Difference between revisions of "Team:Munich/Testflow"

 
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<head>
 
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+
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+
 
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</style>
 
</style>
</head><body>
+
</head></html>
 +
{{Munich/Menu}}
 +
<html>
 +
<body>
 
<table width=100% height=100% cellpadding=0 cellspacing=0 border=0>
 
<table width=100% height=100% cellpadding=0 cellspacing=0 border=0>
 
<!-- Bar -->
 
<tr><td height="50" bgcolor=#ffffff></td><td class="no-padding" bgcolor=#ffffff height="32" width="960" align=center>
 
<div class="dropdown">
 
  <a href="/Team:Munich"><button class="dropbtnCascAID dropbtn"><img src="https://static.igem.org/mediawiki/2017/0/08/T--Munich--Overlay.png"></button></a>
 
</div><div class="dropdown">
 
  <a href="project"><button class="dropbtnProject dropbtn"><img src="https://static.igem.org/mediawiki/2017/0/08/T--Munich--Overlay.png"><p><b>Project</b></p></button></a>  <div class="dropdown-contentDescription dropdown-content">
 
    <a href="description"><p><b>Description</b></p></a>
 
  </div>
 
  <div class="dropdown-contentDesign dropdown-content">
 
    <a href="design"><p><b>Design</b></p></a>
 
  </div>
 
  <div class="dropdown-contentProofofConcept dropdown-content">
 
    <a href="proofofconcept"><p><b>Proof of Concept</b></p></a>
 
  </div>
 
  <div class="dropdown-contentDemonstration dropdown-content">
 
    <a href="demonstration"><p><b>Demonstration</b></p></a>
 
  </div>
 
  <div class="dropdown-contentApplication dropdown-content">
 
    <a href="application"><p><b>Application</b></p></a>
 
  </div>
 
  <div class="dropdown-contentFinalResults dropdown-content">
 
    <a href="finalresults"><p><b>Final Results</b></p></a>
 
  </div>
 
  <div class="dropdown-contentEntrepreneurship dropdown-content">
 
    <a href="entrepreneurship"><p><b>Entrepeneurship</b></p></a>
 
  </div>
 
  <div class="dropdown-contentAchievements dropdown-content">
 
    <a href="achievements"><p><b>Achievements</b></p></a>
 
  </div>
 
</div><div class="dropdown" valign=center>
 
<a href="wetlab"><button class="dropbtnWetlab dropbtn" valign=center><img src="https://static.igem.org/mediawiki/2017/0/08/T--Munich--Overlay.png"><p><b>Wetlab</b></p></button></a>
 
  <div class="dropdown-contentProtocolsMethods dropdown-content">
 
    <a href="protocolsmethods"><p><b>Protocols and<br> Methods</b></p></a>
 
  </div>
 
  <div class="dropdown-contentMaterials dropdown-content">
 
    <a href="materials"><p><b>Materials</b></p></a>
 
  </div>
 
  <div class="dropdown-contentLabJournal dropdown-content">
 
    <a href="labjournal"><p><b>LabJournal</b></p></a>
 
  </div>
 
  <div class="dropdown-contentSafety dropdown-content">
 
    <a href="safety"><p><b>Safety</b></p></a>
 
  </div>
 
  <div class="dropdown-contentParts dropdown-content">
 
    <a href="parts"><p><b>Parts</b></p></a>
 
  </div>
 
  <div class="dropdown-contentInterlab dropdown-content">
 
    <a href="interlab"><p><b>Interlab</b></p></a>
 
  </div>
 
</div><div class="dropdown">
 
  <a href="model"><button class="dropbtnModel dropbtn"><img src="https://static.igem.org/mediawiki/2017/0/08/T--Munich--Overlay.png"><p><b>Modelling</b></p></button></a></div><div class="dropdown">
 
  <a href="softhardware"><button class="dropbtnSoftHardware dropbtn"><img src="https://static.igem.org/mediawiki/2017/0/08/T--Munich--Overlay.png"><p><b>Software/Hardware</b></p></button></a>
 
  <div class="dropdown-contentSoftware dropdown-content">
 
    <a href="software"><p><b>Software</b></p></a>
 
  </div>
 
  <div class="dropdown-contentHardware dropdown-content">
 
    <a href="hardware"><p><b>Hardware</b></p></a>
 
  </div>
 
</div><div class="dropdown">
 
  <a href="hp"><button class="dropbtnHP dropbtn"><img src="https://static.igem.org/mediawiki/2017/0/08/T--Munich--Overlay.png"><p><b>Human Practices</b></p></button></a>
 
  <div class="dropdown-contentHPSilver dropdown-content">
 
    <a href="hpsilver"><p><b>Human Practices (Silver)</b></p></a>
 
  </div>
 
  <div class="dropdown-contentIHPgold dropdown-content">
 
    <a href="ihpgold"><p><b>Human Practices (Gold)</b></p></a>
 
  </div>
 
  <div class="dropdown-contentPublicEngagement dropdown-content">
 
    <a href="publicengagement"><p><b>Public Engagement</b></p></a>
 
  </div>
 
  <div class="dropdown-contentCollaborations dropdown-content">
 
    <a href="collaborations"><p><b>Collaborations</b></p></a>
 
  </div>
 
</div><div class="dropdown">
 
  <a href="/Team:Munich/Team"><button class="dropbtnTeam dropbtn"><img src="https://static.igem.org/mediawiki/2017/0/08/T--Munich--Overlay.png"><p><b>Team</b></p></button></a>
 
  <div class="dropdown-contentTeamMembers dropdown-content">
 
    <a href="/Team:Munich/Team"><p><b>Team members</b></p></a>
 
  </div>
 
  <div class="dropdown-contentSupervisors dropdown-content">
 
    <a href="supervisors"><p><b>Supervisors</b></p></a>
 
  </div>
 
  <div class="dropdown-contentPIs dropdown-content">
 
    <a href="supervisors"><p><b>PIs</b></p></a>
 
  </div>
 
  <div class="dropdown-contentCollaboratingInstitutions dropdown-content">
 
    <a href="supervisors"><p><b>Institutions</b></p></a>
 
  </div>
 
  <div class="dropdown-contentSponsors dropdown-content">
 
    <a href="sponsors"><p><b>Sponsor
 
s</b></p></a>
 
  </div>
 
  <div class="dropdown-contentAttributions dropdown-content">
 
    <a href="/Team:Munich/Team"><p><b>Attributions</b></p></a>
 
  </div>
 
</div>
 
</td><td height="32" bgcolor=#ffffff></td></tr>
 
 
<!-- Content -->
 
<!-- Content -->
<tr><td width="100%" colspan=3>
+
<tr><td width="100%" colspan=4>
 
<table width=100% height=100% cellpadding=0 cellspacing=0 border=0>
 
<table width=100% height=100% cellpadding=0 cellspacing=0 border=0>
 
<tr>
 
<tr>
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<!-- Head End -->
 
<!-- Head End -->
 
<!-- Content Begin -->
 
<!-- Content Begin -->
<img width="960" src="http://www.startupremarkable.com/wp-content/uploads/2015/02/a-book-a-week-image.jpg" style="margin-bottom: 15px">
+
<img id="TopPicture" width="960" src="https://static.igem.org/mediawiki/2017/0/04/T--Munich--FrontPagePictrues_FinalResults.jpg">
<table width="900" border=0 cellspacing=0 cellpadding=10>
+
<table width="960" border=0 cellspacing=0 cellpadding=10>
<tr><td colspan=3 align=left valign=center>
+
<font size=7 color=#787878><b>Sponsors</b></font>
+
</td></tr>
+
 
<tr>
 
<tr>
<td  colspan = 3 align="left">
+
<td width=160></td>
<p class="introduction">
+
<td width=160></td>
We'd like to thank our sponsors. With their generous financial support and helpful guidance, we were able to develop CascAID to be the project we had envisioned. Their sponsorship allowed us to make the most out of the iGEM-competition and attend the Giant Jamboree.</p>
+
<td width=160></td>
 +
<td width=160></td>
 +
<td width=160></td>
 +
<td width=160></td>
 +
</tr>
 +
<tr><td  colspan=6 align=left valign=center>
 +
<font size=7 color=#51a7f9><b style="color: #51a7f9">Final Results</b></font>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td style="background-color: #51a7f9;" colspan = 6 align="left">
 +
<ul class="menuList" id="menu">
 +
  <li><a href="/Team:Munich/Cas13a">Cas13a</a></li>
 +
  <li><a href="/Team:Munich/Readouts">Readouts</a></li>
 +
  <li><a href="/Team:Munich/Targets">Targets</a></li>
 +
  <li><a href="/Team:Munich/Detection Chip">Detection Chip</a></li>
 +
  <li><a href="/Team:Munich/Amplification">Amplification</a></li>
 +
  <li><a href="/Team:Munich/Biobrick">Biobrick</a></li>
 +
</ul> 
  
 
</td>
 
</td>
 
</tr>
 
</tr>
<tr><td align=center valign=center>
 
<h3>eurofins</h3>
 
<p> 
 
According to all known laws
 
of aviation,
 
  
 
 
there is no way a bee
 
should be able to fly.
 
  
 
+
<tr><td colspan=6 align=center valign=center>
Its wings are too small to get
+
<h1>Overview</h1>
its fat little body off the ground.
+
 
+
 
+
The bee, of course, flies anyway
+
 
+
 
+
because bees don't care
+
what humans think is impossible.
+
 
+
 
+
Yellow, black. Yellow, black.
+
Yellow, black. Yellow, black.
+
 
+
 
+
Ooh, black and yellow!
+
Let's shake it up a little.
+
 
+
 
+
Barry! Breakfast is ready!
+
 
+
 
+
Ooming!
+
 
+
 
+
Hang on a second.
+
 
+
 
+
Hello?
+
 
+
 
+
- Barry?
+
- Adam?
+
 
+
 
+
- Oan you believe this is happening?
+
- I can't. I'll pick you up.
+
 
+
 
+
Looking sharp.
+
 
+
 
+
Use the stairs. Your father
+
paid good money for those.
+
 
+
 
+
Sorry. I'm excited.
+
 
+
 
+
Here's the graduate.
+
We're very proud of you, son.
+
 
+
 
+
A perfect report card, all B's.
+
 
+
 
+
Very proud.
+
 
+
 
+
Ma! I got a thing going here.
+
 
+
 
+
- You got lint on your fuzz.
+
- Ow! That's me!
+
 
+
 
+
- Wave to us! We'll be in row 118,000.
+
- Bye!
+
 
+
 
+
Barry, I told you,
+
stop flying in the house!
+
 
+
 
+
- Hey, Adam.
+
- Hey, Barry.
+
 
+
 
+
- Is that fuzz gel?
+
- A little. Special day, graduation.
+
 
+
 
+
Never thought I'd make it.
+
 
+
 
+
Three days grade school,
+
three days high school.
+
 
+
 
+
Those were awkward.
+
 
+
 
+
Three days college. I'm glad I took
+
a day and hitchhiked around the hive.
+
 
+
 
+
You did come back different.
+
</p>
+
 
+
 
+
</td>
+
<td align=center valign=center>
+
<img src="https://static.igem.org/mediawiki/2017/6/65/T--Munich--Logo_Eurofins.png" width="270">
+
</td></tr>
+
<tr><td align=center valign=center>
+
<h3>New England Biolabs</h3>
+
 
<p>   
 
<p>   
According to all known laws
+
We demonstrated that each of the modules of our platform (extraction, amplification and detection of pathogenic RNA) is functional, although we did not yet fully integrate all the modules into a final product.  
of aviation,
+
 
+
 
+
there is no way a bee
+
should be able to fly.
+
 
+
 
+
Its wings are too small to get
+
its fat little body off the ground.
+
 
+
 
+
The bee, of course, flies anyway
+
 
+
 
+
because bees don't care
+
what humans think is impossible.
+
 
+
 
+
Yellow, black. Yellow, black.
+
Yellow, black. Yellow, black.
+
 
+
 
+
Ooh, black and yellow!
+
Let's shake it up a little.
+
 
+
 
+
Barry! Breakfast is ready!
+
 
+
 
+
Ooming!
+
 
+
 
+
Hang on a second.
+
 
+
 
+
Hello?
+
 
+
 
+
- Barry?
+
- Adam?
+
 
+
 
+
- Oan you believe this is happening?
+
- I can't. I'll pick you up.
+
 
+
 
+
Looking sharp.
+
 
+
 
+
Use the stairs. Your father
+
paid good money for those.
+
 
+
 
+
Sorry. I'm excited.
+
 
+
 
+
Here's the graduate.
+
We're very proud of you, son.
+
 
+
 
+
A perfect report card, all B's.
+
 
+
 
+
Very proud.
+
 
+
 
+
Ma! I got a thing going here.
+
 
+
 
+
- You got lint on your fuzz.
+
- Ow! That's me!
+
 
+
 
+
- Wave to us! We'll be in row 118,000.
+
- Bye!
+
 
+
 
+
Barry, I told you,
+
stop flying in the house!
+
 
+
 
+
- Hey, Adam.
+
- Hey, Barry.
+
 
+
 
+
- Is that fuzz gel?
+
- A little. Special day, graduation.
+
 
+
 
+
Never thought I'd make it.
+
 
+
 
+
Three days grade school,
+
three days high school.
+
 
+
 
+
Those were awkward.
+
 
+
 
+
Three days college. I'm glad I took
+
a day and hitchhiked around the hive.
+
 
+
 
+
You did come back different.
+
 
</p>
 
</p>
  
 
+
<h3>What worked</h3>
 +
  <ul class="listResults">
 +
          <li><a href="/Team:Munich/Cas13a">Demonstrated functionality of Lbu and Lwa Cas13a.</a></li>
 +
          <li><a href="/Team:Munich/Cas13a">Modelled the detection limit of our circuit and confirmed it experimentally (~10 nM RNA).</a></li>
 +
          <li><a href="/Team:Munich/Cas13a">Detected pathogen RNA sequence from <i> in vitro </i> and <i> in vivo </i> sources.</a></li>
 +
          <li><a href="/Team:Munich/Targets">Differentiated viral sequences from bacterial sequences.</a></li>
 +
          <li><a href="/Team:Munich/Readouts">Used RNase Alert and Spinach aptamer read-out circuits.</a></li>
 +
          <li><a href="/Team:Munich/Readouts">Used gold nanoparticles to detect general RNase activity.</a></li>
 +
          <li><a href="/Team:Munich/Detection">Detected RNA in bulk, on paper, and from lyophilized Cas13a.</a></li>
 +
          <li><a href="/Team:Munich/Detection">Constructed a functional fluorescence detector with high sensitivity and low production cost.</a></li>
 +
          <li><a href="/Team:Munich/Cas13a">Detected RNA in bulk, on paper, and from lyophilized Cas13a.</a></li>
 +
          <li><a href="/Team:Munich/Amplification">Amplified target with RPA and transcription on paper.</a></li>
 +
          <li><a href="/Team:Munich/Parts">Improved the biobrick BBa_K1319008 by adding a 6x His-tag and provided Cas13a Lwa as three different composite biobricks.</a></li>
 +
          <li><a href="/Team:Munich/Part_Collection">Characterized the GFP degradation tags and sent them as a part collection.</a></li>
 +
  </ul>
 +
<h3>What presented issues</h3>
 +
  <ul class="listResults">
 +
          <li><a href="/Team:Munich/Cas13a">Optimizing the purification protocol for Cas13a.</a></li>
 +
          <li><a href="/Team:Munich/Cas13a">Demonstrating functionality of Lsh Cas13a.</a></li>
 +
          <li><a href="/Team:Munich/Cas13a">Ruling out RNase contamination from heat-lysed in vivo samples.</a></li>
 +
          <li><a href="/Team:Munich/Targets">Detecting Q5 beta RNA.</a></li>
 +
          <li><a href="/Team:Munich/Targets">Reducing cross-talk between <i> E.coli </i> crRNA and <i> B.subtilitis </i> target RNA.</a></li>
 +
          <li><a href="/Team:Munich/Readouts">Developing colorimetric read-outs.</a></li>
 +
          <li><a href="/Team:Munich/Detection">Optimizing the lyophilization and stability of Cas13a.</a></li>
 +
          <li><a href="/Team:Munich/Amplification">Performing RPA and transcription on chip.</a></li>
 +
  </ul>
 
</td>
 
</td>
<td align=center valign=center>
+
</tr>
<img src="https://static.igem.org/mediawiki/2017/8/87/T--Munich--wiki_image_sponsors_neb.svg" width="270">
+
</td></tr>  
+
 
+
<tr><td align=center valign=center>
+
<h3>biomers.net</h3>
+
<p> 
+
According to all known laws
+
of aviation,
+
 
+
 
+
there is no way a bee
+
should be able to fly.
+
 
+
 
+
Its wings are too small to get
+
its fat little body off the ground.
+
 
+
 
+
The bee, of course, flies anyway
+
 
+
 
+
because bees don't care
+
what humans think is impossible.
+
 
+
 
+
Yellow, black. Yellow, black.
+
Yellow, black. Yellow, black.
+
 
+
 
+
Ooh, black and yellow!
+
Let's shake it up a little.
+
 
+
 
+
Barry! Breakfast is ready!
+
 
+
 
+
Ooming!
+
 
+
 
+
Hang on a second.
+
 
+
 
+
Hello?
+
 
+
 
+
- Barry?
+
- Adam?
+
 
+
 
+
- Oan you believe this is happening?
+
- I can't. I'll pick you up.
+
 
+
 
+
Looking sharp.
+
 
+
 
+
Use the stairs. Your father
+
paid good money for those.
+
 
+
 
+
Sorry. I'm excited.
+
 
+
 
+
Here's the graduate.
+
We're very proud of you, son.
+
 
+
 
+
A perfect report card, all B's.
+
 
+
 
+
Very proud.
+
 
+
 
+
Ma! I got a thing going here.
+
 
+
 
+
- You got lint on your fuzz.
+
- Ow! That's me!
+
 
+
 
+
- Wave to us! We'll be in row 118,000.
+
- Bye!
+
 
+
 
+
Barry, I told you,
+
stop flying in the house!
+
 
+
 
+
- Hey, Adam.
+
- Hey, Barry.
+
 
+
 
+
- Is that fuzz gel?
+
- A little. Special day, graduation.
+
 
+
 
+
Never thought I'd make it.
+
 
+
 
+
Three days grade school,
+
three days high school.
+
 
+
 
+
Those were awkward.
+
 
+
 
+
Three days college. I'm glad I took
+
a day and hitchhiked around the hive.
+
 
+
 
+
You did come back different.
+
</p>
+
 
+
  
 +
<tr><td align=center valign=center colspan=3>
 +
<img width=440 src="https://static.igem.org/mediawiki/2017/7/7d/Detector_hw_startpage.jpeg">
 
</td>
 
</td>
<td align=center valign=center>
+
<td align=center valign=center colspan=3>
<img src="https://static.igem.org/mediawiki/2017/a/a9/T--Munich--wiki_image_sponsors_biomers.png" width="270">
+
<img width=440 src="https://static.igem.org/mediawiki/2017/e/e2/T--Munich--Hardware_kinetic.png">
</td></tr>
+
 
+
 
+
<tr><td align=center valign=center>
+
<h3>GATC Biotech</h3>
+
<p> 
+
According to all known laws
+
of aviation,
+
 
+
 
+
there is no way a bee
+
should be able to fly.
+
 
+
 
+
Its wings are too small to get
+
its fat little body off the ground.
+
 
+
 
+
The bee, of course, flies anyway
+
 
+
 
+
because bees don't care
+
what humans think is impossible.
+
 
+
 
+
Yellow, black. Yellow, black.
+
Yellow, black. Yellow, black.
+
 
+
 
+
Ooh, black and yellow!
+
Let's shake it up a little.
+
 
+
 
+
Barry! Breakfast is ready!
+
 
+
 
+
Ooming!
+
 
+
 
+
Hang on a second.
+
 
+
 
+
Hello?
+
 
+
 
+
- Barry?
+
- Adam?
+
 
+
 
+
- Oan you believe this is happening?
+
- I can't. I'll pick you up.
+
 
+
 
+
Looking sharp.
+
 
+
 
+
Use the stairs. Your father
+
paid good money for those.
+
 
+
 
+
Sorry. I'm excited.
+
 
+
 
+
Here's the graduate.
+
We're very proud of you, son.
+
 
+
 
+
A perfect report card, all B's.
+
 
+
 
+
Very proud.
+
 
+
 
+
Ma! I got a thing going here.
+
 
+
 
+
- You got lint on your fuzz.
+
- Ow! That's me!
+
 
+
 
+
- Wave to us! We'll be in row 118,000.
+
- Bye!
+
 
+
 
+
Barry, I told you,
+
stop flying in the house!
+
 
+
 
+
- Hey, Adam.
+
- Hey, Barry.
+
 
+
 
+
- Is that fuzz gel?
+
- A little. Special day, graduation.
+
 
+
 
+
Never thought I'd make it.
+
 
+
 
+
Three days grade school,
+
three days high school.
+
 
+
 
+
Those were awkward.
+
 
+
 
+
Three days college. I'm glad I took
+
a day and hitchhiked around the hive.
+
 
+
 
+
You did come back different.
+
</p>
+
 
+
 
+
 
</td>
 
</td>
<td align=center valign=center>
+
</tr>
<img src="https://static.igem.org/mediawiki/2017/5/59/T--Munich--wiki_image_sponsors_gatc.png" width="270">
+
<tr><td colspan=6 align=center valign=center>
</td></tr>  
+
<h1>Discussion</h1>
 
+
<tr><td align=center valign=center>
+
<h3>GE Healthcare</h3>
+
 
<p>   
 
<p>   
According to all known laws
+
Our project CascAID is a universal solution for low cost, point of care diagnostics of infectious diseases. Currently, the available diagnostic tools are based on PCR, antibodies or microbiological methods which all need trained personal and lab equipments. Therefore, these methods are cost and time consuming. This gives rise to the need of developing effective, affordable and portable devices.</p><p>
of aviation,
+
In our project, we first successfully replicated the Cas13a-based detection of RNA pathogens that was demonstrated by Gootenberg et al. Although this result is not novel, we thoroughly characterized the target detection limit for different bacterial and viral targets, from <i> in vitro </i> and <i> in vivo </i> sources, and proved the possibility to discriminate between viruses and bacteria with high specificity. We laid the groundwork for colorimetric read-outs that will add another layer of amplification in our cascade detection (gold nanoparticles, intein-extein and ssDNA amplification). Those readouts should allow for a practical readability of the diagnosis by the user without the need of digital analysis. Additionally, their amplification scheme should also lower the detection limit of the Cas13a without the need for pre-amplification of the target. </p><p>
 
+
However, we worked in parallel on a scheme for amplifying the target using RPA and transcription. Although the reaction worked on paper, it did not work on chip due to the toxicity of the PDMS to the reaction.  
 
+
We built a fluorescence detector with high sensitivity to cost ratio, and used it successfully to detect Cas13a activity. However, the product itself needs to be redesigned for market distribution: in general, a fluorescence detector is not necessarily user-friendly, the extraction of the RNA on chip needs to be optimized, and the costs of the whole product must be lowered. </p><p>
there is no way a bee
+
Nevertheless, we are glad to have created a functional platform that allows the detection of nanomolar concentrations of pathogens within 30 minutes. With our modular approach, we have shown at least proof-of-concept results for each part, and are confident that no fundamental gap prevents our platform from being usable, only optimization.  
should be able to fly.
+
 
+
 
+
Its wings are too small to get
+
its fat little body off the ground.
+
 
+
 
+
The bee, of course, flies anyway
+
 
+
 
+
because bees don't care
+
what humans think is impossible.
+
 
+
 
+
Yellow, black. Yellow, black.
+
Yellow, black. Yellow, black.
+
 
+
 
+
Ooh, black and yellow!
+
Let's shake it up a little.
+
 
+
 
+
Barry! Breakfast is ready!
+
 
+
 
+
Ooming!
+
 
+
 
+
Hang on a second.
+
 
+
 
+
Hello?
+
 
+
 
+
- Barry?
+
- Adam?
+
 
+
 
+
- Oan you believe this is happening?
+
- I can't. I'll pick you up.
+
 
+
 
+
Looking sharp.
+
 
+
 
+
Use the stairs. Your father
+
paid good money for those.
+
 
+
 
+
Sorry. I'm excited.
+
 
+
 
+
Here's the graduate.
+
We're very proud of you, son.
+
 
+
 
+
A perfect report card, all B's.
+
 
+
 
+
Very proud.
+
 
+
 
+
Ma! I got a thing going here.
+
 
+
 
+
- You got lint on your fuzz.
+
- Ow! That's me!
+
 
+
 
+
- Wave to us! We'll be in row 118,000.
+
- Bye!
+
 
+
 
+
Barry, I told you,
+
stop flying in the house!
+
 
+
 
+
- Hey, Adam.
+
- Hey, Barry.
+
 
+
 
+
- Is that fuzz gel?
+
- A little. Special day, graduation.
+
 
+
 
+
Never thought I'd make it.
+
 
+
 
+
Three days grade school,
+
three days high school.
+
 
+
 
+
Those were awkward.
+
 
+
 
+
Three days college. I'm glad I took
+
a day and hitchhiked around the hive.
+
 
+
 
+
You did come back different.
+
 
</p>
 
</p>
 
 
 
</td>
 
</td>
<td align=center valign=center>
+
</tr>
<img src="https://static.igem.org/mediawiki/2017/1/1b/T--Munich--wiki_image_sponsors_gehealthcare.svg" width="270">
+
</td></tr>  
+
<tr><td align=center valign=center>
+
<h3>Integrated DNA Technologies</h3>
+
<p> 
+
According to all known laws
+
of aviation,
+
  
 
+
<tr><td colspan=6 align=center valign=center>
there is no way a bee
+
<h1>Outlook</h1>
should be able to fly.
+
 
+
 
+
Its wings are too small to get
+
its fat little body off the ground.
+
 
+
 
+
The bee, of course, flies anyway
+
 
+
 
+
because bees don't care
+
what humans think is impossible.
+
 
+
 
+
Yellow, black. Yellow, black.
+
Yellow, black. Yellow, black.
+
 
+
 
+
Ooh, black and yellow!
+
Let's shake it up a little.
+
 
+
 
+
Barry! Breakfast is ready!
+
 
+
 
+
Ooming!
+
 
+
 
+
Hang on a second.
+
 
+
 
+
Hello?
+
 
+
 
+
- Barry?
+
- Adam?
+
 
+
 
+
- Oan you believe this is happening?
+
- I can't. I'll pick you up.
+
 
+
 
+
Looking sharp.
+
 
+
 
+
Use the stairs. Your father
+
paid good money for those.
+
 
+
 
+
Sorry. I'm excited.
+
 
+
 
+
Here's the graduate.
+
We're very proud of you, son.
+
 
+
 
+
A perfect report card, all B's.
+
 
+
 
+
Very proud.
+
 
+
 
+
Ma! I got a thing going here.
+
 
+
 
+
- You got lint on your fuzz.
+
- Ow! That's me!
+
 
+
 
+
- Wave to us! We'll be in row 118,000.
+
- Bye!
+
 
+
 
+
Barry, I told you,
+
stop flying in the house!
+
 
+
 
+
- Hey, Adam.
+
- Hey, Barry.
+
 
+
 
+
- Is that fuzz gel?
+
- A little. Special day, graduation.
+
 
+
 
+
Never thought I'd make it.
+
 
+
 
+
Three days grade school,
+
three days high school.
+
 
+
 
+
Those were awkward.
+
 
+
 
+
Three days college. I'm glad I took
+
a day and hitchhiked around the hive.
+
 
+
 
+
You did come back different.
+
</p>
+
 
+
 
+
</td>
+
<td align=center valign=center>
+
<img src="https://static.igem.org/mediawiki/2017/1/1a/T--Munich--wiki_image_sponsors_idt.png" width="270">
+
</td></tr>
+
<tr><td align=center valign=center>
+
<h3>Promega</h3>
+
 
<p>   
 
<p>   
According to all known laws
+
We still have some project sections that we need to improve in the future. We have therefore listed the following points that need to be optimized below.
of aviation,
+
 
+
 
+
there is no way a bee
+
should be able to fly.
+
 
+
 
+
Its wings are too small to get
+
its fat little body off the ground.
+
 
+
 
+
The bee, of course, flies anyway
+
 
+
 
+
because bees don't care
+
what humans think is impossible.
+
 
+
 
+
Yellow, black. Yellow, black.
+
Yellow, black. Yellow, black.
+
 
+
 
+
Ooh, black and yellow!
+
Let's shake it up a little.
+
 
+
 
+
Barry! Breakfast is ready!
+
 
+
 
+
Ooming!
+
 
+
 
+
Hang on a second.
+
 
+
 
+
Hello?
+
 
+
 
+
- Barry?
+
- Adam?
+
 
+
 
+
- Oan you believe this is happening?
+
- I can't. I'll pick you up.
+
 
+
 
+
Looking sharp.
+
 
+
 
+
Use the stairs. Your father
+
paid good money for those.
+
 
+
 
+
Sorry. I'm excited.
+
 
+
 
+
Here's the graduate.
+
We're very proud of you, son.
+
 
+
 
+
A perfect report card, all B's.
+
 
+
 
+
Very proud.
+
 
+
 
+
Ma! I got a thing going here.
+
 
+
 
+
- You got lint on your fuzz.
+
- Ow! That's me!
+
 
+
 
+
- Wave to us! We'll be in row 118,000.
+
- Bye!
+
 
+
 
+
Barry, I told you,
+
stop flying in the house!
+
 
+
 
+
- Hey, Adam.
+
- Hey, Barry.
+
 
+
 
+
- Is that fuzz gel?
+
- A little. Special day, graduation.
+
 
+
 
+
Never thought I'd make it.
+
 
+
 
+
Three days grade school,
+
three days high school.
+
 
+
 
+
Those were awkward.
+
 
+
 
+
Three days college. I'm glad I took
+
a day and hitchhiked around the hive.
+
 
+
 
+
You did come back different.
+
 
</p>
 
</p>
 
+
  <ul class="listResults">
 
+
          <li><i> In vivo </i> heat lysis: During our experiments, we realized that the RNA extraction of <i> E. coli </i> using heat lysis is not always optimal for our experimental setup due to the fact that we have RNase contamination in the extracted RNA samples. Although our Cas13a cleavage assays are performed in presence RNase Inhibitor to suppress the activity of the RNases that could be present, we saw that the heat lysed samples show relatively higher fluorescence activity in comparison to the phenol chloroform extracted samples</li>
 +
          <li>RNA extraction and amplification: The RNA extraction from the <i> Bacillus subtilis </i> was particularly difficult in our case since <i> B. subtilis </i> is a gram positive, spore forming bacteria. Also the amount and the quality of the RNA extracted from the <i> B. subtilis </i> and <i> E.coli </i> cultures were sufficiently good. We therefore should find methods to improve either the RNA extraction protocol or use a better amplification steps after the extraction.</li>
 +
          <li>Cost of the chip: Now, the cost of our chip is less than 15 dollars per chip. We could still try to minimize the costs by reducing the chip size and making it fully recyclable. However, at industrial level one could potentially reduce the cost of the chip.</li>
 +
          <li>Lyophilization of Cas13a: We also figured out that the lyophilization protocol of the Cas13a has to be improved in order to make our paper chip portable and sustainable. We also tried drying the Cas13a with the tardigrade intrinsically disordered proteins (TDPs) from team Delft but still it wasn’t that effective as expected. Therefore, we have to integrate some better methods to lyophilize the Cas13a without losing its activity.</li>
 +
          <li>Readouts with color and amplification: The colorimetric readout is also something we need to work on and improve since we only managed to partially succeed with the colorimetric assays. We however think that it is possible to realize this using more elegant ways of RNA detection and this is something we could try in future.</li>
 +
          <li>Integration of all the modules of the platform: Although all our modules parts are functional, we were only able to integrate them partially. So, with more time, we believe that we can have a fully functional and integrated module system.
 +
</li>
 +
  </ul>
 
</td>
 
</td>
<td align=center valign=center>
+
</tr>
<img src="https://static.igem.org/mediawiki/2017/3/3f/T--Munich--wiki_image_sponsors_promega.png" width="270">
+
</td></tr>  
+
  
  
<tr><td class="no-padding" colspan=2 align=right valign=center height=10>
+
<tr><td class="no-padding" colspan=6 align=right valign=center height=10>
 
<br><br><br><center><hr></center>
 
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</td></tr>
 
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Latest revision as of 19:24, 31 October 2017


Final Results

Overview

We demonstrated that each of the modules of our platform (extraction, amplification and detection of pathogenic RNA) is functional, although we did not yet fully integrate all the modules into a final product.

What worked

What presented issues

Discussion

Our project CascAID is a universal solution for low cost, point of care diagnostics of infectious diseases. Currently, the available diagnostic tools are based on PCR, antibodies or microbiological methods which all need trained personal and lab equipments. Therefore, these methods are cost and time consuming. This gives rise to the need of developing effective, affordable and portable devices.

In our project, we first successfully replicated the Cas13a-based detection of RNA pathogens that was demonstrated by Gootenberg et al. Although this result is not novel, we thoroughly characterized the target detection limit for different bacterial and viral targets, from in vitro and in vivo sources, and proved the possibility to discriminate between viruses and bacteria with high specificity. We laid the groundwork for colorimetric read-outs that will add another layer of amplification in our cascade detection (gold nanoparticles, intein-extein and ssDNA amplification). Those readouts should allow for a practical readability of the diagnosis by the user without the need of digital analysis. Additionally, their amplification scheme should also lower the detection limit of the Cas13a without the need for pre-amplification of the target.

However, we worked in parallel on a scheme for amplifying the target using RPA and transcription. Although the reaction worked on paper, it did not work on chip due to the toxicity of the PDMS to the reaction. We built a fluorescence detector with high sensitivity to cost ratio, and used it successfully to detect Cas13a activity. However, the product itself needs to be redesigned for market distribution: in general, a fluorescence detector is not necessarily user-friendly, the extraction of the RNA on chip needs to be optimized, and the costs of the whole product must be lowered.

Nevertheless, we are glad to have created a functional platform that allows the detection of nanomolar concentrations of pathogens within 30 minutes. With our modular approach, we have shown at least proof-of-concept results for each part, and are confident that no fundamental gap prevents our platform from being usable, only optimization.

Outlook

We still have some project sections that we need to improve in the future. We have therefore listed the following points that need to be optimized below.

  • In vivo heat lysis: During our experiments, we realized that the RNA extraction of E. coli using heat lysis is not always optimal for our experimental setup due to the fact that we have RNase contamination in the extracted RNA samples. Although our Cas13a cleavage assays are performed in presence RNase Inhibitor to suppress the activity of the RNases that could be present, we saw that the heat lysed samples show relatively higher fluorescence activity in comparison to the phenol chloroform extracted samples
  • RNA extraction and amplification: The RNA extraction from the Bacillus subtilis was particularly difficult in our case since B. subtilis is a gram positive, spore forming bacteria. Also the amount and the quality of the RNA extracted from the B. subtilis and E.coli cultures were sufficiently good. We therefore should find methods to improve either the RNA extraction protocol or use a better amplification steps after the extraction.
  • Cost of the chip: Now, the cost of our chip is less than 15 dollars per chip. We could still try to minimize the costs by reducing the chip size and making it fully recyclable. However, at industrial level one could potentially reduce the cost of the chip.
  • Lyophilization of Cas13a: We also figured out that the lyophilization protocol of the Cas13a has to be improved in order to make our paper chip portable and sustainable. We also tried drying the Cas13a with the tardigrade intrinsically disordered proteins (TDPs) from team Delft but still it wasn’t that effective as expected. Therefore, we have to integrate some better methods to lyophilize the Cas13a without losing its activity.
  • Readouts with color and amplification: The colorimetric readout is also something we need to work on and improve since we only managed to partially succeed with the colorimetric assays. We however think that it is possible to realize this using more elegant ways of RNA detection and this is something we could try in future.
  • Integration of all the modules of the platform: Although all our modules parts are functional, we were only able to integrate them partially. So, with more time, we believe that we can have a fully functional and integrated module system.