Difference between revisions of "Team:Bielefeld-CeBiTec"

 
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<h2> Welcome to iGEM Bielefeld-CeBiTec 2016! </h2>
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<p>Your team has been approved and you are ready to start the iGEM season! </p>
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<h5> Abstract </h5>
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<p>We have created these wiki template pages to help you get started and to help you think about how your team will be evaluated. You can find a list of all the pages tied to awards here at the <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions">Pages for awards</a> link. You must edit these pages to be evaluated for medals and awards, but ultimately the design, layout, style and all other elements of your team wiki is up to you!</p>
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<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.
  
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<p>On this page you can document your project, introduce your team members, document your progress and share your iGEM experience with the rest of the world! </p>
 
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<p> <a href="https://2016.igem.org/wiki/index.php?title=Team:Example&action=edit"> Click here to edit this page! </a></p>
 
  
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As the starting point of our system, we designed and synthesized genetic libraries encoding binding proteins based on Nanobodies as well as Monobodies.
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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.
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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.
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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.
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<h5>Tips</h5>
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<p>This wiki will be your team’s first interaction with the rest of the world, so here are a few tips to help you get started: </p>
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<li>State your accomplishments! Tell people what you have achieved from the start. </li>
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<li>You have a global audience! Consider the different backgrounds that your users come from.</li>
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<li>Make sure information is easy to find; nothing should be more than 3 clicks away. </li>
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<li>Avoid using very small fonts and low contrast colors; information should be easy to read.  </li>
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<li>Start documenting your project as early as possible; don’t leave anything to the last minute before the Wiki Freeze. For a complete list of deadlines visit the <a href="https://2016.igem.org/Calendar">iGEM 2016 calendar</a> </li>
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<li>Have lots of fun! </li>
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<h5>Inspiration</h5>
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<p> You can also view other team wikis for inspiration! Here are some examples:</p>
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<li> <a href="https://2014.igem.org/Team:SDU-Denmark/"> 2014 SDU Denmark </a> </li>
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<li> <a href="https://2014.igem.org/Team:Aalto-Helsinki">2014 Aalto-Helsinki</a> </li>
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<li> <a href="https://2014.igem.org/Team:LMU-Munich">2014 LMU-Munich</a> </li>
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<li> <a href="https://2014.igem.org/Team:Michigan"> 2014 Michigan</a></li>
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<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>
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<li> <a href="https://2014.igem.org/Team:ITESM-Guadalajara">2014 ITESM-Guadalajara </a></li>
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<h3 class="textHeadline"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Library"
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>Library</a></h3>
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<p class="stdText"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Library"
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>Overview</a> <br><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Library/Overview">Results</a></p>
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<h3 class="textHeadline"> <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Mutation">Mutation</a> </h3>
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<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>
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<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>
 
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<h3 class="textHeadline"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Selection/Motivation">Selection</a></h3>
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<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>
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<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
  
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<h5> Uploading pictures and files </h5>
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When you upload, set the "Destination Filename" to <code>Team:YourOfficialTeamName/NameOfFile.jpg</code>. (If you don't do this, someone else might upload a different file with the same "Destination Filename", and your file would be erased!)</p>
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<h3 class="textHeadline"><a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Model"> Modeling</a></h3>
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<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>
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<div class="container text_header"><h3>Achievements</h3></div>
  
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<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>
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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>
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<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>
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Over 100,000 clones per <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Project/Library/Overview" target="_blank">library</a> generated  </td>
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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>
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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>
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<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>
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<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>
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<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>
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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>
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<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>
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<td style="text-align:left; border:none;">
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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>
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<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>
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<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>
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<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>
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<td style="text-align:left; border:none;"> <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Results/Modeling" target="_blank">
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Prediction </a> of the outcome of our system</td>
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<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>
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<td style="text-align:left; border:none;"> <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Human_Practices" target="_blank">
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Evolution-based human practice projects </a> were perfectly integrated</td>
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<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>
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<td style="text-align:left; border:none;">
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Concept development for  <a href="https://2016.igem.org/Team:Bielefeld-CeBiTec/Entrepreneurship" target="_blank">industrial upscaling</a> </td>
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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