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

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<h1 class="text-wall-heading">Software</h1>
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        <p class="text-content">Cell-free systems are becoming an increasingly popular in vitro tool to study biological processes as it is accompanied by less intrinsic and extrinsic noise. Relying on fundamental concepts of synthetic biology, we apply a bottom-up forward engineering approach to create a novel cell-free system for unorthodox protein-evolution. The core of this system is cell-sized liposomes that serve as excellent artificial membrane models. By encapsulating genetic material and full in vitro protein transcription and translation systems within the liposomes, we create reliable and incredibly efficient nanofactories for the production of target proteins. Even though there are many alternative proteins that can be synthesized, our main focus is directed towards membrane proteins, which occupy approximately one third of living-cells’ genomes. Considering their significance, membrane proteins are spectacularly understudied since synthesis and thus characterization of them remain prevailing obstacles to this day. We aim to utilize liposomes as nanofactories for directed evolution of membrane proteins. Furthermore, by means of directed membrane protein-evolution, a universal exposition system will be designed in order to display any protein of interest on the surface of the liposome. This way, a system is built where a phenotype of a particular protein is expressed on the outside while containing its genotype within the liposome. To prove the concept, small antibody fragments will be displayed to create a single-chain variable fragment (scFv) library for rapid screening of any designated target.</p>
  
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        <button class="read-more-button">Read More</button>
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<h1>Software</h1>
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<div class="pagination">
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<h3>Best Software Tool Special Prize</h3>
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    <div class="pagination-item-wrapper">
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<p>Regardless of the topic, iGEM projects often create or adapt computational tools to move the project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can be surprisingly useful for other teams. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honor such "nuggets" of computational work.
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        <a class="pagination-anchor">
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            <div class="pagination-item"></div>
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            <span class="pagination-text">Description</span>
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        </a>
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</div>
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<div class="modal">
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    <div class="modal-close"></div>
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    <div class="modal-content">
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        <h1>Description</h1>
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        <p></p>
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        <p></p>
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        <h2>What is SynORI?</h2>
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        <p>SynORI stands for synthetic origin of replication. It is a framework designed to make working with single
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            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>
  
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<br><br>
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        <p></p>
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To compete for the <a href="https://2018.igem.org/Judging/Awards">Best Software Tool prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a>.
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        <p>The framework also includes a possibility of adding a selection system that reduces the usage of antibiotics
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<br><br>
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            (only 1 antibiotic for up to 5 different plasmids!) and an active partitioning system to make sure that low
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You must also delete the message box on the top of this page to be eligible for this prize.
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            copy number plasmid groups are not lost during the division.
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</p>
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        </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>
 +
                A multi-plasmid system that is easy to assemble and control. With our framework the need to limit your
 +
                research to a particular plasmid copy number just because there are not enough right replicons to
 +
                choose from, is eliminated. With SynORI you can easily create a vector with a desired copy number that
 +
                suits your needs.</li>
 +
            </p>
 +
            <h5>Biological computing</h5>
 +
            <p>
 +
                The ability to choose a wide range of copy number options and their control types will make the
 +
                synthetic biology engineering much more flexible and predictable. Introduction of plasmid copy number
 +
                regulation is equivalent to adding a global parameter to a computer system. It enables the coordination
 +
                of multiple gene group expression.
 +
            </p>
 +
            <h5>Smart assembly of large protein complexes</h5>
 +
            <p>
 +
                The co-expression of multi-subunit complexes using different replicons brings incoherency to an already
 +
                chaotic cell system. This can be avoided by using SynORI, as in this framework every plasmid group uses
 +
                the same type of control, and in addition can act in a group-specific manner.</p>
  
 +
            <h5>Metabolic engineering</h5>
 +
            <p>
 +
                A big challenge for heterologous expression of multiple gene pathways is to accurately adjust the
 +
                levels of each enzyme to achieve optimal production efficiency. Precise promoter tuning in
 +
                transcriptional control and synthetic ribosome binding sites in translational control are already
 +
                widely used to maintain expression levels. In addition to current approaches, our framework allows a
 +
                simultaneous multiple gene control. Furthermore, an inducible regulation that we offer, can make the
 +
                search for perfect conditions a lot easier.
  
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<div class="column third_size">
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<div class="highlight decoration_A_full">
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            </p>
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<h3> Inspiration </h3>
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<p>
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Here are a few examples from previous teams:
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        </p>
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</p>
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        <p>
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<ul>
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        </p>
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<li><a href="https://2016.igem.org/Team:BostonU_HW">2016 BostonU HW</a></li>
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        <table style="width:100%">
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<li><a href="https://2016.igem.org/Team:Valencia_UPV">2016 Valencia UPV</a></li>
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<thead>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Software">2014 Heidelberg</a></li>
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<td align='center'>Species sign in ODE system</td>
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<li><a href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#Software">2014 Aachen</a></li>
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<td align='center'>Species</td>
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</ul>
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<td align='center'>Initial concentration (M)</td>
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</div>
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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>
 +
<tr>
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<td align='center'>B</td>
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<td align='center'>pDNA+RNA II short</td>
 +
<td align='center'>0</td>
 +
</tr>
 +
<tr>
 +
<td align='center'>RNAI</td>
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<td align='center'>RNA I</td>
 +
<td align='center'>1E-6</td>
 +
</tr>
 +
<tr>
 +
<td align='center'>D</td>
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<td align='center'>pDNA+RNA II long</td>
 +
<td align='center'>0</td>
 +
</tr>
 +
<tr>
 +
<td align='center'>E</td>
 +
<td align='center'>pDNA+RNAII primer</td>
 +
<td align='center'>0</td>
 +
</tr>
 +
<tr>
 +
<td align='center'>F</td>
 +
<td align='center'>RNA II long</td>
 +
<td align='center'>0</td>
 +
</tr>
 +
<tr>
 +
<td align='center'>G</td>
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<td align='center'>pDNA</td>
 +
<td align='center'>4E-8*</td>
 +
</tr>
 +
<tr>
 +
<td align='center'>H</td>
 +
<td align='center'>pDNA+RNA II+RNA I late</td>
 +
<td align='center'>0</td>
 +
</tr>
 +
<tr>
 +
<td align='center'>RNA II</td>
 +
<td align='center'>RNA II</td>
 +
<td align='center'>0</td>
 +
</tr>
 +
<tr>
 +
<td align='center'>J</td>
 +
<td align='center'>RNAI+RNAII</td>
 +
<td align='center'>0</td>
 +
</tr>
 +
</tbody>
 +
</table>
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    </div>
 
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Revision as of 13:46, 16 October 2018

Software

Lorem ipsum, dolor sit amet consectetur adipisicing

Cell-free systems are becoming an increasingly popular in vitro tool to study biological processes as it is accompanied by less intrinsic and extrinsic noise. Relying on fundamental concepts of synthetic biology, we apply a bottom-up forward engineering approach to create a novel cell-free system for unorthodox protein-evolution. The core of this system is cell-sized liposomes that serve as excellent artificial membrane models. By encapsulating genetic material and full in vitro protein transcription and translation systems within the liposomes, we create reliable and incredibly efficient nanofactories for the production of target proteins. Even though there are many alternative proteins that can be synthesized, our main focus is directed towards membrane proteins, which occupy approximately one third of living-cells’ genomes. Considering their significance, membrane proteins are spectacularly understudied since synthesis and thus characterization of them remain prevailing obstacles to this day. We aim to utilize liposomes as nanofactories for directed evolution of membrane proteins. Furthermore, by means of directed membrane protein-evolution, a universal exposition system will be designed in order to display any protein of interest on the surface of the liposome. This way, a system is built where a phenotype of a particular protein is expressed on the outside while containing its genotype within the liposome. To prove the concept, small antibody fragments will be displayed to create a single-chain variable fragment (scFv) library for rapid screening of any designated target.

Description

What is SynORI?

SynORI stands for synthetic origin of replication. It is a framework designed to make working with single and multi-plasmid systems precise, easy and on top of that - more functional.

The SynORI framework enables scientists to build a multi-plasmid system in a standardized manner by:

  1. Selecting the number of plasmid groups
  2. Choosing the copy number of each group
  3. Picking the type of copy number control (specific to one group or regulating all of them at once).

The framework also includes a possibility of adding a selection system that reduces the usage of antibiotics (only 1 antibiotic for up to 5 different plasmids!) and an active partitioning system to make sure that low copy number plasmid groups are not lost during the division.

img

Applications

Everyday lab work

A multi-plasmid system that is easy to assemble and control. With our framework the need to limit your research to a particular plasmid copy number just because there are not enough right replicons to choose from, is eliminated. With SynORI you can easily create a vector with a desired copy number that suits your needs.

Biological computing

The ability to choose a wide range of copy number options and their control types will make the synthetic biology engineering much more flexible and predictable. Introduction of plasmid copy number regulation is equivalent to adding a global parameter to a computer system. It enables the coordination of multiple gene group expression.

Smart assembly of large protein complexes

The co-expression of multi-subunit complexes using different replicons brings incoherency to an already chaotic cell system. This can be avoided by using SynORI, as in this framework every plasmid group uses the same type of control, and in addition can act in a group-specific manner.

Metabolic engineering

A big challenge for heterologous expression of multiple gene pathways is to accurately adjust the levels of each enzyme to achieve optimal production efficiency. Precise promoter tuning in transcriptional control and synthetic ribosome binding sites in translational control are already widely used to maintain expression levels. In addition to current approaches, our framework allows a simultaneous multiple gene control. Furthermore, an inducible regulation that we offer, can make the search for perfect conditions a lot easier.

Species sign in ODE system Species Initial concentration (M)
A pDNA+RNA I+RNAII early 0
B pDNA+RNA II short 0
RNAI RNA I 1E-6
D pDNA+RNA II long 0
E pDNA+RNAII primer 0
F RNA II long 0
G pDNA 4E-8*
H pDNA+RNA II+RNA I late 0
RNA II RNA II 0
J RNAI+RNAII 0
invert