Biomod/2011/HKBU/NBgamers:Results: Difference between revisions

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<h3>Content</h3>
<h3>Contents</h3>
<ol>
<ol>
   <li><a href="#Intensity Optimization">Intensity Optimization</a></li>
   <li><a href="#Optimization">Optimization</a></li>
   <li><a href="#Calibration">Calibration</a></li>
   <li><a href="#Calibration">Calibration</a></li>
  <li><a href="#Multiplex Detection">Multiplex Detection</a></li>
</ol>
</ol>
<br />
<br />


<h3><a name="Intensity Optimization">Intensity Optimization</a></h3>
<h1><a name="Optimization">Optimization</h1>
<p>
<p align="center">
In our project, each individual fibril is labeled by quantum dots (QD). The intensity of the output fluorescence signal from the QDs determines the ability of indentifying the fibrils. Therefore, maximizing the QD fluorescence signal intensity is one of our tasks. There are several factors influencing the output intensity:
<a href="http://openwetware.org/images/a/af/NBgamers_Intensity_Optimization_Images.jpg">
</p>
<img src="http://openwetware.org/images/5/50/NBgamers_Intensity_Optimization_Images_Small.png" width="500" height="400">
<ol>
</a>
  <li>The ratio between the free Aβ monomers and biotinylated Aβ monomers.</li>
  <p>Imagining you put the free Aβ monomers and the biotinylated Aβ monomers into buffers to let them self-assemble into fibrils. If we choose a large proportion of free Aβ monomers, we may get a relatively long length distribution of fibrils. But since QD labeled streptavidin only "sits" on biotinylated Aβ monomers, there may not be enough seats for them to sit on. Therefore, in this case, the average intensity on each fibril may be low.</p>
  <li>The dilution factor of fibrils.</li>
  <p>After you assembled the fibrils, don't rush to let the QD labeled streptavidin sit on the seats. If there are a huge amount of fibrils, even though the number of seats on each fibril is sufficiently large, there may not be enough QDs to fully occupy them and hence result in a low average intensity on each fibril. On the contary, if we first dilute the buffer of fibrils, QDs may be able to fully occupy each of the fibrils and hence result in a high average intensity on each fibril.</p>
</ol>
<p>
The bar chart below shows the measured output intensity from the QDs under different conditions:
</p>
</p>
<br />
<table border="1" align="center" cellpadding="5" cellspacing="0">
<tr>
  <td>Percentage of biotinylated Aβ peptide </td>
  <td>2%</td>
  <td>5%</td>
  <td>10%</td>
  <td>20%</td>
</tr>
<tr>
  <td>10 fold dilution</td>
  <td>3089.69</td>
  <td>3550.09</td>
  <td>2641.94</td>
  <td>5181.44</td></tr>
<tr>
  <td>20 fold dilution</td>
  <td>1112.01</td>
  <td>652.74</td>
  <td>2750.81</td>
  <td>5779.05</td></tr>
<tr>
  <td>50 fold dilution</td>
  <td>1111.80</td>
  <td>1712.92</td>
  <td>2468.71</td>
  <td>6092.45</td></tr>
</table>
<br />
<p align="center">
<p align="center">
<a href="http://openwetware.org/images/6/6a/Intensity_Optimization.png">
<a href="http://openwetware.org/images/6/6a/Intensity_Optimization.png">
<img src="http://openwetware.org/images/6/6a/Intensity_Optimization.png" width="454.5" height="373.5" alt="Intensity measurement (Clikc to enlarge.)" title="Intensity measurement (Clikc to enlarge.)">
<img src="http://openwetware.org/images/6/6a/Intensity_Optimization.png" width="450" height="400">
</a>
</a>
</p>
<p>
The result of the intensity optimization gives us a suggestion: A condition with 20% biotin ratio and 50X dilution factor should be a good choice.
</p>
</p>
<br />
<br />


<h3><a name="Calibration">Calibration</a></h3>
<h1><a name="Calibration">Calibration</a></h1>
<p>
<p align="center">
We believe that, the fluorescence intensity emitted from YOYO will be proportional to the DNA target concentration: The more the targets are, the stronger the signal will be! Therefore, we performed calibration with a set of target concentration. The experiment result is shown in the figure below:
<a href="http://openwetware.org/images/8/87/NBgamers_Target_Concentration_Images.png">
<img src="http://openwetware.org/images/0/00/NBgamers_Target_Concentration_Images_Small.png" width="600" height="150">
</a>
</p>
</p>
<br />
<table border="1" align="center" cellpadding="5" cellspacing="0">
<tr>
  <td>Target concentration (pM)</td>
  <td>250</td>
  <td>750</td>
  <td>1000</td>
  <td>1500</td>
  <td>5000</td>
</tr>
<tr>
  <td>Target concentration (pM)</td>
  <td>250</td>
  <td>750</td>
  <td>1000</td>
  <td>1500</td>
  <td>5000</td>
</tr>
<tr>
  <td>Intensity</td>
  <td>650.02</td>
  <td>712.37</td>
  <td>793.52</td>
  <td>864.46</td>
  <td>1513.83</td>
</tr>
<tr>
  <td>Standard Error of Mean (SEM)</td>
  <td>46.36</td>
  <td>15.37</td>
  <td>33.46</td>
  <td>79.17</td>
  <td>117.43</td>
</tr>
</table>
<br />
<p align="center">
<p align="center">
<a href="http://openwetware.org/images/a/ae/NBgamers_calibration.png" alt="Calibration (Click to enlarge.)" title="Calibration (Click to enlarge.)">
<a href="http://openwetware.org/images/a/ae/NBgamers_calibration.png">
<img src="http://openwetware.org/images/a/ae/NBgamers_calibration.png" width="346" height="243">
<img src="http://openwetware.org/images/a/ae/NBgamers_calibration.png" width="450" height="350">
</a>
</a>
</p>
</p>
<br />
<h3><a name="Multiplex Detection">Multiplex Detection</a></h3>
<br />
<br />


Latest revision as of 14:55, 2 November 2011

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 <a href="http://openwetware.org/wiki/Biomod/2011/HKBU/NBgamers" style="color:black; font-size:20px;" onmouseover="this.style.color='white';" onmouseout="this.style.color='black';">
 Home
 </a>
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 <td align="center" height="50">
 <a href="http://openwetware.org/wiki/Biomod/2011/HKBU/NBgamers:Mission" style="color:black; font-size:20px;" onmouseover="this.style.color='white';" onmouseout="this.style.color='black';">
 Mission
 </a>
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 <td align="center" height="50">
 <a href="http://openwetware.org/wiki/Biomod/2011/HKBU/NBgamers:Project" style="color:black; font-size:20px;" onmouseover="this.style.color='white';" onmouseout="this.style.color='black';">
 Project
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 Results
 </a>
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 <a href="http://openwetware.org/wiki/Biomod/2011/HKBU/NBgamers:Video" style="color:black; font-size:20px;" onmouseover="this.style.color='white';" onmouseout="this.style.color='black';">
 Video
 </a>
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 <a href="http://openwetware.org/wiki/Biomod/2011/HKBU/NBgamers:Team" style="color:black; font-size:20px;" onmouseover="this.style.color='white';" onmouseout="this.style.color='black';">
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 </a>
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 <a href="http://openwetware.org/wiki/Biomod/2011/HKBU/NBgamers:Resources" style="color:black; font-size:20px;" onmouseover="this.style.color='white';" onmouseout="this.style.color='black';">
 Resources
 </a>
 </td>

</tr> </table> </td> </tr>

<tr> <td bgcolor="#fcec00" align="center"> <img src="http://openwetware.org/images/5/53/NBgamers_team_logo.png" width="453" height="143" alt="NBgamers (Team of NanoBiotechnology)" title="NBgamers (Team of NanoBiotechnology)"> </td> </tr>

<tr> <td bgcolor="#fcec00" height="50"> &nbsp; </td> </tr>

<tr> <td bgcolor="#232323" align="center"> <h3 align="center" style="color:white; font-size:20px;" >Results</h3> </td> </tr>

<tr> <td bgcolor="#fcec00"> <table align="center" width="85%" cellpadding="20"> <td>

<h3>Contents</h3> <ol> 

 <li><a href="#Optimization">Optimization</a></li>
 <li><a href="#Calibration">Calibration</a></li>

</ol> <br />

<h1><a name="Optimization">Optimization</h1> <p align="center"> <a href="http://openwetware.org/images/a/af/NBgamers_Intensity_Optimization_Images.jpg"> <img src="http://openwetware.org/images/5/50/NBgamers_Intensity_Optimization_Images_Small.png" width="500" height="400"> </a> </p> <br /> <table border="1" align="center" cellpadding="5" cellspacing="0"> <tr> 

 <td>Percentage of biotinylated Aβ peptide </td>
 <td>2%</td>
 <td>5%</td>
 <td>10%</td>
 <td>20%</td>

</tr> <tr> 

 <td>10 fold dilution</td>
 <td>3089.69</td>
 <td>3550.09</td>
 <td>2641.94</td>
 <td>5181.44</td></tr>

<tr> 

 <td>20 fold dilution</td>
 <td>1112.01</td>
 <td>652.74</td>
 <td>2750.81</td>
 <td>5779.05</td></tr>

<tr> 

 <td>50 fold dilution</td>
 <td>1111.80</td>
 <td>1712.92</td>
 <td>2468.71</td>
 <td>6092.45</td></tr>

</table> <br /> <p align="center"> <a href="http://openwetware.org/images/6/6a/Intensity_Optimization.png"> <img src="http://openwetware.org/images/6/6a/Intensity_Optimization.png" width="450" height="400"> </a> </p> <br />

<h1><a name="Calibration">Calibration</a></h1> <p align="center"> <a href="http://openwetware.org/images/8/87/NBgamers_Target_Concentration_Images.png"> <img src="http://openwetware.org/images/0/00/NBgamers_Target_Concentration_Images_Small.png" width="600" height="150"> </a> </p> <br /> <table border="1" align="center" cellpadding="5" cellspacing="0"> <tr> 

 <td>Target concentration (pM)</td>
 <td>250</td>
 <td>750</td>
 <td>1000</td>
 <td>1500</td>
 <td>5000</td>

</tr> <tr> 

 <td>Target concentration (pM)</td>
 <td>250</td>
 <td>750</td>
 <td>1000</td>
 <td>1500</td>
 <td>5000</td>

</tr> <tr> 

 <td>Intensity</td>
 <td>650.02</td>
 <td>712.37</td>
 <td>793.52</td>
 <td>864.46</td>
 <td>1513.83</td>

</tr> <tr> 

 <td>Standard Error of Mean (SEM)</td>
 <td>46.36</td>
 <td>15.37</td>
 <td>33.46</td>
 <td>79.17</td>
 <td>117.43</td>

</tr> </table> <br /> <p align="center"> <a href="http://openwetware.org/images/a/ae/NBgamers_calibration.png"> <img src="http://openwetware.org/images/a/ae/NBgamers_calibration.png" width="450" height="350"> </a> </p> <br />

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