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

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<h1 class="text-wall-heading">Attributions</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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<h1>Attributions</h1>
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    </div>
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<p>This page is your opportunity to explain what parts of your project you did and what was done by technicians, advisers, etc. This requirement is not about literature references - these can and should be displayed throughout your wiki.
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</p>
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<h3> Bronze Medal Criterion #3</h3>
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<p> All of the work done in your project must be attributed correctly on this page. You must clearly state the work that was done by the students on your team and note any work that was done by people outside of your team, including the host labs, advisors, instructors, and individuals not on the team roster.
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<br><br>
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Please see the <a href="https://2018.igem.org/Judging/Medals">Medals requirements page</a> for more details.</p>
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            <span class="pagination-text">Description</span>
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        </a>
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<div class="column third_size">
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    </div>
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<h3> What should this page contain?</h3>
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<ul>
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<li>Clearly state what the team accomplished</li>
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<li>General Support</li>
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<li>Project support and advice</li>
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<li>Fundraising help and advice</li>
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<li>Lab support</li>
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<li>Difficult technique support</li>
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<li>Project advisor support</li>
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<li>Wiki support</li>
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<li>Presentation coaching</li>
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<li>Human Practices support</li>
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<li> Thanks and acknowledgements for all other people involved in helping make a successful iGEM team</li>
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</ul>
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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
 +
            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>
 +
            <li>Selecting the number of plasmid groups</li>
 +
            <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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<div class="column third_size">
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        </ol>
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<p>Tell us if your institution teaches an iGEM or synthetic biology class and when you started your project:</p>
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        </p>
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<ul>
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<li>Does your institution teach an iGEM or synthetic biology course?</li>
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<li>When did you start this course?</li>
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<li>Are the syllabus and course materials freely available online?</li>
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<li>When did you start your brainstorming?</li>
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<li>When did you start in the lab?</li>
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<li>When did you start working on  your project?</li>
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</ul>
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</div>
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        <p></p>
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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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            (only 1 antibiotic for up to 5 different plasmids!) and an active partitioning system to make sure that low
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            copy number plasmid groups are not lost during the division.
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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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        <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
 +
                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>
  
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<div class="column third_size">
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            <h5>Metabolic engineering</h5>
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<div class="highlight decoration_A_full">
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            <p>
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                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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<h3>Inspiration</h3>
 
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<p>Take a look at what other teams have done:</p>
 
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<ul>
 
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<li><a href="https://2011.igem.org/Team:Imperial_College_London/Team">2011 Imperial College London</a> (scroll to the bottom)</li>
 
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<li><a href="https://2014.igem.org/Team:Exeter/Attributions">2014 Exeter </a></li>
 
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<li><a href="https://2014.igem.org/Team:Melbourne/Attributions">2014 Melbourne </a></li>
 
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<li><a href="https://2014.igem.org/Team:Valencia_Biocampus/Attributions">2014 Valencia Biocampus</a></li>
 
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</ul>
 
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</div>
 
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</div>
 
  
  
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            </p>
  
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<div class="clear extra_space"></div>
 
  
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<div class="column two_thirds_size">
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        </p>
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<h3> Why is this page needed? </h3>
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        <p>
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<p>The Attribution requirement helps the judges know what you did yourselves and what you had help with. We don't mind if you get help with difficult or complex techniques, but you must report what work your team did and what work was done by others.</p>
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        </p>
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<p>
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        <table style="width:100%">
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For example, you might choose to work with an animal model during your project. Working with animals requires getting a license and applying far in advance to conduct certain experiments in many countries. This is difficult to achieve during the course of a summer, but much easier if you can work with a postdoc or PI who has the right licenses.</p>
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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>
 +
<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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                    <a class="carrot-anchor-back" href="">
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<h3> Can we base our project on a previous one? </h3>
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                        <img class="carrot-next-icon" src="https://static.igem.org/mediawiki/2018/d/d0/T--Vilnius-Lithuania--next-icon.png" />
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<p>Yes! You can have a project based on a previous team, or based on someone else's idea, <b>as long as you state this fact very clearly and give credit for the original project.</b> </p>
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                    </a>
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        <div class="invert-box">
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        <a class="invert-image">
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            <img src="https://static.igem.org/mediawiki/2018/5/5b/T--Vilnius-Lithuania--Invert-Icon.png"/>
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Revision as of 13:52, 16 October 2018

Attributions

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