Difference between revisions of "Team:Amsterdam"

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      Home
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<h2><a href="#"></a>iGEM Amsterdam</h2>
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<p class="post-info"> written by: iGEM Amsterdam </p>
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        Cyanofactory
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<article>
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      </a>
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<p>We live in a remarkable time. Ever since the 70’s, we’ve been able to
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      </div>
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read, interpret and manipulate DNA ­ the programming language of life
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      <ul class="list-inline nav navbar-right">
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itself. Now, backed by the transformation of biology into an information
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      <li class="list-inline-item dropdown">
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science and Moore’s law, we have complete lists of the basic
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        <a class="nav-link" href="#">
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components that constitute living systems, accessible from any web
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        Project
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browser in the world; we have genetic building blocks that are
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        <span class="caret">
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standardized and cheap, allowing modular use with predictable
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        </span>
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outcomes; and we have computer aided design, analysis and
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        </a>
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modelling to speed up progress even more. Together with rapid gene
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        <ul class="dropdown-menu">
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synthesis and sequencing technologies, engineering life has become
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both more accessible and creative, resulting in a synthetic biology
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          <a class="nav-link" href="#">
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revolution poised to transform industries.
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          Modeling
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In practice, synthetic biology often involves the design of genetic
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          </a>
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circuits ­ sets of interacting genes that perform a desired task ­ and the
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        </li>
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insertion of the designed circuit into living cells. As such, microbes can
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        <li>
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be programmed to produce fuels, smell like banana’s, or sense and
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          <a class="nav-link" href="#">
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break down toxic compounds. We are already remaking ourselves and
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          Glyoxylate Shunt
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our world, redesigning, recoding, and reinventing nature itself
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in the process</p>
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        </li>
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        <li>
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          Transport
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          Biosensor
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        Practices
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          Carbon Efficiency
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          Outreach
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          Articles
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          Entrepreneurship
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          Safety
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          Interlab Study
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          Protocol
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          Methods
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          Sponsors
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        Achievements
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      <video controls="" height="auto" poster="https://static.igem.org/mediawiki/2017/8/8f/Intro_poster.png" width="85%">
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      <source src="https://static.igem.org/mediawiki/2017/c/c5/Intro.mp4" type="video/mp4">
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        Project
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        Practices
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      <img alt="Project logo 1" src="https://static.igem.org/mediawiki/2017/a/a6/Project_logo_1.png"/>
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      <p>
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        Lab
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      <a class="section-button" href="#" id="Team">
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      <img alt="Project logo 1" src="https://static.igem.org/mediawiki/2017/a/a6/Project_logo_1.png"/>
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      <p>
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        Team
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      </p>
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      </a>
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      <a class="section-button" href="#" id="Achievements">
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      <img alt="Project logo 1" src="https://static.igem.org/mediawiki/2017/a/a6/Project_logo_1.png"/>
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      <p>
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        Achievements
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      </p>
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      </a>
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    </div>
 +
    <div class="home-spacer">
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      <img src="https://static.igem.org/mediawiki/2017/0/02/Design_thingy_1.png">
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      </img>
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    </div>
 +
    <div class="summary-container">
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      <div class="summary-col-left">
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      </div>
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      <div class="summary-col-mid">
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      <p class="summary-text">
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        We are running out of oil and the climate is changing drastically due to the emission of polluting gases such as CO
 +
        <sub>
 +
        2
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        </sub>
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        . But what if CO
 +
        <sub>
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        2
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        </sub>
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        were a resource, rather than a wasteful pollutant; and might even replace oil? We aspire to create a bio-based economy – one that meets its energy and production demands by leveraging biotechnology [1]. We can genetically engineer bacteria to produce a compound we need. This is what we call a bacterial ‘cell factory’.
 +
Meet
 +
        <a class="in-text-link" href="#" style="font-size: 24px">
 +
        CYANOFACTORY
 +
        </a>
 +
        , a cyanobacterium that stably and efficiently produces fumarate.
 +
      </p>
 +
      </div>
 +
      <div class="summary-col-right">
 +
      <div class="vertical-text-container">
 +
        <p class="vertical-text">
 +
        OUR GOAL
 +
        </p>
 +
      </div>
 +
      </div>
 +
    </div>
 +
    <div class="home-spacer">
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      <img src="https://static.igem.org/mediawiki/2017/0/02/Design_thingy_1.png">
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      </img>
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    </div>
 +
    <div class="summary-container">
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      <div class="summary-col-left">
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      <img height="260px" src="https://static.igem.org/mediawiki/2017/7/7a/Erlenmeyer_flask.png" width="200px">
 +
      </img>
 +
      </div>
 +
      <div class="summary-col-mid">
 +
      <p class="summary-text">
 +
        We use the cyanobacterium Synechocystis PCC6803, a photosynthetic model organism of which the genetic toolbox is rapidly expanding.
 +
        <br>
 +
        <br>
 +
          <a class="in-text-link" href="#">
 +
          Click here for a live feed with our Synechocystis cultivators.
 +
          </a>
 +
        </br>
 +
        </br>
 +
      </p>
 +
      </div>
 +
      <div class="summary-col-right">
 +
      <div class="vertical-text-container">
 +
        <p class="vertical-text">
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        SYNECHOCYSTIS
 +
        </p>
 +
      </div>
 +
      </div>
 +
    </div>
 +
    <div class="home-spacer">
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      <img src="https://static.igem.org/mediawiki/2017/0/02/Design_thingy_1.png">
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      </img>
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    </div>
 +
    <div class="summary-container">
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      <div class="summary-col-left">
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      <img height="202px" src="https://static.igem.org/mediawiki/2017/2/21/Fumarate.png" width="200px">
 +
      </img>
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      </div>
 +
      <div class="summary-col-mid">
 +
      <p class="summary-text">
 +
        Fumarate is a multifaceted acid that is used as a plastic precursor, an additive for the food industry and a drug against multiple sclerosis and psoriasis.
 +
        <br>
 +
        <br>
 +
          <a class="in-text-link" href="#">
 +
          Click here to see what we did with Fumarate.
 +
          </a>
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        </br>
 +
        </br>
 +
      </p>
 +
      </div>
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      <div class="summary-col-right">
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      <div class="vertical-text-container">
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        <p class="vertical-text">
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        FUMARATE
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        </p>
 +
      </div>
 +
      </div>
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    </div>
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    <div class="summary-container" id="modules">
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      <div class="home-spacer" id="modules">
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      <img src="https://static.igem.org/mediawiki/2017/f/ff/Design_thingy_1_long.png">
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      </img>
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      </div>
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      <div class="summary-col-left">
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      </div>
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      <div class="summary-col-mid">
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      <div class="summary-modules-outer" id="sensor">
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        <img class="animated-module-icon" src="https://static.igem.org/mediawiki/2017/3/3b/Sensor_icon.png">
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        <div class="modules-summary-text">
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          <h1>
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          Biosensor
 +
          </h1>
 +
          <p>
 +
          A biosensor for fumarate is constructed in order to facilitate a high throughput screening of extracellular fumarate. This is essential for low measurement time and costs.
 +
          <br>
 +
            <a class="in-text-link" href="#">
 +
            &gt;&gt;read more
 +
            </a>
 +
          </br>
 +
          </p>
 +
        </div>
 +
        </img>
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      </div>
 +
      <div class="summary-modules-outer" id="transporter">
 +
        <img class="animated-module-icon" src="https://static.igem.org/mediawiki/2017/8/86/Transporter_icon.png">
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        <div class="modules-summary-text">
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          <h1>
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          Transporter
 +
          </h1>
 +
          <p>
 +
          In anticipation of high fumarate production, transport of fumarate out of the cell can be a limiting factor. This mechanism is largely unknown in Synechocystis and will therefore be -guided by bioinformatics- characterized by means of knock-out and over- expression experiments.
 +
          <br>
 +
            <a class="in-text-link" href="#">
 +
            &gt;&gt;read more
 +
            </a>
 +
          </br>
 +
          </p>
 +
        </div>
 +
        </img>
 +
      </div>
 +
      <div class="summary-modules-outer" id="shunt">
 +
        <img class="animated-module-icon" src="https://static.igem.org/mediawiki/2017/6/6e/Shunt_icon.png">
 +
        <div class="modules-summary-text">
 +
          <h1>
 +
          Glyoxylate Shunt
 +
          </h1>
 +
          <p>
 +
          We will incorporate two enzymes (the glyoxylate shunt) in the Synechocystis genome, creating a shortcut in the TCA-cycle. Our modeling results show that if this shunt is only expressed at night, and the pentose phosphate pathway is blocked by knocking out the zwf gene, more fumarate will be produced. This means we will create a unique combination of growth- coupled and inducible production.
 +
          <br>
 +
            <a class="in-text-link" href="#">
 +
            &gt;&gt;read more
 +
            </a>
 +
          </br>
 +
          </p>
 +
        </div>
 +
        </img>
 +
      </div>
 +
      <div class="summary-modules-outer" id="stability">
 +
        <img class="animated-module-icon" src="https://static.igem.org/mediawiki/2017/7/7f/Stability_icon.png">
 +
        <div class="modules-summary-text">
 +
          <h1>
 +
          Stability
 +
          </h1>
 +
          <p>
 +
          When an organism is genetically modified to create a product, it causes a decrease in growth rate. This means that a mutated - non- producing - organism will grow faster and take over the population. This problem is tackled by coupling fumarate production to growth. Given that evolution selects heavily on growth rate, we now have a way of naturally selecting for production rate [4]! Knocking out the fumarate degrading reaction in the TCA cycle causes fumarate to be produced in a growth coupled way.
 +
          <br>
 +
            <a class="in-text-link" href="#&gt;">
 +
            &gt;&gt;read more
 +
            </a>
 +
          </br>
 +
          </p>
 +
        </div>
 +
        </img>
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      </div>
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      </div>
 +
      <div class="summary-col-right">
 +
      <div class="vertical-text-container">
 +
        <p class="vertical-text">
 +
        MODULES
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        </p>
 +
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      <a href="https://www.aimms.vu.nl/en/index.aspx">
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Achievements

We are running out of oil and the climate is changing drastically due to the emission of polluting gases such as CO 2 . But what if CO 2 were a resource, rather than a wasteful pollutant; and might even replace oil? We aspire to create a bio-based economy – one that meets its energy and production demands by leveraging biotechnology [1]. We can genetically engineer bacteria to produce a compound we need. This is what we call a bacterial ‘cell factory’. Meet CYANOFACTORY , a cyanobacterium that stably and efficiently produces fumarate.

OUR GOAL

We use the cyanobacterium Synechocystis PCC6803, a photosynthetic model organism of which the genetic toolbox is rapidly expanding.

Click here for a live feed with our Synechocystis cultivators.

SYNECHOCYSTIS

Fumarate is a multifaceted acid that is used as a plastic precursor, an additive for the food industry and a drug against multiple sclerosis and psoriasis.

Click here to see what we did with Fumarate.

FUMARATE

Biosensor

A biosensor for fumarate is constructed in order to facilitate a high throughput screening of extracellular fumarate. This is essential for low measurement time and costs.
>>read more

Transporter

In anticipation of high fumarate production, transport of fumarate out of the cell can be a limiting factor. This mechanism is largely unknown in Synechocystis and will therefore be -guided by bioinformatics- characterized by means of knock-out and over- expression experiments.
>>read more

Glyoxylate Shunt

We will incorporate two enzymes (the glyoxylate shunt) in the Synechocystis genome, creating a shortcut in the TCA-cycle. Our modeling results show that if this shunt is only expressed at night, and the pentose phosphate pathway is blocked by knocking out the zwf gene, more fumarate will be produced. This means we will create a unique combination of growth- coupled and inducible production.
>>read more

Stability

When an organism is genetically modified to create a product, it causes a decrease in growth rate. This means that a mutated - non- producing - organism will grow faster and take over the population. This problem is tackled by coupling fumarate production to growth. Given that evolution selects heavily on growth rate, we now have a way of naturally selecting for production rate [4]! Knocking out the fumarate degrading reaction in the TCA cycle causes fumarate to be produced in a growth coupled way.
>>read more

MODULES

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