Team:Aachen/OD/F device

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(F device)
(OD/F device)
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Also regarding fluorescence, we're not re-inventing the wheel (well, not totally). The 2010 iGEM Cambridge team actually build a very similar device, the [http://2010.igem.org/Team:Cambridge/Tools/Eglometer E.glometer]. However, there's no data available showing an actual comparison of the data from their device, and some proven, commercial system, e.g. to assess linearity of the measurement.
Also regarding fluorescence, we're not re-inventing the wheel (well, not totally). The 2010 iGEM Cambridge team actually build a very similar device, the [http://2010.igem.org/Team:Cambridge/Tools/Eglometer E.glometer]. However, there's no data available showing an actual comparison of the data from their device, and some proven, commercial system, e.g. to assess linearity of the measurement.
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== Development ==
 +
 +
Developing the OD/F device has been an interesting task. On the one hand, this device has been developed mainly by the computer guys. On the other hand, the biologists affected from color-blindness helped to select the correct filters for the LEDs. Not the best combinations to recommend ;) .
 +
 +
Being naive, the computer guys first attached the sensor to the couvette holder at approximately 1.5cm, which was perfectly suited for 3ml cuvettes. However, those are not widely used anymore, and we migrated to 1.6ml cuvettes. As it turns out, if the sensor sits at 1.5cm, it just hits the position where the cuvette enlarges again - and most importantly, where the edge of the sample solution is.
 +
This results in diffraction on the surface of the sample, and finally renders any measurement results into - from a computer scientific point of view - a perfect random number generator.
 +
 +
However, placing the sensor very low brings problems with sedimentation as well as diffractions from the bottom. Finally we place the sensor in 0.75cm height, which, as it turns out later, is very close to one of the standard heights (0.2cm, 0.8cm, 1.2cm) of OD meters.
 +
The main problem here was also to have the sensor as close to the bottom, such that enough lights shines through for the fluorescence measurement, and to have it closer to the top, such that effects from sedimentation are reduced.
 +
 +
It is important to note, that despite the minimal fill heights of the 1.6ml cuvettes of 1.2ml, our device also works with fills of only 1ml, which comes closer to reality in the lab.
 +
 +
The final cuvette holder design is rendered below in a stl-file:
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<html>
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<center>       
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<iframe src="http://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>
{{Team:Aachen/BlockSeparator}}
{{Team:Aachen/BlockSeparator}}

Revision as of 00:35, 10 October 2014

OD/F device

Measuring Optical Density (OD) is a central element in microbiological work and synthetic biology in general. Often the qeustion is, how many cells are in a suspension. The OD can give you a hint.

Commercial OD meters cost several hundred dollars (OD meter), and can limit the spread of synthetic biology. Especially for BioHack-Spaces, DIY laboratories and schools we wanted to develop an alternative.

With our OD/F device we want to enable many to people for good, precise and cheap science.

Especially for the Interlab Study also fluorescence has been of importance. Here the correlation between OD and fluorescence should be measured. Since the taks of measuring OD and fluorescence are often performed at the same time, we want to present a device that can measure both with easy changes. Finally we can tell you, how much fluorescence there is per amount of cells.

In fact, you can find some DIY posts for turbidity meters such as Turbidity sensors. However a proper assessment of their linearity as well as a calculated OD-value is missing.

Also regarding fluorescence, we're not re-inventing the wheel (well, not totally). The 2010 iGEM Cambridge team actually build a very similar device, the E.glometer. However, there's no data available showing an actual comparison of the data from their device, and some proven, commercial system, e.g. to assess linearity of the measurement.

Development

Developing the OD/F device has been an interesting task. On the one hand, this device has been developed mainly by the computer guys. On the other hand, the biologists affected from color-blindness helped to select the correct filters for the LEDs. Not the best combinations to recommend ;) .

Being naive, the computer guys first attached the sensor to the couvette holder at approximately 1.5cm, which was perfectly suited for 3ml cuvettes. However, those are not widely used anymore, and we migrated to 1.6ml cuvettes. As it turns out, if the sensor sits at 1.5cm, it just hits the position where the cuvette enlarges again - and most importantly, where the edge of the sample solution is. This results in diffraction on the surface of the sample, and finally renders any measurement results into - from a computer scientific point of view - a perfect random number generator.

However, placing the sensor very low brings problems with sedimentation as well as diffractions from the bottom. Finally we place the sensor in 0.75cm height, which, as it turns out later, is very close to one of the standard heights (0.2cm, 0.8cm, 1.2cm) of OD meters. The main problem here was also to have the sensor as close to the bottom, such that enough lights shines through for the fluorescence measurement, and to have it closer to the top, such that effects from sedimentation are reduced.

It is important to note, that despite the minimal fill heights of the 1.6ml cuvettes of 1.2ml, our device also works with fills of only 1ml, which comes closer to reality in the lab.

The final cuvette holder design is rendered below in a stl-file:

OD device

Hint: Building it

Aachen ODdevice Steckplatine.png
Our novel biosensor approach
Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.

If you want to build the OD device, make sure to use the following secret ingredients:

  • Filter:
  • LED:

F device

Hint: Building it

Aachen Fdevice Steckplatine.png
Our novel biosensor approach
Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.

If you want to build the OD device, make sure to use the following secret ingredients:

  • Filter:
  • LED:

Getting your Device

Table 1: Number of pieces, components and costs for building your own OD/F device

number of pieces components costs [$] order e.g. from
1arduino UNO R312.66
2light to frequency sensor TSL 235R5.90
1display 2x16 l2C18.97
2LEDs2.50
1taster5.23
1filter slide5.20
20jumper-wire-cable2.36
2small breadboards3.00
1power supply5.00
1 case20.24
2cuvettes-holder15.95
-odds and ends like header sockt/pins2.52-
-total99.53-

Building your own OD/F device

Aachen ODF 9.JPG First we want to assemble the casing. Once you have all the cut parts, you can start to assemble them. For cutting, we really recommend using a laser cutter.
Aachen ODF 8.JPG Attach the cuvette-holder holders such that the cuvette holder is placed directly under the opening hole.
Aachen ODF 4.JPG Next build the lid of the device. At this stage you can already mount the button. We recommend to glue any parts.
Aachen ODF 3.JPG Your lid finally should look like this.
Aachen ODF 11.JPGAachen ODF 10.JPG Next we want to assemble the cuvette holders. On the side with the square hole attach the light-to-frequency sensor with glue. For the OD case place the orange LED opposite, or for fluorescence, the LED in the hole in the bottom. Make sure to close any remaining open hole!
Aachen ODF 12.JPG Your final assembly should then look like this. Now place the correct filter into the cuvette holder, directly in front of the sensor. Make sure that the filter does not degrade due to the glue!
Aachen ODF 14.JPG As the case can be used for both, fluorescence and OD measurement, we use a combined plug. Just three header rows (7 pins) and connect them as we did.
Aachen ODF 1.JPG Now we're doing the wiring. Connect the Arduino 5V and GND such that you have one 5V and one GND line on your breadboard.
Aachen ODF 2.JPG Then connect the button to 5V on the one side, and to GND via a resistor on the other side. Connect this side also to port __ on your Arduino. This will sense the blank. Next connect the display to the Arduino and our connector. See the Fritzing diagram at the bottom for a detailed information.
Aachen ODF 13.JPG Now put everything into the case and ...
Aachen ODF 6.JPG ... also place the cuvette holder into the device. Attach the display to the device lid and close the casing.
Aachen ODF 7.JPG Congratulations! You have finished constructing your own OD/F device!