Difference between revisions of "Team:Vilnius-Lithuania/Demonstrate"

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         <h1>Description</h1>
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         <h1>Proof</h1>
         <p></p>
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         <p>The proof of SynDrop’s concept consists of several critical steps:</p>
        <p></p>
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<ul>
        <h2>What is SynORI?</h2>
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    <li>We have specified the parameters for cell-sized liposome (5-30 µm) synthesis by using our COMSOL model.</li>
        <p>SynORI stands for synthetic origin of replication. It is a framework designed to make working with single
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</ul>
            and multi-plasmid systems precise, easy and on top of that - more functional.</p>
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        <p>The SynORI framework enables scientists to build a multi-plasmid system in a standardized manner by:</p>
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        <ol>
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            <li>Selecting the number of plasmid groups</li>
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            <li>Choosing the copy number of each group</li>
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            <li>Picking the type of copy number control (specific to one group or regulating all of them at once).</li>
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        </ol>
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<p>We have concluded that modifications to microfluidic channels affect our system the most (5 µm change in width increased liposome diameter by almost 6 µm), while viscosity and flow rate regulations proved to be an efficient way to fine-tune liposome size in a range of few micrometers (Fig. 1). Moreover, critical value of flow rate ratio was found (Q = 0.7), at which liposomes stopped forming.
        </p>
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    </p>
  
        <p></p>
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                  <div class="image-container">
        <p>The framework also includes a possibility of adding a selection system that reduces the usage of antibiotics
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                          <img src="https://static.igem.org/mediawiki/2018/e/ed/T--Vilnius-Lithuania--dv_fig1a_Model.gif" style="max-width:100%" />
            (only 1 antibiotic for up to 5 different plasmids!) and an active partitioning system to make sure that low
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                          <p><strong>Fig. 1 </strong> Visual representation of liposome formation based on baseline experimental parametric values. Phase variables A, B and C here have values of 1, 2 and 3 respectively.</p>
            copy number plasmid groups are not lost during the division.
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              </div>
        </p>
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        <p></p>
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        <div class="img-cont">
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            <img src="https://static.igem.org/mediawiki/parts/8/84/Collect.png" alt="img">
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            <div class="img-label">
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            </div>
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        </div>
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        <h2>Applications</h2>
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        <p>
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            <h5>Everyday lab work</h5>
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            <p>
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                A multi-plasmid system that is easy to assemble and control. With our framework the need to limit your
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                research to a particular plasmid copy number just because there are not enough right replicons to
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                choose from, is eliminated. With SynORI you can easily create a vector with a desired copy number that
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                suits your needs.</li>
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            </p>
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            <h5>Biological computing</h5>
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            <p>
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                The ability to choose a wide range of copy number options and their control types will make the
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                synthetic biology engineering much more flexible and predictable. Introduction of plasmid copy number
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                regulation is equivalent to adding a global parameter to a computer system. It enables the coordination
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                of multiple gene group expression.
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            </p>
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            <h5>Smart assembly of large protein complexes</h5>
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            <p>
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                The co-expression of multi-subunit complexes using different replicons brings incoherency to an already
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                chaotic cell system. This can be avoided by using SynORI, as in this framework every plasmid group uses
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                the same type of control, and in addition can act in a group-specific manner.</p>
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            <h5>Metabolic engineering</h5>
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            <p>
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                A big challenge for heterologous expression of multiple gene pathways is to accurately adjust the
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                levels of each enzyme to achieve optimal production efficiency. Precise promoter tuning in
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                transcriptional control and synthetic ribosome binding sites in translational control are already
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                widely used to maintain expression levels. In addition to current approaches, our framework allows a
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                simultaneous multiple gene control. Furthermore, an inducible regulation that we offer, can make the
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                search for perfect conditions a lot easier.
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            </p>
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        </p>
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        <p>
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        </p>
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        <table style="width:100%">
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<thead>
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<td align='center'>Species sign in ODE system</td>
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<td align='center'>Species</td>
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<td align='center'>Initial concentration (M)</td>
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</thead>
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<tbody>
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<tr>
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<td align='center'>A</td>
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<td align='center'>pDNA+RNA I+RNAII early</td>
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<td align='center'>0</td>
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</tr>
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<tr>
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<td align='center'>B</td>
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<td align='center'>pDNA+RNA II short</td>
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<td align='center'>0</td>
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</tr>
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<tr>
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<td align='center'>RNAI</td>
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<td align='center'>RNA I</td>
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<td align='center'>1E-6</td>
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</tr>
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<tr>
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<td align='center'>D</td>
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<td align='center'>pDNA+RNA II long</td>
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<td align='center'>0</td>
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</tr>
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<tr>
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<td align='center'>E</td>
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<td align='center'>pDNA+RNAII primer</td>
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<td align='center'>0</td>
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</tr>
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<tr>
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<td align='center'>F</td>
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<td align='center'>RNA II long</td>
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<td align='center'>0</td>
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</tr>
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<tr>
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<td align='center'>G</td>
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<td align='center'>pDNA</td>
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<td align='center'>4E-8*</td>
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</tr>
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<tr>
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<td align='center'>H</td>
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<td align='center'>pDNA+RNA II+RNA I late</td>
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<td align='center'>0</td>
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</tr>
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<tr>
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<td align='center'>RNA II</td>
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<td align='center'>RNA II</td>
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<td align='center'>0</td>
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</tr>
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<tr>
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<td align='center'>J</td>
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<td align='center'>RNAI+RNAII</td>
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<td align='center'>0</td>
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</tr>
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</tbody>
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</table>
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Revision as of 21:16, 4 November 2018

Proof of Concept

The Composite Proof

We proved that our SynDrop system worked as intended by successfully implementing several critical wet lab and dry lab experiments. First, we have created a model to determine microfluidics variables for optimal liposome synthesis. Second, we synthesized stable biocompatible liposomes and demonstrated an internal transcription and translation of functional proteins. Third, we demonstrated that membrane proteins can successfully integrate into our liposomes. Finally, we constructed working fusion proteins that were able to display a designated tag on the outer membrane.

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