Team:Aachen/OD/F device

From 2014.igem.org

(Difference between revisions)
(Measuring Principle)
(Achievements)
 
(63 intermediate revisions not shown)
Line 4: Line 4:
{{Team:Aachen/Header}}
{{Team:Aachen/Header}}
-
= OD/F device =
+
= OD/F Device =
-
Measuring Optical Density (OD) is a '''central element in microbiological work and synthetic biology'''. One question that has to be answered often is how many cells are in a suspension. Here, the OD can give you a hint. Unfortunately, commercially available OD meters '''cost several hundred dollars''' ([http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php OD meter]), and can '''limit''' the spread of synthetic biology.  
+
Measuring '''Optical Density''' (OD) or absorbance is one of the indispensable elements in the field of microbiology. One question that has to be answered often is '''how many cells are in a suspension'''? Here, the OD can give a hint. However, the commercially available [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php OD meters] are expensive and limit its application and usage in low budget institutions.
-
Therefore, we wanted to devenlop an alternative for measuring OD, '''specifically designed for Biohackspaces, DIY and community laboratories and schools'''. With our OD/F device, we want to enable many people to do good, precise and inexpensive science research.
+
Therefore, here we present our OD/F Device. The device is specifically designed for biohackspaces, Do It Yourself (DIY), community laboratories and schools. With our OD/F Device, we aim to enable precise and inexpensive scientific research.
-
Especially for the [[Interlab Study]] fluorescence, too, has been of importance. One aim of this study was to measure the correlation between OD and fluorescence. 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 fluorescence and OD''' with just some easy adjustments. This way, we can measure how much fluorescence there is per amount of cells.
+
Further, in Synthetic Biology, the task of measuring OD and fluorescence are often performed at the same time. Hence, here we present a device that can be configured to '''simultaneously measure both fluorescence and OD'''. With such a configuration of the OD/F Device, the production of fluorescence signal can be correlated to cell growth using a single and a portable device.
-
 
+
-
In fact, you can find some DIY posts for turbidity meters such as [http://www.thingiverse.com/thing:74415 turbidity sensors]. However, a proper assessment of their linearity as well as a calculated OD-value are missing.
+
-
+
-
Regarding fluorescence, we are of course not re-inventing the wheel (well, not totally). The [https://2010.igem.org/Team:Cambridge 2010 iGEM Cambridge] team actually built a very similar device, the [https://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 to, for example, assess linearity of the measurement.
+
<html>
<html>
Line 22: Line 18:
   <li>
   <li>
-
     <a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#measuringprinciple" style="color:black">
+
     <a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfmeasuringprinciple" style="color:black">
-
     <div class="menusmall-item menusmall-info" ><div class="menukachel">Measuring Principle</div></div>
+
     <div class="menusmall-item menusmall-info" ><div class="menukachel" style="top:25%; line-height:1.5em;">Measuring Principle</div></div>
-
     <div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0b/Aachen_14-10-13_GFP_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%">
+
     <div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/0/0f/Aachen_14-10-10_ODF_Button_ipo.png); norepeat scroll 0% 0% transparent; background-size:100%">
     </div>
     </div>
     </a>
     </a>
Line 31: Line 27:
   <li>
   <li>
     <a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfapplication" style="color:black">
     <a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfapplication" style="color:black">
-
     <div class="menusmall-item menusmall-info" ><div class="menukachel">Application</div></div>
+
     <div class="menusmall-item menusmall-info" ><div class="menukachel" style="top:35%; line-height:1.5em;">Application</div></div>
-
     <div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/6/65/Aachen_14-10-13_REACh_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%">
+
     <div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/5/55/Aachen_17-10-14_Glowing_cuvette-ipo.png); norepeat scroll 0% 0% transparent; background-size:100%">
     </div>
     </div>
     </a>
     </a>
Line 39: Line 35:
  <li>
  <li>
     <a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfachievements" style="color:black">
     <a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfachievements" style="color:black">
-
     <div class="menusmall-item menusmall-info" ><div class="menukachel">Achieve-<br/>ments</div></div>
+
     <div class="menusmall-item menusmall-info" ><div class="menukachel" style="top:25%; line-height:1.5em;">Achieve-<br/>ments</div></div>
     <div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%">
     <div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/e/ef/Aachen_14-10-15_Medal_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%">
 +
    </div>
 +
    </a>
 +
  </li>
 +
 +
<li>
 +
    <a class="menulink" href="https://2014.igem.org/Team:Aachen/OD/F_device#odfoutlook" style="color:black">
 +
    <div class="menusmall-item menusmall-info" ><div class="menukachel" style="top:35%; line-height:1.5em;">Outlook</div></div>
 +
    <div class="menusmall-item menusmall-img" style="background: url(https://static.igem.org/mediawiki/2014/6/67/Aachen_14-10-16_Outlook_Cellocks_iNB.png); norepeat scroll 0% 0% transparent; background-size:100%">
     </div>
     </div>
     </a>
     </a>
Line 51: Line 55:
{{Team:Aachen/BlockSeparator}}
{{Team:Aachen/BlockSeparator}}
 +
 +
[[File:Aachen_14-10-10_ODF_Button_ipo.png|right|150px]]
== Measuring Principle ==
== Measuring Principle ==
<span class="anchor" id="odfmeasuringprinciple"></span>
<span class="anchor" id="odfmeasuringprinciple"></span>
-
The measuring principle for both optical density (OD) and fluorescence measurement is depicted below.
+
The measuring principle for both optical density (OD) and fluorescence measurement is shown below. For OD measurementthe sample is illuminated with an LED and a fixed slit width. A filter blocks any light less than 600 nm. In this way, the sensor mainly senses the 600 nm light which is needed for OD{{sub|600}} measurement.
-
For OD measurement we shine through the sample with an LED and a fixed width. A filter blocks any other light but 600&nbsp;nm. This way, the sensor mainly senses the 600&nbsp;nm light which is needed for OD<sub>600</sub> measurement.
+
-
For fluorescence measurement a similar approach is chosen. The filter again is used to block the exciting light from being sensed. That way only the emitted light from the fluorescence protein is measured.
+
For the fluorescence measurement, a similar approach is followed. The filter, again, is used to block the exciting light from being sensed. In this way, only the emitted light from the fluorescence protein is detected and measured.
 +
 
 +
Further details about selecting filters, code, a construction manual and evaluation can be found [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF here].
<center>
<center>
-
{{Team:Aachen/Figure|Aachen_odf_schemes.png|title=Measuring principle for OD/F device|subtitle=The left image shows the measurement approach for the optical density. The light shines through the sample with a fixed width. The right image shows the fluorescence measurement approach, exciting the fluorescence proteins from below and measuring from the side.|width=500px}}
+
{{Team:Aachen/Figure|Aachen_odf_schemes.png|title=Measuring principle for OD/F Device|subtitle=The left image shows the measurement approach for the optical density. The light shines through the sample with a fixed width. The right image shows the fluorescence measurement approach, exciting the fluorescence proteins from below and measuring from the side.|width=500px}}
</center>
</center>
-
Further details about selecting filters, code, a construction manual and evaluation can be found [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF here].
+
<center>
 +
{{Team:Aachen/Figure|Aachen_ODF_7.JPG|title=The combined OD/F Device for optical density and fluorescence measurement.|subtitle= |width=650px}}
 +
</center>
-
{{Team:Aachen/Figure|Aachen_ODF_7.JPG|title=Our OD/F device|subtitle= |width=500px}}
 
{{Team:Aachen/BlockSeparator}}
{{Team:Aachen/BlockSeparator}}
-
== Application ==
+
[[File:Aachen 17-10-14 Glowing cuvette-ipo.png|right|150px]]
-
<span class="anchor" id="pdfapplication"></span>
+
-
Using the presented device is easy and works as with any other device, too.
+
== ''Modus operandi'' of the OD/F Device==
-
First you will have to take a blank reference, e.g. pure medium without cells.
+
<span class="anchor" id="odfapplication"></span>
-
After placing the cuvette in the device, press the red button to take the blank and take out your blank again.
+
 
-
In the following do all your measurements which you would like to do compared to your medium. Again, take the cuvette, fill it with the sample and put it into the device.
+
The device is constructed to make it easy-to-handle for the end users. The standard operating procedure to operate and measure optical density or fluorescence is schematically shown in the figure below.
-
The measured value will be displayed on the device. Do not press the red button again until you want to take another blank/reference.
+
 
 +
{{Team:Aachen/Figure|Aachen 14-10-09 Flowsheet OD-device ipo.png|title=|subtitle=|width=1000px}}
-
{{Team:Aachen/Figure|Aachen 14-10-09 Flowsheet OD-device ipo.png|title=How to use our OD/F device|subtitle=|width=1000px}}
 
{{Team:Aachen/BlockSeparator}}
{{Team:Aachen/BlockSeparator}}
Line 90: Line 97:
When building the OD/F Device, '''our goal''' was to develop a system that
When building the OD/F Device, '''our goal''' was to develop a system that
-
* is straightforward to use
+
* easy-to-handle and portable
-
* is at least as accurate as commercially available systems but at the same time costs significantly less
+
* precise, stable, and reproducible results
-
* produces stable, reproducible results
+
* easy to build from Open Source parts
-
* weights little and is easy to carry around
+
* combined measurement of optical density and fluorescence
-
* uses widely available parts and is easy to build
+
* low cost
-
* can measured both optical density and fluorescence
+
 +
Commercially available equipment uses lasers and a set of two fine filters, one between laser and sample and one between sample and sensor. To reduce the cost, our OD/F Device uses a simpler measuring principle: it is designed with one low-cost filter, between sample and sensor, and illuminates with an LED instead of a laser. Nevertheless, one main goal was to produce an inexpensive device. Given that, we therefore had to compromise some of the measurement quality, were we still able to produce stable, precise and good data?
-
Commercially available equipment uses lasers and a set of two fine filters, one between laser and sample and one between sample and sensor. To '''beat down the price''', our OD/F Device uses a simpler measuring principle: It has just one rather low-quality filter, between sample and sensor, and illuminates with an LED instead of a laser. However, the LED is not as accurate as a laser and has a non-optimal spectrum. On top of that, due to the missing filter between laser and sample, stray light might influence the measurement. Nevertheless, one main goal was to produce an inexpensive device. Given that we therefore had to '''compromise some of the measurement quality''', were we still able to produce stable, precise and good data?
+
{{Team:Aachen/Figure|Aachen_ODallstrains1.png|title=Transmission of different cell types at OD-values from 0.001-1|subtitle=The transmittance data of NIH&nbsp;3T3 (mouse fibroblasts) cells align with the transmittance of ''P.&nbsp;putida'' and ''S.&nbsp;cerevisiae'' strains, even though the measured optical densities are lower by 1-2 orders of magnitude.|width=800px}}
 +
 
 +
The answer is: Yes! With the optimal design of our cuvette holder we achieved good-quality results albeit using the cheap filter. The transmission to true OD conversion is stable for all cell types as expected.
 +
 
 +
Have we been re-inventing the wheel? No!
 +
In fact, you can find some DIY posts for turbidity meters such as [http://www.thingiverse.com/thing:74415 turbidity sensors]. However, a proper assessment of their linearity as well as a calculated OD-value are missing.  
 +
 +
Regarding fluorescence, we are also not re-inventing the wheel. The [https://2010.igem.org/Team:Cambridge 2010 iGEM Cambridge] team actually built a very similar device, the [https://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 to, for example, assess linearity of the measurement.
 +
 
 +
We made a commercial assessment of the OD/F Device that results in a total cost of $60. The unit is built from acrylic glass for the casing. The compact design results in a weight which is less than 200g. The device can be easily connected to any power adapter via USB. The technical details and a construction manual of OD/F Device is [https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy published] on our engineering page.
 +
 
 +
 
 +
{{Team:Aachen/BlockSeparator}}
-
The answer is: Yes! With the optimal design of our cuvette holder we '''achieved good-quality results''' albeit using the cheap filter.
+
[[File:Aachen_14-10-16_Outlook_Cellocks_iNB.png|right|150px]]
-
[graphs showing the awesomeness of our OD/F device]
+
== Outlook ==
 +
<span class="anchor" id="odfoutlook"></span>
-
On top of that, we also achieved all other goals we set in the beginning: The device makes do with '''one button''', the blank button, only and is thus really straightforward to use. With a '''cost of just [https://2014.igem.org/Team:Aachen/PolicyPractices/Economics#economicsodf 60$]''', the OD/F beats any commercially available system by far. Due to the use of light plexiglass for the casing and the compact design, one unit '''weighs less than 500&nbsp;g''' and can be easily connected to any power adapter via USB. We also managed to build the device with common, inexpensive and easily available parts, and '''[https://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF#diy published] all technical details and a construction manual on our wiki'''. At least, though we actually built two separate devices for OD and fluorescence measurement, both work really well and putting the two units into one case would just require to laser cut a new top.  
+
We have proven that our device is capable of delivering good results, even in hard conditions as low cell concentrations.
 +
Yet there is room for improvement.
 +
The calibration process is quite intensive work. An application to do this automatically would help for this process.
 +
For the ease of use and to prevent data loss from noting down measured values manually, a smartphone application that can directly correlate OD and fluorescence values would be a great addition. This addition will be implemented in the next version.
{{Team:Aachen/Footer}}
{{Team:Aachen/Footer}}

Latest revision as of 03:48, 18 October 2014

OD/F Device

Measuring Optical Density (OD) or absorbance is one of the indispensable elements in the field of microbiology. One question that has to be answered often is how many cells are in a suspension? Here, the OD can give a hint. However, the commercially available [http://www.laboratory-equipment.com/laboratory-equipment/cell-density-meter.php OD meters] are expensive and limit its application and usage in low budget institutions.

Therefore, here we present our OD/F Device. The device is specifically designed for biohackspaces, Do It Yourself (DIY), community laboratories and schools. With our OD/F Device, we aim to enable precise and inexpensive scientific research.

Further, in Synthetic Biology, the task of measuring OD and fluorescence are often performed at the same time. Hence, here we present a device that can be configured to simultaneously measure both fluorescence and OD. With such a configuration of the OD/F Device, the production of fluorescence signal can be correlated to cell growth using a single and a portable device.


Aachen 14-10-10 ODF Button ipo.png

Measuring Principle

The measuring principle for both optical density (OD) and fluorescence measurement is shown below. For OD measurement, the sample is illuminated with an LED and a fixed slit width. A filter blocks any light less than 600 nm. In this way, the sensor mainly senses the 600 nm light which is needed for OD600 measurement.

For the fluorescence measurement, a similar approach is followed. The filter, again, is used to block the exciting light from being sensed. In this way, only the emitted light from the fluorescence protein is detected and measured.

Further details about selecting filters, code, a construction manual and evaluation can be found here.

Aachen odf schemes.png
Measuring principle for OD/F Device
The left image shows the measurement approach for the optical density. The light shines through the sample with a fixed width. The right image shows the fluorescence measurement approach, exciting the fluorescence proteins from below and measuring from the side.
Aachen ODF 7.JPG
The combined OD/F Device for optical density and fluorescence measurement.


Aachen 17-10-14 Glowing cuvette-ipo.png

Modus operandi of the OD/F Device

The device is constructed to make it easy-to-handle for the end users. The standard operating procedure to operate and measure optical density or fluorescence is schematically shown in the figure below.

Aachen 14-10-09 Flowsheet OD-device ipo.png
'


Aachen 14-10-15 Medal Cellocks iNB.png

Achievements

When building the OD/F Device, our goal was to develop a system that

  • easy-to-handle and portable
  • precise, stable, and reproducible results
  • easy to build from Open Source parts
  • combined measurement of optical density and fluorescence
  • low cost

Commercially available equipment uses lasers and a set of two fine filters, one between laser and sample and one between sample and sensor. To reduce the cost, our OD/F Device uses a simpler measuring principle: it is designed with one low-cost filter, between sample and sensor, and illuminates with an LED instead of a laser. Nevertheless, one main goal was to produce an inexpensive device. Given that, we therefore had to compromise some of the measurement quality, were we still able to produce stable, precise and good data?

Aachen ODallstrains1.png
Transmission of different cell types at OD-values from 0.001-1
The transmittance data of NIH 3T3 (mouse fibroblasts) cells align with the transmittance of P. putida and S. cerevisiae strains, even though the measured optical densities are lower by 1-2 orders of magnitude.

The answer is: Yes! With the optimal design of our cuvette holder we achieved good-quality results albeit using the cheap filter. The transmission to true OD conversion is stable for all cell types as expected.

Have we been re-inventing the wheel? No! In fact, you can find some DIY posts for turbidity meters such as [http://www.thingiverse.com/thing:74415 turbidity sensors]. However, a proper assessment of their linearity as well as a calculated OD-value are missing.

Regarding fluorescence, we are also not re-inventing the wheel. The 2010 iGEM Cambridge team actually built 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 to, for example, assess linearity of the measurement.

We made a commercial assessment of the OD/F Device that results in a total cost of $60. The unit is built from acrylic glass for the casing. The compact design results in a weight which is less than 200g. The device can be easily connected to any power adapter via USB. The technical details and a construction manual of OD/F Device is published on our engineering page.


Aachen 14-10-16 Outlook Cellocks iNB.png

Outlook

We have proven that our device is capable of delivering good results, even in hard conditions as low cell concentrations. Yet there is room for improvement. The calibration process is quite intensive work. An application to do this automatically would help for this process. For the ease of use and to prevent data loss from noting down measured values manually, a smartphone application that can directly correlate OD and fluorescence values would be a great addition. This addition will be implemented in the next version.