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Our new parts
- 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
-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?- 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
- 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)
- 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)
Here we explain the concept of regulatory element and we explain that the RBS variation has the purpose to stretch the induction curve thus modulating the PoPS-OUT range of the device. In particular, we have seen that:
-RBS32 works as expected
-RBS30 and 34 are not quite bad (even if we had some problems with fitting
-RBS31 gives an RFP output that is not detectable by our instrument (is under the detectability threshold).
Here we have to insert 4 panels with the Hill functions fitted (Tom) with double Y-axes. 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?)
- 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
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BBa_K516030 (wiki name: E5 ) RBS30-mRFP-TT Rebuilt existing part from BBa_S04180 (DNA planning) with
- 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
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BBa_K516031 (wiki name: E6 ) RBS31-mRFP-TT with
- 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
- BBa_K516032 (wiki name: E7 ) RBS32-mRFP-TT Rebuilt existing part from BBa_ J133000 (DNA planning) with
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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
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BBa_K516232 (wiki name: E23 ) pTet-RBS32-mRFP-TT Rebuilt existing part from BBa_I20252 (DNA planning)
- BBa_I13521 RBS34-mRFP-TT with
- 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
- 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_K516031 (wiki name: E6 ) RBS31-mRFP-TT
BBa_K516231 (wiki name: E22 ) pTet-RBS31-mRFP-TT - 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_I13521 RBS34-mRFP-TT
BBa_I13521 pTet-RBS34-mRFP-TT - 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) - 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)
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
- 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!
- 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!- 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)
