Difference between revisions of "Part:BBa K1045015:Experience"

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This composite part was used to construct our DarR reporter system [[Part:BBa_K1045017|BBa_K1045017]]. As from this system, both DarR and GFP were expressed, we conclude that '''BBa_K1045015''' is functional, as well. For experimental data, see sections below:
 
This composite part was used to construct our DarR reporter system [[Part:BBa_K1045017|BBa_K1045017]]. As from this system, both DarR and GFP were expressed, we conclude that '''BBa_K1045015''' is functional, as well. For experimental data, see sections below:
  
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== Microscope data ==
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== Microscope Data ==
  
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TFor characterization, ''E. coli'' BL21 was transformed either with [[Part:BBa_K1045017|BBa_K1045017]] or with [[Part:BBa_K1045013|BBa_K1045013]] as a control. Both strains were grown in the abscence of c-di-AMP and subjected to fluorescence microscopy.
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For characterization, ''E. coli'' BL21 was transformed either with [[Part:BBa_K1045017|BBa_K1045017]] or with [[Part:BBa_K1045013|BBa_K1045013]] as a control. Both strains were grown in the abscence of c-di-AMP and subjected to fluorescence microscopy.
  
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In [[Part:BBa_K1045013|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 [[Part:BBa_K1045013|BBa_K1045013]] ('''Fig. 1''' ''top'') indicated that GFP was expressed. However, when transformed with [[Part:BBa_K1045017|BBa_K1045017]] ('''Fig. 1''' ''bottom''), the cells showed almost no fluorescence. In contrast to [[Part:BBa_K1045013|BBa_K1045013]], [[Part:BBa_K1045017|BBa_K1045017]] encodes for DarR. The low fluorescence suggested that DarR was expressed and active as a repressor down-regulating ''gfp'' transcription. Thus, all regulatory parts in [[Part:BBa_K1045017|BBa_K1045017]] seemed to be functional. Since this part contains [[Part:BBa_K1045015|BBa_K1045015]], [[Part:BBa_K1045015|BBa_K1045015]] is likely to be functional, as well.
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In [[Part:BBa_K1045013|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 [[Part:BBa_K1045013|BBa_K1045013]] ('''Fig. 1''' ''top'') indicated that GFP was expressed. However, when transformed with [[Part:BBa_K1045017|BBa_K1045017]] ('''Fig. 1''' ''bottom''), the cells showed almost no fluorescence. In contrast to [[Part:BBa_K1045013|BBa_K1045013]], [[Part:BBa_K1045017|BBa_K1045017]] encodes for DarR. The low fluorescence suggested that DarR was expressed and active as a repressor down-regulating ''gfp'' transcription. Thus, all regulatory parts in [[Part:BBa_K1045017|BBa_K1045017]] seemed to be functional. Since this part contains '''BBa_K1045015''', '''BBa_K1045015''' is likely to be functional, as well.
  
  
  
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[[File:-DarR.jpg|420px|thumb|'''Fig. 1.''': ''Top'': ''E. coli'' transformed with a plasmid encoding [[Part:BBa_K1045013|BBa_K1045013]] shows a strong green fluorescence under the fluorescence microscope. ''Bottom'': ''E. coli'' transformed with a plasmid harboring the DarR reporter system [[Part:BBa_K1045017|BBa_K1045017]] barely shows fluorescence. 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. [[File:+DarR.jpg|420px]]|center]]
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[[File:-DarR.jpg|420px|thumb|'''Fig. 1.''': ''Top'': ''E. coli'' transformed with a control plasmid encoding [[Part:BBa_K1045013|BBa_K1045013]]. ''Bottom'': ''E. coli'' transformed with a plasmid harboring the DarR reporter system [[Part:BBa_K1045017|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. [[File:+DarR.jpg|420px]]|center]]
  
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== Plate reader data ==
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'''Experimental details''':
 +
''E. coli'' cells were grown in LB medium until log phase. A culture aliquot was prepared on slides covered with 1 % agarose (in water) and the cells observed under the fluorescence microscope. For all images, the same exposure time was used. Microscope: Axioskop 40 FL fluorescence microscope; Camera: digital camera AxioCam MRm; Software for image processing: AxioVision Rel version 4.8 (Carl Zeiss, Göttingen, Germany); Objective: Neofluar series objective (×100 primary magnification); Filter set: eGFP HC-Filterset (band-pass [BP] 472/30, FT 495, and long-pass [LP] 520/35; AHF Analysentechnik, Tübingen, Germany) for GFP detection.
  
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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.
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==Characterization of the Reporter System in a Multi-Well Plate Reader==
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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
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[[File:DarR_Growth_cdiAMP.png|400px|thumb|'''Fig. 2''': ''Top'': Growth curve of the cells with the DarR construct; ''Bottom'': Growth curve of the GFP Control (Cells transformed with the reporter system, but without the repressor DarR).Please enlarge the pictures for better reading. (click on them)[[File:GFP_Control_Growth_cdiAMP.png|400px|]]|left]]
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We furthermore analyzed 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 employed ''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.
 +
 
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Using the plate reader, we quantified the strength of the DarR construct in ''E. coli''. 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.
 +
 
 +
'''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'''). All graphs show the mean value of three technical replicates of one biological replicate. The error bars indicate the standard deviation.
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 +
'''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
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[[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]]
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[[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]]
  
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[[File:DarR_Fluorescence_cdiAMP.png|400px|thumb|'''Fig. 2''': ''Top'': Fluorescence curve of the cells with the riboswitch construct; ''Bottom'': Fluorescence curve of the GFP Control. Please enlarge the pictures for better reading (click on them).[[File:GFP_Control_Fluorescence_cdiAMP.png|400px|]]|right]]
 
  
 
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<br style="clear:both;"/>
  
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As in the microscope experiments described above, the expression of the reporter was prevented (even without c-di-AMP), when DarR was encoded in the vector. Hence, DarR and GFP seemed to be expressed from [[Part:BBa_K1045017|BBa_K1045017]] indicating that this part is functional. Since [[Part:BBa_K1045017|BBa_K1045017]] was constructed using [[Part:BBa_K1045015|BBa_K1045015]], [[Part:BBa_K1045015|BBa_K1045015]] might be functional, as well.
+
As in the microscope experiments described above, the expression of the reporter was prevented (even without c-di-AMP), when DarR was encoded in the vector. Hence, DarR and GFP seemed to be expressed from [[Part:BBa_K1045017|BBa_K1045017]] indicating that this part is functional. Since [[Part:BBa_K1045017|BBa_K1045017]] was constructed using '''BBa_K1045015''', '''BBa_K1045015''' might be functional, as well.
  
 
===User Reviews===
 
===User Reviews===

Latest revision as of 16:32, 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_K1045015

This composite part was used to construct our DarR reporter system BBa_K1045017. As from this system, both DarR and GFP were expressed, we conclude that BBa_K1045015 is functional, as well. 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. Thus, all regulatory parts in BBa_K1045017 seemed to be functional. Since this part contains BBa_K1045015, BBa_K1045015 is likely to be functional, as well.


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. +DarR.jpg

Experimental details: E. coli cells were grown in LB medium until log phase. A culture aliquot was prepared on slides covered with 1 % agarose (in water) and the cells observed under the fluorescence microscope. For all images, the same exposure time was used. Microscope: Axioskop 40 FL fluorescence microscope; Camera: digital camera AxioCam MRm; Software for image processing: AxioVision Rel version 4.8 (Carl Zeiss, Göttingen, Germany); Objective: Neofluar series objective (×100 primary magnification); Filter set: eGFP HC-Filterset (band-pass [BP] 472/30, FT 495, and long-pass [LP] 520/35; AHF Analysentechnik, Tübingen, Germany) for GFP detection.

Characterization of the Reporter System in a Multi-Well Plate Reader

We furthermore analyzed 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 employed 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.

Using the plate reader, we quantified the strength of the DarR construct in E. coli. 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.

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). All graphs show the mean value of three technical replicates of one biological replicate. The error bars indicate the standard deviation.

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).DarR 2.png
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).DarR 5.png



As in the microscope experiments described above, the expression of the reporter was prevented (even without c-di-AMP), when DarR was encoded in the vector. Hence, DarR and GFP seemed to be expressed from BBa_K1045017 indicating that this part is functional. Since BBa_K1045017 was constructed using BBa_K1045015, BBa_K1045015 might be functional, as well.

User Reviews

UNIQe1288c79e39f3fe7-partinfo-00000000-QINU UNIQe1288c79e39f3fe7-partinfo-00000001-QINU