Difference between revisions of "Team:Marburg"

 
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      <div class="words">
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        <p class="word glitch" data-text="F A S T E S T .">
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          F A S T E S T .
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        </p>
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        <p class="word glitch" data-text="P H O T O T R O P H I C .">
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          P H O T O T R O P H I C .
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        <p class="word glitch" data-text="O R G A N I S M .">
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          O R G A N I S M .
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        </p>
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    <div class="hero-text">
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      <p class="hero-first">
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        By providing the fastest growing phototrophic chassis to the community, we are paving the way for other
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        phototrophic organisms in Synthetic Biology.
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      </p>
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      <hr class="line" style="transform: unset;">
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      <p class="hero-second">
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        We created an easy to use toolbox for <i>Synechococcus elongatus</i> UTEX 2973 to empower rapid design
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        testing, including genome engineering tools, self-replicating plasmid systems, natural competence and a Golden
 +
        Gate-based part library. By providing the fastest growing phototrophic chassis with a doubling time of <b>under 80 minutes</b> to the community, we are paving the way
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        for other phototrophic organisms in Synthetic Biology.
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      </p>
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    </div>
 
     <div>
 
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       <img src="https://static.igem.org/mediawiki/2019/d/d4/T--Marburg--m_team.jpg" alt="Team">
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        <img id="strain" src="https://static.igem.org/mediawiki/2019/9/91/T--Marburg--hero_strain.jpg"
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          alt="Strain Engineering Logo">
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        <h1 class="heading">
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          S T R A I N
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          <br><br>
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          E N G I N E E R I N G
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        </h1>
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        <hr class="line">
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        <p class="text">
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          We created an "easy to use" phototrophic chassis by restoring the natural competence of <i>S. elongatus</i>
 +
          UTEX 2973 in order to enormously simplify the transformation process. We established a genome modification
 +
          system via the CRISPR/Cas12a and enabled the usage of self-replicating plasmids overcoming the drawbacks of time
 +
          intensive genome integration for genetic design testing.
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        </p>
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      </div>
 
     </div>
 
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         <img src="https://static.igem.org/mediawiki/2019/b/b9/T--Marburg--m_logo-text.jpg" alt="Syntex Logo">
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         <img id="toolbox" src="https://static.igem.org/mediawiki/2019/c/ca/T--Marburg--hero_toolbox.jpg" alt="Toolbox Photo">
 
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         <img src="https://static.igem.org/mediawiki/2019/a/a9/T--Marburg--logo_toolbox.svg" class="logo" alt="Toolbox Logo">
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         <p>
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        <h1 class="heading">
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          <span>Our Project</span> <br>
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          T O O L B O X
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        </h1>
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        <hr class="line">
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        <p class="text">
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          We constructed the green expansion, a set of biobricks to accompany our new chassis. It contains the first
 +
          MoClo compatible shuttle vector for cyanobacteria. Additionally users can design plasmids for genomic
 +
          integrations using novel rationally designed integration sites. To improve standardization in phototrophic
 +
          research we deliver standardized measurement entry vectors to test BioBricks in cyanobacteria.
 
         </p>
 
         </p>
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        <p>
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      </div>
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          With rising atmospheric CO<sub>2</sub> concentrations and declining oil reserves,
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    </div>
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          we saw that the worldwide effort to change from a petroleum based industry to a carbon neutral industry needs to increase drastically. One
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    <div>
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          of the most promising key technologies right now is the use of phototrophic organisms for biotechnological applications. Hence, we decided
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      <div class="box-light">
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          quite early this year to devote ourselves to a photosynthetic project. During the design phase, which we initially thought about a project
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        <img id="measurement" src="https://static.igem.org/mediawiki/2019/c/c3/T--Marburg--hero_measurement.jpg"
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          around the model moss <i>Physcomitrella patens</i>, we soon stumbled upon many common obstacles characteristic to phototrophic chassis due
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           alt="Measurement Photo">
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          to our choice of organism. Issues like time intensive culturing and complicated techniques to perform basic molecular biological methods
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      </div>
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          eventually showed us, why only very few iGEM teams every year decide to use a phototrophic chassis. We saw a need to tackle these issues
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      <div class="box-dark left">
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          and were determined to find a solution.
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        <img src="https://static.igem.org/mediawiki/2019/8/8a/T--Marburg--logo_measurement.svg" class="logo"
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           <br> <br>
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           alt="Measurement Logo">
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          Consequently, our choice fell on the cyanobacterial strain <i>Synechococcus elongatus</i> UTEX 2973, due to its highly potential doubling
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        <h1 class="heading" style="margin-top: 3em;">
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          time of about 2 hours <sup>1</sup>. This could have a huge impact, as the time consumed by many workflows is mainly dictated by the growth
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           M E A S U R E M E N T
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          of your chassis. Our strain could compete with common heterotrophic chassis like yeast, which would be a novelty in photosynthetic
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        </h1>
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          research. We are dedicated to develop this strain as a chassis for the scientific community and future iGEM teams. To restore its natural
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        <hr class="line">
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           competence, which it has lost after isolation, we will integrate a CRISPR/Cpf1 system into our toolbox, enabling easy genomic manipulation
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        <p class="text">
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           and thus giving us the tools to construct various strains and revert the point mutation responsible for the loss of natural competence.
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           Following the call for long needed standardization in the cyanobacterial community, we ventured out to rationalize important measurements hugely affecting the growth of our cultures. As using fluorescence for part characterization proves difficult in self-fluorescent cyanobacteria, we showed that the use of bioluminescence reporters as well as the use of flow cytometry offer promising alternatives to improve these characterizations.
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          Additionally, we remove the wild type plasmid pANS from <i>Synechococcus</i> to use it’s origin of replication in our “Marburg Collection
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          2.0”: a versatile Golden Gate based modular cloning library for fast state of the art assembly of genetic constructs based on a “one step
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           - one pot” reaction. By designing “operon connectors”, our toolbox is the first to assemble complete operons in the span of two days. This
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          assembly technique can be performed in our open source liquid handler OT-2 from Opentrons, paving the way for our vision of fully
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          automated cloning in molecular and synthetic biology - from ordered primers to the finished construct. To add to this vision, we are the
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          first to establish several laboratory practices in this robot such as colony picking, plating and plasmid purification. By making full
+
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          cloning processes possible in the Opentron environment, we give iGEM teams access to an affordable way to accelerate their undertaking,
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          allowing them to allocate more time to the design of their project. In our metabolic engineering project we prove the value of the tools
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          we hereby provide: Using our cloning system, we modify our established chassis to produce limonene and farnesene, two valuable
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          biochemicals that can be used as a biofuel. The chassis’ capabilities are not limited to terpene production but can be expanded to other
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          areas of biotechnological applications as well as to academic experimental setups. Customized strains offer the opportunity of sustainable
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          growth in drug development and manufacturing, helping us all to achieve our vision of a more sustainable future on this planet.
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          <br> <br>
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         </p>
 
         </p>
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        <p>
 
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          <sup>1</sup> Yu, J.; Liberton M.; Cliften, P. F.; Head, R. D.; Jacobs, J. M.; Smith, R. D.; Koppenaal, D. W.; Brand J. J.; Pakrasi, H. B.:
 
−
          <i>Synechococcus elongatus</i> UTEX 2973, a
 
−
          fast growing cyanobacterial chassis for
 
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          biosynthesis using light and CO<sub>2</sub>. Scientific Reports. 5:8132. DOI: 10.1038/srep08132 (2015)
 
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        <ul>
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        <img id="automation" src="https://static.igem.org/mediawiki/2019/f/f9/T--Marburg--hero_automation.jpg"
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          <li><a href="https://www.facebook.com/IGEMMarburg2019/"><img src='https://static.igem.org/mediawiki/2019/b/b1/T--Marburg--m_icon_fa.svg' /></a>
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           alt="Automation Photo">
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          </li>
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          <li><a href="https://twitter.com/igemmarburg2019"><img src='https://static.igem.org/mediawiki/2019/4/43/T--Marburg--m_icon_tw.svg' /></a></li>
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          <li><a href="https://www.instagram.com/igem.marburg.2019"><img src='https://static.igem.org/mediawiki/2019/e/e7/T--Marburg--m_icon_in.svg' /></a>
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           </li>
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          <li><a href="mailto:igem2019@synmikro.uni-marburg.de"><img src='https://static.igem.org/mediawiki/2019/2/2c/T--Marburg--m_icon_ma.svg' /></a>
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          </li>
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        </ul>
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       </div>
 
       </div>
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      <div class="box-dark right">
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        <img src="https://static.igem.org/mediawiki/2019/3/3f/T--Marburg--logo_automation.svg" class="logo"
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          alt="Automation Logo">
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        <h1 class="heading">
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          A U T O M A T I O N
 +
        </h1>
 +
        <hr class="line">
 +
        <p class="text">
 +
          The goal of the automation lab was to completely automate the process of cloning using OT-2 Pipetting robots. This was achieved using a state of the art faster-RCNN neural network and a self made camera module and light table for colony picking. We also automated large scale purification of plasmids. Our
 +
          software as well as the hardware blueprints are published on GitHub to give everybody access to scalable and affordable automation.
 +
        </p>
 +
      </div>
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    </div>
 +
    <div id="awards" class="box-light awards" onclick="window.location.href = '/Team:Marburg/MedalCriteria'">
 +
      <h1 class="award-title title">Achievements</h1>
 +
      <img class="award" src="https://static.igem.org/mediawiki/2019/a/ae/T--Marburg--medal_bronze.svg">
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      <img class="award" src="https://static.igem.org/mediawiki/2019/c/cc/T--Marburg--medal_silver.svg">
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      <img class="award" src="https://static.igem.org/mediawiki/2019/6/6f/T--Marburg--medal_gold.svg">
 +
      <img class="award" src="https://static.igem.org/mediawiki/2019/b/bd/T--Marburg--medal_special.svg">
 
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Latest revision as of 17:00, 11 December 2019

F A S T E S T .

P H O T O T R O P H I C .

O R G A N I S M .

By providing the fastest growing phototrophic chassis to the community, we are paving the way for other phototrophic organisms in Synthetic Biology.

We created an easy to use toolbox for Synechococcus elongatus UTEX 2973 to empower rapid design testing, including genome engineering tools, self-replicating plasmid systems, natural competence and a Golden Gate-based part library. By providing the fastest growing phototrophic chassis with a doubling time of under 80 minutes to the community, we are paving the way for other phototrophic organisms in Synthetic Biology.

Strain Engineering Photo

S T R A I N

E N G I N E E R I N G

We created an "easy to use" phototrophic chassis by restoring the natural competence of S. elongatus UTEX 2973 in order to enormously simplify the transformation process. We established a genome modification system via the CRISPR/Cas12a and enabled the usage of self-replicating plasmids overcoming the drawbacks of time intensive genome integration for genetic design testing.

Toolbox Photo

T O O L B O X

We constructed the green expansion, a set of biobricks to accompany our new chassis. It contains the first MoClo compatible shuttle vector for cyanobacteria. Additionally users can design plasmids for genomic integrations using novel rationally designed integration sites. To improve standardization in phototrophic research we deliver standardized measurement entry vectors to test BioBricks in cyanobacteria.

Measurement Photo

M E A S U R E M E N T

Following the call for long needed standardization in the cyanobacterial community, we ventured out to rationalize important measurements hugely affecting the growth of our cultures. As using fluorescence for part characterization proves difficult in self-fluorescent cyanobacteria, we showed that the use of bioluminescence reporters as well as the use of flow cytometry offer promising alternatives to improve these characterizations.

Automation Photo

A U T O M A T I O N

The goal of the automation lab was to completely automate the process of cloning using OT-2 Pipetting robots. This was achieved using a state of the art faster-RCNN neural network and a self made camera module and light table for colony picking. We also automated large scale purification of plasmids. Our software as well as the hardware blueprints are published on GitHub to give everybody access to scalable and affordable automation.

Achievements