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

(→‎User Reviews)
(→‎User Reviews)
 
(4 intermediate revisions by the same user not shown)
Line 48: Line 48:
  
  
−
<p>Inducible and constitutive promoters were assembled upstream of different coding sequences containing an RBS from the Community collection.</p>
+
<p>The inducible device </html><partinfo>BBa_K081022</partinfo> <html>was assembled upstream of different mRFP coding sequences, containing an RBS from the Community collection.</p>
 
<p>The assembled RBSs are:</p>
 
<p>The assembled RBSs are:</p>
 
<br>
 
<br>
 
<div align='center'>
 
<div align='center'>
−
<table class='data'>
+
<table class='data' border='1'>
 
<tr><td class="row"><b>BioBrick code</b></td><td><b>  Declared efficiency</b></td></tr>
 
<tr><td class="row"><b>BioBrick code</b></td><td><b>  Declared efficiency</b></td></tr>
 
<tr><td class="row">BBa_B0030 </td><td class="row"> 0,6</td></tr>
 
<tr><td class="row">BBa_B0030 </td><td class="row"> 0,6</td></tr>
Line 65: Line 65:
 
<p>For this reason, every combination 'Promoter+RBS' was studied as a different regulatory element. Regulatory elements were characterized using mRFP reporter protein for different RBSs in terms of Synthesis rate per Cell (<b>S<sub>cell</sub></b>) and <b>R.P.U.s</b> (Relative Promoter Units) as explained in <a href='http://2011.igem.org/Team:UNIPV-Pavia/Measurements'>measurements</a> section.</p>
 
<p>For this reason, every combination 'Promoter+RBS' was studied as a different regulatory element. Regulatory elements were characterized using mRFP reporter protein for different RBSs in terms of Synthesis rate per Cell (<b>S<sub>cell</sub></b>) and <b>R.P.U.s</b> (Relative Promoter Units) as explained in <a href='http://2011.igem.org/Team:UNIPV-Pavia/Measurements'>measurements</a> section.</p>
 
</p>
 
</p>
−
<p>Operative parameters of the promoter are derived from the estimated Hill equations obtained by <em>nonlinear least squares</em> fitting (<em>lsqnonlin</em> Matlab routine) of the <a href='http://2011.igem.org/Team:UNIPV-Pavia/Project/Modelling#Equations_for_gene_networks'>Hill function</a> expressed in RPUs. </p>
+
 
−
<br><br>
+
<p align='justify'>
 +
The Hill function relating the induction to the S<sub>cell</sub> is reported below:<br>
 
<p align='center'>
 
<p align='center'>
 
S<sub>cell</sub>=&alpha; * ( &delta; + (1-&delta;)/(1+(K/Induction)<sup>&eta;</sup>) )
 
S<sub>cell</sub>=&alpha; * ( &delta; + (1-&delta;)/(1+(K/Induction)<sup>&eta;</sup>) )
  
 
</p>
 
</p>
 +
 +
</p>
 +
 +
<p>Operative parameters of the promoter are derived from the estimated Hill equations obtained by <em>nonlinear least squares</em> fitting (<em>lsqnonlin</em> Matlab routine) of the <a href='http://2011.igem.org/Team:UNIPV-Pavia/Project/Modelling#Equations_for_gene_networks'>Hill function</a> expressed in RPUs:</p>
 +
 
<p><ol><ul><li><b>
 
<p><ol><ul><li><b>
 
RPU<sub>max</sub></b> is equal to the &alpha; and represents the maximum promoter activity</p>
 
RPU<sub>max</sub></b> is equal to the &alpha; and represents the maximum promoter activity</p>
Line 87: Line 93:
 
</p>
 
</p>
  
−
<table class='data' width='100%'>
+
<table class='data' width='100%' border='1'>
 
<tr>
 
<tr>
 
<td class="row"><b>RBS</b></td>
 
<td class="row"><b>RBS</b></td>
Line 128: Line 134:
 
<p>The operative parameters are summarized in the table below:</p></div>
 
<p>The operative parameters are summarized in the table below:</p></div>
  
−
<table align='center' class='data' width='100%'>
+
<table align='center' class='data' width='100%' border='1'>
 
<tr>
 
<tr>
 
<td class='row'><b>RBS</b></td>
 
<td class='row'><b>RBS</b></td>

Latest revision as of 15:13, 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

UNIQf8c1b78c446c30f5-partinfo-00000000-QINU UNIQf8c1b78c446c30f5-partinfo-00000001-QINU

UNIQf8c1b78c446c30f5-partinfo-00000002-QINU

•••••

UNIPV-Pavia iGEM 2011

Characterized with:

The inducible device BBa_K081022 was assembled upstream of different mRFP coding sequences, containing an RBS from the Community collection.

The assembled RBSs are:


BioBrick code Declared efficiency
BBa_B0030 0,6
BBa_B0031 0,07
BBa_B0032 0,3
BBa_B0034 1

For an inducible device, the RBS variation has the purpose to stretch the induction curve, thus modulating its PoPs-OUT range.

The complex RBS-promoter acts as a whole regulatory element and determines the amount of translated protein. RBSs have been reported to have an un-modular behavior, since the translational efficiency is not independent on the coding sequences, but variates as an effect of different mRNA structure stability [Salis et al., Nat Biotec, 2009]. It is not possible to separate the effects of the sole promoter and of the sole RBS on the total amount/activity of gene product (in this case study, mRFP).

For this reason, every combination 'Promoter+RBS' was studied as a different regulatory element. Regulatory elements were characterized using mRFP reporter protein for different RBSs in terms of Synthesis rate per Cell (Scell) and R.P.U.s (Relative Promoter Units) as explained in measurements section.

The Hill function relating the induction to the Scell is reported below:

Scell=α * ( δ + (1-δ)/(1+(K/Induction)η) )

Operative parameters of the promoter are derived from the estimated Hill equations obtained by nonlinear least squares fitting (lsqnonlin Matlab routine) of the Hill function expressed in RPUs:

    • RPUmax is equal to the α and represents the maximum promoter activity

    • RPUmin is equal to the α * δ represents the minimum promoter activity

    • Switch point is computed as the abscissa of the inflection point of the Hill curve and it is representative of the position of linear region

    • Linearity boundaries are determined as the intersection between the tangent line to the inflection point and the upper and lower horizontal boundaries of the Hill curve.

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.

UNIQf8c1b78c446c30f5-partinfo-00000007-QINU