"
Team:KULeuven/Project/Input
From 2008.igem.org
(Difference between revisions)
m |
|||
| Line 3: | Line 3: | ||
==Input== | ==Input== | ||
| + | Searching for an input signal that was easily turned on and off, we chose to use the light-sensing device '''BBa_M30109'''. This device has already been used by a number of teams: | ||
| + | * '''listing team''' | ||
| + | For the sake of completeness, we describe it here again. | ||
| - | + | ===BioBricks=== | |
| + | ('''figuur input''') | ||
| - | The first step is to produce ''ho1'' (heme | + | ===Components=== |
| + | The first step is to produce ''ho1'' (heme oxigenase 1) that converts heme to biliverdin IXalpha. This enzyme is encoded by '''BBa_I15008'''. The second step is to produce ''PcyA'' (phycocyanobilin:ferredoxin oxidoreductase) that converts the biliverdin IXalpha to phycocyanobilin. This enzyme is encoded by '''BBa_I15009'''. This phycocyanobilin associates with the light receptive domain Cph1 of a Cph1/EnvZ fusion protein, encoded by '''BBa_I15010'''. | ||
| + | ===Action=== | ||
The ''ho1'' and ''PcyA'' coding parts are placed under a Pbad promoter. As AraC is present in the cell, phycocyanobilin will only be made upon activation with arabinose. The coding part for the Cph1/EnvZ fusion protein is placed under control of a pTet promoter, which means that, as TetR is present, the fusion protein will only be produced when aTc is added to the medium. This gives us the possibility to test the system with an exogenous memory instead of the endogenous one, which will then be added later on in the project. | The ''ho1'' and ''PcyA'' coding parts are placed under a Pbad promoter. As AraC is present in the cell, phycocyanobilin will only be made upon activation with arabinose. The coding part for the Cph1/EnvZ fusion protein is placed under control of a pTet promoter, which means that, as TetR is present, the fusion protein will only be produced when aTc is added to the medium. This gives us the possibility to test the system with an exogenous memory instead of the endogenous one, which will then be added later on in the project. | ||
| - | |||
[[Image:input.png|300px|right]] It is the Cph1 part of the fusion protein that acts as the light sensor, the EnvZ part is a kinase. Upon radiation with 660nm (red) light, the fusion protein gets dephosphorylated. This renders the kinase in an inactive state. The active kinase phosphorylates the molecule ompR. A high concentration of the phosphorylated ompR represses the OmpF promoter. A lower concentration activates it. So when 660nm light is irradiated on the input mechanism, the concentration of phosphorylated ompR drops and the OmpF promoter is turned on. | [[Image:input.png|300px|right]] It is the Cph1 part of the fusion protein that acts as the light sensor, the EnvZ part is a kinase. Upon radiation with 660nm (red) light, the fusion protein gets dephosphorylated. This renders the kinase in an inactive state. The active kinase phosphorylates the molecule ompR. A high concentration of the phosphorylated ompR represses the OmpF promoter. A lower concentration activates it. So when 660nm light is irradiated on the input mechanism, the concentration of phosphorylated ompR drops and the OmpF promoter is turned on. | ||
Revision as of 13:48, 30 July 2008
Result:
To have a dropdown for your own team copy over all of the content below. It might be needed to adjust a thing or two. Comments have been added throughout the code what must be changed.
Inspirational websites:
- Most basic dropdown menu, with no submenu's
- The javascript library used to add effects and optimise the dropdown
- How to center a ul list effectively
The dropdown has been created and developed by the KULeuven team.
<html>
<style type="text/css">
#content {z-index:4;}
#ddwrapper * {z-index:8 !important;}
div#ddwrapper {
margin:0;
padding:0;
height:28px;
width:945px; /* change to adjust imperfections in width */
}
div#ddnav {
margin:0 auto; /* needed to center the dropdown */
padding:0;
top:5px;
/* width: 965px */
visibility:hidden; /* dropdown is hidden until properly initalised by javascript */
}
div#ddtoggle {
margin:0;
position:fixed;
right:2px;
top:15px;
height:10px;
width:10px;
z-index:100;
}
#ddnav ul {
display:table-row; /* works only for firefox, later adjusted by javascript for IE */
margin:0 auto;
padding:0;
}
#ddnav ul li {
display:table-cell; /* works only for firefox, later adjusted by javascript for IE */
list-style:none;
margin:0;
padding:0 !important;
border-right:1px solid #FFF; /* creates illusion of spacing between tabs */
}
#ddnav ul li:last-child{border-right:none;}
#ddnav a{
display:block;
margin:0;
padding:4px 14px; /* play with dimensions for size of tabs */
background-color:#075A90; /* background color for tabs */
color:#FFF !important; /* font color for text in tabs */
text-align:center; /* aligning for text in tabs */
text-decoration:none !important;
font:bold 10pt Trebuchet MS; /* font properties for text in tabs */
outline:0;
}
#ddnav ul li a:hover {background-color:#99CCFF;}/* background color for tabs on mouseover */
#ddnav li a:active {outline:none;} /* remove standard dotted border for links when clicked (IE) */
#ddnav li a:focus {-moz-outline-style:none;} /* remove standard dotted border for links when clicked (FF) */
#ddnav div {
display:none;
position:absolute;
width:9em;
background-color:#000; /* bug solution, do not change ! */
border:1px solid #5970B2; /* border color for dropdown menus */
opacity:0.9; /* transparancy of the dropdown menus (FF) */
filter:alpha(opacity=90); /* transparancy of the dropdown menus (IE) */
}
#ddnav div a {
display:block;
padding:5px 10px; /* play with dimensions of block element in dropdown menus */
position:relative;
font:normal 8pt arial; /* font properties for text in dropdown menus */
text-align:left; /* aligning of text in dropdown menus */
cursor:pointer;
}
#ddnav div a:hover, #ddnav span a:hover {color:#000 !important;} /* text color on mouseover */
#ddnav span div {
position:relative;
border:none;
border-bottom:2px groove #5970B2; /* separator for submenus, groove does not work in FF */
opacity:1.0; /* avoid stacking transparancy for submenus (FF) */
filter:alpha(opacity=100); /* avoid stacking transparancy for submenus (IE) */
}
/* may want to upload the following pictures to a new location */
.expand {background: url('https://static.igem.org/mediawiki/2008/e/ef/Icon-expand.png') no-repeat 95% 50%;}
.collapse {background: url('https://static.igem.org/mediawiki/2008/c/cd/Icon-collapse.png') no-repeat 95% 50%;}
.docked {background: #99ccff url("https://static.igem.org/mediawiki/2008/6/62/Ddnavundock.png") no-repeat 50% 50%;}
.undocked {background: #99ccff url("https://static.igem.org/mediawiki/2008/e/e4/Ddnavdock.png") no-repeat 50% 50%;}
</style>
<!-- IMPORTANT: save following script under a personalized webspace or download the library at www.jquery.com -->
<script type="text/javascript" src="http://student.kuleuven.be/~s0173901/wiki/js/jquery.js"></script>
<script type="text/javascript">
function ddnav() {
$('#ddnav ul li').hover(
function () {
$(this).find('div:first').css('display','block');},
function () {
$(this).find('div:first').css('display','none');}
);
}
function ddnavsub() {
$('#ddnav span > a').toggle(
function () {
$(this).removeClass("#ddnav expand").addClass("#ddnav collapse");
$(this).parent().find('div:first').slideDown('fast');
$(this).hover(
function (){$(this).css('background-color','#99AAFF');},
function (){$(this).css('background-color','#99AAFF');});},
function () {
$(this).removeClass("#ddnav collapse").addClass("#ddnav expand");
$(this).parent().find('div:first').css('display','none');
$(this).hover(
function (){$(this).css('background-color','#99CCFF');},
function (){$(this).css('background-color','#075A90');});}
).addClass("#ddnav expand");
}
/* If you wish to omit the docking feature, remove following function ddtoggle() */
function ddtoggle() {
$('#ddtoggle').toggle(
function () {
$(this).removeClass('undocked').addClass('docked');
$('#ddnav').css('position','fixed');},
function () {
$(this).removeClass('docked').addClass('undocked');
$('#ddnav').css('position','static');}
);
}
function ddalign() {
var _windowWidth = $(window).width();
var _leftOffset = (_windowWidth - 965)/2;
$('div#ddnav').css('left',_leftOffset);
}
function ddmsie() {
$('#ddnav a').hover(
function () {$(this).css('background-color','#99ccff');},
function () {$(this).css('background-color','#075a90');}
);
/* toggle doesn't work yet */
$('#ddtoggle').css('display','none');
$('#ddnav ul').css('display','inline-block');
$('#ddnav ul li').css('display','inline');
$('#ddnav ul li').css('position','relative');
$('#ddnav ul li>a').css('display','inline-block');
$('#ddnav ul li>a').css('margin-right','-4px');
$('#ddnav div').css('left','0');
$('#ddnav div').css('top','100%');
$('#ddnav span div').css('top','0');
}
function ddmozilla() {
ddtoggle();
$(window).bind('resize', function() {ddalign();});
}
$(function () {
ddnav();
ddnavsub();
if(jQuery.browser.msie) ddmsie();
if(jQuery.browser.mozilla) ddmozilla();
$('#ddnav').css('visibility','visible');
});
</script>
<!-- If you wish to omit the docking feature omit following line (div with id ddtoggle) -->
<div id="ddtoggle" class="undocked"></div>
<div id="ddwrapper">
<!-- Here the actual links are defined, simply replace with your own links in the appropriate sections -->
<div id="ddnav" align="center">
<ul>
<li>
<a href="https://2008.igem.org/Team:KULeuven">Home</a>
</li>
<li>
<a>The Team</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Team/LabsandGroups">Research Labs and Groups</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Students">Students</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Instructors">Instructors</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Advisors">Advisors</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Pictures">Pictures</a>
</div>
</li>
<li>
<a>The Project</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Project">Summary</a>
<span>
<a>Components</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Project/Input">Input</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Output">Output</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Filter">Filter</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Inverter">Invertimer</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Reset">Reset</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/CellDeath">Cell Death</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Memory">Memory</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Evaluation">End Evaluation</a>
<a href="https://2008.igem.org/Team:KULeuven/Literature">Literature</a>
<a href="https://2008.igem.org/Team:KULeuven/Brainstorm">Brainstorm</a>
</div>
</li>
<li>
<a>Ethics</a>
<div>
</div>
</li>
<li>
<a>Submitted Parts</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Parts">Listing</a>
<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=KULeuven">Sandbox</a>
</div>
</li>
<li>
<a>Modeling</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Model/Overview">Overview</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/KineticConstants">Kinetic Constants</a>
<span>
<a>Components</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Model/Output">Output</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Filter">Filter</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">Invertimer</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Reset">Reset</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/CellDeath">Cell Death</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Memory">Memory</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Model/FullModel">Full Model</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Sensitivity">Sensitivity Analysis</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/MultiCell">Multi-cell Model</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Diffusion">Diffusion</a>
</div>
</li>
<li>
<a>Data Analysis</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Data/Overview">Overview</a>
<span>
<a>New Parts</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Data/GFP">GFP (LVA-tag)</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/T7">T7 (UmuD-tag)</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Antisense">Antisense LuxI</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/ccdB">Celldeath (ccdB)</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/HybridProm">Hybrid Promotor</a>
</div>
</span>
<span>
<a>Components</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Data/Input">Input</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Output">Output</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Filter">Filter</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Inverter">Invertimer</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Reset">Reset</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/CellDeath">Cell Death</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Memory">Memory</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Data/FullModel">Full Model</a>
</div>
</li>
<li>
<a>Software</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Software/MultiCell">Multi-cell Toolbox</a>
<a href="https://2008.igem.org/Team:KULeuven/Software/Simbiology2LaTeX">Simbiology2LaTeX Toolbox</a>
</div>
</li>
<li>
<a>Notebook</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Meeting_Calendar">Calendar</a>
<a href="https://2008.igem.org/Team:KULeuven/SummerHolidays">Summer Holidays</a>
<span>
<a>Reports</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Meeting Reports">Daily</a>
<a href="https://2008.igem.org/Team:KULeuven/Weekly Meetings">Weekly</a>
</div>
</span>
<span>
<a>Lab Data</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Freezer">Freezer</a>
<a href="https://2008.igem.org/Team:KULeuven/Primers">Primers</a>
<a href="https://2008.igem.org/Team:KULeuven/Ligation">Ligation</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Tools">Tools</a>
<a href="https://2008.igem.org/Team:KULeuven/Press">Press</a>
<a href="https://2008.igem.org/Team:KULeuven/Guestbook">Guestbook</a>
</div>
</li>
</ul>
</div>
</div>
</html>
Contents |
Input
Searching for an input signal that was easily turned on and off, we chose to use the light-sensing device BBa_M30109. This device has already been used by a number of teams:
- listing team
For the sake of completeness, we describe it here again.
BioBricks
(figuur input)
Components
The first step is to produce ho1 (heme oxigenase 1) that converts heme to biliverdin IXalpha. This enzyme is encoded by BBa_I15008. The second step is to produce PcyA (phycocyanobilin:ferredoxin oxidoreductase) that converts the biliverdin IXalpha to phycocyanobilin. This enzyme is encoded by BBa_I15009. This phycocyanobilin associates with the light receptive domain Cph1 of a Cph1/EnvZ fusion protein, encoded by BBa_I15010.
Action
The ho1 and PcyA coding parts are placed under a Pbad promoter. As AraC is present in the cell, phycocyanobilin will only be made upon activation with arabinose. The coding part for the Cph1/EnvZ fusion protein is placed under control of a pTet promoter, which means that, as TetR is present, the fusion protein will only be produced when aTc is added to the medium. This gives us the possibility to test the system with an exogenous memory instead of the endogenous one, which will then be added later on in the project.
