Team:UNIPV-Pavia/parts/characterized2.html

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Do we need a 'measurement' page, where all the protocols for Tecan tests are collected?
Should it be included in the Protocols section and then linked when needed?

<groupparts>iGEM011 UNIPV-Pavia</groupparts>

Our new parts

BBa_J23101

BBa_J23101-RBS30-mRFP-TT (J101-E5)
BBa_J23101-RBS31-mRFP-TT (J101-31)
BBa_J23101-RBS32-mRFP-TT (J101-E7)

-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?

LuxI - BBa_C0061

RBS30-LuxI (E2 - Rebuilt existing part BBa_K081008, Registry 2011) -> pTet-RBS30-LuxI (E13)
RBS31-LuxI (E3) -> pTet-RBS31-LuxI (E14)
RBS32-LuxI (E4) -> pTet-RBS32-LuxI (E15)
RBS34-LuxI (BBa_C0261) -> pTet-RBS34-LuxI (E16, rebuilt existing part 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..

AiiA - BBa_C0060

RBS30-AiiA-TT (E9) -> pTet-RBS30-AiiA-TT (E24)
RBS31-AiiA-TT (E10, BBa_I13914, DNA planning) -> pTet-RBS31-AiiA-TT (E25)
RBS32-AiiA-TT (E11, BBa_I13912, DNA planning) -> pTet-RBS32-AiiA-TT (E26, rebuilt existing part BBa_ J22071, 2008 only, Bad sequencing)
RBS34-AiiA-TT (BBa_I0460) -> pTet-RBS34-AiiA-TT (E27)

pTet - BBa_R0040

pTet-RBS30-mRFP-TT (E21)
pTet-RBS31-mRFP-TT (E22)
pTet-RBS32-mRFP-TT (E23, Existing part BBa_I20252, DNA planning)
pTet-RBS34-mRFP-TT (BBa_I13521)
pTet-RBS30-LuxI (E13)
pTet-RBS31-LuxI (E14)
pTet-RBS32-LuxI (E15)
pTet-RBS34-LuxI (E16, rebuilt existing part BBa_S03623, DNA available, only 2008 kit, inconsistent)

RBSs BBa_B0030, BBa_B0031, BBa_B0032, BBa_B0034

RBS30-mRFP-TT(E5, rebuilt existing part from BBa_S04180, DNA planning) -> pTet-RBS30-mRFP-TT (E21)
RBS31-mRFP-TT(E6) -> pTet-RBS31-mRFP-TT (E22)
RBS32-mRFP-TT(E7, rebuilt existing part from BBa_ J133000, DNA planning) -> pTet-RBS32-mRFP-TT (E23, rebuilt existing part from BBa_I20252, DNA planning)
pTet-RBS34-mRFP-TT (BBa_I13521)
RBS30-LuxI (E2 - Rebuilt existing part BBa_K081008, Registry 2011) -> pTet-RBS30-LuxI (E13)
RBS31-LuxI (E3) -> pTet-RBS31-LuxI (E14)
RBS32-LuxI (E4) -> pTet-RBS32-LuxI (E15)
RBS34-LuxI (BBa_C0261) -> pTet-RBS34-LuxI (E16, rebuilt existing part BBa_S03623, DNA available, only 2008 kit, inconsistent)

Improvement of existing pars from the Registry

mRFP

RBS30-mRFP-TT (E5) -> pTet-RBS30-RFP-TT and pLux-RBS30-mRFP-TT (E21)
RBS31-mRFP-TT (E6) -> pTet-RBS31-RFP-TT and pLux-RBS31-mRFP-TT (E22)
RBS32-mRFP-TT (E7) -> pTet-RBS34-RFP-TT and pLux-RBS32-mRFP-TT (E23)
RBS34-mRFP-TT (BBa_I13507) -> pTet-RBS34-mRFP-TT BBa_I13521

pLux

Plambda-RBS30-luxR-T(B1006)-pLux-RBS30-mRFP-TT (E17)
Plambda-RBS30-luxR-T(B1006)-pLux-RBS31-mRFP-TT (E17)
Plambda-RBS30-luxR-T(B1006)-pLux-RBS32-mRFP-TT (E17)
Plambda-RBS30-luxR-T(B1006)-pLux-RBS34-mRFP-TT (E17)

Add the re-built existing parts with DNA planning!