Difference between revisions of "Team:Marburg/MedalCriteria"

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<div>
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  <div class="box-dark">
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    <h1 class="heading">
 +
      A C H I E V E M E N T S
 +
    </h1>
 +
    <hr class="line">
 +
    <img src="https://static.igem.org/mediawiki/2019/a/ac/T--Marburg--logo.svg" class="logo" alt="Syntex Logo">
 +
  </div>
 +
  <div style="margin-top: 11vh;">
 +
    <section class="section">
 +
      <center>“If you do nothing there will be no resultsGreat things are not done by impulse, but by a series of small
 +
        things brought together.” -<b>Vincent van Gogh</b></center>
 +
      <b>Bronze</b>
 +
      <div style="display: flex; flex-direction: row">
 +
        <div>
 +
          <div class="content">
 +
            <ul>
 +
              <li>Competition deliverables
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                We successfully took part in the competition and the Giant Jamboree by creating our wiki, designing our
 +
                poster, holding our presentation and delivering our judging form.
 +
              <li>Attributions
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                Created a clear overview for all our attributions.
 +
              <li>Project inspiration and description
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                We gave a deep insight into our project inspiration and into the project itself by writing our
 +
                descriptions for the different projects.
 +
              <li>Contribution/Characterization
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                We expanded the Marburg Collection by 55 parts and were able to characterize and compare them with a
 +
                second measurement method: FACS.
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                Added two new features for genetic engineering of cyanobacteria.
 +
              </li>
 +
              <li style="margin-left: 60px">
 +
                CRIPSR/Cas12a knock out system.
 +
              </li>
 +
              <li style="margin-left: 60px">
 +
                M.E.G.A. expansion for the knock in of genes.
 +
              </li>
 +
              <li style="margin-left: 60px">
 +
                Designing two novel integration sites based on RNA-seq data.
 +
              </li>
 +
              <li style="margin-left: 60px">
 +
                Created the first MoClo compatible shuttle vector for cyanobacteria.
 +
              </li>
 +
              <li style="margin-left: 90px">
 +
                Used it to build standardized devices for characterization of BioBricks in cyanobacterial chassis.
 +
                (Containing Spaceholders)
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                Implemented luminescence reporters for measurement of cyanobacteria.
 +
              </li>
 +
              <li style="margin-left: 60px">
 +
                Higher accuracy because of the reduced background noise.
 +
              </li>
 +
            </ul>
 +
          </div>
 +
        </div>
 +
      </div>
 +
      <hr>
 +
      <b>Silver</b>
 +
      <div style="display: flex; flex-direction: row">
 +
        <div>
 +
          <div class="content">
 +
            <ul>
 +
              <li>Validated parts
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                Successfully built and validated our new spaceholder parts.
 +
              </li>
 +
              <li style="margin-left: 60px">
 +
                Reducing costs and workload significantly.
 +
              </li>
 +
              <li style="margin-left: 60px">
 +
                Calculated the amount of work required to assemble a promotor library with 20 parts (link to results
 +
                table) compared to the same workload without our spaceholders.
 +
              </li>
 +
              <li style="margin-left: 60px">
 +
                Validated it by using it in our large scale assemblies.
 +
              </li>
 +
              <li>Collaboration
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                Created the colony pictures collaboration.
 +
              </li>
 +
              <li style="margin-left: 60px">
 +
                Asking other teams for pictures of their colony plates to get data to feed our AI with (link collab and
 +
                AI)
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                We expanded the Marburg Collection by 55 parts and were able to characterize and compare them with a
 +
                second measurement method: FACS.
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                Golden Gate Collaboration
 +
              </li>
 +
              <li style="margin-left: 60px">
 +
                Held a webinar to explain the Golden Gate Cloning to other teams and helped them by using a
 +
                Slack-Channel for further questions.
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                Interlab
 +
              </li>
 +
              <li style="margin-left: 60px">
 +
                Investigated the differences of the same test done in different labs.
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                Smaller collaborations
 +
              </li>
 +
              <li style="margin-left: 60px">
 +
                Further we took part in different smaller collaborations and meet ups (Bonn, Düsseldorf, Erlangen,
 +
                Biohackaton LINKS).
 +
              </li>
  
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              <li>Human Practices</li>
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                Since a large part of the population is not aware of green genetic engineering and often has distorted
−
       }
+
                opinions, we have tried to provide more information and insights into this topic by visiting the plant
 +
                market and organizing a panel discussion.
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                Further we talked to politicians to see their views and concerns on this topic.
 +
              </li>
 +
            </ul>
 +
          </div>
 +
        </div>
 +
      </div>
 +
      <hr>
 +
      <b>Gold</b>
 +
      <div style="display: flex; flex-direction: row">
 +
         <div>
 +
          <div class="content">
 +
            <ul>
 +
              <li>Integrated Human Practices
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                during our igem year we were able to establish many interesting contacts with companies and scientists.
 +
                For many experts in the field of cyanobacteria, the standardization of cultivation conditions was a
 +
                major factor, which is why we decided to take a closer look at it. during our igem year we were able to
 +
                establish many interesting contacts with companies and scientists. For many experts in the field of
 +
                cyanobacteria, the standardization of cultivation conditions was a major factor, which is why we decided
 +
                to take a closer look at it.
 +
              <li style="margin-left: 30px">
 +
                Cooperation with promega to automate the plasmid purification with their kit with the opentron.
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                Opentrons (Kristin Ellis), Keoni Gandall and Doulix took part in our biggest cooperation while we worked
 +
                on making the Opentrons OT-2 pick single colonies by adding a camera and a raspberry pi to its arm and
 +
                training a A.I. with colony pictures.
 +
              </li>
 +
              <li>Improve a previous part or project
 +
              </li>
 +
              <li style="margin-left: 30px">
 +
                ???
 +
              </li>
 +
              <li>Model your project</li>
 +
              <li style="margin-left: 60px">
 +
                Light model? growth curve model?
 +
              </li>
 +
              <li>Demonstration of your work</li>
 +
              <li style="margin-left: 60px">
 +
                ??? Testing growth curve model?
 +
              </li>
 +
            </ul>
 +
          </div>
 +
        </div>
 +
       </div>
  
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       <p>
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        This year we expanded the Marburg Collection from 2018 with 55 new parts to the Marburg Collection 2.0. With
−
       }
+
        our
 +
        developed workflow we could characterize our parts and compare them with a second measurement method: FACs. We
 +
        added two new features for genome engineering of cyanobacteria: a CRISPR/cpf1 guided knockout system as well
 +
        as
 +
        a modularized assembly of repair templates for the knock in of genes (M.E.G.A. expansion). This includes
 +
        integration sites that target conventional neutral sites in cyanobacteria but we also rationally designed two
 +
        novel integration sites based on RNA-seq data. Additionally we offer the first MoClo compatible shuttle vector
 +
         for <a href="https://2019.igem.org/Team:Marburg/Basic_Part">cyanobacteria</a> and characterized gene
 +
        expression
 +
        based on that origin of replication. We used our new shuttle vector to build standardized devices for the
 +
        characterization of BioBricks in cyanobacterial chassis to improve the reproducibility of results and to
 +
        simplify large scale assemblies. For this we used placeholders, a novel part type that aids in the
 +
        construction
 +
        of a larger set of parts by reducing the involved cost and workload significantly. Additionally we tested our
 +
        toolbox with PCC 7942 to show that the Marburg Collection 2.0 is also working with similar cyanobacterias. We
 +
        offer free access to the data of our characterization, enabling the iGEM community and scientists to choose
 +
        the
 +
        parts based on this data. To improve the measurement method applicable for cyanobacteria we focused on
 +
        measurements via luminescence reporters over fluorescence reporters, because of the fact that cyanobacteria
 +
        emmit autofluorescence. This way our results are way more accurate, because of the reduced background noise.
 +
        The
 +
        higher accuracy is obviously visible during the measurement of our parts, where we could see a difference of
 +
        5x10<sup>5</sup> between the background noise and the signal, which implements that already a small amount of
 +
        sample has a more intensive signal.
 +
        <br><br>
 +
        Hereby, we want to encourage the community of young scientists to work with the fastest phototrophic organism
 +
        Synechococcus elongatus UTEX 2973 because of its high relevance for biotechnological applications.
 +
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        A C H I E V E M E N T S
 
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      <section class="section">
 
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        <h2 class="subtitle">Great things are not done by impulse, but by a series of small things brought together. –
 
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          Vincent van Gogh</h2>
 
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        <p>
 
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          This year we expanded the Marburg Collection from 2018 with 55 new parts to the Marburg Collection 2.0. With
 
−
          our
 
−
          developed workflow we could characterize our parts and compare them with a second measurement method: FACs. We
 
−
          added two new features for genome engineering of cyanobacteria: a CRISPR/cpf1 guided knockout system as well
 
−
          as
 
−
          a modularized assembly of repair templates for the knock in of genes (M.E.G.A. expansion). This includes
 
−
          integration sites that target conventional neutral sites in cyanobacteria but we also rationally designed two
 
−
          novel integration sites based on RNA-seq data. Additionally we offer the first MoClo compatible shuttle vector
 
−
          for <a href="https://2019.igem.org/Team:Marburg/Basic_Part">cyanobacteria</a> and characterized gene
 
−
          expression
 
−
          based on that origin of replication. We used our new shuttle vector to build standardized devices for the
 
−
          characterization of BioBricks in cyanobacterial chassis to improve the reproducibility of results and to
 
−
          simplify large scale assemblies. For this we used placeholders, a novel part type that aids in the
 
−
          construction
 
−
          of a larger set of parts by reducing the involved cost and workload significantly. Additionally we tested our
 
−
          toolbox with PCC 7942 to show that the Marburg Collection 2.0 is also working with similar cyanobacterias. We
 
−
          offer free access to the data of our characterization, enabling the iGEM community and scientists to choose
 
−
          the
 
−
          parts based on this data. To improve the measurement method applicable for cyanobacteria we focused on
 
−
          measurements via luminescence reporters over fluorescence reporters, because of the fact that cyanobacteria
 
−
          emmit autofluorescence. This way our results are way more accurate, because of the reduced background noise.
 
−
          The
 
−
          higher accuracy is obviously visible during the measurement of our parts, where we could see a difference of
 
−
          5x10<sup>5</sup> between the background noise and the signal, which implements that already a small amount of
 
−
          sample has a more intensive signal.
 
−
          <br><br>
 
−
          Hereby, we want to encourage the community of young scientists to work with the fastest phototrophic organism
 
−
          Synechococcus elongatus UTEX 2973 because of its high relevance for biotechnological applications.
 
−
        </p>
 
−
      </section>
 
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    </div>
 
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Revision as of 16:54, 10 December 2019

A C H I E V E M E N T S

“If you do nothing there will be no resultsGreat things are not done by impulse, but by a series of small things brought together.” -Vincent van Gogh
Bronze
  • Competition deliverables
  • We successfully took part in the competition and the Giant Jamboree by creating our wiki, designing our poster, holding our presentation and delivering our judging form.
  • Attributions
  • Created a clear overview for all our attributions.
  • Project inspiration and description
  • We gave a deep insight into our project inspiration and into the project itself by writing our descriptions for the different projects.
  • Contribution/Characterization
  • We expanded the Marburg Collection by 55 parts and were able to characterize and compare them with a second measurement method: FACS.
  • Added two new features for genetic engineering of cyanobacteria.
  • CRIPSR/Cas12a knock out system.
  • M.E.G.A. expansion for the knock in of genes.
  • Designing two novel integration sites based on RNA-seq data.
  • Created the first MoClo compatible shuttle vector for cyanobacteria.
  • Used it to build standardized devices for characterization of BioBricks in cyanobacterial chassis. (Containing Spaceholders)
  • Implemented luminescence reporters for measurement of cyanobacteria.
  • Higher accuracy because of the reduced background noise.
Silver
  • Validated parts
  • Successfully built and validated our new spaceholder parts.
  • Reducing costs and workload significantly.
  • Calculated the amount of work required to assemble a promotor library with 20 parts (link to results table) compared to the same workload without our spaceholders.
  • Validated it by using it in our large scale assemblies.
  • Collaboration
  • Created the colony pictures collaboration.
  • Asking other teams for pictures of their colony plates to get data to feed our AI with (link collab and AI)
  • We expanded the Marburg Collection by 55 parts and were able to characterize and compare them with a second measurement method: FACS.
  • Golden Gate Collaboration
  • Held a webinar to explain the Golden Gate Cloning to other teams and helped them by using a Slack-Channel for further questions.
  • Interlab
  • Investigated the differences of the same test done in different labs.
  • Smaller collaborations
  • Further we took part in different smaller collaborations and meet ups (Bonn, Düsseldorf, Erlangen, Biohackaton LINKS).
  • Human Practices
  • Since a large part of the population is not aware of green genetic engineering and often has distorted opinions, we have tried to provide more information and insights into this topic by visiting the plant market and organizing a panel discussion.
  • Further we talked to politicians to see their views and concerns on this topic.
Gold
  • Integrated Human Practices
  • during our igem year we were able to establish many interesting contacts with companies and scientists. For many experts in the field of cyanobacteria, the standardization of cultivation conditions was a major factor, which is why we decided to take a closer look at it. during our igem year we were able to establish many interesting contacts with companies and scientists. For many experts in the field of cyanobacteria, the standardization of cultivation conditions was a major factor, which is why we decided to take a closer look at it.
  • Cooperation with promega to automate the plasmid purification with their kit with the opentron.
  • Opentrons (Kristin Ellis), Keoni Gandall and Doulix took part in our biggest cooperation while we worked on making the Opentrons OT-2 pick single colonies by adding a camera and a raspberry pi to its arm and training a A.I. with colony pictures.
  • Improve a previous part or project
  • ???
  • Model your project
  • Light model? growth curve model?
  • Demonstration of your work
  • ??? Testing growth curve model?

This year we expanded the Marburg Collection from 2018 with 55 new parts to the Marburg Collection 2.0. With our developed workflow we could characterize our parts and compare them with a second measurement method: FACs. We added two new features for genome engineering of cyanobacteria: a CRISPR/cpf1 guided knockout system as well as a modularized assembly of repair templates for the knock in of genes (M.E.G.A. expansion). This includes integration sites that target conventional neutral sites in cyanobacteria but we also rationally designed two novel integration sites based on RNA-seq data. Additionally we offer the first MoClo compatible shuttle vector for cyanobacteria and characterized gene expression based on that origin of replication. We used our new shuttle vector to build standardized devices for the characterization of BioBricks in cyanobacterial chassis to improve the reproducibility of results and to simplify large scale assemblies. For this we used placeholders, a novel part type that aids in the construction of a larger set of parts by reducing the involved cost and workload significantly. Additionally we tested our toolbox with PCC 7942 to show that the Marburg Collection 2.0 is also working with similar cyanobacterias. We offer free access to the data of our characterization, enabling the iGEM community and scientists to choose the parts based on this data. To improve the measurement method applicable for cyanobacteria we focused on measurements via luminescence reporters over fluorescence reporters, because of the fact that cyanobacteria emmit autofluorescence. This way our results are way more accurate, because of the reduced background noise. The higher accuracy is obviously visible during the measurement of our parts, where we could see a difference of 5x105 between the background noise and the signal, which implements that already a small amount of sample has a more intensive signal.

Hereby, we want to encourage the community of young scientists to work with the fastest phototrophic organism Synechococcus elongatus UTEX 2973 because of its high relevance for biotechnological applications.