Team:UC Davis

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  <li style='color:#014457; cursor:default'><a>teams</a></li>
  <li style='color:#014457; cursor:default'><a>teams</a></li>
                    <li class='selected'        ><a href="https://2012.igem.org/Team:UC_Davis">Page</a></li>
                    <li class='selected'        ><a href="https://2012.igem.org/Team:UC_Davis">Page</a></li>
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                 <li class='new'><a href="https://2012.igem.org/wiki/index.php?title=Talk:Team:UC_Davis&amp;action=edit&amp;redlink=1">Discussion</a></li>
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         <li ><a href="https://2012.igem.org/Team:UC_Davis/Attributions" title="Attributions">Attributions</a></li>
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         <li ><a href="https://2012.igem.org/Team:UC_Davis/Data" title="Data">Data</a>
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        <li ><a href="https://2012.igem.org/Team:UC_Davis/Notebook" title="Notebook">Notebook</a>
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            <li ><a href="./Notebook.htm ">Week 1</a></li>
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         <li class="selected"><a href="https://2012.igem.org/Team:UC_Davis/Safety" title="Safety">Safety</a></li>
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        <li ><a href="https://2012.igem.org/Team:UC_Davis" title="Home">Home</a></li>
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<h1> Safety </h1>
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<b>1. Would any of your project ideas raise safety issues in terms of: researcher safety, public safety, or environmental safety?</b>
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The accumulation of plastic products poses a hazard to the environment, as well as humans, through drinking water contamination. This threat led us to develop a degradation pathway to turn the polyethylene terephthalate into different substrates. We produce terephthalic acid and ethylene glycol. Ethylene glycol is a moderately toxic substance, which is oxidized to glycolic acid. The glycolic acid is further oxidized to oxalic acid – a toxic substance that affects the central nervous system via the liver. However, in the environment, the ethylene glycol will be degraded by hydroxyl radicals and in sewage sludge, it is readily biodegradable. Because ethylene glycol must be ingested to pose a problem, researchers take extra precaution to make sure there are no splashes of ethylene glycol in the laboratory and the wastes will be disposed of in the appropriate hazardous waste receptacles. Ethylene glycol can also be a mild irritant if it comes in contact with the skin or if it is inhaled, so researchers wear eye protection as well as gloves and lab coats, and always work with ethylene glycol in the confine of a fume hood. Also, in our constructs, we have produced enzymes that will degrade ethylene glycol into glycoaldehyde and then glycolate. The glycolate has the potential to be turned in to oxaloacetate, a metabolic intermediate. In the environment, ethylene glycol can potentially be toxic within waterways, however the team made sure to dispose of ethylene glycol in a responsible way.
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<h1> Welcome </h1>
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<b>2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes, did you document these issues in the Registry? How did you manage to handle the safety issue? How could other teams learn from your experience?</b>
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<p>Welcome to iGEM 2012 at UC Davis!</p>
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<br><br>
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This year's UC Davis team is composed of ten undergraduates, two advisors, and a graduate student. We come from different areas of study, but we're all working together on this year's synthetic biology project. Due to the global impact of plastic pollution, we have decided to focus on biodegradation of polyethylene terephthalate (PET). PET is a commonly and widely used plastic, but only a small percentage of them are recycled, meaning a majority of the trash ends up in landfills and the oceans. It is a global issue, and achieving our goal would have a big impact on the issue of plastic degradation.
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Our BioBrick parts this year do not raise safety issues, despite the ethylene glycol production. The safety management procedures have been discussed in the previous question’s answer. The novel part that we are submitting to the Registry is the cutinase gene, in BioBrick format. This is a lipolytic enzyme that does not pose a threat to humans.
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<b>3. Is there a local biosafety group, committee, or review board at your institution? If yes, what does your local biosafety group think about your project? If no, which specific biosafety rules or guidelines do you have to consider in your country?</b>
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The University of California at Davis has a biosafety group, which heads the disposal and use of hazardous materials. They approve of our project and the procedures that we have followed. Further, they are excited for the potential that this project has, in terms of making the environment safer for ihabitants.
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<b>4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</b>
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<br>  
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<div class="floatbox3">
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<h1> Our Project/Abstract</h1>
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<p>We hope to accomplish:</p><br>
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This year, our team hopes to successfully insert the gene for cutinase, an
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enzyme that has been shown to degrade polyethylene terephthalate (PET), into
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several strains of E. coli. PET is a major kind of plastic used today, and we hope to
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overproduce cutinase within the E. coli and secrete the enzyme into the extracellular
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region to degrade the PET. We hope to test the cutinase out on several kinds of
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PET, such as films from scientific companies and plastic bottles, and test how much
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each is broken down. We also hope to improve the cutinase itself through targeted
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mutations and codon optimization, through programs such as Foldit and SWISS-
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MODEL.<br><br>
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Through our research, we have learned that with cutinase, PET degrades into
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terephthalic acid (TPA) and ethylene glycol. While TPA does not appear to be
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harmful, ethylene glycol is a toxic substance. We hope to degrade ethylene glycol as
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much as possible by enhancing the promoters that express the degradative enzymes
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involved. After ethylene glycol is degraded, we hope to redirect all further
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byproducts into glycolysis within E. coli so that the project would sustain itself.
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We also hope to perform a complete economic and environmental analysis
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of our project to see how feasible it would be in real life and to assess the impact it
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could have.<br><br>
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Lastly, we need to ensure that our parts do not have common restriction
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sites within them so they can be used properly in the standard BioBrick format. We
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hope to create and characterize a part family and to end up with a series of BioBrick
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standard parts to submit to the Parts Registry.
<br><br>
<br><br>
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<p>What We Have Done So Far:</p><br>
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We have outlined a plan for the engineering of the PET degradation circuit
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and we ordered a synthesized sequence for cutinase. We asked for separate strains
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of E. coli from Yale and Barcelona.<br><br>
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We learned basic lab protocols, such as ligation, transformation, and
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digestion and we have worked on the Wiki.<br><br>
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We have done extensive research on past attempts to degrade PET and other
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plastics. We even visited our local landfill to talk about current issues with waste
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degradation, such as control over concentrations of methane.<br><br>
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Two of our members (Nick and Mattan) attended the Biomedical Engineering
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Entrepreneurship Academy to be better informed about the economic implications
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of our project, and what companies might be looking for in terms of a completed
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product.<br><br>
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Lastly, we’ve had team bonding, over sushi buffets, ice cream sandwiches and
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laughs.<br>
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Safety issues could be headed by a designated safety monitor in each iGEM group. This set-up allows all of the teams to have a person who will always make sure that the safest procedures are being followed at all times. Also, the production of potentially hazardous materials should always be controlled by an inducible promoter, so that it may be stopped at any time. The different parts can be made safer by making the parts work only with BioBrick assembly units and nothing else that exists in nature.
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You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples.
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You <strong>MUST</strong> have all of the pages listed in the menu below with the names specified. PLEASE keep all of your pages within your teams namespace. 
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</td><td><div class="thumb tright"><div class="thumbinner" style="width:182px;"><a href="https://2012.igem.org/wiki/index.php?title=Special:Upload&amp;wpDestFile=UC_Davis_logo.png" class="new" title="File:UC Davis logo.png">File:UC Davis logo.png</a>  <div class="thumbcaption">200px</div></div></div>
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<p><i>Tell us more about your project.  Give us background.  Use this as the abstract of your project.  Be descriptive but concise (1-2 paragraphs)</i>
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</td><td><div class="thumb tright"><div class="thumbinner" style="width:182px;"><a href="/wiki/index.php?title=Special:Upload&amp;wpDestFile=UC_Davis_team.png" class="new" title="File:UC Davis team.png">File:UC Davis team.png</a>  <div class="thumbcaption">Your team picture</div></div></div>
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</td><td align="center"><strong class="selflink"> Team UC_Davis</strong>
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</th><th align="center"><a href="https://2012.igem.org/Team:UC_Davis/Team" title="Team:UC Davis/Team">Team</a>
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</th><th align="center"><a href="https://2012.igem.org/Team:UC_Davis/Project" title="Team:UC Davis/Project">Project</a>
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Revision as of 17:11, 24 July 2012

Team:UC Davis - 2012.igem.org



Welcome

Welcome to iGEM 2012 at UC Davis!

This year's UC Davis team is composed of ten undergraduates, two advisors, and a graduate student. We come from different areas of study, but we're all working together on this year's synthetic biology project. Due to the global impact of plastic pollution, we have decided to focus on biodegradation of polyethylene terephthalate (PET). PET is a commonly and widely used plastic, but only a small percentage of them are recycled, meaning a majority of the trash ends up in landfills and the oceans. It is a global issue, and achieving our goal would have a big impact on the issue of plastic degradation.



Our Project/Abstract

We hope to accomplish:


This year, our team hopes to successfully insert the gene for cutinase, an enzyme that has been shown to degrade polyethylene terephthalate (PET), into several strains of E. coli. PET is a major kind of plastic used today, and we hope to overproduce cutinase within the E. coli and secrete the enzyme into the extracellular region to degrade the PET. We hope to test the cutinase out on several kinds of PET, such as films from scientific companies and plastic bottles, and test how much each is broken down. We also hope to improve the cutinase itself through targeted mutations and codon optimization, through programs such as Foldit and SWISS- MODEL.

Through our research, we have learned that with cutinase, PET degrades into terephthalic acid (TPA) and ethylene glycol. While TPA does not appear to be harmful, ethylene glycol is a toxic substance. We hope to degrade ethylene glycol as much as possible by enhancing the promoters that express the degradative enzymes involved. After ethylene glycol is degraded, we hope to redirect all further byproducts into glycolysis within E. coli so that the project would sustain itself. We also hope to perform a complete economic and environmental analysis of our project to see how feasible it would be in real life and to assess the impact it could have.

Lastly, we need to ensure that our parts do not have common restriction sites within them so they can be used properly in the standard BioBrick format. We hope to create and characterize a part family and to end up with a series of BioBrick standard parts to submit to the Parts Registry.

What We Have Done So Far:


We have outlined a plan for the engineering of the PET degradation circuit and we ordered a synthesized sequence for cutinase. We asked for separate strains of E. coli from Yale and Barcelona.

We learned basic lab protocols, such as ligation, transformation, and digestion and we have worked on the Wiki.

We have done extensive research on past attempts to degrade PET and other plastics. We even visited our local landfill to talk about current issues with waste degradation, such as control over concentrations of methane.

Two of our members (Nick and Mattan) attended the Biomedical Engineering Entrepreneurship Academy to be better informed about the economic implications of our project, and what companies might be looking for in terms of a completed product.

Lastly, we’ve had team bonding, over sushi buffets, ice cream sandwiches and laughs.

Retrieved from "http://2012.igem.org/Team:UC_Davis"