Difference between revisions of "Team:Washington"

 
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                                 <a href="https://2015.igem.org/Team:Washington/Aptamer#Introduction">Introduction</a>
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                                 <a href="https://2015.igem.org/Team:Washington/Aptazyme#Introduction">Introduction</a>
 
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                                 <a href="https://2015.igem.org/Team:Washington/Aptamer#Methods">Methods</a>
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                                 <a href="https://2015.igem.org/Team:Washington/Aptazyme#Methods">Methods</a>
 
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                                 <a href="https://2015.igem.org/Team:Washington/Aptamer#Results">Results</a>
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                                 <a href="https://2015.igem.org/Team:Washington/Aptazyme#Results">Results</a>
 
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                                 <a href="https://2015.igem.org/Team:Washington/Aptamer#Conclusion">Conclusion</a>
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                                 <a href="https://2015.igem.org/Team:Washington/Aptazyme#Conclusion">Conclusion</a>
 
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                                 <a href="https://2015.igem.org/Team:Washington/Parts#Aptamer">Aptamer</a>
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                                 <a href="https://2015.igem.org/Team:Washington/Parts#Aptazyme">Biobrick</a>
 
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                             <a href="https://2015.igem.org/Team:Washington/Paper_Device#Methods">Methods</a>
 
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                                <a href="https://2015.igem.org/Team:Washington/Design">Design</a>
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                                <a href="https://2015.igem.org/Team:Washington/Paper_Device#Results">Results</a>
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                                <a href="https://2015.igem.org/Team:Washington/Paper_Device#Conclusion">Conclusion</a>
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                             <a href="https://2015.igem.org/Team:Washington/Modeling#Aptamer">Aptamer</a>
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                             <a href="https://2015.igem.org/Team:Washington/Modeling#Aptazyme">Aptazyme</a>
 
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                             <a href="https://2015.igem.org/Team:Washington/Team#Attributions">Attributions</a>
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                             <a href="https://2015.igem.org/Team:Washington/Attributions">Attributions</a>
 
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         <h2 align=center> Lab on a Strip: Developing a Novel Platform for Yeast Biosensors </h2>
 
         <h2 align=center> Lab on a Strip: Developing a Novel Platform for Yeast Biosensors </h2>
 
         <h2> Project Overview </h2>
 
         <h2> Project Overview </h2>
  
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         <p>Marine toxins are an increasing problem in Washington State waters and the Pacific Ocean at large. Produced in high concentrations by microorganisms during algae blooms, these toxins are ingested by filter-feeding shellfish and get caught within shellfish tissue. Although these toxins are harmful to mammals, causing illness and death in human consumers, they do not affect the shellfish, giving collectors no reason to be suspicious. Furthermore, algal blooms are not always the striking crimson of "red tides," making affected areas difficult to notice. The Washington State Department of Health and commercial shellfish farmers conduct periodic surveys of local beaches to catch contaminations early, but these methods are costly, time-consuming, and not always effective. This is a dilemma especially for individual and recreational shellfish collectors, who do not have the resources to screen their shellfish. With the current methods of shellfish toxin detection, the crowds swarming to Seattle’s famous Pike Place Market and popular raw oyster bars are constantly at risk. Most consumers cannot be completely sure that their seafood is safe. </p>
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         <p>The Pacific Ocean is home to a wide range of marine life, including the food source of many filter-feeders, toxin-producing algae. When algal blooms are ingested by shellfish, the toxins produced by the algae are caught within shellfish tissue. Although these toxins are harmful to us, they aren’t to the shellfish, giving collectors no immediate sign of danger. Biotoxins are also just generally difficult to detect; contrary to popular belief, algal blooms are not always the striking crimson of “red tides.” Thus, blooms may not be discovered until after a poisoned shellfish is found. The Washington State Department of Health and commercial shellfish farmers conduct periodic surveys of local beaches to catch contaminations early, but these methods are costly, time-consuming, and not always effective. This can especially pose a dilemma for individual shellfish hunters, who do not have the resources to screen their shellfish for toxins. With current detection methods, the crowds swarming to Seattle’s famous Pike Place Market and popular raw oyster bars are constantly at risk.</p><p><img src="https://static.igem.org/mediawiki/2015/f/ff/Igem_red_tide.jpeg" width=572 height=500 align="center" ></p>
  
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<p> Now imagine that you could simply dip a sheet of paper into a bucket of shellfish, wait only a few minutes, and determine if your products are safe to consume. With this goal in mind, we've taken the first steps towards a diagnostic test kit that combines the emerging fields of synthetic biology and paper diagnostics to create an affordable, accessible, and accurate biosensor that could detect for harmful biotoxins.  We've developed a paper device and tested it with two proof-of-concept systems we've engineered, which detect the plant hormone auxin and the molecule theophylline, respectively. However, we’ve implemented a number of techniques to ensure the versatility of our systems, making them easily generalizable to a wide variety of other molecules.</p>
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        <p>We have developed a much cheaper diagnostic tool in which genetically-modified baker’s yeast is grown on a paper device and is able to produce an easy-to-read color output in the presence of a target molecule. Imagine if you could simply dip a sheet of paper into your bucket of shellfish, wait only (insert amount of time) and tell if your products are safe to consume. The proof-of-concept systems we’ve engineered detect the plant hormone auxin and the molecule theophylline. However, we’ve implemented a number of techniques to ensure the versatility of our systems thus, they can be easily modified and further developed to test for a wide variety of other molecules.</p>
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<p>This “lab on a strip” will be a critical step forward in marine toxin detection, as it will cut nearly 20 hours off the time needed to obtain results, allowing farmers to screen at a lower cost and empowering individual hunters to confirm the safety of their shellfish. This is also the first project to attempt to grow yeast on a paper device, and if successful, could open the door to a wide range of similar biosensors. Such sensors would have applications in medicine, food, and the environment worldwide. </p>
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      <li><a href="#Paper">Paper Platform:</a></li>
 
 
       <li><a href="#Auxin">Auxin Pathway</a></li>
 
       <li><a href="#Auxin">Auxin Pathway</a></li>
 
       <li><a href="#Theophylline">Theophylline Pathway</a></li>
 
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<p>The auxin pathway produces a color output rather than a fluorescent one….(I will finish this part tomorrow when my computer isn’t dead)
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<p1>In the Auxin detection pathway, a DNA binding domain, a degron domain and a repressor domain are fused to suppress the expression of a reporter gene, LacZ. In the presence of Auxin, a plant hormone, along with a corresponding F-Box protein will lead to the fusion protein suppressing the reporter will be ubiquitinated allowing the reporter to be expressed. </p1>
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Microfluidic design:.....(1% remaining….)</p>
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<p>In this design RNA aptamers are used to sense our target molecule, theophylline.  Aptamers, unlike antibodies, can actually bind to virtually any molecule, allowing for a more versatile system.  We’ve implemented a ribozyme switch which, when active, cleaves the mRNA code of our target sequence, hindering the production of GFP by default.  However, in the presence of theophylline our switch becomes inactive, allowing for the expression of our target gene.  This system is useful because it is faster-acting than more traditional expression pathways, and can be generalized to many other small molecules by changing the aptamer sequence.</p2>
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<p1>In this design RNA aptamers are used to sense our target molecule, theophylline.  Aptamers, unlike antibodies, can actually bind to virtually any molecule, allowing for a more versatile system.  We’ve implemented a ribozyme switch which, when active, cleaves the mRNA code of our target sequence, hindering the production of GFP by default.  However, in the presence of theophylline our switch becomes inactive, allowing for the expression of our target gene.  This system is useful because it is faster-acting than more traditional expression pathways, and can be generalized to many other small molecules by changing the aptamer sequence.</p1>
 
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Latest revision as of 23:56, 18 September 2015





Lab on a Strip: Developing a Novel Platform for Yeast Biosensors

Project Overview

The Pacific Ocean is home to a wide range of marine life, including the food source of many filter-feeders, toxin-producing algae. When algal blooms are ingested by shellfish, the toxins produced by the algae are caught within shellfish tissue. Although these toxins are harmful to us, they aren’t to the shellfish, giving collectors no immediate sign of danger. Biotoxins are also just generally difficult to detect; contrary to popular belief, algal blooms are not always the striking crimson of “red tides.” Thus, blooms may not be discovered until after a poisoned shellfish is found. The Washington State Department of Health and commercial shellfish farmers conduct periodic surveys of local beaches to catch contaminations early, but these methods are costly, time-consuming, and not always effective. This can especially pose a dilemma for individual shellfish hunters, who do not have the resources to screen their shellfish for toxins. With current detection methods, the crowds swarming to Seattle’s famous Pike Place Market and popular raw oyster bars are constantly at risk.



We have developed a much cheaper diagnostic tool in which genetically-modified baker’s yeast is grown on a paper device and is able to produce an easy-to-read color output in the presence of a target molecule. Imagine if you could simply dip a sheet of paper into your bucket of shellfish, wait only (insert amount of time) and tell if your products are safe to consume. The proof-of-concept systems we’ve engineered detect the plant hormone auxin and the molecule theophylline. However, we’ve implemented a number of techniques to ensure the versatility of our systems thus, they can be easily modified and further developed to test for a wide variety of other molecules.

In the Auxin detection pathway, a DNA binding domain, a degron domain and a repressor domain are fused to suppress the expression of a reporter gene, LacZ. In the presence of Auxin, a plant hormone, along with a corresponding F-Box protein will lead to the fusion protein suppressing the reporter will be ubiquitinated allowing the reporter to be expressed.
In this design RNA aptamers are used to sense our target molecule, theophylline. Aptamers, unlike antibodies, can actually bind to virtually any molecule, allowing for a more versatile system. We’ve implemented a ribozyme switch which, when active, cleaves the mRNA code of our target sequence, hindering the production of GFP by default. However, in the presence of theophylline our switch becomes inactive, allowing for the expression of our target gene. This system is useful because it is faster-acting than more traditional expression pathways, and can be generalized to many other small molecules by changing the aptamer sequence.