Team:UNIPV-Pavia/parts/characterized2.html

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Characterized Parts

Our new parts

BBa_J23101

BBa_K516130 (wiki name: J101-E5 ) J101-RBS30-RFP-TT
BBa_K516131 (wiki name: J101-31 ) J101-RBS31-mRFP-TT
BBa_K516132 (wiki name: J101-E7 ) J101-RBS32-mRFP-TT

BBa_J23101 is the reference standard promoter for the computation of RPUs. As discussed in 'data analysis' section, RPUs are relative units for the evaluation of promoter strength, based on a mathematical model of the transcription and the translation of a reporter gene.
The RPUs are supposed to be indepedent on the experimental setup, provided that the reference standard BBa_J23101 must be assayed in the same experimental condition of the studied promoter.
It means that if the studied promoter is in a low copy number plasmid and drives the expression of a reporter protein P, J23101 must be assembled in the same vector upstream of the same reporter P.
This approach is motivated by the assumption that the trascriptional strength of a promoter is independent on the encoded gene and on the experimental setup.
This approach is in accordance with the philosophy of synthetic biology, based on the concept of 'modularity' of the components. According to this approach, the assembly of basic well charcaterized modules to build complex circuits allow whose behaviour can be predicted by knowledge on the basic parts.

-provide Scell with CI 95% (error bar?) and RPU?? with errorbar? -Provide RBS ranking -Discuss that RPUs can be used to compare different promoters in the same exp conditions (i.e: the same RBS), but are not reliable when comparing different RBSs with the same promoter because of the un-modularity of RBS (cit: RBS calculator Salis Nature Biot 2009, 'identical ribosome binding site sequences in different genetic contexts can result in different protein expression levels', 'It is likely that this absence of modularity is caused by the formation of strong secondary structures between the RBS-containing RNA sequence and one protein coding sequence but not another'). Highlight that we are not trying to show that RBSs are modular, since it has been shown to be false. We try to overcome the problem of modularity by considering the complex Promoter-RBS as a whole regulatory element, whose effect can't be split between the two components. Explain that here we provide a library of ready-to-use reference standard in order to easily compute RPUs of promoters with different RBSs. Discuss that it is not totally correct to compare RPUs coming from characterization with different RBSs?

Characterization of existing pars from the Registry

Do we say that we are charcterizing also F2620 or T9002? Or both?
Inducible and constitutive promoters were assembled upstream of different coding sequences containing an RBS from the Community collection.

The assembled RBSs are:

BioBrick code	Estimated 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]. In addition, it is not possible to separate the effects of the sole promoter and of the sole RBS on the total amount of mRFP produced.

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 (S_cell) and R.P.U.s (Relative Promoter Units) as explained in measurements section.

pTet - BBa_R0040

mRFP
- BBa_K516230 (wiki name: E21 ) pTet-RBS30-mRFP-TT
- BBa_K516231 (wiki name: E22 ) pTet-RBS31-mRFP-TT
- BBa_K516232 (wiki name: E23 ) pTet-RBS32-mRFP-TT Rebuilt existing part from BBa_I20252 (DNA planning)
- BBa_I13521 pTet-RBS34-mRFP-TT
AiiA
- BBa_K516220 (wiki name: E24 ) pTet-RBS30-AiiA-TT
- BBa_K516221 (wiki name: E25 ) pTet-RBS31-AiiA-TT
- BBa_K516222 (wiki name: E26 ) pTet-RBS32-AiiA-TT Rebuilt existing part from BBa_ J22071 (2008 only, Bad sequencing)
- BBa_K516224 (wiki name: E27 ) pTet-RBS34-AiiA-TT Rebuilt existing part from BBa_K077047 (Part deleted)
LuxI
- BBa_K516210 (wiki name: E13 ) pTet-RBS30-LuxI
- BBa_K516211 (wiki name: E14 ) pTet-RBS31-LuxI
- BBa_K516212 (wiki name: E15 ) pTet-RBS32-LuxI
- BBa_K516214 (wiki name: E16 ) pTet-RBS34-LuxI Rebuilt existing part from BBa_S03623 (DNA available, only 2008 kit, inconsistent)

The protocols for the characterization of pTet promoter are reported in the pTet measurement section.
This promoter is widely studied and characterized usually using the strong RBS BBa_B0034. Here we have characterized its transcriptional strength as a function of aTc induction (ng/ul) for different RBSs. Four different induction curves were obtained and are reported in figure: INSERIRE 4 CURVE pTET!! The data collected from the mRFP measurement systems were processed as described in data analysis section. The induction curves were obtained by fitting a Hill function as described in modelling section and the estimated parameters for pTet are reported in the table below.

RBS	α_{p_Tet}	δ_{p_Tet}	η_{p_Tet}	k_{p_Tet}
BBa_B0030	215	0.001	4.3	8.3
BBa_B0031	0.7	0	18.84	47.51
BBa_B0032	45.7	0.02	83	8
BBa_B0034	125	0.12	71.8	9.8

Their CV% (coefficient of variation):

RBS	α_{p_Tet}	δ_{p_Tet}	η_{p_Tet}	k_{p_Tet}
BBa_B0030	2.13	888	12	2.54
BBa_B0031	imm	1.47*10^11	imm	imm
BBa_B0032	10.88	411.3	676671474	393179
BBa_B0034	12.22	61.74	2705172	55888.6

While α parameter (representing the maximum trascriptional rate in the studied range of induction) varies as expected with the RBS variation , the K and η parameters (determining the switch-point of the induction curve) are quite constant among all the RBS variations.
This suggests that the RBS variation only modulates the amplitude of the induction curve, but doesn't affect the shape, i.e. the translational promoter activity. 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.
Do we need to insert a table with the most significant measurements for every pTet-RBSx (i.e.: min RPU, max RPU, switch point, saturation threshold?)

pLux

BBa_K516330 (wiki name: E17 ) pLambda-RBS30-LuxR-T-pLux-RBS30-mRFP-TT
BBa_K516331 (wiki name: E18 ) pLambda-RBS30-LuxR-T-pLux-RBS31-mRFP-TT
BBa_K516332 (wiki name: E19 ) pLambda-RBS30-LuxR-T-pLux-RBS32-mRFP-TT
BBa_K516334 (wiki name: E20 ) pLambda-RBS30-LuxR-T-pLux-RBS34-mRFP-TT

RBS	α_{p_Lux}	δ_{p_Lux}	η_{p_Lux}	k_{p_Lux}
BBa_B0030	438	0.05	2	1.88
BBa_B0031	9.8	0.11	1.2	1.5
BBa_B0032	206	0	1.36	1.87
BBa_B0034	1105	0.02	1.33	2.34

Their CV% (coefficient of variation):

RBS	α_{p_Lux}	δ_{p_Lux}	η_{p_Lux}	k_{p_Lux}
BBa_B0030	10.14	180	47.73	27.5
BBa_B0031	7.12	57.04	29.13	25.82
BBa_B0032	2.78	1318	9.75	8.46
BBa_B0034	5.81	187.2	19.3	17.86

RBSs

BBa_B0030
1. BBa_K516030 (wiki name: E5 ) RBS30-mRFP-TT Rebuilt existing part from BBa_S04180 (DNA planning)
  - BBa_K516230 (wiki name: E21 ) pTet-RBS30-mRFP-TT
  - BBa_K516330 (wiki name: E17 ) pLambda-RBS30-LuxR-T-pLux-RBS30-mRFP-TT
  - BBa_K516130 (wiki name: J101-E5 ) J101-RBS30-RFP-TT
2. BBa_K516020 (wiki name: E9 ) RBS30-AiiA-TT
  - BBa_K516220 (wiki name: E24 ) pTet-RBS30-AiiA-TT
3. BBa_K081008 (wiki name: E2 ) RBS30-LuxI
  - BBa_K516210 (wiki name: E13 ) pTet-RBS30-LuxI
BBa_B0031
1. BBa_K516031 (wiki name: E6 ) RBS31-mRFP-TT
  - BBa_K516231 (wiki name: E22 ) pTet-RBS31-mRFP-TT
  - BBa_K516331 (wiki name: E18 ) pLambda-RBS30-LuxR-T-pLux-RBS31-mRFP-TT
  - BBa_K516131 (wiki name: J101-31 ) J101-RBS31-RFP-TT
2. BBa_K516021 (wiki name: E10 ) RBS31-AiiA-TT Rebuilt existing part from BBa_I13914 (DNA planning)
  - BBa_K516221 (wiki name: E25 ) pTet-RBS31-AiiA-TT
3. BBa_K516011 (wiki name: E3 ) RBS31-LuxI
  - BBa_K516211 (wiki name: E14 ) pTet-RBS31-LuxI
BBa_B0032
1. BBa_K516032 (wiki name: E7 ) RBS32-mRFP-TT Rebuilt existing part from BBa_ J133000 (DNA planning)
  - BBa_K516232 (wiki name: E23 ) pTet-RBS32-mRFP-TT Rebuilt existing part from BBa_I20252 (DNA planning)
  - BBa_K516332 (wiki name: E19 ) pLambda-RBS30-LuxR-T-pLux-RBS32-mRFP-TT
  - BBa_K516132 (wiki name: J101-E7 ) J101-RBS32-RFP-TT
2. BBa_K516022 (wiki name: E11 ) RBS32-AiiA-TT Rebuilt existing part from BBa_I13912 (DNA planning)
  - BBa_K516222 (wiki name: E26 ) pTet-RBS32-AiiA-TT Rebuilt existing part from BBa_ J22071 (2008 only, Bad sequencing)
3. BBa_K516012 (wiki name: E4 ) RBS32-LuxI
  - BBa_K516212 (wiki name: E15 ) pTet-RBS32-LuxI
BBa_B0034
1. BBa_I13521 RBS34-mRFP-TT
  - BBa_I13521 pTet-RBS34-mRFP-TT
  - BBa_K516334 (wiki name: E20 ) pLambda-RBS30-LuxR-T-pLux-RBS34-mRFP-TT
  - BBa_J23101 J101-RBS34-RFP-TT
2. BBa_I0460 RBS34-AiiA-TT
  - BBa_K516224 (wiki name: E27 ) pTet-RBS34-AiiA-TT Rebuilt existing part from BBa_K077047 (Part deleted)
3. BBa_C0261 RBS34-LuxI
  - BBa_K516214 (wiki name: E16 ) pTet-RBS34-LuxI Rebuilt existing part from BBa_S03623 (DNA available, only 2008 kit, inconsistent)

Almost everything must be inserted in this section!! How do I evaluate the efficiency of RBSs in case of inducible promoters? We need a summary table with the estimated efficiency in the condition:
-Promoter - Gene

LuxI - BBa_C0061

BBa_K081008 (wiki name: E2 ) RBS30-LuxI
BBa_K516210 (wiki name: E13 ) pTet-RBS30-LuxI
BBa_K516011 (wiki name: E3 ) RBS31-LuxI
BBa_K516211 (wiki name: E14 ) pTet-RBS31-LuxI
BBa_K516012 (wiki name: E4 ) RBS32-LuxI
BBa_K516212 (wiki name: E15 ) pTet-RBS32-LuxI
BBa_C0261 RBS34-LuxI
BBa_K516214 (wiki name: E16 ) pTet-RBS34-LuxI Rebuilt existing part from BBa_S03623 (DNA available, only 2008 kit, inconsistent)

LuxI has been characterized through the Biosensor T9002 (see modeling section). The HSL synthesis rate has been evaluated according to the model (Eq. 2 - dLuxI/dt, Eq. 3 dHSL/dt, Eq. 5 dN/dt). Explain that in all these evaluations we have estimated Nmax, mu, gamma_HSL from previous experiments - see measurement and modelling sections. When do we talk about HSL stability as a function of pH?
Provide parameters of HSL. How do we present these data? It would be nice also to say what's the amount of HSL produced by a liquid 5 ml culture at a given OD600 in M9 medium after tot hours starting from 1:1000 dilution of a saturated ON culture..
We nee a synthetic parameter to express LuxI activity as a function of PoPS in. I suggest to report the HSL vs pH analysis here AND in the AiiA section of registry and, for what concerns our wiki, to add an appendix to the 'measurement section' to wich link when explaining..
Decide figures!

AiiA - BBa_C0060

BBa_K516020 (wiki name: E9 ) RBS30-AiiA-TT
BBa_K516220 (wiki name: E24 ) pTet-RBS30-AiiA-TT
BBa_K516021 (wiki name: E10 ) RBS31-AiiA-TT Rebuilt existing part from BBa_I13914 (DNA planning)
BBa_K516221 (wiki name: E25 ) pTet-RBS31-AiiA-TT
BBa_K516022 (wiki name: E11 ) RBS32-AiiA-TT Rebuilt existing part from BBa_I13912 (DNA planning)
BBa_K516222 (wiki name: E26 ) pTet-RBS32-AiiA-TT Rebuilt existing part from BBa_ J22071 (2008 only, Bad sequencing)
BBa_I0460 RBS34-AiiA-TT
BBa_K516224 (wiki name: E27 ) pTet-RBS34-AiiA-TT Rebuilt existing part from BBa_K077047 (Part deleted)

Tha same as LuxI. Here we report the AiiA equations. Even more fundamental the estimation of gamma_HSL, that is pH dependent, because of the necessity to depurate the observed degradation by the effect not depending on AiiA
Decide figures!

Improvement of existing pars from the Registry

Add the re-built existing parts with DNA planning!

Rebuilt existing parts

BBa_K516021 (wiki name: E10 ) RBS31-AiiA-TT Rebuilt existing part from BBa_I13914 (DNA planning)
BBa_K516022 (wiki name: E11 ) RBS32-AiiA-TT Rebuilt existing part from BBa_I13912 (DNA planning)
BBa_K516030 (wiki name: E5 ) RBS30-mRFP-TT Rebuilt existing part from BBa_S04180 (DNA planning)
BBa_K516032 (wiki name: E7 ) RBS32-mRFP-TT Rebuilt existing part from BBa_ J133000 (DNA planning)
BBa_K516214 (wiki name: E16 ) pTet-RBS34-LuxI Rebuilt existing part from BBa_S03623 (DNA available, only 2008 kit, inconsistent)
BBa_K516222 (wiki name: E26 ) pTet-RBS32-AiiA-TT Rebuilt existing part from BBa_ J22071 (2008 only, Bad sequencing)
BBa_K516224 (wiki name: E27 ) pTet-RBS34-AiiA-TT Rebuilt existing part from BBa_K077047 (Part deleted)
BBa_K516232 (wiki name: E23 ) pTet-RBS32-mRFP-TT Rebuilt existing part from BBa_I20252 (DNA planning)

@@ Line 1: / Line 1: @@
 {{main}}
-<html>
-<a name='indice'></a>
-                                <h2 class="art-postheader">
-                Parts
-                                </h2>
-                <div class="cleared"></div>
-                                <div class="art-postcontent">
+<html>
+<h2 class="art-postheader">Characterized Parts</h2>
 <div class="cleared"></div>
 <div class="art-postcontent">
@@ Line 13: / Line 8: @@
 <table id="toc" class="toc"><tr><td><div id="toctitle"><h2>Contents</h2></div>
 <ul>
-<li class="toclevel-1"><a href="#new"><span class="tocnumber">1</span> <span class="toctext">New Parts</span></a>  <ul>
+<li class="toclevel-1"><a href="#New"><span class="tocnumber">1</span> <span class="toctext">New Parts</span></a>  <ul>
-<li class="toclevel-2"><a href="#J101"><span class="tocnumber">1.1</span> <span class="toctext">J23101x series with different RBSs</span></a></li>
+<li class="toclevel-2"><a href="#J101"><span class="tocnumber">1.2</span> <span class="toctext">J23101 series with different RBSs</span></a></li></ul>
-<li class="toclevel-2"><a href="#pTetAiiA"><span class="tocnumber">1.2</span> <span class="toctext">AiiA Expression cassette driven by aTc</span></a></li>
+<li class="toclevel-1"><a href="#Existing"><span class="tocnumber">2</span> <span class="toctext">Existing parts: characterization</span></a> <ul>
-<li class="toclevel-2"><a href="#pTetLuxI"><span class="tocnumber">1.3</span> <span class="toctext">LuxI Expression cassette driven by aTc</span></a></li></ul>
-<li class="toclevel-1"><a href="#Existing"><span class="tocnumber">2</span> <span class="toctext">Characterization of existing parts</span></a> <ul>
+<li class="toclevel-2"><a href="#pTet"><span class="tocnumber">2.1</span> <span class="toctext">pTet - BBa_R0040</span></a></li>
-<li class="toclevel-2"><a href="#note"><span class="tocnumber">2.1</span> <span class="toctext">Notes on promoter characterization</span></a></li>
+<li class="toclevel-2"><a href="#pLux"><span class="tocnumber">2.2</span> <span class="toctext">pLux - a 3OC6-HSL-in PoPs-out device, with less internal homology, has been characterized with mRFP</span></a></li>
-<li class="toclevel-2"><a href="#rbs"><span class="tocnumber">2.2</span> <span class="toctext">RBSs from the community collection</span></a></li>
+<li class="toclevel-2"><a href="#mRFP"><span class="tocnumber">2.3</span> <span class="toctext">RBSs from the community collection</span></a></li>
-<li class="toclevel-2"><a href="#pLux"><span class="tocnumber">2.3</span> <span class="toctext">pLux - a 3OC6-HSL-in PoPs-out device</span></a></li>
+<li class="toclevel-2"><a href="#LuxI"><span class="tocnumber">2.4</span> <span class="toctext">LuxI - BBa_C0061</span></a></li>
-<li class="toclevel-2"><a href="#pTet"><span class="tocnumber">2.4</span> <span class="toctext">pTet - BBa_R0040</span></a></li>
 <li class="toclevel-2"><a href="#AiiA"><span class="tocnumber">2.5</span> <span class="toctext">AiiA - BBa_C0060</span></a></li>
-<li class="toclevel-2"><a href="#LuxI"><span class="tocnumber">2.6</span> <span class="toctext">LuxI - BBa_C0061</span></a></li>
+</ul>
-<li class="toclevel-2"><a href="#K999"><span class="tocnumber">2.7</span> <span class="toctext">pSB1C3 vector with mRFP between S and P for easy cloning</span></a></li></ul>
+<li class="toclevel-1"><a href="#Improvement"><span class="tocnumber">3</span> <span class="toctext">Existing parts: improvement</span></a><ul>
-<li class="toclevel-1"><a href="#Improvement"><span class="tocnumber">3</span> <span class="toctext">Sequence debugging</span></a></li>
-</ul></td></tr></table>
+<li class="toclevel-2"><a href="#Rebuilt"><span class="tocnumber">3.1</span> <span class="toctext">Rebuilt existing parts from the registry for DNA not available or sequence debugging</span></a></li></ul></ul>
+</td></tr></table>
 </div>
+<a name="New"></a> <h2 class="art-postheader">
+Our new parts
+</h2>
+<div class="art-postcontent">
+<a name="J101"></a><h2> <span class="mw-headline"><partinfo>BBa_J23101</partinfo></h2></div>
+<div class="art-postcontent">
-<a name='new'></a><h1>New parts</h1>
-<a name='J101'></a><h2>J23101x series</h2>
 <ol type='1'>
@@ Line 38: / Line 37: @@
 <li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516132	">	BBa_K516132	</a>	(wiki name:	J101-E7	)	J101-RBS32-mRFP-TT				</li>
 </ol>
+<br>
-<!-- ----------------- -->
-<!-- J23101x description -->
-<!-- ----------------- -->
-<p align='justify'>
 BBa_J23101 is the reference standard promoter for the computation of RPUs. As discussed in '<a href='https://2011.igem.org/Team:UNIPV-Pavia/Measurements'>data analysis</a>' section, RPUs are relative units for the evaluation of promoter strength, based on a mathematical model of the transcription and the translation of a reporter gene. <br>
 The RPUs are supposed to be indepedent on the experimental setup, provided that the reference standard BBa_J23101 must be assayed in the same experimental condition of the studied promoter. <br>It means that if the studied promoter is in a low copy number plasmid and drives the expression of a reporter protein P, J23101 must be assembled in the same vector upstream of the same reporter P.<br>
-This approach is in accordance with the philosophy of synthetic biology, based on the concept of 'modularity' of the components. According to this approach, the assembly of basic well characterized modules to build complex circuits allows the prediction of the circuit behavior starting from the knowledge on the basic parts. <br>
+This approach is motivated by the assumption that the trascriptional strength of a promoter is independent on the encoded gene and on the experimental setup. <br> This approach is in accordance with the philosophy of synthetic biology, based on the concept of 'modularity' of the components. According to this approach, the assembly of basic well charcaterized modules to build complex circuits allow  whose behaviour can be predicted by knowledge on the basic parts.
-Salis et al. [Nat Biotec, 2009] stated that <br><br>
-<em> 'Identical ribosome binding site sequences in different genetic contexts can result in different protein expression levels'</em><br><br>
-and again
-<br><br>
-<em> 'It is likely that this absence of modularity is caused by the formation of strong secondary structures between the RBS-containing RNA sequence and one protein coding sequence but not another.'</em> <br><br>
-For this reason, RPUs might not be reliable when comparing the same promoter with different RBSs because of the un-modularity of the RBS.<br>
-In order to asses what's the effect of RBS 'un-modularity' on RPUs reliability, we have built a set of four constitutive promoters (BBa_J23101) followed by one of the four RBSs tested. These parts were used to evaluate RBS efficiency. Data were collected and analyzed as described in 'Measurements' and 'Data analysis' sections. RPUs and Synthesis rate per cell [AUr] were computed and results are summarized in the table below.
-<br><br><em>
-<b>NB</b>: for the RPU computation, the J23101-RBS34-mRFP-TT construct has been considered as the reference standard. With this assumption, RPUs are identical to the estimated RBS efficiency. </em>
 <br><br>
-If the hypothesis of RBS modularity depending on the promoter is accepted, the J23101-RBSx series we have provided can be used as a library of ready-to-use reference standard for RPU evaluation, that allows to depurate RPU measurement from RBS effect, thus providing only the promoter strength.
+<b>
+-provide Scell with CI 95% (error bar?) and RPU?? with errorbar?
+-Provide RBS ranking
+-Discuss that RPUs can be used to compare different promoters in the same exp conditions (i.e: the same RBS), but are not reliable when comparing different RBSs with the same promoter because of the un-modularity of RBS (cit: RBS calculator Salis Nature Biot 2009, 'identical ribosome binding site sequences in different genetic
+contexts can result in different protein expression levels', 'It is likely that this absence of modularity is caused by the formation of strong secondary structures between the RBS-containing RNA sequence and one protein coding sequence but not another'). Highlight that we are not trying to show that RBSs are modular, since it has been shown to be false. We try to overcome the problem of modularity by considering the complex Promoter-RBS as a whole regulatory element, whose effect can't be split between the two components. Explain that here we provide a library of ready-to-use reference standard in order to easily compute RPUs of promoters with different RBSs. Discuss that it is not totally correct to compare RPUs coming from characterization with different RBSs?
-<table align='center'><tr><td width='50%' >
+</b>
-<table class='data'>
+<br>
-<tr>
-<td class='row'><b>J23101 promoter with RBS</b>
-</td>
-<td class='row'><b>S<sub>cell</sub></b>
-</td>
-<td class='row'><b>R.P.U.s</b>
-</td>
-</tr>
-<tr><td class='row'>RBS30
-</td>
-<td class='row'>150.97 [15.34]</td>
-<td class='row'>3.17</td>
-</tr>
-<tr><td class='row'>RBS31
-</td>
-<td class='row'>2.30 [0.37]</td>
-<td class='row'>0.05</td>
-</tr>
-<tr><td class='row'>RBS32
-</td>
-<td class='row'>17.60 [5.85]</td>
-<td class='row'>0.37</td>
-</tr>
-<tr><td class='row'>RBS34
-</td>
-<td class='row'>47.57 [0.82]</td>
-<td class='row'>1</td>
-</tr>
-</table></td>
-<td width='50%' >
-<div style="text-align:justify"><div class="thumbinner" width='80%'><a href="File:RPU_J101.png" class="image"><img alt="RPUs of J23101 promoter with different RBSs" src="https://static.igem.org/mediawiki/2011/1/12/RPU_J101.png" class="thumbimage" width="80%"></a></div></div>
-</td>
-</tr></table>
-</p>
-<div align="right"><small><a href="#indice" title="">^top</a></small></div>
-<!-- ----------------- -->
-<!-- pLuxAiiA description -->
-<!-- ----------------- -->
-<a name='pTetAiiA'></a><h2>AiiA expression cassette driven by aTc-inducible pTet promoter</h2>
+ <a name="Existing"></a><h2 class="art-postheader">
-<ol>
+Characterization of existing pars from the Registry
-<ul>
+</h2>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516220	">	BBa_K516220	</a>	(wiki name:	E24	)	pTet-RBS30-AiiA-TT				</li>
+<b><font color='red'>Do we say that we are charcterizing also F2620 or T9002? Or both?</font></b>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516221	">	BBa_K516221	</a>	(wiki name:	E25	)	pTet-RBS31-AiiA-TT				</li>
+<br>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516222	">	BBa_K516222	</a>	(wiki name:	E26	)	pTet-RBS32-AiiA-TT		</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516224	">	BBa_K516224	</a>	(wiki name:	E27	)	pTet-RBS34-AiiA-TT		</li></ul></ol>
-<div align="right"><small><a href="#indice" title="">^top</a></small></div>
-<!-- ----------------- -->
-<!-- pTetAiiA description -->
-<!-- ----------------- -->
-<a name='pTetLuxI'></a><h2>LuxI expression cassette driven by aTc-inducible pTet promoter</h2>
-<ol>
-<ul>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516210	">	BBa_K516210	</a>	(wiki name:	E13	)	pTet-RBS30-LuxI				</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516211	">	BBa_K516211	</a>	(wiki name:	E14	)	pTet-RBS31-LuxI				</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516212	">	BBa_K516212	</a>	(wiki name:	E15	)	pTet-RBS32-LuxI				</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516214	">	BBa_K516214	</a>	(wiki name:	E16	)	pTet-RBS34-LuxI		</li></ul></ol>
-<div align="right"><small><a href="#indice" title="">^top</a></small></div>
-<a name='Existing'></a><h1>Existing parts</h1>
-<a name='note'></a><h2>Notes for promoter characterization</h2>
+<font color='#000000'>
-<p align='justify'>
 Inducible and constitutive promoters were assembled upstream of different coding sequences containing an  RBS from the Community collection.
 <br><br>
@@ Line 142: / Line 71: @@
 <div align='center'>
 <table class='data'>
-<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>   	Estimated efficiency</b></td></tr>
 <tr><td class="row">BBa_B0030 </td><td class="row">		0,6</td></tr>
 <tr><td class="row">BBa_B0031 </td><td class="row">		0,07</td></tr>
@@ Line 148: / Line 77: @@
 <tr><td class="row">BBa_B0034 </td><td class="row">	1</td></tr>
 </table></div>
-<br>
 For an inducible device, the RBS variation has the purpose to stretch the induction curve, thus modulating its PoPs-OUT range.
 <br><br>
 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]. In addition, 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). <br><br>
+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]. In addition, it is not possible to separate the effects of the sole promoter and of the sole RBS on the total amount of mRFP produced. <br><br>
 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='https://2011.igem.org/Team:UNIPV-Pavia/Measurements'>measurements</a> section.
-</p>
+</font>
-<p>
-Operative parameters of the promoter are derived from the estimated Hill equations obtained by <em>lsqnonlin</em> fitting of the <a href='https://2011.igem.org/Team:UNIPV-Pavia/Project/Modelling#Equations_for_gene_networks'>Hill function</a> expressed in RPUs :
-<br>
-<ol><ul><li><b>
-RPU<sub>max</sub></b> is equal to the &alpha; and represents the maximum promoter activity,
-</li><li><b>
-RPU<sub>min</sub></b> is equal to the &alpha; * &delta; represents the minimum promoter activity,
-</li><li>
-<b>Switch point</b> is computed as the abscissa of the inflection point of the Hill curve and represents the heart of linear region,
-</li>
-<li>
-<b>Linearity boundaries</b> are determined as the intersection between the tangent line to the inflection point and the upper and lower horizontal boundaries of the Hill curve.</li>
-</ul></ol>
-</p>
-<div align="right"><small><a href="#indice" title="">^top</a></small></div>
-<!-- ----------------- -->
+<div class="art-postcontent">
-<!-- --RBS description-- -->
+<a name="pTet"></a><h2> <span class="mw-headline">pTet - <partinfo>BBa_R0040</partinfo></h2></div>
-<!-- ----------------- -->
+<ol>
+<li>mRFP<ul>
-<a name='rbs'></a><h2>RBSs</h2>
-<p align='justify'>
-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]. In addition, it is not possible to separate the effects of the sole promoter and of the sole RBS on the total amount of mRFP produced.
-For this reason, every combination 'Promoter+RBS' was studied as a different regulatory element.
-The evaluation of RBS efficiency can be performed in a very intuitive fashion:<br>
-<ol><ul>
-<li> select the RBSs you want to study, </li>
-<li> assemble them in a Promoter - XX - Coding sequence circuit, </li></ul></ol>
-<div style="text-align:justify"><div class="thumbinner" width='80%'><a href="File:Vettore_base.jpg" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/d/d1/Vettore_base.jpg" class="thumbimage"  width="50%"></a></div></div>
-<ol><ul>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516230	">	BBa_K516230	</a>	(wiki name:	E21	)	pTet-RBS30-mRFP-TT				</li>
-<li> measure the output of the circuits and calculate the RBS efficiency as the ratio of the output relative to the output of the circuit with the standard RBS. </li>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516231	">	BBa_K516231	</a>	(wiki name:	E22	)	pTet-RBS31-mRFP-TT				</li>
-</ul></ol><br>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516232	">	BBa_K516232	</a>	(wiki name:	E23	)	pTet-RBS32-mRFP-TT	Rebuilt existing part from	BBa_I20252	(DNA planning)	</li>
-This simple measurement system allows the quantification of RBS efficiency depending on the whole measurement system (i.e.: promoter and encoded gene). Today it has not still been completely validated the hypothesis that every functional module in a genetic circuit maintains its behavior when assembled in a complex circuits, even if many researchers implicitly accept this hypothesis when performing characterization experiments. <br>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_I13521	">	BBa_I13521	</a>				pTet-RBS34-mRFP-TT				</li></ul></li>
-To rationally assess the impact that this hypothesis has on the genetic circuit design and fine tuning, several measurement systems were built  to evaluate the dependance of RBS modularity from the promoter or the coding sequence separately.<br>
+<li>AiiA
-In particular, in order to investigate if RBS efficiency depends on the promoter, the same coding devices (RBSx-RFP-TT) were assembled downstream of different promoters (J23101, pTet, pLux). Measuring the system output and evaluating the RBS efficiency. The results are summarized in the table below:<br>
+<ul>
-<table class='data' width='70%'><tr>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516220	">	BBa_K516220	</a>	(wiki name:	E24	)	pTet-RBS30-AiiA-TT				</li>
-<td class='row'><b>RBS</b></td>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516221	">	BBa_K516221	</a>	(wiki name:	E25	)	pTet-RBS31-AiiA-TT				</li>
-<td class='row'><b>eff<sub>pLux</sub></b><sup>*</sup></td>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516222	">	BBa_K516222	</a>	(wiki name:	E26	)	pTet-RBS32-AiiA-TT	Rebuilt existing part from	BBa_ J22071	(2008 only, Bad sequencing)	</li>
-<td class='row'><b>eff<sub>pTet</sub></b><sup>*</sup></td>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516224	">	BBa_K516224	</a>	(wiki name:	E27	)	pTet-RBS34-AiiA-TT	Rebuilt existing part from	BBa_K077047	(Part deleted)	</li></ul></li>
-<td class='row'><b>eff<sub>J23101</sub></b><sup>**</sup></td>
+<li>LuxI<ul>
-<td class='row'><b>Declared efficiency</b></td>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516210	">	BBa_K516210	</a>	(wiki name:	E13	)	pTet-RBS30-LuxI				</li>
-</tr><tr>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516211	">	BBa_K516211	</a>	(wiki name:	E14	)	pTet-RBS31-LuxI				</li>
-<td class='row'>B0030</td><td class='row'>0.40</td><td class='row'>1.72</td><td class='row'>3.17</td><td class='row'>0,6</td>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516212	">	BBa_K516212	</a>	(wiki name:	E15	)	pTet-RBS32-LuxI				</li>
-</tr><tr>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516214	">	BBa_K516214	</a>	(wiki name:	E16	)	pTet-RBS34-LuxI	Rebuilt existing part from	BBa_S03623	 (DNA available, only 2008 kit, inconsistent)	</li></ul></li>
-<td class='row'>B0031</td><td class='row'>0.01</td><td class='row'>0.03</td><td class='row'>0.05</td><td class='row'>0,07</td>
+</ol>
-</tr><tr>
-<td class='row'>B0032</td><td class='row'>0.19</td><td class='row'>0.37</td><td class='row'>0.37</td><td class='row'>0,3</td>
-</tr><tr>
-<td class='row'>B0034</td><td class='row'>1</td><td class='row'>1</td><td class='row'>1</td><td class='row'>1</td>
-</tr></table>
-<br>
+The protocols for the characterization of pTet promoter are reported in the <a href='https://2011.igem.org/Team:UNIPV-Pavia/Measurements#pTet_protocol'>pTet measurement section</a>. <br>
-On the other end, to investigate the dependance of RBS modularity on the coding sequence, the same regulatory elements (pTet-RBSx) were assembled upstream of different encoded gene (mRFP, AiiA and LuxI). RBS efficiency was assessed and the results are summarized in the table below:<br>
+This promoter is widely studied and characterized usually using the strong RBS BBa_B0034. Here we have characterized its transcriptional strength as a function of aTc induction (ng/ul) for different RBSs. Four different induction curves were obtained and are reported in figure:
-<table class='data' width='70%'><tr>
+<font face='red'><b>INSERIRE 4 CURVE pTET!!</b></font>
-<td class='row'><b>RBS</b></td>
-<td class='row'><b>eff<sub>mRFP</sub></b><sup>**</sup></td>
-<td class='row'><b>eff<sub>AiiA</sub></b><sup>***</sup></td>
-<td class='row'><b>eff<sub>LuxI</sub><sup>****</sup></b></td>
-<td class='row'><b>Declared efficiency</b></td>
-</tr><tr>
-<td class='row'>B0030</td><td class='row'>1.72</td><td class='row'>0.53</td><td class='row'>0.64</td><td class='row'>0,6</td>
-</tr><tr>
-<td class='row'>B0031</td><td class='row'>0.03</td><td class='row'>0.83</td><td class='row'>0.08</td><td class='row'>0,07</td>
-</tr><tr>
-<td class='row'>B0032</td><td class='row'>0.37</td><td class='row'>0.50</td><td class='row'>N.D.</td><td class='row'>0.3</td>
-</tr><tr>
-<td class='row'>B0034</td><td class='row'>1</td><td class='row'>1</td><td class='row'>1</td><td class='row'>1</td>
-</tr></table>
-<p align='justify'>
-<sup>*</sup> The RBS efficiency for inducible devices expressing mRFP was estimated as the ratio of the AUCs (Area under the curve) of the induction curve of the system with the studied RBS and the B0034 reference: AUC<sub>P, RBSx</sub>/AUC<sub>P, B0034</sub><br>
-<sup>**</sup> The RBS efficiency for constitutive promoters expressing mRFP was computed as the ratio between S<sub>cell<sub>P, RBSx</sub></sub>/S<sub>cell<sub>P, B0034</sub></sub><br>
-<sup>***</sup> The RBS efficiency for promoters driving the expression of AiiA enzyme was computed for the systems pTet-RBSx-aiiA-TT as the ratio between the percentage of degraded HSL in 4 hours of the device bearing the studied RBS and of the one bearing BBa_B0034. pTet was tested at full induction (100 ng/ml).<br>
-<sup>****</sup>The RBS efficiency for promoters driving the expression of LuxI was computed as the ratio between the amount of HSL produced by the device with the studied promoter and with BBa_B0034.<br>
-<br>
+The data collected from the mRFP measurement systems were processed as described in <a href='https://2011.igem.org/Team:UNIPV-Pavia/Measurements'> data analysis section</a>. The induction curves were obtained by fitting a Hill function as described in <a href='https://2011.igem.org/Team:UNIPV-Pavia/Project/Modelling#Ptet_&_Plux'>modelling section</a> and the estimated <a href='https://2011.igem.org/Team:UNIPV-Pavia/Project/Modelling#Table_of_parameters'>parameters</a> for pTet are reported in the table below.
-</p>
 <br><br>
-The parts we used to characterize the RBSs are listed here:
+<table class='data' width='70%' title='parameter value'>
-<ol>
-<ul><li>mRFP expression with different promoters</li>
-<ul>
-<li>J23101</li>
-<ul>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516130	">	BBa_K516130	</a>	J101-RBS30-RFP-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516131	">	BBa_K516131	</a>	J101-RBS31-mRFP-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516132	">	BBa_K516132	</a>	J101-RBS32-mRFP-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_J23101	">	BBa_J23101	</a>	J101-RBS34-mRFP-TT	</li>
-</ul>
-<li>pTet</li>
-<ul>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516230	">	BBa_K516230	</a>	pTet-RBS30-mRFP-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516231	">	BBa_K516231	</a>	pTet-RBS31-mRFP-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516232	">	BBa_K516232	</a>	pTet-RBS32-mRFP-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_I13521	">	BBa_I13521	</a>	pTet-RBS34-mRFP-TT	</li>
-</ul>
-<li>pLux</li>
-<ul>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516330	">	BBa_K516330	</a>	pLambda-RBS30-LuxR-T-pLux-RBS30-mRFP-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516331	">	BBa_K516331	</a>	pLambda-RBS30-LuxR-T-pLux-RBS31-mRFP-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516332	">	BBa_K516332	</a>	pLambda-RBS30-LuxR-T-pLux-RBS32-mRFP-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516334	">	BBa_K516334	</a>	pLambda-RBS30-LuxR-T-pLux-RBS34-mRFP-TT	</li>
-</ul>
-</ul>
-<li>pTet driving the expression of different genes</li>
-<ul><li>mRFP</li>
-<ul>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516230	">	BBa_K516230	</a>	pTet-RBS30-mRFP-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516231	">	BBa_K516231	</a>	pTet-RBS31-mRFP-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516232	">	BBa_K516232	</a>	pTet-RBS32-mRFP-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_I13521	">	BBa_I13521	</a>	pTet-RBS34-mRFP-TT	</li>
-</ul>
-<li>AiiA</li>
-<ul>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516220	">	BBa_K516220	</a>	pTet-RBS30-AiiA-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516221	">	BBa_K516221	</a>	pTet-RBS31-AiiA-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516222	">	BBa_K516222	</a>	pTet-RBS32-AiiA-TT	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516224	">	BBa_K516224	</a>	pTet-RBS34-AiiA-TT	</li>
-</ul>
-<li>LuxI</li>
-<ul>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516210	">	BBa_K516210	</a>	pTet-RBS30-LuxI	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516211	">	BBa_K516211	</a>	pTet-RBS31-LuxI	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516212	">	BBa_K516212	</a>	pTet-RBS32-LuxI	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516214	">	BBa_K516214	</a>	pTet-RBS34-LuxI	</li>
-</ul></ul>
-</ul></ol>
-</p>
-<div align="right"><small><a href="#indice" title="">^top</a></small></div>
-<!-- ----------------- -->
-<!-- -pLux description-- -->
-<!-- ----------------- -->
-<a name='pLux'></a><h2>pLux promoter</h2>
-<p align='justify'>
-</p>
-<ol><ul>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516330	">	BBa_K516330	</a>	(wiki name:	E17	)	pLambda-RBS30-LuxR-T-pLux-RBS30-mRFP-TT				</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516331	">	BBa_K516331	</a>	(wiki name:	E18	)	pLambda-RBS30-LuxR-T-pLux-RBS31-mRFP-TT				</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516332	">	BBa_K516332	</a>	(wiki name:	E19	)	pLambda-RBS30-LuxR-T-pLux-RBS32-mRFP-TT				</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516334	">	BBa_K516334	</a>	(wiki name:	E20	)	pLambda-RBS30-LuxR-T-pLux-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='https://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></b></td>
+<td class="row"><b>&alpha;<sub>p<sub>Tet</sub></sub></b></td>
-<td class="row"><b>&delta;<sub>p<sub>Lux</sub></sub></b></td>
+<td class="row"><b>&delta;<sub>p<sub>Tet</sub></sub></b></td>
-<td class="row"><b>&eta;<sub>p<sub>Lux</sub></sub></b></td>
+<td class="row"><b>&eta;<sub>p<sub>Tet</sub></sub></b></td>
-<td class="row"><b>k<sub>p<sub>Lux</sub></sub></b></td>
+<td class="row"><b>k<sub>p<sub>Tet</sub></sub></b></td>
 </tr>
 <tr><td class="row">BBa_B0030</td>
-<td class="row">438 [10]</td>
+<td class="row">215</td>
-<td class="row">0.05 [>100]</td>
+<td class="row">0.001</td>
-<td class="row">2 [47]</td>
+<td class="row">4.3</td>
-<td class="row">1.88 [27]</td>
+<td class="row">8.3</td>
 </tr>
 <tr><td class="row">BBa_B0031</td>
-<td class="row">9.8 [7]</td>
+<td class="row">0.7</td>
-<td class="row">0.11 [57]</td>
+<td class="row">0</td>
-<td class="row">1.2 [29]</td>
+<td class="row">18.84</td>
-<td class="row">1.5 [26]</td>
+<td class="row">47.51</td>
 </tr>
 <tr><td class="row">BBa_B0032</td>
-<td class="row">206 [3]</td>
+<td class="row">45.7</td>
-<td class="row">0 [>>100]</td>
+<td class="row">0.02</td>
-<td class="row">1.36 [10]</td>
+<td class="row">83</td>
-<td class="row">1.87 [9]</td>
+<td class="row">8</td>
 </tr>
 <tr><td class="row">BBa_B0034</td>
-<td class="row">1105 [6]</td>
+<td class="row">125</td>
-<td class="row">0.02 [>100]</td>
+<td class="row">0.12</td>
-<td class="row">1.33 [19]</td>
+<td class="row">71.8</td>
-<td class="row">2.34 [18]</td>
+<td class="row">9.8</td>
 </tr>
 </table>
-Data are provided as average [CV%]
 <br><br>
-<p align='justify'>
+Their CV% (coefficient of variation):
-The operative parameters are summarized in the table below:
-</p>
-<table align='center' class='data' width='100%'>
+<table class='data' width='70%' title='parameter value'>
 <tr>
-<td class='row'><b>RBS</b></td>
+<td class="row"><b>RBS</b></td>
-<td class='row'><b>RPU<sub>max</sub></b></td>
+<td class="row"><b>&alpha;<sub>p<sub>Tet</sub></sub></b></td>
-<td class='row'><b>RPU<sub>min</sub></b></td>
+<td class="row"><b>&delta;<sub>p<sub>Tet</sub></sub></b></td>
-<td class='row'><b>Switch point [nM]</b></td>
+<td class="row"><b>&eta;<sub>p<sub>Tet</sub></sub></b></td>
-<td class='row'><b>Linear boundaries [MIN; MAX] [nM]</b></td>
+<td class="row"><b>k<sub>p<sub>Tet</sub></sub></b></td>
 </tr>
-<tr>
+<tr><td class="row">BBa_B0030</td>
-<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>
+<td class="row">2.13</td>
+<td class="row">888</td>
+<td class="row">12</td>
+<td class="row">2.54</td>
 </tr>
-<tr>
+<tr><td class="row">BBa_B0031</td>
-<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>
+<td class="row">imm</td>
+<td class="row">1.47*10^11</td>
+<td class="row">imm</td>
+<td class="row">imm</td>
 </tr>
-<tr>
+<tr><td class="row">BBa_B0032</td>
-<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>
+<td class="row">10.88</td>
+<td class="row">411.3</td>
+<td class="row">676671474</td>
+<td class="row">393179</td>
 </tr>
-<tr>
+<tr><td class="row">BBa_B0034</td>
-<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>
+<td class="row">12.22</td>
+<td class="row">61.74</td>
+<td class="row">2705172</td>
+<td class="row">55888.6</td>
 </tr>
 </table>
+<br><br>
-<table width='100%'><tr><td width='50%'>
+While &alpha; parameter (representing the maximum trascriptional rate in the studied range of induction) varies as expected with the RBS variation , the K and &eta; parameters (determining the switch-point of the induction curve) are quite constant among all the RBS variations.<br>This suggests that the RBS variation only modulates the amplitude of the induction curve, but doesn't affect the shape, i.e. the translational promoter activity.
-<div style="text-align:justify"><div class="thumbinner" width='100%'><a href="File:PTet_-_mRFP_with_RBS_B0030_RFP_8_0.png" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/f/f6/PTet_-_mRFP_with_RBS_B0030_RFP_8_0.png" class="thumbimage" width="100%"></a></div></div>
+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.
-</td>
-<td width='50%'>
-<div style="text-align:justify"><div class="thumbinner" width='100%'><a href="File:PTet_-_mRFP_with_RBS_B0031_RFP_8_0.png" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/d/d0/PTet_-_mRFP_with_RBS_B0031_RFP_8_0.png" 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="File:PTet_-_mRFP_with_RBS_B0032_RFP_8_0.png" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/6/64/PTet_-_mRFP_with_RBS_B0032_RFP_8_0.png" class="thumbimage" width="100%"></a></div></div>
-</td>
-<td width='50%'>
-<div style="text-align:justify"><div class="thumbinner" width='100%'><a href="File:PTet_-_mRFP_with_RBS_B0034_RFP_8_0.png" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/1/12/PTet_-_mRFP_with_RBS_B0034_RFP_8_0.png" class="thumbimage" width="100%"></a></div></div>
-</td></tr>
-</table>
-<div align="right"><small><a href="#indice" title="">^top</a></small></div>
+<b><br>
-<!-- ----------------- -->
+Do we need to insert a table with the most significant measurements for every pTet-RBSx (i.e.: min RPU, max RPU, switch point, saturation threshold?)
-<!-- -pTet description-- -->
+</br></b>
-<!-- ----------------- -->
-<a name='pTet'></a><h2>pTet promoter</h2>
+<div class="art-postcontent"><a name="pLux"></a><h2> <span class="mw-headline">pLux</h2></div>
 <ol>
-<ul>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516230	">	BBa_K516230	</a>	(wiki name:	E21	)	pTet-RBS30-mRFP-TT				</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516231	">	BBa_K516231	</a>	(wiki name:	E22	)	pTet-RBS31-mRFP-TT				</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516232	">	BBa_K516232	</a>	(wiki name:	E23	)	pTet-RBS32-mRFP-TT
-</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_I13521	">	BBa_I13521	</a>				pTet-RBS34-mRFP-TT
-</li></ul>
-</ul>
-</ol>
-<p align='justify'>
-The protocols for the characterization of pTet promoter are reported in the <a href='https://2011.igem.org/Team:UNIPV-Pavia/Measurements#pTet_protocol'>pTet measurement section</a>. <br>
-This promoter is widely studied and characterized usually using the strong RBS BBa_B0034. Here we have characterized its transcriptional strength as a function of aTc induction (ng/ul) for different RBSs. Four different induction curves were obtained and are reported in figure:
-<br><br><br><br>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516330	">	BBa_K516330	</a>	(wiki name:	E17	)	pLambda-RBS30-LuxR-T-pLux-RBS30-mRFP-TT				</li>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516331	">	BBa_K516331	</a>	(wiki name:	E18	)	pLambda-RBS30-LuxR-T-pLux-RBS31-mRFP-TT				</li>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516332	">	BBa_K516332	</a>	(wiki name:	E19	)	pLambda-RBS30-LuxR-T-pLux-RBS32-mRFP-TT				</li>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516334	">	BBa_K516334	</a>	(wiki name:	E20	)	pLambda-RBS30-LuxR-T-pLux-RBS34-mRFP-TT				</li>
+</ol>
-The data collected from the mRFP measurement systems were processed as described in <a href='https://2011.igem.org/Team:UNIPV-Pavia/Measurements'> data analysis section</a>. The induction curves were obtained by fitting a Hill function as described in <a href='https://2011.igem.org/Team:UNIPV-Pavia/Project/Modelling#Ptet_&_Plux'>modelling section</a> and the estimated <a href='https://2011.igem.org/Team:UNIPV-Pavia/Project/Modelling#Table_of_parameters'>parameters</a> for pTet are reported in the pictures and in table below. </p>
-<table width='100%'><tr><td width='50%'>
+<table class='data' width='70%'>
-<div style="text-align:justify"><div class="thumbinner" width='100%'><a href="File:PTet_-_mRFP_with_RBS_B0030_RFP_8_0.png" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/f/f6/PTet_-_mRFP_with_RBS_B0030_RFP_8_0.png" class="thumbimage" width="100%"></a></div></div>
-</td>
-<td width='50%'>
-<div style="text-align:justify"><div class="thumbinner" width='100%'><a href="File:PTet_-_mRFP_with_RBS_B0031_RFP_8_0.png" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/d/d0/PTet_-_mRFP_with_RBS_B0031_RFP_8_0.png" 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="File:PTet_-_mRFP_with_RBS_B0032_RFP_8_0.png" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/6/64/PTet_-_mRFP_with_RBS_B0032_RFP_8_0.png" class="thumbimage" width="100%"></a></div></div>
-</td>
-<td width='50%'>
-<div style="text-align:justify"><div class="thumbinner" width='100%'><a href="File:PTet_-_mRFP_with_RBS_B0034_RFP_8_0.png" class="image"><img alt="" src="https://static.igem.org/mediawiki/2011/1/12/PTet_-_mRFP_with_RBS_B0034_RFP_8_0.png" class="thumbimage" width="100%"></a></div></div>
-</td></tr>
-</table>
-The estimated parameters of the Hill curves described in the figures are summarized in the table below:
-<br><br>
-<table class='data' width='100%' title='parameter value'>
 <tr>
 <td class="row"><b>RBS</b></td>
-<td class="row"><b>&alpha;<sub>p<sub>Tet</sub></sub></b></td>
+<td class="row"><b>&alpha;<sub>p<sub>Lux</sub></sub></b></td>
-<td class="row"><b>&delta;<sub>p<sub>Tet</sub></sub></b></td>
+<td class="row"><b>&delta;<sub>p<sub>Lux</sub></sub></b></td>
-<td class="row"><b>&eta;<sub>p<sub>Tet</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>Tet</sub></sub></b></td>
+<td class="row"><b>k<sub>p<sub>Lux</sub></sub></b></td>
 </tr>
 <tr><td class="row">BBa_B0030</td>
-<td class="row">215 [2]</td>
+<td class="row">438</td>
-<td class="row">0.001 [>>100]</td>
+<td class="row">0.05</td>
-<td class="row">4.3 [12]</td>
+<td class="row">2</td>
-<td class="row">8.3 [2]</td>
+<td class="row">1.88</td>
 </tr>
 <tr><td class="row">BBa_B0031</td>
-<td class="row">0.7 [>>100]</td>
+<td class="row">9.8</td>
-<td class="row">0[>>100]</td>
+<td class="row">0.11</td>
-<td class="row">18.84[>>100]</td>
+<td class="row">1.2</td>
-<td class="row">47.51[>>100]</td>
+<td class="row">1.5</td>
 </tr>
 <tr><td class="row">BBa_B0032</td>
-<td class="row">45.7 [11]</td>
+<td class="row">206</td>
-<td class="row">0.02 [>>100]</td>
+<td class="row">0</td>
-<td class="row">83 [>>100]</td>
+<td class="row">1.36</td>
-<td class="row">8 [>>100]</td>
+<td class="row">1.87</td>
 </tr>
 <tr><td class="row">BBa_B0034</td>
-<td class="row">125 [12]</td>
+<td class="row">1105</td>
-<td class="row">0.12 [61]</td>
+<td class="row">0.02</td>
-<td class="row">71.8 [>>100]</td>
+<td class="row">1.33</td>
-<td class="row">9.8 [>>100]</td>
+<td class="row">2.34</td>
 </tr>
 </table>
-Data are provided as average [CV%]
-<br><br>
-<p align='justify'>
-While &alpha; parameter (representing the maximum trascriptional rate in the studied range of induction) varies as expected with the RBS variation , the K and &eta; parameters (determining the switch-point of the induction curve) are quite constant among all the RBS variations.<br>This suggests that the RBS variation only modulates the amplitude of the induction curve, but doesn't affect the shape, i.e. the translational promoter activity.
-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 align='justify'>
-The operative parameters are summarized in the table below:
-</p>
-<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>max</sub></b></td>
-<td class='row'><b>Switch point [ng/&mu;]</b></td>
-<td class='row'><b>Linear boundaries [MIN; MAX] [ng/&mu;]</b></td>
-</tr>
-<tr>
-<td class='row'>B0030</td><td class='row'>1.43</td><td class='row'>~0</td><td class='row'>7.47</td><td class='row'>[4.66;11.99]</td>
-</tr>
-<tr>
-<td class='row'>B0031</td><td class='row'>0.33</td><td class='row'>~0</td><td class='row'>ND</td><td class='row'>ND</td>
-</tr>
-<tr>
-<td class='row'>B0032</td><td class='row'>2.60</td><td class='row'>0.04</td><td class='row'>8.03</td><td class='row'>[7.85;8.24]</td>
-</tr>
-<tr>
-<td class='row'>B0034</td><td class='row'>2.63</td><td class='row'>0.31</td><td class='row'>9.79</td><td class='row'>[9.52;10.07]</td>
-</tr>
-</table>
-<div align="right"><small><a href="#indice" title="">^top</a></small></div>
-<!-- ----------------- -->
-<!-- --AiiA description-- -->
-<!-- ----------------- -->
-<a name='AiiA'></a><h2>AiiA gene - BBa_C0060</h2>
-<p align='justify'>
-The activity of AiiA enzyme has been evaluated by testing the measurement systems <a href='<a href='https://2011.igem.org/Team:UNIPV-Pavia/Parts/Characterized#pTetAiiA'>pTet-RBSx-AiiA-TT</a>.
-The HSL synthesis rate has been evaluated according to the <a href='https://2011.igem.org/Team:UNIPV-Pavia/Project/Modelling#Equations_for_gene_networks'>model equations</a>, properly adjusted. In particular, the ODE system is reported here:
-</p>
 <br><br>
-dAiiA/dt=&alpha;<sub>pTet</sub>*(&delta;<sub>pTet</sub>+(1-&delta;<sub>pTet</sub>)/(1+(K<sub>pTet</sub>/aTc)<sup>&eta;</sup>))<br><br>
+Their CV% (coefficient of variation):
-d[HSL]/dt=N*K<sub>cat</sub>*AiiA*HSL/(K<sub>M, AiiA</sub>+AiiA))
-<br><br>
-dN/dt=N*&mu;*(N<sub>max</sub>-N)/N<sub>max</sub>
-<br><br>
- <p align='justify'>
-The parameters of the first equation (estimated from the part pTet-RBSx-mRFP-TT) and N<sub>max</sub>, &mu; and &gamma;<sub>HSL</sub> (see the <a href='https://2011.igem.org/Team:UNIPV-Pavia/Project/Results'>Results section</a> for more details) are known. <br> These parameters are summarized in the table below:
-<table class='data' width='100%' title='parameter value'>
+<table class='data' width='70%' title='parameter value'>
 <tr>
 <td class="row"><b>RBS</b></td>
-<td class="row"><b>&alpha;<sub>p<sub>Tet</sub></sub></b></td>
+<td class="row"><b>&alpha;<sub>p<sub>Lux</sub></sub></b></td>
-<td class="row"><b>&delta;<sub>p<sub>Tet</sub></sub></b></td>
+<td class="row"><b>&delta;<sub>p<sub>Lux</sub></sub></b></td>
-<td class="row"><b>&eta;<sub>p<sub>Tet</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>Tet</sub></sub></b></td>
+<td class="row"><b>k<sub>p<sub>Lux</sub></sub></b></td>
-<td class="row"><b>N<sub>max</sub></sub></b></td>
-<td class="row"><b>&mu;</b></td>
-<td class="row"><b>&gamma;<sub>HSL</sub></b></td>
 </tr>
 <tr><td class="row">BBa_B0030</td>
-<td class="row">215 [2]</td>
+<td class="row">10.14</td>
-<td class="row">0.001 [>>100]</td>
+<td class="row">180</td>
-<td class="row">4.3 [12]</td>
+<td class="row">47.73</td>
-<td class="row">8.3 [2]</td>
+<td class="row">27.5</td>
-<td class='row' rowspan='4'>1*10<sup>9</sup></td>
-<td class='row' rowspan='4'>0.003152</td>
-<td class='row' rowspan='4'>0</td>
 </tr>
 <tr><td class="row">BBa_B0031</td>
-<td class="row">0.7 [>>100]</td>
+<td class="row">7.12</td>
-<td class="row">0[>>100]</td>
+<td class="row">57.04</td>
-<td class="row">18.84[>>100]</td>
+<td class="row">29.13</td>
-<td class="row">47.51[>>100]</td>
+<td class="row">25.82</td>
 </tr>
 <tr><td class="row">BBa_B0032</td>
-<td class="row">45.7 [11]</td>
+<td class="row">2.78</td>
-<td class="row">0.02 [>>100]</td>
+<td class="row">1318</td>
-<td class="row">83 [>>100]</td>
+<td class="row">9.75</td>
-<td class="row">8 [>>100]</td>
+<td class="row">8.46</td>
 </tr>
 <tr><td class="row">BBa_B0034</td>
-<td class="row">125 [12]</td>
+<td class="row">5.81</td>
-<td class="row">0.12 [61]</td>
+<td class="row">187.2</td>
-<td class="row">71.8 [>>100]</td>
+<td class="row">19.3</td>
-<td class="row">9.8 [>>100]</td>
+<td class="row">17.86</td>
 </tr>
 </table>
-</p>
-<p align='justify'>
-The parameters K<sub>cat</sub> and K<sub>M,AiiA</sub> were estimated with a simultaneous fitting of the data collected as described in <a href='https://2011.igem.org/Team:UNIPV-Pavia/Measurements#AiiA'>measurement section</a> for the four measurement parts <a href='https://2011.igem.org/Team:UNIPV-Pavia/Parts/Characterized#pTetAiiA'>pTet-RBSx-AiiA-TT</a> assayed by <a href='https://2011.igem.org/Team:UNIPV-Pavia/Measurements#T9002'>BBa_T9002 biosensor</a> section.
-The estimated parameters for the enzymatic activity of AiiA are reported in the table below:
-<table align='center' width='50%'>
-<tr><td width='100%'>
-<table class='data' width='100%'>
-<tr>
-<td class='row'><b>K<sub>cat</sub></b></td>
-<td class='row'><b>K<sub>M, AiiA</sub></b></td>
-</tr>
-<tr><td class='row'></td>
-<td class='row'></td>
-</tr></table></td></tr></table>
 <br><br>
+<div class="art-postcontent"><a name="mRFP"></a><h2> <span class="mw-headline">RBSs</h2></div>
-</p>
+<ol>
+  <li> <A HREF="http://partsregistry.org/wiki/index.php/Part:BBa_B0030">BBa_B0030</a>
+     <ol type='a'>
+        <li>
+           <A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516030	">	BBa_K516030	</a>	(wiki name:	E5	)	RBS30-mRFP-TT	Rebuilt existing part from	BBa_S04180	(DNA planning)
+            <ul>
+              <li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516230	">	BBa_K516230	</a>	(wiki name:	E21	)	pTet-RBS30-mRFP-TT</li>
+		<li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516330	">	BBa_K516330	</a>	(wiki name:	E17	)	pLambda-RBS30-LuxR-T-pLux-RBS30-mRFP-TT</li>
+		<li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516130	">	BBa_K516130	</a>	(wiki name:	J101-E5	)	J101-RBS30-RFP-TT</li>
+            </ul>
+        </li>
+        <li> <A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516020	">	BBa_K516020	</a>	(wiki name:	E9	)	RBS30-AiiA-TT
+		<ul><li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516220	">	BBa_K516220	</a>	(wiki name:	E24	)	pTet-RBS30-AiiA-TT	</li></ul>
+        </li>
+        <li> <A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K081008	">	BBa_K081008	</a>	(wiki name:	E2	)	RBS30-LuxI
+		<ul><li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516210	">	BBa_K516210	</a>	(wiki name:	E13	)	pTet-RBS30-LuxI	</li></ul>
+        </li>
+     </ol>
+  </li>
+  <li>  <A HREF="http://partsregistry.org/wiki/index.php/Part:BBa_B0031">BBa_B0031</a>
+     <ol type='a'>
+        <li>
+           <A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516031	">	BBa_K516031	</a>	(wiki name:	E6	)	RBS31-mRFP-TT
+            <ul>
+              <li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516231	">	BBa_K516231	</a>	(wiki name:	E22	)	pTet-RBS31-mRFP-TT	</li>
+		<li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516331	">	BBa_K516331	</a>	(wiki name:	E18	)	pLambda-RBS30-LuxR-T-pLux-RBS31-mRFP-TT</li>
+		<li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516131	">	BBa_K516131	</a>	(wiki name:	J101-31	)	J101-RBS31-RFP-TT</li>
+            </ul>
+        </li>
+        <li> <A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516021	">	BBa_K516021	</a>	(wiki name:	E10	)	RBS31-AiiA-TT	Rebuilt existing part from	BBa_I13914 	(DNA planning)
+		<ul><li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516221	">	BBa_K516221	</a>	(wiki name:	E25	)	pTet-RBS31-AiiA-TT	</li></ul>
+        </li>
+        <li> <A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516011	">	BBa_K516011	</a>	(wiki name:	E3	)	RBS31-LuxI
+		<ul><li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516211	">	BBa_K516211	</a>	(wiki name:	E14	)	pTet-RBS31-LuxI	</li></ul>
+        </li>
+     </ol>
+  </li>
-<div align="right"><small><a href="#indice" title="">^top</a></small></div>
+  <li>  <A HREF="http://partsregistry.org/wiki/index.php/Part:BBa_B0032">BBa_B0032</a>
+     <ol type='a'>
+        <li>
+           <A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516032	">	BBa_K516032	</a>	(wiki name:	E7	)	RBS32-mRFP-TT	Rebuilt existing part from	BBa_ J133000	(DNA planning)
+            <ul>
+              <li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516232	">	BBa_K516232	</a>	(wiki name:	E23	)	pTet-RBS32-mRFP-TT	Rebuilt existing part from	BBa_I20252	(DNA planning)</li>
+		<li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516332	">	BBa_K516332	</a>	(wiki name:	E19	)	pLambda-RBS30-LuxR-T-pLux-RBS32-mRFP-TT</li>
+		<li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516130	">	BBa_K516132	</a>	(wiki name:	J101-E7	)	J101-RBS32-RFP-TT</li>
+            </ul>
+        </li>
+        <li> <A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516022	">	BBa_K516022	</a>	(wiki name:	E11	)	RBS32-AiiA-TT	Rebuilt existing part from	BBa_I13912	(DNA planning)
+		<ul><li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516222	">	BBa_K516222	</a>	(wiki name:	E26	)	pTet-RBS32-AiiA-TT	Rebuilt existing part from	BBa_ J22071	(2008 only, Bad sequencing)</li></ul>
+        </li>
+        <li> <A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516012	">	BBa_K516012	</a>	(wiki name:	E4	)	RBS32-LuxI
+		<ul><li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516212	">	BBa_K516212	</a>	(wiki name:	E15	)	pTet-RBS32-LuxI	</li></ul>
+        </li>
+     </ol>
+  </li>
-<!-- ----------------- -->
+  <li>  <A HREF="http://partsregistry.org/wiki/index.php/Part:BBa_B0034">BBa_B0034</a>
-<!-- --LuxI description-- -->
+     <ol type='a'>
-<!-- ----------------- -->
+        <li>
+          <A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_I13521	">	BBa_I13521	</a>				RBS34-mRFP-TT
+            <ul>
+              <li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_I13521	">	BBa_I13521	</a>				pTet-RBS34-mRFP-TT	</li>
+		<li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516334	">	BBa_K516334	</a>	(wiki name:	E20	)	pLambda-RBS30-LuxR-T-pLux-RBS34-mRFP-TT</li>
+		<li> <A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_J23101	">	BBa_J23101	</a>		J101-RBS34-RFP-TT </li>
+            </ul>
+        </li>
+        <li> 	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_I0460	">	BBa_I0460	</a>				RBS34-AiiA-TT
+		<ul><li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516224	">	BBa_K516224	</a>	(wiki name:	E27	)	pTet-RBS34-AiiA-TT	Rebuilt existing part from	BBa_K077047	(Part deleted)</li></ul>
+        </li>
+        <li> <A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_C0261	">	BBa_C0261	</a>				RBS34-LuxI
+		<ul><li><A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516214	">	BBa_K516214	</a>	(wiki name:	E16	)	pTet-RBS34-LuxI	Rebuilt existing part from	BBa_S03623	 (DNA available, only 2008 kit, inconsistent)</li></ul>
+        </li>
+     </ol>
+  </li>
-<a name='LuxI'></a><h2>LuxI gene - BBa_C0061</h2>
+</ol>
+<br><b>
+Almost everything must be inserted in this section!! How do I evaluate the efficiency of RBSs in case of inducible promoters? We need a summary table with the estimated efficiency in the condition:
+<br>-Promoter - Gene<br>
-<p align='justify'>
-LuxI has been characterized through the Biosensor BBa_T9002 (see <a href='https://2011.igem.org/Team:UNIPV-Pavia/Project/Modelling#t9002'>modeling section</a>).
+</b></br>
-<br>The HSL synthesis rate has been evaluated according to the <a href='https://2011.igem.org/Team:UNIPV-Pavia/Project/Modelling#Equations_for_gene_networks'>model equations</a>, properly adjusted. In particular, the ODE system is reported here:
-<br><br>
-dLuxI/dt=&alpha;<sub>pTet</sub>*(&delta;<sub>pTet</sub>+(1-&delta;<sub>pTet</sub>)/(1+(K<sub>pTet</sub>/aTc)<sup>&eta;</sup>))<br><br>
-d[HSL]/dt=N*V<sub>max</sub>*1/(1+(K<sub>M, LuxI</sub>/LuxI))
-<br><br>
-dN/dt=N*&mu;*(N<sub>max</sub>-N)/N<sub>max</sub>
-<br><br>
-The parameters of the first equation (estimated from the part pTet-RBSx-mRFP-TT) and N<sub>max</sub>, &mu; and &gamma;<sub>HSL</sub> (see the <a href='https://2011.igem.org/Team:UNIPV-Pavia/Project/Results'>Results section</a> for more details) are known. <br> These parameters are summarized in the table below:
+<div class="art-postcontent">
+<a name="LuxI"></a><h2> <span class="mw-headline">LuxI - <partinfo>BBa_C0061</partinfo></h2></div>
+<ol>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K081008	">	BBa_K081008	</a>	(wiki name:	E2	)	RBS30-LuxI				<br>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516210	">	BBa_K516210	</a>	(wiki name:	E13	)	pTet-RBS30-LuxI				</li>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516011	">	BBa_K516011	</a>	(wiki name:	E3	)	RBS31-LuxI				<br>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516211	">	BBa_K516211	</a>	(wiki name:	E14	)	pTet-RBS31-LuxI				</li>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516012	">	BBa_K516012	</a>	(wiki name:	E4	)	RBS32-LuxI				<br>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516212	">	BBa_K516212	</a>	(wiki name:	E15	)	pTet-RBS32-LuxI				</li>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_C0261	">	BBa_C0261	</a>				RBS34-LuxI				<br>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516214	">	BBa_K516214	</a>	(wiki name:	E16	)	pTet-RBS34-LuxI	Rebuilt existing part from	BBa_S03623	 (DNA available, only 2008 kit, inconsistent)	</li>
+</ol>
+<br><b>
+LuxI has been characterized through the Biosensor T9002 (see modeling section). The HSL synthesis rate has been evaluated according to the model (Eq. 2 - dLuxI/dt, Eq. 3 dHSL/dt, Eq. 5 dN/dt). Explain that in all these evaluations we have estimated Nmax, mu, gamma_HSL from previous experiments - see measurement and modelling sections. When do we talk about HSL stability as a function of pH?<br> Provide parameters of HSL. How do we present these data? It would be nice also to say what's the amount of HSL produced by a liquid 5 ml culture at a given OD600 in M9 medium after tot hours starting from 1:1000 dilution of a saturated ON culture..<br>
+We nee a synthetic parameter to express LuxI activity as a function of PoPS in.
+I suggest to report the HSL vs pH analysis here AND in the AiiA section of registry and, for what concerns our wiki, to add an appendix to the 'measurement section' to wich link when explaining..
+<br>Decide figures!
+</b></br>
-<table class='data' width='100%' title='parameter value'>
+<div class="art-postcontent">
-<tr>
+<a name="AiiA"></a><h2> <span class="mw-headline">AiiA - <partinfo>BBa_C0060</partinfo></h2></div>
-<td class="row"><b>RBS</b></td>
+<ol>
-<td class="row"><b>&alpha;<sub>p<sub>Tet</sub></sub></b></td>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516020	">	BBa_K516020	</a>	(wiki name:	E9	)	RBS30-AiiA-TT				<br>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516220	">	BBa_K516220	</a>	(wiki name:	E24	)	pTet-RBS30-AiiA-TT				</li>
-<td class="row"><b>&delta;<sub>p<sub>Tet</sub></sub></b></td>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516021	">	BBa_K516021	</a>	(wiki name:	E10	)	RBS31-AiiA-TT	Rebuilt existing part from	BBa_I13914 	(DNA planning)	<br>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516221	">	BBa_K516221	</a>	(wiki name:	E25	)	pTet-RBS31-AiiA-TT				</li>
-<td class="row"><b>&eta;<sub>p<sub>Tet</sub></sub></b></td>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516022	">	BBa_K516022	</a>	(wiki name:	E11	)	RBS32-AiiA-TT	Rebuilt existing part from	BBa_I13912	(DNA planning)	<br>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516222	">	BBa_K516222	</a>	(wiki name:	E26	)	pTet-RBS32-AiiA-TT	Rebuilt existing part from	BBa_ J22071	(2008 only, Bad sequencing)	</li>
-<td class="row"><b>k<sub>p<sub>Tet</sub></sub></b></td>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_I0460	">	BBa_I0460	</a>				RBS34-AiiA-TT				<br>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516224	">	BBa_K516224	</a>	(wiki name:	E27	)	pTet-RBS34-AiiA-TT	Rebuilt existing part from	BBa_K077047	(Part deleted)	</li>
-<td class="row"><b>N<sub>max</sub></sub></b></td>
+</ol>
-<td class="row"><b>&mu;</b></td>
-<td class="row"><b>&gamma;<sub>HSL</sub></b></td>
-</tr>
-<tr><td class="row">BBa_B0030</td>
-<td class="row">215 [2]</td>
-<td class="row">0.001 [>>100]</td>
-<td class="row">4.3 [12]</td>
-<td class="row">8.3 [2]</td>
-<td class='row' rowspan='4'>1*10<sup>9</sup></td>
-<td class='row' rowspan='4'>0.003152</td>
-<td class='row' rowspan='4'>0</td>
-</tr>
-<tr><td class="row">BBa_B0031</td>
-<td class="row">0.7 [>>100]</td>
-<td class="row">0[>>100]</td>
-<td class="row">18.84[>>100]</td>
-<td class="row">47.51[>>100]</td>
-</tr>
-<tr><td class="row">BBa_B0032</td>
-<td class="row">45.7 [11]</td>
-<td class="row">0.02 [>>100]</td>
-<td class="row">83 [>>100]</td>
-<td class="row">8 [>>100]</td>
-</tr>
-<tr><td class="row">BBa_B0034</td>
-<td class="row">125 [12]</td>
-<td class="row">0.12 [61]</td>
-<td class="row">71.8 [>>100]</td>
-<td class="row">9.8 [>>100]</td>
-</tr>
-</table>
-<p align='justify'>
+<br><b>
-The parameters V<sub>max</sub> and K<sub>M,LuxI</sub> were estimated with a simultaneous fitting of the data collected as described in <a href='https://2011.igem.org/Team:UNIPV-Pavia/Measurements#LuxI'>measurement section</a> for the four measurement parts <a href='https://2011.igem.org/Team:UNIPV-Pavia/Parts/Characterized#pTetLuxI'>pTet-RBSx-LuxI-TT</a> assayed by <a href='https://2011.igem.org/Team:UNIPV-Pavia/Measurements#T9002'>BBa_T9002 biosensor</a> section.
+Tha same as LuxI. Here we report the AiiA equations. Even more fundamental the estimation of gamma_HSL, that is pH dependent, because of the necessity to depurate the observed degradation by the effect not depending on AiiA
+<br>Decide figures!
+</b></br>
-The estimated parameters for the enzymatic activity of LuxI are reported in the table below:
-<table align='center' width='50%'>
-<tr><td width='100%'>
-<table class='data' width='100%'>
-<tr>
-<td class='row'><b>K<sub>M, LuxI</sub></b></td>
-<td class='row'><b>V<sub>max</sub></b></td>
-</tr>
-<tr><td class='row'></td>
-<td class='row'></td>
-</tr></table></td></tr></table>
-<br><br>
+ <a name="Improvement"></a><h2 class="art-postheader">
+Improvement of existing pars from the Registry
-Explain that in all these evaluations we have estimated Nmax, mu, gamma_HSL from previous experiments - see measurement and modelling sections. When do we talk about HSL stability as a function of pH?
+</h2>
-Provide parameters of HSL. How do we present these data? It would be nice also to say what's the amount of HSL produced by a liquid 5 ml culture at a given OD600 in M9 medium after tot hours starting from 1:1000 dilution of a saturated ON culture..
-We nee a synthetic parameter to express LuxI activity as a function of PoPS in. I suggest to report the HSL vs pH analysis here AND in the AiiA section of registry and, for what concerns our wiki, to add an appendix to the 'measurement section' to wich link when explaining..
-Decide figures!
-</p>
-</p>
-<div align="right"><small><a href="#indice" title="">^top</a></small></div>
+<b><font color='red'>Add the re-built existing parts with DNA planning!</font></b>
-<!-- ----------------- -->
-<!-- ---pSB1C3-mRFP-- -->
-<!-- ----------------- -->
-<a name='K999'></a><h2>pSB1C3 plasmid with mRFP between S and P bearing pTet (easy-to-clone)</h2>
+<div class="art-postcontent"><a name="Rebuilt"></a><h2> <span class="mw-headline">Rebuilt existing parts</h2></div>
-<div align="right"><small><a href="#indice" title="">^top</a></small></div>
+<ol>
-<a name='Improvement'></a><h1>Existing parts: sequence debugging</h1>
-<ol><ul>
 <li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516021	">	BBa_K516021	</a>	(wiki name:	E10	)	RBS31-AiiA-TT	Rebuilt existing part from	BBa_I13914 	(DNA planning)	</li>
 <li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516022	">	BBa_K516022	</a>	(wiki name:	E11	)	RBS32-AiiA-TT	Rebuilt existing part from	BBa_I13912	(DNA planning)	</li>
@@ Line 706: / Line 423: @@
 <li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516222	">	BBa_K516222	</a>	(wiki name:	E26	)	pTet-RBS32-AiiA-TT	Rebuilt existing part from	BBa_ J22071	(2008 only, Bad sequencing)	</li>
 <li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516224	">	BBa_K516224	</a>	(wiki name:	E27	)	pTet-RBS34-AiiA-TT	Rebuilt existing part from	BBa_K077047	(Part deleted)	</li>
-<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516232	">	BBa_K516232	</a>	(wiki name:	E23	)	pTet-RBS32-mRFP-TT	Rebuilt existing part from	BBa_I20252	(DNA planning)	</li></ul></ol>
+<li>	<A HREF="http://partsregistry.org/wiki/index.php/Part:	BBa_K516232	">	BBa_K516232	</a>	(wiki name:	E23	)	pTet-RBS32-mRFP-TT	Rebuilt existing part from	BBa_I20252	(DNA planning)	</li>
-<div align="right"><small><a href="#indice" title="">^top</a></small></div>
+</ol>
+<div class="cleared"></div>
+<div class="art-postcontent">
+<p>
+</p>
+<p style="text-align:left;">