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

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<img src="http://openwetware.org/images/5/53/NBgamers_team_logo.png" width="679.2" height="214.4" alt="NBgamers (Team of NanoBiotechnology)" title="NBgamers (Team of NanoBiotechnology)">
<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)">
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<h3 align="center" style="color:white; font-size:30px;" >Results</h3>
<h3 align="center" style="color:white; font-size:20px;" >Results</h3>
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<h3>Intensity Optimization</h3>
<h3>Contents</h3>
<ol>
  <li><a href="#Optimization">Optimization</a></li>
  <li><a href="#Calibration">Calibration</a></li>
</ol>
<br />


<p>
<h1><a name="Optimization">Optimization</h1>
In our project, each individual fibril is labeled by quantum dots (QD). The intensity of the output fluorescence signal from the QD's 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:
<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>
</p>
 
<br />
<p>
<table border="1" align="center" cellpadding="5" cellspacing="0">
1. The ratio between the free Aβ monomers and biotinylated Aβ monomers.
<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>
</p>
<br />


<p>
<h1><a name="Calibration">Calibration</a></h1>
Imagining you put the free Aβ monomers and the biotinylated Aβ monomers into buffers to let them spontaneously assemble into fibrils. A large proportion of free ones may result in a relatively long fibril length distribution, but since QD labeled streptavidin only "sits" on biotinylated Aβ monomers, the average intensity on each fibril may be low.
<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>
</p>
 
<br />
<p>
<table border="1" align="center" cellpadding="5" cellspacing="0">
2. The dilution factor of fibrils.
<tr>
</p>
  <td>Target concentration (pM)</td>
 
  <td>250</td>
<p>
  <td>750</td>
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 QD's 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, QD's may be able to fully occupy each of the fibrils and hence result in a high average intensity on each fibril.
  <td>1000</td>
</p>
  <td>1500</td>
 
  <td>5000</td>
<p>
</tr>
The bar chart below shows the measured output intensity from the QD's under different conditions:
<tr>
</p>
  <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/6/6a/Intensity_Optimization.png">
<a href="http://openwetware.org/images/a/ae/NBgamers_calibration.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/a/ae/NBgamers_calibration.png" width="450" height="350">
</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 />

Latest revision as of 14:55, 2 November 2011

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<tr> <td bgcolor="#fcec00"> <table border="0" align="center" cellpadding="20" cellspacing="0"> <tr bgcolor="#fcec00"> 

 <td align="center" height="50">
 <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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 <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>
 </td>
 <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
 </a>
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 Results
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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 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
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 </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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