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Team:UANL Mty-Mexico/Modeling
From 2013.igem.org
Overview
Figure 1. Predicted secondary structures of synthetic RNATs used in this project, as calculated by Mfold. The orange rectangles highlight nucleotides belonging to the SD sequence. a) 37ºC responsive RNAT b)32ºC responsive RNAT.
All our experiments were performed in E. coli K12. Figure 1 shows the predicted secondary structures of the two synthetic RNATs implemented in our project. So far, we detected fluorescence only with the 37ºC responsive RNAT, which controls mCherry's translation.
Figure 2 shows the visual appearance of cultures grown at 37ºC containing the 37ºC RNAT_mCherry construction (figure 2a), a non-fluorescent control (figure 2b), and a standard constitutively expressing RFP (figure 2c).
Figure 2. Visual appearance of cultures incubated for 17h at 37ºC. a)37ºC RNAT mCherry b)Non-fluorescent control c)Standard constitutively expressing RFP.
Figure 3. Average relative fluorescence values of cultures carrying our construction (37ºC RNAT mCherry) incubated at 31 and 37ºC.
Fluorescence of cultures carrying our construction increases almost 4x from 31 to 37ºC (figure 3).
Surprisingly, we obtained different behaviors in clones transformed with the same DNA (figure 4). We identified variations in plasmid copy number as the potential cause of phenotypic discrepancies among clones.
Figure 3. Behavior of different clones transformed with this construction (M1, 2, 11 and 12). Relative fluorescence at 25, 30, 37 and 42 ºC. All measurements were performed at least in triplicate, the aritmethic mean is shown.
Mathematically, we found that a simple gaussian function fits our data well, and it provides us a way to quantify the strength (amplitude), optimal value (horizontal shift), and definition or clearness (width) of our RNAT activity (figure 4). We believe positive slope is due to RNAT melting, while negative slope is due to increase in the overall protein degradation rate due to higher temperatures. This function also allows for comparisons between different RNAT, as well as being potentially predictive for non verified temperatures.
Figure 4. Gaussian Function fitting of the experimental data shown in figure 3.
What is in the charts?
For each measure in a given temperature, the system was left until a point in which we were sure the O.D of the cell culture and the production of the protein were in equilibrium, steady, and uniform, before the cells population started to decrease (which we found was 17h). The charts in our wiki show the fluorescence of our constructions relative to a standard constitutively expressing RFP, with values that go from 0 to 1. We took as a standard for the RFUs the amount of fluorescence emitted by an E. coli K12 culture transformed with a constitutively expressed part BBa_E1010 (the amount of fluorescence emitted by our culture was calculated by dividing the fluorescence of the sample by the fluorescence of the standard). Fluorescence values of a non-fluorescent control (noise) were subtracted from each measurement before calculating the relative fluorescence.
