Difference between revisions of "Team:UC Davis"

 
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      <li><a href="https://2018.igem.org/Team:UC_Davis/Project_Overview">Team</a></li>
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    <p class="centertext"><a href="https://2018.igem.org/Team:UC_Davis/Project_Overview">
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Project Overview</a>
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    </p>
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    <p class="centertext"><a href="https://2018.igem.org/Team:UC_Davis/Human_Practices">
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Human Practices</a>
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    <p class="centertext">
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      <h1 style="color:gold;">
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<i><b>Cenozoic: </b></h1>
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      <h2="color:000080;">Mammmalian Cell Based Biosensor For Physiological Effects of Toxins</i>
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        </h2>
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    <a href="https://2018.igem.org/Team:UC_Davis/Policy_Practices_Overview">
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      <b>An idealized finding from our project would be in the form: </b><br><br> “We have evidence to support the finding that (COC) is correlated with the expression of (reporter genes) coupled with promoters associated with physiological stress (e.g.
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}
−
      oxidative) in mammalian cells.”<br><br> After visiting a Superfund site, it became clear that to have a real positive impact regarding their problems with pollution and health, it would be necessary to draw a clear narrative between sources of pollution,
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      measurements of a specific toxin in the environment using a high quality field test, demonstration of an effect on human health at these concentrations, and a specific policy change.<br><br> Polluters –> Environment (Field Test) –> Human Disease
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−
      –> Policy Change –| Polluters<br><br> For best outcomes, every link in this chain needs to be well documented and backed by substantial evidence/data. It needs to be clear which organizations are responsible for introducing which toxins into the
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−
      environment, that they are present in meaningful concentrations in the environment, that these toxins have a known causal effect on human disease, and what set of policy changes can help improve public health.<br><br> This model suggests an obvious
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−
      guiding narrative to a project, with a very strong human practices component involving “cultural competencies” working with, and respecting the views and opinions of an indigenous people, and designing policy change to improve public health. <br><br>      After initially focusing on the possibility of developing a new field test to help detect COCs in the environment, upon further research, it was determined that the current state of the art field tests, ELISA immunoassays, are of high quality and
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−
      effectiveness. In light of this finding, we determined that our efforts were best spent studying the effect of COCs, including chemicals which have not been previously studied in detail, on the physiological health of mammalian cells.<br><br> A
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      limitation of our research is that we will not be able to show a definitive causal link between COCs and human disease, but it is our intention to find links between COCs and physiological stress in mammalian systems, with the hope that our findings
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      may motivate and inform further studies to find out if there is a causal link between these COCs and human disease.<br><br> A possible extension of our research would be to determine the effect of multiple COCs on the physiological health of mammalian
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      cells. This would be of value in assessing and creating sane standards for pollution, as organisms in the natural environment are exposed to a variety of COCs at once, which may not have been previously screened in conjunction with each other. A
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      possible finding from this might be that COC “A,” at a concentration below what is currently considered to be harmful, in the presence of COC “B,” also at a concentration below what is currently considered to be harmful, interact together to trigger
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      a response associated with stress in mammalian cells.
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      <br><br>
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.info {
 +
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<body>
 +
<div class="content">
 +
  <div class="contentb">
 +
  <!-- Page content -->
 +
  <div style='padding-top: 50px;'></div>
 +
<!--______________UC Davis logo____________-->
 +
 +
  <div class="logos" style="background-color: #002855;">
 +
      <div class="UCD">
 +
      <a href="http://ucdavis.com">
 +
      <img src="https://static.igem.org/mediawiki/2018/a/a5/T--UC_Davis--whitelogo.png"  alt="uc davis logo" style="margin-left: auto;margin-right:auto; width: 50%;" Padding: "0";>
 +
      </a>
 +
    </div>
 +
</div>
 +
  <!--_____________Cenozoic logo_____________-->
 +
 +
  <div class="logos" style="background-color: #002855">
 +
      <div class="Cenozoic"style='padding-bottom: 50px;'>
 +
      <a href="https://2018.igem.org/Team:UC_Davis">
 +
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 +
onmouseout="this.src='https://static.igem.org/mediawiki/2018/6/66/T--UC_Davis--Cenozoi_Transp.jpg'
 +
"  alt="Cenozoic logo" style="width: 80%; margin-left: auto;margin-right: auto;"Padding: "0";>
 +
      </a>
 +
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  <!--______________iGEM logo____________-->
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  <div class="logos" style="background-color: #002855">
 +
        <div class="iGEM">
 +
    <a href="https://2018.igem.org">
 +
    <img src="https://static.igem.org/mediawiki/2018/2/2b/T--UC_Davis--iGEM.png"  alt="iGEM logo" style="width: 40%; margin-left: auto;margin-right: auto;" ;Padding: "0";>
 +
    </a>
 +
  </div>
 +
</div>
 +
 +
 +
 +
 +
 +
</div>
 +
 +
<div style='padding-top: 200px;'></div>
 +
 +
<!--______________Top Navigation Bar____________-->
 +
  <ul class="topnav" id="topnav">
 +
 +
      <!--______________Project____________-->
 +
      <div class="dropdown">
 +
        <button class="dropbtn">PROJECT</button>
 +
          <div class="dropdown-content">
 +
            <a href="https://2018.igem.org/Team:UC_Davis/Design">Design</a>
 +
<a href="https://2018.igem.org/Team:UC_Davis/Measurement">Measurement</a>
 +
            <a href="https://2018.igem.org/Team:UC_Davis/Demonstrate">Results</a>
 +
            <a href="https://2018.igem.org/Team:UC_Davis/Modeling">Modeling</a>
 +
            <a href="https://2018.igem.org/Team:UC_Davis/InterLab">InterLab</a>
 +
           
 +
 +
          </div>
 +
      </div>
 +
<!--______________Human Resources____________-->
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      <div class="dropdown">
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    <div style = ' padding-right: 100PX; padding-left: 60PX; padding-bottom: 25px;padding-top: 100px; font-size: 25px; color: #d9a900; line-height: 25px'; ><b>Mammalian Cell Based Bioassay For Environmental Toxicology</b></div>
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    Hello, we are team Cenozoic from the University of California, Davis. This year we developed a mammalian cell-based bioassay for detecting physiological stress, for use in environmental toxicology.
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          <div style = 'padding-left: 10PX; padding-bottom: 20px;padding-top: 20px; font-size: 25px; color: #d9a900'; ><b>Inspiration</b></div>
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            <img src="https://static.igem.org/mediawiki/2018/3/35/T--UC_Davis--Klamath.jpg" style="width:300px; height: 300px;padding-left: 20PX; padding-right:20px;padding-bottom: 20px;padding-top: 5px;">
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          In the far northern end of California, a Native American tribe lives at the mouth of the Klamath River, where their people have lived for countless generations. This community exists in close relation with the local ecosystem, which they rely upon for food, materials for their traditional ceremonies, and recreation. In recent years this tribe has reported elevated rates of cancer, miscarriage, and other illnesses. Our team joined fellow researchers from our university to visit the tribe and learn about the problems they face.
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            <br></br> Upriver from this community, industrial agriculture and forestry corporations manage the land. As part of their routine practices, these corporations apply herbicides, pesticides, and other industrial chemicals on the land under their control. These chemicals have been detected in the water of the river and in local flora and fauna Additionally, illegal marijuana growers in the region have been found to be using warfarin, a potent rat poison, to protect their crops from pests. This chemical has also been measured in the environment.
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            <br></br> The tribe has presented the hypothesis that their health crisis is linked to the presence of these chemicals in their environment.
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          <div style = 'padding-left: 10PX; padding-bottom: 20px;padding-top: 20px; font-size: 25px; color: #d9a900'; ><b>Biosensor Design</b></div>
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            We designed a mammalian cell-based bioassay that reports activation of specific stress pathways via fluorescence, for use in environmental toxicology. To do this, we selected transcriptionally regulated target genes which are present in mammalian cells and are involved in stress pathways. We isolated the promoters with transcription factor binding sites from these target genes and coupled them to a fluorescent reporter gene. When a chemical of concern is screened using our assay, if it triggers a specific stress response, the reporter gene will be expressed, causing the assay to fluoresce. The fluorescence of the assay can be quantitatively measured and analyzed. This assay will provide data on the effect of chemicals of concern on the physiological health of mammalian cells.
 +
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<br></br>For a full report on our bioassay design, please visit our <a style='color: #d9a900' href="https://2018.igem.org/Team:UC_Davis/Design">project design page.</a>
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        <div style = 'padding-left: 10PX; padding-bottom: 20px;padding-top: 20px; font-size: 25px; color: #d9a900'; ><b>Integrating Human Practices</b></div>
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          After learning about the problems facing this community, we became very interested in the cultural context in which any proposed solution involving synthetic biology would be used.
 +
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            <br></br> The tribe has previously voiced concerns about biotechnology. In 2015, the tribal leadership council passed the “Genetically Engineered Organism Ordinance,” which made illegal the creation, growth, or release of genetically engineered organisms within the tribe’s territory. Interestingly, when our team read through the law in question, we learned that the ban has generous exceptions, including all of bacterial synthetic biology. When we reached out to a member of the tribe’s scientific body for clarification, the tribe’s scientist told us that some forms of biotechnology were incompatible with this community’s values, other forms were not.
 +
 +
            <br></br> With a better understanding of the cultural context in hand, we set out to help solve this problem. The tribe’s concern was not about identifying the chemicals in their environment. Their question, to paraphrase a tribal member we met with, was “is this water going to make my kids sick?” They already knew what chemicals were present— what they wanted to know was what effect they had on the health of people in their community.
 +
 +
            <br></br> For a full report on what we learned from working with this indigenous community and how we integrated human practices into our project, please visit our <a style ='color:  #d9a900;' href="https://2018.igem.org/Team:UC_Davis/Human_Practices">Human Practices page.</a>
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          <div style = 'padding-left: 10PX; padding-bottom: 20px;padding-top: 20px; font-size: 25px; color: #d9a900'; ><b>Mammalian Synthetic Biology</b></div>
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          Our project represents the first time that an iGEM team from our university has worked with mammalian cells. Mammalian synthetic biology in the iGEM competition is less well developed than bacterial systems, and we hope to help future teams work in this space. Mammalian cells offer unique challenges and opportunities, and there are very large gaps in shared knowledge and protocols for working with mammalian cells in iGEM. To this end, we have created comprehensive protocols for culturing of two mammalian cell lines, AML-12 and CHO-DG44, as well as protocols for transfection and characterization of EGFP expression. To download these protocols, please visit our  <a style ='color:  #d9a900;' href="https://2018.igem.org/Team:UC_Davis/Experiments">Experiments page</a>.
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Latest revision as of 01:08, 18 October 2018

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Mammalian Cell Based Bioassay For Environmental Toxicology
Hello, we are team Cenozoic from the University of California, Davis. This year we developed a mammalian cell-based bioassay for detecting physiological stress, for use in environmental toxicology.
Inspiration
In the far northern end of California, a Native American tribe lives at the mouth of the Klamath River, where their people have lived for countless generations. This community exists in close relation with the local ecosystem, which they rely upon for food, materials for their traditional ceremonies, and recreation. In recent years this tribe has reported elevated rates of cancer, miscarriage, and other illnesses. Our team joined fellow researchers from our university to visit the tribe and learn about the problems they face.

Upriver from this community, industrial agriculture and forestry corporations manage the land. As part of their routine practices, these corporations apply herbicides, pesticides, and other industrial chemicals on the land under their control. These chemicals have been detected in the water of the river and in local flora and fauna Additionally, illegal marijuana growers in the region have been found to be using warfarin, a potent rat poison, to protect their crops from pests. This chemical has also been measured in the environment.

The tribe has presented the hypothesis that their health crisis is linked to the presence of these chemicals in their environment.
Biosensor Design
We designed a mammalian cell-based bioassay that reports activation of specific stress pathways via fluorescence, for use in environmental toxicology. To do this, we selected transcriptionally regulated target genes which are present in mammalian cells and are involved in stress pathways. We isolated the promoters with transcription factor binding sites from these target genes and coupled them to a fluorescent reporter gene. When a chemical of concern is screened using our assay, if it triggers a specific stress response, the reporter gene will be expressed, causing the assay to fluoresce. The fluorescence of the assay can be quantitatively measured and analyzed. This assay will provide data on the effect of chemicals of concern on the physiological health of mammalian cells.

For a full report on our bioassay design, please visit our project design page.
Integrating Human Practices
After learning about the problems facing this community, we became very interested in the cultural context in which any proposed solution involving synthetic biology would be used.

The tribe has previously voiced concerns about biotechnology. In 2015, the tribal leadership council passed the “Genetically Engineered Organism Ordinance,” which made illegal the creation, growth, or release of genetically engineered organisms within the tribe’s territory. Interestingly, when our team read through the law in question, we learned that the ban has generous exceptions, including all of bacterial synthetic biology. When we reached out to a member of the tribe’s scientific body for clarification, the tribe’s scientist told us that some forms of biotechnology were incompatible with this community’s values, other forms were not.

With a better understanding of the cultural context in hand, we set out to help solve this problem. The tribe’s concern was not about identifying the chemicals in their environment. Their question, to paraphrase a tribal member we met with, was “is this water going to make my kids sick?” They already knew what chemicals were present— what they wanted to know was what effect they had on the health of people in their community.

For a full report on what we learned from working with this indigenous community and how we integrated human practices into our project, please visit our Human Practices page.
Mammalian Synthetic Biology
Our project represents the first time that an iGEM team from our university has worked with mammalian cells. Mammalian synthetic biology in the iGEM competition is less well developed than bacterial systems, and we hope to help future teams work in this space. Mammalian cells offer unique challenges and opportunities, and there are very large gaps in shared knowledge and protocols for working with mammalian cells in iGEM. To this end, we have created comprehensive protocols for culturing of two mammalian cell lines, AML-12 and CHO-DG44, as well as protocols for transfection and characterization of EGFP expression. To download these protocols, please visit our Experiments page.