Team:UPO-Sevilla/Project/Improving Flip Flop/Data Page

From 2011.igem.org

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<html>
<html>
 +
 +
<script type="text/javascript">
 +
            ddmenuactual = 1;
 +
            $("#menuPImproved").addClass("TopMenuSelected");
 +
</script>
                     <div id="principal">
                     <div id="principal">
                         <div class="main">
                         <div class="main">
Line 16: Line 21:
                         </ul>
                         </ul>
-
                             <h1>Data Page</h1>
+
                             <h1>Data Page</h1>   
 +
                           
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<style type="text/css">
 +
        .dataPage{width:700px; height:475px; background: url(https://static.igem.org/mediawiki/2011/d/df/UPOSevillaImprovingFlipFlop.png);}
 +
              .tour_PcI{
 +
        border: 3px solid transparent;
 +
    bottom: -2.5em;
 +
    display: inline-block;
 +
    height: 1em;
 +
    left: 15.5em;
 +
    position: relative;
 +
    width: 3.7em;}
 +
.tour_LacI_Das{     
 +
      border: 3px solid transparent;
 +
    bottom: -2.5em;
 +
    display: inline-block;
 +
    height: 1em;
 +
    left: 9em;
 +
    position: relative;
 +
    width: 2em;}
 +
.tour_GFP_DAS{
 +
    border: 3px solid transparent;
 +
    bottom: -2.5em;
 +
    display: inline-block;
 +
    height: 1em;
 +
    left: 1.5em;
 +
    position: relative;
 +
    width: 4em;}
 +
        .tour_asRNA{    border: 3px solid transparent;
 +
    bottom: -6em;
 +
    display: inline-block;
 +
    height: 1em;
 +
    left: 22em;
 +
    position: relative;
 +
    width: 6.5em;}
 +
  .tour_PLac{
 +
    border: 3px solid transparent;
 +
    display: inline-block;
 +
    height: 1em;
 +
    position: relative;
 +
    right: 2.8em;
 +
    top: 21.5em;
 +
    width: 6.7em;}
 +
        .tour_cI{      border: 3px solid transparent;
 +
    display: inline-block;
 +
    height: 1em;
 +
    left: -6em;
 +
    position: relative;
 +
    top: 21.5em;
 +
    width: 4em;}
 +
.tour_OmpN_RFP{ 
 +
    border: 3px solid transparent;
 +
    display: inline-block;
 +
    height: 1em;
 +
    left: -4.5em;
 +
    position: relative;
 +
    top: 21.8em;
 +
    width: 4.7em;}
 +
.tour_OmpN_SspB{
 +
    border: 3px solid transparent;
 +
    display: inline-block;
 +
    height: 4em;
 +
    left: -14.5em;
 +
    position: relative;
 +
    top: 24.5em;
 +
    width: 6.7em;}
 +
.tour_IPTG{ 
 +
    border: 3px solid transparent;
 +
    display: inline-block;
 +
    height: 4em;
 +
    left: 3.5em;
 +
    position: relative;
 +
    top: 7em;
 +
    width: 4.7em;}
 +
</style>
 +
<div class="wrapper">
 +
<div class="content">
 +
 +
                            <div class="dataPage">
 +
                              <div class="tour_PcI"></div>
 +
 
 +
                              <div class="tour_LacI_Das"></div>
 +
 
 +
                              <div class="tour_GFP_DAS"></div>
 +
 
 +
                              <div class="tour_asRNA"></div>
 +
 
 +
                              <div class="tour_PLac"></div>
 +
 
 +
                              <div class="tour_cI"></div>
 +
 
 +
                              <div class="tour_OmpN_RFP"></div>
 +
 
 +
                              <div class="tour_OmpN_SspB"></div>
 +
 
 +
                              <div class="tour_IPTG"></div>
 +
 
 +
 
 +
                </div>
 +
</div>
 +
 
 +
</div>
 +
 
 +
<!-- The JavaScript -->
 +
      <script src="https://2011.igem.org/Team:UPO-Sevilla/js/jqueryeasing.js?action=raw&ctype=text/javascript" type="text/javascript"></script>
 +
        <script type="text/javascript">
 +
$(function() {
 +
/*
 +
the json config obj.
 +
name: the class given to the element where you want the tooltip to appear
 +
bgcolor: the background color of the tooltip
 +
color: the color of the tooltip text
 +
text: the text inside the tooltip
 +
time: if automatic tour, then this is the time in ms for this step
 +
position: the position of the tip. Possible values are
 +
TL top left
 +
TR  top right
 +
BL  bottom left
 +
BR  bottom right
 +
LT  left top
 +
LB  left bottom
 +
RT  right top
 +
RB  right bottom
 +
T  top
 +
R  right
 +
B  bottom
 +
L  left
 +
*/
 +
var config = [
 +
{
 +
"name" : "tour_PcI",
 +
"bgcolor" : "white",
 +
"color" : "black",
 +
"position" : "T",
 +
"text" : "When we give a heat shock to our bacteria (42 ºC) cI promoter (PcI) is activated, expressing LacI::Das+4 and GFP::Das+4 proteins. Now we are in Green State. ",
 +
"time" : 5000
 +
},
 +
{
 +
"name" : "tour_LacI_Das",
 +
"bgcolor" : "white",
 +
"color" : "black",
 +
"text" : "LacI::Das+4 is Lac promoter repressor. This protein represses PLac and, therefore, Red State. This will assure de maintenance of Green State over Red State in absence of Red State stimulus.",
 +
"position" : "T",
 +
"time" : 5000
 +
},
 +
{
 +
"name" : "tour_GFP_DAS",
 +
"bgcolor" : "white",
 +
"color" : "black",
 +
"text" : "GFP::Das+4 is Green State reporter, which makes our bacteria glow in green when exposed to UV.",
 +
"position" : "T",
 +
"time" : 5000
 +
},
 +
{
 +
"name" : "tour_asRNA",
 +
"bgcolor" : "white",
 +
"color" : "black",
 +
"text" : "Additionally, RybB asRNA is also regulated by PcI promoter so that it is also expressed when we give the heat shock. RybB bind Red State OmpN::SspB’s and OmpN::RFP’s mRNA as they have its binding sequence fused (OmpN protein start sequence). This union prevents these mRNA’s translation, so that we are also eliminating Red State reporter and SspB adaptor when expressing Green State.",
 +
"position" : "T",
 +
"time" : 5000
 +
},
 +
{
 +
"name" : "tour_PLac",
 +
"bgcolor" : "white",
 +
"color" : "black",
 +
"text" : "When we give an IPTG pulse to our bacteria Lac promoter (PLac) is activated, expressing cI (temperature-sensitive), OmpN::SspB and OmpN::RFP proteins. Now we are in Red State. ",
 +
"position" : "B",
 +
"time" : 5000
 +
},
 +
{
 +
"name" : "tour_cI",
 +
"bgcolor" : "white",
 +
"color" : "black",
 +
"text" : "cI is cI promoter repressor. This protein represses PcI and, therefore, Green State. This will assure de maintenance of Red State over Green State in absence of State Green stimulus. As this cI is temperature sensitive it is degraded when we give our bacteria the heat shock necessary for Green State activation.",
 +
"position" : "B",
 +
"time" : 5000
 +
},
 +
{
 +
"name" : "tour_OmpN_RFP",
 +
"bgcolor" : "white",
 +
"color" : "black",
 +
"text" : "OmpN::RFP is Red State reporter, which makes our bacteria glow in red when exposed to UV.",
 +
"position" : "B",
 +
"time" : 5000
 +
},
 +
{
 +
"name" : "tour_OmpN_SspB",
 +
"bgcolor" : "white",
 +
"color" : "black",
 +
"text" : "SspB is the adaptor protein that allows the ClpXP protease to degrade DAS+4 tagged proteins, in this case LacI::DAS+4  and GFP::DAS+4. Therefore, Red State expression also eliminates Green State reporter and Red State repressor. ",
 +
"position" : "B",
 +
"time" : 5000
 +
},
 +
{
 +
"name" : "tour_IPTG",
 +
"bgcolor" : "white",
 +
"color" : "black",
 +
"text" : "This State won’t change again until we give our bacterias the heat shock.",
 +
"position" : "B",
 +
"time" : 5000
 +
},
 +
 
 +
],
 +
//define if steps should change automatically
 +
autoplay = false,
 +
//timeout for the step
 +
showtime,
 +
//current step of the tour
 +
step = 0,
 +
//total number of steps
 +
total_steps = config.length;
 +
 +
//show the tour controls
 +
showControls();
 +
 +
/*
 +
we can restart or stop the tour,
 +
and also navigate through the steps
 +
*/
 +
$('#activatetour').live('click',startTour);
 +
$('#canceltour').live('click',endTour);
 +
$('#endtour').live('click',endTour);
 +
$('#restarttour').live('click',restartTour);
 +
$('#nextstep').live('click',nextStep);
 +
$('#prevstep').live('click',prevStep);
 +
 +
function startTour(){
 +
$('#activatetour').remove();
 +
$('#endtour,#restarttour').show();
 +
if(!autoplay)
 +
                                          if(total_steps > 1)
 +
$('#nextstep').show();
 +
showOverlay();
 +
nextStep();
 +
}
 +
 +
function nextStep(){
 +
if(!autoplay){
 +
if(step > 0)
 +
$('#prevstep').show();
 +
else
 +
$('#prevstep').hide();
 +
if(step == total_steps-1)
 +
$('#nextstep').hide();
 +
else
 +
$('#nextstep').show();
 +
}
 +
if(step >= total_steps){
 +
//if last step then end tour
 +
endTour();
 +
return false;
 +
}
 +
++step;
 +
showTooltip();
 +
}
 +
 +
function prevStep(){
 +
if(!autoplay){
 +
if(step > 2)
 +
$('#prevstep').show();
 +
else
 +
$('#prevstep').hide();
 +
if(step == total_steps)
 +
$('#nextstep').show();
 +
}
 +
if(step <= 1)
 +
return false;
 +
--step;
 +
showTooltip();
 +
}
 +
 +
function endTour(){
 +
step = 0;
 +
if(autoplay) clearTimeout(showtime);
 +
removeTooltip();
 +
hideControls();
 +
hideOverlay();
 +
}
 +
 +
function restartTour(){
 +
step = 0;
 +
if(autoplay) clearTimeout(showtime);
 +
nextStep();
 +
}
 +
 +
function showTooltip(){
 +
//remove current tooltip
 +
removeTooltip();
 +
 +
var step_config = config[step-1];
 +
var $elem = $('.' + step_config.name);
 +
 +
if(autoplay)
 +
showtime = setTimeout(nextStep,step_config.time);
 +
 +
var bgcolor = step_config.bgcolor;
 +
var color = step_config.color;
 +
 +
var $tooltip = $('<div>',{
 +
id : 'tour_tooltip',
 +
className : 'tooltip',
 +
html : '<p>'+step_config.text+'</p><span class="tooltip_arrow"></span>'
 +
}).css({
 +
'display' : 'none',
 +
'background-color' : bgcolor,
 +
'color' : color
 +
});
 +
 +
//position the tooltip correctly:
 +
 +
//the css properties the tooltip should have
 +
var properties = {};
 +
 +
var tip_position = step_config.position;
 +
 +
//append the tooltip but hide it
 +
$('BODY').prepend($tooltip);
 +
 +
//get some info of the element
 +
var e_w = $elem.outerWidth();
 +
var e_h = $elem.outerHeight();
 +
var e_l = $elem.offset().left;
 +
var e_t = $elem.offset().top;
 +
 +
 +
switch(tip_position){
 +
case 'TL' :
 +
properties = {
 +
'left' : e_l,
 +
'top' : e_t + e_h + 'px'
 +
};
 +
$tooltip.find('span.tooltip_arrow').addClass('tooltip_arrow_TL');
 +
break;
 +
case 'TR' :
 +
properties = {
 +
'left' : e_l + e_w - $tooltip.width() + 'px',
 +
'top' : e_t + e_h + 'px'
 +
};
 +
$tooltip.find('span.tooltip_arrow').addClass('tooltip_arrow_TR');
 +
break;
 +
case 'BL' :
 +
properties = {
 +
'left' : e_l + 'px',
 +
'top' : e_t - $tooltip.height() + 'px'
 +
};
 +
$tooltip.find('span.tooltip_arrow').addClass('tooltip_arrow_BL');
 +
break;
 +
case 'BR' :
 +
properties = {
 +
'left' : e_l + e_w - $tooltip.width() + 'px',
 +
'top' : e_t - $tooltip.height() + 'px'
 +
};
 +
$tooltip.find('span.tooltip_arrow').addClass('tooltip_arrow_BR');
 +
break;
 +
case 'LT' :
 +
properties = {
 +
'left' : e_l + e_w + 'px',
 +
'top' : e_t + 'px'
 +
};
 +
$tooltip.find('span.tooltip_arrow').addClass('tooltip_arrow_LT');
 +
break;
 +
case 'LB' :
 +
properties = {
 +
'left' : e_l + e_w + 'px',
 +
'top' : e_t + e_h - $tooltip.height() + 'px'
 +
};
 +
$tooltip.find('span.tooltip_arrow').addClass('tooltip_arrow_LB');
 +
break;
 +
case 'RT' :
 +
properties = {
 +
'left' : e_l - $tooltip.width() + 'px',
 +
'top' : e_t + 'px'
 +
};
 +
$tooltip.find('span.tooltip_arrow').addClass('tooltip_arrow_RT');
 +
break;
 +
case 'RB' :
 +
properties = {
 +
'left' : e_l - $tooltip.width() + 'px',
 +
'top' : e_t + e_h - $tooltip.height() + 'px'
 +
};
 +
$tooltip.find('span.tooltip_arrow').addClass('tooltip_arrow_RB');
 +
break;
 +
case 'T' :
 +
properties = {
 +
'left' : e_l + e_w/2 - $tooltip.width()/2 + 'px',
 +
'top' : e_t + e_h + 'px'
 +
};
 +
$tooltip.find('span.tooltip_arrow').addClass('tooltip_arrow_T');
 +
break;
 +
case 'R' :
 +
properties = {
 +
'left' : e_l - $tooltip.width() + 'px',
 +
'top' : e_t + e_h/2 - $tooltip.height()/2 + 'px'
 +
};
 +
$tooltip.find('span.tooltip_arrow').addClass('tooltip_arrow_R');
 +
break;
 +
case 'B' :
 +
properties = {
 +
'left' : e_l + e_w/2 - $tooltip.width()/2 + 'px',
 +
'top' : e_t - $tooltip.height() + 'px'
 +
};
 +
$tooltip.find('span.tooltip_arrow').addClass('tooltip_arrow_B');
 +
break;
 +
case 'L' :
 +
properties = {
 +
'left' : e_l + e_w  + 'px',
 +
'top' : e_t + e_h/2 - $tooltip.height()/2 + 'px'
 +
};
 +
$tooltip.find('span.tooltip_arrow').addClass('tooltip_arrow_L');
 +
break;
 +
}
 +
 +
 +
/*
 +
if the element is not in the viewport
 +
we scroll to it before displaying the tooltip
 +
*/
 +
var w_t = $(window).scrollTop();
 +
var w_b = $(window).scrollTop() + $(window).height();
 +
//get the boundaries of the element + tooltip
 +
var b_t = parseFloat(properties.top,10);
 +
 +
if(e_t < b_t)
 +
b_t = e_t;
 +
 +
var b_b = parseFloat(properties.top,10) + $tooltip.height();
 +
if((e_t + e_h) > b_b)
 +
b_b = e_t + e_h;
 +
 +
 +
if((b_t < w_t || b_t > w_b) || (b_b < w_t || b_b > w_b)){
 +
$('html, body').stop()
 +
.animate({scrollTop: b_t}, 500, 'easeInOutExpo', function(){
 +
//need to reset the timeout because of the animation delay
 +
if(autoplay){
 +
clearTimeout(showtime);
 +
showtime = setTimeout(nextStep,step_config.time);
 +
}
 +
//show the new tooltip
 +
$tooltip.css(properties).show();
 +
});
 +
}
 +
else
 +
//show the new tooltip
 +
$tooltip.css(properties).show();
 +
}
 +
 +
function removeTooltip(){
 +
$('#tour_tooltip').remove();
 +
}
 +
 +
function showControls(){
 +
/*
 +
we can restart or stop the tour,
 +
and also navigate through the steps
 +
*/
 +
var $tourcontrols  = '<div id="tourcontrols" class="tourcontrols">';
 +
$tourcontrols += '<p>Data Page. Step by Step</p>';
 +
$tourcontrols += '<span class="button" id="activatetour">Start the tour</span>';
 +
if(!autoplay){
 +
$tourcontrols += '<div class="nav"><span class="button" id="prevstep" style="display:none;">< Previous</span>';
 +
$tourcontrols += '<span class="button" id="nextstep" style="display:none;">Next ></span></div>';
 +
}
 +
$tourcontrols += '<a id="restarttour" style="display:none;">Restart the tour</span>';
 +
$tourcontrols += '<a id="endtour" style="display:none;">End the tour</a>';
 +
$tourcontrols += '<span class="close" id="canceltour"></span>';
 +
$tourcontrols += '</div>';
 +
 +
$('BODY').prepend($tourcontrols);
 +
$('#tourcontrols').animate({'right':'30px'},500);
 +
}
 +
 +
function hideControls(){
 +
$('#tourcontrols').remove();
 +
}
 +
 +
function showOverlay(){
 +
var $overlay = '<div id="tour_overlay" class="overlay"></div>';
 +
$('BODY').prepend($overlay);
 +
}
 +
 +
function hideOverlay(){
 +
$('#tour_overlay').remove();
 +
}
 +
 +
});
 +
        </script> 
 +
 
 +
<br>
 +
                          <p>The <strong>Improved Flip Flop</strong> (Part: <a href="http://partsregistry.org/Part:BBa_K510019" target="_blank">BBa_K510019</a> and Part: <a href="http://partsregistry.org/Part:BBa_K510036" target="_blank">BBa_K510036</a>) is based on the basic flip flop (Part: <a href="http://partsregistry.org/Part:BBa_K177038" target="_blank">BBa_K177038</a>) and was built with devices which are in the Registry of Standard Biological Parts. As for the different sequences used in our construction, here it is a brief description of each one:</p>
 +
<br>
 +
<ol>
 +
<li><p> <strong>cI promoter </strong>(Part: <a href="http://partsregistry.org/Part:BBa_R0051" target="_blank">BBa_R0051</a>): The cI regulated promoter is based on the pR promoter from bacteriophage lambda. The promoter has two DNA binding sites for lambda cI repressor BBa_C0051. cI binding results in repression of transcription. The specific sequence used here is based on the cI repressible promoter used in the Elowitz repressilator (and references therein).</p></li>
 +
<li><p><strong>Lac promoter </strong>(Part: <a href="http://partsregistry.org/Part:BBa_R0010" target="_blank">BBa_R0010</a>): This part is an inverting regulator sensitive to LacI and CAP. It contains two protein binding sites. The first binds CAP protein, which is generally present in E.coli and is associated with cell health and availability of glucose. The second one binds LacI protein.</p> </li>
 +
 
 +
<li><p><strong>RBS.3 medium </strong> (Part: <a href="http://partsregistry.org/Part:BBa_B0032" target="_blank">BBa_B0032</a>):This part is a weak RBS based on Ron Weiss thesis.</p> </li>
 +
<li><p><strong>LacI:</strong> Our LacI was taken from E. coli strain K-12 substrain MG1655 chromosome genome and it has a total of 1083 bp.</p></li>
 +
<li><p><strong>GFP </strong>(Part: <a href="http://partsregistry.org/Part:BBa_E0040" target="_blank">BBa_E0040</a>): Green fluorescent protein derived from jellyfish Aequeora victoria wild-type GFP.</p></li>
 +
<li><p><strong>DAS+4:</strong> Short tag at the end of the proteins. For more information see Figure 2 of Proteolysis section.</p></li>
 +
<li><p><strong>Temperature sensitive cI </strong>(Part: <a href="http://partsregistry.org/Part:BBa_K177050" target="_blank">BBa_K177050</a>): Thermosensitive version of the lambda phage repressor. Functions in 30°C and it's inactivated in 42°C</p></li>
 +
<li><p><strong>SspB:</strong> Taken from <a href="http://www.ncbi.nlm.nih.gov/pubmed/16762842" target="_blank">McGinness et al. (2006)</a>. For more information, see Proteolysis section. The OmpN::SspB fusion is detailed in Figure 5 of the asRNA section.</p> </li>
 +
<li><p><strong>RFP </strong>(Part: <a href="http://partsregistry.org/Part:BBa_E1010" target="_blank">BBa_E1010</a>): Highly engineered mutant of red fluorescent protein from Discosoma striata (coral). Monomeric RFP with its excitation peak at  584 nm and its emission peak at 607 nm. The OmpN::RFP fusion is detailed in Figure 5 of the asRNA section.</p></li>
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<li><p><strong>Double terminator </strong>(Part <a href="http://partsregistry.org/Part:BBa_B0015" target="_blank">BBa_B0015</a>): Double terminator consisting of <a href="http://partsregistry.org/Part:BBa_B0010" target="_blank">BBa_B0010</a> and <a href="http://partsregistry.org/Part:BBa_B0012" target="_blank">BBa_B0012</a>.This is the most commonly used terminator and it seems to be reliable.</p></li>
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<li><p><strong>RybB asRNA:</strong> Taken from <a href="http://www.ncbi.nlm.nih.gov/pubmed/19111662"_blank">Bouvier et al.(2008)</a>. For further information see Figure 2 of the asRNA section.</p></li>
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Latest revision as of 22:14, 27 October 2011

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Data Page


The Improved Flip Flop (Part: BBa_K510019 and Part: BBa_K510036) is based on the basic flip flop (Part: BBa_K177038) and was built with devices which are in the Registry of Standard Biological Parts. As for the different sequences used in our construction, here it is a brief description of each one:


  1. cI promoter (Part: BBa_R0051): The cI regulated promoter is based on the pR promoter from bacteriophage lambda. The promoter has two DNA binding sites for lambda cI repressor BBa_C0051. cI binding results in repression of transcription. The specific sequence used here is based on the cI repressible promoter used in the Elowitz repressilator (and references therein).

  2. Lac promoter (Part: BBa_R0010): This part is an inverting regulator sensitive to LacI and CAP. It contains two protein binding sites. The first binds CAP protein, which is generally present in E.coli and is associated with cell health and availability of glucose. The second one binds LacI protein.

  3. RBS.3 medium (Part: BBa_B0032):This part is a weak RBS based on Ron Weiss thesis.

  4. LacI: Our LacI was taken from E. coli strain K-12 substrain MG1655 chromosome genome and it has a total of 1083 bp.

  5. GFP (Part: BBa_E0040): Green fluorescent protein derived from jellyfish Aequeora victoria wild-type GFP.

  6. DAS+4: Short tag at the end of the proteins. For more information see Figure 2 of Proteolysis section.

  7. Temperature sensitive cI (Part: BBa_K177050): Thermosensitive version of the lambda phage repressor. Functions in 30°C and it's inactivated in 42°C

  8. SspB: Taken from McGinness et al. (2006). For more information, see Proteolysis section. The OmpN::SspB fusion is detailed in Figure 5 of the asRNA section.

  9. RFP (Part: BBa_E1010): Highly engineered mutant of red fluorescent protein from Discosoma striata (coral). Monomeric RFP with its excitation peak at 584 nm and its emission peak at 607 nm. The OmpN::RFP fusion is detailed in Figure 5 of the asRNA section.

  10. Double terminator (Part BBa_B0015): Double terminator consisting of BBa_B0010 and BBa_B0012.This is the most commonly used terminator and it seems to be reliable.

  11. RybB asRNA: Taken from Bouvier et al.(2008). For further information see Figure 2 of the asRNA section.

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