Difference between revisions of "Team:Bielefeld-CeBiTec"

 
(4 intermediate revisions by one other user not shown)
Line 1: Line 1:
 
{{Template:Bielefeld-CeBiTec/header}}
 
{{Template:Bielefeld-CeBiTec/header}}
 
<html>
 
<html>
 +
<style>
 +
 +
 +
.equalheight {
 +
overflow: hidden;
 +
position:relative;
 +
}
 +
.equal {
 +
margin-bottom: -99999px;
 +
padding-bottom: 99999px;
 +
position:relative;
 +
}
 +
.space_around{
 +
height:70px;
 +
}
 +
 +
 +
 +
</style>
  
  
Line 7: Line 26:
 
<!--<div class="row">-->
 
<!--<div class="row">-->
 
     <center>
 
     <center>
−
<img class="picture" src="https://static.igem.org/mediawiki/2016/0/03/Bielefeld_CeBiTec_2016_10_13_X_Evobodies_animation.gif" >
+
<img style="heigth:100px;" class="picture" src="https://static.igem.org/mediawiki/2016/0/03/Bielefeld_CeBiTec_2016_10_13_X_Evobodies_animation.gif" >
 
</center>
 
</center>
−
<div class="container text">We developed a novel and easy to use system for the generation of binding proteins in <i>E. coli</i> via <i>in vivo</i> directed evolution. Resulting proteins called Evobodies have the potential to bind specific to target proteins enabling varies medical and analytical applications. Big advantages of our low-cost system are the short hands on time and the short generation time.
 
 
<br>
 
<br>
 +
<div class="container text">We developed a novel and easy to use system for the generation of binding proteins in <i>E. coli</i> via <i>in vivo</i> directed evolution. Resulting proteins called Evobodies have the potential to bind specifically to target proteins enabling various medical and analytical applications. Great advantages of our low-cost system are the short hands on time and the short generation time.
 +
 +
 +
 +
 
<br>
 
<br>
−
As the starting point of our system, we designed and synthesized a library of a new entity of BioBricks encoding binding proteins in <i>E. coli</i> based on Nanobodies as well as Monobodies. The diversity of the library in <i>E. coli</i> is continuously increased by co-expressing a special DNA-Polymerase conferring plasmid restricted error-prone replication of the binding protein expressing plasmids. Finally, binding proteins with high affinity to the target protein are selected using a bacterial two-hybrid system providing growth advantage to antibiotics in relation to protein-protein interaction strength. Ultimately, desired clones are enriched during fermentation in batch or in continuous culture.
+
<br>
 +
As the starting point of our system, we designed and synthesized genetic libraries encoding binding proteins based on Nanobodies as well as Monobodies.  
 +
The diversity of the respective library in <i>E. coli</i> is continuously increased by co-expressing a special DNA-Polymerase conferring plasmid restricted error-prone replication of the binding protein expressing plasmids.
 +
Finally, binding proteins with high affinity to the target protein are selected using a bacterial two-hybrid system providing growth advantage to antibiotics in relation to protein-protein interaction strength. Ultimately, desired clones are enriched during fermentation in batch or in continuous culture.
 
<br>
 
<br>
 
<br>  
 
<br>  
−
Binding capacities of our libraries, efficiency of our selection system and potential of our mutagenesis system were demonstrated. Moreover, library diversity and mutation system characteristics were analyzed in detail by high-throughput sequencing.
+
Binding capability of our libraries, efficiency of our selection system and potential of our mutagenesis system were demonstrated. Moreover, library diversity and mutation system characteristics were analyzed in detail by high-throughput sequencing.  
 +
<br>
 
</div>
 
</div>
  
Line 50: Line 77:
 
</a>
 
</a>
 
</div>-->
 
</div>-->
 +
<br>
 
<div class="row">
 
<div class="row">
 
<div class="col-md-12 ">
 
<div class="col-md-12 ">
Line 57: Line 85:
 
 
 
</div>
 
</div>
 +
<br>
 +
<br>
  
 
 
−
<div class="row">
+
<div class="row equalheight">
 
<div class="col-xs-6 col-md-6">
 
<div class="col-xs-6 col-md-6">
 
<div class="thumbnail">  
 
<div class="thumbnail">  
−
<div class="row">
+
<div class="row equal" id="top_left">
−
<div class="col-xs-7 col-md-7">  
+
<div class="col-xs-3 col-md-3 ">  
 
<figure class="figure">
 
<figure class="figure">
−
<a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Library"><img class="picture figure-image" src="https://static.igem.org/mediawiki/2016/c/c9/Bielefeld_CeBiTec_2016_10_18_LIB_project_overview_library.png" /> </a>
+
<a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Library"><img class="picture figure-image" src="https://static.igem.org/mediawiki/2016/c/c9/Bielefeld_CeBiTec_2016_10_18_LIB_project_overview_library.png" /> </a>
 
</figure>
 
</figure>
 
</div>
 
</div>
−
<div class="col-xs-5 col-md-5">
+
<div class="col-xs-9 col-md-9">
 
<h3 class="textHeadline"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Library"
 
<h3 class="textHeadline"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Library"
 
>Library</a></h3>
 
>Library</a></h3>
Line 79: Line 109:
 
<div class="col-xs-6 col-md-6">
 
<div class="col-xs-6 col-md-6">
 
<div class="thumbnail">  
 
<div class="thumbnail">  
−
<div class="row">
+
<div class="row equal" id="top_right">
−
<div class="col-xs-7 col-md-7">  
+
<div class="col-xs-3 col-md-3">  
−
<a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Mutation"><img class="picture" src="https://static.igem.org/mediawiki/2016/d/d4/Bielefeld_CeBiTec_2016_10_14_project_description_mutation.png" />
+
<a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Mutation"><img class="picture" src="https://static.igem.org/mediawiki/2016/d/d4/Bielefeld_CeBiTec_2016_10_14_project_description_mutation.png" />
 
</div>
 
</div>
−
<div class="col-xs-5 col-md-5">
+
<div class="col-xs-9 col-md-9">
−
<h3 class="textHeadline"> <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Mutation">Mutation</a> </h3>
+
<h3 class="textHeadline"> <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Mutation">Mutation</a> </h3>
 
<p class="stdText"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Mutation">Overview</a><br><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Mutation">Results</a></p>
 
<p class="stdText"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Mutation">Overview</a><br><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Mutation">Results</a></p>
 
</div>
 
</div>
Line 94: Line 124:
 
<div class="col-xs-6 col-md-6">
 
<div class="col-xs-6 col-md-6">
 
<div class="thumbnail">  
 
<div class="thumbnail">  
−
<div class="row">
+
<div class="row" id="botton_left">
−
<div class="col-xs-7 col-md-7">  
+
<div class="col-xs-3 col-md-3">  
−
<a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Selection"><img class="picture" src="https://static.igem.org/mediawiki/2016/9/9e/Bielefeld_CeBiTec_2016_10_14_project_description_selection.png" /></a>
+
<a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Selection/Motivation"><img class="picture" src="https://static.igem.org/mediawiki/2016/9/9e/Bielefeld_CeBiTec_2016_10_14_project_description_selection.png" /></a>
−
</div>
+
</div>
−
<div class="col-xs-5 col-md-5">
+
<div class="col-xs-9 col-md-9">
−
<h3 class="textHeadline"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Selection">Selection</a></h3>
+
<h3 class="textHeadline"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Selection/Motivation">Selection</a></h3>
−
<p class="stdText"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Selection">Overview</a><br><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Selection">Results</a></p>
+
<p class="stdText"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Selection/Motivation">Overview</a><br><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Selection">Results</a></p>
 
</div>
 
</div>
 
</div>
 
</div>
Line 107: Line 137:
 
<div class="col-xs-6 col-md-6">
 
<div class="col-xs-6 col-md-6">
 
<div class="thumbnail">  
 
<div class="thumbnail">  
−
<div class="row">
+
<div class="row" id="bottom_right">
−
<div class="col-xs-7 col-md-7">  
+
<div class="col-xs-3 col-md-3">  
−
<a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Model"><img class="picture" src="https://static.igem.org/mediawiki/2016/6/6b/Bielefeld_CeBiTec_2016_10_16_Mod_3D.png
+
<a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Model"><img class="picture" src="https://static.igem.org/mediawiki/2016/d/db/Bielefeld_CeBiTec_2016_10_16_Mod_3D_2.png
 +
 
 
" /></a>
 
" /></a>
 
</div>
 
</div>
−
<div class="col-xs-5 col-md-5">
+
<div class="col-xs-9 col-md-9">
 
<h3 class="textHeadline"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Model"> Modeling</a></h3>
 
<h3 class="textHeadline"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Model"> Modeling</a></h3>
 
<p class="stdText"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Model">Overview</a><br><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Modeling">Results</a></p>
 
<p class="stdText"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Model">Overview</a><br><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Modeling">Results</a></p>
Line 127: Line 158:
 
      
 
      
 
     <tbody style="border:none;">
 
     <tbody style="border:none;">
−
<tr style="border:none;">
+
        <tr style="border:none;">
 
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
 
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
−
<td style="text-align:left; border:none;">Establishment of <i>in vivo</i> <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Mutation" target="_blank">mutagenesis systems</a> for the iGEM community </td>
+
<td style="text-align:left; border:none;">
 +
Design and construction of an <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Library/Overview" target="_blank">Evobody library</a> and invention of a new BioBrick class  </td>
 
</tr>
 
</tr>
 +
<tr style="border:none;">
 +
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
 +
<td style="text-align:left; border:none;">
 +
Over 100,000 clones per <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Library/Overview" target="_blank">library</a> generated  </td>
 +
</tr>
 +
 +
</tr>
 +
<tr style="border:none;">
 +
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
 +
<td style="text-align:left; border:none;">
 +
High diversity of the plasmid library confirmed by <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Library/Sequencing" target="_blank">high-throughput sequencing </a> </td>
 +
</tr>
 +
 +
<tr style="border:none;">
 +
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
 +
<td style="text-align:left; border:none;">
 +
Functionality of the <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Library/Phage" target="_blank">library </a>  was demonstrated by binding to various targets </td>
 +
</tr>
 +
 +
 +
 
<tr style="border:none;">
 
<tr style="border:none;">
 
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
 
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
−
<td style="text-align:left; border:none;">Design and construction of a <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Library/Overview" target="_blank">library</a> </td>
+
<td style="text-align:left; border:none;">Construction and detailed characterization via high-throughput sequencing of a plasmid-specific <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Mutation" target="_blank"> mutagenesis system </a> </td>
 
</tr>
 
</tr>
 +
 +
<tr style="border:none;">
 +
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
 +
<td style="text-align:left; border:none;">
 +
Construction and characterization of several parts for <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Mutation/Reversion" target="_blank"> reversion assays </a>  </td>
 +
</tr>
 +
 +
 +
 +
 +
<tr style="border:none;">
 +
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
 +
<td style="text-align:left; border:none;">
 +
Plasmid sequence improvement by <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Mutation/Sequencing" target="_blank"> re-sequencing </a> and  <i>de novo</i> assembly  </td>
 +
</tr>
 +
 +
 
<tr style="border:none;">
 
<tr style="border:none;">
 
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
 
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
−
<td style="text-align:left; border:none;">Establishment of a functional <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Selection" target="_blank">selection system</a> </td>
+
<td style="text-align:left; border:none;">Construction and characterization of a <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Selection" target="_blank"> bacterial two-hybrid selection system </a> </td>
 
</tr>
 
</tr>
 
<tr style="border:none;">
 
<tr style="border:none;">
 
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
 
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
−
<td style="text-align:left; border:none;"> <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Model" target="_blank">Predict</a> how our system work</td>
+
<td style="text-align:left; border:none;"> <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Modeling" target="_blank">
 +
Prediction </a> of the outcome of our system</td>
 
</tr>
 
</tr>
 
<tr style="border:none;">
 
<tr style="border:none;">
 
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
 
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
−
<td style="text-align:left; border:none;"> Several <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Human_Practices" target="_blank">human practice projects</a> </td>
+
<td style="text-align:left; border:none;"> <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Human_Practices" target="_blank">
 +
Evolution-based human practice projects </a> were perfectly integrated</td>
 +
</tr>
 +
<tr style="border:none;">
 +
<td style="border:none; width:20px"><img src="https://static.igem.org/mediawiki/2016/4/48/Bielefeld_CeBiTec_2016_10_18_XXXX_tick.png" class="check" width="40px"></td>
 +
<td style="text-align:left; border:none;">
 +
Concept development for  <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Entrepreneurship" target="_blank">industrial upscaling</a> </td>
 
</tr>
 
</tr>
  
Line 151: Line 228:
 
   </table>
 
   </table>
 
</div>
 
</div>
 +
 +
 +
 +
 +
 +
  
 
   </div>
 
   </div>
Line 156: Line 239:
  
 
  </div>
 
  </div>
 +
 
   
 
   
  
  
 
</html>
 
</html>

Latest revision as of 16:24, 1 December 2016




We developed a novel and easy to use system for the generation of binding proteins in E. coli via in vivo directed evolution. Resulting proteins called Evobodies have the potential to bind specifically to target proteins enabling various medical and analytical applications. Great advantages of our low-cost system are the short hands on time and the short generation time.

As the starting point of our system, we designed and synthesized genetic libraries encoding binding proteins based on Nanobodies as well as Monobodies. The diversity of the respective library in E. coli is continuously increased by co-expressing a special DNA-Polymerase conferring plasmid restricted error-prone replication of the binding protein expressing plasmids. Finally, binding proteins with high affinity to the target protein are selected using a bacterial two-hybrid system providing growth advantage to antibiotics in relation to protein-protein interaction strength. Ultimately, desired clones are enriched during fermentation in batch or in continuous culture.

Binding capability of our libraries, efficiency of our selection system and potential of our mutagenesis system were demonstrated. Moreover, library diversity and mutation system characteristics were analyzed in detail by high-throughput sequencing.



Achievements

Design and construction of an Evobody library and invention of a new BioBrick class
Over 100,000 clones per library generated
High diversity of the plasmid library confirmed by high-throughput sequencing
Functionality of the library was demonstrated by binding to various targets
Construction and detailed characterization via high-throughput sequencing of a plasmid-specific mutagenesis system
Construction and characterization of several parts for reversion assays
Plasmid sequence improvement by re-sequencing and de novo assembly
Construction and characterization of a bacterial two-hybrid selection system
Prediction of the outcome of our system
Evolution-based human practice projects were perfectly integrated
Concept development for industrial upscaling