Difference between revisions of "Part:BBa K1045009:Experience"

Revision as of 14:15, 26 October 2013

This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.

Applications of BBa_K1045009

We used this part to construct our DarR reporter system BBa_K1045017. From this system, both DarR and GFP were expressed. We assume that the inverted terminator BBa_K1045009 does not interfere with the operation of the DarR reporter system. For experimental data, see sections below:

Microscope data

For characterization, E. coli BL21 was transformed either with BBa_K1045017 or with BBa_K1045013 as a control. Both strains were grown in the abscence of c-di-AMP and subjected to fluorescence microscopy.

In BBa_K1045013, gfp is placed downstream of a strong promoter and the DarR operator. This vector does not encode for DarR. The strong fluorescence of the cells transformed with BBa_K1045013 (Fig. 1 top) indicated that GFP was expressed. However, when transformed with BBa_K1045017 (Fig. 1 bottom), the cells showed almost no fluorescence. In contrast to BBa_K1045013, BBa_K1045017 encodes for DarR. The low fluorescence suggested that DarR was expressed and active as a repressor down-regulating gfp transcription.

Fig. 1.: Top: E. coli transformed with a control plasmid encoding BBa_K1045013. Bottom: E. coli transformed with a plasmid harboring the DarR reporter system BBa_K1045017. Cells of both strains were cultured without c-di-AMP and analyzed by fluorescence microscopy. Both pictures represent merges of a bright field image and a GFP fluorescence image. The exposure time used to record GFP fluorescence was in both cases 2 seconds.

Plate reader data

We furthermore produced quantitative data characterizing the growth and the fluorescence over time of the BL21 E. colis we transformed with the DarR reporter system construct BBa_K1045017. As a control, we used E. coli cells harboring the BBa_K1045013 plasmid. This plasmid carries only the GFP expression unit with a strong promoter and the DarR operator. It does not encode for DarR.

Plate reader experiments were performed to quantify the strength of the DarR construct in E. coli. In these experiments, a dilution series of c-di-AMP (0, 50, 100, 150, 300, 500 and 1000 nmol c-di-AMP) was used to test the reaction of the DarR reporter system to the nucleotide. Two biological replicates were done. For each biological replicate, three technical replicates were analyzed. The graphs below show the mean value of the technical replicates of one biological replicate. The error bars indicate the standard deviation.

Fig. 2 shows the growth curves recorded via the optical density (OD) at the wavelength 600 nm. The GFP fluorescence was measured at 509 nm over the time, as well. Since the fluorescence depends on the growth of the E. coli cells, the GFP fluorescence was normalized to the OD at 600 nm for each time point (Fig. 3).

Experimental setup: total time 21 h; 15 min measurement interval; 37°C, medium shaking; 96-well titer plate; Synergy Mx Monochromator-Based Multi-Mode Microplate Reader; Gen5 V2.01

Fig. 2: The growth of the E. coli cells was measured in a plate reader via the OD at 600 nm. To facilitate the differentiation between the growth phases, the OD at 600 nm is depicted in log scale. Top: E. coli cells carrying the control plasmid BBa_K1045013; Bottom: E. coli cells transformed with the DarR reporter system BBa_K1045017. The cells were cultured with c-di-AMP in different concentrations or without c-di-AMP. Please enlarge the pictures for better reading (click on them).

Fig. 3: The GFP fluorescence measured at 509 nm was normalized to the OD at 600 nm. Top: E. coli cells carrying the control plasmid BBa_K1045013; Bottom: E. coli cells transformed with the DarR reporter system BBa_K1045017. The cells were cultured with c-di-AMP in different concentrations or without c-di-AMP. Please enlarge the pictures for better reading (click on them).

As in the microscope experiments described above, the expression of the reporter was prevented, when DarR was encoded in the vector. This was even the case when c-di-AMP was absent. Hence, DarR and GFP seemed to be expressed from BBa_K1045017 indicating that this part is functional. We assume that the strong repression of the GFP fluorescence might result from the strong binding of DarR to its operator sequence in E. coli. Mutation of the DarR operator or the DNA binding domain of DarR could possibly reduce the binding strength. This could lead to a DarR reporter system which might be controlled by different c-di-AMP concentrations.

User Reviews

UNIQd3f167b3e969cc6b-partinfo-00000000-QINU UNIQd3f167b3e969cc6b-partinfo-00000001-QINU

@@ Line 20: / Line 20: @@
 == Plate reader data ==
-We furthermore produced quantitative data characterizing the growth and the fluorescence over time of the BL21 ''E. coli''s we transformed with the DarR reporter system construct [[Part:BBa_K1045017|BBa_K1045017]]. As a control, we used ''E. coli'' cells harboring the [[Part:BBa_K1045013|BBa_K1045013]] plasmid.
+We furthermore produced quantitative data characterizing the growth and the fluorescence over time of the BL21 ''E. coli''s we transformed with the DarR reporter system construct [[Part:BBa_K1045017|BBa_K1045017]]. As a control, we used ''E. coli'' cells harboring the [[Part:BBa_K1045013|BBa_K1045013]] plasmid. This plasmid carries only the GFP expression unit with a strong promoter and the DarR operator. It does not encode for DarR.
-The following graphs show the results of the plate reader experiments performed to quantify the strength of the DarR construct in ''E. coli''. Shown are growth curves measured at the wavelength 600 nm for the cell density ('''Fig. 2''') and 509 nm for the GFP ('''Fig. 3'''), which is encoded in the construct. For each measurement, three technical and two biological replicates were done. The graphs show the mean value of the technical replicates and one of the biological replicates. As written in the legend, a dilution series of c-di-AMP was used to test the reaction of the DarR reporter system to the nucleotide. Experimental setup: total time 21 h; 15 min measurement interval; 37°C, medium shaking; 96-well titer plate; Synergy Mx Monochromator-Based Multi-Mode Microplate Reader; Gen5 V2.01
-[[File:DarR_Growth_cdiAMP.png|400px|thumb|'''Fig. 2''': ''Top'': Growth curve of the ''E. coli'' cells carrying the DarR reporter system [[Part:BBa_K1045017|BBa_K1045017]]; ''Bottom'': Growth curve of ''E. coli'' cells transformed with the control plasmid [[Part:BBa_K1045013|BBa_K1045013]]. The cells were cultured with c-di-AMP in different concentrations or without c-di-AMP. The growth was measured via the OD at 600 nm in a plate reader. Please enlarge the pictures for better reading (click on them).[[File:GFP_Control_Growth_cdiAMP.png|400px|]]|left]]
+Plate reader experiments were performed to quantify the strength of the DarR construct in ''E. coli''. In these experiments, a dilution series of c-di-AMP (0, 50, 100, 150, 300, 500 and 1000 nmol c-di-AMP) was used to test the reaction of the DarR reporter system to the nucleotide. Two biological replicates were done. For each biological replicate, three technical replicates were analyzed. The graphs below show the mean value of the technical replicates of one biological replicate. The error bars indicate the standard deviation.
+'''Fig. 2''' shows the growth curves recorded via the optical density (OD) at the wavelength 600 nm. The GFP fluorescence was measured at 509 nm over the time, as well. Since the fluorescence depends on the growth of the ''E. coli'' cells, the GFP fluorescence was normalized to the OD at 600 nm for each time point ('''Fig. 3''').
+'''Experimental setup''': total time 21 h; 15 min measurement interval; 37°C, medium shaking; 96-well titer plate; Synergy Mx Monochromator-Based Multi-Mode Microplate Reader; Gen5 V2.01
+[[File:DarR_1.png|400px|thumb|'''Fig. 2''': The growth of the ''E. coli'' cells was measured in a plate reader via the OD at 600 nm. To facilitate the differentiation between the growth phases, the OD at 600 nm is depicted in log scale. ''Top'': ''E. coli'' cells carrying the control plasmid [[Part:BBa_K1045013|BBa_K1045013]]; ''Bottom'': ''E. coli'' cells transformed with the DarR reporter system [[Part:BBa_K1045017|BBa_K1045017]]. The cells were cultured with c-di-AMP in different concentrations or without c-di-AMP. Please enlarge the pictures for better reading (click on them).[[File:DarR_2.png|400px|]]|center]]
+[[File:DarR_6.png|400px|thumb|'''Fig. 3''': The GFP fluorescence measured at 509 nm was normalized to the OD at 600 nm. ''Top'': ''E. coli'' cells carrying the control plasmid [[Part:BBa_K1045013|BBa_K1045013]]; ''Bottom'': ''E. coli'' cells transformed with the DarR reporter system [[Part:BBa_K1045017|BBa_K1045017]]. The cells were cultured with c-di-AMP in different concentrations or without c-di-AMP. Please enlarge the pictures for better reading (click on them).[[File:DarR_5.png|400px|]]|center]]
-[[File:DarR_Fluorescence_cdiAMP.png|400px|thumb|'''Fig. 2''': ''Top'': Fluorescence curve of the ''E. coli'' cells with the DarR reporter system [[Part:BBa_K1045017|BBa_K1045017]]; ''Bottom'': Fluorescence curve of ''E. coli'' cells transformed with the control plasmid [[Part:BBa_K1045013|BBa_K1045013]]. The cells were cultured with c-di-AMP in different concentrations or without c-di-AMP. The fluorescence was measured at 509 nm in a plate reader. Please enlarge the pictures for better reading (click on them).[[File:GFP_Control_Fluorescence_cdiAMP.png|400px|]]|right]]