Page79

From 2010.igem.org

(Difference between revisions)
 
(47 intermediate revisions not shown)
Line 40: Line 40:
   text-align:right;
   text-align:right;
   font-size: 1em;
   font-size: 1em;
 +
  color: #a5a5a5;
 +
  margin-right:2.5%;
 +
  vertical-align: middle;
 +
  height: 2.5em;
 +
  display: inline;
 +
}
 +
 +
#navbar2
 +
{
 +
  background: #3b3b3b;
 +
  float: left;
 +
  padding: 0em;
   color: #a5a5a5;
   color: #a5a5a5;
   margin-right:2.5%;
   margin-right:2.5%;
Line 73: Line 85:
   padding: 0em;
   padding: 0em;
   height: 3px;
   height: 3px;
 +
}
 +
 +
#pop-up
 +
{
 +
  background: #656565;
 +
  width: 69em;
 +
  height: 100%;
 +
  padding: 1em;
 +
  border: 0.5em solid #3b3b3b;
 +
  margin: 2em;
 +
  font-family: "Trebuchet MS", Times;
 +
  color: #ffffff;
 +
  float: left;
}
}
Line 91: Line 116:
/* Calendar Coding */
/* Calendar Coding */
-
 
+
/* div for the calendar markup - text must be centered */
-
#calendar  
+
div#calendar  
{
{
-
   width:21.875em; height:19.125em; border:2em solid #000; background:#3b3b3b; margin:0 auto 6.25em auto;
+
   float: left;
 +
  margin: 0 auto;
 +
  padding: 1em 0.1em 2.5em 2.5em;
 +
  text-align: center;
 +
  width: 24em;
 +
  border: 0.2em solid #000000;
 +
  background: #3b3b3b;
}
}
-
#calendar h2  
+
/* calendar heading color */
 +
h2.calendar
{
{
-
   width:15em; left:6.875em; top:9.375em; text-align:center; font-size:2em;font-family: "Trebuchet MS", Times;
+
   color : #fff200;
 +
  font-size: 2.5em;
 +
  font-family: "Trebuchet MS", Times;
}
}
-
#year a
+
/* list info */
 +
ul#days, ul.weeks
{
{
-
   text-decoration:none; color:#fff200;
+
   font-family: "Trebuchet MS", Times;
 +
  margin: 2em 0 2em 0;
 +
  list-style: none;
}
}
-
#year
+
/* day-box span styles - adjust with padding */
 +
ul#days li span
{
{
-
   padding:3.375em 0 0 0; margin:0; list-style-type:none; width:6.875em;
+
   background-color: #757575;
 +
  border: 0.2em solid #ffffff;
 +
  color: #ffffff;
 +
  margin: 0.1em 0.1em;
 +
  padding: 0.8em;
 +
  display: block;
 +
  width: 1em;
}
}
-
#year li  
+
/* basic style for all calendar boxes */
 +
ul.weeks li a
{
{
-
   display:block; width:100px; height:17px; line-height:17px; padding-left:10px; background:transparent;
+
   color: #ffffff;
 +
  text-decoration: underline;
 +
  background-color: #a5a5a5;
 +
  border: 0.2em solid #ffffff;
 +
  padding: 0.8em;
 +
  margin: 0.1em 0.1em;
 +
  width: 1em;
 +
  display: block;
}
}
-
#year table
+
ul.weeks li, ul#days li {
-
{
+
   float: left;
-
   border-collapse:collapse; width:240px; height:270px;
+
}
}
-
#year table td
+
ul.weeks
{
{
-
   height:33px; width:35px; text-align:center; line-height:33px;
+
   clear: both;
}
}
-
#year table caption
+
/* all states of not-used links */
-
{
+
ul.weeks li a.na, ul.weeks li a.na:hover, ul.weeks li a.na:focus, ul.weeks li a.na:active 
-
   color:#a5a5a5; height:32px; line-height:32px; padding:0; margin:0; background:#e1e5a6; font-size:1.5em;
+
{  
 +
   background: transparent;
 +
  text-decoration: none;
 +
  color: #ffffff;
 +
  background-color: #656565;
}
}
-
#year table thead th
+
/* hover and focus state of active links */
-
{
+
ul.weeks li a.al:hover, ul.weeks li a.al:focus, ul.weeks li a.al:active {
-
   text-align:center; background:#6d8666; color:#fff;
+
   color: #fff200;
 +
  background-color: #3b3b3b;
 +
  border: 0.2em solid #ffffff;
 +
  text-decoration: underline;
}
}
-
#year li table
+
/* not used link boxes - color and background should match - adjust with padding */
-
{
+
ul.weeks li a.nu
-
   display:none;
+
{  
 +
   color: #656565;
 +
  border: 0.2em solid #ffffff;
 +
  background-color: #656565;
}
}
-
#year li:hover
+
/* this needs to be in conditional comment for IE only */
 +
div#calendar
{
{
-
   cursor:default; background:#3b3b3b; color:#a5a5a5;
+
   font-size: 0.9em;
 +
  letter-spacing: 0.001em;
}
}
-
#year li:hover table
+
/* tab content next to calendar*/
-
{
+
 
-
  display:block; position:absolute; left:110px; top:0; background:#a5a5a5;
+
content {font-size: 1.5em; font-family: 'Trebuchet MS', Times; float: right; width: 40em;}
 +
     
 +
ul#tabs {list-style-type: none; margin: 0.2em 0em 0 0; padding: 0em; position: absolute; right: 1.5em;}
 +
     
 +
ul#tabs li {display: inline;}
 +
     
 +
ul#tabs li a {color: #ffffff; background-color: #757575; border: 0.3em solid #000000; border-bottom: none; padding: 0.18em; text-decoration: none;}
 +
 
 +
ul#tabs li a:hover {background-color: #3b3b3b; color: #fff200;}
 +
     
 +
ul#tabs li a.selected {color: #fff200; background-color: #3b3b3b; font-weight: bold; padding: 0.18em;}
 +
     
 +
div.tabContent {float: right; width: 50.5em; border: 0.5em solid #3b3b3b; padding: 0em; background-color: #656565; color: #ffffff; white-space: pre-wrap; position: absolute; right: 0.5em; top: 10.5em;}
 +
     
 +
div.tabContent.hide {display: none;}
 +
 
 +
.h2 {text-decoration: none; color: #ffffff; font-size: 2em; font-family: "Trebuchet MS", Times; line-height: 120%; margin: 0em;}
 +
 
 +
.p {text-decoration: none; color: #ffffff; font-size: 1.5em; font-family: "Trebuchet MS", Times; text-align: left; padding: 1em; margin: 1em;}
 +
 
 +
/*hiding toggle content on initial load*/
 +
div.hideme { display: none }
 +
 
 +
</style>
 +
 
 +
<script type="text/javascript">
 +
 
 +
//<![CDATA[
 +
 
 +
    var tabLinks = new Array();
 +
    var contentDivs = new Array();
 +
 
 +
    function init() {
 +
 
 +
// Grab the tab links and content divs from the page
 +
      var tabListItems = document.getElementById('tabs').childNodes;
 +
      for ( var i = 0; i < tabListItems.length; i++ ) {
 +
        if ( tabListItems[i].nodeName == "LI" ) {
 +
          var tabLink = getFirstChildWithTagName( tabListItems[i], 'A' );
 +
          var id = getHash( tabLink.getAttribute('href') );
 +
          tabLinks[id] = tabLink;
 +
          contentDivs[id] = document.getElementById( id );
 +
}
}
}
-
#year td a
+
// Assign onclick events to the tab links, and
-
{
+
// highlight the first tab
-
  display:block; border:1px solid #000; margin:-1px; color:#fff;
+
      var i = 0;
 +
 
 +
      for ( var id in tabLinks ) {
 +
        tabLinks[id].onclick = showTab;
 +
        tabLinks[id].onfocus = function() { this.blur() };
 +
        if ( i == 0 ) tabLinks[id].className = 'selected';
 +
        i++;
}
}
-
#year td a:hover
+
// Hide all content divs except the first
-
{
+
      var i = 0;
-
  display:block; background:#fff; color:#000;
+
 
 +
      for ( var id in contentDivs ) {
 +
        if ( i != 0 ) contentDivs[id].className = 'tabContent hide';
 +
        i++;
 +
}
}
}
-
</style>
+
    function showTab() {
 +
      var selectedId = getHash( this.getAttribute('href') );
 +
 
 +
      // Highlight the selected tab, and dim all others.
 +
      // Also show the selected content div, and hide all others.
 +
      for ( var id in contentDivs ) {
 +
        if ( id == selectedId ) {
 +
          tabLinks[id].className = 'selected';
 +
          contentDivs[id].className = 'tabContent';
 +
        } else {
 +
          tabLinks[id].className = '';
 +
          contentDivs[id].className = 'tabContent hide';
 +
        }
 +
      }
 +
 
 +
      // Stop the browser following the link
 +
      return false;
 +
}
 +
 
 +
    function getFirstChildWithTagName( element, tagName ) {
 +
      for ( var i = 0; i < element.childNodes.length; i++ ) {
 +
        if ( element.childNodes[i].nodeName == tagName ) return element.childNodes[i];
 +
      }
 +
    }
 +
 
 +
    function getHash( url ) {
 +
      var hashPos = url.lastIndexOf ( '#' );
 +
      return url.substring( hashPos + 1 );
 +
    }
 +
 
 +
//]]>
 +
 
 +
  function toggleMe(a){
 +
       
 +
  // add # to id name
 +
  var selector = "#" + a;
 +
 
 +
  // select the pop-up div with jquery and hide everything in it
 +
  $("#pop-up").children().hide();
 +
 
 +
  // show the div we want
 +
  $(selector).show();
 +
 
 +
  // since we want to use this function in onlick, we need to return false
 +
  return false;
 +
}
 +
 
 +
</script>
</head>
</head>
Line 179: Line 341:
<!-- NAVBAR -->
<!-- NAVBAR -->
-
<div id="navbar"><span class="llink2"><a href="https://2010.igem.org/Team:Alberta/JTest"> home</a> |  <a href="project"> project</a> | <a href="ethics"> ethics</a> | <a href="parts"> parts</a> | <a href="software"> software</a> | <a href="https://2010.igem.org/Team:Alberta/Notebook"> notebook</a> | <a href="team"> team</a></span>  
+
<div id="navbar"><span class="llink2"><a href="https://2010.igem.org/Team:Alberta/JTest"> home</a> |  <a href="project"> project</a> | <a href="ethics"> ethics</a> | <a href="parts"> parts</a> | <a href="software"> software</a> | <a href="https://2010.igem.org/Team:Alberta/Notebook"> notebook</a> | <a href="https://2010.igem.org/Team:Alberta/team"> team</a></span>  
</div>
</div>
Line 187: Line 349:
<div id="calendar">
<div id="calendar">
-
<h2>Calendar<br />2010</h2>
+
<div id="navbar2">
 +
<span class="llink2"><a href="https://2010.igem.org/Team:Alberta/Notebook_May">May</a> |  <a href="https://2010.igem.org/Team:Alberta/Notebook_June">June</a> | <a href="https://2010.igem.org/Team:Alberta/Notebook_July">July</a> | <a href="https://2010.igem.org/Team:Alberta/Notebook_August">August</a> | <a href="https://2010.igem.org/Team:Alberta/Notebook_September">September</a> | <a href="https://2010.igem.org/Team:Alberta/Notebook_October">October</a> | <a href="https://2010.igem.org/Team:Alberta/Notebook_November">November</a></span>
 +
</div><br><br>
-
<ul id="year">
+
<h2 class="calendar">May 2010</h2>
-
<li> MAY
+
 
-
  <table>
+
<ul id="days">
-
   <caption>MAY 2010</caption>
+
   <li><span title="Sunday">Su</span></li>
-
  <thead>
+
   <li class= "day" ><span title="Monday">Mo</span></li>
-
   <tr>
+
   <li class= "day" ><span title="Tuesday">Tu</span></li>  
-
  <th scope="col">Sun</th>
+
   <li class= "day" ><span title="Wednesday">We</span></li>
-
   <th scope="col">Mon</th>
+
   <li class= "day" ><span title="Thursday">Th</span></li>
-
  <th scope="col">Tue</th>
+
   <li class= "day" ><span title="Friday">Fr</span></li>
-
   <th scope="col">Wed</th>
+
   <li class= "day" ><span title="Saturday">Sa</span></li>
-
   <th scope="col">Thu</th>
+
</ul>
-
   <th scope="col">Fri</th>
+
-
   <th scope="col">Sat</th>
+
-
  </tr>
+
<!-- On links Below: NU = Not Used; NA = Not Active; AL = Active Link -->
-
  </thead>
+
  <ul class="weeks">
-
  <tbody>
+
    <li class="day"><a title="" onclick="return toggleMe('div30')" return false;" href="#" class="al">30</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div31')" return false;" href="#" class="al">31</a></li>  
 +
    <li class="day"><a title="" onclick="return toggleMe('div32')" return false;" href="#" class="nu">--</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div33')" return false;" href="#" class="nu">--</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div34')" return false;" href="#" class="nu">--</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div35')" return false;" href="#" class="nu">--</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div1')" return false;" href="#" class="na">01</a></li>
 +
  </ul>
-
  <tr><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>01</td></tr>
+
  <ul class="weeks">
-
  <tr><td>02</td><td>03</td><td>04</td><td>05</td><td>06</td><td>07</td><td>08</td></tr>
+
    <li class="day"><a title="" onclick="return toggleMe('div2')" return false;" href="#" class="na">02</a></li>  
-
  <tr><td>09</td><td>10</td><td>11</td><td>12</td><td>13</td><td>14</td><td>15</td></tr>
+
    <li class="day"><a title="" onclick="return toggleMe('div3')" return false;" href="#" class="na">03</a></li>  
-
  <tr><td>16</td><td>17</td><td>18</td><td>19</td><td>20</td><td>21</td><td>22</td></tr>
+
    <li class="day"><a title="" onclick="return toggleMe('div4')" return false;" href="#" class="na">04</a></li>  
-
  <tr><td>23</td><td>24</td><td>25</td><td>26</td><td>27</td><td>28</td><td>29</td></tr>
+
    <li class="day"><a title="" onclick="return toggleMe('div5')" return false;" href="#" class="na">05</a></li>  
-
  <tr><td>30</td><td>31</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td></tr>
+
    <li class="day"><a title="" onclick="return toggleMe('div6')" return false;" href="#" class="na">06</a></li>  
 +
    <li class="day"><a title="" onclick="return toggleMe('div7')" return false;" href="#" class="na">07</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div8')" return false;" href="#" class="na">08</a></li>  
 +
  </ul>
 +
  <ul class="weeks">
 +
    <li class="day"><a title="" onclick="return toggleMe('div9')" return false;" href="#" class="na">09</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div10')" return false;" href="#" class="al">10</a></li>  
 +
    <li class="day"><a title="" onclick="return toggleMe('div11')" return false;" href="#" class="al">11</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div12')" return false;" href="#" class="na">12</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div13')" return false;" href="#" class="na">13</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div14')" return false;" href="#" class="na">14</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div15')" return false;" href="#" class="na">15</a></li>  
 +
  </ul>
 +
  <ul class="weeks">
 +
    <li class="day"><a title="" onclick="return toggleMe('div16')" return false;" href="#" class="na">16</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div17')" return false;" href="#" class="al">17</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div18')" return false;" href="#" class="al">18</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div19')" return false;" href="#" class="al">19</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div20')" return false;" href="#" class="al">20</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div21')" return false;" href="#" class="na">21</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div22')" return false;" href="#" class="na">22</a></li>  
 +
  </ul>
 +
  <ul class="weeks">
 +
    <li class="day"><a title="" onclick="return toggleMe('div23')" return false;" href="#" class="na">23</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div24')" return false;" href="#" class="na">24</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div25')" return false;" href="#" class="al">25</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div26')" return false;" href="#" class="al">26</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div27')" return false;" href="#" class="al">27</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div28')" return false;" href="#" class="al">28</a></li>
 +
    <li class="day"><a title="" onclick="return toggleMe('div29')" return false;" href="#" class="na">29</a></li>  
 +
  </ul>
 +
</div>
 +
   
 +
<ul id="tabs">
 +
  <li><a href="#Notebook">Notebook</a></li>
 +
  <li><a href="#Building">Building Parts</a></li>
 +
  <li><a href="#Testing">Testing Parts</a></li>
 +
  <li><a href="#Assembly">Assembly Method</a></li>
 +
  <li><a href="#Plates">Plates</a></li>
 +
  <li><a href="#Cells">Competent Cells</a></li>
 +
  <li><a href="#Software">Software</a></li>
 +
</ul>
-
  </tbody>
+
<body onload="init()">
-
  </table>
+
-
  </li>
+
-
<li> JUNE
+
<div class="tabContent" id="Notebook">
-
  <table>
+
<span class="h2">iGEM 2010 Notebook</span>
-
  <caption>JUNE 2010</caption>
+
-
  <thead>
+
-
  <tr>
+
-
  <th scope="col">S</th>
+
<p>The lab notebook chronicles our journey in the creation of the Genomikon kit. Many paths were woven together in space and time to reach this finished masterpiece. To help you navigate through these trials with us we have laid out our notebook in a layered fashion. This page gives a sketch of each project and how it interacts with each other. Then follow the links to a projects page for time line of the major landmarks and accomplishments.  If you require more details on the project the links within that page will take you to our day-by-day work log.
-
  <th scope="col">M</th>
+
</p>
-
  <th scope="col">T</th>
+
</div>
-
  <th scope="col">W</th>
+
-
  <th scope="col">T</th>
+
-
  <th scope="col">F</th>
+
-
  <th scope="col">S</th>
+
-
  </tr>
+
-
  </thead>
+
-
  <tbody>
+
-
   
+
-
  <tr><td>..</td><td>..</td><td>01</td><td>02</td><td>03</td><td>04</td><td>05</td></tr>
+
-
  <tr><td>06</td><td>07</td><td>08</td><td>09</td><td>10</td><td>11</td><td>12</td></tr>
+
-
  <tr><td>13</td><td>14</td><td>15</td><td>16</td><td>17</td><td>18</td><td>19</td></tr>
+
-
  <tr><td>20</td><td>21</td><td>22</td><td>23</td><td>24</td><td>25</td><td>26</td></tr>
+
-
  <tr><td>27</td><td>28</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td></tr>
+
-
  <tr><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td></tr>
+
-
  </tbody>
+
<div class="tabContent" id="Building">
-
  </table>
+
<span class="h2">Building Parts</span>
-
  </li>
+
     
 +
<p>The Building Parts project was responsible to first build a plasmid (plasmid 01)that contained our own specialized prefix and suffix nested inside of the standard BioBrick prefix and suffix.  After plasmid 01 existed we inserted the CcdB gene (the "death" gene) between our prefix and suffix removing the gene for Kanamycin resistance (plasmid 02).  Plasmid 02 is fantastic base plasmid from which we are able to amplify any part at all because it provides a positive selection marker when transformed into DH5&alpha;. At this point we were able to make parts en masse to put in our kit. After obtaining a particular part in a plasmid we PCRed the part and digested it ready to use in Assembly or to Test the plasmid.</p>
 +
</div>
-
<li> JULY
+
<div class="tabContent" id="Testing">  
-
  <table>
+
<span class="h2">Testing Parts</span>
-
   <caption>JULY 2010</caption>
+
     
-
  <thead>
+
<p>Before we were able to test parts we created 2 base testing plasmids (vector 01 and vector 02).  Vector 01 is designed to test Open Reading Frame parts, or parts that code for proteins.   The part is flanked by a promoter and the start codon on one side and a stop codon and terminator on the other.  Vector 02 is designed to test linker parts, or parts that control the expression of the Open Reading Frame parts they are next two.  In Vector 02 the part is flanked by two distinct reporter genes, that by comparing the relative expression of the 2 reporter genes we can determine the behavior of the linking part.</p>
-
  <tr>
+
</div>
 +
 +
<div class="tabContent" id="Assembly">
 +
<span class="h2">Assembly Method</span>
 +
     
 +
<p>Insert description here.</p>
 +
</div>
-
  <th scope="col">S</th>
+
<div class="tabContent" id="Plates">
-
  <th scope="col">M</th>
+
<span class="h2">Plates</span>
-
  <th scope="col">T</th>
+
     
-
  <th scope="col">W</th>
+
<p>Insert description here.</p>
-
  <th scope="col">T</th>
+
</div>
-
  <th scope="col">F</th>
+
-
  <th scope="col">S</th>
+
-
  </tr> 
+
-
  </thead>
+
-
  <tbody>
+
-
  <tr><td>..</td><td>..</td><td>..</td><td>..</td><td>01</td><td>02</td><td>03</td></tr>
+
<div class="tabContent" id="Cells">
-
  <tr><td>04</td><td>05</td><td>06</td><td>07</td><td>08</td><td>09</td><td>10</td></tr>
+
<span class="h2">Competent Cells</span>
-
  <tr><td>11</td><td>12</td><td>13</td><td>14</td><td>15</td><td>16</td><td>17</td></tr>
+
     
-
  <tr><td>18</td><td>19</td><td>20</td><td>21</td><td>22</td><td>23</td><td>24</td></tr>
+
<p>Insert description here.</p>
-
  <tr><td>25</td><td>26</td><td>27</td><td>28</td><td>29</td><td>30</td><td>31</td></tr>
+
</div>
-
  <tr><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td></tr>
+
-
  </tbody>
+
<div class="tabContent" id="Software">
-
  </table>
+
<span class="h2">Software</span>
-
  </li>
+
     
 +
<p>Insert description here.</p>
 +
</div>
-
<li> AUGUST
+
<div id="pop-up">
-
  <table>
+
<div align="left" id='div30' class="hideme">
-
  <caption>AUGUST 2010</caption>
+
<span class="h2">May 30, 2010<br><br>
-
  <thead>
+
Building Parts</span>
-
  <tr>
+
<p>From the transformation of DH5&alpha; cells with pSB1C3-KanR performed on <a style="color: #fff200" href="" onclick="return toggleMe('div28')" return false;">28-05-2010</a>, we took 12 distinct colonies of each KanA/B' and KanB/A', streaked them on a new chloramphenicol plate and inoculated 5ml liquid cultures with the appropriate antibiotics overnight at 37<sup>o</sup>C. We also picked colonies of pSB4A5-J04450, pSB4C5-J04450 and pSB3T5-J04450, streaked and made 5mL liquid cultures of them too.</p>
 +
</div>
-
  <th scope="col">S</th>
+
<div align="left" id='div31' class="hideme">
-
  <th scope="col">M</th>
+
<span class="h2">May 31, 2010<br><br>
-
  <th scope="col">T</th>
+
Building Parts</span>
-
  <th scope="col">W</th>
+
<p>9/12 of the pSB1C3-KanA/B' Liquid cultures [[#30-05-2010|30-05-2010]] were successful and only 1/12 of the pSB1C3-KanB/A' liquid cultures were successful.  The pSB4A5, pSB3T5 and pSB4C5 liquid cultures worked.  Miniprepped all the liquid cultures that worked. However, the streaks on the plates worked.</p>
-
  <th scope="col">T</th>
+
<p>Performed a restriction digest of an aliquot of the pSB1C3-KanA/B' and pSB1C3-KanB/A' minipreps.  Digested with XbaI at 37<sup>o</sup>C for one hour and then with EcoRI at 37<sup>o</sup>C for one hour.  Ran a 1% agarose gel of the digests to determine the orientation of the KanR fragments. </p>
-
  <th scope="col">F</th>
+
<!--who did this digest!! we need an image-->
-
  <th scope="col">S</th>
+
<p>KanA/B' and KanB/A' fragements PCRed on [[#11-05-2010|11-05-2010]], digested with BsaI at 37<sup>o</sup>C for 1.5hours, heat inactivated at 65<sup>o</sup>C for 30 minutes. Tried to ligate KanA/B' fragments to each other and tried to ligate KanB/A' fragments to each other.  Also tried to ligate KanA/B' fragments with KanB/A'.  Ligated with T4 DNA ligase overnight at 16<sup>o</sup>C.</p>
-
  </tr>   
+
</div>
-
  </thead>
+
-
  <tbody>
+
-
  <tr><td>01</td><td>02</td><td>03</td><td>04</td><td>05</td><td>06</td><td>07</td></tr>
+
<div align="left" id='div10' class="hideme">
-
  <tr><td>08</td><td>09</td><td>10</td><td>11</td><td>12</td><td>13</td><td>14</td></tr>
+
<span class="h2">May 10, 2010<br><br>
-
  <tr><td>15</td><td>16</td><td>17</td><td>18</td><td>19</td><td>20</td><td>21</td></tr>
+
Building Parts</span>
-
  <tr><td>22</td><td>23</td><td>24</td><td>25</td><td>26</td><td>27</td><td>28</td></tr>
+
<p>PCR a Kanamycin resistance cassette fragment from p1003 with primers containing either the A/B' ends or the B/A' ends. (Fragments formed called KanR A/B'-Bsa and KanR B/A'-Bsa respectively)</p>
-
  <tr><td>29</td><td>30</td><td>31</td><td>..</td><td>..</td><td>..</td><td>..</td></tr>
+
<p>Recipe:</br>  
-
  <tr><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td></tr>
+
<ul>1&mu;L p1003 (approx. 1ng)</ul>
 +
<ul>2.5&mu;L prA_p1003+</ul>
 +
<ul>2.5&mu;L prB'_p1003-</ul>
 +
<ul>5&mu;L 10X PCR buffer</ul>
 +
<ul>1&mu;L 10uM dNTPs</ul>
 +
<ul>2&mu;L 50uM MgCl<sub>2</sub></ul>
 +
<ul>0.5&mu;L Taq polymerase</ul>
 +
<ul>35.5&mu;L MilliQ H<sub>2</sub>O</ul></p>
 +
<p>Same recipe for KanR B/A'-Bsa except primers are prB_p1003+ and prA'_p1003-. </p>
 +
<p>Program:
 +
<ul>5 min-94<sup>o</sup>C</ul>
 +
<ul>45 sec-94<sup>o</sup>C</ul>
 +
<ul>1 min-60<sup>o</sup>C</ul>
 +
<ul>1 min-72<sup>o</sup>C</ul>
 +
<ul>Repeat 2 through 4 35 times</ul>
 +
<ul>5 min-72<sup>o</sup>C</ul></p>
 +
<!--Image of gel performed that day. 5&mu;L of each PCR reaction, 1&mu;L of 10X loading dye and 4&mu;L MilliQ water in a 1% agarose gel -->
 +
</div>
-
  </tbody>
+
<div align="left" id='div11' class="hideme">
-
  </table>
+
<span class="h2">May 11, 2010<br><br>
-
  </li>
+
Building Parts</span>
 +
<p>PCR purification of KanR A/B'-Bsa and KanR B/A'-Bsa created <a style="color: #fff200" href="" onclick="return toggleMe('div10')" return false;">10-05-2010</a> with Qiagen PCR cleanup kit.</p>
 +
<p>Determined concentrations by nanodrop.  KanA/B'-Bsa: 101.1ng/&mu;L KanB/A'-Bsa:89.6ng/&mu;L</p>
 +
</div>
-
<li> SEPTEMBER
+
<div align="left" id='div17' class="hideme">
-
  <table>
+
<span class="h2">May 17, 2010<br><br>
-
  <caption>SEPTEMBER 2010</caption>
+
Building Parts</span>
-
  <thead>
+
<p>Innoculated 250mL overnight cultures with 10mL,4mL and 2mL of a starter culture of DH5&alpha;.  Left shaking at 18<sup>o</sup>C overnight. </p>
-
  <tr>
+
</div>
-
  <th scope="col">S</th>
+
<div align="left" id='div18' class="hideme">
-
  <th scope="col">M</th>
+
<span class="h2">May 18, 2010<br><br>
-
  <th scope="col">T</th>
+
Building Parts</span>
-
  <th scope="col">W</th>
+
<p>Prepared DH5&alpha; E.Coli competent cells using the Inoue Method. </p>
-
  <th scope="col">T</th>
+
<p>Transformed DH5&alpha; cells with pSB1C3-J04450 and grew overnight at 37<sup>o</sup>C on Chloramphenicol plates</p>
-
  <th scope="col">F</th>
+
</div>
-
  <th scope="col">S</th>
+
-
  </tr> 
+
-
  </thead>
+
-
  <tbody>
+
-
+
-
  <tr><td>..</td><td>..</td><td>..</td><td>01</td><td>02</td><td>03</td><td>04</td></tr>
+
-
  <tr><td>05</td><td>06</td><td>07</td><td>08</td><td>09</td><td>10</td><td>11</td></tr>
+
-
  <tr><td>12</td><td>13</td><td>14</td><td>15</td><td>16</td><td>17</td><td>18</td></tr>
+
-
  <tr><td>19</td><td>20</td><td>21</td><td>22</td><td>23</td><td>24</td><td>25</td></tr>
+
-
  <tr><td>26</td><td>27</td><td>28</td><td>29</td><td>30</td><td>..</td><td>..</td></tr>
+
-
  <tr><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td></tr>
+
-
  </tbody>
+
<div align="left" id='div19' class="hideme">
-
  </li>
+
<span class="h2">May 19, 2010<br><br>
 +
Building Parts</span>
 +
<p>From the transformation of DH5&alpha; cells with pSB1C3-J04450 performed on <a style="color: #fff200" href="" onclick="return toggleMe('div18')" return false;">18-05-2010</a>, we took 4 distinct colonies, streaked them on a new chloramphenicol plate and inoculated 5ml liquid cultures.</p>
 +
</div>
-
<li> OCTOBER
+
<div align="left" id='div20' class="hideme">
-
  <table>
+
<span class="h2">May 20, 2010<br><br>
-
  <caption>OCT 2010</caption>
+
Building Parts</span>
-
  <thead>
+
<p>Performed a Miniprep of 3 of the 4 5ml liquid cultures of DH5&alpha; cells with pSB1C3-J04450 from <a style="color: #fff200" href="" onclick="return toggleMe('div19')" return false;">19-05-2010</a>.  Took a 1&mu;L sample of the Miniprep solutions and digested with NotI at 37<sup>o</sup>C for 1 hour. </p>
-
  <tr>
+
<p>Digestion Recipe:
 +
<ul>1&mu;L Miniprep (between 153.2 ng/&mu;l and 302.7ng/&mu;l determined by nanodrop)</ul>
 +
<ul>1&mu;L NotI</ul>
 +
<ul>1&mu;L 10X ReACT 3</ul>
 +
<ul>7&mu;L MilliQ</ul></p>
 +
<p>Ran Digestion on a 1% agarose gel to check that the plasmid obtained with what we expected. </p>
 +
<!-- Image of Gel-->
 +
</div>
-
  <th scope="col">S</th>
+
<div align="left" id='div25' class="hideme">
-
  <th scope="col">M</th>
+
<span class="h2">May 25, 2010<br><br>
-
  <th scope="col">T</th>
+
Building Parts</span>
-
  <th scope="col">W</th>
+
<p>Made 1.5mL LB liquid cultures of pSB1C3 from the plate streaked on <a style="color: #fff200" href="" onclick="return toggleMe('div19')" return false;">19-05-2010</a> and added chloramphenicol.</p>
-
  <th scope="col">T</th>
+
</div>
-
  <th scope="col">F</th>
+
-
  <th scope="col">S</th>
+
-
  </tr> 
+
-
  </thead>
+
-
  <tbody>
+
-
+
-
  <tr><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>01</td><td>02</td></tr>
+
-
  <tr><td>03</td><td>04</td><td>05</td><td>06</td><td>07</td><td>08</td><td>09</td></tr>
+
-
  <tr><td>10</td><td>11</td><td>12</td><td>13</td><td>14</td><td>15</td><td>16</td></tr>
+
-
  <tr><td>17</td><td>18</td><td>19</td><td>20</td><td>21</td><td>22</td><td>23</td></tr>
+
-
  <tr><td>24</td><td>25</td><td>26</td><td>27</td><td>28</td><td>29</td><td>30</td></tr>
+
-
  <tr><td>31</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td></tr>
+
-
  </tbody>
+
<div align="left" id='div26' class="hideme">
-
  </table>
+
<span class="h2">May 26, 2010<br><br>
-
  </li>
+
Building Parts</span>
 +
<p>Made 3 glycerol stocks of pSB1C3 from overnight made <a style="color: #fff200" href="" onclick="return toggleMe('div25')" return false;">25-05-2010</a>.</p>
 +
</div>
-
<li> NOVEMBER
+
<div align="left" id='div27' class="hideme">
-
  <table>
+
<span class="h2">May 27, 2010<br><br>
-
  <caption>NOVEMBER 2010</caption>
+
Building Parts</span>
-
  <thead>
+
<p>Digested both A/B' and B/A' Kanamycin Resistance cassettes fragments from <a style="color: #fff200" href="" onclick="return toggleMe('div11')" return false;">11-05-2010</a> and pSB1C3 from <a style="color: #fff200" href="" onclick="return toggleMe('div20')" return false;">20-05-2010</a> with NotI at 37<sup>o</sup>C for 1 hour. Heat inactivated the NotI for 10 minutes at 65<sup>o</sup>C.  Ligated the Kanamycin Resistance cassettes into pSB1C3 at 16<sup>o</sup>C for 1 hour then took 15&mu;L to room temperature for 2 hours.  Transformed 100&mu;L of DH5&alpha; cells with 5&mu;L of RT ligation reaction. Plated transformation on plates with both Chloramphenicol and Kanamycin.</p>
-
  <tr>
+
<p>Digestion Recipe:
 +
<ul>1&mu;L Miniprep (302.7ng/&mu;l determined by nanodrop)</ul>
 +
<ul>2&mu;L either A/B' or B/A' Kanamycin resistance cassette (approx. 100ng/&mu;L)</ul>
 +
<ul>1&mu;L NotI</ul>
 +
<ul>1&mu;L 10X ReACT 3</ul>
 +
<ul>:5&mu;L MilliQ</ul></p>
 +
<p>Ligation Recipe:
 +
<ul>10&mu;L of Digest solution</ul>
 +
<ul>1&mu;L T4 DNA ligase</ul>
 +
<ul>6&mu;L 5X Buffer</ul>
 +
<ul>13&mu;L MilliQ H<sub>2</sub>O</ul></p>
 +
<p>Also transformed pSB4A5-J04450, pSB4C5-J04450 and pSB3T5-J04450 from the 2010 biobrick parts into DH5&alpha; cells.</p>
 +
<p>Performed PCR reactions to create parts with antibiotic resistance with negative controls.</p>
 +
<p>PCR Recipe:
 +
<ul>3&mu;L 10X PCR Buffer</ul>
 +
<ul>1&mu;L 10 uM dNTPs</ul>
 +
<ul>2&mu;L 50 uM MgCl<sub>2</sub></ul>
 +
<ul>17.5&mu;L MilliQ H<sub>2</sub>O</ul>
 +
<ul>0.5&mu;L Taq Polymerase</ul>
 +
<ul>1&mu;L Template (psB4A5-J04450, psB4C5-J04450 or psB3T5-J04450)</ul>
 +
<ul>2.5&mu;L Primer + (PrA psB4A5 ApR+, PrA psB4C5 ChR+ or PrA psB3T5 TR+)</ul>
 +
:2.5&mu;L Primer - (PrB psB4A5 ApR-, PrB psB4C5 ChR- or PrB psB3T5 TR-)</p>
 +
<p>PCR Program:
 +
<ul>5 min-94<sup>o</sup>C</ul>
 +
<ul>45 sec-94<sup>o</sup>C</ul>
 +
<ul>1 min-60<sup>o</sup>C</ul>
 +
<ul>1 min-72<sup>o</sup>C</ul>
 +
<ul>Repeat 2 through 4 35 times</ul>
 +
<ul>5 min-72<sup>o</sup>C</ul></p>
 +
<!--gel images of PCR Products (Alina's) and ligated and pre-digested samples (Jeremy's)-->
 +
</div>
-
  <th scope="col">S</th>
+
<div align="left" id='div28' class="hideme">
-
  <th scope="col">M</th>
+
<span class="h2">May 28, 2010<br><br>
-
  <th scope="col">T</th>
+
Building Parts</span>
-
  <th scope="col">W</th>
+
<p>We got colonies!! (it's a fantastic feeling) We then lovingly put them in the cold room to await our return from Calgary</p>
-
  <th scope="col">T</th>
+
</div>
-
  <th scope="col">F</th>
+
-
  <th scope="col">S</th>
+
-
  </tr> 
+
-
  </thead>
+
-
  <tbody>
+
-
+
-
  <tr><td>..</td><td>01</td><td>02</td><td>03</td><td>04</td><td>05</td><td>06</td></tr>
+
-
  <tr><td>07</td><td>08</td><td>09</td><td>10</td><td>11</td><td>12</td><td>13</td></tr>
+
-
  <tr><td>14</td><td>15</td><td>16</td><td>17</td><td>18</td><td>19</td><td>20</td></tr>
+
-
  <tr><td>21</td><td>22</td><td>23</td><td>24</td><td>25</td><td>26</td><td>27</td></tr>
+
-
  <tr><td>28</td><td>29</td><td>30</td><td>..</td><td>..</td><td>..</td><td>..</td></tr>
+
-
  <tr><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td><td>..</td></tr>
+
-
  </tbody>
 
-
  </table>
 
-
  </li>
 
-
 
-
</ul>
 
</div>
</div>
Line 393: Line 609:
<a href="Site_Map">site map</a>|<a href="Sponsors">sponsors</a>|<a href="Contact">contact us</a>
<a href="Site_Map">site map</a>|<a href="Sponsors">sponsors</a>|<a href="Contact">contact us</a>
</span></div>
</span></div>
 +
 +
</body>
</body>

Latest revision as of 22:22, 8 July 2010

genomikon


May 2010

  • Su
  • Mo
  • Tu
  • We
  • Th
  • Fr
  • Sa
iGEM 2010 Notebook

The lab notebook chronicles our journey in the creation of the Genomikon kit. Many paths were woven together in space and time to reach this finished masterpiece. To help you navigate through these trials with us we have laid out our notebook in a layered fashion. This page gives a sketch of each project and how it interacts with each other. Then follow the links to a projects page for time line of the major landmarks and accomplishments. If you require more details on the project the links within that page will take you to our day-by-day work log.

Building Parts

The Building Parts project was responsible to first build a plasmid (plasmid 01)that contained our own specialized prefix and suffix nested inside of the standard BioBrick prefix and suffix. After plasmid 01 existed we inserted the CcdB gene (the "death" gene) between our prefix and suffix removing the gene for Kanamycin resistance (plasmid 02). Plasmid 02 is fantastic base plasmid from which we are able to amplify any part at all because it provides a positive selection marker when transformed into DH5α. At this point we were able to make parts en masse to put in our kit. After obtaining a particular part in a plasmid we PCRed the part and digested it ready to use in Assembly or to Test the plasmid.

Testing Parts

Before we were able to test parts we created 2 base testing plasmids (vector 01 and vector 02). Vector 01 is designed to test Open Reading Frame parts, or parts that code for proteins. The part is flanked by a promoter and the start codon on one side and a stop codon and terminator on the other. Vector 02 is designed to test linker parts, or parts that control the expression of the Open Reading Frame parts they are next two. In Vector 02 the part is flanked by two distinct reporter genes, that by comparing the relative expression of the 2 reporter genes we can determine the behavior of the linking part.

Assembly Method

Insert description here.

Plates

Insert description here.

Competent Cells

Insert description here.

Software

Insert description here.

May 30, 2010

Building Parts

From the transformation of DH5α cells with pSB1C3-KanR performed on 28-05-2010, we took 12 distinct colonies of each KanA/B' and KanB/A', streaked them on a new chloramphenicol plate and inoculated 5ml liquid cultures with the appropriate antibiotics overnight at 37oC. We also picked colonies of pSB4A5-J04450, pSB4C5-J04450 and pSB3T5-J04450, streaked and made 5mL liquid cultures of them too.

May 31, 2010

Building Parts

9/12 of the pSB1C3-KanA/B' Liquid cultures [[#30-05-2010|30-05-2010]] were successful and only 1/12 of the pSB1C3-KanB/A' liquid cultures were successful. The pSB4A5, pSB3T5 and pSB4C5 liquid cultures worked. Miniprepped all the liquid cultures that worked. However, the streaks on the plates worked.

Performed a restriction digest of an aliquot of the pSB1C3-KanA/B' and pSB1C3-KanB/A' minipreps. Digested with XbaI at 37oC for one hour and then with EcoRI at 37oC for one hour. Ran a 1% agarose gel of the digests to determine the orientation of the KanR fragments.

KanA/B' and KanB/A' fragements PCRed on [[#11-05-2010|11-05-2010]], digested with BsaI at 37oC for 1.5hours, heat inactivated at 65oC for 30 minutes. Tried to ligate KanA/B' fragments to each other and tried to ligate KanB/A' fragments to each other. Also tried to ligate KanA/B' fragments with KanB/A'. Ligated with T4 DNA ligase overnight at 16oC.

May 10, 2010

Building Parts

PCR a Kanamycin resistance cassette fragment from p1003 with primers containing either the A/B' ends or the B/A' ends. (Fragments formed called KanR A/B'-Bsa and KanR B/A'-Bsa respectively)

Recipe:

    1μL p1003 (approx. 1ng)
    2.5μL prA_p1003+
    2.5μL prB'_p1003-
    5μL 10X PCR buffer
    1μL 10uM dNTPs
    2μL 50uM MgCl2
    0.5μL Taq polymerase
    35.5μL MilliQ H2O

Same recipe for KanR B/A'-Bsa except primers are prB_p1003+ and prA'_p1003-.

Program:

    5 min-94oC
    45 sec-94oC
    1 min-60oC
    1 min-72oC
    Repeat 2 through 4 35 times
    5 min-72oC

May 11, 2010

Building Parts

PCR purification of KanR A/B'-Bsa and KanR B/A'-Bsa created 10-05-2010 with Qiagen PCR cleanup kit.

Determined concentrations by nanodrop. KanA/B'-Bsa: 101.1ng/μL KanB/A'-Bsa:89.6ng/μL

May 17, 2010

Building Parts

Innoculated 250mL overnight cultures with 10mL,4mL and 2mL of a starter culture of DH5α. Left shaking at 18oC overnight.

May 18, 2010

Building Parts

Prepared DH5α E.Coli competent cells using the Inoue Method.

Transformed DH5α cells with pSB1C3-J04450 and grew overnight at 37oC on Chloramphenicol plates

May 19, 2010

Building Parts

From the transformation of DH5α cells with pSB1C3-J04450 performed on 18-05-2010, we took 4 distinct colonies, streaked them on a new chloramphenicol plate and inoculated 5ml liquid cultures.

May 20, 2010

Building Parts

Performed a Miniprep of 3 of the 4 5ml liquid cultures of DH5α cells with pSB1C3-J04450 from 19-05-2010. Took a 1μL sample of the Miniprep solutions and digested with NotI at 37oC for 1 hour.

Digestion Recipe:

    1μL Miniprep (between 153.2 ng/μl and 302.7ng/μl determined by nanodrop)
    1μL NotI
    1μL 10X ReACT 3
    7μL MilliQ

Ran Digestion on a 1% agarose gel to check that the plasmid obtained with what we expected.

May 25, 2010

Building Parts

Made 1.5mL LB liquid cultures of pSB1C3 from the plate streaked on 19-05-2010 and added chloramphenicol.

May 26, 2010

Building Parts

Made 3 glycerol stocks of pSB1C3 from overnight made 25-05-2010.

May 27, 2010

Building Parts

Digested both A/B' and B/A' Kanamycin Resistance cassettes fragments from 11-05-2010 and pSB1C3 from 20-05-2010 with NotI at 37oC for 1 hour. Heat inactivated the NotI for 10 minutes at 65oC. Ligated the Kanamycin Resistance cassettes into pSB1C3 at 16oC for 1 hour then took 15μL to room temperature for 2 hours. Transformed 100μL of DH5α cells with 5μL of RT ligation reaction. Plated transformation on plates with both Chloramphenicol and Kanamycin.

Digestion Recipe:

    1μL Miniprep (302.7ng/μl determined by nanodrop)
    2μL either A/B' or B/A' Kanamycin resistance cassette (approx. 100ng/μL)
    1μL NotI
    1μL 10X ReACT 3
    :5μL MilliQ

Ligation Recipe:

    10μL of Digest solution
    1μL T4 DNA ligase
    6μL 5X Buffer
    13μL MilliQ H2O

Also transformed pSB4A5-J04450, pSB4C5-J04450 and pSB3T5-J04450 from the 2010 biobrick parts into DH5α cells.

Performed PCR reactions to create parts with antibiotic resistance with negative controls.

PCR Recipe:

    3μL 10X PCR Buffer
    1μL 10 uM dNTPs
    2μL 50 uM MgCl2
    17.5μL MilliQ H2O
    0.5μL Taq Polymerase
    1μL Template (psB4A5-J04450, psB4C5-J04450 or psB3T5-J04450)
    2.5μL Primer + (PrA psB4A5 ApR+, PrA psB4C5 ChR+ or PrA psB3T5 TR+)
:2.5μL Primer - (PrB psB4A5 ApR-, PrB psB4C5 ChR- or PrB psB3T5 TR-)

PCR Program:

    5 min-94oC
    45 sec-94oC
    1 min-60oC
    1 min-72oC
    Repeat 2 through 4 35 times
    5 min-72oC

May 28, 2010

Building Parts

We got colonies!! (it's a fantastic feeling) We then lovingly put them in the cold room to await our return from Calgary

Retrieved from "http://2010.igem.org/Page79"