Difference between revisions of "Part:BBa K911001:Experience"

(→‎Applications of BBa_K911001)
(→‎Applications of BBa_K911001)
 
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[[Image:MgConstruct1.jpg|800px|center]]
 
[[Image:MgConstruct1.jpg|800px|center]]
  
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The sequence of this construct has been verified.
+
The sequence of this construct has been verified. E.coli colonies containing this construct expressed sfGFP, which was expected due to the leakiness of the lacI repressor, as well as the fact that the LB on which the cells were grown will have contained magnesium.
  
−
In order to test it, we transformed the construct into e.coli and attempted to induce GFP expression with both increasing magnesium concentrations and increasing IPTG concentrations. The cells were then interrogated at the correct GFP absorbtion and emission wavelengths (450nm and 545nm respectively) in a plate reader.
+
In order to test it, we attempted to induce GFP expression in transformed e.coli cells with both increasing magnesium concentrations and increasing IPTG concentrations. The cells were then interrogated at wavelengths close to peak absorbence and emission for GFP (450nm and 545nm respectively) in a plate reader.
  
−
The results of this assay are shown below.
+
The results of our initial assay are shown below.
  
−
[[Image:MgEcoliAssay.tif|500px|center]]
+
[[Image:MgEcoliAssay.png|500px|center]]
  
 
As can be seen, the assay did not give the expected results. At differing IPTG concentrations, the response to magnesium seems to have inverted.
 
As can be seen, the assay did not give the expected results. At differing IPTG concentrations, the response to magnesium seems to have inverted.
  
−
The construct was then transformed into Bacillus subtilis, with a view to repeat the same assay in this new chassis. Because the part originally comes from bacillus, we hoped that this might give more useful data.
+
[[Image:AssayGrowthCurves.png|left|500px|thumb|Typical growth curves of our construct in minimal medium. Magnesium concentrations varied from 1 μM (most red) to 5mM (most blue).]]
 +
 
 +
We repeated this experiment, using a different range of magnesium concentrations (1μM - 5mM) and doing duplicates in alternate rows. The cells grew well, although they did not appear to do so in an exponential fashion. It is believed that this may be a feature of the minimal medium in which we were performing the assay, as failed tests using a rich defined medium (which, unfortunately, autofluoresced at GFP wavelengths due to the aromatic amino acids it contained) showed normal exponential growth with the same construct and at identical magnesium concentrations.
 +
 
 +
Having collected OD620 data as well as fluorescence data, we hoped to generate graphs containing fluorescence readings normalized to cell density. We used the following formula to normalize our data:
 +
 
 +
[[Image:NormalisationFormula.png|center|400px]]
 +
 
 +
Initial analysis produced fairly convincing data, as shown in the graphs below (top images). Certainly, the part appeared to produce a convincing response to magnesium between 1 μM and ~10μM, within the sensitivity range of the original paper. A more modest increase can be seen past this point. More careful analysis of the raw data indicated that this apparent trend may have been an artifact of the normalization formula, as no particularly convincing trend can be seen in the raw final fluorescence data (bottom images).
 +
 
 +
[[Image:MgSurfs.png|center|thumb|900px|Surface plots of our plate reader assay data. Top images have been normalized to cell population, while bottom images have not. Images on the right leave out the outlier at 1μM.]]
 +
 
 +
[[Image:MgLines.png|center|thumb|900px|Line graphs of our plate reader assay data. Top images have been normalized to cell population, while bottom images have not. Images on the right leave out the outlier at 1μM.]]
 +
 
 +
However, visual inspection under the fluorescence microscope demonstrated that the low magnesium cultures had very different fluorescent properties, both in quantity and quality of the light produced (higher magnesium cultures had a more yellow hue). We took this as a sign that our plate reader may not be producing reliable data, perhaps not surprising given that we were having to use non-optimal emission and excitation filters. Additionally, the final fluorescence was lower than the initial fluorescence despite the fact that visual inspection demonstrated that it increased considerably from start to finish. This just goes to show the dangers of normalizing data without looking at it first! It also shows the importance of an internal ratiometric control channel which is measured in the same way - this should eliminate the normalization artifacts that we have found from using OD620 as our normalization channel. If the plate reader was unable to measure one fluorescence channel, it is unlikely that it would be able to measure the second, eliminating the artifacts.
 +
 
 +
We then attempted to transform the construct into Bacillus subtilis, with a view to repeat the same assay in this new chassis. Because the part originally comes from bacillus, we hoped that this might give more useful data. Unfortunately, we did not have time to characterise the part in this chassis, as our transformation attempts failed. This may be an excellent starting point for any future teams seeking to explore this part.
  
 
===User Reviews===
 
===User Reviews===

Latest revision as of 22:49, 26 September 2012

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_K911001

BBa_K911001 has been inserted into the following construct:

MgConstruct1.jpg

The sequence of this construct has been verified. E.coli colonies containing this construct expressed sfGFP, which was expected due to the leakiness of the lacI repressor, as well as the fact that the LB on which the cells were grown will have contained magnesium.

In order to test it, we attempted to induce GFP expression in transformed e.coli cells with both increasing magnesium concentrations and increasing IPTG concentrations. The cells were then interrogated at wavelengths close to peak absorbence and emission for GFP (450nm and 545nm respectively) in a plate reader.

The results of our initial assay are shown below.

MgEcoliAssay.png

As can be seen, the assay did not give the expected results. At differing IPTG concentrations, the response to magnesium seems to have inverted.

Typical growth curves of our construct in minimal medium. Magnesium concentrations varied from 1 μM (most red) to 5mM (most blue).

We repeated this experiment, using a different range of magnesium concentrations (1μM - 5mM) and doing duplicates in alternate rows. The cells grew well, although they did not appear to do so in an exponential fashion. It is believed that this may be a feature of the minimal medium in which we were performing the assay, as failed tests using a rich defined medium (which, unfortunately, autofluoresced at GFP wavelengths due to the aromatic amino acids it contained) showed normal exponential growth with the same construct and at identical magnesium concentrations.

Having collected OD620 data as well as fluorescence data, we hoped to generate graphs containing fluorescence readings normalized to cell density. We used the following formula to normalize our data:

NormalisationFormula.png

Initial analysis produced fairly convincing data, as shown in the graphs below (top images). Certainly, the part appeared to produce a convincing response to magnesium between 1 μM and ~10μM, within the sensitivity range of the original paper. A more modest increase can be seen past this point. More careful analysis of the raw data indicated that this apparent trend may have been an artifact of the normalization formula, as no particularly convincing trend can be seen in the raw final fluorescence data (bottom images).

Surface plots of our plate reader assay data. Top images have been normalized to cell population, while bottom images have not. Images on the right leave out the outlier at 1μM.
Line graphs of our plate reader assay data. Top images have been normalized to cell population, while bottom images have not. Images on the right leave out the outlier at 1μM.

However, visual inspection under the fluorescence microscope demonstrated that the low magnesium cultures had very different fluorescent properties, both in quantity and quality of the light produced (higher magnesium cultures had a more yellow hue). We took this as a sign that our plate reader may not be producing reliable data, perhaps not surprising given that we were having to use non-optimal emission and excitation filters. Additionally, the final fluorescence was lower than the initial fluorescence despite the fact that visual inspection demonstrated that it increased considerably from start to finish. This just goes to show the dangers of normalizing data without looking at it first! It also shows the importance of an internal ratiometric control channel which is measured in the same way - this should eliminate the normalization artifacts that we have found from using OD620 as our normalization channel. If the plate reader was unable to measure one fluorescence channel, it is unlikely that it would be able to measure the second, eliminating the artifacts.

We then attempted to transform the construct into Bacillus subtilis, with a view to repeat the same assay in this new chassis. Because the part originally comes from bacillus, we hoped that this might give more useful data. Unfortunately, we did not have time to characterise the part in this chassis, as our transformation attempts failed. This may be an excellent starting point for any future teams seeking to explore this part.

User Reviews

UNIQf99aa15753073c9e-partinfo-00000000-QINU UNIQf99aa15753073c9e-partinfo-00000001-QINU