Difference between revisions of "Team:HKUST-Rice/Design"

 
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<div id="MYicon1">
 
<div id="MYicon1">
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<a href="https://2015.igem.org/Team:HKUST-Rice/Expression"><img src="https://static.igem.org/mediawiki/2015/e/ea/HKUST-Rice15_leftarrow.png">
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<a href="https://2015.igem.org/Team:HKUST-Rice/Application"><img src="https://static.igem.org/mediawiki/2015/e/ea/HKUST-Rice15_leftarrow.png">
 
<p style="color:#5570b0; font-size: 130%"> Application </p></a>
 
<p style="color:#5570b0; font-size: 130%"> Application </p></a>
 
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</div>
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<div class="project_content">
 
<div class="project_content">
 
<div class="project_row">
 
<div class="project_row">
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<h1>Why Gel imaging is important to synthetic biology? </h1>
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<h1>Motivation</h1>
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<p>Gel electrophoresis is one of the most essential tools in biology, it is an essential part for restriction diagnostic test for nucleic acid, resolving PCR products, etc. Having a gel imaging tool in proximity can increase the productivity of the lab. In our case, since the closest gel imaging tools is far away from HKUST iGEM lab, we decided to build a gel imaging station for our own use, using simple and easy-to-get materials. </p>
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<table>
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<tr>
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<td style="width:48.5%">
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<figure>
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<img  src="https://static.igem.org/mediawiki/2015/9/97/HKUST_Rice15_still_image_diy_gel_doc_webWithinlet.png" style="width:110%;">
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</figure>
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</td>
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<td style="width:2%">
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</td>
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<td style="width:48.5%">
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<video width="320px" height="240px" controls>
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  <source src="https://static.igem.org/mediawiki/2015/a/a6/Team_HKUST-Rice_2015_gel1.mp4" type="video/mp4">
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</video>
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</td>
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</tr>
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<tr>
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<td style="width:48.5%">
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<br>
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<p style="font-size:110%; padding-left:2%; padding-right: 2% ; height'90px';"><strong>A.</strong> A photo was taken using this model of DIY Gel imaging station to prove the functionality of the station. This is the 1<sup>st</sup> photo taken!</p>
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<td style="width:3%">
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</td>
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<td style="width:48.5%">
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<p style="font-size:110%; padding-left:2;height:'90px'; padding-right: 2%"  ><strong>B.</strong> This is a video showing how the Gel Imaging Station actually works.</p>
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</td>
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</tr>
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</table>
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<p>Since its establishment, HKUST iGEM team has been working in small lab pretty far away from the centralized equipment complex. Every time when we want to document our gel or perform gel extraction, we have to carry our gels, walk through a corridor and up a floor to reach the commercial gel documentation system. Starting from this year though, we no longer have to suffer! We have built our own gel imaging system from affordable and easy to get-to-materials, and would like to share with the iGEM community how they make their own.</p>
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</div>
 
</div>
 
<div class="project_row">
 
<div class="project_row">
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<h1>Material for  DIY Gel imaging Station</h1>
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<hr class="para">
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<h1>Materials for  DIY Gel imaging Station</h1>
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<p>The DIY Gel imaging station mainly consists of six parts:</p>
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<p>The DIY Gel imaging station mainly consist of six parts:</p>
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<div class="project_image">
 
<div class="project_image">
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<img src="https://static.igem.org/mediawiki/2015/thumb/c/c4/HKUST_Rice15_still_whole_gel_doc_web_annotated.png/800px-HKUST_Rice15_still_whole_gel_doc_web_annotated.png" alt="Parts of DIY Gel Imaging station " width= "800px">
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<img src="https://static.igem.org/mediawiki/2015/thumb/c/c4/HKUST_Rice15_still_whole_gel_doc_web_annotated.png/800px-HKUST_Rice15_still_whole_gel_doc_web_annotated.png" alt="Parts of DIY Gel Imaging station " width= "700px">
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</div>  
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<br></br></div>  
 
<div class="project_image">
 
<div class="project_image">
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<img src="https://static.igem.org/mediawiki/2015/thumb/0/0f/HKUST_Rice_Green_Filter_annotated.png/800px-HKUST_Rice_Green_Filter_annotated.png" alt="Parts of DIY Gel Imaging station " width= "800px">
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<img src="https://static.igem.org/mediawiki/2015/thumb/0/0f/HKUST_Rice_Green_Filter_annotated.png/800px-HKUST_Rice_Green_Filter_annotated.png" alt="Parts of DIY Gel Imaging station " width= "700px">
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</div>  
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<br></br></div>  
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<div class="project_image">
 
<div class="project_image">
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<img src="https://static.igem.org/mediawiki/2015/thumb/f/f4/HKUST_rice15_UV_trans_illunminator_annotated.png/800px-HKUST_rice15_UV_trans_illunminator_annotated.png" alt="Parts of DIY Gel Imaging station " width= "800px">
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<img src="https://static.igem.org/mediawiki/2015/thumb/f/f4/HKUST_rice15_UV_trans_illunminator_annotated.png/800px-HKUST_rice15_UV_trans_illunminator_annotated.png" alt="Parts of DIY Gel Imaging station " width= "700px">
 
</div>  
 
</div>  
 
<table class= "catalog_table">
 
<table class= "catalog_table">
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<tr><td>2: Camera (Nikon D3200) </td><td>Local electronic store</td><td>$3499</td></tr>
 
<tr><td>2: Camera (Nikon D3200) </td><td>Local electronic store</td><td>$3499</td></tr>
 
<tr><td>3: Computer with monitor for live viewing of Gel</td><td>Laboratory Laptop</td><td>-</td></tr>
 
<tr><td>3: Computer with monitor for live viewing of Gel</td><td>Laboratory Laptop</td><td>-</td></tr>
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<tr><td>4: Green UV filter (PMMA) </td><td>TaoBao</td><td>~$12</td></tr>
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<tr><td>4: Green UV filter (PMMA) </td><td>Taobao</td><td>~$12</td></tr>
 
<tr><td>5: UV trans-illuminator</td><td>HKUST division of life science</td><td>-</td></tr>
 
<tr><td>5: UV trans-illuminator</td><td>HKUST division of life science</td><td>-</td></tr>
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<tr><td>6: Color filters set</td><td>Ebay</td><td>~$124</td></tr>
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<tr><td>6: Color filters set</td><td>ebay</td><td>~$124</td></tr>
 
<tr><td>Total</td><td></td><td>~$3884</td></tr>
 
<tr><td>Total</td><td></td><td>~$3884</td></tr>
 
</table>
 
</table>
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<p> In addition to the materials listed above, a stand and clamp is used to hold the camera in place. A heat block is used as a counter weight to keep the set up balance. The inside of the case is wrapped with two layers of aluminium foil to insulate the UV radiation emitted from the UV trans-illuminator when it is being turned on. </p>
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<p> In addition to the materials listed above, a stand and clamp is used to hold the camera in place. A heat block is used as a counter weight to keep the set up balanced. The inside of the case is wrapped with two layers of aluminium foil to insulate the UV radiation emitted from the UV trans-illuminator when it is being turned on. </p>
 
<p> A small hole is drilled at the back of the plastic case (not shown on picture above). This hole allows connection between the power cord and the UV trans-illuminator. </p>
 
<p> A small hole is drilled at the back of the plastic case (not shown on picture above). This hole allows connection between the power cord and the UV trans-illuminator. </p>
 
<p> For live viewing of gel from computer, <a href="http://digicamcontrol.com/">DigiCamControl</a>, an open source software is used. This software allows the control (including auto focus and capturing picture) of the camera from the connected computer. </p>
 
<p> For live viewing of gel from computer, <a href="http://digicamcontrol.com/">DigiCamControl</a>, an open source software is used. This software allows the control (including auto focus and capturing picture) of the camera from the connected computer. </p>
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<div class="project_row">
 
<div class="project_row">
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<hr class="para">
 
<h1>From Prototype to a Working Model</h1>
 
<h1>From Prototype to a Working Model</h1>
 
<h2>Prototype</h2>
 
<h2>Prototype</h2>
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<li>We obtained a plastic bucket and drilled a 5 cm hole on the bottom of it.  </li>
 
<li>We obtained a plastic bucket and drilled a 5 cm hole on the bottom of it.  </li>
 
<li>We placed a filter on top of the hole and put a camera on top of the filter. </li>
 
<li>We placed a filter on top of the hole and put a camera on top of the filter. </li>
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<li>An electrophoresed agarose gel stained with Midori Green is placed on top of the UV trans-illuminator</li>
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<li>An electrophoresed agarose gel stained with Midori Green is placed on top of the UV trans-illuminator.</li>
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<li>The entire bucket, with the filter and camera are placed on top of the UV trans-illuminator, and a photo was taken </li>
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<li>The entire bucket, with the filter and camera are placed on top of the UV trans-illuminator, and a photo was taken.</li>
 
</ol>
 
</ol>
 
 
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<h2>Working Model</h2>
 
<h2>Working Model</h2>
 
 
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<p>After we confirmed that we could take Gel photo using easy-to-get materials, we proceeded to build a case especially for this purpose. With the case, the imaging station will be more durable. We choose plastic as the material for case. Plastic is resistant to rust and inert to acid and base. Using plastic can <b>prevent rusting</b> and is <b>easy to maintain</b>.</p>
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<p>After we confirmed that we could take gel photo using easy-to-get materials, we proceeded to build a case especially for this purpose. With the case, the imaging station will be more durable. We choose plastic as the material for case. Plastic is inert to acid and base, <b>resistant to rusting</b> and is <b>easy to maintain</b>.</p>
 
<div class="project_image">
 
<div class="project_image">
 
<img src="https://static.igem.org/mediawiki/2015/thumb/a/a9/HKUST_Rice15_still_image_diy_gel_doc_web.png/800px-HKUST_Rice15_still_image_diy_gel_doc_web.png" alt="First image taken by the DIY gel imaging station">
 
<img src="https://static.igem.org/mediawiki/2015/thumb/a/a9/HKUST_Rice15_still_image_diy_gel_doc_web.png/800px-HKUST_Rice15_still_image_diy_gel_doc_web.png" alt="First image taken by the DIY gel imaging station">
 
</div>
 
</div>
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<p>A photo was taken using this model of DIY Gel imaging station to prove the functionality of the station. This is the 1<sup>st</sup> photo taken:</p>
 
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<div class="project_image">
 
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<img src="https://static.igem.org/mediawiki/2015/9/94/HKUST_Rice15_diy_gel_imaging_Gel_web.png">
 
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</div>
 
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<p>The above gel is 0.8% agarose gel pre-stained with Midori Green Gel Advance DNA stain. Each lane is loaded with NEB 1 kb DNA Ladder (N3232, NEB). A green filter is used in taking the photo. As shown on the picture above, each band is clearly shown. Each band is bright enough to be observed. </p>
 
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<h1> Comparison</h1>
 
  
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<img src="#">
 
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                            <h2> Comparison</h2>
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<img src="https://static.igem.org/mediawiki/2015/2/20/HKUST_Rice15_Gel_doc_comparison_web.png" style="width:100%">
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<div class= "des">The Commercial Gel Visualization System is AlphaImager® HP System.</div>
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                            </div>
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<div class="project_row">
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<hr class="para">
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                            <h1> 3D View of Animated DIY Gel Imaging Station</h1>
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<p>Our current working model 1.0 is good enough for daily in-out documentation purposes, but it is not so convenient for gel extraction – the space between the camera and the trans-illuminator is too narrow. We are about to build our 2.0 version and we want to introduce a drawer-like feature for the trans-illuminator. Our design is as below and we will build it pretty soon.</p>
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<a href="https://static.igem.org/mediawiki/2015/6/64/Team_HKUST-Rice_2015_3D_View.pdf " download><img class="button" src="https://static.igem.org/mediawiki/2015/a/ab/Team_HKUST-Rice_2015_3Dimage.png" style="width:60%"></a>
  
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Latest revision as of 17:00, 18 September 2015


DIY Gel Imaging Station

Motivation

A. A photo was taken using this model of DIY Gel imaging station to prove the functionality of the station. This is the 1st photo taken!

B. This is a video showing how the Gel Imaging Station actually works.

Since its establishment, HKUST iGEM team has been working in small lab pretty far away from the centralized equipment complex. Every time when we want to document our gel or perform gel extraction, we have to carry our gels, walk through a corridor and up a floor to reach the commercial gel documentation system. Starting from this year though, we no longer have to suffer! We have built our own gel imaging system from affordable and easy to get-to-materials, and would like to share with the iGEM community how they make their own.

Materials for DIY Gel imaging Station

The DIY Gel imaging station mainly consists of six parts:

Parts of DIY Gel Imaging station

Parts of DIY Gel Imaging station

Parts of DIY Gel Imaging station
ItemSourceCost (HKD)
1: Case Local hard ware store: Pricerite$249
2: Camera (Nikon D3200) Local electronic store$3499
3: Computer with monitor for live viewing of GelLaboratory Laptop-
4: Green UV filter (PMMA) Taobao~$12
5: UV trans-illuminatorHKUST division of life science-
6: Color filters setebay~$124
Total~$3884

In addition to the materials listed above, a stand and clamp is used to hold the camera in place. A heat block is used as a counter weight to keep the set up balanced. The inside of the case is wrapped with two layers of aluminium foil to insulate the UV radiation emitted from the UV trans-illuminator when it is being turned on.

A small hole is drilled at the back of the plastic case (not shown on picture above). This hole allows connection between the power cord and the UV trans-illuminator.

For live viewing of gel from computer, DigiCamControl, an open source software is used. This software allows the control (including auto focus and capturing picture) of the camera from the connected computer.

From Prototype to a Working Model

Prototype

Before we built the DIY Gel imaging station, we built a prototype to prove the feasibility of a DIY gel imaging station. Here is how we build this prototype:

Parts of DIY Gel Imaging station
  1. We obtained a plastic bucket and drilled a 5 cm hole on the bottom of it.
  2. We placed a filter on top of the hole and put a camera on top of the filter.
  3. An electrophoresed agarose gel stained with Midori Green is placed on top of the UV trans-illuminator.
  4. The entire bucket, with the filter and camera are placed on top of the UV trans-illuminator, and a photo was taken.

Working Model

After we confirmed that we could take gel photo using easy-to-get materials, we proceeded to build a case especially for this purpose. With the case, the imaging station will be more durable. We choose plastic as the material for case. Plastic is inert to acid and base, resistant to rusting and is easy to maintain.

First image taken by the DIY gel imaging station

Comparison

The Commercial Gel Visualization System is AlphaImager® HP System.

3D View of Animated DIY Gel Imaging Station

Our current working model 1.0 is good enough for daily in-out documentation purposes, but it is not so convenient for gel extraction – the space between the camera and the trans-illuminator is too narrow. We are about to build our 2.0 version and we want to introduce a drawer-like feature for the trans-illuminator. Our design is as below and we will build it pretty soon.