Difference between revisions of "Part:BBa K389016:Experience"
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===Applications of BBa_K389016=== | ===Applications of BBa_K389016=== | ||
− | ====Transfer function of <partinfo>K389016<partinfo>==== | + | ====Transfer function of <partinfo>K389016</partinfo>==== |
− | + | ||
The data for the transfer function was measured and analyzed as described below. The data was fitted with a dose response function of the form | The data for the transfer function was measured and analyzed as described below. The data was fitted with a dose response function of the form | ||
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− | with the hill coefficient p, the bottom asymptote A1, the top asymptote A2 and the inflection point log(x<sub>0</sub>). | + | with the hill coefficient p, the bottom asymptote A1, the top asymptote A2 and the inflection point log(x<sub>0</sub>). Figure 1 shows the measured normalized specific production rates q<sub>P,n</sub> plotted against the logarithm of the concentration of the inductor acetosyringone in µM. The fit has an R<sup>2</sup> = 0.99. |
− | [[Image:Bielefeld_Final_RFP_fit.jpg|600px|thumb|center|Transfer function for the part <partinfo>K389016</partinfo> (R<sup>2</sup> = 0.99).]] | + | [[Image:Bielefeld_Final_RFP_fit.jpg|600px|thumb|center|'''Fig. 1: Transfer function for the part <partinfo>K389016</partinfo> (R<sup>2</sup> = 0.99).''']] |
− | The important data from the transfer function is summarized in | + | The important data from the transfer function is summarized in table 1: |
<center> | <center> | ||
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The accumulation of mRFP in the cells is always exponential. A typical fitted product accumulation curve is shown below: | The accumulation of mRFP in the cells is always exponential. A typical fitted product accumulation curve is shown below: | ||
− | [[Image:Bielefeld_ExpFit_auf_RFU.jpg|500px|thumb|center|'''Exponential fit on the measured RFU plotted against cultivation time of a cultivation of <partinfo>K389016</partinfo> in ''Escherichia coli'' DB3.1 in LB medium with 10 mg ml<sup>-1</sup> chloramphenicol and 150 µM acetosyringone. ''']] | + | [[Image:Bielefeld_ExpFit_auf_RFU.jpg|500px|thumb|center|'''Fig. 2: Exponential fit on the measured RFU plotted against cultivation time of a cultivation of <partinfo>K389016</partinfo> in ''Escherichia coli'' DB3.1 in LB medium with 10 mg ml<sup>-1</sup> chloramphenicol and 150 µM acetosyringone. ''']] |
The product accumulation in a cultivation can be described as: | The product accumulation in a cultivation can be described as: |
Revision as of 15:23, 25 October 2010
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Applications of BBa_K389016
Transfer function of BBa_K389016
The data for the transfer function was measured and analyzed as described below. The data was fitted with a dose response function of the form
with the hill coefficient p, the bottom asymptote A1, the top asymptote A2 and the inflection point log(x0). Figure 1 shows the measured normalized specific production rates qP,n plotted against the logarithm of the concentration of the inductor acetosyringone in µM. The fit has an R2 = 0.99.
The important data from the transfer function is summarized in table 1:
Table 1: Data from the transfer function for the part BBa_K389016.
Parameter | Value |
---|---|
Hill coefficient | 1.673 |
Inflection point | 26.5 µM |
Top asymptote | 2.62 |
Data analysis for BBa_K389016
The data analysis is made in three steps. First step is the processing of the fluorescence raw data gained by the fluorescence plate reader for every sample:
In the second step the RFUcorrected of every sample is plotted against the cultivation time it was drawn. The data is fitted by an exponential fit of the following style:
The accumulation of mRFP in the cells is always exponential. A typical fitted product accumulation curve is shown below:
The product accumulation in a cultivation can be described as:
with the amount of product P, the cell count X and the specific production rate qP.
RFU is commensurate to the concentration of mRFP (P) and the OD600 is commensurate to the cell count (X) ([http:/parts.igem.org/Part:BBa_F2620:Experience/Endy/Data_analysis Canton and Labno, 2004]):
With these assumptions it is possible to calculate the specific production rate of mRFP qP in the third step: the specific production rate for every sample of a cultivation is calculated by the derivation of the exponential fit line which describes the accumulation of product in the culture (dRFU/dt) and the measured OD600 data:
The specific production rates qP of all samples of all cultivations made with a specific inductor concentration c are averaged and normalized against the specific production rate of the uninduced system qP,0:
This normalized specific production rate we calculated is commensurate to relative promotor units (RPU) which is commensurate to PoPS (polymerase per seconds) (Canton and Labno, 2004; Pasotti et al., 2009):
References
Canton B and Labno A (2004) Data processing of Part BBa_F2620, https://parts.igem.org/Part:BBa_F2620:Experience/Endy/Data_analysis.
Pasotti L, Zucca S, Del Fabbro E (2009) Characterization experiment on BBa_J23100, BBa_J23101, BBa_J23118, https://parts.igem.org/Part:BBa_J23101:Experience.
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