Difference between revisions of "Team:Stuttgart/InterLab"

 
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{{Template:Home}}
 
<html>
 
<html>
  
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<script>
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<!-- start of content -->
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<h1 align=middle>InterLab Study</h1>
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    // This is the jquery part of your template. 
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<div class="container">
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    // Try not modify any of this code too much since it makes your menu work.
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      <div class="row section">
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         <div class="col-xs-12 col-sm-12 col-md-12">
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    $(document).ready(function() {
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          <h2>Introduction</h2>
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        $("#HQ_page").attr('id','');
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        // call the functions that control the menu
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        menu_functionality();
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        hide_show_menu();
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        //this function controls the expand and collapse buttons of the menu and changes the +/- symbols
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        function menu_functionality() {
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            //when clicking on a "menu_button", it will change the "+/-" accordingly and it will show/hide the corresponding submenu
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            $(".menu_button").click(function(){
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                // add or remove the class "open" , this class holds the "-"
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                $(this).children().toggleClass("open");
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                // show or hide the submenu
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                $(this).next('.submenu_wrapper').fadeToggle(400);
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            });
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            // when the screen size is smaller than 800px, the display_menu_control button appears and will show/hide the whole menu
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            $("#display_menu_control").click(function(){
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                $('#menu_content').fadeToggle(400);
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            });
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            // call the current page highlight function
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            highlight_current_page();
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        }
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        // call the highlight current page function to show it on the menu with a different background color
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        function highlight_current_page() {
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            // select a page from the menu based on the id assigned to it and the current page name and add the class "current page" to make it change background color
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            $("#"+  wgPageName.substring(wgPageName.lastIndexOf("/")+1, wgPageName.length ) + "_page").addClass("current_page");
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            // now that the current_page class has been added to a menu item, make the submenu fade in
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            $(".current_page").parents(".submenu_wrapper").fadeIn(400);
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            // change the +/- symbol of the corresponding menu button
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            $(".current_page").parents(".submenu_wrapper").prev().children().toggleClass("open");
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        }
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        // allow button on the black menu bar to show/hide the side menu
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        function hide_show_menu() {
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            // in case you preview mode is selected, the menu is hidden for better visibility
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            if (window.location.href.indexOf("submit") >= 0) {
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                $(".igem_2017_menu_wrapper").hide();
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            // if the black menu bar has been loaded
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            if (document.getElementById('bars_item')) {
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                // when the "bars_item" has been clicked
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                $("#bars_item").click(function() {
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                    $("#sideMenu").hide();
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                    // show/hide the menu wrapper
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                    $(".igem_2017_menu_wrapper").fadeToggle("100");
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                });
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            }
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            // because the black menu bars loads at a different time than the rest of the page, this function is set on a time out so it can run again in case it has not been loaded yet
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            else {
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                setTimeout(hide_show_menu, 15);
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            }
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        }
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    });
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</script>
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<style>
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    /***************************************************** DEFAULT WIKI SETTINGS  ****************************************************/
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    /* Clear the default wiki settings */
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    #home_logo, #sideMenu { display:none; }
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    #sideMenu, #top_title, .patrollink  {display:none;}
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    #content { width:100%; padding:0px;  margin-top:-7px; margin-left:0px;}
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    body {background:#190707 }
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    #bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 { margin-bottom: 0px; }
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  table {background}
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    .igem_2017_menu_wrappe::-webkit-scrollbar {
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    .igem_2017_menu_wrapper a {
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    .menu_button.direct_to_page {
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    .igem_2017_menu_wrapper .menu_button .expand_collapse_icon::before {
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        content: "+";
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    .open::before {
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        content: "-" !important;
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    /* styling for the menu buttons on hover */
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    .igem_2017_menu_wrapper .menu_button:hover, .igem_2017_menu_wrapper .submenu_button:hover ,  .submenu_button.current_page:hover {
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        background-color: #F8CE63;
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        text-decoration: none;
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        color:#190707;
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    }
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    /* styling for the menu button when it is the current page */
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    .current_page {
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        background-color:#190707  !important;
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        color:#F8CE63 !important;
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    /* styling for the submenu buttons */
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    .igem_2017_menu_wrapper .submenu_button {
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        width: 100%;
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        padding: 10px 0px 10px 34px;
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        float:left;
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        background-color:#190707;
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        border-bottom: 1px solid #F8CE63;
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        color: #F8CE63;
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    /* wrapper for the submenu items, they are hidden by default*/
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    /***************************************************** CONTENT OF THE PAGE ****************************************************/
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    /* Wrapper for the content */
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    .igem_2017_content_wrapper {
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        width: 81%;
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        margin: 2%;
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        display:block;
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        float:left;
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        background-color: #190707;
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        font-family:Tahoma, Geneva, sans-serif;
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    }
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    /********************************* HTML STYLING  *********************************/
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    /* styling for the titles h1 h2 */
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    .igem_2017_content_wrapper h1, .igem_2017_content_wrapper h2 {
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        color:#F8CE63;
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        padding:15px 0 25px 0;
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        border-bottom: 0;
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    /* styling for the titles  h3 h4 h5 h6*/
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    .igem_2017_content_wrapper h3, .igem_2017_content_wrapper h4, .igem_2017_content_wrapper h5, .igem_2017_content_wrapper h6 {
+
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        padding:5px 15px;
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        border-bottom:0;
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−
    }
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−
 
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    /* font and text */
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    .igem_2017_content_wrapper p {
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        padding: 15px 0;
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        font-size: 16px;
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    }
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    .igem_2017_content_wrapper img {
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        padding: 15px 0;
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    }
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−
 
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    /* Links */
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    .igem_2017_content_wrapper a {
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        font-weight: bold;
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        text-decoration: underline;
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        text-decoration-color: #190707;
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−
        color:  #3399ff;
+
−
        -webkit-transition: all 0.4s ease;
+
−
        -moz-transition: all 0.4s ease;
+
−
        -ms-transition: all 0.4s ease;
+
−
        -o-transition: all 0.4s ease;
+
−
        transition: all 0.4s ease;
+
−
    }
+
−
 
+
−
    /* hover for the links */
+
−
    .igem_2017_content_wrapper a:hover {
+
−
        text-decoration:none;
+
−
        color:#000000;
+
−
    }
+
−
 
+
−
    /* non numbered lists */
+
−
    .igem_2017_content_wrapper ul {
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−
        padding:0px 20px;
+
−
        font-size: 15px;
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        font-family:Tahoma, Geneva, sans-serif;
+
−
    }
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−
 
+
−
    /* numbered lists */
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−
    .igem_2017_content_wrapper ol {
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        padding:0px;
+
−
        font-size: 15px;
+
−
        font-family:Tahoma, Geneva, sans-serif;
+
−
    }
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−
 
+
−
    /* Table */
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−
    .igem_2017_content_wrapper table {
+
−
        width: 97%;
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−
        margin:15px 10px;
+
−
        border: 2px solid #190707;
+
−
        border-collapse: collapse;
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−
        background: ;
+
−
    }
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−
 
+
−
    /* table cells */
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−
    .igem_2017_content_wrapper  td {
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        padding: 10px;
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        vertical-align: text-top;
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        border: 1px solid #190707;
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        border-collapse: collapse;
+
−
    }
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−
 
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−
    /* table headers */
+
−
    .igem_2017_content_wrapper th {
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−
        padding: 10px;
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−
        vertical-align: text-top;
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        border: 1px solid #190707;
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−
        border-collapse: collapse;
+
−
       
+
−
    }
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−
 
+
−
 
+
−
    /**********************************LAYOUT CLASSES **********************************/
+
−
 
+
−
    /* general class for column divs */
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−
    .igem_2017_content_wrapper .column  {
+
−
        padding: 10px 0px;
+
−
        float:left;
+
−
    }
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−
 
+
−
    /* class for a full width column */
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−
    .column .full_size {
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−
        width:100%;
+
−
    }
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−
 
+
−
    /* styling for images in a full width column*/
+
−
    .column.full_size img {
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−
        width:97%;
+
−
        padding: 10px 15px;
+
−
    }
+
−
 
+
−
    /* class for a half width column */
+
−
    .column.half_size {
+
−
        width: 50%;
+
−
    }
+
−
    /* styling for images in a half width column*/
+
−
    .column.half_size img {
+
−
        width: 94.5%;
+
−
        padding: 10px 15px;
+
−
    }
+
−
 
+
−
 
+
−
 
+
−
 
+
−
    /********************************* SUPPORT CLASSES ********************************/
+
−
 
+
−
    /* class that clears content below*/
+
−
    .igem_2017_content_wrapper .clear {
+
−
        clear:both;
+
−
    }
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−
 
+
−
 
+
−
    /* adds extra spacing when clearing content */
+
−
    .igem_2017_content_wrapper  .clear.extra_space {
+
−
        height: 30px;
+
−
    }
+
−
 
+
−
 
+
−
    /* highlight class, makes content slightly smaller */
+
−
    .igem_2017_content_wrapper .highlight {
+
−
        margin: 0px 15px;
+
−
        padding: 15px 0px;
+
−
    }
+
−
 
+
−
 
+
−
    /* highlight class, adds a gray background */
+
−
    .igem_2017_content_wrapper .highlight.gray {
+
−
        background-color: #190707;
+
−
    }
+
−
 
+
−
    /* highlight with decoration blue line on top */
+
−
    .igem_2017_content_wrapper .highlight.blue_top {
+
−
        border-top: 4px solid #190707;
+
−
    }
+
−
 
+
−
    /* highlight with a full blue border decoration */
+
−
    .igem_2017_content_wrapper .highlight.blue_border {
+
−
        border: 4px solid  #190707;
+
−
    }
+
−
 
+
−
 
+
−
    /* button class */
+
−
    .igem_2017_content_wrapper .button{
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−
        max-width: 35%;
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−
        margin: 30px auto;
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−
        padding: 12px 10px;
+
−
        background-color: #190707;
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−
        text-align: center;
+
−
        color: #F8CE63;
+
−
        -webkit-transition: all 0.4s ease;
+
−
        -moz-transition: all 0.4s ease;
+
−
        -ms-transition: all 0.4s ease;
+
−
        -o-transition: all 0.4s ease; transition: all 0.4s ease;
+
−
    }
+
−
 
+
−
    /* styling for button on hover */
+
−
    .igem_2017_content_wrapper .button:hover{
+
−
        background-color: #190707;
+
−
        color: #F8CE63;
+
−
    }
+
−
 
+
−
 
+
−
 
+
−
 
+
−
    /***************************************************** RESPONSIVE STYLING ****************************************************/
+
−
 
+
−
    /* IF THE SCREEN IS LESS THAN 1200PX */
+
−
    @media only screen and (max-width: 1200px) {
+
−
 
+
−
        #content {width:100%; }
+
−
        .igem_2017_menu_wrapper {width:15%; right:0;}
+
−
        .highlight {padding:10px 0px;}
+
−
        .igem_2017_menu_wrapper #display_menu_control { display:none; }
+
−
        #menu_content { display:block;}
+
−
        .menu_button.direct_to_page {padding-left: 17px;}
+
−
 
+
−
    }
+
−
 
+
−
    /* IF THE SCREEN IS LESS THAN 800PX */
+
−
    @media only screen and (max-width: 800px) {
+
−
 
+
−
        .igem_2017_menu_wrapper { width:100%; height: 15%; position:relative; left:0%;}
+
−
        .igem_2017_content_wrapper {width:100%; margin-left:0px;}
+
−
        .column.half_size  {width:100%; }
+
−
        .column.full_size img, .column.half_size img {  width: 100%; padding: 10px 0px;}
+
−
        .highlight {padding:15px 5px;}
+
−
        .igem_2017_menu_wrapper #display_menu_control { display:block; }
+
−
        #menu_content { display:none;}
+
−
        .igem_2017_menu_wrapper .menu_button .expand_collapse_icon { width: 5%; }
+
−
        .menu_bottom_padding {display:none;}
+
−
        .menu_button.direct_to_page { padding-left: 36px; }
+
−
    }
+
−
 
+
−
 
+
−
 
+
−
 
+
−
    /* special class that the system uses to make sure the team wants a page to be evaluated */
+
−
    .judges-will-not-evaluate {
+
−
        width: 96.6%;
+
−
        margin: 5px 15px;
+
−
        display: block;
+
−
        border: 4px solid #3399ff;
+
−
        font-weight: bold;
+
−
    }
+
−
 
+
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</style>
+
−
 
+
−
 
+
−
<!--- THIS IS WHERE THE HTML BEGINS --->
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−
 
+
−
<head>
+
−
 
+
−
    <!-- This tells the browser that your page is responsive -->
+
−
    <meta name="viewport" content="width=device-width, initial-scale=1">
+
−
 
+
−
</head>
+
−
 
+
−
 
+
−
<!--MENU-->
+
−
<div class="igem_2017_menu_wrapper" >
+
−
 
+
−
 
+
−
 
+
−
    <a href="https://2017.igem.org/Team:Stuttgart">
+
−
         <img src="https://static.igem.org/mediawiki/2017/4/45/Bildschirmfoto_2017-10-17_um_14.23.20.png">
+
−
    </a>
+
−
 
+
−
 
+
−
    <!-- this div is hidden by default and will only be displayed if the screen size is too small -->
+
−
    <div class="menu_button" id="display_menu_control">
+
−
        MENU
+
−
    </div>
+
−
 
+
−
    <div id="menu_content">
+
−
 
+
−
 
+
−
 
+
−
 
+
−
        <a href="https://2017.igem.org/Team:Stuttgart">
+
−
            <div class="menu_button direct_to_page">
+
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<b>Figure 1:</b> Workflow InterLab Study, from InterLab_2017_Plate_Reader_Protocol.
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<h1 align=middle>Introduction</h1>
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<p>
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Reproducibility of an experiment and reliable measurement results are important parts of synthetic biology but it is very complicated to find a significant number of laboratories that are able to work on a identical protocol to produce comparable results. Being in many places in the world iGEM seems to be the perfect platform to compare results of one experiment in many different laboratories.
+
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iGEM Stuttgart also took part at the fourth InterLab Measurement Study in 2017. The aim of this years study was to measure GFP fluorescence of 6 different test devices (+negative and positive control). The following eight constructs (iGEM-kit plate 7) were transformed into chemo-competent DH5α E.coli cells:
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<br>
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<img/ src= "https://static.igem.org/mediawiki/2017/7/77/TeamStuttgart_plasmids.png"/ align="middle" width= heigth=><br>
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First step of the experiment is the calibration of the available plate reader with LUDOX SH40 and the generation of a standard curve with fluorescein (both provided in the iGEM-Measurement Kit).  
 
First step of the experiment is the calibration of the available plate reader with LUDOX SH40 and the generation of a standard curve with fluorescein (both provided in the iGEM-Measurement Kit).  
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<br>
+
The next step is the transformation of the mentioned plasmids into DH5alpha <i>E. coli</i> cells followed by the procedure explained in the picture below.
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The next step is the transformation of the mentioned plasmids into DH5alpha E.coli cells followed by the procedure explained in the picture below.
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<br>
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<img/ src= "https://static.igem.org/mediawiki/2017/6/6b/TeamStuttgart_workflow_platereader2.png"/ align=middle>
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<br>
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Results of the measurements of OD600 and fluorescence after 0, 2, 4 and 6 hours will be compared and used to establish a precise GFP measurement protocol.  
 
Results of the measurements of OD600 and fluorescence after 0, 2, 4 and 6 hours will be compared and used to establish a precise GFP measurement protocol.  
−
<br>
 
 
We used a BioTek Synergy 2 plate reader and clear 96-well plates for both measurements.  
 
We used a BioTek Synergy 2 plate reader and clear 96-well plates for both measurements.  
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<br>
 
 
You can find the protocol, the detailed description of the experiment and information about the InterLab Study itself <a href="https://2017.igem.org/Competition/InterLab_Study">here</a>.
 
You can find the protocol, the detailed description of the experiment and information about the InterLab Study itself <a href="https://2017.igem.org/Competition/InterLab_Study">here</a>.
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<h1 align=middle>Results and discussion</h1>
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<img/ src="https://static.igem.org/mediawiki/2017/f/f8/TeamStuttgart_ludox.png"/ hspace=20 vspace=0 align=right>
 
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<h3>LUDOX-OD600-Measurement (calibration)</h3>
 
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<img/ src="https://static.igem.org/mediawiki/2017/4/4b/TeamStuttgart_fluorescin.png"/ weigth=400 height=300 hspace=20 align=right>
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<h2>Results and Discussion</h2>
 +
          <h3>LUDOX-OD600 Measurement (calibration)</h3>
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            <p>For the calibration 100 μL of LUDOX-S40 from the InterLab Measurement Kit was added into the wells A1, B1, C1, and D1. Analogical 100 μL of ddH<sub>2</sub>O was added to the wells A2, B2, C2, D2.  
 +
              The measurement was performed with a plate reader at an absorbance of 600 nm.
 +
</p>
 +
</div>
 +
<div class="col-xs-12 col-sm-7 col-md-7">
 +
  <table>
 +
    <tr> <th></th> <th>LUDOX-HS40</th><th>H<sub>2</sub>O</th> </tr>
 +
    <tr><td>Replicate 1</td><td>0,04</td><td>0,026</td></tr>
 +
    <tr><td>Replicate 2</td><td>0,041</td><td>0,027</td></tr>
 +
    <tr><td>Replicate 3</td><td>0,043</td><td>0,026</td></tr>
 +
    <tr><td>Replicate 4</td><td>0,04</td><td>0,028</td></tr>
 +
    <tr><th>Arith. Mean</th> <th>0,041</th>
 +
    <tr><td>Corrected Abs600</td><td>0,0143</td></tr>
 +
    <tr><td>Reference OD600</td><td>0,043</td></tr>
 +
    <tr><td>OD600/Abs600</td><td>2,98</td></tr>
 +
  </table>
 +
</div>
 +
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 +
<div class="row section">
 +
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<h3>Fluorescein-Fluorescence-Measurement (standard curve)</h3>
 
<h3>Fluorescein-Fluorescence-Measurement (standard curve)</h3>
 +
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 +
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 +
<div class="row section">
 +
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<p>Measurement of different fluorescein concentrations.
 
<p>Measurement of different fluorescein concentrations.
 
excitation wavelength: 485nm; emission wavelength: 528nm</p>
 
excitation wavelength: 485nm; emission wavelength: 528nm</p>
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        <!--<img src="https://static.igem.org/mediawiki/2017/6/63/Interlab1.png">-->
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        <img src="https://static.igem.org/mediawiki/2017/8/8d/Interabfluoro4.png" class="img-responsive"/>
 +
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 +
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<h3>Transformation</h3>
 
<h3>Transformation</h3>
−
<p>We had at least two colonies of every test device except for test device 1 (transformation not successful).<br>
+
  <p> We had at least two colonies of every test device except for test device 1 (transformation not successful).
−
All of the following measurements are without test device 1. <br>Agar-plates with colonies after transformation.</p>
+
All of the following measurements are without test device 1. </p>
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          <!--<img src="https://static.igem.org/mediawiki/2017/3/3b/TeamStuttgart_agarplates.jpeg">-->
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<img/ src="https://static.igem.org/mediawiki/2017/3/3b/TeamStuttgart_agarplates.jpeg"/weight=600 height=550 align="middle" hspace=30 vspace=0>
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Latest revision as of 22:30, 14 December 2017

InterLab Study

Introduction

Reproducibility of an experiment and reliable measurement results are important parts of synthetic biology but it is very complicated to find a significant number of laboratories that are able to work on a identical protocol to produce comparable results. Being in many places in the world iGEM seems to be the perfect platform to compare results of one experiment in many different laboratories. iGEM Stuttgart also took part at the fourth InterLab Measurement Study in 2017. The aim of this years study was to measure GFP fluorescence of 6 different test devices (+negative and positive control). The eight constructs (iGEM-kit plate 7) listed below were transformed into chemo-competent DH5α E. coli cells.

Figure 1: Workflow InterLab Study, from InterLab_2017_Plate_Reader_Protocol.

First step of the experiment is the calibration of the available plate reader with LUDOX SH40 and the generation of a standard curve with fluorescein (both provided in the iGEM-Measurement Kit). The next step is the transformation of the mentioned plasmids into DH5alpha E. coli cells followed by the procedure explained in the picture below. Results of the measurements of OD600 and fluorescence after 0, 2, 4 and 6 hours will be compared and used to establish a precise GFP measurement protocol. We used a BioTek Synergy 2 plate reader and clear 96-well plates for both measurements. You can find the protocol, the detailed description of the experiment and information about the InterLab Study itself here.

Results and Discussion

LUDOX-OD600 Measurement (calibration)

For the calibration 100 μL of LUDOX-S40 from the InterLab Measurement Kit was added into the wells A1, B1, C1, and D1. Analogical 100 μL of ddH2O was added to the wells A2, B2, C2, D2. The measurement was performed with a plate reader at an absorbance of 600 nm.

LUDOX-HS40H2O
Replicate 10,040,026
Replicate 20,0410,027
Replicate 30,0430,026
Replicate 40,040,028
Arith. Mean 0,041
Corrected Abs6000,0143
Reference OD6000,043
OD600/Abs6002,98

Fluorescein-Fluorescence-Measurement (standard curve)

Measurement of different fluorescein concentrations. excitation wavelength: 485nm; emission wavelength: 528nm

Transformation

We had at least two colonies of every test device except for test device 1 (transformation not successful). All of the following measurements are without test device 1.

Cell Measurement

OD600-measurement - growth of E. coli cells.
All cells (with different parts) show the expectable exponential growth.

Fluorescence Measurement of E. coli cells

Test device 2, the positive control and test device 4 show the highest fluorescence after 6 hours followed by test device 5. The remaining test devices do not show any increasing fluorescence and stay on the level of the negative control. (Excitation wavelength: 485nm; emission wavelength: 528nm)