Difference between revisions of "Team:UC Davis/AchalaTestPage"

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<html>
 
<html>
 
<head>
 
<head>
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<title>iGEM-bg</title>
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  <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">
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<title>iGEM-mainpage</title>
 
<meta name="viewport" content="width=device-width, initial-scale=1">
 
<meta name="viewport" content="width=device-width, initial-scale=1">
 
</head>
 
</head>
 
<style>
 
<style>
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   body { margin:0px; background-color: #fff; max-width: 100%; min-width: 600px; font-family:BernardMT;}
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   body { margin:0px; background-color: #fff; max-width: 100%; min-width: 700px; font-family:BernardMT;}
 
   /*------------Get rid of iGEM stuff----------------------------------*/
 
   /*------------Get rid of iGEM stuff----------------------------------*/
 
#home_logo, #sideMenu { display:none; }
 
#home_logo, #sideMenu { display:none; }
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   /*-------------------------------------------------------------------*/
 
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body {
  
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      font-family: 'PT Sans', sans-serif;
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      min-width: 700px;
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      margin-bottom:-17px;
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/*--Top Navigation Styling--*/
 
/*--Top Navigation Styling--*/
 
#topnav {
 
#topnav {
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   display: block;
 
   display: block;
 
   text-align:left;
 
   text-align:left;
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   font-size: 18px;
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}
 
}
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/*-- Add a grey background color to dropdown links on hover-- */
 
 
.dropdown-content a:hover {
 
.dropdown-content a:hover {
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  background-color: #ddd;
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    color:#48fb47;
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}
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  }
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/* --Show the dropdown menu on hover --*/
 
/* --Show the dropdown menu on hover --*/
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.topnav .b-dropdown-content {
 
.topnav .b-dropdown-content {
 
   display: none;
 
   display: none;
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   font-size: 16px;
 
   border-radius: 7px;
 
   border-radius: 7px;
  
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}
 
}
 
#topnav .b-dropdown-content a:hover {
 
#topnav .b-dropdown-content a:hover {
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   color: black;
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   color: #48fb47;
 
}
 
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#topnav .b-dropdown-content {
 
#topnav .b-dropdown-content {
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@media screen and (max-width:750px) {
 
@media screen and (max-width:750px) {
 
   #topnav .dropdown .dropbtn {
 
   #topnav .dropdown .dropbtn {
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     display: none;
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     display: none;
 
   }
 
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   #topnav {
 
   #topnav {
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     justify-content: center;
 
     justify-content: center;
 
     padding-right: 46%;
 
     padding-right: 46%;
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   }
 
   }
 
}
 
}
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}
 
}
  
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.Cenozoic img:hover{
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   box-shadow: 0px 0px 50px green;
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  border-radius: 50%;
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      -o-transition: all 10ms cubic-bezier(0.980, 0.960, 0.975, 0.980);
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          transition: all 10ms cubic-bezier(0.980, 0.960, 0.975, 0.980); /* custom */
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  -webkit-transition-timing-function: cubic-bezier(0.980, 0.960, 0.975, 0.980);
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.rectangleb{
 
.rectangleb{
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background-color: #002855;
 
background-color: #002855;
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}
 
}
 
.rectanglew{
 
.rectanglew{
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background-color: #fff;
 
background-color: #fff;
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height: 10vw;
 
height: 10vw;
 
}
 
}
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.info {
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width: 40%;
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}
 
</style>
 
</style>
  
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  <div class="logos" style="background-color: #002855;">
 
  <div class="logos" style="background-color: #002855;">
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       <a href="http://ucdavis.com">
 
       <a href="http://ucdavis.com">
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      <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";>
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        <img src="https://static.igem.org/mediawiki/2018/a/a5/T--UC_Davis--whitelogo.png" onmouseover="this.src='https://static.igem.org/mediawiki/2018/4/45/T--UC_Davis--UCDgreen.jpg'"
 +
        onmouseout="this.src='https://static.igem.org/mediawiki/2018/a/a5/T--UC_Davis--whitelogo.png'
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        " alt="uc davis logo" style="margin-left: auto;margin-right:auto; width: 50%;" Padding: "0";>
 
       </a>
 
       </a>
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     </div>
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−
 
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</div>
 
  <!--_____________Cenozoic logo_____________-->
 
  <!--_____________Cenozoic logo_____________-->
  
 
  <div class="logos" style="background-color: #002855">
 
  <div class="logos" style="background-color: #002855">
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      <div class="Cenozoic">
 
       <a href="https://2018.igem.org/Team:UC_Davis">
 
       <a href="https://2018.igem.org/Team:UC_Davis">
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      <img src="https://static.igem.org/mediawiki/2018/1/1b/T--UC_Davis--DNA_refined.png" alt="Cenozoic logo" style="width: 80%; margin-left: auto;margin-right: auto;"Padding: "0";>
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      <img src="https://static.igem.org/mediawiki/2018/6/66/T--UC_Davis--Cenozoi_Transp.jpg" onmouseover="this.src='https://static.igem.org/mediawiki/2018/5/5e/T--UC_Davis--Cenozoi_green.jpg'"
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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>
 
       </a>
 
     </div>
 
     </div>
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    </div>
  
 
  <!--______________iGEM logo____________-->
 
  <!--______________iGEM logo____________-->
 +
  
 
  <div class="logos" style="background-color: #002855">
 
  <div class="logos" style="background-color: #002855">
 +
        <div class="iGEM">
 
     <a href="https://2018.igem.org">
 
     <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";>
 
    <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>
 
     </a>
 
  </div>
 
  </div>
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</div>
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</div>
 
</div>
  
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<div style='padding-top: 130px;'></div>
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<div style='padding-top: 200px;'></div>
  
 
<!--______________Top Navigation Bar____________-->
 
<!--______________Top Navigation Bar____________-->
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           <div class="dropdown-content">
 
           <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/Design">Design</a>
−
             <a href="#">Results</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Results">Results</a>
−
             <a href="#">Modelling</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>
 
             <a href="https://2018.igem.org/Team:UC_Davis/InterLab">InterLab</a>
 +
            <a href="https://2018.igem.org/Team:UC_Davis/SupplementalMaterials">Supplementary Material</a>
  
 
           </div>
 
           </div>
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         <button class="dropbtn">HUMAN PRACTICES</button>
 
         <button class="dropbtn">HUMAN PRACTICES</button>
 
           <div class="dropdown-content">
 
           <div class="dropdown-content">
−
             <a href="#">Human Practices</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Human_Practices">Human Practices</a>
−
             <a href="#">Education & Engagement</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Superfund">Superfund Program</a>
−
             <a href="#">Policy</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Education">Education & Outreach</a>
 +
 
 
           </div>
 
           </div>
 
       </div>
 
       </div>
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         <div class="dropdown-content">
 
         <div class="dropdown-content">
 
           <a href="#">Experiments</a>
 
           <a href="#">Experiments</a>
−
           <a href="#">Lab Notebook</a>
+
           <a href="https://2018.igem.org/Team:UC_Davis/Notebook">Lab Notebook</a>
−
           <a href="#">Safety</a>
+
           <a href="https://2018.igem.org/Team:UC_Davis/Safety">Safety</a>
  
 
           </div>
 
           </div>
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       <button class="dropbtn">TEAM</button>
 
       <button class="dropbtn">TEAM</button>
 
           <div class="dropdown-content">
 
           <div class="dropdown-content">
−
             <a href="#">Meet the Team</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Team">Meet the Team</a>
−
             <a href="#">Advisors</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Attributions">Attributions</a>
−
             <a href="#">Sposors</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Sponsors">Sponsors</a>
 
           </div>
 
           </div>
 
     </div>
 
     </div>
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       <button class="dropbtn">ACHIEVEMENTS</button>
 
       <button class="dropbtn">ACHIEVEMENTS</button>
 
         <div class="dropdown-content">
 
         <div class="dropdown-content">
−
           <a href="#">Medal Requirements</a>
+
           <a href="https://2018.igem.org/Team:UC_Davis/Medal_Requirements">Medal Requirements</a>
 
           <a href="#">Awards</a>
 
           <a href="#">Awards</a>
 
           </div>
 
           </div>
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<div class="b-dropdown-content">
 
<div class="b-dropdown-content">
 
             <a href="https://2018.igem.org/Team:UC_Davis/Design">Design</a>
 
             <a href="https://2018.igem.org/Team:UC_Davis/Design">Design</a>
−
             <a href="#">Results</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Results">Results</a>
−
             <a href="#">Modelling</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Modeling">Modeling</a>
−
             <a href="https://2018.igem.org/Team:UC_Davis/InterLab">InterLa
+
             <a href="https://2018.igem.org/Team:UC_Davis/InterLab">InterLab</a>
 +
            <a href="https://2018.igem.org/Team:UC_Davis/SupplementalMaterials">Supplementary Material</a>
 
</div>
 
</div>
 
</div>
 
</div>
 
<div class="b-dropdown"><a href="Practices" class="b-dropdown-main"> Human Practices</a>
 
<div class="b-dropdown"><a href="Practices" class="b-dropdown-main"> Human Practices</a>
 
<div class="b-dropdown-content">
 
<div class="b-dropdown-content">
−
             <a href="#">Human Practices</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Human_Practices">Human Practices</a>
−
             <a href="#">Education & Engagement</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Superfund">Superfund Program</a>
−
             <a href="#">Policy</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Education">Education & Outreach</a>
 +
 
 
</div>
 
</div>
 
</div>
 
</div>
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<div class="b-dropdown-content">
 
<div class="b-dropdown-content">
 
             <a href="#">Experiments</a>
 
             <a href="#">Experiments</a>
−
             <a href="#">Lab Notebook</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Notebook">Lab Notebook</a>
−
             <a href="#">Safety</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Safety">Safety</a>
 
</div>
 
</div>
 
</div>
 
</div>
 
<div class="b-dropdown b-Acknowledgements"><a href="Acknowledgements" class="b-dropdown-main">Team</a>
 
<div class="b-dropdown b-Acknowledgements"><a href="Acknowledgements" class="b-dropdown-main">Team</a>
 
<div class="b-dropdown-content">
 
<div class="b-dropdown-content">
−
<a href="#">Meet the Team</a>
+
<a href="https://2018.igem.org/Team:UC_Davis/Team">Meet the Team</a>
−
<a href="#">Advisors</a>
+
<a href="https://2018.igem.org/Team:UC_Davis/Attributions">Attributions</a>
−
<a href="#">Sponsors</a>
+
<a href="https://2018.igem.org/Team:UC_Davis/Sponsors">Sponsors</a>
 
</div>
 
</div>
 
</div>
 
</div>
 
         <div class="b-dropdown"><a href="Parts" class="b-dropdown-main">Achievements</a>
 
         <div class="b-dropdown"><a href="Parts" class="b-dropdown-main">Achievements</a>
 
           <div class="b-dropdown-content">
 
           <div class="b-dropdown-content">
−
             <a href="#">Medal Requirements</a>
+
             <a href="https://2018.igem.org/Team:UC_Davis/Medal_Requirements">Medal Requirements</a>
 
             <a href="#">Awards</a>
 
             <a href="#">Awards</a>
 
           </div>
 
           </div>
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<div class="rectanglew">
 
<div class="rectanglew">
 
   <center>
 
   <center>
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     <div style = ' padding-right: 100PX; padding-left: 60PX; padding-bottom: 20px;padding-top: 100px; font-size: 25px; color: #d9a900; line-height: 25px'; ><b>Mammailian Cell Based Biosensor For Physiological Effects Of Toxins</b></div>
+
     <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 Biosensor For Environmental Toxicology</b></div>
 
   </center>
 
   </center>
  
 
     <div style='padding-top: 30px;'></div>
 
     <div style='padding-top: 30px;'></div>
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     <div style = 'padding-right: 100PX; padding-left: 100PX; text-indent: 50px;line-height: 25px; font-size: 18px' >
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     <div style = 'padding-right: 100PX; padding-left: 100PX; text-indent: 50px;line-height: 25px; font-size: 16px' >
−
       After visiting the Yurok Tribe, 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, a specific toxin in the environment, a high quality field test, a causal effect on human health, and a specific policy change.
+
       Our project aims to develop mammalian-based biosensors for use in the context of environmental toxicology. Specifically, out biosensors have been designed to co-opt the mammalian cell’s intrinsic stress response pathways and use these to trigger the production of a fluorescent reporter. We hypothesize that a device reporting on the activation of cell stress pathways will provide more physiologically and health relevant information about the potential toxins present in an environment than bioassays which seek to simply measure compound presence and/or abundance. That is, our bioassay asks not whether a compound is there, but rather whether compounds exists that may pose a health hazard. We leave the identification of the specific hazards to more sensitive and quantitative techniques.
 +
      <br></br>Our biosensors use mammalian-derived promoters of genes known to be activated in response to stress-inducing environmental pollutants. These promoters are coupled to a reporter gene (eGFP) and used in in vitro assays to report on the presence of compounds that elicit cell stress.
 +
 
 
</div>
 
</div>
−
        <div style = 'padding-right: 100PX; padding-left: 100PX; text-indent: 50px;line-height: 25px; font-size: 18px' >Polluters –> Environment (Field Test) –> Human Disease –> Policy Change –| </div>
 
−
      <div style = 'padding-right: 100PX; padding-left: 100PX; text-indent: 50px;line-height: 25px; font-size: 18px' >  Polluters 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 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.</div>
 
  
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</div>
 
</div>
  
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     <div style='padding-top: 25px;'></div>
 
     <div style='padding-top: 25px;'></div>
 
       <center>
 
       <center>
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           <div style = 'padding-left: 10PX; padding-bottom: 20px;padding-top: 20px; font-size: 30px; color: #d9a900'; ><b>Process</b></div>
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           <div style = 'padding-left: 10PX; padding-bottom: 20px;padding-top: 20px; font-size: 25px; color: #d9a900'; ><b>Inspiration</b></div>
 
       </center>
 
       </center>
 
           <div style='padding-top: 30px;'></div>
 
           <div style='padding-top: 30px;'></div>
 +
          <div class="info" style = "float:right;">
 +
            <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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          </div>
  
  
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           <div style = 'padding-right: 100PX; padding-left: 100PX;padding-bottom: 60px; text-indent:50px ;line-height: 25px; color: #fff; font-size: 18px'; >
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           <div style = 'padding-right: 100PX; padding-left: 100PX;padding-bottom: 60px; text-indent:50px ;line-height: 25px; color: #fff; font-size: 16px'; >
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             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
+
             Earlier this year, we were really fortunate to visit an indigenous tribe of people who live in Klamath, Ca -  a beautiful city in the coastal regions of northern California.
−
             of the art field tests, ELISA immunoassays, are of high quality and 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>The tribe have reported unusually elevated rates of cancer and miscarriage incidence, and have indicated they have reason to suspect that the cause may be tied to environmental pollution on their tribal land from local agricultural and forestry corporations. Researchers from UC Davis have been collaborating with the tribe’s scientists and governing council to gather data pertaining to environmental and human health.
 
           </div>
 
           </div>
 
</div>
 
</div>
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   <div class="spacer" ></div>
 
   <div class="spacer" ></div>
  
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     <div style='padding-top: 40px;'></div>
 
       <center>
 
       <center>
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         <div style = 'padding-left: 10PX; padding-bottom: 20px;padding-top: 20px; font-size: 27px; color: #d9a900'; ><b>Limitations</b></div>
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         <div style = 'padding-left: 10PX; padding-bottom: 20px;padding-top: 20px; font-size: 25px; color: #d9a900'; ><b>How does it work?</b></div>
 
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       </center>
 
         <div style='padding-top: 30px;'></div>
 
         <div style='padding-top: 30px;'></div>
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        <div class="info" style = "float:left;">
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          <img src="https://static.igem.org/mediawiki/2018/4/43/T--UC_Davis--picFP.jpg" style="width:250px; height: 350px;padding-left: 50PX; padding-right:10px;padding-bottom: 5px;padding-top: 5px;">
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        </div>
  
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        <div style = 'padding-right: 100PX; padding-left: 100PX;padding-bottom: 60px; text-indent:50px ;line-height: 25px; color: #fff; font-size: 16px'; >
 +
          We reasoned that health impacts from exposure to toxins, particularly low level exposure, elicits a very complex cellular response that involves the change in activity and regulation of many genes simultaneously;
 +
          these are very complex pathways that we still have a lot to learn about, but we imagine that they are similar to intricate built in sensors of health that are very hard to engineer ourselves. So we took advantage of that.
 +
          the basic premise of our project is that we are taking advantage of what mammalian cells offer as a chassis and then we engineered them to tell us the stress they are experiencing in a way that we can quantify.
  
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<br></br>The specific promoters we have identified for our project control the expression of the following genes: Metallothionein 1, Metallothionein 2, Fibroblast growth factor(FGF21), and the Growth arrest and DNA Damage(GADD45a and GADD153). The representative environmental toxins that we plan to stimulate our engineered cells with include: 2,4-Dichlorophenoxyacetic acid, Warfarin, Metam Sodium, and Copper Sulfate. We are also using Hydrogen Peroxide as a positive control.
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        A 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 may motivate and inform further studies to find out if there is a causal link between these COCs and human disease.
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           A possible extension of our research would be to determine the effect of multiple COCs on the physiological health of mammalian 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 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 a response associated with stress in mammalian cells.
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           A possible extension of our research would be to determine the effect of multiple chemicals of concern(COCs) on the physiological health of mammalian 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 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 a response associated with stress in mammalian cells.
 
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Revision as of 05:37, 1 October 2018

iGEM-mainpage

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Mammalian Cell Biosensor For Environmental Toxicology
Our project aims to develop mammalian-based biosensors for use in the context of environmental toxicology. Specifically, out biosensors have been designed to co-opt the mammalian cell’s intrinsic stress response pathways and use these to trigger the production of a fluorescent reporter. We hypothesize that a device reporting on the activation of cell stress pathways will provide more physiologically and health relevant information about the potential toxins present in an environment than bioassays which seek to simply measure compound presence and/or abundance. That is, our bioassay asks not whether a compound is there, but rather whether compounds exists that may pose a health hazard. We leave the identification of the specific hazards to more sensitive and quantitative techniques.

Our biosensors use mammalian-derived promoters of genes known to be activated in response to stress-inducing environmental pollutants. These promoters are coupled to a reporter gene (eGFP) and used in in vitro assays to report on the presence of compounds that elicit cell stress.
Inspiration
Earlier this year, we were really fortunate to visit an indigenous tribe of people who live in Klamath, Ca - a beautiful city in the coastal regions of northern California.

The tribe have reported unusually elevated rates of cancer and miscarriage incidence, and have indicated they have reason to suspect that the cause may be tied to environmental pollution on their tribal land from local agricultural and forestry corporations. Researchers from UC Davis have been collaborating with the tribe’s scientists and governing council to gather data pertaining to environmental and human health.
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How does it work?
We reasoned that health impacts from exposure to toxins, particularly low level exposure, elicits a very complex cellular response that involves the change in activity and regulation of many genes simultaneously; these are very complex pathways that we still have a lot to learn about, but we imagine that they are similar to intricate built in sensors of health that are very hard to engineer ourselves. So we took advantage of that. the basic premise of our project is that we are taking advantage of what mammalian cells offer as a chassis and then we engineered them to tell us the stress they are experiencing in a way that we can quantify.

The specific promoters we have identified for our project control the expression of the following genes: Metallothionein 1, Metallothionein 2, Fibroblast growth factor(FGF21), and the Growth arrest and DNA Damage(GADD45a and GADD153). The representative environmental toxins that we plan to stimulate our engineered cells with include: 2,4-Dichlorophenoxyacetic acid, Warfarin, Metam Sodium, and Copper Sulfate. We are also using Hydrogen Peroxide as a positive control.
Future
A possible extension of our research would be to determine the effect of multiple chemicals of concern(COCs) on the physiological health of mammalian 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 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 a response associated with stress in mammalian cells.


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Contact

530-752-1139

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UC Davis iGEM 2018