Difference between revisions of "Team:Utah State/Design"

 
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<h1><a href="index.html" id="logo">Arcana <em>by HTML5 UP</em></a></h1>
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<h2>Utah State University <em>iGEM 2015</em></h2>
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<li><a href="https://2015.igem.org/Team:Utah_State/Results">Results</a></li>
 
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                                         <li><a href="https://2015.igem.org/Team:Utah_State/Design">Design</a></li>
 
                                         <li><a href="https://2015.igem.org/Team:Utah_State/Design">Design</a></li>
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<li><a href="https://2015.igem.org/Team:Utah_State/Basic_Part">Basic Parts</a></li>
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                                        <li><a href="https://2015.igem.org/Team:Utah_State/Part_Collection">Part Collection</a></li>
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<li><a href="https://2015.igem.org/Team:Utah_State/Notebook">Notebook</a></li>
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<li><a href="https://2015.igem.org/Team:Utah_State/Attributions">Attributions</a></li>
 
<li><a href="https://2015.igem.org/Team:Utah_State/Attributions">Attributions</a></li>
 
                                 <li><a href="https://2015.igem.org/Team:Utah_State/Collaborations">Collaborations</a></li>
 
                                 <li><a href="https://2015.igem.org/Team:Utah_State/Collaborations">Collaborations</a></li>
 
                                 <li><a href="https://2015.igem.org/Team:Utah_State/Practices">Human Practices</a></li>
 
                                 <li><a href="https://2015.igem.org/Team:Utah_State/Practices">Human Practices</a></li>
 
                                 <li><a href="https://2015.igem.org/Team:Utah_State/Safety">Safety</a></li>
 
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                                 <li><a href="https://2015.igem.org/Team:Utah_State/Standards">Standards</a></li>
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                                 <li><a href="https://2015.igem.org/Team:Utah_State/Standards">Medal Criteria</a></li>
 
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<h2>Design</h2>
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<p>All content, all the time.</p>
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<p>You imagine it, we build it.</p>
 
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<span class="image featured"><img src="https://static.igem.org/mediawiki/2015/6/63/Team_Utah_State_LactowareCircuitBanner.jpeg" alt="" /></span>
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<span class="image featured"><img src="https://static.igem.org/mediawiki/2015/6/62/Team_Utah_State_LactoWareCheeseFeatured.jpg" alt="" /></span>
  
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<h3>And Yet Another Subheading</h3>
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<h3>Design of Devices for Phage Detection and Control</h3>
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<p>We have designed an experiment leveraging the natural biology of the problematic
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Phasellus sed nisl vitae risus tristique volutpat. Cras rutrum commodo luctus.</p>
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<p>Phasellus odio risus, faucibus et viverra vitae, eleifend ac purus. Praesent mattis, enim
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lactococcal P335 species phage Φ31 to help detect and fight against Φ31 infections of
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quis hendrerit porttitor, sapien tortor viverra magna, sit amet rhoncus nisl lacus nec arcu.
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<i>Lactococcus lactis</i> during cheese fermentations. Our designed experiment investigates the
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use of two Φ31 promoters, a divergent promoter (p2001) located within the genetic switch
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<textarea name="message" id="message" placeholder="Message" rows="5"></textarea>
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region of the phage genome and a middle promoter  (p1997), for detection and a triggered
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<li><a href="#" class="icon fa-twitter"><span class="label">Twitter</span></a></li>
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<li><a href="#" class="icon fa-facebook"><span class="label">Facebook</span></a></li>
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<li><a href="#" class="icon fa-github"><span class="label">GitHub</span></a></li>
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<li><a href="#" class="icon fa-linkedin"><span class="label">LinkedIn</span></a></li>
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defense system. Both promoter systems investigated in this experiment have previously
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<li>&copy; Untitled. All rights reserved</li><li>Design: <a href="http://html5up.net">HTML5 UP</a></li>
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been determined to initiate transcription and subsequent expression in the initial stages of
  
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infection, specifically in the rightward direction of p2001, and only during phage infection. 
  
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Making them excellent candidates for use in a detection and defense triggered system.</p>  
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<script src="https://2015.igem.org/Template:Utah_State/jquerymin?action=raw&ctype=text/javascript"></script>
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<script src="https://2015.igem.org/Template:Utah_State/main?action=raw&ctype=text/javascript"></script>
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<p>Our Φ31 phage detection system was designed utilizing these promoters and the reporter
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</html>
+
  
 +
genes superfolder green fluorescent protein (sfGFP) and mCherry (a red fluorescent protein, RFP),
  
 +
inserted within the lactic acid bacteria (LAB) expression vector pTRKH2.  In this system,
  
 +
transcription and subsequent expression of the fluorescent reporter proteins would only
  
 +
be initiated during Φ31 phage infection of <i>L. lactis</i>, from the designed construct within the
  
 +
cell, and allow for qualitative and quantitative detection by observing and measuring
  
 +
fluorescence, respectively. This detection system provides a rapid detection method that
  
 +
could be implemented within dairy fermentation facilities, allowing for timely monitoring
  
 +
of appearance and presence of the Φ31 phage. </p>
  
 +
<p>The Φ31 phage triggered defense system was designed using the same promoter concept,
  
 +
but with expression of lalR, a three-gene restriction cassette (depicted as a single gene and
  
 +
enzyme for simplicity), after initial phage infection. Expression of this restriction cassette
  
 +
results in digestion of the bacterial chromosomal DNA, and subsequently in cell death.
  
 +
Because transcription from the Φ31 promoters is only expressed during Φ31 infection, cell
  
 +
death would only be induced during an active infection. This system is designed to provide
  
 +
an effective defense against Φ31 infection of <i>L. lactis</i> industrial dairy fermentations that
  
 +
results in cell death of infected cells and prevents propagation of the Φ31 phage, allowing
  
 +
for minimal hindrance of industrial fermentations during Φ31 infections.</p>
  
 +
<p>Additionally, this experiment was designed purposefully incorporating the divergent
  
 +
p2001 promoter because of its conservation and high sequence similarity with the other
  
 +
lytic members of the lactococcal P335 species phage. With the assumption that expression
  
 +
can potentially be induced from this promoter by other lytic members, allowing for
  
 +
broader detection and defense against one of the main phage species that infect and ruin
  
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<!--
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industrial cheese fermentations.</p>
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<html>
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<h2>Design</h2>
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<figure style="text-align:center">
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  <img src="https://static.igem.org/mediawiki/2015/0/06/Team_Utah_State_PromoterFigure1.gif" height="60%" alt="#"/>
 +
  <figcaption>Fluorescent detection of Φ31: Upon injection of the Φ31 chromosome expression from the p2001 rightward promoter or the p1997 promoter is activated in our designed construct, resulting in production of green fluorescent protein.
 +
</figcaption>
 +
</figure>
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<br>
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<figure style="text-align:center">
 +
  <img src="https://static.igem.org/mediawiki/2015/2/23/Team_Utah_State_PromoterFigure2.png" height="60%" alt="#"/>
 +
  <figcaption>Triggered defense of Φ31: Upon injection of the Φ31 chromosome expression from the p2001 rightward promoter or the p1997 promoter is activated in our designed construct, resulting in expression of the three-gene restriction cassette lalR. Subsequently leading to restriction digestion of the host chromosome, and cell death.
  
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<p>
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By talking about your design work on this page, there is one medal criterion that you can attempt to meet, and one award that you can apply for. If your team is going for a gold medal by building a functional prototype, you should tell us what you did on this page. If you are going for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Applied Design award</a>, you should also complete this page and tell us what you did.
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<h4>Note</h4>
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<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Applied Design award</a> and/or the <a href="https://2015.igem.org/Judging/Awards#Medals">functional prototype gold medal criterion</a>, you must fill out this page.</p>
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</div>
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<p>This is a prize for the team that has developed a synthetic biology product to solve a real world problem in the most elegant way. The students will have considered how well the product addresses the problem versus other potential solutions, how the product integrates or disrupts other products and processes, and how its lifecycle can more broadly impact our lives and environments in positive and negative ways.</p>
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</div>
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</div>
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</section>
  
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<p>
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<!-- Footer -->
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If you are working on art and design as your main project, please join the art and design track. If you are integrating art and design into the core of your main project, please apply for the award by completing this page.
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</p>
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<div class="container">
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<section> <!--class="3u 6u(narrower) 12u$(mobilep)"-->
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<h3 style="text-align: center">Links to Stuff</h3>
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<table class="links">
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<tr>
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<td><a href="https://2015.igem.org/Team:Utah_State">Home</a></td>
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<td><a href="https://2015.igem.org/Team:Utah_State/Team">Team</a></td>
 +
<td><a href="https://2015.igem.org/Team:Utah_State/Standards">Medal Criteria</a></td>
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<td><a href="https://2015.igem.org/Team:Utah_State/Attributions">Attributions</a></td>
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</tr>
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<tr>
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<td><a href="https://2015.igem.org/Team:Utah_State/Description">Project Description</a></td>
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<td><a href="https://2015.igem.org/Team:Utah_State/Experiments">Experiments and Protocols</a></td>
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<td><a href="https://2015.igem.org/Team:Utah_State/Results">Results</a></td>
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<td><a href="https://2015.igem.org/Team:Utah_State/Design">Design</a></td>
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</tr>
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<td><a href="https://2015.igem.org/Team:Utah_State/Interlab">Interlab Study</a></td>
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<td><a href="https://2015.igem.org/Team:Utah_State/Practices">Human Practices</a></td>
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<td><a href="https://2015.igem.org/Team:Utah_State/Collaborations">Collaborations</a></td>
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<td><a href="https://2015.igem.org/Team:Utah_State/Safety">Safety</a></td>
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<tr>
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<td><a href="https://2015.igem.org/Team:Utah_State/Parts">All Parts</a></td>
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<td><a href="https://2015.igem.org/Team:Utah_State/Basic_Part">Favorite Parts</a></td>
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</tr>
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</table>
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</section>
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<hr>
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<!-- LOGO BANNER -->
  
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<ul class="icons" style="text-align:center">
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<li><img src="https://static.igem.org/mediawiki/2015/c/cb/Team_Utah_State_IDTLogopic.png" alt="IDT" height="41" width="150" class="icon"></li>
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<li><img src="https://static.igem.org/mediawiki/2015/7/7e/Team_Utah_State_CellularEngineeringpic.png" alt="Cellular Engineering" height="46" width="150" class="icon"></li>
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<li><img src="https://static.igem.org/mediawiki/2015/8/8e/Team_Utah_State_SponsorLogo_Monsato.png" alt="Monsanto" height="51" width="150" class="icon"></li>
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<li><img src="https://static.igem.org/mediawiki/2015/3/30/Team_Utah_State_SponsorLogo_IMFlash.png" alt="IMFlash" height="43" width="150" class="icon"></li>
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<li><img src="https://static.igem.org/mediawiki/2015/1/19/Team_Utah_State_SponsorLogo_Schreiber.png" alt="Schriber Foods" height="52" width="150" class="icon"></li>
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</ul>
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<ul class="icons" style="text-align:center">
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<li><img src="https://static.igem.org/mediawiki/2015/7/7a/Team_Utah_State_SponsorLogo_Conagra.png" alt="ConAgra Foods" height="70" width="113" class="icon"></li>
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<li><img src="https://static.igem.org/mediawiki/2015/1/16/Team_Utah_State_USUBELogo.png" class="icon"></li>
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<li><img src="https://static.igem.org/mediawiki/2015/0/08/Team_Utah_State_USUCollegeELogo.png" height="82" width="250" class="icon"></li>
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<li><img src="https://static.igem.org/mediawiki/2015/1/1e/Team_Utah_State_SponsorLogo_USUSA.png" alt="USUSA" height="140" width="150" class="icon"></li>
 +
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 +
</ul> 
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<li>&copy; Untitled. All rights reserved</li><li>Design: <a href="http://html5up.net">HTML5 UP</a></li>
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</ul>
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</div>
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</div>
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<script src="https://2015.igem.org/Template:Utah_State/jquerymin?action=raw&ctype=text/javascript"></script>
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<script src="https://2015.igem.org/Template:Utah_State/jquerydropotronmin?action=raw&ctype=text/javascript"></script>
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<script src="https://2015.igem.org/Template:Utah_State/skelmin?action=raw&ctype=text/javascript"></script>
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<script src="https://2015.igem.org/Template:Utah_State/util?action=raw&ctype=text/javascript"></script>
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Latest revision as of 03:46, 19 September 2015

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Design

You imagine it, we build it.

Design of Devices for Phage Detection and Control

We have designed an experiment leveraging the natural biology of the problematic lactococcal P335 species phage Φ31 to help detect and fight against Φ31 infections of Lactococcus lactis during cheese fermentations. Our designed experiment investigates the use of two Φ31 promoters, a divergent promoter (p2001) located within the genetic switch region of the phage genome and a middle promoter (p1997), for detection and a triggered defense system. Both promoter systems investigated in this experiment have previously been determined to initiate transcription and subsequent expression in the initial stages of infection, specifically in the rightward direction of p2001, and only during phage infection. Making them excellent candidates for use in a detection and defense triggered system.

Our Φ31 phage detection system was designed utilizing these promoters and the reporter genes superfolder green fluorescent protein (sfGFP) and mCherry (a red fluorescent protein, RFP), inserted within the lactic acid bacteria (LAB) expression vector pTRKH2. In this system, transcription and subsequent expression of the fluorescent reporter proteins would only be initiated during Φ31 phage infection of L. lactis, from the designed construct within the cell, and allow for qualitative and quantitative detection by observing and measuring fluorescence, respectively. This detection system provides a rapid detection method that could be implemented within dairy fermentation facilities, allowing for timely monitoring of appearance and presence of the Φ31 phage.

The Φ31 phage triggered defense system was designed using the same promoter concept, but with expression of lalR, a three-gene restriction cassette (depicted as a single gene and enzyme for simplicity), after initial phage infection. Expression of this restriction cassette results in digestion of the bacterial chromosomal DNA, and subsequently in cell death. Because transcription from the Φ31 promoters is only expressed during Φ31 infection, cell death would only be induced during an active infection. This system is designed to provide an effective defense against Φ31 infection of L. lactis industrial dairy fermentations that results in cell death of infected cells and prevents propagation of the Φ31 phage, allowing for minimal hindrance of industrial fermentations during Φ31 infections.

Additionally, this experiment was designed purposefully incorporating the divergent p2001 promoter because of its conservation and high sequence similarity with the other lytic members of the lactococcal P335 species phage. With the assumption that expression can potentially be induced from this promoter by other lytic members, allowing for broader detection and defense against one of the main phage species that infect and ruin industrial cheese fermentations.

#
Fluorescent detection of Φ31: Upon injection of the Φ31 chromosome expression from the p2001 rightward promoter or the p1997 promoter is activated in our designed construct, resulting in production of green fluorescent protein.

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Triggered defense of Φ31: Upon injection of the Φ31 chromosome expression from the p2001 rightward promoter or the p1997 promoter is activated in our designed construct, resulting in expression of the three-gene restriction cassette lalR. Subsequently leading to restriction digestion of the host chromosome, and cell death.

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