Difference between revisions of "Team:TU Delft"

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        <title>iGEM TU Delft</title>
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<img src="https://static.igem.org/mediawiki/2016/5/58/TUDelft_Header.jpeg">
 
</div>
 
  
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<h2> Welcome to iGEM 2016! </h2>
 
<p>Your team has been approved and you are ready to start the iGEM season! </p>
 
  
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<h5>Before you start: </h5>
 
<p> Please read the following pages:</p>
 
<ul>
 
<li>  <a href="https://2016.igem.org/Requirements">Requirements page </a> </li>
 
<li> <a href="https://2016.igem.org/Wiki_How-To">Wiki Requirements page</a></li>
 
<li> <a href="https://2016.igem.org/Resources/Template_Documentation"> Template Documentation </a></li>
 
</ul>
 
</div>
 
  
<div class="column half_size" >
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              <div class="carousel-inner" role="listbox">
<div class="highlight">
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<h5> Styling your wiki </h5>
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<p>You may style this page as you like or you can simply leave the style as it is. You can easily keep the styling and edit the content of these default wiki pages with your project information and completely fulfill the requirement to document your project.</p>
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<p>While you may not win Best Wiki with this styling, your team is still eligible for all other awards. This default wiki meets the requirements, it improves navigability and ease of use for visitors, and you should not feel it is necessary to style beyond what has been provided.</p>
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<div class="column full_size" >
 
<h5> Wiki template information </h5>
 
<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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                  <img src="https://static.igem.org/mediawiki/2016/2/2e/T--TU_Delft--header.jpg" alt="">
  
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                  <div class="container">
  
<div class="column half_size" >
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                    <div class="carousel-caption">
<h5> Editing your wiki </h5>
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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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                      <h2 class="carousel-title bounceInDown animated slow">TU Delft 2016</h2>
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                      <h4 class="carousel-subtitle bounceInUp animated slow ">OPTICOLI</h4>
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                      <h5 class="carousel-subsubtitle bounceInUp animated slow">Producing biological lenses and lasers using synthetic biology</h5>
  
  
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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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<ul>
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<li>State your accomplishments! Tell people what you have achieved from the start. </li>
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<li>Be clear about what you are doing and how you plan to do this.</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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</ul>
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                </div> <!-- /.item --></a>
<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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<ul>
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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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<li> <a href="https://2014.igem.org/Team:ITESM-Guadalajara">2014 ITESM-Guadalajara </a></li>
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<li> <a href="https://2014.igem.org/Team:SCU-China"> 2014 SCU-China </a></li>
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</ul>
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</div>
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<div class="column half_size" >
 
<h5> Uploading pictures and files </h5>
 
<p> You can upload your pictures and files to the iGEM 2016 server. Remember to keep all your pictures and files within your team's namespace or at least include your team's name in the file name. <br />
 
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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UPLOAD FILES
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        <div class="section-home about-us">
  
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                            <h3 class="col-title">Project</h3></a>
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                            <a href="https://2016.igem.org/Team:TU_Delft/Attributions#sponsors"><i class="fa fa-money fa-5x"></i>
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                            <h3 class="col-title">Sponsors</h3></a>
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                        <div class="col-icon-wrapper">
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                          <a href="https://2016.igem.org/Team:TU_Delft/Model"><i class="fa fa-area-chart fa-5x"></i>
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                          <h3 class="col-title">Modeling</h3></a>
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                            <a href="https://2016.igem.org/Team:TU_Delft/Hardware"><i class="fa fa-cog fa-spin-hover fa-5x"></i>
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                            <h3 class="col-title">Hardware</h3></a>
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                            <a href="https://2016.igem.org/Team:TU_Delft/Parts"><i class="fa fa-puzzle-piece fa-5x"></i>
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                            <h3 class="col-title">Parts</h3></a>
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                            <a href="https://2016.igem.org/Team:TU_Delft/Practices"><i class="fa fa-users fa-5x"></i>
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                            <h3 class="col-title">Practices</h3></a>
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        <div class="section-home home-reasons">
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                                <h3 class="reasons-title">Producing biological lenses and lasers to improve microscopy</h3>
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                            <div class="reasons-intro">
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                                <p>Microscopes have been around for hundreds of years and the technology behind these devices has been quickly developing over the past centuries. Microscopy has already helped us to image cells into great detail, which is essential for the identification of mechanisms behind diseases such as Alzheimer’s, of which we still don’t know the exact mechanism, but also for developing synthetic biology even further. In this age, the technology and knowledge of microscopy is no longer limiting for making detailed images of the cell; it’s the cells itself. When using fluorescence microscopy, a fluorescent cell only emits a limited number of photons, a part of this will not reach the detector. This year’s TU Delft team is using synthetic biology with the aim of improving fluorescence microscopy. There are two research lines: producing biological lenses and inventing a bacterial laser. <strong>Hover</strong> over the pictures underneath to find out more.</p>
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                                <h3 class="reasons-title">BIOLENSES</h3>
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                            <img src="https://static.igem.org/mediawiki/2016/5/50/T--TU_Delft--Lens_frontpage.png" alt="lenses">                   
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                                <p>The goal of our <strong>biological microlenses</strong> is to increase the fraction of light captured by the detector of a microscope. Lenses are known to focus light onto a surface. By applying a layer of our biological microlenses on the detector of a microscope, we can increase the fraction of light captured. To produce microlenses, we expressed the enzyme <strong>silicatein</strong> in our cells, which catalyzes polymerization of silicic acid <a href="#references">(Cha et al., 1999)</a>. This results in a <strong>biosilica layer</strong> around the cell <a href="#references">(Muller et al., 2008)</a>, allowing the cell to function as a microlens. Since the shape of the lenses is a crucial property, we also overexpressed the gene <i>bolA</i> in our silica covered cells, which produces a round cell shape when overexpressed <a href="#references">(Aldea & Concha, 1988)</a>, to produce round lenses. Apart from using the lenses for microscopy, we can also use the lenses for improving the efficiency of solar panels, thin lightweight cameras with high resolution or 3D screens.</p>
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                                <h3 class="reasons-title">BIOLASERS</h3>
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                            <img src="https://static.igem.org/mediawiki/2016/2/2a/T--TU_Delft--Laser_frontpage2.png" alt="laser">
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                                <p>By turning a cell into a <strong>biolaser</strong>, we will increase the light intensity emitted by the fluorescent cell. The cell will then emit more photons  without changing the fluorophore concentration. When more photons are emitted, more photons can be detected by the microscope. A laser works by resonating photons within a closed space, in this case a cell of E. coli. We approached this by expressing <strong>fluorescent proteins</strong> within our <strong>biosilica</strong>-covered cells we used for our biolenses. When exciting the fluorophores, a fraction of the photons are trapped inside the cell by the biosilica layer. When these photons meet other excited fluorescent proteins they cause them to emit a photon with the same wavelength and direction, this process is called <strong>‘stimulated emission’</strong> <a href="#references">(Einstein, A. 1917)</a> and results in light with a higher intensity and thus more emitted photons compared to conventional fluorescence.</p>
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            <h4 class="footer-title">References</h4>
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                <li>Aldea, M., & Concha, H. C. (1988). Identification, Cloning, and Expression of bolA, an ftsZ-Dependent Morphogene of Escherichia coli. <i>Journal of Bacteriology</i>.</li>
 +
                <li>Cha, J. N., Shimizu, K., Zhou, Y., Christiansen, S. C., Chmelka, B. F., Stucky, G. D., & Morse, D. E. (1999). Silicatein filaments and subunits from a marine sponge direct the polymerization of silica and silicones in vitro.<i> Biochemistry, 96</i>, 361–365.</li>
 +
<li>Einstein, A. (1917): "Zur Quantentheorie der Strahlung". <i>Physikalische Zeitschrift 18</i>, 121-128</li>
 +
                <li>Muller, W., Engel, S., Wang, X., Wolf, S., Tremel, W., Thakur, N., … Schrodel, H. (2008). Bioencapsulation of living bacteria (Escherichia coli) with poly(silicate) after transformation with silicatein-α gene. <i>Biomaterials</i>, 29(7), 771–779. http://doi.org/10.1016/j.biomaterials.2007.10.038</li>
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{{:Team:TU_Delft/Footer}}

Latest revision as of 21:56, 19 October 2016

iGEM TU Delft

Producing biological lenses and lasers to improve microscopy

Microscopes have been around for hundreds of years and the technology behind these devices has been quickly developing over the past centuries. Microscopy has already helped us to image cells into great detail, which is essential for the identification of mechanisms behind diseases such as Alzheimer’s, of which we still don’t know the exact mechanism, but also for developing synthetic biology even further. In this age, the technology and knowledge of microscopy is no longer limiting for making detailed images of the cell; it’s the cells itself. When using fluorescence microscopy, a fluorescent cell only emits a limited number of photons, a part of this will not reach the detector. This year’s TU Delft team is using synthetic biology with the aim of improving fluorescence microscopy. There are two research lines: producing biological lenses and inventing a bacterial laser. Hover over the pictures underneath to find out more.

BIOLENSES

lenses

The goal of our biological microlenses is to increase the fraction of light captured by the detector of a microscope. Lenses are known to focus light onto a surface. By applying a layer of our biological microlenses on the detector of a microscope, we can increase the fraction of light captured. To produce microlenses, we expressed the enzyme silicatein in our cells, which catalyzes polymerization of silicic acid (Cha et al., 1999). This results in a biosilica layer around the cell (Muller et al., 2008), allowing the cell to function as a microlens. Since the shape of the lenses is a crucial property, we also overexpressed the gene bolA in our silica covered cells, which produces a round cell shape when overexpressed (Aldea & Concha, 1988), to produce round lenses. Apart from using the lenses for microscopy, we can also use the lenses for improving the efficiency of solar panels, thin lightweight cameras with high resolution or 3D screens.

BIOLASERS

laser

By turning a cell into a biolaser, we will increase the light intensity emitted by the fluorescent cell. The cell will then emit more photons without changing the fluorophore concentration. When more photons are emitted, more photons can be detected by the microscope. A laser works by resonating photons within a closed space, in this case a cell of E. coli. We approached this by expressing fluorescent proteins within our biosilica-covered cells we used for our biolenses. When exciting the fluorophores, a fraction of the photons are trapped inside the cell by the biosilica layer. When these photons meet other excited fluorescent proteins they cause them to emit a photon with the same wavelength and direction, this process is called ‘stimulated emission’ (Einstein, A. 1917) and results in light with a higher intensity and thus more emitted photons compared to conventional fluorescence.

  1. Aldea, M., & Concha, H. C. (1988). Identification, Cloning, and Expression of bolA, an ftsZ-Dependent Morphogene of Escherichia coli. Journal of Bacteriology.
  2. Cha, J. N., Shimizu, K., Zhou, Y., Christiansen, S. C., Chmelka, B. F., Stucky, G. D., & Morse, D. E. (1999). Silicatein filaments and subunits from a marine sponge direct the polymerization of silica and silicones in vitro. Biochemistry, 96, 361–365.
  3. Einstein, A. (1917): "Zur Quantentheorie der Strahlung". Physikalische Zeitschrift 18, 121-128
  4. Muller, W., Engel, S., Wang, X., Wolf, S., Tremel, W., Thakur, N., … Schrodel, H. (2008). Bioencapsulation of living bacteria (Escherichia coli) with poly(silicate) after transformation with silicatein-α gene. Biomaterials, 29(7), 771–779. http://doi.org/10.1016/j.biomaterials.2007.10.038