Difference between revisions of "Team:Humboldt Berlin/Attributions"

 
(15 intermediate revisions by 3 users not shown)
Line 82: Line 82:
 
                         </div>
 
                         </div>
 
                         <div class="devider"></div>
 
                         <div class="devider"></div>
                         <a href="https://igem.org/2019_Judging_Form?team=Humboldt_Berlin">
+
                         <a href="/Team:Humboldt_Berlin/Achievements">
 
                             For Judges
 
                             For Judges
 
                         </a>
 
                         </a>
Line 117: Line 117:
 
                         <h3 class="headline3">Supporters</h3>
 
                         <h3 class="headline3">Supporters</h3>
 
                         <p class="block-text medium-sized">
 
                         <p class="block-text medium-sized">
                             Our team accomplished great things in the project <i>Chlamylicious</i> over the course of this year’s iGEM competition: We adapted a toolkit for the green algae <i>C. reinhardtii</i> with parts for successful and easy cloning of any transcription unit, which we implemented for the expression of the PET-degrading enzyme PETase by the algae and designed a bioreactor for its cultivation under constant monitoring of all parameters. These were our greatest supporters:
+
                             Our team accomplished great things in the project <i>Chlamylicious</i> over the course of this year’s iGEM competition: We adapted a toolkit for the green alga <i>C. reinhardtii</i> with parts for successful and easy cloning of any transcription unit, which we implemented for the expression of the PET-degrading enzyme PETase by the alga and designed a bioreactor for its cultivation under constant monitoring of all parameters. These were our greatest supporters:
 
                         </br>
 
                         </br>
 
                         <ul style="font-size:18px">
 
                         <ul style="font-size:18px">
                         <LI>our host laboratories <b>Experimental Biophysics and Molecular Genetics</b> from the Humboldt University of Berlin, who shared their infrastructure with us
+
                         <LI>our host laboratories <b>Experimental Biophysics and Molecular Genetics</b> from the Humboldt University of Berlin, who shared their infrastructure with us</li>
                       <LI>our supervisors <b>Prof. Dr. Schmitz-Linneweber and Prof. Dr. Hegemann</b>
+
                       <LI>our supervisors <b>Prof. Dr. Schmitz-Linneweber and Prof. Dr. Hegemann</b></li>
                         <LI>the principal investigator <b>Simon Kelterborn</b>, who guided us with his expertise in transformations of <i>Chlamydomonas</i> and CRISPR-aided genetic engineering
+
                         <LI>the principal investigator <b>Simon Kelterborn</b>, who guided us with his expertise in transformations of <i>Chlamydomonas</i> and CRISPR-aided genetic engineering</li>
                         <LI>the <b>biological technical assistants</b> Heide (Biophysics lab), Conny, Thea and Irina (all Genetics lab), who enabled us to launch the wet-lab
+
                         <LI>the <b>biological technical assistants</b> Irina, Heide (Biophysics lab), Conny, Thea and Irina (all Genetics lab), who enabled us to launch the wet-lab</li>
                         <LI>computer scientist <b>Vincent Will</b>, who implemented the design for our website
+
                         <LI>computer scientist <b>Vincent Will</b>, who implemented the design for our website</li>
                         <LI><b>Prof. Dr. Ringrose</b>, who coached us on how to create a good scientific poster
+
                        <LI><b>Dr. Ralf Steuer</b>, who helped us developing the bioreactor</li>
                         <LI>electrical engineer <b>Markus Schulz</b>, who helped designing and wiring the electronics for our bioreactor
+
                         <LI><b>Prof. Dr. Ringrose</b>, who coached us on how to create a good scientific poster</li>
                         <LI>technical engineering student <b>Alejandro Gómez Jiménez</b> from the Technical University of Berlin, who made the CAD-models for all parts of our bioreactor
+
                         <LI>electronic engineer <b>Markus Schulz</b>, who helped designing and wiring the electronics for our bioreactor</li>
                         <LI>the Interdisciplinary Workshop <b>„Matters of Activity“</b> of Humboldt University, who laser-cut our hardware
+
                         <LI>technical engineering student <b>Alejandro Gómez Jiménez</b> from the Technical University of Berlin, who made the CAD-models for all parts of our bioreactor</li>
                         <LI>the <b>Mechanical Workshop</b> of the Physics Department of our university
+
                         <LI>the Interdisciplinary Workshop <b>„Matters of Activity“</b> of Humboldt University, who laser-cut our hardware</li>
 +
                         <LI>the <b>Mechanical Workshop</b> of the Physics Department of our university</li>
 +
<LI><b>Dr. Nina Siragusa</b> from Merck KGaA, who presented us to her broad scientific network and supported our outreach</li>
 +
<LI><b>Arne Kuczmera</b> from the Berliner Wasserbetriebe, who supported our research at the waste water treatment plant</li>
 
                         </ul>
 
                         </ul>
 
                         </p>
 
                         </p>
 
</br>
 
</br>
<img src="https://static.igem.org/mediawiki/2019/b/b6/T--Humboldt_Berlin--attribution_thank_you.png"/>
 
 
                     </div>
 
                     </div>
 
              
 
              
Line 139: Line 141:
 
                 <!--------------------------------------- TWO COLUMN IMG LEFT END -----------------------------------------------></br></br>
 
                 <!--------------------------------------- TWO COLUMN IMG LEFT END -----------------------------------------------></br></br>
 
<div class="width-limit padding-container" style="width: 70%; margin-left:auto;margin-right:auto">
 
<div class="width-limit padding-container" style="width: 70%; margin-left:auto;margin-right:auto">
<p><b>Re-used parts from different sources</b></p>
+
<h3 class="headline3">Re-used parts from different sources</h3>
 
<table>
 
<table>
 
                                                     <tr>
 
                                                     <tr>
Line 147: Line 149:
 
                                                     <tr>
 
                                                     <tr>
 
                                                       <td style="padding-left: 15px">AR</td>
 
                                                       <td style="padding-left: 15px">AR</td>
                                                         <td>Plasmid p114, Hegemann lab (Biophysics Department, Humboldt University of Berlin)</td>
+
                                                         <td>Plasmid p114, Hegemann lab (Biophysics Department, Humboldt Universität zu Berlin)</td>
 
                                                     </tr>
 
                                                     </tr>
 
                                                     <tr>
 
                                                     <tr>
 
                                                       <td style="padding-left: 15px">ARS</td>
 
                                                       <td style="padding-left: 15px">ARS</td>
                                                         <td>Ordered oligos from IDT</br>Sequence:https://www.uniprot.org/blast/?about=A8ISJ6[1-26]&key=Signal%20peptide </td>
+
                                                         <td>Ordered oligos from IDT</br>Sequence: A8ISJ6[1-26] <i>(Uniprot)</i> </td>
 
                                                     </tr>
 
                                                     </tr>
 
                                                     <tr>
 
                                                     <tr>
 
                                                       <td style="padding-left: 15px">AmpOri </td>
 
                                                       <td style="padding-left: 15px">AmpOri </td>
                                                         <td>Amplified from MoClo plasmid <a href="https://www.addgene.org/48000/">pICH47732</a></td>
+
                                                         <td>Amplified from MoClo plasmid pICH47732 <i>(Addgene)</i></td>
 
                                                     </tr>
 
                                                     </tr>
 
                                                     <tr>
 
                                                     <tr>
Line 163: Line 165:
 
                                                     <tr>
 
                                                     <tr>
 
                                                       <td style="padding-left: 15px">GLE </td>
 
                                                       <td style="padding-left: 15px">GLE </td>
                                                         <td><a href="https://www.uniprot.org/blast/?about=Q93WN9[1-28]&key=Signal%20peptide">Uniprot Q93WN9[1 - 28]</a></td>
+
                                                         <td>Sequence: Q93WN9[1 - 28] <i>(Uniprot)</i> </td>
 
                                                     </tr>
 
                                                     </tr>
                                                     <tr>
+
                                                     <tr>  
 
                                                       <td style="padding-left: 15px">3xHA-Tag</td>
 
                                                       <td style="padding-left: 15px">3xHA-Tag</td>
 
                                                         <td>Ordered oligos from IDT</td>
 
                                                         <td>Ordered oligos from IDT</td>
Line 175: Line 177:
 
                                                     <tr>
 
                                                     <tr>
 
                                                       <td style="padding-left: 15px">Hyg</td>
 
                                                       <td style="padding-left: 15px">Hyg</td>
                                                         <td>Amplified from p360, Hegemann lab (Biophysics Department, Humboldt University of Berlin)</td>
+
                                                         <td>Amplified from p360, Hegemann lab (Biophysics Department, Humboldt Universität zu Berlin)</td>
 
                                                     </tr>
 
                                                     </tr>
 
                                                     <tr>
 
                                                     <tr>
Line 191: Line 193:
 
                                                     <tr>
 
                                                     <tr>
 
                                                       <td style="padding-left: 15px">Paro</td>
 
                                                       <td style="padding-left: 15px">Paro</td>
                                                         <td> Amplified from p114, Hegemann lab (Biophysics Department, Humboldt University of Berlin)
+
                                                         <td> Amplified from p114, Hegemann lab (Biophysics Department, Humboldt Universität zu Berlin)
 
</td>
 
</td>
 
                                                     </tr>
 
                                                     </tr>
Line 202: Line 204:
 
                                                       <tr>
 
                                                       <tr>
 
                                                         <td style="padding-left: 15px">PETase (<i>E. coli</i>)</td>
 
                                                         <td style="padding-left: 15px">PETase (<i>E. coli</i>)</td>
                                                           <td> <a href="https://www.addgene.org/112203/
+
                                                           <td> Adgene's plasmid: plasmid #112203</td>
">Adgene's plasmid: plasmid #112203</a></td>
+
 
   </td>
 
   </td>
 
                                                       </tr>
 
                                                       </tr>
Line 209: Line 210:
 
                                                     <tr>
 
                                                     <tr>
 
                                                       <td style="padding-left: 15px">PtxD</td>
 
                                                       <td style="padding-left: 15px">PtxD</td>
                                                         <td> Sequence: <a href="https://www.ncbi.nlm.nih.gov/nuccore/AF061070">AF061070.1</a></br>Ordered from GeneCust
+
                                                         <td> Sequence: AF061070.1 <i>(ncbi)</i></br>Ordered from GeneCust
 
                                                     </tr>
 
                                                     </tr>
 
                                                     <tr>
 
                                                     <tr>
 
                                                       <td style="padding-left: 15px">PsaD</td>
 
                                                       <td style="padding-left: 15px">PsaD</td>
                                                         <td>Plasmid 51, Hegemann lab (Biophysics Department, Humboldt University of Berlin)</td>
+
                                                         <td>Plasmid 51, Hegemann lab (Biophysics Department, Humboldt Universität zu Berlin)</td>
 
                                                     </tr>
 
                                                     </tr>
 
                                                     <tr>
 
                                                     <tr>
Line 225: Line 226:
 
                                                     <tr>
 
                                                     <tr>
 
                                                       <td style="padding-left: 15px">RFP</td>
 
                                                       <td style="padding-left: 15px">RFP</td>
                                                         <td>p42, Hegemann lab (Biophysics Department, Humboldt University of Berlin)</td>
+
                                                         <td>p42, Hegemann lab (Biophysics Department, Humboldt Universität zu Berlin)</td>
 
                                                     </tr>
 
                                                     </tr>
 
                                                     <tr>
 
                                                     <tr>
 
                                                       <td style="padding-left: 15px">Spec</td>
 
                                                       <td style="padding-left: 15px">Spec</td>
                                                         <td>Amplified from an Addgene MoClo Plasmid <a href="https://www.addgene.org/51833/">pAGM9121</a></td>
+
                                                         <td>Amplified from the MoClo Plasmid pAGM9121 <i>(Addgene)</i></td>
 
                                                     </tr>
 
                                                     </tr>
 
                                                     <tr>
 
                                                     <tr>
 
                                                       <td style="padding-left: 15px">YFP</td>
 
                                                       <td style="padding-left: 15px">YFP</td>
 
                                                         <td>Amplified from YFP Sequenz of p135 pCr3-Ble2-YFP-Sp-APH plasmid
 
                                                         <td>Amplified from YFP Sequenz of p135 pCr3-Ble2-YFP-Sp-APH plasmid
>pAGM9121</br>Overhang PCR: Amplification</a></td>
+
pAGM9121</br>Overhang PCR: Amplification</a></td>
 
                                                     </tr>
 
                                                     </tr>
 
                                                 </table>
 
                                                 </table>
Line 248: Line 249:
 
                             As the first team from the Humboldt University ever to form and participate in the iGEM competition we had to organize the following to establish <i>C. reinhardtii</i> as a chassis for synthetic biology in the iGEM community:</br>
 
                             As the first team from the Humboldt University ever to form and participate in the iGEM competition we had to organize the following to establish <i>C. reinhardtii</i> as a chassis for synthetic biology in the iGEM community:</br>
 
                         <UL style="font-size:18px">
 
                         <UL style="font-size:18px">
                         <LI>Find a professor and department able to supervise the iGEM project. As there is no course of synthetic biology taught at our university we referred to the Molecular Genetics and Biophysics lab groups.
+
                         <LI>Find a professor and department able to supervise the iGEM project. As there is no course of synthetic biology taught at our university we referred to the Molecular Genetics and Biophysics lab groups.</li>
                         <LI>Found a team of students, who were able to conduct the project research during their studies without earning credits for it. Our university so far does not offer any courses for the participation of students as an iGEM team. By <b>June 2018</b> the main core of our iGEM team was brought together.
+
                         <LI>Found a team of students, who were able to conduct the project research during their studies without earning credits for it. Our university so far does not offer any courses for the participation of students as an iGEM team. By <b>June 2018</b> the main core of our iGEM team was brought together.</li>
                         <LI>Brainstorm for interesting and viable SynBio projects, which took place in <b>July 2018</b>. Most of us had little or no prior knowledge in synthetic biology.
+
                         <LI>Brainstorm for interesting and viable SynBio projects, which took place in <b>July 2018</b>. Most of us had little or no prior knowledge in synthetic biology.</li>
                         <LI>Research more on the possibilities of <i>C. reinhardtii</i> as a SynBio tool and familiarize ourselves with project management conducts from <b>July-October 2018</b>. 
+
                         <LI>Research more on the possibilities of <i>C. reinhardtii</i> as a SynBio tool and familiarize ourselves with project management conducts from <b>July-October 2018</b>. </li>
                         <LI>Start fundraising initiatives in <b>July 2018</b>. 
+
                         <LI>Start fundraising initiatives in <b>July 2018</b>. </li>
                         <LI>Get part of the team started with working in the wet lab in <b>November 2018</b>.
+
                         <LI>Get part of the team started with working in the wet lab in <b>October 2018</b>.</li>
                         <LI>Organize Human Practice events and possibilities of outreach to the broader public from <b>November 2018 - October 2019</b>.
+
                         <LI>Organize Human Practice events and possibilities of outreach to the broader public from <b>November 2018 - October 2019</b>.</li>
                         <LI>Get a second lab team to finish the wet lab work from <b>April-October 2019</b>.
+
                         <LI>Get a second lab team to finish the wet lab work from <b>April-October 2019</b>.</li>
 +
                        <LI>Conceptualize a bioreactor for optimal cultivation and build it from <b>June-October 2019</b>.</li>
 
                         </UL>
 
                         </UL>
 
                         </p>
 
                         </p>
Line 261: Line 263:
 
                    
 
                    
 
                 <!--------------------------------------- TWO COLUMN IMG RIGHT END ------------------------------------------------>
 
                 <!--------------------------------------- TWO COLUMN IMG RIGHT END ------------------------------------------------>
 +
 +
<!--------------------------------------- TO TOP LINK ----------------------------------------------->
 +
                </br>
 +
<a href="#" class="to-top-link">
 +
                    <img src="https://static.igem.org/mediawiki/2019/3/3e/T--Humboldt_Berlin--ArrowDown.jpg" /> Go to top
 +
                </a>
 +
                <!--------------------------------------- TO TOP LINK END ------------------------------------------->
 +
  
 
         </section>
 
         </section>

Latest revision as of 21:05, 21 October 2019

notebook

Attributions

Supporters

Our team accomplished great things in the project Chlamylicious over the course of this year’s iGEM competition: We adapted a toolkit for the green alga C. reinhardtii with parts for successful and easy cloning of any transcription unit, which we implemented for the expression of the PET-degrading enzyme PETase by the alga and designed a bioreactor for its cultivation under constant monitoring of all parameters. These were our greatest supporters:

  • our host laboratories Experimental Biophysics and Molecular Genetics from the Humboldt University of Berlin, who shared their infrastructure with us
  • our supervisors Prof. Dr. Schmitz-Linneweber and Prof. Dr. Hegemann
  • the principal investigator Simon Kelterborn, who guided us with his expertise in transformations of Chlamydomonas and CRISPR-aided genetic engineering
  • the biological technical assistants Irina, Heide (Biophysics lab), Conny, Thea and Irina (all Genetics lab), who enabled us to launch the wet-lab
  • computer scientist Vincent Will, who implemented the design for our website
  • Dr. Ralf Steuer, who helped us developing the bioreactor
  • Prof. Dr. Ringrose, who coached us on how to create a good scientific poster
  • electronic engineer Markus Schulz, who helped designing and wiring the electronics for our bioreactor
  • technical engineering student Alejandro Gómez Jiménez from the Technical University of Berlin, who made the CAD-models for all parts of our bioreactor
  • the Interdisciplinary Workshop „Matters of Activity“ of Humboldt University, who laser-cut our hardware
  • the Mechanical Workshop of the Physics Department of our university
  • Dr. Nina Siragusa from Merck KGaA, who presented us to her broad scientific network and supported our outreach
  • Arne Kuczmera from the Berliner Wasserbetriebe, who supported our research at the waste water treatment plant




Re-used parts from different sources

Part name Source
AR Plasmid p114, Hegemann lab (Biophysics Department, Humboldt Universität zu Berlin)
ARS Ordered oligos from IDT
Sequence: A8ISJ6[1-26] (Uniprot)
AmpOri Amplified from MoClo plasmid pICH47732 (Addgene)
Ble/Scp: Ordered oligos from IDT
GLE Sequence: Q93WN9[1 - 28] (Uniprot)
3xHA-Tag Ordered oligos from IDT
His-Tag Ordered oligos from IDT
Hyg Amplified from p360, Hegemann lab (Biophysics Department, Humboldt Universität zu Berlin)
MHETase (wildtype) 2019 iGEM team University of Kaiserslautern, (C. reinhardtii)
MHETase (wildtype II) Weber lab (Molecular Structural Biology, University of Greifswald), (E. coli)
MHETase (Mutant W397A) Weber lab (Molecular Structural Biology, University of Greifswald), (E. coli)
Paro Amplified from p114, Hegemann lab (Biophysics Department, Humboldt Universität zu Berlin)
PETase Ordered oligos from IDT, Codon usage is for C. reinhardtii
PETase (E. coli) Adgene's plasmid: plasmid #112203
PtxD Sequence: AF061070.1 (ncbi)
Ordered from GeneCust
PsaD Plasmid 51, Hegemann lab (Biophysics Department, Humboldt Universität zu Berlin)
PsadIntron Self designed, intron designed after those of the AR-Promoter
RbcS2 Amplified from p141 pCrP2-SaCas9 (RBCS2, G), p016
RFP p42, Hegemann lab (Biophysics Department, Humboldt Universität zu Berlin)
Spec Amplified from the MoClo Plasmid pAGM9121 (Addgene)
YFP Amplified from YFP Sequenz of p135 pCr3-Ble2-YFP-Sp-APH plasmid pAGM9121
Overhang PCR: Amplification

Timeline and responsibilities

As the first team from the Humboldt University ever to form and participate in the iGEM competition we had to organize the following to establish C. reinhardtii as a chassis for synthetic biology in the iGEM community:

  • Find a professor and department able to supervise the iGEM project. As there is no course of synthetic biology taught at our university we referred to the Molecular Genetics and Biophysics lab groups.
  • Found a team of students, who were able to conduct the project research during their studies without earning credits for it. Our university so far does not offer any courses for the participation of students as an iGEM team. By June 2018 the main core of our iGEM team was brought together.
  • Brainstorm for interesting and viable SynBio projects, which took place in July 2018. Most of us had little or no prior knowledge in synthetic biology.
  • Research more on the possibilities of C. reinhardtii as a SynBio tool and familiarize ourselves with project management conducts from July-October 2018
  • Start fundraising initiatives in July 2018
  • Get part of the team started with working in the wet lab in October 2018.
  • Organize Human Practice events and possibilities of outreach to the broader public from November 2018 - October 2019.
  • Get a second lab team to finish the wet lab work from April-October 2019.
  • Conceptualize a bioreactor for optimal cultivation and build it from June-October 2019.


Go to top