Difference between revisions of "Template:Team:Utrecht/MainBody"

 
(27 intermediate revisions by the same user not shown)
Line 762: Line 762:
  
 
<script id="page-home" type="text/template"><!--
 
<script id="page-home" type="text/template"><!--
 +
<div style="position: absolute;top: 0;right: -250px;width: 200px;text-align: center;border: 1px solid gold;padding: 10px;border-radius: 10px;box-sizing: border-box;background: #ffedb8;">
 +
<div style="
 +
    font-weight: bold;
 +
    font-size: 20px;
 +
    color: #c48b00;
 +
    border-bottom: 1px solid #ffd700;
 +
padding-bottom: 15px;
 +
    margin-bottom: 15px;
 +
">Awards</div>
 +
<img width="100" src="https://static.igem.org/mediawiki/2017/thumb/a/a2/UU_gold_medal.png/240px-UU_gold_medal.png"><br><div style="font-size: 15px;color: #c48b00; border-bottom: 1px solid #ffd700; padding-bottom: 15px; margin-top: 5px;">Gold medal</div>
 +
<div style="margin-top: 15px; margin-bottom: 10px; font-size: 15px;color: #c48b00;"><b>Nominated</b><br />Best integrated human practices</div>
 +
</div>
 +
 
<div class="page-heading">The OUTCASST two-component system</div>
 
<div class="page-heading">The OUTCASST two-component system</div>
−
This year, Utrecht University participates in the iGEM for the first time.  
+
This year is the debut year for the Utrecht University iGEM team. Our team has developed an easy to use and cheap DNA detection kit for disease diagnosis in areas of the world where advanced diagnostic technologies are not available. We call our system ‘OUTCASST’, which stands for ‘Out-of-cell Crispr-Activated Sequence-specific Signal Transducer’.
−
We aim to create a cheap DNA detection kit for disease diagnosis that is easy to use and does not rely on complicated sequencing technologies.  
+
−
We call our system ‘OUTCASST’, which stands for ‘Out-of-cell Crispr-Activated Sequence-specific Signal Transducer’.
+
 
 
 
<br />
 
<br />
Line 778: Line 789:
 
<h2 class="subhead" id="subhead-2">The problem</h2>
 
<h2 class="subhead" id="subhead-2">The problem</h2>
 
Disease diagnosis is of great importance for healthcare.  
 
Disease diagnosis is of great importance for healthcare.  
−
In developing countries, diagnoses are often based on limited information, even though accurate disease determination based on pathogen specific DNA is possible through sequencing technologies. These technologies, however, require specialised equipment and expertise that simply is not available everywhere.  
+
In developing countries, diagnoses are often based on limited information, even though accurate disease determination based on pathogen specific DNA is possible through sequencing technologies. These technologies, however, require specialised equipment and expertise that simply is not available in developing parts of the world.  
−
With the OUTCASST two-component system and detection kit, we hope to alleviate this problem.
+
The OUTCASST two-component system and detection kit was designed to alleviate this problem.
  
 
<center>
 
<center>
Line 789: Line 800:
 
 
 
<div id="popover-1" style="display: none;">
 
<div id="popover-1" style="display: none;">
−
Binding of components with search-specific gRNA sequences.
+
First, guide RNA (gRNA) needs to be added, which is complementary to the DNA sequence you want to detect.
 
<br>
 
<br>
 
<br>
 
<br>
Line 796: Line 807:
 
 
 
<div id="popover-2" style="display: none;">
 
<div id="popover-2" style="display: none;">
−
DNA sample fragment binds to one of the components.
+
dCas9 and dCpf1 will bind their corresponding gRNA.
 
<br>
 
<br>
 
<br>
 
<br>
Line 803: Line 814:
 
 
 
<div id="popover-3" style="display: none;">
 
<div id="popover-3" style="display: none;">
−
Fragment binding with both components induces co-localization.
+
DNA from the sample that matches the gRNA will first bind to one of the proteins.
 
<br>
 
<br>
 
<br>
 
<br>
Line 810: Line 821:
 
 
 
<div id="popover-4" style="display: none;">
 
<div id="popover-4" style="display: none;">
−
Protease cleaves, transcription factor is released from complex.
+
Once the DNA fragment binds the other protein, the system will co-localize. This allows the protease to release the transcription factor from the complex, resulting in an intracellular signal.
 
<br>
 
<br>
 
<br>
 
<br>
Line 833: Line 844:
 
 
 
<h2 class="subhead" id="subhead-3">The system</h2>
 
<h2 class="subhead" id="subhead-3">The system</h2>
−
The OUTCASST two-component system consists of two proteins that span the membrane.  
+
The OUTCASST two-component system consists of two synthetic receptors that span the membrane.  
 
One of the proteins has a Cas9 protein attached as an extracellular domain, the other has a Cpf1 protein attached.  
 
One of the proteins has a Cas9 protein attached as an extracellular domain, the other has a Cpf1 protein attached.  
 
Both proteins can be given a guide RNA that makes them bind to a specific, user-chosen, complementary sequence.  
 
Both proteins can be given a guide RNA that makes them bind to a specific, user-chosen, complementary sequence.  
−
When both proteins bind a single DNA fragment from a sample, possibly containing pathogen DNA, they co-localize, so that a protease releases a transcription factor which then induces an intracellular reporter mechanism, resulting in a stained or fluorescent cell.
+
When both proteins bind a single DNA fragment from a sample, possibly containing pathogen DNA, they co-localize, so that a protease releases a transcription factor which then induces an intracellular reporter mechanism such as a luminescent or fluorescent signal.
 +
<br><br>
 +
A final product would include the use of so-called anhydrobiotic insect <i>Polypedilum vanderplanki</i> cells, which can be air-dried, allowing them to be stored for prolonged periods of time at room temperature. The OUTCASST system is cheap to produce, store and ship, and requires nothing more then a simple microscope as a readout.
 
 
 +
 +
 
 +
 
 +
 
 +
 +
 
 +
 +
 
 +
 +
 +
 
 +
 
<script type="text/javascript" language="JavaScript">
 
<script type="text/javascript" language="JavaScript">
 
function tut_goto(step)
 
function tut_goto(step)
Line 848: Line 873:
 
{
 
{
 
jQuery("#link-" + i).removeClass("selected");
 
jQuery("#link-" + i).removeClass("selected");
 +
jQuery("#link-" + i).removeClass("pulsing");
 
jQuery("#popover-" + i).dxPopover("hide");
 
jQuery("#popover-" + i).dxPopover("hide");
 
jQuery("#figure-" + i).fadeOut("5");
 
jQuery("#figure-" + i).fadeOut("5");
Line 869: Line 895:
 
{
 
{
 
jQuery("#link-" + i).removeClass("selected");
 
jQuery("#link-" + i).removeClass("selected");
 +
jQuery("#link-" + i).removeClass("pulsing");
 
jQuery("#popover-" + i).dxPopover("hide");
 
jQuery("#popover-" + i).dxPopover("hide");
 
jQuery("#figure-" + i).fadeOut("5");
 
jQuery("#figure-" + i).fadeOut("5");
Line 898: Line 925:
 
var title;
 
var title;
 
 
−
if(i == 1)
+
/*if(i == 1)
 
title = "Guide RNA";
 
title = "Guide RNA";
 
else if(i == 2)
 
else if(i == 2)
Line 904: Line 931:
 
else if(i == 3)
 
else if(i == 3)
 
title = "Signal transduction";
 
title = "Signal transduction";
 +
else if(i == 4)
 +
title = "Signal transduction";*/
 +
 +
if(i == 1)
 +
title = "Start";
 +
else if(i == 2)
 +
title = "gRNA binding";
 +
else if(i == 3)
 +
title = "DNA binding";
 
else if(i == 4)
 
else if(i == 4)
 
title = "Signal transduction";
 
title = "Signal transduction";
Line 1,037: Line 1,073:
 
<br><br>
 
<br><br>
 
Additionally, together with team Wageningen_UR a final experiment was done to verify that the protein in the medium was indeed secreted instead of due to involuntary cell lysis (see <a onclick="return change_page('collaborations', 1)" href="collaborations">Collaborations</a>).  
 
Additionally, together with team Wageningen_UR a final experiment was done to verify that the protein in the medium was indeed secreted instead of due to involuntary cell lysis (see <a onclick="return change_page('collaborations', 1)" href="collaborations">Collaborations</a>).  
−
This experiment was done in duplo, by members from both team Wageningen_UR and team Utrecht, individually, to provide independent verification of the result. This final experiment was done according to a collaboration protocol that was shared with the Wageningen_UR team [Experimental\Protocols\Wiki ready\Experimental\Protocols\Wiki ready.pdf].
+
This experiment was done in duplo, by members from both team Wageningen_UR and team Utrecht, individually, to provide independent verification of the result. This final experiment was done according to a collaboration protocol that was shared with the Wageningen_UR team <a target=_BLANK href="https://static.igem.org/mediawiki/2017/4/40/UuProtocolCollaborationWageningen.pdf" class="pdf pdf-inline"></a>.
 
<br><br>
 
<br><br>
 
<b>Endonuclease activity assay</b>
 
<b>Endonuclease activity assay</b>
Line 1,372: Line 1,408:
 
<h2 class="subhead" id="subhead-6">Supplementary</h2>
 
<h2 class="subhead" id="subhead-6">Supplementary</h2>
  
−
Plasmid nanodrop results can be found in a downloadable <a href="">document</a>.
+
Plasmid nanodrop results can be downloaded here: <a target=_BLANK href="https://static.igem.org/mediawiki/2017/b/b1/UU_-_Assembly_supplementary.pdf" class="pdf pdf-inline"></a>.
 
</script>
 
</script>
  
Line 1,421: Line 1,457:
 
<br><br>
 
<br><br>
 
By comparing the two figures, we can now see that the probability of cleavage for the slow cleaver is much smaller than that of the fast cleaver in the timespan that the transient complex persists. Of course, the concentration of the substrate-mediated complex decreases over time, so the total cleavage decreases when it cleaves later. To investigate how much the transient and substrate-mediated complex contribute to signal development for both Protease Chain variants, we define:
 
By comparing the two figures, we can now see that the probability of cleavage for the slow cleaver is much smaller than that of the fast cleaver in the timespan that the transient complex persists. Of course, the concentration of the substrate-mediated complex decreases over time, so the total cleavage decreases when it cleaves later. To investigate how much the transient and substrate-mediated complex contribute to signal development for both Protease Chain variants, we define:
−
<br><br>
+
 
−
S'(t) = p_c (t)⋅C(t)⋅(1-∫_0^t p_c  dt)
+
<center><img height="75" src="https://static.igem.org/mediawiki/2017/b/b5/UuModelingEquation1.png"></center>
−
<br><br>
+
 
 
Wherein S’ is the increase in signal, given by the probability of cleavage (p<sub>c</sub>) for the remaining uncleaved complex. The remaining uncleaved complex is given by the remaining complex fraction (C) and how likely it is that it has not already been cleaved (one minus the integral of p<sub>c</sub> from 0 until that timepoint).
 
Wherein S’ is the increase in signal, given by the probability of cleavage (p<sub>c</sub>) for the remaining uncleaved complex. The remaining uncleaved complex is given by the remaining complex fraction (C) and how likely it is that it has not already been cleaved (one minus the integral of p<sub>c</sub> from 0 until that timepoint).
 
<br><br>
 
<br><br>
Line 1,514: Line 1,550:
 
<br><br>
 
<br><br>
 
From these relations, it is already clear that there can only be a stable signal potential, i.e. a stable fraction of the target chains remains uncleaved, when the production of target chain outweighs the decay and cleavage of it, whilst the acquisition of cleaved target chain is balanced by its decay, such that the following conditions apply:
 
From these relations, it is already clear that there can only be a stable signal potential, i.e. a stable fraction of the target chains remains uncleaved, when the production of target chain outweighs the decay and cleavage of it, whilst the acquisition of cleaved target chain is balanced by its decay, such that the following conditions apply:
−
<br><br>
+
<center><img height="50" src="https://static.igem.org/mediawiki/2017/9/91/UuModelingEquation2.png"></center>
−
p_T=d ([T]+[T:S]+[T:S:P])+k_5 [T:S:P]
+
<center><img height="45" src="https://static.igem.org/mediawiki/2017/e/e0/UuModelingEquation3.png"></center>
−
<br><br>
+
−
k_5 [T:S:P]=d([T_c]+[T_c:S]+[T_c:S:P])
+
−
<br><br>
+
 
Which together forms:
 
Which together forms:
−
<br><br>
+
<br>
−
p_T=d ([T]+[T:S]+[T:S:P]+[T_c]+[T_c:S]+[T_c:S:P])
+
<center><img height="45" src="https://static.igem.org/mediawiki/2017/9/90/UuModelingEquation4.png"></center>
−
<br><br>
+
<br>
 
However, the concentrations of the intermediary complexes is dependent on the concentration and hence production of protease chain P. We know that, at equilibrium concentrations, the following must hold:
 
However, the concentrations of the intermediary complexes is dependent on the concentration and hence production of protease chain P. We know that, at equilibrium concentrations, the following must hold:
 
<br><br>
 
<br><br>
−
p_P=d([P]+[P:S]+[T:S:P]+[T_c:S:P])
+
<center><img height="45" src="https://static.igem.org/mediawiki/2017/4/4b/UuModelingEquation5.png"></center>
−
<br><br>
+
<br>
 
By combining these equations, we can get an expression for T depending on the production, decay and complex concentrations:
 
By combining these equations, we can get an expression for T depending on the production, decay and complex concentrations:
 
<br><br>
 
<br><br>
−
[T]=p_T/p_P ([P]+[P:S]+(p_T/p_P -1)([T:S:P]+[T_c:S:P])-([T:S]+[T_c]+[T_c:S])
+
<center><img height="50" src="https://static.igem.org/mediawiki/2017/b/b9/UuModelingEquation6.png"></center>
−
<br><br>
+
<br>
 
By assuming that the DNA binding dynamics of the system occur at much faster timescales than protein production and decay, we can assume that the substrate binding of the protease and target chains is at steady state, yielding the following expressions:
 
By assuming that the DNA binding dynamics of the system occur at much faster timescales than protein production and decay, we can assume that the substrate binding of the protease and target chains is at steady state, yielding the following expressions:
 
<br><br>
 
<br><br>
−
[T:S] = (k_1  [S] [T] + k_4  [T:S:P])/(d + k_2  + k_3  [P])
+
<center><img height="75" src="https://static.igem.org/mediawiki/2017/0/0d/UuModelingEquation7.png"></center>
 +
<center><img height="75" src="https://static.igem.org/mediawiki/2017/1/19/UuModelingEquation8.png"></center>
 +
<center><img height="75" src="https://static.igem.org/mediawiki/2017/e/ee/UuModelingEquation9.png"></center>
 +
<br>
 +
We could then substitute these three concentrations for their expressions in the expression of the target chain concentration. Making further quasi steady state assumptions on the formation of the pre-cleavage and post-cleavage complexes reduces the expression by two more dependencies. This was done in mathematica notebook, found <a target=_BLANK href="https://static.igem.org/mediawiki/2017/2/21/UuModelingQSSAWorkouts.txt" class="url_external">here</a>.
 
<br><br>
 
<br><br>
−
[T_c:S] =  (k_1  [S] [T_c] + k_4  [T_c:S:P])/(d + k_2  + k_3  [P])
+
 
 +
The resulting expression shows that the concentration of target chain depends on: 1) The concentrations of its production relative to the production of the protease chain. 2) The concentration of protease chain. 3) The concentration of substrate. 4) How much cleaved target chain is available to trap said substrate.
 
<br><br>
 
<br><br>
−
[P:S]=(k_3  [P] [S] + k_2  [T_c:S:P] + k_2  [T:S:P])/(d + k_4  + k_1 ([T] + [Tc]))
+
The fraction of the total target chain that is cleaved is a saturation function that depends on substrate and protease chain concentrations with respect to how quickly the function's saturation point is attained. We can minimize the cleaved target chain fraction, and the occurrence of substrate trapping with it, by simply having a target chain amount that is much larger than that of the substrate.
 
<br><br>
 
<br><br>
−
We could then substitute these three concentrations for their expressions in the expression of the target chain concentration. Making further quasi steady state assumptions on the formation of the pre-cleavage and post-cleavage complexes reduces the expression by two more dependencies. This was done in mathematica notebook, found <a target=_BLANK href="https://static.igem.org/mediawiki/2017/2/21/UuModelingQSSAWorkouts.txt" class="url_external">here</a>.
+
In short, the more substrate there is available per target chain, the less signal per substrate molecule we can get as ineffectual target chain concentration increases.  
 
<br><br>
 
<br><br>
−
[INSERT WILL FOLLOW]
+
The equations suggest that there is a theoretical optimum for the production rates of both chains, relative to the substrate concentration in the system. Due to time constraints, the expression for this optimum could not be given. The methods given in the mathematica script provided here should be able to reach this solution, given enough time. The meaning of such an optimum, however, is questionable. As the substrate concentrations in our toolkit may differ greatly depending on severity of infection and chance, optimization through growth-rates would need to be different per sample. In conclusion, the only effective optimization of protein productions is to make sure that the protein concentrations greatly exceed the sample concentration of DNA sequence we wish to detect.
  
 
<br><br>
 
<br><br>
Line 1,658: Line 1,696:
  
 
<script id="page-stakeholders" type="text/template">
 
<script id="page-stakeholders" type="text/template">
−
As OUTCASST is a system with a very broad application, we wanted to find the most suitable end users and focus our design on their needs and restrictions. To achieve this goal, we have interviewed multiple professionals from different backgrounds. In these conversations, we tried to discover strengths and weaknesses of our system and design with regard to existing techniques and whether the OUTCASST system would be useful in the professions of the interviewed individuals. If not, we tried to figure out in what direction it might prove more useful or what aspects needed to be improved. In addition, we also discussed safety issues and technical aspects of our toolkit design.  
+
As OUTCASST is a system with a very broad application, we wanted to find the most suitable end users and focus our design on their needs and restrictions. To achieve this goal, we have interviewed multiple professionals from different backgrounds. In these conversations, we tried to discover strengths and weaknesses of our system and design with regard to existing techniques and whether the OUTCASST system would be useful in the professions of the interviewed individuals. If not, we tried to figure out in what direction it might prove more useful or what aspects needed to be improved. In addition, we also discussed safety issues and technical aspects of our toolkit design, of which the outcomes were compiled on their own respective pages:  <a onclick="return change_page('safety', 1)" href="safety">Safety</a> and <a onclick="return change_page('product-design', 1)" href="product-design">Design & Integration</a>.
 
<br><br>
 
<br><br>
 
In the short video below, we show a summary of the journey we made to get to our end users. Besides this summary, more elaborate descriptions of each interview can be found below.
 
In the short video below, we show a summary of the journey we made to get to our end users. Besides this summary, more elaborate descriptions of each interview can be found below.
 
<br><br>
 
<br><br>
−
<video style="width: 100%;" poster="" controls>
+
 
−
<source src="" type='video/mp4'/>
+
<video onclick="this.paused?this.play():this.pause();" style="width: 100%; cursor: pointer;" poster="https://static.igem.org/mediawiki/2017/8/8d/UU-stakeholders-video-poster.png" controls>
−
<source src="" type='video/ogg; codecs="theora, vorbis"'/>
+
<source src="https://static.igem.org/mediawiki/2017/6/6f/UuHPEndUsersVid.mp4" type='video/mp4'/>
−
<source src="" type='video/webm; codecs="vp8, vorbis"'/>
+
−
<a href=""><img border="0" src="" alt="Click to view on Youtube" width="100%"></a>
+
 
<p style="font-style:italic;color:red;border-style:solid;border-width:2px;border-color:red">Your browser either does not support HTML5 or cannot handle MediaWiki open video formats. Please consider upgrading your browser, installing the appropriate plugin or switching to a Firefox or Chrome install.</p>
 
<p style="font-style:italic;color:red;border-style:solid;border-width:2px;border-color:red">Your browser either does not support HTML5 or cannot handle MediaWiki open video formats. Please consider upgrading your browser, installing the appropriate plugin or switching to a Firefox or Chrome install.</p>
 
</video>
 
</video>
 +
 
<div class="shuffle-container" style="position: relative; margin-top: 30px; margin-bottom: 50px; width: 900px; margin-left: -75px;">
 
<div class="shuffle-container" style="position: relative; margin-top: 30px; margin-bottom: 50px; width: 900px; margin-left: -75px;">
 
<div style="position: absolute; top: 200px; left: 350px; z-index: 1;">
 
<div style="position: absolute; top: 200px; left: 350px; z-index: 1;">
Line 1,674: Line 1,711:
 
</div>
 
</div>
 
   <div class="js-grid my-shuffle shuffle" style="height: 520.262px; transition: height 250ms cubic-bezier(0.4, 0, 0.2, 1);">
 
   <div class="js-grid my-shuffle shuffle" style="height: 520.262px; transition: height 250ms cubic-bezier(0.4, 0, 0.2, 1);">
−
   <figure class="js-item column col-span shuffle-item shuffle-item--visible" style="position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity; transform: translate(0px, 0px) scale(1);">
+
   <figure class="js-item column col-span shuffle-item shuffle-item--visible" onclick="jQuery('html, body').animate({scrollTop: jQuery('#item-doctors').offset().top - 150}, 500);" style="cursor: pointer; position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity; transform: translate(0px, 0px) scale(1);">
 
       <div class="aspect aspect--32x9">
 
       <div class="aspect aspect--32x9">
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/f/fe/Marit_de_Wit.jpg"></div>
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/f/fe/Marit_de_Wit.jpg"></div>
−
<div style="position: absolute; bottom: 5px; left: 5px; right: 5px; color: white; font-size: 13px; line-height: 100%;">
 
−
Marit de Wit<br>
 
−
<span style="font-style: italic;">Doctors without borders</span>
 
−
</div>
 
 
       </div>
 
       </div>
 
     </figure>
 
     </figure>
−
     <figure class="js-item column shuffle-item shuffle-item--visible" style="position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(450px, 0px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
+
     <figure class="js-item column shuffle-item shuffle-item--visible" onclick="jQuery('html, body').animate({scrollTop: jQuery('#item-westerdijk').offset().top - 150}, 500);" style="cursor: pointer; position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(450px, 0px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
 
       <div class="aspect aspect--9x80">
 
       <div class="aspect aspect--9x80">
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/f/fc/Bert_Gerrits_van_den_Ende.jpg"></div>
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/f/fc/Bert_Gerrits_van_den_Ende.jpg"></div>
 
       </div>
 
       </div>
 
     </figure>
 
     </figure>
−
<figure class="js-item column shuffle-item shuffle-item--visible" style="position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(675px, 0px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
+
<figure class="js-item column shuffle-item shuffle-item--visible" onclick="jQuery('html, body').animate({scrollTop: jQuery('#item-cancer').offset().top - 150}, 500);" style="cursor: pointer; position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(675px, 0px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
 
       <div class="aspect aspect--9x80">
 
       <div class="aspect aspect--9x80">
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/6/63/Hans_Bos.jpg"></div>
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/6/63/Hans_Bos.jpg"></div>
 
       </div>
 
       </div>
 
     </figure>
 
     </figure>
−
<figure class="js-item column shuffle-item shuffle-item--visible" style="position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(225px, 129px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
+
<figure class="js-item column shuffle-item shuffle-item--visible" onclick="jQuery('html, body').animate({scrollTop: jQuery('#item-parasitology').offset().top - 150}, 500);" style="cursor: pointer; position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(225px, 129px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
 
       <div class="aspect aspect--16x9">
 
       <div class="aspect aspect--16x9">
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/8/8e/Jaap_van_Hellemond.jpg"></div>
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/8/8e/Jaap_van_Hellemond.jpg"></div>
 
       </div>
 
       </div>
 
     </figure>
 
     </figure>
−
<figure class="js-item column col-span shuffle-item shuffle-item--visible" style="position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(225px, 260px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
+
<figure class="js-item column col-span shuffle-item shuffle-item--visible" onclick="jQuery('html, body').animate({scrollTop: jQuery('#item-amca').offset().top - 150}, 500);" style="cursor: pointer; position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(225px, 260px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
 
       <div class="aspect aspect--32x9">
 
       <div class="aspect aspect--32x9">
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/4/4b/Jet_and_Ruud.jpg"></div>
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/4/4b/Jet_and_Ruud.jpg"></div>
 
       </div>
 
       </div>
 
     </figure>
 
     </figure>
−
<figure class="js-item column col-span shuffle-item shuffle-item--visible" style="position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(0px, 389px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
+
<figure class="js-item column col-span shuffle-item shuffle-item--visible" onclick="jQuery('html, body').animate({scrollTop: jQuery('#item-genomediagnostics').offset().top - 150}, 500);" style="cursor: pointer; position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(0px, 389px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
 
       <div class="aspect aspect--32x9">
 
       <div class="aspect aspect--32x9">
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/c/cd/Patrick_en_Pieter-Jaap.jpg"></div>
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/c/cd/Patrick_en_Pieter-Jaap.jpg"></div>
 
       </div>
 
       </div>
 
     </figure>
 
     </figure>
−
<figure class="js-item column shuffle-item shuffle-item--visible" style="position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(0px, 129px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
+
<figure class="js-item column shuffle-item shuffle-item--visible" onclick="jQuery('html, body').animate({scrollTop: jQuery('#item-cancer').offset().top - 150}, 500);" style="cursor: pointer; position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(0px, 129px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
 
       <div class="aspect aspect--9x80">
 
       <div class="aspect aspect--9x80">
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/5/59/Hugo_Snippert_%282%29.jpg"></div>
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/5/59/Hugo_Snippert_%282%29.jpg"></div>
 
       </div>
 
       </div>
 
     </figure>
 
     </figure>
−
<figure class="js-item column shuffle-item shuffle-item--visible" style="position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(675px, 260px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
+
<figure class="js-item column shuffle-item shuffle-item--visible" onclick="jQuery('html, body').animate({scrollTop: jQuery('#item-nfi').offset().top - 150}, 500);" style="cursor: pointer; position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(675px, 260px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
 
       <div class="aspect aspect--9x80">
 
       <div class="aspect aspect--9x80">
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/d/d0/Titia_Sijen.JPG"></div>
 
         <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/d/d0/Titia_Sijen.JPG"></div>
 +
      </div>
 +
    </figure>
 +
<figure class="js-item column shuffle-item shuffle-item--visible" style="position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(450px, 389px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
 +
      <div class="aspect aspect--9x80" style="padding-bottom: 70%;">
 +
        <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/1/10/Uu-hp-team-photo.png"></div>
 
       </div>
 
       </div>
 
     </figure>
 
     </figure>
Line 1,724: Line 1,762:
 
<section class="timeline" style="width: 1000px; margin-left: -100px;">
 
<section class="timeline" style="width: 1000px; margin-left: -100px;">
 
   <div class="timeline-container" style="width: 100%;">
 
   <div class="timeline-container" style="width: 100%;">
−
     <div class="timeline-item">
+
     <div id="item-westerdijk" class="timeline-item">
  
 
       <div class="timeline-img"></div>
 
       <div class="timeline-img"></div>
Line 1,737: Line 1,775:
  
 
     </div>
 
     </div>
−
     <div class="timeline-item">
+
     <div id="item-genomediagnostics" class="timeline-item">
  
 
       <div class="timeline-img"></div>
 
       <div class="timeline-img"></div>
Line 1,756: Line 1,794:
 
     </div>
 
     </div>
 
 
−
<div class="timeline-item">
+
<div id="item-amca" class="timeline-item">
  
 
       <div class="timeline-img"></div>
 
       <div class="timeline-img"></div>
Line 1,771: Line 1,809:
 
     </div>
 
     </div>
 
 
−
<div class="timeline-item">
+
<div id="item-cancer" class="timeline-item">
  
 
       <div class="timeline-img"></div>
 
       <div class="timeline-img"></div>
Line 1,788: Line 1,826:
 
     </div>   
 
     </div>   
 
 
−
<div class="timeline-item">
+
<div id="item-nfi" class="timeline-item">
  
 
       <div class="timeline-img"></div>
 
       <div class="timeline-img"></div>
Line 1,805: Line 1,843:
 
     </div>   
 
     </div>   
 
 
−
<div class="timeline-item">
+
<div id="item-doctors" class="timeline-item">
  
 
       <div class="timeline-img"></div>
 
       <div class="timeline-img"></div>
Line 1,821: Line 1,859:
 
     </div>   
 
     </div>   
 
 
−
<div class="timeline-item">
+
<div id="item-parasitology" class="timeline-item">
  
 
       <div class="timeline-img"></div>
 
       <div class="timeline-img"></div>
Line 1,837: Line 1,875:
 
     </div>
 
     </div>
 
 
−
<div class="timeline-item">
+
<div id="item-clinical" class="timeline-item">
  
 
       <div class="timeline-img"></div>
 
       <div class="timeline-img"></div>
Line 1,875: Line 1,913:
 
sub { vertical-align: sub; font-size: smaller; }
 
sub { vertical-align: sub; font-size: smaller; }
 
sup { vertical-align: super; font-size: smaller; }
 
sup { vertical-align: super; font-size: smaller; }
 +
 +
.uu-table { border: 0 !important; margin: 0 !important; }
 +
.uu-table td { border: 0 !important; padding: 0 !important; }
  
 
#modal-overlay
 
#modal-overlay
Line 2,068: Line 2,109:
 
</script>
 
</script>
  
−
<script id="page-product-design" type="text/template">
+
<script id="page-product-design" type="text/template"><!--
 
<div class="page-heading">Integrated human practices: design of OUTCASST</div>
 
<div class="page-heading">Integrated human practices: design of OUTCASST</div>
 
Altogether, we gathered information from many different fields and perspectives. All of these views helped us to optimize our design to use OUTCASST as a tool for diagnosing Chagas disease. Since we want our tool to be easy to use in the field and rural areas, there are different aspects that should be taken into account. Robustness and resistance of the toolkit to temperature fluctuations and humidity are chief among these. In addition, it is important not to rely on material and storage containers such as fridges or freezers (Marit de Wit, Doctors without borders).  
 
Altogether, we gathered information from many different fields and perspectives. All of these views helped us to optimize our design to use OUTCASST as a tool for diagnosing Chagas disease. Since we want our tool to be easy to use in the field and rural areas, there are different aspects that should be taken into account. Robustness and resistance of the toolkit to temperature fluctuations and humidity are chief among these. In addition, it is important not to rely on material and storage containers such as fridges or freezers (Marit de Wit, Doctors without borders).  
 
<br><br>
 
<br><br>
  
−
<b>INTERACTIVE SCREEN</b>
+
<style type="text/css">
 +
.tutorial-design .tutorial_button { width: 25px; height: 25px;
 +
    font-size: 1.2em;
 +
    line-height: 25px;
 +
border: 3px solid #ffb252
 +
}
  
−
<br><br>
+
.tutorial-design .container { background: transparent; z-index: 1; }
 +
</style>
 +
 
 +
<div class="tutorial tutorial-design" style="position: relative; width: 100%; display: inline-block;">
 +
<img id="figure-1" style="position: absolute; top: 0; right: 25px; width: 600px;" src="https://static.igem.org/mediawiki/2017/9/97/UU-hp-0.png">
 +
<img id="figure-2" style="position: absolute; top: 0; right: 25px; width: 600px; display: none;" src="https://static.igem.org/mediawiki/2017/4/4a/UU-hp-1.png">
 +
<img id="figure-3" style="position: absolute; top: 0; right: 25px; width: 600px; display: none;" src="https://static.igem.org/mediawiki/2017/4/49/UU-hp-2.png">
 +
<img id="figure-4" style="position: absolute; top: 0; right: 25px; width: 600px; display: none;" src="https://static.igem.org/mediawiki/2017/6/61/UU-hp-3.png">
 +
<img id="figure-5" style="position: absolute; top: 0; right: 25px; width: 600px; display: none;" src="https://static.igem.org/mediawiki/2017/3/37/UU-hp-4.png">
 +
<img id="figure-6" style="position: absolute; top: 0; right: 25px; width: 600px; display: none;" src="https://static.igem.org/mediawiki/2017/5/56/UU-hp-5.png">
 +
<img id="figure-7" style="position: absolute; top: 0; right: 25px; width: 600px; display: none;" src="https://static.igem.org/mediawiki/2017/c/c8/UU-hp-6.png">
 +
<img id="figure-8" style="position: absolute; top: 0; right: 25px; width: 600px; display: none;" src="https://static.igem.org/mediawiki/2017/d/dd/UU-hp-7.png">
 +
<img id="figure-9" style="position: absolute; top: 0; right: 25px; width: 600px; display: none;" src="https://static.igem.org/mediawiki/2017/4/4d/UU-hp-8.png">
 +
 +
<div style="clear: both;"></div>
 +
 +
<div id="popover-1" style="display: none;">
 +
The OUTCASST toolkit consists of dried cells in a closed off compartment, two medium compartments (green) and a lysis and reset buffer compartment (purple).
 +
<br>
 +
<br>
 +
<a href="javascript: void(0);" class="btn blue" id="goto-2" style="margin: 0; padding: 10px 25px; font-size: 18px;">Next</a>
 +
</div>
 +
 
 +
<div id="popover-2" style="display: none;">
 +
First, the seal on one of the medium compartments is broken so medium goes onto the cells. The cells will now be rejuvenated and allowed to acclimatize in 12 hours.
 +
<br>
 +
<br>
 +
<a href="javascript: void(0);" class="btn blue" id="goto-3" style="margin: 0; padding: 10px 25px; font-size: 18px;">Next</a>
 +
</div>
 +
 
 +
<div id="popover-3" style="display: none;">
 +
After 12 hours, a patient's sample can be added to the test kit. The sample will enter the filtering compartment, which contains chemicals that bind all sorts of unwanted chemicals.
 +
<br>
 +
<br>
 +
<a href="javascript: void(0);" class="btn blue" id="goto-4" style="margin: 0; padding: 10px 25px; font-size: 18px;">Next</a>
 +
</div>
 +
 
 +
<div id="popover-4" style="display: none;">
 +
The seal on the lysis buffer compartment is broken. The lysis buffer causes any intact cells to burst, releasing their DNA and internal contents. Unwanted cell debris is bound by the filter molecules, coated to the inside of the filtering compartment.
 +
<br>
 +
<br>
 +
<a href="javascript: void(0);" class="btn blue" id="goto-5" style="margin: 0; padding: 10px 25px; font-size: 18px;">Next</a>
 +
</div>
 +
 +
<div id="popover-5" style="display: none;">
 +
The seal on the reset buffer compartment is broken. Reset buffer, sample and lysis buffer mingle, neutralizing each other and resulting in an isotonic mixture that will not harm the sensor cells.
 +
<br>
 +
<br>
 +
<a href="javascript: void(0);" class="btn blue" id="goto-6" style="margin: 0; padding: 10px 25px; font-size: 18px;">Next</a>
 +
</div>
 +
 +
<div id="popover-6" style="display: none;">
 +
The second medium pocket is used to resuspend the gRNA. We kept the gRNA dry until now to prevent degradation of this sensitive chemical.
 +
<br>
 +
<br>
 +
<a href="javascript: void(0);" class="btn blue" id="goto-7" style="margin: 0; padding: 10px 25px; font-size: 18px;">Next</a>
 +
</div>
 +
 +
<div id="popover-7" style="display: none;">
 +
The dissolved gRNA is released onto the sensor cells. The protein chains on the surface of these cells can now bind with the gRNA, making the sensor cells specific for DNA that is complementary to the gRNA they were provided with.
 +
<br>
 +
<br>
 +
<a href="javascript: void(0);" class="btn blue" id="goto-8" style="margin: 0; padding: 10px 25px; font-size: 18px;">Next</a>
 +
</div>
 +
 +
<div id="popover-8" style="display: none;">
 +
The seal to the waste compartment is broken. As this compartment was under a slight vacuum, a part of the medium is sucked away from the cells, making room for the sample.
 +
<br>
 +
<br>
 +
<a href="javascript: void(0);" class="btn blue" id="goto-9" style="margin: 0; padding: 10px 25px; font-size: 18px;">Next</a>
 +
</div>
 +
 +
<div id="popover-9" style="display: none;">
 +
The seal to the waste compartment is closed again and so are the seals to the medium pockets. The lysed and filtered sample, containing the patient's DNA, is now brought to the cells. If the right DNA sequence is present, the cells will detect it and give an output signal.
 +
</div>
 +
 +
<div class="container" style="position: absolute; top: 20px; left: 20px; width: 40px; z-index: 2;">
 +
<span id="link-1" class="tutorial_button selected pulsing" style="font-size: 17px; width: 40px; height: 40px; line-height: 40px; border: 5px solid #ffb252;">Start</span>
 +
</div>
 +
 +
<div class="container" style="position: absolute; top: 80px; left: 30px;">
 +
<span id="link-2" class="tutorial_button">2</span>
 +
</div>
 +
 +
<div class="container" style="position: absolute; top: 120px; left: 30px;">
 +
<span id="link-3" class="tutorial_button">3</span>
 +
</div>
 +
 +
<div class="container" style="position: absolute; top: 160px; left: 30px;">
 +
<span id="link-4" class="tutorial_button">4</span>
 +
</div>
 +
 +
<div class="container" style="position: absolute; top: 200px; left: 30px;">
 +
<span id="link-5" class="tutorial_button">5</span>
 +
</div>
 +
 +
<div class="container" style="position: absolute; top: 240px; left: 30px;">
 +
<span id="link-6" class="tutorial_button">6</span>
 +
</div>
 +
 +
<div class="container" style="position: absolute; top: 280px; left: 30px;">
 +
<span id="link-7" class="tutorial_button">7</span>
 +
</div>
 +
 +
<div class="container" style="position: absolute; top: 320px; left: 30px;">
 +
<span id="link-8" class="tutorial_button">8</span>
 +
</div>
 +
 +
<div class="container" style="position: absolute; top: 360px; left: 30px;">
 +
<span id="link-9" class="tutorial_button">9</span>
 +
</div>
 +
</div>
 +
 
 +
<script type="text/javascript" language="JavaScript">
 +
function tut_goto(step)
 +
{
 +
if(step == 1)
 +
{
 +
for(var i = 1; i <= 9; i++)
 +
{
 +
if(i != step)
 +
{
 +
jQuery("#link-" + i).removeClass("selected");
 +
jQuery("#link-" + i).removeClass("pulsing");
 +
jQuery("#popover-" + i).dxPopover("hide");
 +
jQuery("#figure-" + i).fadeOut("5");
 +
}
 +
else
 +
{
 +
jQuery("#popover-" + i).dxPopover("show");
 +
jQuery("#link-" + i).addClass("selected");
 +
jQuery("#link-" + i).removeClass("pulsing");
 +
jQuery("#figure-" + i).fadeIn("5");
 +
}
 +
}
 +
 +
//jQuery('html, body').animate({scrollTop: jQuery('.tutorial').offset().top - 200}, 500);
 +
}
 +
else
 +
{
 +
for(var i = 1; i <= 9; i++)
 +
{
 +
if(i != step)
 +
{
 +
jQuery("#link-" + i).removeClass("selected");
 +
jQuery("#link-" + i).removeClass("pulsing");
 +
jQuery("#popover-" + i).dxPopover("hide");
 +
jQuery("#figure-" + i).fadeOut("5");
 +
}
 +
else
 +
{
 +
jQuery("#popover-" + i).dxPopover("show");
 +
jQuery("#link-" + i).addClass("selected");
 +
jQuery("#figure-" + i).fadeIn("5");
 +
}
 +
}
 +
 +
//jQuery('html, body').animate({scrollTop: jQuery('.tutorial').offset().top - 200}, 500);
 +
}
 +
}
 +
 
 +
jQuery(function(){
 +
for(var i = 1; i <= 9; i++)
 +
{
 +
var position = "left";
 +
var showEvent = "";
 +
 +
var content = jQuery("#popover-" + i)[0].innerHTML;
 +
 +
jQuery("#popover-" + i).dxPopover({
 +
target: "#link-" + i,
 +
showEvent: "",
 +
hideEvent: "",
 +
closeOnBackButton: false,
 +
closeOnOutsideClick: false,
 +
position: {
 +
my: (position == "left" ? "right" : "left"),
 +
at: position,
 +
of: $("#link-" + i)
 +
},
 +
width: 0,
 +
height: 0,
 +
showTitle: false,
 +
visible: true,
 +
animation: { show: { type: 'fade', from: 0, to: 1, duration: 0 }, hide: { type: 'fade', to: 0, duration: 0 } },
 +
contentTemplate: "",
 +
closeOnTargetScroll: function(){
 +
return true;
 +
}
 +
}).dxPopover("hide");
 +
 +
jQuery("#popover-" + i).dxPopover({
 +
width: 300,
 +
height: "auto",
 +
animation: { show: { type: 'fade', from: 0, to: 1 }, hide: { type: 'fade', to: 0 } },
 +
contentTemplate: content
 +
});
 +
}
 +
 +
for(var i = 1; i <= 9; i++)
 +
{
 +
jQuery("#link-" + i).click(function()
 +
{
 +
tut_goto(this.id.split("-")[1]);
 +
});
 +
}
 +
 +
jQuery('body').on('click', 'a', function(event) {
 +
var id = event.target.id;
 +
 +
if(id.indexOf("goto-") > -1)
 +
{
 +
tut_goto(parseInt(id.split("-")[1]));
 +
}
 +
});
 +
});
 +
</script>
 +
 
 +
<div style="clear: both;"></div>
  
 
The tool should be cheap to produce and easy to use. To achieve this goal, the tool needs to have a closed box design wherein only the blood sample has to be added and a simple protocol can be followed to perform the test (Jet Bliek and Ruud van den Bogaard, Academical Medical Center Amsterdam: clinical genetics). Disposal of the system also needs to be considered (collaboration RIVM National Insitute for Public Health and the Environment).
 
The tool should be cheap to produce and easy to use. To achieve this goal, the tool needs to have a closed box design wherein only the blood sample has to be added and a simple protocol can be followed to perform the test (Jet Bliek and Ruud van den Bogaard, Academical Medical Center Amsterdam: clinical genetics). Disposal of the system also needs to be considered (collaboration RIVM National Insitute for Public Health and the Environment).
Line 2,138: Line 2,402:
 
<script id="page-outreach" type="text/template">
 
<script id="page-outreach" type="text/template">
 
<div class="page-heading">Outreach</div>
 
<div class="page-heading">Outreach</div>
−
Science can have an impact on the world in many ways. With our project, we are not only trying to make a difference by creating a diagnostic tool, but by reaching out to the public we hope to make science accessible for everyone as well. We tried to achieve this by collaborating with ‘de Kennis van Nu’, a platform of the Dutch national public broadcasting corporation that brings different scientific themes to the general public in an understandable way. They aim to make science accessible to everyone, old and young, and encourage everyone to be curious and bring out the scientist in themselves!  
+
Science impacts the world in many ways. With our project, we are not only aiming to make a difference by creating a diagnostic tool, but also to reach out to the public to create awareness and make science accessible for everyone. We collaborated with ‘de Kennis van Nu’, a well-known national TV program and internet platform that brings different scientific themes to the general public in an understandable way. They aim to make science accessible to everyone, old and young, and encourage everyone to be curious and bring out the scientist in themselves!  
 
On their platform, we explain the formation of Utrecht’s very first team, our design and how we are trying to solve healthcare problems.  
 
On their platform, we explain the formation of Utrecht’s very first team, our design and how we are trying to solve healthcare problems.  
−
Through our whole iGEM experience, they follow us from lab bench to Boston.
+
Through our whole iGEM experience, they follow us from lab bench to Boston. Their special about our team can be found <a target=_BLANK href="https://dekennisvannu.nl/site/special/iGEM-2017-studenten-ontwerpen-nieuw-leven/111#!/" class="url_external">here</a>.
 
<br><br>
 
<br><br>
 
Below, you can find the short movies, articles and infographics that were so far made in cooperation with Kennis van Nu to reach out to the public.  
 
Below, you can find the short movies, articles and infographics that were so far made in cooperation with Kennis van Nu to reach out to the public.  
Line 2,191: Line 2,455:
 
</video>
 
</video>
  
−
<div class="description">The lab can be a treacherous environment. One tiny mistake, and it might be your last.. We answer important questions about how to stay safe in the lab.</div>
+
<div class="description">The lab can be a treacherous environment. One tiny mistake, and it could be your last.. We answer important questions about how to stay safe in the lab.</div>
  
 
</div>
 
</div>
Line 2,198: Line 2,462:
  
 
<div style="clear: both;"></div>
 
<div style="clear: both;"></div>
−
 
−
<div style="clear: both;">
 
−
For a link to the special on our team on the website of de Kennis van Nu, <a target=_BLANK href="https://dekennisvannu.nl/site/special/iGEM-2017-studenten-ontwerpen-nieuw-leven/111#!/" class="url_external">click here</a>.
 
−
</div>
 
  
 
<style type="text/css">
 
<style type="text/css">
Line 2,363: Line 2,623:
 
<span class="team-duties">
 
<span class="team-duties">
 
&rsaquo; Experimental - Secreted Cas9 and Cpf1<br>
 
&rsaquo; Experimental - Secreted Cas9 and Cpf1<br>
−
&rsaquo; Human Practices - Application
+
&rsaquo; Human Practices - Application<br>
 +
&rsaquo; Biobricks
 
</span>
 
</span>
 
 
Line 2,424: Line 2,685:
 
&rsaquo; Human Practices -<br>&nbsp;&nbsp;Application/Safety/Design<br>
 
&rsaquo; Human Practices -<br>&nbsp;&nbsp;Application/Safety/Design<br>
 
&rsaquo; Experimental - Assembly/InterLab Study<br>
 
&rsaquo; Experimental - Assembly/InterLab Study<br>
−
&rsaquo; Funding & Sponsoring
+
&rsaquo; Funding & Sponsoring<br>
 +
&rsaquo; Treasurer
 
</span>
 
</span>
 
 
 
<div style="margin-top: 10px; font-weight: bold;">Bio</div>
 
<div style="margin-top: 10px; font-weight: bold;">Bio</div>
−
<div class="team-bio">
+
<div class="team-bio" style="height: 61px;">
 
Hi! I'm Lishi (21), a first year master student in Pharmacy at Utrecht University. After that, I want to become a hospital pharmacist.
 
Hi! I'm Lishi (21), a first year master student in Pharmacy at Utrecht University. After that, I want to become a hospital pharmacist.
 
<div class="lb"></div>
 
<div class="lb"></div>
Line 2,804: Line 3,066:
 
         </div>
 
         </div>
 
         <span style="display: block; font-size: 12px; padding: 0 20px;">
 
         <span style="display: block; font-size: 12px; padding: 0 20px;">
−
TODO<br>
+
Professor of Regenerative Medicine<br>
−
+
 
<div style="margin-top: 10px; font-weight: bold;">Bio</div>
 
<div style="margin-top: 10px; font-weight: bold;">Bio</div>
−
<div class="team-bio" style="height: 201px;">
+
<div class="team-bio" style="height: 239px;">
−
bio
+
Hello, I’m Niels Geijsen, and supervising the very first iGEM team of Utrecht University has been an immensely fun and inspiring adventure. Scientific challenges require for our brightest minds with diverse perspectives and backgrounds to come together. This is the Utrecht iGEM team: they are a group of smart, creative and ambitious students who have contributed a wide range of knowledge backgrounds, life experiences and hobbies to the project. It was such a fantastic experience to see how each member brought a special talent ranging from artistic drawing skills and video animation to photography, coding and web design. Together, they have truly outdone themselves.
 +
<div class="lb"></div>
 +
As a professor in regenerative medicine at the Hubrecht Institute and Utrecht University, my research team works work at the boundaries of stem cell biology and technology development with a particular focus on (genetic) muscle disease. I spent 10 years in Boston, as post-doctoral fellow at the Whitehead Institute and faculty at Massachusetts General Hospital, Harvard Medical School and the Harvard Stem Cell Institute, and I'm particularly looking forward to joining the team in Boston for the Giant Jamboree.
 +
<div class="lb"></div>
 +
Aside from science, I experiment in the kitchen, have a passion for food and wine, and enjoy outdoor activities such as sailing, hiking and skiing. My three active young boys  are a daily joy and challenge. <br>
 
<div class="team-bio-grad"></div>
 
<div class="team-bio-grad"></div>
 
</div>
 
</div>
Line 2,815: Line 3,080:
 
</span>
 
</span>
 
</div>
 
</div>
−
<div class="back"></div></div>
+
<div class="back" style="line-height: 15px; font-size: 11px;"></div></div>
 
       </div>
 
       </div>
 
   
 
   
Line 2,828: Line 3,093:
 
<div class="team-bio" style="height: 215px;">
 
<div class="team-bio" style="height: 215px;">
 
Hi all, I am Roos Masereeuw, and since June 2015 I am full professor of Experimental Pharmacology at Utrecht Institute for Pharmaceutical Sciences in The Netherlands. I did a master’s in Biopharmaceutical Sciences at Leiden University, and my PhD in Pharmacology and Toxicology at Radboud University in Nijmegen (January 1997).
 
Hi all, I am Roos Masereeuw, and since June 2015 I am full professor of Experimental Pharmacology at Utrecht Institute for Pharmaceutical Sciences in The Netherlands. I did a master’s in Biopharmaceutical Sciences at Leiden University, and my PhD in Pharmacology and Toxicology at Radboud University in Nijmegen (January 1997).
−
<br><br>
+
<div class="lb"></div>
 
Part of my PhD research and a postdoc period I did at National Institute for Environmental Sciences (NIEHS/NIH) in Research Triangle Park, North Carolina of USA. Between 1998 and 2015, I was first assistent and then associate professor at Radboud University Medical Centre in Nijmegen, after which I moved to Utrecht University.
 
Part of my PhD research and a postdoc period I did at National Institute for Environmental Sciences (NIEHS/NIH) in Research Triangle Park, North Carolina of USA. Between 1998 and 2015, I was first assistent and then associate professor at Radboud University Medical Centre in Nijmegen, after which I moved to Utrecht University.
−
<br><br>
+
<div class="lb"></div>
 
My research is focused on understanding the pathways that can be pharmacologically triggered to enhance repair and regeneration processes after organ injury. An example is the development of a bioartificial kidney device to partly replace kidney function. Next to science, I mostly enjoy outdoor sports when I can. This includes mountain hiking, mountain biking and running, but I also love watching Netflix series with my family, and visiting concerts and festivals.
 
My research is focused on understanding the pathways that can be pharmacologically triggered to enhance repair and regeneration processes after organ injury. An example is the development of a bioartificial kidney device to partly replace kidney function. Next to science, I mostly enjoy outdoor sports when I can. This includes mountain hiking, mountain biking and running, but I also love watching Netflix series with my family, and visiting concerts and festivals.
 
<div class="team-bio-grad"></div>
 
<div class="team-bio-grad"></div>
Line 2,851: Line 3,116:
 
<div class="team-bio" style="height: 201px;">
 
<div class="team-bio" style="height: 201px;">
 
Hello, I’m Guido van den Ackerveken and it is my privilege to be one of the supervisors of the energetic and bright team of Utrecht University. I am trained as a molecular biologist in the field of plant- and microbiology, and have always worked of plant-pathogen interactions. I have a research team of about 10 people and in our research we reveal molecular mechanisms in the dialogue between plants and microorganisms, which we then try to translate to improve the resistance of food crops to infectious diseases. It is real fun to work with the iGEM bunch and to support the starting researchers in their ambitious programme.
 
Hello, I’m Guido van den Ackerveken and it is my privilege to be one of the supervisors of the energetic and bright team of Utrecht University. I am trained as a molecular biologist in the field of plant- and microbiology, and have always worked of plant-pathogen interactions. I have a research team of about 10 people and in our research we reveal molecular mechanisms in the dialogue between plants and microorganisms, which we then try to translate to improve the resistance of food crops to infectious diseases. It is real fun to work with the iGEM bunch and to support the starting researchers in their ambitious programme.
−
<br><br>
+
<div class="lb"></div>
 
Outside of my busy work I try to find time for playing squash and running (I ran my first marathon this year), but also of course to enjoy being with my family. Never a dull moment :-)
 
Outside of my busy work I try to find time for playing squash and running (I ran my first marathon this year), but also of course to enjoy being with my family. Never a dull moment :-)
 
<div class="team-bio-grad"></div>
 
<div class="team-bio-grad"></div>
Line 2,872: Line 3,137:
 
<div class="team-bio" style="height: 215px;">
 
<div class="team-bio" style="height: 215px;">
 
I am a microbiologist and work at Utrecht University. My research interest focusses on two topics. One is to unravel the mechanisms involved in secretion of proteins and the role of secreted proteins in bacteria. This knowledge is important to understand how bacteria interact with their environment and can be used  to  optimize large scale production of proteins and vaccine development.
 
I am a microbiologist and work at Utrecht University. My research interest focusses on two topics. One is to unravel the mechanisms involved in secretion of proteins and the role of secreted proteins in bacteria. This knowledge is important to understand how bacteria interact with their environment and can be used  to  optimize large scale production of proteins and vaccine development.
−
<br><br>
+
<div class="lb"></div>
 
My second topic of interest is teaching, and especially how to stimulate students to become independent and critical researchers. Therefore, assisting the first Utrecht iGEM team has been a great experience. In my spare time, I like to eat, watch movies and spend time with my family, which includes two daughters and a lazy cat.
 
My second topic of interest is teaching, and especially how to stimulate students to become independent and critical researchers. Therefore, assisting the first Utrecht iGEM team has been a great experience. In my spare time, I like to eat, watch movies and spend time with my family, which includes two daughters and a lazy cat.
 
<div class="team-bio-grad"></div>
 
<div class="team-bio-grad"></div>
Line 2,893: Line 3,158:
 
<div class="team-bio" style="height: 201px;">
 
<div class="team-bio" style="height: 201px;">
 
Hello, my name is Clara (23) and I’m a first year Cancer, Stem Cells and Developmental biology Master student in Utrecht. I finished a Bachelor’s degree in Genetics in Barcelona last year and came to the Netherlands with a fellowship for post-graduate internships abroad, which allowed me to join Niels Geijsen’s lab for six months.
 
Hello, my name is Clara (23) and I’m a first year Cancer, Stem Cells and Developmental biology Master student in Utrecht. I finished a Bachelor’s degree in Genetics in Barcelona last year and came to the Netherlands with a fellowship for post-graduate internships abroad, which allowed me to join Niels Geijsen’s lab for six months.
−
<br><br>
+
<div class="lb"></div>
 
I’m really happy to have been asked to write a piece as part of the team, even if I haven’t been there for the whole process. I joined the team during the summer period to help with some lab work that was being carried out in my former lab. It has been a great experience to help supervising the Utrecht iGEM team and its amazing people, full of joy and stress I have to admit. Now the deadline is getting closer and we are all preparing for the big final! Thank you, guys, for this opportunity!  
 
I’m really happy to have been asked to write a piece as part of the team, even if I haven’t been there for the whole process. I joined the team during the summer period to help with some lab work that was being carried out in my former lab. It has been a great experience to help supervising the Utrecht iGEM team and its amazing people, full of joy and stress I have to admit. Now the deadline is getting closer and we are all preparing for the big final! Thank you, guys, for this opportunity!  
 
<div class="team-bio-grad"></div>
 
<div class="team-bio-grad"></div>
Line 3,025: Line 3,290:
 
<div class="slider_for" style="float: left; width: 400px;">
 
<div class="slider_for" style="float: left; width: 400px;">
 
<div><b>Utrecht University is a Dutch public university with over 50.000 students.</b> As our home university, they were our first sponsor. They have helped us generously with great financial support, meeting space, PR-facilities and the opportunity to use several labspaces on campus.</div>
 
<div><b>Utrecht University is a Dutch public university with over 50.000 students.</b> As our home university, they were our first sponsor. They have helped us generously with great financial support, meeting space, PR-facilities and the opportunity to use several labspaces on campus.</div>
 +
<div><b>The Jong Alumni Netwerk (JAN) organizes activities and events to help support the careers of recent graduates by providing networking opportunities.</b> JAN agreed to financially support us to make this project possible.</div>
 +
<div><b>The Hubrecht Institute is a leading research centre focusing on developmental biology and stem cell research.</b> Hubrecht institute offered us guidance and assistance with our project by facilitating a lab assistant for the work we had to do for our project.</div>
 
<div><b>RIVM is the National Institute for Public Health and the Environment, which belongs to the Ministry of Health, Welfare and Sport of the Dutch government.</b> They offered a sponsorship to the Dutch iGEM teams based on an assignment titled ‘think before you do’, stimulating us to think about the societal implications that our project could have. We submitted a proposal and the RIVM offered us a €1500 grant to further our project.</div>
 
<div><b>RIVM is the National Institute for Public Health and the Environment, which belongs to the Ministry of Health, Welfare and Sport of the Dutch government.</b> They offered a sponsorship to the Dutch iGEM teams based on an assignment titled ‘think before you do’, stimulating us to think about the societal implications that our project could have. We submitted a proposal and the RIVM offered us a €1500 grant to further our project.</div>
 
<div><b>DSM is a science-based company focusing on health, nutrition and materials to drive sustainable innovation.</b> DSM is active in many different markets, including medicine, energy and food, so developments in synthetic biology are of major interest to them. For our project, they sponsored us with €1000.</div>
 
<div><b>DSM is a science-based company focusing on health, nutrition and materials to drive sustainable innovation.</b> DSM is active in many different markets, including medicine, energy and food, so developments in synthetic biology are of major interest to them. For our project, they sponsored us with €1000.</div>
Line 3,046: Line 3,313:
 
<div class="sponsors_slider" style="width: 100%;">
 
<div class="sponsors_slider" style="width: 100%;">
 
<div style="width: 150px;"><img src="https://static.igem.org/mediawiki/2017/e/e0/Uu17logo.png"></div>
 
<div style="width: 150px;"><img src="https://static.igem.org/mediawiki/2017/e/e0/Uu17logo.png"></div>
 +
<div style="width: 250px;"><img src="https://static.igem.org/mediawiki/2017/8/85/Uu-jongealumninetwerk.png"></div>
 +
<div style="width: 200px;"><img src="https://static.igem.org/mediawiki/2017/2/2a/Uu-logo-hubrecht.png"></div>
 
<div style="width: 300px;"><img src="https://static.igem.org/mediawiki/2017/e/e6/Uurivm.png"></div>
 
<div style="width: 300px;"><img src="https://static.igem.org/mediawiki/2017/e/e6/Uurivm.png"></div>
 
<div style="width: 250px;"><img src="https://static.igem.org/mediawiki/2017/5/5b/Uudsm.jpeg"></div>
 
<div style="width: 250px;"><img src="https://static.igem.org/mediawiki/2017/5/5b/Uudsm.jpeg"></div>
Line 3,107: Line 3,376:
 
Our team collaborated with the Wageningen team to obtain independent validations of both our and their biobricks.
 
Our team collaborated with the Wageningen team to obtain independent validations of both our and their biobricks.
 
<br><br>
 
<br><br>
 +
<div style="float: right; margin-left: 35px; margin-bottom: 10px;">
 +
<img src="https://static.igem.org/mediawiki/2017/thumb/f/f5/Collab_WUR_UU.jpg/320px-Collab_WUR_UU.jpg">
 +
<br>
 +
<span class="text-figure">
 +
Our collaboration with Wageningen has been great fun.
 +
</span>
 +
</div>
 
Wageningen validated the secreted-Cas9 and secreted-Cpf1 biobricks for us (BB_numbers).  
 
Wageningen validated the secreted-Cas9 and secreted-Cpf1 biobricks for us (BB_numbers).  
 
Members of the Wageningen team came to Utrecht to perform this validation together with members of the Utrecht team in our lab.  
 
Members of the Wageningen team came to Utrecht to perform this validation together with members of the Utrecht team in our lab.  
Line 3,112: Line 3,388:
 
Medium of the cells was analysed on a western blot to compare extracellular protein expression.  
 
Medium of the cells was analysed on a western blot to compare extracellular protein expression.  
 
This tells us whether Cas9 and Cpf1 are truly being secreted or if they just leak out of the cells.  
 
This tells us whether Cas9 and Cpf1 are truly being secreted or if they just leak out of the cells.  
−
The results of this validation can be found on the <a onclick="return change_page('basicparts', 1)" href="basicparts">Parts Page</a> and the experimental page on <a onclick="return change_page('secretion', 1)" href="secretion">secreted Cas9 and Cpf1</a>.
+
The results of this validation can be found on the <a onclick="return change_page('basic_part', 1)" href="basic_part">Parts Page</a> and the experimental page on <a onclick="return change_page('secretion', 1)" href="secretion">secreted Cas9 and Cpf1</a>.
 
<br><br>
 
<br><br>
 
In return, for the Wageningen team, we did a blind validation of some of their biobricks.  
 
In return, for the Wageningen team, we did a blind validation of some of their biobricks.  
Line 3,119: Line 3,395:
 
We also performed a leucine zipper BiFC measurement, where we transformed split sfGFP and split Venus to E.coli K12 and also full sfGFP and full Venus as controls.  
 
We also performed a leucine zipper BiFC measurement, where we transformed split sfGFP and split Venus to E.coli K12 and also full sfGFP and full Venus as controls.  
 
Cells were then lysed and fluorescence was measured in the cell lysate <a target=_BLANK href="https://2017.igem.org/Team:Wageningen_UR/Collaborations" class="url_external">(link)</a>.
 
Cells were then lysed and fluorescence was measured in the cell lysate <a target=_BLANK href="https://2017.igem.org/Team:Wageningen_UR/Collaborations" class="url_external">(link)</a>.
−
 
−
<br><br>
 
−
<b>NICE PICTURE OF US AND WAGENINGEN GUYS IN SOME LAB</b>
 
  
 
<br><br>
 
<br><br>
Line 3,130: Line 3,403:
  
 
<br><br>
 
<br><br>
−
<b>NICE PICTURE OF RAWAN AND LISHI AT THE RIVM</b>
+
 
 +
<center>
 +
<img onclick="openmodal('rivm-event')" style="cursor: pointer;" src="https://static.igem.org/mediawiki/2017/thumb/f/f7/8997_Kennisparade_%281%29.jpg/240px-8997_Kennisparade_%281%29.jpg">
 +
<br>
 +
<span class="text-figure">
 +
Attending a RIVM event. <a href="javascript:void(0)" onclick="openmodal('rivm-event')" style="font-size: 11px;">Click for full size.</a>
 +
</span>
 +
</center>
  
 
<br><br>
 
<br><br>
Line 3,142: Line 3,422:
  
 
<br><br>
 
<br><br>
−
<b>PICTURE OF POSTCARDS LISHI IS GONNA MAKE</b>
+
 
 +
<center>
 +
<img width="100%" src="https://static.igem.org/mediawiki/2017/thumb/b/be/Collab_dusseldorf_postcards.jpg/800px-Collab_dusseldorf_postcards.jpg">
 +
</center>
  
 
</script>
 
</script>
  
 
<script id="page-achievements" type="text/template">
 
<script id="page-achievements" type="text/template">
 +
<div style="position: absolute;top: 0;right: -250px;width: 200px;text-align: center;border: 1px solid gold;padding: 10px;border-radius: 10px;box-sizing: border-box;background: #ffedb8;">
 +
<div style="
 +
    font-weight: bold;
 +
    font-size: 20px;
 +
    color: #c48b00;
 +
    border-bottom: 1px solid #ffd700;
 +
padding-bottom: 15px;
 +
    margin-bottom: 15px;
 +
">Awards</div>
 +
<img width="100" src="https://static.igem.org/mediawiki/2017/thumb/a/a2/UU_gold_medal.png/240px-UU_gold_medal.png"><br><div style="font-size: 15px;color: #c48b00; border-bottom: 1px solid #ffd700; padding-bottom: 15px; margin-top: 5px;">Gold medal</div>
 +
<div style="margin-top: 15px; margin-bottom: 10px; font-size: 15px;color: #c48b00;"><b>Nominated</b><br />Best integrated human practices</div>
 +
</div>
 
<div class="page-heading">Achievements</div>
 
<div class="page-heading">Achievements</div>
  
−
This page will give an overview of the achievements of our team. These will be presented as the medal criteria we fulfilled to acquire the various medals. For several criteria we will provide a link to the page with more information on that item.
+
This page gives an overview of the achievements of our team. These will be presented as the medal criteria we fulfilled to acquire the various medals. For several criteria we will provide a link to the page with more information on that item.
  
 
<br><br>
 
<br><br>
Line 3,162: Line 3,457:
 
<b>Deliverables</b><br>
 
<b>Deliverables</b><br>
 
We have delivered all the required items on the iGEM deliverables page.<br>
 
We have delivered all the required items on the iGEM deliverables page.<br>
−
<table border="0" cellspacing="0" cellpadding="0" width="600">
+
<table class="uu-table" border="0" cellspacing="0" cellpadding="0" width="600" style="margin-top: 10px !important;">
 
<tr>
 
<tr>
 
<td width="250">
 
<td width="250">
 
<ul>
 
<ul>
−
<li /><a href="">Team wiki</a>
+
<li /><a onclick="return change_page('home', 1)" href="https://2017.igem.org/Team:Utrecht/">Team wiki</a>
−
<li /><a href="">Project attribution</a>
+
<li /><a onclick="return change_page('attributions', 1)" href="attributions">Project attribution</a>
−
<li /><a href="">Team poster</a>
+
<li /><a onclick="return change_page('posters', 1)" href="posters">Team poster</a>
−
<li /><a href="">Team presentation</a>
+
<li />Team presentation
−
<li /><a href="">Safety forms</a>
+
<li /><a target=_BLANK href="https://2017.igem.org/Safety/Final_Safety_Form?team_id=2351" class="url_external">Safety forms</a>
 
</ul>
 
</ul>
 
</td>
 
</td>
 
<td width="350">
 
<td width="350">
 
<ul>
 
<ul>
−
<li /><a href="">Judging form</a>
+
<li /><a target=_BLANK href="https://igem.org/2017_Judging_Form?id=2351" class="url_external">Judging form</a>
−
<li /><a href="">Registry part pages</a>
+
<li /><a onclick="return change_page('basic_part', 1)" href="basic_part">Registry part pages</a>
−
<li /><a href="">Sample submission</a>
+
<li /><a target=_BLANK href="http://parts.igem.org/cgi/dna_transfer/batch_list.cgi?group_id=2850" class="url_external">Sample submission</a>
−
<li /><a href="">Project attribution</a>
+
<li /><a onclick="return change_page('interlab-study', 1)" href="interlab-study">Contribution to InterLab Study</a>
−
<li /><a href="">Contribution to InterLab Study</a>
+
 
</ul>
 
</ul>
 
</td>
 
</td>
Line 3,194: Line 3,488:
 
<div style="float: left; width: 100%; margin: 0;">
 
<div style="float: left; width: 100%; margin: 0;">
 
<b>Validate functionality of BioBrick</b><br>
 
<b>Validate functionality of BioBrick</b><br>
−
<li /><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351012">Part BBa_K2351012 (secreted Cpf1)</a><br>
+
BioBrick Part <a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351012" class="url_external">BBa_K2351012</a> (secreted Cpf1) has been validated. This BioBrick is very special since our team successfully secreted CRISPR-associated proteins from HEK293 cells.  
−
BioBrick Part BBa_K2351012 (secreted Cpf1) has been validated. This BioBrick is very special since our team successfully secreted CRISPR-associated proteins from HEK293 cells.  
+
 
To our knowledge, this is the first time that Cpf1 has ever been expressed outside of the cell.
 
To our knowledge, this is the first time that Cpf1 has ever been expressed outside of the cell.
 +
<br><br>
 +
&rsaquo; <a onclick="return change_page('basic_part', 1)" href="basic_part">View submitted parts.</a>
 
</div>
 
</div>
 
<div style="float: left; width: 100%; margin: 0; margin-top: 20px;">
 
<div style="float: left; width: 100%; margin: 0; margin-top: 20px;">
Line 3,202: Line 3,497:
 
Our team collaborated with the Wageningen team to obtain independent validations of both our and their biobricks. In addition, we worked with the Rathenau Institute and the RIVM on our Human Practices and safety considerations.
 
Our team collaborated with the Wageningen team to obtain independent validations of both our and their biobricks. In addition, we worked with the Rathenau Institute and the RIVM on our Human Practices and safety considerations.
 
<br><br>
 
<br><br>
−
Furthermore, we contributed a postcard design to the Düsseldorf Cologne postcards campaign. Although these are not, strictly speaking, collaborations, we have attended several meet-ups with Dutch and other European iGEM teams to exchange ideas. An overview of our collaboration efforts can be found on the Collaborations page (> Links to [Collaborations page]).
+
Furthermore, we contributed a postcard design to the Düsseldorf Cologne postcards campaign. Although these are not, strictly speaking, collaborations, we have attended several meet-ups with Dutch and other European iGEM teams to exchange ideas. An overview of our collaboration efforts can be found on the <a onclick="return change_page('collaborations', 1)" href="collaborations">Collaborations page</a>.
 
</div>
 
</div>
 
<div style="float: left; width: 100%; margin: 0; margin-top: 20px;">
 
<div style="float: left; width: 100%; margin: 0; margin-top: 20px;">
 
<b>Human Practices</b><br>
 
<b>Human Practices</b><br>
−
Our team has contacted professionals from many different backgrounds to find the setting wherein the OUTCASST system would be of most use and to identify where the requirements of the intended application affect the design of our tool. Through a series of interviews with several experts, we came to the conclusion that our tool would be most useful in diagnostics and pathogen detection in particular. By talking to a representative from ‘Doctors without borders’ and a parasitology expert, we discovered that Chagas disease is a neglected tropical disease with a large impact, yet a good diagnostic tool for this disease is still missing. Therefore, we chose to focus on Chagas disease in the further design of our tool. (> Links to [Human Practices] [End User])
+
Our team has contacted professionals from many different backgrounds to find the setting wherein the OUTCASST system would be of most use and to identify where the requirements of the intended application affect the design of our tool. Through a series of interviews with several experts, we came to the conclusion that our tool would be most useful in diagnostics and pathogen detection in particular. By talking to a representative from ‘Doctors without borders’ and a parasitology expert, we discovered that Chagas disease is a neglected tropical disease with a large impact, yet a good diagnostic tool for this disease is still missing. Therefore, we chose to focus on Chagas disease in the further design of our tool. Read more about our <a onclick="return change_page('stakeholders', 1)" href="stakeholders">end users</a>.
 
<br><br>
 
<br><br>
−
Besides the interviews to find the focus of our project, we also worked on outreach. In collaboration with ‘De Kennis van Nu’, a Dutch platform that brings different scientific themes to the general public, we made videos and wrote blogs about synthetic biology, the iGEM competition, lab safety, tropical diseases and our project. To raise more awareness for the competition and our project within our university, we wrote articles in several student magazines. (> Links to [Human Practices] [Outreach])  
+
Besides the interviews to find the focus of our project, we also worked on outreach. In collaboration with ‘De Kennis van Nu’, a Dutch platform that brings different scientific themes to the general public, we made videos and wrote blogs about synthetic biology, the iGEM competition, lab safety, tropical diseases and our project. To raise more awareness for the competition and our project within our university, we wrote articles in several student magazines. Read more about our <a onclick="return change_page('outreach', 1)" href="outreach">outreach</a>.
 
</div>
 
</div>
 
</div>
 
</div>
Line 3,219: Line 3,514:
 
<div style="float: left; width: 100%; margin: 0;">
 
<div style="float: left; width: 100%; margin: 0;">
 
<b>Integrated Human Practices</b><br>
 
<b>Integrated Human Practices</b><br>
−
We incorporated the feedback we got from various professionals into the design of our final product. Not only did the information we gained make us choose for Chagas disease as the focus of our project, it also made us think about the way our system could be used on location. Through our conversations with specialists, we realized the importance of simplicity in use and resistance to varying temperatures and humidity. Only tools which take these factors into account can be used without a need for further lab equipment or trained personnel. Furthermore, with safety considerations in mind, we designed our device to keep our system separated from the outside world, making it impossible for the GMO’s to escape into the environment. (> Link to [Human Practices][Design])
+
We incorporated the feedback we got from various professionals into the design of our final product. Not only did the information we gained make us choose for Chagas disease as the focus of our project, it also made us think about the way our system could be used on location. Through our conversations with specialists, we realized the importance of simplicity in use and resistance to varying temperatures and humidity. Only tools which take these factors into account can be used without a need for further lab equipment or trained personnel. Furthermore, with safety considerations in mind, we designed our device to keep our system separated from the outside world, making it impossible for the GMO’s to escape into the environment. Read more about our <a onclick="return change_page('product-design', 1)" href="product-design">design considerations</a>.
 
</div>
 
</div>
 
<div style="float: left; width: 100%; margin: 0; margin-top: 20px;">
 
<div style="float: left; width: 100%; margin: 0; margin-top: 20px;">
 
<b>Model your project</b><br>
 
<b>Model your project</b><br>
−
At the same time, our team worked on modeling our system. They first summarized the kinetics of our fusion proteins in a network of reactions. With this reaction network, we demonstrated that the system contains negative feedback on its own sensitivity and give some suggestions on how to alleviate that problem with additional bio-circuitry components. In addition, we show that the precision of the system may be increased by usage of a weaker protease. We subsequently used ODE reaction equations to test if differences in substrate affinity or protein production rates can alleviate sensitivity problems and if so, how.
+
At the same time, our team worked on modeling our system. They first summarized the kinetics of our fusion proteins in a network of reactions. With this reaction network, we demonstrated that the system contains negative feedback on its own sensitivity and give some suggestions on how to alleviate that problem with additional bio-circuitry components. In addition, we show that the precision of the system may be increased by usage of a weaker protease. We subsequently used ODE reaction equations to test if differences in substrate affinity or protein production rates can alleviate sensitivity problems and if so, how. Read more about our <a onclick="return change_page('modeling-and-mathematics', 1)" href="modeling-and-mathematics">modeling efforts</a>.
 +
</div>
 +
<div style="float: left; width: 100%; margin: 0; margin-top: 20px;">
 +
<b>Improve a previous part</b><br>
 +
The part we improved is <a target=_BLANK href="http://parts.igem.org/Part:BBa_K1774001" class="url_external">BBa_K1774001</a>. This part is <i>S. pyogenes</i> Cas9, submitted by the University of Hong Kong 2015 iGEM team. To improve this part we did three things: codon optimize it for mammalian cells, add a signal sequence for secretion from mammalian cells and add a His-tag. Modifying the Cas9 protein in this way makes it possible to get it produced and secreted from mammalian cells instead of bacteria. It can then be easily isolated and purified using the His-tag. Isolating the protein from mammalian cells instead of bacteria makes this Cas9 more suitable for clinical applications in humans or human cells. We therefore think this version of S. pyogenes Cas9 has added value in future medicine and thus is an improvement over the bacterial-produced version of <i>S. pyogenes</i> Cas9.
 +
<br><br>
 +
The improved part was submitted as <a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351013" class="url_external">BBa_K2351013</a>.
 +
<br><br>
 +
&rsaquo; <a onclick="return change_page('basic_part', 1)" href="basic_part">View all submitted parts.</a>
 
</div>
 
</div>
 
</div>
 
</div>
Line 3,234: Line 3,537:
 
<div class="page-heading">Attribution and acknowledgement</div>
 
<div class="page-heading">Attribution and acknowledgement</div>
  
−
The Utrecht iGEM team performed most of the experiments, funding, PR and human practices on their own. All additional help is acknowledged here:
+
The Utrecht iGEM team performed most of the experiments, funding, PR, human practices and other tasks on their own. All additional help is acknowledged below.
 +
For a breakdown of the contribution of individual team members, see the <a onclick="return change_page('team', 1)" href="team">Team page</a>.
  
 
<br><br>
 
<br><br>
Line 3,272: Line 3,576:
 
<br><br>
 
<br><br>
 
Thank you!
 
Thank you!
 +
</script>
 +
 +
<script id="page-basic_part" type="text/template">
 +
<div class="page-heading">BioBricks - Basic Parts</div>
 +
 +
This page contains an overview of all the basic BioBricks we created for our project.<br>
 +
Interested in our composite parts? You can find them <a onclick="return change_page('composite_part', 1)" href="composite_part">here</a>.
 +
 +
<br><br>
 +
 +
<table class="biobricktable" style="width: 100%; font-size: 12px; text-align: left;">
 +
<tr style="font-size: 15px; font-weight: bold;">
 +
<td width="150">Number</td>
 +
<td width="200">Name</td>
 +
<td>Short description</td>
 +
</tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351000" class="url_external">BBa_K2351000</a></td><td>Ig lambda-2 chain V region signal sequence</td><td>Allows for proteins to be secreted</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351001" class="url_external">BBa_K2351001</a></td><td><b>Best basic part:</b> dAsCpf1</td><td>DNA and gRNA binding properties are maintained but no endonuclease activity is exhibited.</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351002" class="url_external">BBa_K2351002</a></td><td>nCas9 </td><td>A cas9 variant without first Methionine and without stopcodon, such that it can be used as a fusion protein component that contains illegal restriction sites.</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351003" class="url_external">BBa_K2351003</a></td><td>nCpf1</td><td>A cpf1 variant without first Methionine and without stopcodon, such that it can be used as a fusion protein component that contains illegal restriction sites.</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351004" class="url_external">BBa_K2351004</a></td><td>Glycine [3x] linked histidine[6x] tag</td><td>Basic histidine tag with preceding glycine linker.</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351007" class="url_external">BBa_K2351007</a></td><td>nCas9 </td><td>A cas9 variant without first Methionine and without stopcodon, such that it can be used as a fusion protein component.</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351008" class="url_external">BBa_K2351008</a></td><td>nCpf1</td><td>A cpf1 variant without first Methionine and without stopcodon, such that it can be used as a fusion protein component.</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351011" class="url_external">BBa_K2351011</a></td><td>dCpf1</td><td>DNA and gRNA binding properties are maintained but no endonuclease activity is exhibited.</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351012" class="url_external">BBa_K2351012</a></td><td>sCpf1</td><td>Phytobrick* // Cpf1 that will be secreted from humane cells.</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351013" class="url_external">BBa_K2351013</a></td><td>dCpf1</td><td>Phytobrick*// DNA and gRNA binding properties are maintained but no endonuclease activity is exhibited.</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351014" class="url_external">BBa_K2351014</a></td><td>sCas9</td><td>Phytobrick* // Cas9 that will be secreted from humane cells.</td></tr>
 +
</table>
 +
 +
<style type="text/css">
 +
.biobricktable { border: 0 !important; margin: 0 !important; }
 +
.biobricktable tr:nth-child(even) td { background: #f7f7f7; }
 +
.biobricktable td { padding: 5px !important; border: 0 !important; vertical-align: middle !important; }
 +
</style>
 +
 +
</script>
 +
 +
<script id="page-composite_part" type="text/template">
 +
<div class="page-heading">BioBricks - Composite Parts</div>
 +
 +
This page contains an overview of all the composite BioBricks we created for our project.<br>
 +
Interested in our basic parts? You can find them <a onclick="return change_page('basic_part', 1)" href="basic_part">here</a>.
 +
 +
<br><br>
 +
 +
<table class="biobricktable" style="width: 100%; font-size: 12px; text-align: left;">
 +
<tr style="font-size: 15px; font-weight: bold;">
 +
<td width="150">Number</td>
 +
<td width="200">Name</td>
 +
<td>Short description</td>
 +
</tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351005" class="url_external">BBa_K2351005</a></td><td><b>Best composite part:</b> secreted Cas9</td><td>Cas9 that will be secreted from humane cells.</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351006" class="url_external">BBa_K2351006</a></td><td>Secreted Cpf1</td><td>Cpf1 that will be secreted from humane cells.</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351009" class="url_external">BBa_K2351009</a></td><td>sCas9</td><td>Cas9 that will be secreted from humane cells.</td></tr>
 +
<tr><td><a target=_BLANK href="http://parts.igem.org/Part:BBa_K2351010" class="url_external">BBa_K2351010</a></td><td>sCpf1</td><td>Cpf1 that will be secreted from humane cells.</td></tr>
 +
</table>
 +
 +
<style type="text/css">
 +
.biobricktable { border: 0 !important; margin: 0 !important; }
 +
.biobricktable tr:nth-child(even) td { background: #f7f7f7; }
 +
.biobricktable td { padding: 5px !important; border: 0 !important; vertical-align: middle !important; }
 +
</style>
 +
 +
</script>
 +
 +
<script id="page-posters" type="text/template">
 +
<div class="page-heading">Team Posters</div>
 +
 +
Displayed here are the posters that we used to present our team during various events.
 +
 +
<br><br>
 +
 +
<div style="width: 100%; text-align: center;">
 +
 +
<div class="outreach-video">
 +
<div style="width: 100%; text-align: center;">
 +
<img style="width: 150px;" src="https://static.igem.org/mediawiki/2017/thumb/b/b8/UU-poster-portrait.png/423px-UU-poster-portrait.png">
 +
</div>
 +
 +
<div class="description"><a target=_BLANK href="https://static.igem.org/mediawiki/2017/5/56/UU-poster-portrait-fullsize.pdf" class="pdf">Download poster</a></div>
 +
</div>
 +
 +
<div class="outreach-video">
 +
<div style="width: 100%; text-align: center;">
 +
<img style="width: 200px;" src="https://static.igem.org/mediawiki/2017/d/da/UU-poster-landscape.png">
 +
</div>
 +
 +
<div class="description"><a target=_BLANK href="https://static.igem.org/mediawiki/2017/4/4e/UU-poster-landscape-fullsize.pdf" class="pdf">Download poster</a></div>
 +
</div>
 +
 +
</div>
 +
 +
<div style="clear: both;"></div>
 +
 +
<style type="text/css">
 +
.outreach-video
 +
{
 +
width: 230px;
 +
    padding: 20px;
 +
    background: #fafafa;
 +
    float: left;
 +
    border: 2px solid #f6f6f6;
 +
    margin: 0 30px 0 0;
 +
display: inline-block;
 +
text-align: center;
 +
}
 +
 +
.outreach-video.right { float: right; margin-right: 0; }
 +
 +
.outreach-video>h2 { font-size: 17px; color: black; font-weight: bold; padding-bottom: 10px; border-bottom: 2px solid #f6f6f6; }
 +
 +
.outreach-video .description { font-size: 12px; line-height: 20px; display: inline-block; }
 +
</style>
 +
 
</script>
 
</script>
 
 
Line 3,479: Line 3,897:
 
6: "Administrative assistance",
 
6: "Administrative assistance",
 
7: "Final word"
 
7: "Final word"
−
}
+
},
 +
"basic_part" : {},
 +
"composite_part" : {},
 +
"posters" : {}
 
};
 
};
  
Line 3,499: Line 3,920:
 
if($$("body")[0].getAttribute("data-page") == "home")
 
if($$("body")[0].getAttribute("data-page") == "home")
 
{
 
{
−
for(var i = 1; i <= 4; i++)
+
if(same_page)
 
{
 
{
−
if(same_page)
+
for(var i = 1; i <= 4; i++)
 
{
 
{
−
for(var i = 1; i <= 4; i++)
+
jQuery("#popover-" + i).dxPopover("hide");
 +
 +
if(i == 1)
 
{
 
{
−
jQuery("#popover-" + i).dxPopover("hide");
+
jQuery("#link-" + i).addClass("selected");
−
+
jQuery("#link-" + i).addClass("pulsing");
−
if(i == 1)
+
jQuery("#figure-" + i).fadeIn("5");
−
{
+
}
−
jQuery("#link-" + i).addClass("selected");
+
else
−
jQuery("#link-" + i).addClass("pulsing");
+
{
−
jQuery("#figure-" + i).fadeIn("5");
+
jQuery("#link-" + i).removeClass("selected");
−
}
+
jQuery("#figure-" + i).fadeOut("5");
−
else
+
−
{
+
−
jQuery("#link-" + i).removeClass("selected");
+
−
jQuery("#figure-" + i).fadeOut("5");
+
−
}
+
 
}
 
}
 
}
 
}
−
else
+
}
 +
else
 +
{
 +
for(var i = 1; i <= 4; i++)
 +
{
 +
jQuery("#popover-" + i).dxPopover({
 +
animation: { show: { type: 'fade', from: 0, to: 1, duration: 0 }, hide: { type: 'fade', to: 0, duration: 0 } }
 +
}).dxPopover("hide");
 +
}
 +
}
 +
}
 +
else if($$("body")[0].getAttribute("data-page") == "product-design")
 +
{
 +
if(same_page)
 +
{
 +
for(var i = 1; i <= 9; i++)
 +
{
 +
jQuery("#popover-" + i).dxPopover("hide");
 +
 +
if(i == 1)
 +
{
 +
jQuery("#link-" + i).addClass("selected");
 +
jQuery("#link-" + i).addClass("pulsing");
 +
jQuery("#figure-" + i).fadeIn("5");
 +
}
 +
else
 +
{
 +
jQuery("#link-" + i).removeClass("selected");
 +
jQuery("#figure-" + i).fadeOut("5");
 +
}
 +
}
 +
}
 +
else
 +
{
 +
for(var i = 1; i <= 9; i++)
 
{
 
{
 
jQuery("#popover-" + i).dxPopover({
 
jQuery("#popover-" + i).dxPopover({
Line 3,645: Line 4,097:
 
 
 
if(return_false)
 
if(return_false)
 +
{
 +
history.pushState({page: page}, page, page);
 +
 
return false;
 
return false;
 +
}
 
}
 
}
 +
 +
jQuery(window).on("popstate", function(e) {
 +
if(typeof e.originalEvent !== "undefined")
 +
{
 +
if(e.originalEvent.state !== "undefined")
 +
{
 +
if(e.originalEvent.state == null)
 +
change_page("home");
 +
else if(e.originalEvent.state.page !== "undefined")
 +
change_page(e.originalEvent.state.page);
 +
}
 +
}
 +
});
  
 
function getSectionByPage(page)
 
function getSectionByPage(page)
Line 3,656: Line 4,125:
 
else
 
else
 
{
 
{
−
var section = $$(".section[data-url='" + page + "']")[0];
+
if($$(".section[data-url='" + page + "']").length == 0)
−
+
key = "home";
−
key = section.up(".sections").getAttribute("data-key");
+
else
 +
{
 +
var section = $$(".section[data-url='" + page + "']")[0];
 +
 +
if(typeof section.up(".sections") !== "undefined")
 +
key = section.up(".sections").getAttribute("data-key");
 +
else
 +
key = "home";
 +
}
 
}
 
}
 
 
Line 3,678: Line 4,155:
 
"contribution": "interlab-study",
 
"contribution": "interlab-study",
 
"model": "modeling-and-mathematics",
 
"model": "modeling-and-mathematics",
−
"improve": "",
+
"improve": "achievements",
−
"attributions": "team",
+
−
"basic_part": "",
+
−
"composite_part": "",
+
 
"hp/silver": "stakeholders",
 
"hp/silver": "stakeholders",
 
"hp/gold_integrated": "product-design",
 
"hp/gold_integrated": "product-design",
Line 3,736: Line 4,210:
 
var page = element.getAttribute("data-url");
 
var page = element.getAttribute("data-url");
 
 
−
history.pushState({}, title, page);
+
history.pushState({page: page}, title, page);
 
 
 
change_page(page);
 
change_page(page);
Line 3,766: Line 4,240:
 
page = "/igemsite/";
 
page = "/igemsite/";
 
 
−
history.pushState({}, title, page);
+
history.pushState({page: page}, title, page);
 
}
 
}
 
});
 
});
Line 3,820: Line 4,294:
 
});
 
});
 
});
 
});
 +
</script>
 +
 +
<script id="modal-rivm-event" type="text/template">
 +
<img width="650" src="https://static.igem.org/mediawiki/2017/f/f7/8997_Kennisparade_%281%29.jpg">
 
</script>
 
</script>
  

Latest revision as of 00:24, 15 December 2017

<!DOCTYPE html>

  • Home
  • Experimental
  • Human practices
  • Team & Sponsors
Cas9 & Cpf1 secretion
and activity
Comparison of endonuclease activity for Cas9 and Cpf1 that has been produced in, and excreted by, HEK293 cells.
MESA two-component system replication
Details on the MESA two-component system, explanation of its relation to our design and the results of its reproduction.
OUTCASST system production
Detailed explanation of the OUTCASST mechanism, experimental progress and technical prospects.
Modeling and
mathematics
Ordinary differential equations, cellular automaton and an object based model for optimal linker-length estimation.
InterLab study participation
Results and details of our measurements for the iGEM 2017 InterLab Study.
Stakeholders & opinions
Interviews and dialogues with stakeholders, potential users, third parties and experts relating to pathogen detection or DNA-based diagnostics.
Risks & safety-issues
Implications and design considerations relating to safety in the usage and implementation of OUTCASST as a diagnostics tool.
Design & integration
OUTCASST toolkit and product design with factors such as bio-safety and user-friendliness taken into account.
Outreach
Videos we made for the dutch public, together with 'de Kennis van Nu'.
Meet our team
About us, our interests and roles in the team and our supervisors.
Sponsors
A listing of our sponsors, how they assisted us and our gratitude for their assistance.
Collaborations
Read about our exchanges with other iGEM teams and government agencies.
Achievements
A short description of all that we have achieved during our participation in the iGEM.
Attributions
A thank-you for everyone that assited us, both in and outside the lab.
Intro
The problem
The system