Difference between revisions of "Team:Dundee/Experiments"

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                 <li><a href="https://2016.igem.org/Team:Dundee/Design">Design</a></li>
 
                 <li><a href="https://2016.igem.org/Team:Dundee/Design">Design</a></li>
 
                 <li><a href="https://2016.igem.org/Team:Dundee/Results">Results</a></li>
 
                 <li><a href="https://2016.igem.org/Team:Dundee/Results">Results</a></li>
−
  <li><a href="https://2016.igem.org/Team:Dundee/Hardware">Hardware</a></li>
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  <li class="active" ><a href="https://2016.igem.org/Team:Dundee/Hardware">Hardware</a></li>
 
               </ul>
 
               </ul>
 
</li>
 
</li>
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               <ul class="dropdown-menu">
 
               <ul class="dropdown-menu">
 
<li><a href="https://2016.igem.org/Team:Dundee/Team">Meet The Agents</a></li>
 
<li><a href="https://2016.igem.org/Team:Dundee/Team">Meet The Agents</a></li>
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                 <li class="active"><a href="https://2016.igem.org/Team:Dundee/Attributions">Attributions</a></li>
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                 <li><a href="https://2016.igem.org/Team:Dundee/Attributions">Attributions</a></li>
 
                 <li><a href="https://2016.igem.org/Team:Dundee/Collaborations">Collaboration</a></li>
 
                 <li><a href="https://2016.igem.org/Team:Dundee/Collaborations">Collaboration</a></li>
 
               </ul>
 
               </ul>
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                   <div id="BackImg">
 
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<img src="https://static.igem.org/mediawiki/2016/f/fa/T--Dundee--Medals.jpg" />
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<img src="https://static.igem.org/mediawiki/2016/5/55/T--Dundee--Hardware.JPG" />
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                                <h1><span>Hardware</span></h1>
 
</div>
 
</div>
  
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<div class="container">
 
<div class="container">
 
<div id = "SplashTitle">
 
<div id = "SplashTitle">
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<p>Judging Criteria</p>
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<p></p>
 
</div>
 
</div>
  
 
<div id="SplashTitleUnder">
 
<div id="SplashTitleUnder">
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<p>Dundee 2016 </p>
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<p>ACME Stomach Masher</p>
 
</div>
 
</div>
 
</div>
 
</div>
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<div class="container">
 
<div class="container">
 
<div  id= "ProjectDesCon">
 
<div  id= "ProjectDesCon">
−
<h3>Bronze</h3>
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<h3>Introduction</h3>
−
+
−
<div id="FlaskImg1">
+
−
<img src="https://static.igem.org/mediawiki/2016/f/f1/T--Dundee--BronzeMedal.png"/>
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−
</div>
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−
<div id="FlaskPos1">
 
−
<p>1. We have registered the team, had a great summer and plan to have fun at the Jamboree.</p>
 
−
<p>2. We have met all deliverables, documented our work on the wiki page, plan to present a poster and presentation at the Jamboree.</p>
 
−
<ul>
 
−
<li>We have also attributed all of the work done for our project. </li>
 
−
<li>We have also created and documented our Part pages on the Registry for the Parts </li>
 
−
<li>We have submitted. And all part samples have been submitted to the Registry. </li>
 
−
<li>We have completed the following forms: About Our Lab, About Project, Final Safety Form and the Judging Form.  </li>
 
−
</ul>
 
−
</li>
 
−
<p>3. We have clearly attributed each aspect of our project.</p>
 
−
<p>4. We have documented the following BioBrick Parts: </p>
 
 
 
−
<ul>
 
−
<li>BBa_K1962000</li>
 
−
<li>BBa_K1962001</li>
 
−
<li>BBa_K1962002</li>
 
−
<li>BBa_K1962004</li>
 
−
<li>BBa_K1962005</li>
 
−
<li>BBa_K1962006</li>
 
−
<li>BBa_K1962015</li>
 
−
<li>BBa_K1962016</li>
 
−
<li>BBa_K1962017</li>
 
−
</ul>
 
−
</div>
 
 
 
 +
<div id="FlaskImg">
 +
<img src="https://static.igem.org/mediawiki/2016/9/97/T--Dundee--Hardware1st.png"/>
 +
</div>
 +
 +
<div id="FlaskPos">
 +
<p>According to Kozu, et al. a simple compressing, rolling motion adequately simulates the stomach’s mechanical stress. With that in mind reusing the internals of a printer came to mind as rollers and motors would be among the recovered parts. Not only was this an economical option but also a environmentally friendly one. The contents of the stomach would be put in a plastic bag that would be passed back and forth through the recovered rollers. To put it all together the Dundee Maker Space laser cutter would be put to
 +
use extensively.</p>
 +
</div>
 
 
 
</div>
 
</div>
 
</div>
 
</div>
−
+
 
 
 
 
<div class="container">
 
<div class="container">
 
<div  id= "ProjectDesCon">
 
<div  id= "ProjectDesCon">
−
<h3>Silver</h3>
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<h3>Planning</h3>
−
+
−
<div id="FlaskImg1">
+
<p>The stomach was modeled in OnShape, a free cloud based CAD suite. Initially the design took advantage of the printer’s linear scanner drive since linear motion was required for the stomach. This choice is reflected in the image above. Unfortunately the motor for the scanner motion was not powerful enough to properly move the contents of the stomach. </p>
−
<img src="https://static.igem.org/mediawiki/2016/3/39/T--Dundee--SilverMedal.png"/>
+
 +
<div id="CytoGifAlign">
 +
<img src="https://static.igem.org/mediawiki/2016/f/f0/T--Dundee--Hardware4.png"/>
 
</div>
 
</div>
−
+
−
<div id="FlaskPos1">
+
−
<p>1. We have experimentally validated that at least one new BioBrick Part of our own design works as expected. </p>
+
−
<ul>
+
−
<li>BBa_K1962003</li>
+
−
<li>BBa_K1962007</li>
+
−
<li>BBa_K1962008</li>
+
−
<li>BBa_K1962009</li>
+
−
<li>BBa_K19620010</li>
+
−
<li>BBa_K19620011</li>
+
−
<li>BBa_K19620012</li>
+
−
<li>BBa_K19620013</li>
+
−
<li>BBa_K19620014</li>
+
−
</ul>
+
−
<p>2. We have helped other iGEM teams by characterizing a part, mentoring a high school team and attending iGEM meetups.</p>
+
−
<p>3. Human practices – silver. Identified and investigated important issues including the sustainability of antibiotics, public concerns on the ethics of using GMOs. We were also involved in organizing a debate with the Edniburgh iGEM team to tackle some misconceptions that the public had on GMOs.</p>
+
 
</div>
 
</div>
 
</div>
 
</div>
−
</div>
+
−
 
+
 
<div class="container">
 
<div class="container">
 
<div  id= "ProjectDesCon">
 
<div  id= "ProjectDesCon">
−
<h3>Gold</h3>
+
<h3>Building</h3>
−
+
−
+
<p>As mentioned, initially the motion was to be provided by the scanner motor. Using this would have simplified the design since it already created a linear motion. Also, controlling it would have been very simple. A double pole double throw (DPDT) switch can easily be used as a mechanical H-Bridge (bi-directional motor controller). When in one position the motor will rotate clockwise, and when flipped to the other position it rotates counter-clockwise. The red end-stops in the image above were positioned to actuate the switch when it reached each end. As soon as it hit the end of travel it would immediately reverse direction. The dead-spot in the switch where it is in neither positions
−
<div id="FlaskImg1">
+
and therefore not conducting electricity was too large and resulted in no motion.
−
<img src="https://static.igem.org/mediawiki/2016/4/45/T--Dundee--GoldMedal.png"/>
+
</p>
 +
<div id="CytoGifAlign">
 +
<img src="https://static.igem.org/mediawiki/2016/1/1e/T--Dundee--Hardware3.png">
 
</div>
 
</div>
 
 
−
<div id="FlaskPos1">
+
<p>With the scanner not working, a spool and thread was turned to. Printers also contain several gear trains, which reduce speed and increase torque, something the scanner motor could have used more of. The string had trouble staying positively engaged with the spool unless under extreme tension. At that point
 +
though the motor needed to do extra work to overcome the added friction. Another issue was that the string would always jam up on one side or the other, depending on the direction of rotation. Looking back, both
 +
problems could have been solved by a much wider spool with the string fastened in the middle. As the string unspooled from one side, it would be taken in on the other. So long as the width of the spool is sufficient, the string will never encounter the edge. Without the benefit of hindsight in the moment, a new method of motion was devised.
 +
</p>
  
−
<p>1. Human practices - gold. Our initial idea was to target infections that cause food poisoning, however we gained valuable feedback from our human practices which made us think about targeting infections at the source of the problem. We also created a BactiFeed product in the lab to explore the real world applications of the device.    </p>
+
<div id="CytoGifAlign">
−
<p>2. We have improved the characterization of a number of parts and documented them in the parts page on the registry.
+
<img src="https://static.igem.org/mediawiki/2016/a/ae/T--Dundee--Hardware2.png">
−
</p>
+
</div>
−
+
 
−
<p>- Improved the characterization of two pH sensitive promoters. We improved them by cloning GFP downstream of the two promoters and measuring GFP fluorescence in different pH conditions.
+
</div>
−
</p>
+
</div>
−
<ul>
+
−
<li>Pasr- BBa_K1231000 </li>
+
<div class="container">
−
<li>PgadA – BBa_K1231001</li>
+
<div  id= "ProjectDesCon">
−
<li>BBa_E0840</li>
+
<h3 style = "color:#3D72A4; text-align:center;" >References</h3>
−
</ul>
+
<div id ="CytoGifHeader">
−
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                          <p>Hiroyuki Kozu, Yuki Nakata, Mitsutoshi Nakajima, Marcos A. Neves, Kunihiko Uemura, Seigo Sato, Isao Kobayashi, Sosaku Ichikawa “Development of a Human Gastric Digestion Simulator Equipped with Peristalsis Function for the Direct Observation and Analysis of the Food Digestion Process”, Food Science and Technology Research, 20 (2), p.225-233</p>
−
<p>- We have also improved the characterization of the acrRA promoter. By cloning the gfp gene downstream and measuring gfp fluorescence. </p>
+
−
+
−
<ul>
+
−
<li>Pasr- BBa_K1231000 </li>
+
−
</ul>
+
−
<p>3. We have created a piece of hardware that will mimic the churning motion in the gut of a chicken in order to test our bactifeed. </p>
+
 
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</div>
 
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<div  id = "BBSRC" class="SponserLink">
 
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<a href="http://www.bbsrc.ac.uk/">
 
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<img class="grayscale" src="https://static.igem.org/mediawiki/2016/8/8b/T--Dundee--BBSRCFooter.png" />
 
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</a>
 
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</div>
 
−
<div class="SponserLink">
 
−
<a href="https://www.sebiology.org/">
 
−
<img  class="grayscale"src="https://static.igem.org/mediawiki/2016/f/f0/T--Dundee--SEBFooter.png" />
 
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</a>
 
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<div id = "WellcomeT" class="SponserLink">
 
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<a href="https://wellcome.ac.uk/">
 
−
<img class="grayscale"src="https://static.igem.org/mediawiki/2016/2/22/T--Dundee--WELLTFooter.png" />
 
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<a href="https://www.facebook.com/DundeeiGEM2016">
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<img src="https://static.igem.org/mediawiki/2016/2/24/T--Dundee--FBFooter.png" />
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</a>
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</div>
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<div id = "MiddleTxt" class="footerImg">
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<img src="https://static.igem.org/mediawiki/2016/b/be/T--Dundee--MiddleFooter.png" />
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<div class="footerImg">
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<a  style="padding-right:0px;"href="https://twitter.com/DundeeiGEMTeam">
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<img  src="https://static.igem.org/mediawiki/2016/4/4f/T--Dundee--TWFooter.png" />
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Revision as of 15:01, 19 October 2016

Dundee 2016

Hardware

ACME Stomach Masher

Introduction

According to Kozu, et al. a simple compressing, rolling motion adequately simulates the stomach’s mechanical stress. With that in mind reusing the internals of a printer came to mind as rollers and motors would be among the recovered parts. Not only was this an economical option but also a environmentally friendly one. The contents of the stomach would be put in a plastic bag that would be passed back and forth through the recovered rollers. To put it all together the Dundee Maker Space laser cutter would be put to use extensively.

Planning

The stomach was modeled in OnShape, a free cloud based CAD suite. Initially the design took advantage of the printer’s linear scanner drive since linear motion was required for the stomach. This choice is reflected in the image above. Unfortunately the motor for the scanner motion was not powerful enough to properly move the contents of the stomach.

Building

As mentioned, initially the motion was to be provided by the scanner motor. Using this would have simplified the design since it already created a linear motion. Also, controlling it would have been very simple. A double pole double throw (DPDT) switch can easily be used as a mechanical H-Bridge (bi-directional motor controller). When in one position the motor will rotate clockwise, and when flipped to the other position it rotates counter-clockwise. The red end-stops in the image above were positioned to actuate the switch when it reached each end. As soon as it hit the end of travel it would immediately reverse direction. The dead-spot in the switch where it is in neither positions and therefore not conducting electricity was too large and resulted in no motion.

With the scanner not working, a spool and thread was turned to. Printers also contain several gear trains, which reduce speed and increase torque, something the scanner motor could have used more of. The string had trouble staying positively engaged with the spool unless under extreme tension. At that point though the motor needed to do extra work to overcome the added friction. Another issue was that the string would always jam up on one side or the other, depending on the direction of rotation. Looking back, both problems could have been solved by a much wider spool with the string fastened in the middle. As the string unspooled from one side, it would be taken in on the other. So long as the width of the spool is sufficient, the string will never encounter the edge. Without the benefit of hindsight in the moment, a new method of motion was devised.

References

Hiroyuki Kozu, Yuki Nakata, Mitsutoshi Nakajima, Marcos A. Neves, Kunihiko Uemura, Seigo Sato, Isao Kobayashi, Sosaku Ichikawa “Development of a Human Gastric Digestion Simulator Equipped with Peristalsis Function for the Direct Observation and Analysis of the Food Digestion Process”, Food Science and Technology Research, 20 (2), p.225-233