Difference between revisions of "Team:Chalmers-Gothenburg/Model"

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{{Chalmers-Gothenburg}}
 
 
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<style type="text/css"> /*------------------ bootstrap.min.css START ----------------------------------*/
  
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/*!
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* Bootstrap v3.3.7 (http://getbootstrap.com)
<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
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<h1> Modeling</h1>
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
 
  
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<h3> Gold Medal Criterion #3</h3>
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To complete for the gold medal criterion #3, please describe your work on this page and fill out the description on your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>. To achieve this medal criterion, you must convince the judges that your team has gained insight into your project from modeling. You may not convince the judges if your model does not have an effect on your project design or implementation.
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Please see the <a href="https://2017.igem.org/Judging/Medals"> 2017 Medals Page</a> for more information.
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<h3>Best Model Special Prize</h3>
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<p>
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#content {
To compete for the <a href="https://2017.igem.org/Judging/Awards">Best Model prize</a>, please describe your work on this page  and also fill out the description on the <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>. Please note you can compete for both the gold medal criterion #3 and the best model prize with this page.
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<br><br>
+
    padding: 0;
You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
+
    margin-left: 0;
</p>
+
    margin-top: -12px; /*Couldn't figure out why we got a white bar above all content, so I cheated a bit*/
 +
}
  
</div>
 
<div class="clear"></div>
 
  
<div class="column full_size">
+
/*This changes margins that messed with the header navbar*/
<h5> Inspiration </h5>
+
.mw-content-ltr ul, .mw-content-rtl .mw-content-ltr ul {
<p>
+
    margin: 0;
Here are a few examples from previous teams:
+
}
</p>
+
<ul>
+
<li><a href="https://2016.igem.org/Team:Manchester/Model">Manchester 2016</a></li>
+
<li><a href="https://2016.igem.org/Team:TU_Delft/Model">TU Delft 2016  </li>
+
<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
+
<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
+
</ul>
+
  
 +
/*This is the forced heading and logo. Why? :( */
 +
#top_title {
 +
    display: none;
 +
}
 +
 +
/*Something caused the sideMenu to start out displayed instead of hidden. This fixes that.*/
 +
#sideMenu {
 +
    display: none;
 +
}
 +
 +
/*---------------Index page header (above header nav bar)------------------------------*/
 +
 +
/*This is for the part above the header navbar with the title and logo*/
 +
#header_navbar_top {
 +
  background-color: #000000;
 +
  background-image: url("pictures_17/backgrounds/korsvagen_5.png"); /*linear-gradient(to bottom, #7bac78, #016243);*/ 
 +
background-repeat: no-repeat;
 +
  background-position: center;
 +
background-size: 100% 100%; /*60% 100%*/
 +
/*border: 3px solid #000000;*/
 +
text-align: left;
 +
position:top;
 +
  min-height: 750px;
 +
height:auto;
 +
background-attachment: fixed;
 +
  background-position: center;
 +
  background-repeat: no-repeat;
 +
  background-size: cover;
 +
 +
  /*padding-right: 10px; /*100--> 250*/
 +
  /*padding-left: 10px; /*250--> 250px*/
 +
 +
/*height: 270px;/*220px
 +
  min-width: 70%; /*minimum width of header. Don't change from 1200px, title fucks up
 +
  min-height: 70%; /*don't think does anything
 +
margin-left: auto; /*The width of the header. Keep on auto to avoid gray edges
 +
  margin-right: auto; /* --"--
 +
  padding: 40px;/*Find another way to move the logo down a bit?*/
 +
  border-bottom: 5px solid transparent; /*A lot of code for the line between the header and the body */
 +
  -moz-border-image: -moz-linear-gradient(left, #000000 0%, #404040, #000000 100%); /*(left, #016243 0%, #b5deca, #016243 100%);*/
 +
  -webkit-border-image: -webkit-linear-gradient(left, #000000 0%, #404040, #000000 100%); /*(left, #016243 0%, #b5deca, #016243 100%)*/
 +
  border-image: linear-gradient(to right, #000000 0%, #404040, #000000 100%); /*(to right, #016243 0%, #b5deca, #016243 100%);*/
 +
  border-image-slice: 1;
 +
  -webkit-touch-callout: none;
 +
  -webkit-user-select: none;
 +
  -khtml-user-select: none;
 +
  -moz-user-select: none;
 +
  -ms-user-select: none;
 +
  user-select: none;
 +
  cursor: default;
 +
 +
}
 +
 +
/*This is the title of the project*/
 +
#header_navbar_top_title {
 +
/*Sizes in px*/
 +
display:inline-block;
 +
padding-top:650px;
 +
  padding-right:20%;
 +
  font-size: 100px;
 +
  line-height: 45px;
 +
  color: #c91a03;
 +
text-shadow: 3px 3px #000000;
 +
  font-family:'Lato', cursive; /*Dancing Script, Marck Script (meh), Tangerine (ok), Sacramento (meh), Allura (nej), Parisienne (meh), Montez(meh)*/
 +
font-weight: bold;
 +
text-align:left;
 +
margin-left:10%;
 +
 +
/*margin-right:10px; */
 +
/*For the title on index*/
 +
/*background-color: transparent;
 +
  font-size: 60pt; /*35pt
 +
font-family:"Lato", cursive; /*Dancing Script, Marck Script, Tangerine, Sacramento, Allura, Parisienne, Montez
 +
  color:#c91a03;
 +
line-height: 45pt;
 +
  padding-top: 35%;
 +
font-weight: bold;
 +
text-align:left;
 +
margin-left:200px;*/
 +
}
 +
 +
#header_navbar_top_subtitle {
 +
  color:#c91a03;
 +
  font-size: 40pt;
 +
line-height: 30pt;
 +
  padding-top: 1%;
 +
  padding-bottom: 20px;
 +
font-family:"Lato", cursive;
 +
text-align:left;
 +
margin-left:10%;
 +
margin-right:25%;
 +
text-shadow: 3px 3px #000000;
 +
}
 +
 +
.subheader{
 +
color:#808080; /*#7e1002;*/
 +
text-align:center;
 +
font-size:50pt;
 +
padding-top:150px;
 +
padding-bottom:200px;
 +
}
 +
 +
 +
#header_navbar_top_logo {
 +
  display:inline-block;
 +
position: absolute;
 +
  width:9vw; /*20% 20%*/
 +
    height:9vw;
 +
    right:10%;
 +
    bottom:12%;
 +
 +
}
 +
 +
.overview {
 +
padding-bottom:100px;
 +
}
 +
 +
/*logo in the right corner*/
 +
.logo_pos_right{
 +
position: fixed;
 +
/*position in px*/ 
 +
/*  width:20px;
 +
    height:20px;
 +
    right:150px;
 +
    bottom:150px;*/
 +
/*position in percent*/ 
 +
  width:7vw; /*20% 20%*/
 +
    height:7vw;
 +
    right:3%;
 +
    bottom:5%;
 +
}
 +
 +
 +
#header_navbar_top_logo {
 +
  display:inline-block;
 +
}
 +
 +
 +
/*--------------------Header navbar--------------------------------------------*/
 +
 +
 +
/*body {
 +
    font-family: helvetica;
 +
margin:0;
 +
}*/
 +
 +
/*The wrapper and the nav bar have to be the same height, or the page will jump when the nav bar sticks.*/
 +
#header_navbar_wrapper, .header_navbar_ul {
 +
    height: 70px;
 +
}
 +
 +
.header_navbar_ul {
 +
  list-style-type: none; /*No bullet points*/
 +
  margin: 0;
 +
  padding: 0;
 +
  background-repeat: no-repeat;
 +
  background-color: #c91a03;
 +
border-bottom: 2px solid black;
 +
 +
top: 0;
 +
  width: 100%;
 +
  min-width: 1440px;
 +
  z-index:9999;
 +
  -webkit-touch-callout: none;
 +
  -webkit-user-select: none;
 +
  -khtml-user-select: none;
 +
  -moz-user-select: none;
 +
  -ms-user-select: none;
 +
  user-select: none;
 +
}
 +
 +
/*Having the header navbar stick to the top of the screen after it reaches that position*/
 +
.header-nav_stick {
 +
    position: fixed;
 +
    width: 100%;
 +
    top: 16px;
 +
    z-index: 9999;
 +
}
 +
 +
/*Current page header highlight*/
 +
.home #home_link,
 +
.team #team_link,
 +
.achievements #achievements_link,
 +
.HP #HP_link,
 +
.modelling #modelling_link,
 +
.notebook #notebook_link,
 +
.parts #parts_link,
 +
.project #project_link,
 +
.safety #safety_link
 +
{
 +
    color: white;
 +
text-decoration:underline;
 +
 +
}
 +
 +
 +
.dropbtn {
 +
    background-color: transparent;
 +
    color: white;
 +
    padding: 8px;
 +
    /*font-size: 16px;*/
 +
    border: none;
 +
    cursor: pointer;
 +
}
 +
 +
.dropdown,
 +
#header_navbar_home {
 +
    position: relative;
 +
    display: inline-block;
 +
    z-index:9999;
 +
    font-family:'Lato', sans-serif;
 +
}
 +
 +
.dropdown a,
 +
#header_navbar_home a {
 +
  display: block; /*Displaying the links as block elements makes the whole link
 +
  area clickable (not just the text), and it allows us to specify padding (and
 +
  height, width, margins, etc. if you want)*/
 +
  color: #e6e6e6;/*b5deca*/
 +
  text-align: left;
 +
  text-decoration: bold;
 +
  padding: 8px; /*Since block elements take up the full width available, they
 +
  cannot float next to each other. Therefore, specify some padding to make them look good*/
 +
  font-size: 14pt;
 +
  font-weight:bold;
 +
  line-height: 54px;
 +
}
 +
 +
 +
/*Size settings for the dropdown menu content*/
 +
.dropdown-content a {
 +
    line-height: 30px;
 +
    font-size: 12pt;
 +
}
 +
 +
/* Change the link color on hover over either dropdown button, or the dropdown menu items. Also, rounded top borders */
 +
.header_navbar_ul li:hover > a {
 +
    background-color: #7e1002; /*#7e1002*/
 +
    color: white;
 +
    border-radius: 10px 10px 0 0;
 +
text-decoration:none;
 +
 +
}
 +
 +
 +
#header_navbar_home a:hover {
 +
    color: white;
 +
    border-radius: 10px 10px 0 0;
 +
border-bottom: 2px solid black;
 +
}
 +
 +
 +
/*Top right rounded highlight for first list element in dropdown menu*/
 +
.dropdown-content a:first-child:hover {
 +
    border-radius: 0 10px 0 0;
 +
}
 +
 +
/*bottom rounded highlights for last list element in dropdown menu*/
 +
.dropdown-content a:last-child:hover {
 +
    border-radius: 0 0 10px 10px;
 +
}
 +
 +
.dropdown-content {
 +
    display: none;
 +
    position: absolute;
 +
    background-color: #c91a03;
 +
    box-shadow: 0px 8px 16px 0px rgba(0,0,0,0.2);
 +
    width: auto !important; /*to avoid line breaks*/
 +
    white-space: nowrap; /*to avoid line breaks*/
 +
    min-width: 200px;
 +
    border-radius: 0 10px 10px 10px;
 +
}
 +
 +
.dropdown-content a {
 +
    color: white;
 +
    padding: 12px 16px;
 +
    text-decoration: none;
 +
    font-weight: bold;
 +
    display: block;
 +
}
 +
 +
.dropdown-content a:hover {
 +
    background-color: #7e1002;/*#7e1002*/
 +
    /*border-radius: 10px 10px 10px 10px; /*Temprorary solution. I'd prefer to only round the corners that touch the corners of the menu*/
 +
    color: white;
 +
}
 +
 +
.dropdown:hover .dropdown-content {
 +
    display: block;
 +
}
 +
 +
/*Styling for <hr> between menu items in the dropdown menus*/
 +
.header_navbar_ul hr {
 +
    border: 0;
 +
    height: 1px;
 +
    background-image: linear-gradient(to right,  rgba(0, 0, 0, 0), #ccc,  rgba(0, 0, 0, 0));
 +
    margin-top: 0;
 +
    margin-bottom: 0;
 +
}
 +
 +
/*I don't think this one does anything. Probably because of "".dropdown-content a:hover" covering it.*/
 +
.dropdown:hover .dropbtn {
 +
    background-color: #111;
 +
}
 +
 +
 +
 +
/*---------------------------Footer with sponsor logos----------------------------*/
 +
 +
footer hr  {
 +
    border: 0;
 +
    height: 0;
 +
    /*border-top: 1px solid rgba(0, 0, 0, 0.1);*/
 +
    border-bottom: 1px solid rgba(255, 255, 255, 0.3);
 +
    width: 80%;
 +
    text-align: center;
 +
    margin-left: 10%;
 +
    margin-top: 50px;
 +
}
 +
 +
#footer-contact-row {
 +
  padding-bottom: 50px;
 +
}
 +
 +
#footer-contact-row a {
 +
  color: #999999;
 +
  text-decoration: none;
 +
  padding-left: 15px;
 +
  padding-right: 15px;
 +
}
 +
 +
#footer-contact-row a:hover {
 +
  color: #c91a03;
 +
}
 +
 +
#footer-contact-row hr  {
 +
    border: 0;
 +
    height: 0;
 +
    /*border-top: 1px solid rgba(0, 0, 0, 0.1);*/
 +
    border-bottom: 1px solid rgba(255, 255, 255, 0.3);
 +
    width: 30%;
 +
    text-align: center;
 +
    margin-left: 35%;
 +
}
 +
 +
#logorow {
 +
  width: 80%;
 +
  padding: 0;
 +
  margin: 0 auto 0 auto;
 +
}
 +
 +
.footerimg {
 +
  max-height: 100px;
 +
  max-width: 250px;
 +
}
 +
 +
.footerlogo {
 +
  display: inline-block;
 +
  vertical-align: bottom;
 +
  padding: 1em 1.5em 1em 1.5em;
 +
}
 +
 +
.footerlogo .on {
 +
  display: inline-block;
 +
}
 +
 +
.footerlogo:hover .on, .footerlogo .off {
 +
  display: none;
 +
}
 +
 +
.footerlogo:hover .off {
 +
  display: inline-block;
 +
}
 +
 +
/*---------------------------Center page styling---------------------------------*/
 +
 +
/*The wrap class is used for <div> in order to define a space where the
 +
side navigation bar and the page content (text, images etc) is kept*/
 +
 +
 +
.wrap {
 +
  /*width: 100%; /*auto--> 50%
 +
  text-align: center;
 +
  margin: auto; /*auto--> %
 +
  margin-top: 0px; /*40px --> 0px */
 +
 +
width: cover;
 +
  min-width:1440px;
 +
  text-align: center;
 +
  margin: auto;
 +
  margin-top: 0px;
 +
 +
background:#e6e6e6; 
 +
}
 +
 +
/*Attempt to wrap header*/
 +
.wrap-header {
 +
padding-right: auto; /*100--> 250*/
 +
  padding-left: auto; /*250--> 250px*/
 +
background-color: #e6e6e6;
 +
}
 +
 +
/*This is the content of the page, i.e. text images etc. Fits inside <div> with the wrap class*/
 +
.wrap-content {
 +
/*margin-top:75px;
 +
  padding-right: 25%; /*100--> 450*/ /*25%
 +
  padding-left: 25%; /*250--> 450px*/ /*25%
 +
background-color: transparent;
 +
border-style:dashed;*/
 +
 +
margin-top:100px;
 +
padding-right: 22%;
 +
  padding-left: 22%;
 +
background-color: transparent;
 +
 +
/*background-size:50px;*/
 +
}
 +
 +
/*Like .wrap-content, except with even margins, for pages where a side navigation bar is superfluous*/
 +
.wrap-content-no-side-nav {
 +
  padding-right: 75px;/*50px*/
 +
  padding-left: 75px;
 +
}
 +
 +
.wrap-content, .wrap-content-no-side-nav {
 +
  padding-top: 25px;
 +
}
 +
 +
.dashed_line_left_first {
 +
background-color:transparent;
 +
 +
border-style: none none dashed dashed;
 +
border-width:5px;
 +
border-color:#7e1002;
 +
padding-left:50px;
 +
padding-right:50px;
 +
padding-bottom:50px;
 +
padding-top:0px;
 +
}
 +
 +
.dashed_line_left {
 +
background-color:transparent;
 +
 +
border-style: none none dashed dashed;
 +
border-width:5px;
 +
border-color:#7e1002;
 +
padding:50px;
 +
}
 +
 +
.dashed_line_right {
 +
background-color:transparent;
 +
border-style: none dashed dashed none;
 +
border-width:5px;
 +
border-color:#7e1002;
 +
padding:50px;
 +
}
 +
 +
.dashed_line_right_last { /*No bottom border, only left*/
 +
background-color:transparent;
 +
border-style: none dashed none none;
 +
border-width:5px;
 +
border-color:#7e1002;
 +
padding:50px;
 +
}
 +
 +
.dashed_line_left_last { /*No bottom border, only right*/
 +
background-color:transparent;
 +
border-style: none none none dashed;
 +
border-width:5px;
 +
border-color:#7e1002;
 +
padding:50px;
 +
}
 +
 +
 +
/*----------------------------Side navigation bar-------------------------------*/
 +
 +
#side-nav {
 +
    width: 25%;
 +
}
 +
 +
#side-nav nav {
 +
    /*width: 225px;
 +
    padding-left: 25px;
 +
    padding-top:80px;
 +
    float: left;
 +
border-style:dashed;*/
 +
 +
  width: 175px;
 +
    margin-left: 25px;
 +
    margin-top:140px;
 +
    float: left;
 +
border-style:solid;
 +
border-width:2px;
 +
border-color:#000000;
 +
 +
}
 +
 +
#side-nav a {
 +
    color: #333;
 +
    display: block;
 +
    padding: 10px;
 +
    text-align: left;
 +
    text-decoration: none;
 +
background: #f2f2f2;
 +
font-size:12pt !important;
 +
}
 +
 +
#side-nav a.active {
 +
    background: #c91a03;/*before: fff7b5*/
 +
    color: #1a1a1a;
 +
font-size:12pt !important;
 +
}
 +
 +
#side-nav .sub-level {
 +
    padding-left: 30px;
 +
    /*font-size: 12pt;*/
 +
}
 +
 +
#side-nav a:hover {
 +
  background: #ffffff; /*Before: #dcdbdb;*/
 +
  color: black;
 +
font-size:12pt !important;
 +
font-weight:bold;
 +
text-decoration:underline;
 +
text-decoration-color:#c91a03;
 +
}
 +
 +
 +
.side-nav_stick {
 +
    position: fixed;
 +
    top: 0;
 +
    z-index: 0;
 +
    margin-top:120px;
 +
}
 +
 +
.hidden-sidenav {
 +
  opacity: 0;
 +
}
 +
 +
#side-nav nav {
 +
-webkit-transition: opacity 200ms ease-in-out;
 +
    -moz-transition: opacity 200ms ease-in-out;
 +
    -ms-transition: opacity 200ms ease-in-out;
 +
    -o-transition: opacity 200ms ease-in-out;
 +
}
 +
 +
/*---------------------------Profile card styling-------------------------------------*/
 +
.profile-table {
 +
  margin: 80px auto 0 auto;
 +
  border-spacing: 30px;
 +
 +
}
 +
 +
.profile-main {
 +
  height: 350px;
 +
  width: 300px;
 +
  position: relative;
 +
  margin: 20px;
 +
}
 +
 +
.profile-container {
 +
  height: 350px;
 +
  width: 300px;
 +
  position: absolute;
 +
  display: block;
 +
  top: 0;
 +
  left: 0;
 +
-webkit-border-radius: 5px;
 +
-moz-border-radius: 5px;
 +
border-radius: 5px;
 +
box-shadow: 1px 1px 4px #666;
 +
padding: 1%;
 +
background: #fffef9;
 +
background: rgb(252,255,244); /* Old browsers */
 +
background: -moz-linear-gradient(top,  #fffffb 0%, #fffef9 100%); /* FF3.6+ */
 +
background: -webkit-gradient(linear, left top, left bottom, color-stop(0%,rgba(252,255,244,1)), color-stop(100%,rgba(219,218,201,1))); /* Chrome,Safari4+ */
 +
background: -webkit-linear-gradient(top,  #fffffb 0%,#fffef9 100%); /* Chrome10+,Safari5.1+ */
 +
background: -o-linear-gradient(top,  #fffffb 0%,#fffef9 100%); /* Opera 11.10+ */
 +
background: -ms-linear-gradient(top,  #fffffb 0%,#fffef9 100%); /* IE10+ */
 +
background: linear-gradient(top,  #fffffb 0%,#fffef9 100%); /* W3C */
 +
filter: progid:DXImageTransform.Microsoft.gradient( startColorstr='#fcfff4', endColorstr='#dbdac9',GradientType=0 ); /* IE6-9 */
 +
}
 +
 +
.profile-image {
 +
  margin: 15px auto 0 auto;
 +
  height: 250px;
 +
  width: 250px;
 +
  position:relative;
 +
}
 +
 +
.profile-content {
 +
  display: none;
 +
  width: 300px;
 +
  margin: 70px auto 0 auto;
 +
  text-align: justify;
 +
}
 +
 +
.profile-container:hover .profile-content {
 +
  display: block;
 +
}
 +
 +
.profile-container:hover .profile-image {
 +
  position: relative;
 +
}
 +
 +
.profile-name {
 +
  padding-top: 15px;
 +
  color: #c91a03;
 +
  font-weight: bold;
 +
  font-size: 15pt;
 +
text-align:center;
 +
}
 +
 +
.profiletext {
 +
  font-size: 12pt;
 +
  margin-top: 10px;
 +
  line-height: 150%;
 +
  text-align: justify;
 +
}
 +
 +
/*-------------------------------GENERAL STUFF-------------------------------------*/
 +
 +
div {
 +
  text-align: center;
 +
}
 +
 +
.header_test {
 +
background-position: top;
 +
background-attachment: fixed;
 +
background-repeat: no-repeat;
 +
-webkit-background-size: cover;
 +
-moz-background-size: cover;
 +
-o-background-size: cover;
 +
background-size: cover;
 +
        padding-top: 100vh;
 +
        background-image: url("https://static.igem.org/mediawiki/2017/e/e3/T--Chalmers-Gothenburg--Project_Modeling.jpg");
 +
 +
/*A lot of code for the line between the header and the body */
 +
border-bottom: 3px solid transparent;
 +
  -moz-border-image: -moz-linear-gradient(left, #000000 0%, #404040, #000000 100%); /*(left, #016243 0%, #b5deca, #016243 100%);*/
 +
  -webkit-border-image: -webkit-linear-gradient(left, #000000 0%, #404040, #000000 100%); /*(left, #016243 0%, #b5deca, #016243 100%)*/
 +
  border-image: linear-gradient(to right, #000000 0%, #404040, #000000 100%); /*(to right, #016243 0%, #b5deca, #016243 100%);*/
 +
  border-image-slice: 1;
 +
  -webkit-touch-callout: none;
 +
  -webkit-user-select: none;
 +
  -khtml-user-select: none;
 +
  -moz-user-select: none;
 +
  -ms-user-select: none;
 +
  user-select: none;
 +
  cursor: default;
 +
}
 +
 +
 +
/* Banner: name of the page */
 +
#banner {
 +
height: 100%;
 +
        position: relative;
 +
        bottom: 50px;
 +
    float: left;
 +
    width: 100%;
 +
        font-size: 80pt; /*35pt*/
 +
font-family:"Lato", cursive;
 +
        color:#c91a03 ;
 +
line-height: 65pt;
 +
        text-shadow: 5px 5px #000000;
 +
}
 +
 +
#banner h3 {
 +
display: block;
 +
position: absolute;
 +
bottom: 50px;
 +
left: 200px;
 +
        font-size: 80pt; /*35pt*/
 +
font-family:"Lato", cursive;
 +
        color:#c91a03 ;
 +
line-height: 65pt;
 +
        text-shadow: 5px 5px #000000;
 +
        /*border-style:dashed;*/
 +
padding: 20px 20px 20px 20px;
 +
 +
}
 +
 +
#banner h4 {
 +
display: block;
 +
position: absolute;
 +
bottom: -40px;
 +
left: 200px;
 +
        font-size: 40pt; /*35pt*/
 +
font-family:"Lato", cursive;
 +
        color:#c91a03 ;
 +
line-height: 65pt;
 +
        text-shadow: 3px 3px #000000;
 +
        /*border-style:dashed;*/
 +
padding: 20px 20px 20px 20px;
 +
}
 +
 +
 +
.header-text {
 +
  background-color: transparent;
 +
  font-size: 80pt;
 +
font-family:"Lato", cursive;
 +
  color:#c91a03 ;
 +
line-height: 65pt;
 +
  padding-top: 30%;
 +
font-weight: bold;
 +
text-align:left;
 +
margin-left:200px;
 +
text-shadow: 5px 5px #000000;
 +
 +
 +
}
 +
 +
.header-subtitle {
 +
  color:#c91a03;
 +
  font-size: 40pt;
 +
line-height: 30pt;
 +
  padding-top: 2%;
 +
  padding-bottom: 20px;
 +
font-family:"Lato", cursive;
 +
text-align:left;
 +
margin-left:200px;
 +
text-shadow: 2px 2px #000000;
 +
}
 +
 +
/*--------------Basic text and content styling---------------------------------*/
 +
p {
 +
  font-size: 12pt !important;
 +
  text-align: justify;
 +
  text-justify: inter-word;
 +
  /*text-indent: 20px;*/
 +
  line-height: 200%;
 +
  margin-bottom: 10px;
 +
color:#1a1a1a;
 +
}
 +
 +
h2 {
 +
text-align:left;
 +
        font-size:18pt; !important
 +
}
 +
 +
.h2style {
 +
color:#1a1a1a;
 +
font-size:25pt;
 +
text-align:center;
 +
}
 +
 +
h3 {
 +
  text-align: left;
 +
 
 +
}
 +
 +
figcaption {
 +
  color: black;
 +
  font-size: 11pt;
 +
  text-align: justify;
 +
  padding-left: 80px;
 +
margin-left:50px;
 +
 
 +
}
 +
 +
figcaption b {
 +
  color: #c91a03;
 +
}
 +
 +
.subtitle {
 +
 +
color:#000000;
 +
font-size:30pt !important;
 +
text-align:center;
 +
 +
border-bottom: 2px solid transparent; /*A lot of code for the line between the header and the body */
 +
  -moz-border-image: -moz-linear-gradient(left, #1a1a1a 0%, #808080, #1a1a1a 100%); /*(left, #016243 0%, #b5deca, #016243 100%);*/
 +
  -webkit-border-image: -webkit-linear-gradient(left, #1a1a1a 0%, #808080, #1a1a1a 100%); /*(left, #016243 0%, #b5deca, #016243 100%)*/
 +
  border-image: linear-gradient(to right, #1a1a1a 0%, #808080, #1a1a1a 100%); /*(to right, #016243 0%, #b5deca, #016243 100%);*/
 +
  border-image-slice: 1;
 +
  -webkit-touch-callout: none;
 +
  -webkit-user-select: none;
 +
  -khtml-user-select: none;
 +
  -moz-user-select: none;
 +
  -ms-user-select: none;
 +
  user-select: none;
 +
  cursor: default;
 +
}
 +
 +
.list {
 +
  margin-left:50px;
 +
  list-style-position: outside;
 +
  text-align: justify;
 +
  text-justify: inter-word;
 +
  margin-top: 10px;
 +
  font-size: 12pt;
 +
  line-height: 125%;
 +
}
 +
 +
.sponsor-picture {
 +
display: inline-block;
 +
border-style:dashed;
 +
width: 500px;
 +
  height:170px;
 +
padding: 10px;
 +
}
 +
 +
.sponsor-picture2 {
 +
width: 200px;
 +
  margin-left: 50px;
 +
margin-bottom:10px;
 +
float:right;
 +
}
 +
 +
.sidetitle {
 +
 +
color:#1a1a1a;
 +
font-size:30pt;
 +
text-align:center;
 +
 +
border-bottom: 2px solid transparent; /*A lot of code for the line between the header and the body */
 +
  -moz-border-image: -moz-linear-gradient(left, #000000 0%, #808080, #000000 100%); /*(left, #016243 0%, #b5deca, #016243 100%);*/
 +
  -webkit-border-image: -webkit-linear-gradient(left, #000000 0%, #808080, #000000 100%); /*(left, #016243 0%, #b5deca, #016243 100%)*/
 +
  border-image: linear-gradient(to right, #000000 0%, #808080, #000000 100%); /*(to right, #016243 0%, #b5deca, #016243 100%);*/
 +
  border-image-slice: 1;
 +
  -webkit-touch-callout: none;
 +
  -webkit-user-select: none;
 +
  -khtml-user-select: none;
 +
  -moz-user-select: none;
 +
  -ms-user-select: none;
 +
  user-select: none;
 +
  cursor: default;
 +
 +
}
 +
 +
.figure-caption {
 +
    display: table-caption;
 +
    caption-side: bottom; 
 +
}
 +
 +
.table-caption {
 +
    display: table-caption;
 +
    caption-side: top;   
 +
  color: black;
 +
  font-size: 11pt;
 +
  text-align: justify;
 +
  padding-left: 0px;
 +
  padding-right:0px;
 +
margin-left:0px;
 +
margin-right:0px;
 +
}
 +
 +
th {
 +
    text-align: center;
 +
}
 +
 +
figure {
 +
  display:table;
 +
  text-align:center;
 +
  margin: auto;
 +
  margin-bottom: 25px;
 +
  margin-top: 25px;
 +
}
 +
 +
/*---Reference List---*/
 +
 +
.reference_list {
 +
    text-align: left;
 +
    font-size:10pt; !important
 +
}
 +
 +
.reference_list ul {
 +
    list-style-type: none;
 +
    list-style-image: none;
 +
}
 +
 +
.reference_list li {
 +
    padding-bottom: 10px;
 +
}
 +
 +
/*--------------Links in text and lists are red when hovered------------------*/
 +
 +
 +
 +
p a:link {
 +
  text-decoration: none;
 +
  color: #c91a03;
 +
 
 +
}
 +
 +
p a:link:hover {
 +
  color: #7e1002;
 +
}
 +
 +
p a:visited {
 +
  text-decoration: none;
 +
  color: #c91a03;
 +
 
 +
}
 +
 +
h1 a:link {
 +
  font-weight: bold;
 +
color: #c91a03;
 +
}
 +
 +
h1 a:link:hover {
 +
  font-weight: bold;
 +
  color: #7e1002;
 +
}
 +
 +
h1 a:visited {
 +
  /*font-weight: bold;*/
 +
color:#c91a03;
 +
}
 +
 +
/*Commented before, want to know what it does*/
 +
.list a:link {
 +
  text-decoration: none;
 +
  color: #c91a03;
 +
}
 +
 +
.list a:visited {
 +
  text-decoration: none;
 +
  color: #c91a03;
 +
}
 +
 +
.list a:hover {
 +
  text-decoration: none;
 +
  color: #7e1002;
 +
}
 +
 +
.text a:link {
 +
  text-decoration: none;
 +
  color: #c91a03;
 +
}
 +
 +
.text a:visited {
 +
  text-decoration: none;
 +
  color: #c91a03;
 +
}
 +
 +
.text a:hover {
 +
  text-decoration: none;
 +
  color: #7e1002;
 +
}
 +
 +
.profiletext a:link {
 +
  text-decoration: none;
 +
  color: #c91a03;
 +
  font-weight: bold;
 +
}
 +
 +
.profiletext a:visited {
 +
  text-decoration: none;
 +
  color: #c91a03;
 +
  font-weight: bold;
 +
}
 +
 +
 +
.profiletext a:hover {
 +
  text-decoration: none;
 +
  color: #7e1002;
 +
}
 +
 +
/*superscript and subscript modification so it doesn't fuck up line-height in multiple lined text*/
 +
sub, sup {
 +
font-size: 75%;
 +
line-height: 0;
 +
position: relative;
 +
vertical-align: baseline;
 +
}
 +
sup {
 +
top: -0.5em;
 +
}
 +
sub {
 +
bottom: -0.25em;
 +
}
 +
 +
.thankyoutext {
 +
  font-size: 16pt;
 +
  text-align: justify;
 +
  text-justify: inter-word;
 +
  margin-top: 10px;
 +
  text-indent: 20px;
 +
  line-height: 150%;
 +
  font-weight: 500;
 +
}
 +
 +
 +
/*---------------------------BUTTON---------------------------------*/
 +
.button {
 +
  display: inline-block;
 +
  border-radius: 10px;
 +
  background-color: #5B9E00;
 +
  border: none;
 +
  color: #FFFFFF;
 +
  text-align: center;
 +
  font-size: 28px;
 +
  padding: 20px;
 +
  width: 250px;
 +
  transition: all 0.6s;
 +
  cursor: pointer;
 +
  margin: 5px;
 +
}
 +
 +
.button span {
 +
  cursor: pointer;
 +
  display: inline-block;
 +
  position: relative;
 +
  transition: 0.5s;
 +
}
 +
 +
.button span:after {
 +
  content: '»';
 +
  position: absolute;
 +
  opacity: 0;
 +
  top: 0;
 +
  right: -20px;
 +
  transition: 0.5s;
 +
}
 +
 +
.button:hover span {
 +
  padding-right: 25px;
 +
}
 +
 +
.button:hover span:after {
 +
  opacity: 1;
 +
  right: 0;
 +
}
 +
 +
/*-----------------------long button----------------------------------------*/
 +
.button_long {
 +
  display: inline-block;
 +
  border-radius: 10px;
 +
  background-color: #5B9E00;
 +
  border: none;
 +
  color: black;
 +
  text-align: left;
 +
  font-weight:600;
 +
  font-size: 15pt;
 +
  padding: 10px;
 +
  width: 100%;
 +
  transition: all 0.6s;
 +
  cursor: pointer;
 +
  margin-top: 10px;
 +
  box-shadow: 0 8px 16px 0 rgba(0,0,0,0.2), 0 6px 20px 0 rgba(0,0,0,0.19);
 +
}
 +
 +
.button_long span {
 +
  cursor: pointer;
 +
  display: inline-block;
 +
  position: relative;
 +
  transition: 0.5s;
 +
}
 +
 +
.button_long span:after {
 +
  content: '»';
 +
  position: absolute;
 +
  opacity: 0;
 +
  top: 0;
 +
  right: -20px;
 +
  transition: 0.5s;
 +
}
 +
 +
.button_long:hover span {
 +
  padding-right: 25px;
 +
}
 +
 +
.button_long:hover span:after {
 +
  opacity: 1;
 +
  right: 0;
 +
}
 +
 +
/*-------------------------------------- NOTE!!!!!!!!!!!! Do not add the code for the slider. The buttons for previewing and save the wiki ------------------------------------------*/
 +
 +
</style> <!------------------ style_170803.css STOP ---------------------------------->
 +
 +
<!---------------------------------------- Insert jquery and script.js here, when you figure out how to make them work...------------------------------>
 +
 +
<!-------------------------------- jquery-3.0.0.min.js START ----------------------->
 +
<!-- WORKING!!!!!! -->
 +
<script type="application/javascript">
 +
 +
/*! jQuery v3.0.0 | (c) jQuery Foundation | jquery.org/license */
 +
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        <h4 class="subtitle">Introduction</h4>
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        <p class="text">
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The modeling part of our project was to simulate our biosensor <i>in silico</i> to gain insight in how the output might look, and what may be changed or modified in it to produce a better result.
 +
        </p>
 +
        <p class="text">
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One of the main parts of our biosensor uses the <b>yeast pheromone pathway</b> with custom GPCRs that will make the cells sense volatile organic compounds (VOCs) that are lung cancer biomarkers. These receptors, when activated by the VOCs in the breath of patients will trigger a proteolytic cascade, <b>the MAPK cascade</b>, in the pheromone pathway which ultimately leads to increased levels <b>of a transcription factor called Ste12</b> [1]. Ste12 acts as a “first checkpoint” in our biosensor as its values will correlate with the downstream processes. This transcription factor will then promote expression of <b>the protein Fus1</b>, whose function involves coordinating cell polarization and fusion in order to make the yeast mate with the opposing mating type [3]. Therefore, the promoter region (P<sub><i>FUS1</i></sub>) was used as a way to signal when the pheromone pathway is activated.
 +
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        <p class="text">
 +
In parallel to the normal pheromone pathway, a construct containing <b>Cre recombinase</b> with P<sub><i>FUS1</i></sub> in front of it was added, which causes it to be co-expressed by pheromone pathway activation. Cre in turn flips the constitutive promoter P<sub><i>TEF</i></sub>  by recombining two <b>loxP-sites</b> surrounding the promoter. This leads to expression of <b>Cas9 in one mating type</b> and <b>a gRNA in the other</b>. When the cells of opposing mating types then mate to form a diploid, the Cas9 and gRNA will bind to each other. This will in turn cause the Cas9-gRNA complex to cut the <i>ADE2</i> gene in yeast and turn the cells red.
 +
        </p>
 +
        </div>
 +
        </div>
 +
         
 +
        <div class="target" id="results">
 +
        <div class="dashed_line_right">
 +
          <h4 class="sidetitle">Modeling and results</h4>
 +
        <p class="text">
 +
To model this system, we decided to use a set of <b>coupled ordinary differential equations (ODEs)</b> that correspond to the different species involved in the <b>pheromone pathway</b>. The model <b>relies upon the work of Kofahl and Klipp</b> [1], whose model of this pathway has been used extensively by many iGEM teams throughout the years and has produced good results [4,5,6]. The model is very detailed and involves 36 different species with almost 50 reactions between them [1]. The modeling part of the project uses all of the ODEs and parameter from their original paper, along with other ODEs stated in Table 3.
 +
        </p>
 +
        <figure>
 +
<img src="https://static.igem.org/mediawiki/2017/6/63/T--Chalmers-Gothenburg--Modeling_pathway_gray.png" style="height:967px; width:625px;">
 +
<figcaption><b>Figure 1.</b>The reaction network used in the model by Kofahl and Klipp [1].</figcaption>
 +
        </figure>
 +
        </div>
 +
 +
        <div class="dashed_line_left">
 +
        <p class="text">
 +
As seen in the bottom right corner of Figure 1, the cascade ends with an activation of Ste12 which makes it possible for it to bind into DNA and begin transcriptional activation. This was therefore used as a first step into validating the function of the biosensor. The concentration of Ste12 should be higher in lung cancer patients compared to healthy people, due to the fact that they produce a higher amount of VOCs that can activate the pheromone pathway [7]. To check this, <b>data on different VOC levels was used</b>, both in in lung cancer patients and compared to a healthy control group and a group consisting of smokers [7]. The data of the median level of each group is presented in Table 1 and consists only of n-octanal levels. The choice of only studying the n-octanal levels is due to the fact that no data (kinetic rates <i>v<sub>1</sub></i> to <i>v<sub>5</sub></i> in Kofahl and Klipp’s model, see Figure 1) is available for the two receptors used in this project, thus the 2-butanone levels were omitted. The original yeast parameters of these reactions were used together with the n-octanal concentrations from the three patient groups.
 +
        </p>
 +
 +
          <figure>
 +
            <figcaption class="table-caption"><b>Table 1.</b> Median n-octanal level values for different patient groups [7]. </figcaption>
 +
            <table>
 +
                <tr>
 +
                  <th><b>Patient group (n=12) </b></th> <th><b>Controls</b></th>  <th><b>Smokers</b></th> <th><b>Lung cancer patients</b></th>
 +
                </tr>
 +
                <tr>
 +
                    <td>Median n-octanal values (nmol/L)</td> <td>0,011</td> <td>0,006</td> <td>0,052</td>
 +
                </tr>
 +
            </table>
 +
          </figure>
 +
        </div>
 +
       
 +
        <div class="dashed_line_right"> 
 +
        <p class="text">
 +
Given these assumptions, the simulation for the Ste12 concentration can be run on the three different patient groups, which gives the result presented in Figure 2a. Even though the n-octanal level is about <b>five times higher in lung cancer patients</b> compared to the controls, this only leads to a <b>50% increase in peak Ste12 concentration</b>. To study whether this affected expression of Cre recombinase another ODE was added into the system, see Table 2, that models binding and gene expression of Ste12 onto P<sub><i>FUS1</sub></i>.
 +
        </p>
 +
        <figure>
 +
<img src="https://static.igem.org/mediawiki/2017/0/03/T--Chalmers-Gothenburg--Modeling_graphs.png" style="height:631px; width:601px;">
 +
<figcaption><b>Figure 2.</b> Time course plots for the different species in our model.</figcaption>
 +
        </figure>
 +
 +
          <figure>
 +
            <figcaption class="table-caption"><b>Table 2.</b> ODEs describing the temporal behavior of different species in the model. The parameter values are either randomly chosen or from literature.</figcaption>
 +
            <table>
 +
                <tr>
 +
                  <th><b>ODEs added to Kofahl & Klipp's model </b></th> <th><b>Parameter values</b></th>
 +
                </tr>
 +
                <tr>
 +
                    <td> Cre/Fus1 production: <img src="https://static.igem.org/mediawiki/2017/b/bd/T--Chalmers-Gothenburg--table_eq_1.png" style="height:50px; width:284px;"></td> <td>[2,8]</td>
 +
                </tr>
 +
                <tr>
 +
                    <td> Cas9/gRNA formation: <img src="https://static.igem.org/mediawiki/2017/4/44/T--Chalmers-Gothenburg--table_eq_2.png" style="height:45px; width:111px;"></td> <td>Arbitrary value</td>
 +
                </tr>
 +
                <tr>
 +
                    <td> Diploid formation: <img src="https://static.igem.org/mediawiki/2017/e/ee/T--Chalmers-Gothenburg--table_eq_3.png" style="height:40px; width:350px;"></td> <td>Arbitrary value</td>
 +
                </tr>
 +
                <tr>
 +
                    <td> Haploid mating: <img src="https://static.igem.org/mediawiki/2017/a/a5/T--Chalmers-Gothenburg--table_eq_4.png" style="height:42px; width:337px;"></td> <td>Arbitrary value</td>
 +
                </tr>
 +
                <tr>
 +
                    <td> Cas9:gRNA complex formation: <img src="https://static.igem.org/mediawiki/2017/e/e2/T--Chalmers-Gothenburg--table_eq_5.png" style="height:45px; width:485px;"></td> <td>Arbitrary value</td>
 +
                </tr>
 +
            </table>
 +
          </figure>
 +
        </div>
 +
 +
 +
        <div class="dashed_line_left"> 
 +
        <p class="text">
 +
The binding kinetics are assumed to be of <b>Hill type</b> with values found in the literature [2,8]. The initial concentrations of Fus1 and Cre recombinase are assumed to be zero. The time courses for Cre/Fus1 are shown in Figure 2b. Notice that we now have about double the Fus1/Cre recombinase amounts for the lung cancer patients compared to the controls. The Cre recombinase will flip a constitutive promoter P<sub><i>TEF1</i></sub> flanked between two LoxP sites. This will in turn activate transcription of the gRNA for <i>ADE2</i> disruption in one mating type and transcription of the protein Cas9 in the other. Since the production rate of P<sub><i>TEF1</sub></i> is unknown, we set it to an arbitrary value of 1mmol/min/L. Setting an arbitrary production rate does not allow us to make any quantitative predictions about the gRNA/Cas9 levels. However, due to the fact that the original yeast parameters are used for the receptors, quantitative information is lost anyway. Although we can still estimate relative concentrations of these species between our patient groups.
 +
        </p>
 +
 +
        <p class="text">
 +
The mating rate in this model is assumed to be proportional to the amount of haploid cells in the culture and the Fus1 concentration. Given an initial 1000 haploids, we produce the corresponding amount of diploids for each patient group, shown in Figure 2d.
 +
For the concentration of activated Cas9-gRNA complex per diploid cell we assumed it to be proportional to the amount of haploids, the gRNA concentration in each cell and the Cas9 concentration in each cell. The result from this simulation is shown in Figure 2e. After 24 hours there is about a <b>50% increase in Cas9:gRNA dimers</b> compared with the controls. This increase will in turn promote deletion of the <i>ADE2</i> gene, causing the cell to turn red. Although this can be modeled, since there were not any parameters at all for the <i>ADE2</i> pathway in the literature, we decided to only model up until the Cas9:gRNA dimer formation.
 +
        </p>
 +
        <p class="text">
 +
From this we can conclude that it might be possible to differentiate between lung cancer patients and controls since we get a 50% higher level of Cas9:dimers after 24 hours.
 +
        </p>
 +
        </div>
 +
        </div>
 +
     
 +
        <div class="target" id="code">
 +
          <div class="dashed_line_right">
 +
        <h4 class="subtitle">MATLAB code</h4>
 +
        <p class="text">
 +
The MATLAB code used in this project can be found here:
 +
        </p>
 +
<h2>pheromonepathway.m</h2>
 +
        <p class="text">
 +
This is the main .m-file that should be run. Available <a href="https://static.igem.org/mediawiki/2017/9/9d/T--Chalmers-Gothenburg--pheromonepathway.m.txt" target="blank">here.</a>
 +
        </p>
 +
<h2>f.m</h2>
 +
        <p class="text">
 +
This function is called by the ODE solver and contains all of the ODEs. Available <a href="https://static.igem.org/mediawiki/2017/8/8d/T--Chalmers-Gothenburg--f.txt" target="blank">here.</a>
 +
        </p>
 +
        </div>
 +
        </div>
 +
       
 +
        <div class="target" id="references">
 +
        <div class="dashed_line_left_last">
 +
        <h4 class="sidetitle">References</h4>
 +
 +
            <div class="reference_list">
 +
              <ul>
 +
                <li>[1]&#160;&#160; Kofahl B,Klipp E Modelling the dynamics of the yeast pheromone pathway. Yeast 2004; 21: 831–850.</li>
 +
 +
                <li>[2]&#160;&#160; Dyjack N, Azeredo-Tseng C, Yildirim N Mathematical modeling reveals differential regulation of MAPK activity by phosphatase proteins in the yeast pheromone response pathway. Mol. BioSyst. Mol. BioSyst 2017; 13: 1323-1335.</li>
 +
 +
                <li>[3]&#160;&#160; Yeastgenome.org. (2017). FUS1 | SGD. [online] Available at: https://www.yeastgenome.org/locus/S000000532 [Accessed 17 Sep. 2017].</li>
 +
 +
                <li>[4]&#160;&#160; 2012.igem.org. (2017). Team:TU-Delft/Modeling/SingleCellModel - 2012.igem.org. [online] Available at: https://2012.igem.org/Team:TU-Delft/Modeling/SingleCellModel [Accessed 17 Sep. 2017].</li>
 +
 +
                <li>[5]&#160;&#160; 2015.igem.org. (2017). Team:CGU Taiwan/Modeling - 2015.igem.org. [online] Available at: https://2015.igem.org/Team:CGU_Taiwan/Modeling [Accessed 17 Sep. 2017].</li>
 +
 +
                <li>[6]&#160;&#160;2015.igem.org. (2017). Team:Chalmers-Gothenburg/Detection - 2015.igem.org. [online] Available at: https://2015.igem.org/Team:Chalmers-Gothenburg/Detection [Accessed 17 Sep. 2017]. </li>
 +
 +
                <li>[7]&#160;&#160; Fuchs P, Loeseken C, Schubert J. K. , Miekisch W Breath gas aldehydes as biomarkers of lung cancer. International Journal of Cancer 2010.</li>
 +
 +
                <li>[8]&#160;&#160; Groves B, Khakhar A, Nadel C. M. , Gardner R. G. ,Seelig G, Rewiring MAP kinases in Saccharomyces cerevisiae to regulate novel targets through ubiquitination. eLife 2016. </li>
 +
 +
              </ul>
 +
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 +
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Latest revision as of 08:18, 1 November 2017

Chalmers Gothenburg iGEM 2017

Introduction

The modeling part of our project was to simulate our biosensor in silico to gain insight in how the output might look, and what may be changed or modified in it to produce a better result.

One of the main parts of our biosensor uses the yeast pheromone pathway with custom GPCRs that will make the cells sense volatile organic compounds (VOCs) that are lung cancer biomarkers. These receptors, when activated by the VOCs in the breath of patients will trigger a proteolytic cascade, the MAPK cascade, in the pheromone pathway which ultimately leads to increased levels of a transcription factor called Ste12 [1]. Ste12 acts as a “first checkpoint” in our biosensor as its values will correlate with the downstream processes. This transcription factor will then promote expression of the protein Fus1, whose function involves coordinating cell polarization and fusion in order to make the yeast mate with the opposing mating type [3]. Therefore, the promoter region (PFUS1) was used as a way to signal when the pheromone pathway is activated.

In parallel to the normal pheromone pathway, a construct containing Cre recombinase with PFUS1 in front of it was added, which causes it to be co-expressed by pheromone pathway activation. Cre in turn flips the constitutive promoter PTEF by recombining two loxP-sites surrounding the promoter. This leads to expression of Cas9 in one mating type and a gRNA in the other. When the cells of opposing mating types then mate to form a diploid, the Cas9 and gRNA will bind to each other. This will in turn cause the Cas9-gRNA complex to cut the ADE2 gene in yeast and turn the cells red.

Modeling and results

To model this system, we decided to use a set of coupled ordinary differential equations (ODEs) that correspond to the different species involved in the pheromone pathway. The model relies upon the work of Kofahl and Klipp [1], whose model of this pathway has been used extensively by many iGEM teams throughout the years and has produced good results [4,5,6]. The model is very detailed and involves 36 different species with almost 50 reactions between them [1]. The modeling part of the project uses all of the ODEs and parameter from their original paper, along with other ODEs stated in Table 3.

Figure 1.The reaction network used in the model by Kofahl and Klipp [1].

As seen in the bottom right corner of Figure 1, the cascade ends with an activation of Ste12 which makes it possible for it to bind into DNA and begin transcriptional activation. This was therefore used as a first step into validating the function of the biosensor. The concentration of Ste12 should be higher in lung cancer patients compared to healthy people, due to the fact that they produce a higher amount of VOCs that can activate the pheromone pathway [7]. To check this, data on different VOC levels was used, both in in lung cancer patients and compared to a healthy control group and a group consisting of smokers [7]. The data of the median level of each group is presented in Table 1 and consists only of n-octanal levels. The choice of only studying the n-octanal levels is due to the fact that no data (kinetic rates v1 to v5 in Kofahl and Klipp’s model, see Figure 1) is available for the two receptors used in this project, thus the 2-butanone levels were omitted. The original yeast parameters of these reactions were used together with the n-octanal concentrations from the three patient groups.

Table 1. Median n-octanal level values for different patient groups [7].
Patient group (n=12) Controls Smokers Lung cancer patients
Median n-octanal values (nmol/L) 0,011 0,006 0,052

Given these assumptions, the simulation for the Ste12 concentration can be run on the three different patient groups, which gives the result presented in Figure 2a. Even though the n-octanal level is about five times higher in lung cancer patients compared to the controls, this only leads to a 50% increase in peak Ste12 concentration. To study whether this affected expression of Cre recombinase another ODE was added into the system, see Table 2, that models binding and gene expression of Ste12 onto PFUS1.

Figure 2. Time course plots for the different species in our model.
Table 2. ODEs describing the temporal behavior of different species in the model. The parameter values are either randomly chosen or from literature.
ODEs added to Kofahl & Klipp's model Parameter values
Cre/Fus1 production: [2,8]
Cas9/gRNA formation: Arbitrary value
Diploid formation: Arbitrary value
Haploid mating: Arbitrary value
Cas9:gRNA complex formation: Arbitrary value

The binding kinetics are assumed to be of Hill type with values found in the literature [2,8]. The initial concentrations of Fus1 and Cre recombinase are assumed to be zero. The time courses for Cre/Fus1 are shown in Figure 2b. Notice that we now have about double the Fus1/Cre recombinase amounts for the lung cancer patients compared to the controls. The Cre recombinase will flip a constitutive promoter PTEF1 flanked between two LoxP sites. This will in turn activate transcription of the gRNA for ADE2 disruption in one mating type and transcription of the protein Cas9 in the other. Since the production rate of PTEF1 is unknown, we set it to an arbitrary value of 1mmol/min/L. Setting an arbitrary production rate does not allow us to make any quantitative predictions about the gRNA/Cas9 levels. However, due to the fact that the original yeast parameters are used for the receptors, quantitative information is lost anyway. Although we can still estimate relative concentrations of these species between our patient groups.

The mating rate in this model is assumed to be proportional to the amount of haploid cells in the culture and the Fus1 concentration. Given an initial 1000 haploids, we produce the corresponding amount of diploids for each patient group, shown in Figure 2d. For the concentration of activated Cas9-gRNA complex per diploid cell we assumed it to be proportional to the amount of haploids, the gRNA concentration in each cell and the Cas9 concentration in each cell. The result from this simulation is shown in Figure 2e. After 24 hours there is about a 50% increase in Cas9:gRNA dimers compared with the controls. This increase will in turn promote deletion of the ADE2 gene, causing the cell to turn red. Although this can be modeled, since there were not any parameters at all for the ADE2 pathway in the literature, we decided to only model up until the Cas9:gRNA dimer formation.

From this we can conclude that it might be possible to differentiate between lung cancer patients and controls since we get a 50% higher level of Cas9:dimers after 24 hours.

MATLAB code

The MATLAB code used in this project can be found here:

pheromonepathway.m

This is the main .m-file that should be run. Available here.

f.m

This function is called by the ODE solver and contains all of the ODEs. Available here.

References

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