Difference between revisions of "Team:Wageningen UR/InterLab"

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                         <h1> InterLab</h1>
 
                         <h1> InterLab</h1>
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                         <p> The iGEM InterLab study was set up 4 years ago to develop a robust measurement protocol for green fluorescent protein, which will allow for accurate comparison of results between labs. Creating such a robust protocol requires fluorescence data from labs around the world, which is why all iGEM teams are encouraged to participate in this study and submit their results. To contribute to this important study we of the Wageningen iGEM team were proud to be able to participate.
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                         <p> The iGEM InterLab study was set up 4 years ago to develop a robust measurement protocol for Green Fluorescent Protein (GFP), which will allow for accurate comparison of results between labs. Creating such a robust protocol requires fluorescence data from labs around the world, which is why all iGEM teams are encouraged to participate in this study and submit their results. To contribute to this study, the Wageningen iGEM team was proud to be able to participate.
 
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                             Repetition of experiments is an essential process within all science-related fields. First and foremost, it is the main way of verifying experimental results. By repeating a scientific experiment the impact of random variation can be reduced due to a larger dataset giving a more representative view of the measured system. This allows for more accurate interpretation of results. However, repetition of measurements can be difficult due to variations in lab environments, equipment specifics, and human handling. This can lead to problems with the comparison of data obtained from similar experiments around the world.</p>
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                             Repetition of experiments is an essential process within all science-related fields. First and foremost, it is the main way of verifying experimental results. By repeating a scientific experiment, the impact of random variation can be reduced owing to the larger dataset giving a more representative view of the measured system. This allows for more accurate interpretation of results. However, repetition of measurements can be difficult due to variations in lab environments, equipment specifications, and human handling. This can lead to problems with the comparison of data obtained from similar experiments around the world.</p>
 
                              
 
                              
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<p>To allow for more accurate interpretation of results in different labs, the iGEM Measurement Committee has been developing a robust measurement procedure in the InterLab study, specifically for the measurement of green fluorescent protein (GFP). Fluorescence is an important tool in synthetic biology, as it acts as an easy to use reporter for engineered systems. By creating this robust procedure the Committee hopes to solve the challenge of comparing fluorescence data between labs. In the InterLab study iGEM teams from around the world are asked to perform a standard GFP measurement on a set of bacterial 'devices' in their own labs. Data generated by the teams are then used to improve upon the measurement procedure.</p>
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<p>To allow for more accurate interpretation of results in different labs, the iGEM Measurement Committee has been developing a robust measurement procedure in the InterLab study, specifically for the measurement of GFP. Fluorescence is an important tool in synthetic biology, as it acts as an easy reporter for engineered systems. By creating this robust procedure, the Committee hopes to solve the data variations in fluorescence data between labs. In the InterLab study, iGEM teams from around the world were asked to perform a standard GFP measurement on a set of bacterial 'devices' in their own labs. Data generated by these teams are then used to improve upon the measurement procedure.</p>
 
                              
 
                              
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<p>We of the Wageningen iGEM 2017 team were happy to participate in this important study.
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<p>We, of the Wageningen iGEM 2017, team were happy to participate in this study.
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                         On this page we will present this measurement protocol, as well as the results we obtained from it.
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                         On this page we will present the measurement protocol, as well as the results we obtained with it.
 
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                                         For this study, we had the choice performing fluorescence measurements either with a plate reader or flow cytometer. As the use of the latter is restricted in our laboratory we decided to adhere to the <a href="https://static.igem.org/mediawiki/2017/8/85/InterLab_2017_Plate_Reader_Protocol.pdf">plate reader protocol</a>. Using the BioTek&rsquo;s Synergy Mx Monochromator-based Microplate Reader we measured culture samples of the following 8 devices:
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                                         For this study, we had the choice of performing fluorescence measurements either with a plate reader or flow cytometer. As the use of the latter is restricted in our laboratory, we decided to adhere to the <a href="https://static.igem.org/mediawiki/2017/8/85/InterLab_2017_Plate_Reader_Protocol.pdf">plate reader protocol</a>. Using the BioTek&rsquo;s Synergy Mx Monochromator-based Microplate Reader, we measured culture samples of the following 8 devices:
 
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                                                 Successful transformation of these devices to <i>E. coli</i> DH5&alpha; cells resulted in the colonies that were used to inoculate 50 mL Greiner tubes containing 10 mL LB medium + Chloramphenicol. These liquid cultures were incubated at 37 degrees Celcius, during which samples were taken at timepoints 0, 2, 4 and 6 hours after inoculation. They were then used to measure fluorescence and OD<sub>600nm</sub> in the plate reader.
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                                                 Successful transformation of these devices to <i>E. coli</i> DH5&alpha; cells resulted in the colonies that were used to inoculate 50 mL Greiner tubes containing 10 mL LB medium + Chloramphenicol. These liquid cultures were incubated at 37 degrees Celsius, during which samples were taken at timepoints 0, 2, 4 and 6 hours after inoculation. They were then used to measure fluorescence and OD<sub>600nm</sub> in the plate reader.
 
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                                                 To make sense of the data we first needed to make calibrations of both the OD<sub>600nm</sub> and fluorescence at 395nm/509nm (emission/excitation). For the former, we used LUDOX-HS40 and H<sub>2</sub>O, provided by iGEM; for the latter, we used fluorescein, also provided by iGEM.
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                                                 To make sense of this data, we first needed to make calibrations of both the OD<sub>600nm</sub> and fluorescence at 395nm/509nm (emission/excitation). For the former, we used LUDOX-HS40 and H<sub>2</sub>O, provided by iGEM; for the latter, we used fluorescein, also provided by iGEM.
 
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                             Measurement of the 96 wells plate in the BioTek&rsquo;s Synergy Mx Monochromator-based Microplate Reader was performed at 27 &deg;C with a wavelength of 600nm for the OD and wavelengths of 395nm and 509nm for the fluorescence excitation and emission respectively. Furthermore, path length correction was turned off in the absorbance measurement and a slit width of 9 mm with a gain of 75 was selected for the fluorescence measurement. Data obtained from these measurements were added to the calculation sheet provided by the iGEM Committee, resulting in data as presented in the final graph:
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                             Measurement of the 96-wells plate in the BioTek&rsquo;s Synergy Mx Monochromator-based Microplate Reader was performed at 27&deg;C with a wavelength of 600nm for the OD and wavelengths of 395nm and 509nm for the fluorescence excitation and emission, respectively. Furthermore, path length correction was turned off in the absorbance measurement and a slit width of 9 mm with a gain of 75 was selected for the fluorescence measurement. Data obtained from these measurements was added to the calculation sheet provided by the iGEM Committee, resulting in data as presented in the final graph:
 
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Revision as of 16:17, 1 November 2017

InterLab

The iGEM InterLab study was set up 4 years ago to develop a robust measurement protocol for Green Fluorescent Protein (GFP), which will allow for accurate comparison of results between labs. Creating such a robust protocol requires fluorescence data from labs around the world, which is why all iGEM teams are encouraged to participate in this study and submit their results. To contribute to this study, the Wageningen iGEM team was proud to be able to participate.

Details

Repetition of experiments is an essential process within all science-related fields. First and foremost, it is the main way of verifying experimental results. By repeating a scientific experiment, the impact of random variation can be reduced owing to the larger dataset giving a more representative view of the measured system. This allows for more accurate interpretation of results. However, repetition of measurements can be difficult due to variations in lab environments, equipment specifications, and human handling. This can lead to problems with the comparison of data obtained from similar experiments around the world.

To allow for more accurate interpretation of results in different labs, the iGEM Measurement Committee has been developing a robust measurement procedure in the InterLab study, specifically for the measurement of GFP. Fluorescence is an important tool in synthetic biology, as it acts as an easy reporter for engineered systems. By creating this robust procedure, the Committee hopes to solve the data variations in fluorescence data between labs. In the InterLab study, iGEM teams from around the world were asked to perform a standard GFP measurement on a set of bacterial 'devices' in their own labs. Data generated by these teams are then used to improve upon the measurement procedure.

We, of the Wageningen iGEM 2017, team were happy to participate in this study. On this page we will present the measurement protocol, as well as the results we obtained with it.

For this study, we had the choice of performing fluorescence measurements either with a plate reader or flow cytometer. As the use of the latter is restricted in our laboratory, we decided to adhere to the plate reader protocol. Using the BioTek’s Synergy Mx Monochromator-based Microplate Reader, we measured culture samples of the following 8 devices:

Successful transformation of these devices to E. coli DH5α cells resulted in the colonies that were used to inoculate 50 mL Greiner tubes containing 10 mL LB medium + Chloramphenicol. These liquid cultures were incubated at 37 degrees Celsius, during which samples were taken at timepoints 0, 2, 4 and 6 hours after inoculation. They were then used to measure fluorescence and OD600nm in the plate reader.

To make sense of this data, we first needed to make calibrations of both the OD600nm and fluorescence at 395nm/509nm (emission/excitation). For the former, we used LUDOX-HS40 and H2O, provided by iGEM; for the latter, we used fluorescein, also provided by iGEM.

Table 1: OD600nm reference point.
LUDOX-HS40 H20
Replicate 1 0.122 0.087
Replicate 2 0.095 0.089
Replicate 3 0.098 0.088
Replicate 4 0.099 0.089
Arith. Mean 0.1035 0.08825
Corrected Abs600 0.01525
Reference Abs600 0.0425
OD600/Abs600 2.786885246

Samples taken from the liquid cultures of the devices at the different time points were added to a black, clear bottomed 96 wells plate in order to measure them in the plate reader. Each well contained 100 μL of the sample following the scheme provided in the protocol:

Results

Measurement of the 96-wells plate in the BioTek’s Synergy Mx Monochromator-based Microplate Reader was performed at 27°C with a wavelength of 600nm for the OD and wavelengths of 395nm and 509nm for the fluorescence excitation and emission, respectively. Furthermore, path length correction was turned off in the absorbance measurement and a slit width of 9 mm with a gain of 75 was selected for the fluorescence measurement. Data obtained from these measurements was added to the calculation sheet provided by the iGEM Committee, resulting in data as presented in the final graph: