Difference between revisions of "Part:BBa K516334:Experience"

 
(→‎User Reviews)
Line 1: Line 1:
−
 
 
__NOTOC__
 
__NOTOC__
 
This experience page is provided so that any user may enter their experience using this part.<BR>Please enter
 
This experience page is provided so that any user may enter their experience using this part.<BR>Please enter
Line 18: Line 17:
 
|};
 
|};
 
<!-- End of the user review template -->
 
<!-- End of the user review template -->
 +
<!-- DON'T DELETE --><partinfo>BBa_K516334 EndReviews</partinfo>
 +
 +
<!-- DON'T DELETE --><partinfo>BBa_K516334 StartReviews</partinfo>
 +
<!-- Template for a user review
 +
{|width='80%' style='border:1px solid gray'
 +
|-
 +
|width='10%'|
 +
<partinfo>BBa_K516334 AddReview 1</partinfo>
 +
<I>Username</I>
 +
|width='60%' valign='top'|
 +
Enter the review inofrmation here.
 +
|};
 +
<!-- End of the user review template -->
 +
{|width='80%' style='border:1px solid gray'
 +
|-
 +
|width='10%'|
 +
<partinfo>BBa_K516334 AddReview 5</partinfo>
 +
<I>UNIPV-Pavia iGEM 2011</I>
 +
|width='60%' valign='top'|
 +
<html>
 +
 +
 +
Characterized with:
 +
<ol><ul>
 +
<li> <A HREF="https://parts.igem.org/wiki/index.php/Part: BBa_K516330 "> BBa_K516330 </a> pLambda-RBS30-LuxR-T-p<sub>Lux</sub>-RBS30-mRFP-TT </li>
 +
<li> <A HREF="https://parts.igem.org/wiki/index.php/Part: BBa_K516331 "> BBa_K516331 </a> pLambda-RBS30-LuxR-T-p<sub>Lux</sub>-RBS31-mRFP-TT </li>
 +
<li> <A HREF="https://parts.igem.org/wiki/index.php/Part: BBa_K516332 "> BBa_K516332 </a> pLambda-RBS30-LuxR-T-p<sub>Lux</sub>-RBS32-mRFP-TT </li>
 +
<li> <A HREF="https://parts.igem.org/wiki/index.php/Part: BBa_K516334 "> BBa_K516334 </a> pLambda-RBS30-LuxR-T-p<sub>Lux</sub>-RBS34-mRFP-TT </li></ul>
 +
</ol>
 +
 +
<p align='justify'>
 +
The estimated parameters for the Hill functions are summarized in the table below. For more details on parameter estimation, see the <a href='http://2011.igem.org/Team:UNIPV-Pavia/Project/Modelling#Ptet_&_Plux'>model section</a>.
 +
</p>
 +
 +
<table class='data' width='100%'>
 +
<tr>
 +
<td class="row"><b>RBS</b></td>
 +
<td class="row"><b>&alpha;<sub>p<sub>Lux</sub></sub> [(AUr/min)/cell]</b></td>
 +
<td class="row"><b>&delta;<sub>p<sub>Lux</sub></sub> [-]</b></td>
 +
<td class="row"><b>&eta;<sub>p<sub>Lux</sub></sub> [-]</b></td>
 +
<td class="row"><b>k<sub>p<sub>Lux</sub></sub> [ng/ml]</b></td>
 +
</tr>
 +
<tr><td class="row">BBa_B0030</td>
 +
<td class="row">438 [10]</td>
 +
<td class="row">0.05 [>100]</td>
 +
<td class="row">2 [47]</td>
 +
<td class="row">1.88 [27]</td>
 +
</tr>
 +
<tr><td class="row">BBa_B0031</td>
 +
<td class="row">9.8 [7]</td>
 +
<td class="row">0.11 [57]</td>
 +
<td class="row">1.2 [29]</td>
 +
<td class="row">1.5 [26]</td>
 +
</tr>
 +
<tr><td class="row">BBa_B0032</td>
 +
<td class="row">206 [3]</td>
 +
<td class="row">0 [>>100]</td>
 +
<td class="row">1.36 [10]</td>
 +
<td class="row">1.87 [9]</td>
 +
</tr>
 +
<tr><td class="row">BBa_B0034</td>
 +
<td class="row">1105 [6]</td>
 +
<td class="row">0.02 [>100]</td>
 +
<td class="row">1.33 [19]</td>
 +
<td class="row">2.34 [18]</td>
 +
</tr>
 +
</table>
 +
<div align="center">Data are provided as average [CV%].</div><br>
 +
 +
 +
<div align="justify">
 +
<p>From this table, it is evident that, whilst &alpha;<sub>p<sub>Lux</sub></sub> assumes significantly different values for different RBSs, &eta;<sub>pLux</sub> and k<sub>pLux</sub> assume very similar values. This result shows that RBS variation modulates the amplitude of Hill function, not affecting the shape of the curve. The four induction curves result to be the same Hill function modulated in amplitude by a parameter, that is the estimated RBS efficiency for this measurement system.</p>
 +
<p>These results are quite encouraging, because suggest that, given the non-modular behavior of RBS dpending on the encoded gene, the RBS has a modular behaviour respect to the promoter.</p>
 +
<p>The operative parameters are summarized in the table below:</p></div>
 +
 +
<table align='center' class='data' width='100%'>
 +
<tr>
 +
<td class='row'><b>RBS</b></td>
 +
<td class='row'><b>RPU<sub>max</sub></b></td>
 +
<td class='row'><b>RPU<sub>min</sub></b></td>
 +
<td class='row'><b>Switch point [nM]</b></td>
 +
<td class='row'><b>Linear boundaries [MIN; MAX] [nM]</b></td>
 +
</tr>
 +
<tr>
 +
<td class='row'>B0030</td><td class='row'>4.28</td><td class='row'>0.20</td><td class='row'>1.08</td><td class='row'>[0.36; 3.27]</td>
 +
</tr>
 +
<tr>
 +
<td class='row'>B0031</td><td class='row'>4.93</td><td class='row'>0.55</td><td class='row'>0.25</td><td class='row'>[0.03; 2.30]</td>
 +
</tr>
 +
<tr>
 +
<td class='row'>B0032</td><td class='row'>9.49</td><td class='row'>0.02</td><td class='row'>0.47</td><td class='row'>[0.07; 3.07]</td>
 +
</tr>
 +
<tr>
 +
<td class='row'>B0034</td><td class='row'>21.53</td><td class='row'>0.51</td><td class='row'>0.53</td><td class='row'>[0.08; 3.77]</td>
 +
</tr>
 +
</table>
 +
<p align='justify'>These operative parameters provide useful information on the behavior of this 3OC6-HSL inducible device. RPU<sub>max</sub> assumes very different values in terms of RPUs.
 +
This can't be explained by RBS modulation, since RPUs have been evaluated by normalizing S<sub>cell</sub> of p<sub>Lux</sub>-RBSx for the one of J23101-RBSx. It is evident that some nonlinear effect on maximum strength, maybe due to saturation phenomena on protein expression, occur.
 +
The same RPUs should be observed for every RBS, since the normalization by the standard reference used for RPUs computation should eliminate the RBS contribute. Here different RPUs are observed, maybe due to nonlinear RBS behavior or to saturation phenomena occurring with this very strong promoter. The switch point and linear boundaries are quite constant in all the cases, showing that the linear region of this system is not affected by RBS changes.</p>
 +
 +
<table width='100%'><tr><td width='50%'>
 +
<div style="text-align:justify"><div class="thumbinner" width='100%'><a href="https://static.igem.org/mediawiki/2011/5/50/E17_RPU_80.jpg" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/5/50/E17_RPU_80.jpg" class="thumbimage" width="100%"></a></div></div>
 +
</td>
 +
<td width='50%'>
 +
<div style="text-align:justify"><div class="thumbinner" width='100%'><a href="https://static.igem.org/mediawiki/2011/c/c4/E18_RPU_80.jpg" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/c/c4/E18_RPU_80.jpg" class="thumbimage" width="100%"></a></div></div>
 +
</td></tr>
 +
<tr><td width='50%'>
 +
<div style="text-align:justify"><div class="thumbinner" width='100%'><a href="https://static.igem.org/mediawiki/2011/7/78/E19_RPU_80.jpg" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/7/78/E19_RPU_80.jpg" class="thumbimage" width="100%"></a></div></div>
 +
</td>
 +
<td width='50%'>
 +
<div style="text-align:justify"><div class="thumbinner" width='100%'><a href="https://static.igem.org/mediawiki/2011/5/55/E20_RPU_80.jpg" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/5/55/E20_RPU_80.jpg" class="thumbimage" width="100%"></a></div></div>
 +
</td></tr>
 +
</table>
 +
 +
 +
 +
</html>
 +
|}
 +
 
<!-- DON'T DELETE --><partinfo>BBa_K516334 EndReviews</partinfo>
 
<!-- DON'T DELETE --><partinfo>BBa_K516334 EndReviews</partinfo>

Revision as of 14:56, 23 September 2011

This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.

Applications of BBa_K516334

User Reviews

UNIQ63c53d57b2fe55b3-partinfo-00000000-QINU UNIQ63c53d57b2fe55b3-partinfo-00000001-QINU

UNIQ63c53d57b2fe55b3-partinfo-00000002-QINU

•••••

UNIPV-Pavia iGEM 2011

Characterized with:

The estimated parameters for the Hill functions are summarized in the table below. For more details on parameter estimation, see the model section.

RBS αpLux [(AUr/min)/cell] δpLux [-] ηpLux [-] kpLux [ng/ml]
BBa_B0030 438 [10] 0.05 [>100] 2 [47] 1.88 [27]
BBa_B0031 9.8 [7] 0.11 [57] 1.2 [29] 1.5 [26]
BBa_B0032 206 [3] 0 [>>100] 1.36 [10] 1.87 [9]
BBa_B0034 1105 [6] 0.02 [>100] 1.33 [19] 2.34 [18]
Data are provided as average [CV%].

From this table, it is evident that, whilst αpLux assumes significantly different values for different RBSs, ηpLux and kpLux assume very similar values. This result shows that RBS variation modulates the amplitude of Hill function, not affecting the shape of the curve. The four induction curves result to be the same Hill function modulated in amplitude by a parameter, that is the estimated RBS efficiency for this measurement system.

These results are quite encouraging, because suggest that, given the non-modular behavior of RBS dpending on the encoded gene, the RBS has a modular behaviour respect to the promoter.

The operative parameters are summarized in the table below:

RBS RPUmax RPUmin Switch point [nM] Linear boundaries [MIN; MAX] [nM]
B00304.280.201.08[0.36; 3.27]
B00314.930.550.25[0.03; 2.30]
B00329.490.020.47[0.07; 3.07]
B003421.530.510.53[0.08; 3.77]

These operative parameters provide useful information on the behavior of this 3OC6-HSL inducible device. RPUmax assumes very different values in terms of RPUs. This can't be explained by RBS modulation, since RPUs have been evaluated by normalizing Scell of pLux-RBSx for the one of J23101-RBSx. It is evident that some nonlinear effect on maximum strength, maybe due to saturation phenomena on protein expression, occur. The same RPUs should be observed for every RBS, since the normalization by the standard reference used for RPUs computation should eliminate the RBS contribute. Here different RPUs are observed, maybe due to nonlinear RBS behavior or to saturation phenomena occurring with this very strong promoter. The switch point and linear boundaries are quite constant in all the cases, showing that the linear region of this system is not affected by RBS changes.

UNIQ63c53d57b2fe55b3-partinfo-00000005-QINU