Difference between revisions of "Team:Vilnius-Lithuania/Human Practices"

Line 1: Line 1:
−
{{Vilnius-Lithuania}}
+
{{Vilnius-Lithuania/InnerPage}}
 +
 
 
<html>
 
<html>
 +
<h1 class="text-wall-heading">HP Overview</h1>
 +
<div class="text-wall-area-box">
 +
    <h2 class="text-wall-area-box-heading">Lorem ipsum, dolor sit amet consectetur adipisicing</h2>
 +
    <div class="scroll-area">
 +
        <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>
  
−
<div class="column full_size">
+
        </p>
−
 
+
        <button class="read-more-button">Read More</button>
−
<h1>Human Practices</h1>
+
    </div>
−
<p>
+
−
At iGEM we believe societal considerations should be upfront and integrated throughout the design and execution of synthetic biology projects. “Human Practices” refers to iGEM teams’ efforts to actively consider how the world affects their work and the work affects the world. Through your Human Practices activities, your team should demonstrate how you have thought carefully and creatively about whether your project is responsible and good for the world. We invite you to explore issues relating (but not limited) to the ethics, safety, security, and sustainability of your project, and to show how this exploration feeds back into your project purpose, design and execution.
+
−
</p>
+
−
 
+
−
 
+
−
 
+
−
<p>For more information, please see the <a href="https://2018.igem.org/Human_Practices">Human Practices Hub</a>. There you will find:</p>
+
−
+
−
<ul>
+
−
<li> an <a href="https://2018.igem.org/Human_Practices/Introduction">introduction</a> to Human Practices at iGEM </li>
+
−
<li>tips on <a href="https://2018.igem.org/Human_Practices/How_to_Succeed">how to succeed</a> including explanations of judging criteria and advice about how to conduct and document your Human Practices work</li>
+
−
<li>descriptions of <a href="https://2018.igem.org/Human_Practices/Examples">exemplary work</a> to inspire you</li>
+
−
<li>links to helpful <a href="https://2018.igem.org/Human_Practices/Resources">resources</a></li>
+
−
<li>And more! </li>
+
−
</ul>
+
−
+
−
 
+
−
 
+
−
 
+
−
 
+
−
<p>On this page, your team should document all of your Human Practices work and activities. You should write about the Human Practices topics you considered in your project, document any activities you conducted to explore these topics (such as engaging with experts and stakeholders), describe why you took a particular approach (including referencing any work you built upon), and explain if and how you integrated takeaways from your Human Practices work back into your project purpose, design and/or execution. </p>
+
−
+
−
<p>If your team has gone above and beyond in work related to safety, then you should document this work on your Safety wiki page and provide a description and link on this page. If your team has developed education and public engagement efforts that go beyond a focus on your particular project, and for which would like to nominate your team for the Best Education and Public Engagement Special Prize, you should document this work on your Education and Education wiki page and provide a description and link here. </p>
+
−
</div>
+
−
+
−
<div class="clear"></div>
+
−
 
+
−
+
−
<div class="column full_size">
+
−
<div class="highlight decoration_background">
+
−
<p>The iGEM judges will review this page to assess whether you have met the Silver and/or Gold medal requirements based on the Integrated Human Practices criteria listed below. If you nominate your team for the <a href="https://2018.igem.org/Judging/Awards">Best Integrated Human Practices Special Prize</a> by filling out the corresponding field in the <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a>, the judges will also review this page to consider your team for that prize.
+
−
</p>
+
 
</div>
 
</div>
 +
<div class="pagination">
 +
    <div class="pagination-item-wrapper">
 +
        <a class="pagination-anchor">
 +
            <div class="pagination-item"></div>
 +
            <span class="pagination-text">Description</span>
 +
        </a>
 +
    </div>
 
</div>
 
</div>
 +
<div class="modal">
 +
    <div class="modal-close"></div>
 +
    <div class="modal-content">
 +
        <h1>Description</h1>
 +
        <p></p>
 +
        <p></p>
 +
        <h2>What is SynORI?</h2>
 +
        <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>
 +
        <p>The SynORI framework enables scientists to build a multi-plasmid system in a standardized manner by:</p>
 +
        <ol>
 +
            <li>Selecting the number of plasmid groups</li>
 +
            <li>Choosing the copy number of each group</li>
 +
            <li>Picking the type of copy number control (specific to one group or regulating all of them at once).</li>
  
−
<div class="clear extra_space"></div>
+
        </ol>
 +
        </p>
  
 +
        <p></p>
 +
        <p>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.
 +
        </p>
 +
        <p></p>
 +
        <div class="img-cont">
 +
            <img src="https://static.igem.org/mediawiki/parts/8/84/Collect.png" alt="img">
 +
            <div class="img-label">
 +
            </div>
 +
        </div>
 +
        <h2>Applications</h2>
 +
        <p>
 +
            <h5>Everyday lab work</h5>
 +
            <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.
  
−
<div class="column full_size">
 
−
 
−
<h3>Silver Medal Criterion #3</h3>
 
−
<p>Convince the judges you have thought carefully and creatively about whether your work is responsible and good for the world. Document how you have investigated these issues and engaged with your relevant communities, why you chose this approach, and what you have learned. Please note that surveys will not fulfill this criteria unless you follow scientifically valid methods. </p>
 
  
  
−
<h3>Gold Medal Criterion #1</h3>
+
            </p>
−
<p>Expand on your silver medal activity by demonstrating how you have integrated the investigated issues into the purpose, design and/or execution of your project. Document how your project has changed based upon your human practices work.
+
−
</p>
+
−
</div>
+
  
  
 +
        </p>
 +
        <p>
 +
        </p>
 +
        <table style="width:100%">
 +
<thead>
 +
<td align='center'>Species sign in ODE system</td>
 +
<td align='center'>Species</td>
 +
<td align='center'>Initial concentration (M)</td>
 +
</thead>
 +
<tbody>
 +
<tr>
 +
<td align='center'>A</td>
 +
<td align='center'>pDNA+RNA I+RNAII early</td>
 +
<td align='center'>0</td>
 +
</tr>
 +
<tr>
 +
<td align='center'>B</td>
 +
<td align='center'>pDNA+RNA II short</td>
 +
<td align='center'>0</td>
 +
</tr>
 +
<tr>
 +
<td align='center'>RNAI</td>
 +
<td align='center'>RNA I</td>
 +
<td align='center'>1E-6</td>
 +
</tr>
 +
<tr>
 +
<td align='center'>D</td>
 +
<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>
 +
<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>
 +
    </div>
 +
</div>
 +
            </div>
 +
                <div class="carrot-back">
 +
                    <a class="carrot-anchor-back" href="">
 +
                        <img class="carrot-next-icon" src="https://static.igem.org/mediawiki/2018/d/d0/T--Vilnius-Lithuania--next-icon.png" />
 +
                    </a>
 +
                </div>
 +
                <div class="carrot-next">
 +
                    <a class="carrot-anchor" href="">
 +
                        <img class="carrot-next-icon" src="https://static.igem.org/mediawiki/2018/d/d0/T--Vilnius-Lithuania--next-icon.png" />
 +
                    </a>
 +
                </div>
 +
            </div>
 +
        </div>
 +
    </div>
 +
        <div class="invert-box">
 +
        <a class="invert-image">
 +
            <img src="https://static.igem.org/mediawiki/2018/5/5b/T--Vilnius-Lithuania--Invert-Icon.png"/>
 +
        </a>
 +
        <span class="invert-text">invert</span>
 +
    </div>
 +
<script type="text/javascript" src="https://2018.igem.org/wiki/index.php?title=Template:Vilnius-Lithuania/MainJS&action=raw&ctype=text/javascript"></script>
 +
</body>
  
−
<div class="clear extra_space"></div>
+
</html>
−
 
+
−
 
+
−
 
+
−
<div class="column full_size">
+
−
<h3>Best Integrated Human Practices Special Prize</h3>
+
−
 
+
−
<p>To compete for the Best Integrated Human Practices prize, please describe your work on this page and also fill out the description on the judging form. </p>
+
−
 
+
−
<p>How does your project affect society and how does society influence the direction of your project? How might ethical considerations and stakeholder input guide your project purpose and design and the experiments you conduct in the lab? How does this feedback enter into the process of your work all through the iGEM competition? Document a thoughtful and creative approach to exploring these questions and how your project evolved in the process to compete for this award!</p>
+
−
<p>You must also delete the message box on the top of this page to be eligible for this prize.</p>
+
−
 
+
−
</div>
+

Revision as of 13:49, 16 October 2018

HP Overview

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