Difference between revisions of "Team:Washington"

 
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                            <a href="https://2015.igem.org/Team:Washington">
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        <ul>
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                                <li>Home</li>
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            <a href="https://2015.igem.org/Team:Washington">
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                            </a>
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                <li>Home
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                            <a href="https://2015.igem.org/Team:Washington/Auxin">
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                  <ul>
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                                <li>Auxin
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                    <li><a href="https://2014.igem.org/Team:Washington">UW 2014</a></li>
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                    <li><a href="https://2013.igem.org/Team:Washington">UW 2013</a></li>
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                                    <ul class="nav navbar-nav">
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                    <li><a href="https://2012.igem.org/Team:Washington">UW 2012</a></li>
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                                        <li>
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                    <li><a href="https://2011.igem.org/Team:Washington">UW 2011</a></li>
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                                          <a href="https://2015.igem.org/Team:Washington/Auxin">Description</a>
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                    <li><a href="https://2010.igem.org/Team:Washington">UW 2010</a></li>
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                                        </li>
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                    <li><a href="https://2009.igem.org/Team:Washington">UW 2009</a></li>
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                                        <li>
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                    <li><a href="https://2008.igem.org/Team:University_of_Washington">UW 2008</a></li>
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                                            <a href="https://2015.igem.org/Team:Washington/Auxin">Experiments</a>
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                    <li><a href="https://2013.igem.org/Main_Page">iGEM Homepage</a></li>
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                                        </li>
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</li>
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                                            <a href="https://2015.igem.org/Team:Washington/Auxin">Results</a>
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            </a>
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                                        </li>
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            <a href="https://2015.igem.org/Team:Washington/Auxin">
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                                        <li>
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                <li>Auxin
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                                            <a href="https://2015.igem.org/Team:Washington/Auxin">Parts</a>
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                                        </li>
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                                    </ul>
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                            </a>
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                            <a href="https://2015.igem.org/Team:Washington/Aptamer">
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                                <li>Aptamer
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                                            <a href="https://2015.igem.org/Team:Washington/Aptamer_Description">Description</a>
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                            <li>
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                                        </li>
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                                <a href="https://2015.igem.org/Team:Washington/Auxin#Introduction">Introduction</a>
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                                        <li>
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                            </li>
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                                            <a href="https://2015.igem.org/Team:Washington/Aptamer_Experiments">Experiments</a>
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                            <li>
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                                        </li>
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                                 <a href="https://2015.igem.org/Team:Washington/Auxin#Methods">Methods</a>
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                                        <li>
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                             </li>
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                                            <a href="https://2015.igem.org/Team:Washington/Aptamer_Results">Results</a>
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                             <li>
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                                        </li>
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                                 <a href="https://2015.igem.org/Team:Washington/Auxin#Results">Results</a>
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                                        <li>
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                            </li>
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                                            <a href="https://2015.igem.org/Team:Washington/Aptamer_Parts">Parts</a>
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                            <li>
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                                        </li>
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                                <a href="https://2015.igem.org/Team:Washington/Auxin#Conclusion">Conclusion</a>
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                                <a href="https://2015.igem.org/Team:Washington/Parts#Auxin">Biobrick</a>
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                            <a href="https://2015.igem.org/Team:Washington/Outreach">
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                            </li>
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                                <li>Outreach</li>
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                            </a>
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                             <a href="https://2015.igem.org/Team:Washington/Protocols">
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                                <li>Protocols</li>
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                            <a href="https://2015.igem.org/Team:Washington/Team">
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                                 <li>Team
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                                            <a href="https://2015.igem.org/Team:Washington/Team_Members">Members</a>
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                                        </li>
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                                            <a href="https://2015.igem.org/Team:Washington/Team_Attributions">Attributions</a>
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                                        <li>
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                                            <a href="https://2015.igem.org/Team:Washington/Team_Sponsors">Sponsors</a>
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                                        </li>
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                                    </ul>
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            <a href="https://2015.igem.org/Team:Washington/Aptazyme">
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                <li>Aptazyme
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<h2> Lab on a Strip: Developing a Novel Platform for Yeast Biosensors </h2>
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                     <ul>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Introduction">Introduction</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Methods">Methods</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Results">Results</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Conclusion">Conclusion</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Parts#Aptazyme">Biobrick</a>
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                            </li>
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                     </ul>
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                </li>
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            </a>
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            <a href="https://2015.igem.org/Team:Washington/Paper_Device">
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                <li>Paper Device             
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                    <ul>
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                         <li>
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                            <a href="https://2015.igem.org/Team:Washington/Paper_Device#Introduction">Introduction</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Paper_Device#Methods">Methods</a>
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                        </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Design">Design</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Paper_Device#Results">Results</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Paper_Device#Conclusion">Conclusion</a>
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                            </li>
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                    </ul>
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                </li>
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            </a>
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            <a href="https://2015.igem.org/Team:Washington/Modeling">
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                <li>Modeling             
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                    <ul>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Modeling#Paper_Device">Paper Device</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Modeling#Aptazyme">Aptazyme</a>
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                        </li>
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                    </ul>
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                </li>
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            </a>
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            <a href="https://2015.igem.org/Team:Washington/Practices">
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                <li>Human Practices             
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                    <ul>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Practices#Outreach">Outreach</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Practices#Integrated">Integrated</a>
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                        </li>
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                    </ul>
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                </li>
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            </a>
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            <a href="https://2015.igem.org/Team:Washington/Protocols">
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                <li>Protocols
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                    <ul>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Protocols#Experiments">Experiments</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Protocols#Safety">Safety</a>
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                        </li>
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                    </ul>
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                </li>
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            </a>
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            <a href="https://2015.igem.org/Team:Washington/Team">
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                <li>Team                       
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                    <ul>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Team#Members">Members</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Attributions">Attributions</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Team#Sponsors">Sponsors</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Team#Judging_Form">Judging Form</a>
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                        </li>
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                    </ul>
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<h2>Overview </h2>
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<p>Biosensors for detecting small molecules have many applications in medicine, food, and the environment. Our project aims to combine the emerging fields of synthetic biology and paper diagnostics to create an affordable and accessible platform for a new class of biological sensors that could detect a wide variety of molecules. We first developed a paper microfluidic device housing Saccharomyces cerevisiae, which was then modified to accommodate two different biological detection systems. In one system, the Auxin/IAA-Degron pathway is used in conjunction with beta-galactosidase to produce a visible signal in response to the plant hormone auxin. In the other system, aptazymes, a combination of RNA aptamers and ribozymes, are used to bind theophylline and allow fluorescent protein to be produced. Both pathways serve as models for future real-world applications of our device, including the detection of marine biotoxins in the Pacific Northwest.  </p>
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        <h2 align=center> Lab on a Strip: Developing a Novel Platform for Yeast Biosensors </h2>
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        <h2> Project Overview </h2>
  
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<p>For commercial shellfish farmers and recreational hunters alike, marine biotoxins pose a significant threat to health and welfare. With this project, we aim to create an inexpensive and easy-to-use test kit for the detection of the shellfish toxin okadaic acid using engineered yeast strains and DNA aptamers on a paper device. We also hope that this project paves the way for a new class of biosensors capable of detecting a wide range of small molecules. </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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<h2>What is the context of this research? </h2>
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<p>Marine toxins are an increasing problem in Washington State waters. Produced in high concentrations by microorganisms during algae blooms, they are ingested by filter-feeding shellfish, causing illness and death in human consumers. Biotoxins are also 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. </p>
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<br></br>
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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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<h2>What is the significance of this project? </h2>
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      <li><a href="#Auxin">Auxin Pathway</a></li>
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      <li><a href="#Theophylline">Theophylline Pathway</a></li>
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    </ul>
  
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<p>Our project aims to combine the emerging fields of synthetic biology and paper diagnostics to create an affordable, accessible, and accurate diagnostic test kit that would allow farmers and the public to test shellfish for common biotoxins. 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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<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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<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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<p><br><br></br></br></p>
  
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<h2>What are the goals of the project?</h2>
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                                </div>
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<p>1. Develop a paper microfluidic device that houses yeast; it will provide adequate nutrients for cell growth, but will also be freeze-dried for long-term storage.
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                            </div>
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<p>2. Create a detection system for the plant hormone auxin in which yeast produce a color in response to an auxin input; test it in cells growing on normal media.
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</div>
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<p>3. Clone each part from this system into standard plasmids for submission to BioBrick registry.
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<p>4. Show that when grown on paper, yeast can reliably detect auxin.
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<p>5. Use aptamers (short DNA sequences) to detect for okadaic acid, a shellfish toxin that causes Diarrhetic Shellfish Poisoning.
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<p>6. Show that the aptamer system for detection can be implemented on our paper platform and reliably detect for okadaic acid.
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<p>7. Improve safety of shellfish consumers in the NW and the world!
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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.