026 (TEF1-FKBP-yEGFP)</a>, <a href="http://parts.igem.org/Part:BBa_K2601027">K2601027 (PDH3-FKBP-yEGFP)</a>. </p>
+
                                     <p>Then we characterized the expression of Frb-yEGFP and FKBP-yEGFP with 4 promoters pUra3, pTet07, pTEF1 and PDH3. The expression of these promoters was measured through flow cytometry (Fig. 1).  
 +
<br/>
 +
We made these improved prats:
 +
<br/>
 +
Tet07-Frb-yEGFP<a href="http://parts.igem.org/Part:BBa_K2601021"> (BBa_K2601021) </a>;
 +
<br/>
 +
PDH3-Frb-yEGFP<a href="http://parts.igem.org/Part:BBa_K2601023"> (BBa_K2601023) </a>;
 +
<br/>
 +
Tet07-FKBP-yEGFP<a href="http://parts.igem.org/Part:BBa_K2601025"> (BBa_K2601025) </a>;
 +
<br/>
 +
TEF1-FKBP-yEGFP<a href="http://parts.igem.org/Part:BBa_K2601026"> (BBa_K2601026) </a>;
 +
<br/>
 +
PDH3-FKBP-yEGFP<a href="http://parts.igem.org/Part:BBa_K2601027"> (BBa_K2601027) </a>.
 +
</p>
 +
<br/>
 +
<img src="https://static.igem.org/mediawiki/parts/f/f7/T--Peking--promoter-strength-new.png">
 +
<br/>
 +
<p>Figure. 1 The strength of three different yeast promoters tested through flow cytometry.</p>
 +
 
  
 
                                 </div>
 
                                 </div>
Line 343: Line 357:
 
                                     <p></a></p><br/><br/><br/>       
 
                                     <p></a></p><br/><br/><br/>       
 
                                 </div>
 
                                 </div>
−
                            </div>
+
 
−
         
+
          <div class="texttitle">Phase separation system
 +
<a id="B"></a></div>  
 +
                            <hr style="border:2px dashed; height:2px" color="#666666">
 
  <div class="coll">
 
  <div class="coll">
 
                                  
 
                                  
 
                                 <div class="content">
 
                                 <div class="content">
−
                                     <p>What's more, we fused Frb-yEGFP with HOtag6 and fused FKBP-yEGFP with HOtag3. These two parts can form phase separation in the presence of rapamycin (Fig. 2). The original part <a href="http://parts.igem.org/Part:BBa_K209496">BBa_K209496</a> (Frb) and <a href="http://parts.igem.org/Part:BBa_K209496">BBa_K209023</a> (FKBP) have not this function. We uploaded 2 parts: <a href="http://parts.igem.org/Part:BBa_K2601010">BBa_K2601010</a> (Frb-yEGFP-HOTag6) and <a href="http://parts.igem.org/Part:BBa_K2601011">BBa_K2601011</a> (FKBP-yEGFP-HOTag3).<br/>
+
                                     <p>Moreover, we fused Frb-yEGFP with HOtag6 and FKBP-yEGFP with HOtag3. These parts can form phase separation in the presence of rapamycin (Fig. 2). The original part Frb<a href="http://parts.igem.org/Part:BBa_K209496"> (BBa_K209496) </a>and FKBP<a href="http://parts.igem.org/Part:BBa_K209023"> (BBa_K209023) </a>doesn't have this function.  
 +
<br/>
 +
We uploaded 2 parts:
 +
<br/>
 +
Frb-yEGFP-HOTag6<a href="http://parts.igem.org/Part:BBa_K2601010"> (BBa_K2601010) </a>;
 +
<br/>
 +
FKBP-yEGFP-HOTag3<a href="http://parts.igem.org/Part:BBa_K2601011"> (BBa_K2601011) </a>.
 +
</p>
 +
<br/>
 +
<img src="https://static.igem.org/mediawiki/2018/9/97/T--Peking--Demof4.png">
 +
<br/>
 +
<figcaption style="text-align:justify; text-justify:inter-ideograph;">
 +
<br/>
 +
<br/>
 +
Figure. 2  The improvement of Frb and FKBP fused with yEGFP.
 +
<br/>
 +
Figure. 2A The structure of Frb and FKBP. Rapamycin induces the interaction between them.
 +
<br/>
 +
Figure. 2B Design of RapaSPOT. FKBP is fused with mCherry and HOTag3 while Frb is fused with yEGFP and HOTag6. After adding rapamycin, they are expected self-organizing to form large assemblies, which will be organelles in cells.
 +
<br/>
 +
Figure. 2C Granules formed in chemical-induced SPOT after adding rapamycin. Ura3-FKBP-HOTag3 with mCherry and PDH3-Frb-HOTag6 with yEGFP are transferred and expressed in S. cerevisiae. Fluorescence images in both GFP and mCherry channels of cells are taken after adding 10 μM Figure. 2D Growth curves of wild-type yeast (black curve) and yeast strains of Ura3-FKBP-HOTag3 and PDH3-Frb-HOTag6 (red curve). They are measured after adding different concentration of rapamycin for 24 hours. Wild-type yeast cannot grow and reproduce normally while recombination yeast strains of FKBP-HOTag3 and Frb-HOTag6 can survive when exposed to rapamycin.
 +
<br/><br/><br/>
 +
<p>
 +
Then we characterized the expression of Frb-yEGFP-HOTag6 with 3 promoters pUra3, pTEF1 and PDH3. As our <a href="https://2018.igem.org/Team:Peking/Model">Modeling</a> work predicts, the kinetics of a system depends on the concentration of the components and the interaction strength(Fig .3). We successfully uploaded 5 parts form them:
 +
<br/>
 +
pTet07-Frb-yEGFP-HOTag6<a href="http://parts.igem.org/Part:BBa_K2601032"> (BBa_K2601032) </a>;
 +
<br/>
 +
pTEF1-Frb-yEGFP-HOTag6<a href="http://parts.igem.org/Part:BBa_K2601033"> (BBa_K2601033) </a>;
 +
<br/>
 +
PDH3-Frb-yEGFP-HOTag6<a href="http://parts.igem.org/Part:BBa_K2601034"> (BBa_K2601034) </a>;
 +
<br/>
 +
pTEF1-FKBP-yEGFP-HOTag3<a href="http://parts.igem.org/Part:BBa_K2601011"> (BBa_K2601011) </a>;
 +
<br/>
 +
PDH3-yEGFP-HOTag3<a href="http://parts.igem.org/Part:BBa_K2601011"> (BBa_K2601011) </a>.
 +
</p>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<br/>
  
−
Then, we drive the expression of Frb-yEGFP-HOTag6 with 3 promoters pUra3, pTEF1 and PDH3. As our <a href="https://2018.igem.org/Team:Peking/Model">Modeling</a> work predicts, the kinetics of a system depends on the concentration of the components and the interaction strength(Fig .3).
 
 
<img src="https://static.igem.org/mediawiki/2018/d/d8/T--Peking--Demof5.png"><br/>
 
<img src="https://static.igem.org/mediawiki/2018/d/d8/T--Peking--Demof5.png"><br/>
 
<figcaption style="text-align:justify; text-justify:inter-ideograph;">
 
<figcaption style="text-align:justify; text-justify:inter-ideograph;">
−
Figure. 3A The formation of SPOT can be described as a phase separation process of three components. Two important variable, the concentration of components and the interaction strength are marked in the figure.
+
Figure. 3  The improvement of Frb and FKBP fused with yEGFP regulated by four kinds of promoters.  
 
<br/>
 
<br/>
−
Figure. 3B Flow Cytometry results of three promoters (Ura3, Tef2, and PDH3). The expression level of Ura3 is lowest while PDH3 is the strongest promoter.
+
Figure. 3A The formation of SPOT can be described as a phase separation process of three components. Two important variables, the concentration of components and the interaction strength are marked in the figure.
 
<br/>
 
<br/>
−
Figure. 3C RapaSPOT of different promoter combinations after 10 μM rapamycin induction. Two axes stand for the expression level of components. After 3 hours, Only SPOT system with high level of Frb can be observed.
+
Figure. 3B Flow cytometry results of three promoters (pUra3, pTEF2, and PDH3). The expression level of Ura3 is the lowest while PDH3 is the strongest promoter.
 
<br/>
 
<br/>
−
Figure. 3D Proportion of yeasts with granules after rapamycin induction. The rapamycin is from 1μM to 100 μM.
+
Figure. 3C RapaSPOT of different promoter combinations after 10 μM rapamycin induction. Two axes stand for the expression level of components. After 3 hours, only SPOT system with high level of Frb can be observed.
 +
Figure. 3D Proportion of yeast with granules after rapamycin induction. The rapamycin concentration range is from 1μM to 100 μM.
 
</figcaption>
 
</figcaption>
  
 
<br/>
 
<br/>
 +
 +
<p>
 
  </p>
 
  </p>
  
Line 436: Line 494:
 
                     <ul class="copyright">
 
                     <ul class="copyright">
 
                         <!--<li>&copy; 2014 Sparrow</li> -->
 
                         <!--<li>&copy; 2014 Sparrow</li> -->
−
                         <li><a href="https://2018.igem.org/Team:Peking">Home</a>&nbsp;&nbsp;&nbsp;<a href="mailto:indigomad@pku.edu.cn">Contact</a></li>
+
                         <li><a href="https://2018.igem.org/Team:Peking">Home</a>&nbsp;&nbsp;&nbsp;<a href="mailto:pekingigem2018@126.com">Contact</a></li>
 
                         <span> &copy;2018 PEKING IGEM. All Rights Reserved.</span>
 
                         <span> &copy;2018 PEKING IGEM. All Rights Reserved.</span>
 
                         <li><a href="http://getbootstrap.com/2.3.2/">Based on Bootstrap</a></li>
 
                         <li><a href="http://getbootstrap.com/2.3.2/">Based on Bootstrap</a></li>

Latest revision as of 00:27, 18 October 2018

Improvement

Fused with yEGFP

We fused part Frb (BBa_K209496) and FKBP (BBa_K209023) with yEGFP, which made it visible in the yeast under fluorescent microscope. Then we got part Frb-yEGFP (BBa_K2601007) and FKBP-yEGFP (BBa_K2601008) .

Then we characterized the expression of Frb-yEGFP and FKBP-yEGFP with 4 promoters pUra3, pTet07, pTEF1 and PDH3. The expression of these promoters was measured through flow cytometry (Fig. 1).
We made these improved prats:
Tet07-Frb-yEGFP (BBa_K2601021) ;
PDH3-Frb-yEGFP (BBa_K2601023) ;
Tet07-FKBP-yEGFP (BBa_K2601025) ;
TEF1-FKBP-yEGFP (BBa_K2601026) ;
PDH3-FKBP-yEGFP (BBa_K2601027) .



Figure. 1 The strength of three different yeast promoters tested through flow cytometry.




Phase separation system

Moreover, we fused Frb-yEGFP with HOtag6 and FKBP-yEGFP with HOtag3. These parts can form phase separation in the presence of rapamycin (Fig. 2). The original part Frb (BBa_K209496) and FKBP (BBa_K209023) doesn't have this function.
We uploaded 2 parts:
Frb-yEGFP-HOTag6 (BBa_K2601010) ;
FKBP-yEGFP-HOTag3 (BBa_K2601011) .





Figure. 2 The improvement of Frb and FKBP fused with yEGFP.
Figure. 2A The structure of Frb and FKBP. Rapamycin induces the interaction between them.
Figure. 2B Design of RapaSPOT. FKBP is fused with mCherry and HOTag3 while Frb is fused with yEGFP and HOTag6. After adding rapamycin, they are expected self-organizing to form large assemblies, which will be organelles in cells.
Figure. 2C Granules formed in chemical-induced SPOT after adding rapamycin. Ura3-FKBP-HOTag3 with mCherry and PDH3-Frb-HOTag6 with yEGFP are transferred and expressed in S. cerevisiae. Fluorescence images in both GFP and mCherry channels of cells are taken after adding 10 μM Figure. 2D Growth curves of wild-type yeast (black curve) and yeast strains of Ura3-FKBP-HOTag3 and PDH3-Frb-HOTag6 (red curve). They are measured after adding different concentration of rapamycin for 24 hours. Wild-type yeast cannot grow and reproduce normally while recombination yeast strains of FKBP-HOTag3 and Frb-HOTag6 can survive when exposed to rapamycin.


Then we characterized the expression of Frb-yEGFP-HOTag6 with 3 promoters pUra3, pTEF1 and PDH3. As our Modeling work predicts, the kinetics of a system depends on the concentration of the components and the interaction strength(Fig .3). We successfully uploaded 5 parts form them:
pTet07-Frb-yEGFP-HOTag6 (BBa_K2601032) ;
pTEF1-Frb-yEGFP-HOTag6 (BBa_K2601033) ;
PDH3-Frb-yEGFP-HOTag6 (BBa_K2601034) ;
pTEF1-FKBP-yEGFP-HOTag3 (BBa_K2601011) ;
PDH3-yEGFP-HOTag3 (BBa_K2601011) .



Figure. 3 The improvement of Frb and FKBP fused with yEGFP regulated by four kinds of promoters.
Figure. 3A The formation of SPOT can be described as a phase separation process of three components. Two important variables, the concentration of components and the interaction strength are marked in the figure.
Figure. 3B Flow cytometry results of three promoters (pUra3, pTEF2, and PDH3). The expression level of Ura3 is the lowest while PDH3 is the strongest promoter.
Figure. 3C RapaSPOT of different promoter combinations after 10 μM rapamycin induction. Two axes stand for the expression level of components. After 3 hours, only SPOT system with high level of Frb can be observed. Figure. 3D Proportion of yeast with granules after rapamycin induction. The rapamycin concentration range is from 1μM to 100 μM.