Team:Hong Kong HKUST/riboregulator/CR TA Feature Page

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<ul>
<ul>
                 <li><a href="#">Overview</a></li>
                 <li><a href="#">Overview</a></li>
-
                 <li><a href="#">module one </a></li>
+
                 <li><a href="#">Module one </a></li>
-
                 <li><a href="#">module two</a></li>
+
                 <li><a href="#">Module two</a></li>
-
<li><a href="#">data</a></li>
+
<li><a href="#">Data</a></li>
-
<li><a href="#">characterization</a></li>
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<li><a href="#">Characterization</a></li>
             </ul></li>
             </ul></li>
             <li><a href="#">Side Project</a>
             <li><a href="#">Side Project</a>
<ul>
<ul>
-
                 <li><a href="#">overview</a></li>
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                 <li><a href="#">Overview</a></li>
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                 <li><a href="#">part</a></li>
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                 <li><a href="#">Parts</a></li>
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                 <li><a href="#">catalogue</a></li>
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                 <li><a href="#">Catalogue</a></li>
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<li><a href="#">feature pages</a></li>
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<li><a href="#">Feature pages</a></li>
             </ul></li>
             </ul></li>
        
        
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         <li><a href="#">Human Practice</a>
         <li><a href="#">Human Practice</a>
<ul>
<ul>
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                 <li><a href="#">overview</a></li>
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                 <li><a href="#">Overview</a></li>
                 <li><a href="#">Start up kit</a>
                 <li><a href="#">Start up kit</a>
<ul>
<ul>
-
<li><a href="#">interview</a></li>
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<li><a href="#">Interview</a></li>
<li><a href="#">Report</a></li>
<li><a href="#">Report</a></li>
<li><a href="#">Database</a></li>
<li><a href="#">Database</a></li>
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<li><a href="#">Protocol</a></li>
<li><a href="#">Protocol</a></li>
<li><a href="#">Notebook</a></li>
<li><a href="#">Notebook</a></li>
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<li><a href="#">safety</a></li>
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<li><a href="#">Safety</a></li>
</ul></li>
</ul></li>
         <li><a href="#">Achievement</a>
         <li><a href="#">Achievement</a>
<ul>
<ul>
<li><a href="#">Medal Requirement</a></li>
<li><a href="#">Medal Requirement</a></li>
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<li><a href="#">deliverable</a></li>
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<li><a href="#">Deliverable</a></li>
</ul></li>
</ul></li>
 +
<li class= "logo"><a href="https://2014.igem.org/Main_Page"> <img src="Igemlogo_whiteletters.png" height="45px"> </a> </li>
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<li class= "logo"><a href="http://www.ust.hk/"> <img src="HKUST_logo.png" height="45px"> </a></li>
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</ul>
</ul>
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</div>
</div>
<hr>
<hr>
-
<div id="description_area">
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<div class="feature_page_content">
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<h2>Riboregulator Feature Page</h2>
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<h2>Riboregulator Feature Page</h2>
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<div class="content_image_large"><!--for image with 900px width-->
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<h6>-HKUST iGEM 2014 Team-</h6>
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<img src= "figure1.png">
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<hr>
-
<h5>Figure 1. Artificial riboregulator system used to control post-transcriptional regulation (Isaacs et al.,2004). </h5>
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<h2>Introduction to riboregulators</h2>
-
</div>
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<hr>
-
<p>Regulatory RNAs are small RNA that regulates biological processes such as transcription or translation.  
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<div class = "feature_page_image_container">
-
The use of regulatory RNAs has been a great interest in the field of synthetic biology because it provides an  
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<img src="riboregulator_figure.png">
-
additional level of regulation for biological circuits and systems. Regulatory RNAs have also used by many iGEM  
+
<h3>Figure 1. </h3>
-
teams. We have identified 7 teams that have used cis-repressing (CR) and trans-activating (TA) riboregulator system
+
<h4> Artificial riboregulator system used to control post-transcriptional regulation (Isaacs et al.,2004). </h4>
-
and more teams that have used riboswitches. For example, Isaacs 2005, UC Berkeley 2006 and Caltech 2007  
+
</div>
-
contributed many CR and TA devices to the Registry.   
+
<p>
 +
Regulatory RNAs are small RNA that regulates biological  
 +
processes such as transcription or translation. The use of  
 +
regulatory RNAs has been a great interest in the field of
 +
synthetic biology because it provides an additional level  
 +
of regulation for biological circuits and systems. Regulatory
 +
RNAs have also used by many iGEM teams. We have identified 7 teams
 +
that have used cis-repressing (CR) and trans-activating (TA)  
 +
riboregulator system and more teams that have used riboswitches.  
 +
For example, Isaacs 2005, UC Berkeley 2006 and Caltech 2007  
 +
contributed many CR and TA devices to the Registry.  
 +
</p>
 +
<p>
 +
Artificial cis-repressing and trans-activating riboregulator system was introduced to the iGEM community by the UC Berkeley iGEM 2005 team.
 +
The riboregulator system as a whole acts to regulate translation
 +
at the RNA level. One component of the system ,crRNA, which contains
 +
a cis-repressing sequence 5&#39; of the RBS, RBS, and gene of interest. The cis-repressing sequence can form a loop form complementary
 +
base pairs with the RBS to prevent the recognition of RBS by ribosomes. The translation crRNA is also commonly described as a &quot;lock&quot; because it &quot;locks&quot;
 +
the RBS and prevent translation. The &quot;key&quot; to this system is the taRNA.
 +
taRNA can interact (in trans) with the cis-repressing sequence to unlock the RBS and therefore to activate translation (Figure 1.).
 +
</p>
 +
<p>
 +
The benefits of this system, as described in Isaacs et al.&#39;s paper,
 +
are leakage minimization, fast response time, tunability,
 +
independent regulation of multiple genes etc<sup>1</sup>.
 +
</p>
 +
 +
<table id= "team_info_table">
 +
<tr>
 +
<th>Team</th>
 +
<th>Track</th>
 +
<th>Chassis </th>
 +
</tr>
 +
<tr>
 +
<td>Berkeley 2006 </td>
 +
<td>This team has not been assigned to a track.</td>
 +
<td>E. coli </td>
 +
</tr>
 +
<tr>
 +
<td>Caltech 2007</td>
 +
<td>Foundational Research</td>
 +
<td>E. coli </td>
 +
</tr>
 +
<tr>
 +
<td>Delft 2009</td>
 +
<td>Information Processing</td>
 +
<td>E. coli </td>
 +
</tr>
 +
<tr>
 +
<td>Groningen 2011</td>
 +
<td>Information Processing</td>
 +
<td>E. coli </td>
 +
</tr>
 +
<tr>
 +
<td>K.U. Leuven 2008</td>
 +
<td>This team has not been assigned to a track.</td>
 +
<td>E. coli </td>
 +
</tr>
 +
<tr>
 +
<td>K.U. Leuven 2009</td>
 +
<td>Manufacturing</td>
 +
<td>E. coli</td>
 +
</tr>
 +
<tr>
 +
<td>Melbourne 2008</td>
 +
<td>This team has not been assigned to a track.</td>
 +
<td>E. coli</td>
 +
</tr>
 +
<tr>
 +
<td>Peking 2007</td>
 +
<td>Information Processing</td>
 +
<td>E. coli</td>
 +
</tr>
 +
<tr>
 +
<td>Victoria BC 2009</td>
 +
<td>Manufacturing</td>
 +
<td>E. coli</td>
 +
</tr>
 +
 +
</table>
 +
 +
 +
 +
 +
</div>
 +
<hr>
 +
 +
<div class="feature_page_content">
 +
<h2>Riboregulator parts in the Registry</h2>
 +
<hr>
 +
 +
<table id= "part_info_table">
 +
<tr>
 +
<th>Name</th>
 +
<th>Description</th>
 +
<th>Length</th>
 +
<th>Designed by</th>
 +
<th>Group </th>
 +
</tr>
 +
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_J01008">BBa_J01008</a></td>
 +
<td>Riboregulator  key 1 </td>
 +
<td>94</td>
 +
<td>Golden Bear</td>
 +
<td>iGEM2005 </td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_J01010">BBa_J01010</a></td>
 +
<td>Riboregulator Lock 1</td>
 +
<td>40</td>
 +
<td>Golden Bear</td>
 +
<td>iGEM2005 </td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_J01086">BBa_J01086</a></td>
 +
<td>Key3 </td>
 +
<td>94</td>
 +
<td>Golden Bear</td>
 +
<td>iGEM2005 </td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_J01080">BBa_J01080</a></td>
 +
<td>Lock3 </td>
 +
<td>40</td>
 +
<td>Golden Bear</td>
 +
<td>iGEM2005 </td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K175029">BBa_K175029</a></td>
 +
<td>Lock for weak RBS (B0031) from the lock/key library TUD09</td>
 +
<td>49</td>
 +
<td>Daniel Solis Escalante</td>
 +
<td>iGEM09_TUDelft </td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K175030">BBa_K175030</a></td>
 +
<td>Key for lock of weak (K175029) RBS (B0031) from the lock/key library TUD09</td>
 +
<td>86</td>
 +
<td>Daniel Solis Escalante  </td>
 +
<td>iGEM09_TUDelft </td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K175031">BBa_K175031</a></td>
 +
<td>Lock for medium RBS (B0032) from the lock/key library TUD09</td>
 +
<td>47</td>
 +
<td>Daniel Solis Escalante  </td>
 +
<td>iGEM09_TUDelft </td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_K175032">BBa_K175032</a></td>
 +
<td>Key for lock of medium (K175031) RBS (B0032) from the lock/key library TUD09</td>
 +
<td>84</td>
 +
<td>Daniel Solis Escalante  </td>
 +
<td>iGEM09_TUDelft </td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_I759036">BBa_I759036</a></td>
 +
<td>Ptet_cis3_YFP</td>
 +
<td>829</td>
 +
<td>Kat Pak </td>
 +
<td>iGEM07_Caltech</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_I759022">BBa_I759022</a></td>
 +
<td>pBAD-trans1</td>
 +
<td>1693</td>
 +
<td>Kat Pak </td>
 +
<td>iGEM07_Caltech</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_I759023">BBa_I759023</a></td>
 +
<td>pBAD-trans2</td>
 +
<td>1706</td>
 +
<td>Kat Pak </td>
 +
<td>iGEM07_Caltech</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_J23066">BBa_J23066</a></td>
 +
<td>[key3c][key3d][B0015]</td>
 +
<td>336</td>
 +
<td>Will Bosworth</td>
 +
<td>iGEM2006_Berkeley</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_J23078">BBa_J23078</a></td>
 +
<td>lock3i</td>
 +
<td>52</td>
 +
<td>John Anderson </td>
 +
<td>iGEM2006_Berkeley</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_J23008">BBa_J23008</a></td>
 +
<td>key3c</td>
 +
<td>94</td>
 +
<td>Kaitlin Davis </td>
 +
<td>iGEM2006_Berkeley</td>
 +
</tr>
 +
<tr>
 +
<td><a href="http://parts.igem.org/Part:BBa_J23032">BBa_J23032</a></td>
 +
<td>lock3d</td>
 +
<td>43</td>
 +
<td>John Anderson </td>
 +
<td>iGEM2006_Berkeley</td>
 +
</tr>
 +
 +
</table>
 +
 +
</div>
 +
 +
<div class="feature_page_content">
 +
<h2>Usage of riboregulator by different iGEM teams</h2>
 +
<hr>
 +
 +
<p>
 +
The usage of the riboregulator system can be versatile; Different
 +
teams utilized the system in different ways. In general, introducing the
 +
riboregulator system to a certain circuit allows another level regulation. The new
 +
level of regulation then can give possible outcomes such as: specific interaction/communication
 +
(UC Berekeley 2006/ Caltech 2007); minimization of leakage by introducing post-transcriptional
 +
repression (Calgary 2007); and modulation of different concentrations of desired outcome (K.U. Leuven 2009).   
</p>
</p>
 +
 +
</div>
 +
 +
 +
<div class="feature_page_content">
 +
<h2><a href="https://2006.igem.org/wiki/index.php/University_of_California_Berkeley_2006">UC Berkeley 2006</a></h2>
 +
<hr>
 +
<h5 class= "page_link"><a href="https://2006.igem.org/wiki/index.php/Berkeley2006-RiboregulatorsMain"> Berkeley riboregulator page </a></h5>
 +
<img src="UC_berkeley_2006.png">
 +
<p>
<p>
-
Artificial cis-repressing and trans-activating riboregulator system was introduced to the  
+
<strong>Abstract: </strong>
-
iGEM community by Isaacs in 2005. The riboregulator system as a whole acts to regulate
+
Networks of interacting cells provide the basis for neural learning.  
-
translation at the RNA level. One component of the system ,crRNA, which contains a cis-repressing sequence 5&#39;
+
We have developed the process of addressable conjugation for
-
of the RBS, RBS, and gene of interest. The cis-repressing sequence can form a loop form
+
communication within a network of E. coli bacteria. Here, bacteria
-
complementary base pairs with the RBS to prevent the recognition of RBS by ribosomes.
+
send messages to one another via conjugation of plasmid DNAs, but
-
The translation  crRNA is also commonly described as a &quot;lock&quot; because it &quot;locks&quot; the RBS and prevent
+
the message is only meaningful to cells with a matching address
-
translation. The &quot;key&quot; to this system is the taRNA. taRNA can interact (in trans) with the cis-repressing
+
sequence. In this way, the Watson Crick base-pairing of addressing
-
sequence to unlock the RBS and therefore to activate translation (Figure 1.).  
+
sequences replaces the spatial connectivity present in neural systems.
 +
To construct this system, we have adapted natural conjugation systems
 +
as the communication device. Information contained in the transferred
 +
plasmids is only accessible by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures.  
 +
Ultimately, this will allow us to develop networks of bacteria capable of
 +
trained learning.  
</p>
</p>
 +
 +
<img src="UC_berkeley_2006_3.png" class= "large_img">
 +
<p>Berkeley Riboregulator Reference :</p>
 +
<ol>
 +
 +
<li>Isaacs, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. "Engineered riboregulators enable post-transcriptional control of gene expression"</li>
 +
 +
</ol>
 +
</div>
 +
 +
 +
 +
<div class="feature_page_content">
 +
<h2><a href="https://2007.igem.org/Calgary">Calgary 2007</a></h2>
 +
<hr>
 +
<h5 class= "page_link"><a href="https://2007.igem.org/Calgary/constructing_wetlab">Calgary riboregulator page </a></h5>
<p>
<p>
-
The benefits of this system, as described in Isaacs et al.&#39 s paper, are leakage minimization,  
+
<strong>Abstract: </strong>
-
fast response time, tunability, independent regulation of multiple genes etc<sup>1</sup>.  
+
The project we selected was to design and build a biomechanical printer; composed of a two dimensional plotter
 +
equipped with a red laser, software to translate computer images into instructions for the plotter, and E. coli
 +
cells engineered to respond to the laser light. Bacteria are spread in a solid lawn on the plate,
 +
or mixed in the media before pouring the plate. The response triggered by this biological circuit will produce beta agarase,  
 +
an enzyme which degrades the agar polymer that the cells rest on.
</p>
</p>
 +
<p>The printer can then be used to "draw" high resolution images on the bacteria with the laser. The bacteria will then dissolve the agar where the laser was shone. This results in Bacterial Lithography, where the dissolved agar forms a picture.</p>
 +
<p>We also chose a second project to include in our entry to the competition this year. That is an in Silico Biobrick Evolution system. The purpose of this project is to design a system that will accept user entered parameters and use them to search through the registry database. Using the given parameters the system will try to construct circuits (a series of biobricks) that will produce the desired  product. More information on this project can be found in our evoGEM sections.</p>
 +
</div>
 +
 +
 +
<div class="feature_page_content">
 +
<h2><a href="https://2007.igem.org/wiki/index.php/Caltech/Highlights">Caltech 2007</a></h2>
 +
<hr>
 +
<h5 class= "page_link"><a href="http://openwetware.org/wiki/IGEM:Caltech/2007/Project/Riboregulator">Caltech riboregulator page </a></h5>
 +
 +
<img src ="caltech2007.png">
 +
<p>
 +
<strong>Abstract: </strong>
 +
Our project attacks the following problem: can one engineer viruses to selectively kill or modify specific subpopulations of target cells, based on their RNA or protein expression profiles?
 +
</p>
 +
<p>
 +
This addresses an important issue in gene therapy, where viruses engineered for fine target discrimination would selectively kill only those cells over- or under-expressing specific disease or cancer associated genes. Alternatively, these viruses could be used to discriminate between strains in a bacterial co-culture, allowing strain-specific modification or lysis.
 +
</p>
 +
<p>
 +
This is clearly an ambitious goal, so we brainstormed a simple model of this problem suitable for undergraduates working over a summer. The bacteriophage λ is a classic, well studied virus capable of infecting E. coli, another classic model genetic system. We therefore seek to engineer a λ strain targeted to lyse specific subpopulations of E. coli based on their transcriptional profiles. Together, λ and E. coli provide a tractable genetic model for this larger problem, while hopefully providing lessons applicable to more ambitious, future projects.
 +
</p>
 +
<p>
 +
Caltech Riboregulator references
 +
</p>
 +
 +
<ol>
 +
 +
<li>Isaacs, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. "Engineered riboregulators enable post-transcriptional control of gene expression"</li>
 +
 +
</ol>
</div>
</div>
-
<!-- one row of content , two column-->
+
<div class="feature_page_content">
-
<div class='content_1'>
+
<h2><a href="https://2009.igem.org/Team:TUDelft">Delft 2009</a></h2>
-
<h3>This will be a title </h3>
+
<hr>
-
<table class="content_table" align= "center" >
+
<h5 class= "page_link"><a href="https://2009.igem.org/Team:TUDelft/Lock/Key_library">Delft Riboregulator page </a></h5>
-
<tr class= "content_row">
+
-
<td class= "content_cell">
+
-
<div class= "content_area">
+
-
<p>The meaning of life is a philosophical question concerning the significance of life or existence in general.  
+
-
It can also be expressed in different forms, such as "Why are we here?", "What is life all about?",
+
-
and "What is the purpose of existence?" It has been the subject of much philosophical, scientific,
+
-
and theological speculation throughout history.  
+
-
There have been a large number of proposed answers to these questions from many different cultural and ideological backgrounds.
+
-
The meaning of life is in the philosophical and religious conceptions of existence, social ties, consciousness, and happiness,
+
-
and borders on many other issues, such as symbolic meaning, ontology, value, purpose, ethics, good and evil, free will,
+
-
the existence of one or multiple gods, conceptions of God, the soul, and the afterlife. </p>
+
-
</div>
+
-
</td>
+
-
<td class= "content_cell">
+
-
+
-
<div class= "content_area">
+
-
<div class="content_image">
+
-
<img src= "potato.jpg"/>
+
-
<h5>Fig 1 . Here is the potato.</h5>
+
-
<h6> Here is the description of the potato: it is a potato!</h6>
+
-
</div>
+
-
<p>
+
-
Scientific contributions focus primarily on describing related empirical facts about the universe,
+
-
exploring the context and parameters concerning the 'how' of life.
+
-
Science also studies and can provide recommendations for the pursuit of well-being and a related conception of morality.
+
-
</p>
+
-
</div>
+
-
</td>
+
-
</tr>
+
<p>
 +
<strong>Abstract: </strong>
 +
Our project aims to design a genetic device able to count and memorize the occurrences of an input signal. We achieved this by utilization of auto-inducing loops, that act as memory units, and an engineered riboregulator, acting as an AND gate. The design of the device is modular, allowing free change of both input and output signals. Each increase of the counter results in a different output signal. The design allows implementation of any number of memory units, as the AND gate design enables to extend the system in a hassle-free way. In order to tweak bistable autoinducing loops we need a very fast and robust method for characterizing parts. For this we have created a genetic algorithm that will enable us to find parameters of the parts used in the design. It also allows the combination of data from multiple experiments across models with overlapping components
 +
</p>
 +
 +
<p>
 +
Delft Riboregulator references 
 +
</p>
 +
<ol>
 +
 +
<li>Smolke C, 2009, It&#39;s the DNA That Counts, Science, 324:1156-1157.</li>
 +
<li>Sprinzak D and Elowitz M, 2005, Reconstruction of genetic circuits, Nature, 438-24:443-448.</li>
 +
<li>Isaacs F, Dwyer d and Collins J, 2006, RNA synthetic biology, Nature Biotech., 24:545-554.</li>
 +
<li>Anderson C, Voigt C and Arkin A, 2007, Environmental signal integration by a modular AND gate, Molecular systems biology, 3-133:1-8.</li>
 +
<li>Isaacs F, Dwyer d and Collins J, 2004, Engineered riboregulators enable post-transcriptional control of gene expression, Nature Biotechnology, 22-7:841-847.</li>
 +
</ol>
 +
 +
</div>
 +
<div class="feature_page_content">
 +
<h2><a href="https://2011.igem.org/Team:Groningen">Groningen 2011</a></h2>
 +
<hr>
 +
<h5 class= "page_link"><a href="https://2011.igem.org/Team:Groningen/project_AND_gate">Groningen Riboregulator page </a></h5>
 +
 +
<img src ="Groningen_2011_2.png">
 +
<p>
 +
<strong>Abstract: </strong>
 +
In our project we aim to create a cell-to-cell communication system that allows the propagation of a multi-task message with the capability of being reset. To achieve this, the system will include a reengineered conjugation system, a time-delay genetic circuit and a self-destructive plasmid. This system could be the basis for creating a long distance biosensor and/or be applied in reducing antibiotic resistance of bacteria. Furthermore, we have done a parallel research on the different perceptions of iGEM participants and supervisors on ethical issues in synthetic biology. We focused on the consequences of the ultimate conditions of the top-down and bottom-up approaches as applied in biology.
 +
</p>
 +
<p>
 +
Groningen Riboregulator reference
 +
</p>
 +
 +
<ol>
 +
<li>Isaacs, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. "Engineered riboregulators enable post-transcriptional control of gene expression"</li>
 +
</ol>
 +
 +
</div>
 +
<div class="feature_page_content">
 +
<h2><a href="https://2008.igem.org/Team:KULeuven">K.U. Leuven 2008 </a></h2>
 +
<hr>
 +
<h5 class= "page_link"><a href="https://2008.igem.org/Team:KULeuven/Project/Reset">K.U Leuven 2008 Riboregulator page</a></h5>
 +
 +
<p>
 +
<strong>Abstract: </strong>
 +
Imagine a bacterium that produces a drug when and where it is needed in the human body. It would have several advantages over classical drugs and could have many medical applications. In this framework we proudly present our team's project: Dr. Coli, the bacterial drug delivery system. Dr. Coli senses the disease signal and produces the appropriate amount of drugs to meet the individual patient's needs. And when the patient is cured, Dr. Coli self-destructs. To do this, a molecular timer registers the time since the last disease signal sensed. But when the disease flares up again, this timer is reset and drug production is resumed. Within the time frame of the iGEM competition, we developed a proof of concept of Dr. Coli. The most important assets are massive reuse of standard biobricks, different control mechanisms and extensive modeling.
 +
</p>
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</div>
</div>
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<div class="feature_page_content">
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<h2><a href="https://2009.igem.org/Team:KULeuven">K.U. Leuven 2009 </a></h2>
 +
<hr>
 +
<h5 class= "page_link"><a href="https://2009.igem.org/Team:KULeuven/Design/Key_Antikey">K.U Leuven 2009 Riboregulator page</a></h5>
 +
 +
<p>
 +
<strong>Abstract: </strong>
 +
'Essencia coli' is a vanillin producing bacterium equipped with a control system that keeps the concentration of vanillin at a constant level. The showpiece of the project is the feedback mechanism. Vanillin synthesis is initiated by irradiation with blue light. The preferred concentration can be modulated using the intensity of that light. At the same time the bacterium measures the amount of vanillin outside the cell and controls its production to maintain the set point. The designed system is universal in nature and has therefore potential benefits in different areas. The concept can easily be applied to other flavours and odours. In fact, any application that requires a constant concentration of a molecular substance is possible.
 +
</p>
 +
</div>
 +
<div class="feature_page_content">
 +
<h2><a href="https://2008.igem.org/Team:Melbourne">Melbourne 2008</a></h2>
 +
<hr>
 +
<h5 class= "page_link"><a href="https://2009.igem.org/Team:KULeuven/Design/Key_Antikey">Melbourne 2008 Riboregulator page</a></h5>
 +
 +
<p>
 +
<strong>Abstract: </strong>
 +
This year Melbourne iGEM competition team seeks to build a temporal controller in E. coli. The idea is to build a system, which is modular, has all components in the form of biobricks, and expresses gene(s) at a specific time in a sequential manner. In this study, we show the design, modeling and some experimental results towards a proof of principle of the system. The design uses the leverage of existing biobricks of red light bacterial photography system, positive feedback loops and riboswitches. We propose that the architecture presented should scale well with increasing number of genes to be temporally regulated. It is anticipated that such system will be useful in metabolic engineering because enzymes can be turn on and off in a sequential manner.
 +
</p>
 +
<p>
 +
Melbourne Riboregulator reference
 +
</p>
 +
<ol>
 +
<li>Bauer et al. (2006). Engineered riboswitches as novel tools in molecular biology. J Biotechnol vol. 124 (1), 4-11.2.</li>
 +
<li>Ray, S.K. (2004). Riboswitch: A new mechanism of gene regulation in bacteria, Current Science, Vol. 87 (No. 9).</li>
 +
<li>Isaacs et al. (2004). Engineered riboregulators enable post-transcriptional control of gene expression, Nature Biotechnology, 22 (7), 841-847.</li>
 +
</ol>
 +
</div>
 +
<div class="feature_page_content">
 +
<h2><a href="https://2007.igem.org/Peking">Peking 2007</a></h2>
 +
<hr>
 +
<h5 class= "page_link"><a href="https://2007.igem.org/wiki/index.php/Peking_Hop-Count">Peking 2007 Riboregulator page</a></h5>
 +
<img src ="peking_2007.png">
 +
<p>
 +
<strong>Abstract: </strong>
 +
Our projects concern with the ability for bacterial cells to differentiate out of homogeneous conditions into populations with the division of labor. We aim at devices conferring host cells with the ability to form cooperating groups spontaneously and to take consecutive steps sequentially even when the genetic background and environmental inputs are identical. To break the mirror in such homogeneous condition, we need two devices respectively responsible for temporal and spatial differentiation. The implementation and application of such devices will lead to bioengineering where complex programs consisted of sequential steps (structure oriented programs) and cooperating agencies (forked instances of a single class, object and event oriented) can be embedded in a single genome. Although this "differentiation" process resemble the development of multicellular organism, we tend to use a more bioengineering style analogy: assembly line. Or maybe after some years from now, this will not be just an analogy.
 +
</p>
 +
</div>
 +
<div class="feature_page_content">
 +
<h2><a href="https://2009.igem.org/Team:VictoriaBC">Victoria BC 2009</a></h2>
 +
<hr>
 +
<p>
 +
<strong>Abstract: </strong>
 +
This project explores some of the ways that the secondary structure of messenger RNA can be used to control the rate of protein expression. The 32oC ribothermometer made by the 2008 TUDelft team will be coupled to fluorescent proteins to visually confirm temperature-dependent translation. The "ribolock" made by the 2006 Berkeley team will be tested at various temperatures to determine if it could double for use as a ribothermometer. Finally, a proof-of-concept NAND logic gate will be constructed: a ribolock will be used to interpret two concurrent environmental signals into an on/off control for mCherry output.
 +
 
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<td class= 'site_map_column'><h4>Home</h4>
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<td class= 'site_map_column'><a href="#"><h4>Home</h4></a>
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<li class='site_link'>Team</li>
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<li class='site_link'><a href="#">Team</li></a>
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<li class='site_link'><a href="#">Project</li></a>
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<li class='site_link'>WetLab</li>
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<li class='site_link'><a href="#">WetLab</li></a>
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<li class='site_link'>Achievement</li>
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<li class='site_link'><a href="#">Achievement</li></a>
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<li class='site_link'>Human Practice</li>
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<li class='site_link'><a href="#">Human Practice</li></a>
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<li class='site_link'>Side Project</li>
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<li class='site_link'><a href="#">Side Project</li></a>
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</td>
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<td class= 'site_map_column'><h4>Team</h4>
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<ul class= 'site_list'>
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<li class='site_link'>Member</li>
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<li class='site_link'>Advisor</li>
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<td class= 'site_map_column'><h4>Project</h4>
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<ul class= 'site_list'>
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<li class='site_link'>Overview</li>
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<li class='site_link'>Advisor</li>
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<li class='site_link'>Instructor</li>
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<li class='site_link'>Attribution</li>
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<li class='site_link'>Acknowledgement</li>
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<td class= 'site_map_column'><h4>WetLab</h4>
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<td class= 'site_map_column'><h4>Achievement</h4>
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<td class= 'site_map_column'><h4>Human Practice</h4>
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</td>
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<td class= 'site_map_column'><a href="#"><h4>Team</h4></a>
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<td class= 'site_map_column'><a href="#"><h4>Main Project</h4></a>
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<ul class= 'site_list'>
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<li class='site_link'><a href="#">Overview</li></a>
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<li class='site_link'><a href="#">Module one</li></a>
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<li class='site_link'><a href="#">Module two</li></a>
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<li class='site_link'><a href="#">Data</li></a>
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<li class='site_link'><a href="#">Characterisation</li></a>
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Revision as of 18:30, 19 September 2014

Riboregulator Feature Page

-HKUST iGEM 2014 Team-

Introduction to riboregulators

Figure 1.

Artificial riboregulator system used to control post-transcriptional regulation (Isaacs et al.,2004).

Regulatory RNAs are small RNA that regulates biological processes such as transcription or translation. The use of regulatory RNAs has been a great interest in the field of synthetic biology because it provides an additional level of regulation for biological circuits and systems. Regulatory RNAs have also used by many iGEM teams. We have identified 7 teams that have used cis-repressing (CR) and trans-activating (TA) riboregulator system and more teams that have used riboswitches. For example, Isaacs 2005, UC Berkeley 2006 and Caltech 2007 contributed many CR and TA devices to the Registry.

Artificial cis-repressing and trans-activating riboregulator system was introduced to the iGEM community by the UC Berkeley iGEM 2005 team. The riboregulator system as a whole acts to regulate translation at the RNA level. One component of the system ,crRNA, which contains a cis-repressing sequence 5' of the RBS, RBS, and gene of interest. The cis-repressing sequence can form a loop form complementary base pairs with the RBS to prevent the recognition of RBS by ribosomes. The translation crRNA is also commonly described as a "lock" because it "locks" the RBS and prevent translation. The "key" to this system is the taRNA. taRNA can interact (in trans) with the cis-repressing sequence to unlock the RBS and therefore to activate translation (Figure 1.).

The benefits of this system, as described in Isaacs et al.'s paper, are leakage minimization, fast response time, tunability, independent regulation of multiple genes etc1.

Team Track Chassis
Berkeley 2006 This team has not been assigned to a track. E. coli
Caltech 2007 Foundational Research E. coli
Delft 2009 Information Processing E. coli
Groningen 2011 Information Processing E. coli
K.U. Leuven 2008 This team has not been assigned to a track. E. coli
K.U. Leuven 2009 Manufacturing E. coli
Melbourne 2008 This team has not been assigned to a track. E. coli
Peking 2007 Information Processing E. coli
Victoria BC 2009 Manufacturing E. coli

Riboregulator parts in the Registry

Name Description Length Designed by Group
BBa_J01008 Riboregulator key 1 94 Golden Bear iGEM2005
BBa_J01010 Riboregulator Lock 1 40 Golden Bear iGEM2005
BBa_J01086 Key3 94 Golden Bear iGEM2005
BBa_J01080 Lock3 40 Golden Bear iGEM2005
BBa_K175029 Lock for weak RBS (B0031) from the lock/key library TUD09 49 Daniel Solis Escalante iGEM09_TUDelft
BBa_K175030 Key for lock of weak (K175029) RBS (B0031) from the lock/key library TUD09 86 Daniel Solis Escalante iGEM09_TUDelft
BBa_K175031 Lock for medium RBS (B0032) from the lock/key library TUD09 47 Daniel Solis Escalante iGEM09_TUDelft
BBa_K175032 Key for lock of medium (K175031) RBS (B0032) from the lock/key library TUD09 84 Daniel Solis Escalante iGEM09_TUDelft
BBa_I759036 Ptet_cis3_YFP 829 Kat Pak iGEM07_Caltech
BBa_I759022 pBAD-trans1 1693 Kat Pak iGEM07_Caltech
BBa_I759023 pBAD-trans2 1706 Kat Pak iGEM07_Caltech
BBa_J23066 [key3c][key3d][B0015] 336 Will Bosworth iGEM2006_Berkeley
BBa_J23078 lock3i 52 John Anderson iGEM2006_Berkeley
BBa_J23008 key3c 94 Kaitlin Davis iGEM2006_Berkeley
BBa_J23032 lock3d 43 John Anderson iGEM2006_Berkeley

Usage of riboregulator by different iGEM teams

The usage of the riboregulator system can be versatile; Different teams utilized the system in different ways. In general, introducing the riboregulator system to a certain circuit allows another level regulation. The new level of regulation then can give possible outcomes such as: specific interaction/communication (UC Berekeley 2006/ Caltech 2007); minimization of leakage by introducing post-transcriptional repression (Calgary 2007); and modulation of different concentrations of desired outcome (K.U. Leuven 2009).

UC Berkeley 2006

Berkeley riboregulator page

Abstract: Networks of interacting cells provide the basis for neural learning. We have developed the process of addressable conjugation for communication within a network of E. coli bacteria. Here, bacteria send messages to one another via conjugation of plasmid DNAs, but the message is only meaningful to cells with a matching address sequence. In this way, the Watson Crick base-pairing of addressing sequences replaces the spatial connectivity present in neural systems. To construct this system, we have adapted natural conjugation systems as the communication device. Information contained in the transferred plasmids is only accessible by "unlocking" the message using RNA based 'keys'. The resulting addressable conjugation process is being adapted to construct a network of NAND logic gates in bacterial cultures. Ultimately, this will allow us to develop networks of bacteria capable of trained learning.

Berkeley Riboregulator Reference :

  1. Isaacs, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. "Engineered riboregulators enable post-transcriptional control of gene expression"

Calgary 2007

Calgary riboregulator page

Abstract: The project we selected was to design and build a biomechanical printer; composed of a two dimensional plotter equipped with a red laser, software to translate computer images into instructions for the plotter, and E. coli cells engineered to respond to the laser light. Bacteria are spread in a solid lawn on the plate, or mixed in the media before pouring the plate. The response triggered by this biological circuit will produce beta agarase, an enzyme which degrades the agar polymer that the cells rest on.

The printer can then be used to "draw" high resolution images on the bacteria with the laser. The bacteria will then dissolve the agar where the laser was shone. This results in Bacterial Lithography, where the dissolved agar forms a picture.

We also chose a second project to include in our entry to the competition this year. That is an in Silico Biobrick Evolution system. The purpose of this project is to design a system that will accept user entered parameters and use them to search through the registry database. Using the given parameters the system will try to construct circuits (a series of biobricks) that will produce the desired product. More information on this project can be found in our evoGEM sections.

Caltech 2007

Caltech riboregulator page

Abstract: Our project attacks the following problem: can one engineer viruses to selectively kill or modify specific subpopulations of target cells, based on their RNA or protein expression profiles?

This addresses an important issue in gene therapy, where viruses engineered for fine target discrimination would selectively kill only those cells over- or under-expressing specific disease or cancer associated genes. Alternatively, these viruses could be used to discriminate between strains in a bacterial co-culture, allowing strain-specific modification or lysis.

This is clearly an ambitious goal, so we brainstormed a simple model of this problem suitable for undergraduates working over a summer. The bacteriophage λ is a classic, well studied virus capable of infecting E. coli, another classic model genetic system. We therefore seek to engineer a λ strain targeted to lyse specific subpopulations of E. coli based on their transcriptional profiles. Together, λ and E. coli provide a tractable genetic model for this larger problem, while hopefully providing lessons applicable to more ambitious, future projects.

Caltech Riboregulator references

  1. Isaacs, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. "Engineered riboregulators enable post-transcriptional control of gene expression"

Delft 2009

Delft Riboregulator page

Abstract: Our project aims to design a genetic device able to count and memorize the occurrences of an input signal. We achieved this by utilization of auto-inducing loops, that act as memory units, and an engineered riboregulator, acting as an AND gate. The design of the device is modular, allowing free change of both input and output signals. Each increase of the counter results in a different output signal. The design allows implementation of any number of memory units, as the AND gate design enables to extend the system in a hassle-free way. In order to tweak bistable autoinducing loops we need a very fast and robust method for characterizing parts. For this we have created a genetic algorithm that will enable us to find parameters of the parts used in the design. It also allows the combination of data from multiple experiments across models with overlapping components

Delft Riboregulator references

  1. Smolke C, 2009, It's the DNA That Counts, Science, 324:1156-1157.
  2. Sprinzak D and Elowitz M, 2005, Reconstruction of genetic circuits, Nature, 438-24:443-448.
  3. Isaacs F, Dwyer d and Collins J, 2006, RNA synthetic biology, Nature Biotech., 24:545-554.
  4. Anderson C, Voigt C and Arkin A, 2007, Environmental signal integration by a modular AND gate, Molecular systems biology, 3-133:1-8.
  5. Isaacs F, Dwyer d and Collins J, 2004, Engineered riboregulators enable post-transcriptional control of gene expression, Nature Biotechnology, 22-7:841-847.

Groningen 2011

Groningen Riboregulator page

Abstract: In our project we aim to create a cell-to-cell communication system that allows the propagation of a multi-task message with the capability of being reset. To achieve this, the system will include a reengineered conjugation system, a time-delay genetic circuit and a self-destructive plasmid. This system could be the basis for creating a long distance biosensor and/or be applied in reducing antibiotic resistance of bacteria. Furthermore, we have done a parallel research on the different perceptions of iGEM participants and supervisors on ethical issues in synthetic biology. We focused on the consequences of the ultimate conditions of the top-down and bottom-up approaches as applied in biology.

Groningen Riboregulator reference

  1. Isaacs, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR, Collins JJ. "Engineered riboregulators enable post-transcriptional control of gene expression"

K.U. Leuven 2008

K.U Leuven 2008 Riboregulator page

Abstract: Imagine a bacterium that produces a drug when and where it is needed in the human body. It would have several advantages over classical drugs and could have many medical applications. In this framework we proudly present our team's project: Dr. Coli, the bacterial drug delivery system. Dr. Coli senses the disease signal and produces the appropriate amount of drugs to meet the individual patient's needs. And when the patient is cured, Dr. Coli self-destructs. To do this, a molecular timer registers the time since the last disease signal sensed. But when the disease flares up again, this timer is reset and drug production is resumed. Within the time frame of the iGEM competition, we developed a proof of concept of Dr. Coli. The most important assets are massive reuse of standard biobricks, different control mechanisms and extensive modeling.

K.U. Leuven 2009

K.U Leuven 2009 Riboregulator page

Abstract: 'Essencia coli' is a vanillin producing bacterium equipped with a control system that keeps the concentration of vanillin at a constant level. The showpiece of the project is the feedback mechanism. Vanillin synthesis is initiated by irradiation with blue light. The preferred concentration can be modulated using the intensity of that light. At the same time the bacterium measures the amount of vanillin outside the cell and controls its production to maintain the set point. The designed system is universal in nature and has therefore potential benefits in different areas. The concept can easily be applied to other flavours and odours. In fact, any application that requires a constant concentration of a molecular substance is possible.

Melbourne 2008

Melbourne 2008 Riboregulator page

Abstract: This year Melbourne iGEM competition team seeks to build a temporal controller in E. coli. The idea is to build a system, which is modular, has all components in the form of biobricks, and expresses gene(s) at a specific time in a sequential manner. In this study, we show the design, modeling and some experimental results towards a proof of principle of the system. The design uses the leverage of existing biobricks of red light bacterial photography system, positive feedback loops and riboswitches. We propose that the architecture presented should scale well with increasing number of genes to be temporally regulated. It is anticipated that such system will be useful in metabolic engineering because enzymes can be turn on and off in a sequential manner.

Melbourne Riboregulator reference

  1. Bauer et al. (2006). Engineered riboswitches as novel tools in molecular biology. J Biotechnol vol. 124 (1), 4-11.2.
  2. Ray, S.K. (2004). Riboswitch: A new mechanism of gene regulation in bacteria, Current Science, Vol. 87 (No. 9).
  3. Isaacs et al. (2004). Engineered riboregulators enable post-transcriptional control of gene expression, Nature Biotechnology, 22 (7), 841-847.

Peking 2007

Peking 2007 Riboregulator page

Abstract: Our projects concern with the ability for bacterial cells to differentiate out of homogeneous conditions into populations with the division of labor. We aim at devices conferring host cells with the ability to form cooperating groups spontaneously and to take consecutive steps sequentially even when the genetic background and environmental inputs are identical. To break the mirror in such homogeneous condition, we need two devices respectively responsible for temporal and spatial differentiation. The implementation and application of such devices will lead to bioengineering where complex programs consisted of sequential steps (structure oriented programs) and cooperating agencies (forked instances of a single class, object and event oriented) can be embedded in a single genome. Although this "differentiation" process resemble the development of multicellular organism, we tend to use a more bioengineering style analogy: assembly line. Or maybe after some years from now, this will not be just an analogy.

Victoria BC 2009

Abstract: This project explores some of the ways that the secondary structure of messenger RNA can be used to control the rate of protein expression. The 32oC ribothermometer made by the 2008 TUDelft team will be coupled to fluorescent proteins to visually confirm temperature-dependent translation. The "ribolock" made by the 2006 Berkeley team will be tested at various temperatures to determine if it could double for use as a ribothermometer. Finally, a proof-of-concept NAND logic gate will be constructed: a ribolock will be used to interpret two concurrent environmental signals into an on/off control for mCherry output.

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