Team:Aachen/Interlab Study/Hardware

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= Commercial Hardware =
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For the interlab study we used several devices to measure optical density (OD) and fluorescence.
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{{Team:Aachen/BlockSeparator}}
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= Open Source DIY Hardware =
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Being in the measurement track and having a team of highly motivated engineering and computer science students, we tackled the challenge to build, document and evaluate our open source hardware approach.
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For our daily tasks in the lab, two key devices were detected: fluorometer and OD-meter. As we use GFP most of the time, the fluorometer is designed to work best with GFP. For modularity reasons, and re-usability, it is designed such that a change to another fluorescence protein is easy.
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Besides the mandatory $\mu$-controller architecture, we worked together with the [https://hci.rwth-aachen.de/fablab Fablab Aachen] to construct the device. There we have the chance to use laser cutters and 3D printers.
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The core component for detecting the light intensity is the cuvette holder. Please find the 3D model we printed below:
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<html>
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<center>       
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<iframe src="https://2014.igem.org/Team:Aachen/Notebook/Engineering/Cuvette3D?action=render
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" width=500px height=500px frameBorder="0"></iframe>
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</center>
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</html>
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This cuvette holder can be used for both devices: the hole in the bottom is used for fluorescence measurement, the two opposite hole are used for the light sensor and the LED for optical density measurement respectively.
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=== Hardware Requirements ===
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The key ingredients for our combined optical density/fluorescence (OD/F) device then are:
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* Arduino UNO R3 ''(or equivalent)''
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* breadboard and jumperwires ''(or: circuit board)''
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* bluetooth modem ''optional''
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* cuvette holder [https://2014.igem.org/Template:Team:Aachen/cuvette.stl?action=raw stl file download]
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* TSL235R-LF light to frequency sensor
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* LED for optical density (for 600nm we recommend: DIALIGHT - 550-2505F )
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* LED for fluorescence (any 450nm blue works for iLOV, 480nm for wtGFP )
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* [http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm Filters] Medium Yellow 010 and Twickenham Green 736
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The case is from acrylic glass. The construction plan can be downloaded from [https://2014.igem.org/Team:Aachen iGEM].
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A detailled instruction is available on [http://instructables.com instructables.com]
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== Fluorescence ==
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[[File:Aachen_gfp_ecoli_plate_1.jpg|center|thumb|E. coli plate fluorescence|400px]]
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When measuring fluorescence, two approaches can be followed
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* measure the light intensity sent to fluorescence protein, measure returning light intensity and compare
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* measure two samples, and detect the increase in light returned
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which follows either an absolute or relative quantification. For most tasks however the relative increase in fluorescence is needed, and therefore this approach is also used for this device.
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''Figure 2'' shows the schematic principle of the fluorescence measurement with our device.
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{{Team:Aachen/Figure|Aachen_gfp_ecoli_plate_1.jpg|alignment=float:center|title=Figure 2|subtitle=Schematics of fluorescence measurement|width=300px}}
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=== Characteristic Curve ===
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An important observation for fluorescence measurement is that the linearity of the measurement highly depends on the chosen light sensor.
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If the light sensor is not linear over the spectrum of measurement, linearity would be needed to be corrected by software. Fortunately the characteristic curve of the TSL 235 R shows perfect linearity such that no software correction is needed.
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This needed to be confirmed by measurements. We used an E. coli dilution series to perform this experiment.
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''Figure 3'' shows the recorded values. The linearity clearly can be seen, the regression coefficient of 0.99 also supports this.
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== Optical Density ==
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Some general information
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=== calibration ===
{{Team:Aachen/Footer}}
{{Team:Aachen/Footer}}

Latest revision as of 14:38, 27 September 2014

Commercial Hardware

For the interlab study we used several devices to measure optical density (OD) and fluorescence.


Open Source DIY Hardware

Being in the measurement track and having a team of highly motivated engineering and computer science students, we tackled the challenge to build, document and evaluate our open source hardware approach.

For our daily tasks in the lab, two key devices were detected: fluorometer and OD-meter. As we use GFP most of the time, the fluorometer is designed to work best with GFP. For modularity reasons, and re-usability, it is designed such that a change to another fluorescence protein is easy.

Besides the mandatory $\mu$-controller architecture, we worked together with the Fablab Aachen to construct the device. There we have the chance to use laser cutters and 3D printers.

The core component for detecting the light intensity is the cuvette holder. Please find the 3D model we printed below:

This cuvette holder can be used for both devices: the hole in the bottom is used for fluorescence measurement, the two opposite hole are used for the light sensor and the LED for optical density measurement respectively.

Hardware Requirements

The key ingredients for our combined optical density/fluorescence (OD/F) device then are:

  • Arduino UNO R3 (or equivalent)
  • breadboard and jumperwires (or: circuit board)
  • bluetooth modem optional
  • cuvette holder stl file download
  • TSL235R-LF light to frequency sensor
  • LED for optical density (for 600nm we recommend: DIALIGHT - 550-2505F )
  • LED for fluorescence (any 450nm blue works for iLOV, 480nm for wtGFP )
  • [http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm Filters] Medium Yellow 010 and Twickenham Green 736

The case is from acrylic glass. The construction plan can be downloaded from iGEM.

A detailled instruction is available on [http://instructables.com instructables.com]

Fluorescence

E. coli plate fluorescence

When measuring fluorescence, two approaches can be followed

  • measure the light intensity sent to fluorescence protein, measure returning light intensity and compare
  • measure two samples, and detect the increase in light returned

which follows either an absolute or relative quantification. For most tasks however the relative increase in fluorescence is needed, and therefore this approach is also used for this device. Figure 2 shows the schematic principle of the fluorescence measurement with our device.

Aachen gfp ecoli plate 1.jpg
Figure 2
Schematics of fluorescence measurement

Characteristic Curve

An important observation for fluorescence measurement is that the linearity of the measurement highly depends on the chosen light sensor. If the light sensor is not linear over the spectrum of measurement, linearity would be needed to be corrected by software. Fortunately the characteristic curve of the TSL 235 R shows perfect linearity such that no software correction is needed.

This needed to be confirmed by measurements. We used an E. coli dilution series to perform this experiment. Figure 3 shows the recorded values. The linearity clearly can be seen, the regression coefficient of 0.99 also supports this.

Optical Density

Some general information

calibration

Contact Disclaimer

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