Difference between revisions of "Team:UPF CRG Barcelona/Experimental Validation"
| Line 85: | Line 85: | ||
genetic circuits.</p> | genetic circuits.</p> | ||
<p>We have used these tools to model two of our constructs: pFadBA_34_RFP and pFadba_34_luxR_plux_32_RFP.</p> | <p>We have used these tools to model two of our constructs: pFadBA_34_RFP and pFadba_34_luxR_plux_32_RFP.</p> | ||
| − | <p class=" | + | <p class="subapart3">Regarding the model for pFadBA_34_RFP:</p> |
<p>To analyze the response of pFadBA promoter to palmitic acid (PA) presence, we have used the RFP reporter protein to | <p>To analyze the response of pFadBA promoter to palmitic acid (PA) presence, we have used the RFP reporter protein to | ||
obtain fluorescence measurements. The issue of those experiments was that the PA has effects in the fluorescence | obtain fluorescence measurements. The issue of those experiments was that the PA has effects in the fluorescence | ||
| Line 93: | Line 93: | ||
the curve that fitted the best our non-noisy data. (REFERENCIA) With this, we were able to estimate the whole | the curve that fitted the best our non-noisy data. (REFERENCIA) With this, we were able to estimate the whole | ||
transfer function of our construct. </p> | transfer function of our construct. </p> | ||
| − | <p class=" | + | <p class="subapart3">Regarding the model for pFadba_34_luxR_plux_32_RFP:</p> |
<p>In this case, even if we had the same problem that with pFadBA, since luxR/plux amplifies considerably the signal, | <p>In this case, even if we had the same problem that with pFadBA, since luxR/plux amplifies considerably the signal, | ||
we could obtain the whole curve with acceptable noise levels. Here, we also adapted our parameters to obtain a | we could obtain the whole curve with acceptable noise levels. Here, we also adapted our parameters to obtain a | ||
Revision as of 02:48, 18 October 2018
Single cell model
Motivation:
The last decades have been marked by a high technological development in the field of computation. This has allowed synthetic biology to use modeling tools to predict behaviors and thus make more efficient the construction of genetic circuits.
We have used these tools to model two of our constructs: pFadBA_34_RFP and pFadba_34_luxR_plux_32_RFP.
Regarding the model for pFadBA_34_RFP:
To analyze the response of pFadBA promoter to palmitic acid (PA) presence, we have used the RFP reporter protein to obtain fluorescence measurements. The issue of those experiments was that the PA has effects in the fluorescence over a concentration of 1mM, which generates a lot of noise. Because of this, we could not obtain experimentally the complete transfer function of this construct.
Nevertheless, we have made parameter optimization with weighted non-linear regression functions in order to obtain the curve that fitted the best our non-noisy data. (REFERENCIA) With this, we were able to estimate the whole transfer function of our construct.
Regarding the model for pFadba_34_luxR_plux_32_RFP:
In this case, even if we had the same problem that with pFadBA, since luxR/plux amplifies considerably the signal, we could obtain the whole curve with acceptable noise levels. Here, we also adapted our parameters to obtain a model that reflects the best the behaviour of the construct.
pFadBA model was created to complement and refine the experimental data, in contrast to pFadba_34_luxR_plux_32_RFP whose model was created for a different aim.The pFadba_34_luxR_plux_32_RFP system response is dependent on an eternal inducer: lactone. (ENLACE A MEASUREMENT)Having a model that predicts how much lactone is necessary for the modulation we want will facilitate its use in the future.
The ODE for the pFadBA_34_RFP and pFadba_34_luxR_plux_32_RFP systems are given below:
Both sets of experimental data were convoluted in order to obtain a general deterministic model for pFadBA promoter.
pFadBA_34_luxR_plux_RFP experimental fitting of the model.
pfadBA_34_RFP experimental fitting to the model.
Conclusions:
We can say that with these models we have obtained a consistent way to predict and analyze the pFadBA promoter behaviour.