Difference between revisions of "Team:Washington/Auxin"
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| − | + | <a href="https://2015.igem.org/Team:Washington"> | |
| − | + | <li>Home</li> | |
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| − | + | <a href="https://2015.igem.org/Team:Washington/Auxin"> | |
| − | + | <li>Auxin | |
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| − | + | <a href="#" class="scroll-link" data-id="Description">Description</a> | |
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| − | + | <a href="#" class="scroll-link" data-id="Experiments">Experiments</a> | |
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| − | + | <a href="#" class="scroll-link" data-id="Results">Results</a> | |
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| − | + | <a href="https://2015.igem.org/Team:Washington/Aptamer"> | |
| − | + | <li>Aptamer | |
| − | <div id="main"> | + | <ul> |
| − | + | <li> | |
| − | + | <a href="https://2015.igem.org/Team:Washington/Aptamer#Description">Description</a> | |
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| − | + | <a href="https://2015.igem.org/Team:Washington/Aptamer#Experiments">Experiments</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/Aptamer#Parts">Parts</a> | |
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| − | + | </ul> | |
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| − | + | <a href="https://2015.igem.org/Team:Washington/Outreach"> | |
| − | + | <li>Outreach</li> | |
| − | </div> | + | </a> |
| − | + | <a href="https://2015.igem.org/Team:Washington/Protocols"> | |
| − | + | <li>Protocols</li> | |
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| − | + | <a href="https://2015.igem.org/Team:Washington/Team"> | |
| − | + | <li>Team | |
| − | + | <ul> | |
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| − | < | + | <a href="https://2015.igem.org/Team:Washington/Team#Members">Members</a> |
| − | + | </li> | |
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| − | <p> | + | <a href="https://2015.igem.org/Team:Washington/Team#Attributions">Attributions</a> |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="https://2015.igem.org/Team:Washington/Team#Sponsors">Sponsors</a> | |
| − | <h2><div id="Experiments">What is the context of this research?</div></h2> | + | </li> |
| − | <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> | + | </ul> |
| − | + | </li> | |
| − | <h2>What is the significance of this project? </h2> | + | </a> |
| − | + | </ul> | |
| − | <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> | + | </div> |
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| − | <h2><div id="Results">What are the goals of the project?</div></h2> | + | <!-- Start of content --> |
| − | <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. | + | <div id="main"> |
| − | <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. | + | <div class="container clearfix"> |
| − | <p>3. Clone each part from this system into standard plasmids for submission to BioBrick registry. | + | <div id="sidebar"> |
| − | <p>4. Show that when grown on paper, yeast can reliably detect auxin. | + | <div id="nav-anchor"></div> |
| − | <p>5. Use aptamers (short DNA sequences) to detect for okadaic acid, a shellfish toxin that causes Diarrhetic Shellfish Poisoning. | + | <nav> |
| − | <p>6. Show that the aptamer system for detection can be implemented on our paper platform and reliably detect for okadaic acid. | + | <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1"> |
| − | + | <ul class="nav navbar-nav" style="list-style-type: none;"> | |
| − | + | <li> | |
| + | <a href="#" class="scroll-link" data-id="Description">Description</a> | ||
| + | </li> | ||
| + | <li> | ||
| + | <a href="#" class="scroll-link" data-id="Experiments">Experiments</a> | ||
| + | </li> | ||
| + | <li> | ||
| + | <a href="#" class="scroll-link" data-id="Results">Results</a> | ||
| + | </li> | ||
| + | <li> | ||
| + | <a href="#" class="scroll-link" data-id="Parts">Parts</a> | ||
| + | </li> | ||
| + | </ul> | ||
| + | </div> | ||
| + | </nav> | ||
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| + | <h2> | ||
| + | <div id="Description">Overview</div> | ||
| + | </h2> | ||
| + | <h2> Prior CRISPR transcriptional factors </h2> | ||
| + | |||
| + | <p> CRISPR transcriptional factors are a breakthrough because they enable control of the expression of a particular gene – based on the gRNA. In these systems, the gRNA is attached to a CAS (CRISPR associated) protein, often CAS9. These proteins are degraded so that they do not cleave the dsDNA. The CAS9 protein is attached to either a repressor or an enhancer, which modulates the expression of the gene. Ubiquitination enables a system that can change only once. CRISPR transcriptional factors were first developed by Perez-Pinera et al. in 2013.</p> | ||
| + | <h2> | ||
| + | <div id="Experiments">What is the context of this research?</div> | ||
| + | </h2> | ||
| + | <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> | ||
| + | <h2>What is the significance of this project? </h2> | ||
| + | <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> | ||
| + | <h2> | ||
| + | <div id="Results">What are the goals of the project?</div> | ||
| + | </h2> | ||
| + | <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. | ||
| + | <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. | ||
| + | <p>3. Clone each part from this system into standard plasmids for submission to BioBrick registry. | ||
| + | <p>4. Show that when grown on paper, yeast can reliably detect auxin. | ||
| + | <p>5. Use aptamers (short DNA sequences) to detect for okadaic acid, a shellfish toxin that causes Diarrhetic Shellfish Poisoning. | ||
| + | <p>6. Show that the aptamer system for detection can be implemented on our paper platform and reliably detect for okadaic acid. | ||
| − | < | + | <p>7. Improve safety of shellfish consumers in the NW and the world! |
| − | |||
| − | |||
| − | |||
| − | <h2><div id="Parts">What is the context of this research?</div></h2> | + | <h2> Lab on a Strip: Developing a Novel Platform for Yeast Biosensors </h2> |
| − | <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> | + | <h2>Overview </h2> |
| + | <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> | ||
| + | <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> | ||
| + | <h2> | ||
| + | <div id="Parts">What is the context of this research?</div> | ||
| + | </h2> | ||
| + | <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> | ||
| + | <h2>What is the significance of this project? </h2> | ||
| + | <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> | ||
| + | <h2>What are the goals of the project?</h2> | ||
| + | <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. | ||
| − | < | + | <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. |
| − | <p> | + | <p>3. Clone each part from this system into standard plasmids for submission to BioBrick registry. |
| + | <p>4. Show that when grown on paper, yeast can reliably detect auxin. | ||
| − | + | <p>5. Use aptamers (short DNA sequences) to detect for okadaic acid, a shellfish toxin that causes Diarrhetic Shellfish Poisoning. | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | <p>5. Use aptamers (short DNA sequences) to detect for okadaic acid, a shellfish toxin that causes Diarrhetic Shellfish Poisoning. | + | |
| − | + | ||
| − | + | ||
| + | <p>6. Show that the aptamer system for detection can be implemented on our paper platform and reliably detect for okadaic acid. | ||
| − | < | + | <p>7. Improve safety of shellfish consumers in the NW and the world! |
| − | </html> | + | </div> |
| + | </div> | ||
| + | <!--These are the closing tags for div id="mainContainer" and div id="contentContainer". The corresponding opening tags appear in the template that is {{included}} at the top of this page.--> | ||
| + | </html> | ||
Revision as of 18:16, 14 September 2015
Overview
Prior CRISPR transcriptional factors
CRISPR transcriptional factors are a breakthrough because they enable control of the expression of a particular gene – based on the gRNA. In these systems, the gRNA is attached to a CAS (CRISPR associated) protein, often CAS9. These proteins are degraded so that they do not cleave the dsDNA. The CAS9 protein is attached to either a repressor or an enhancer, which modulates the expression of the gene. Ubiquitination enables a system that can change only once. CRISPR transcriptional factors were first developed by Perez-Pinera et al. in 2013.
What is the context of this research?
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.
What is the significance of this project?
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.
What are the goals of the project?
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.
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.
3. Clone each part from this system into standard plasmids for submission to BioBrick registry.
4. Show that when grown on paper, yeast can reliably detect auxin.
5. Use aptamers (short DNA sequences) to detect for okadaic acid, a shellfish toxin that causes Diarrhetic Shellfish Poisoning.
6. Show that the aptamer system for detection can be implemented on our paper platform and reliably detect for okadaic acid.
7. Improve safety of shellfish consumers in the NW and the world!
Lab on a Strip: Developing a Novel Platform for Yeast Biosensors
Overview
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.
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.
What is the context of this research?
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.
What is the significance of this project?
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.
What are the goals of the project?
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.
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.
3. Clone each part from this system into standard plasmids for submission to BioBrick registry.
4. Show that when grown on paper, yeast can reliably detect auxin.
5. Use aptamers (short DNA sequences) to detect for okadaic acid, a shellfish toxin that causes Diarrhetic Shellfish Poisoning.
6. Show that the aptamer system for detection can be implemented on our paper platform and reliably detect for okadaic acid.
7. Improve safety of shellfish consumers in the NW and the world!