Team:Aachen/OD/F device

(Difference between revisions)
 Revision as of 09:08, 14 October 2014 (view source)Mjoppich (Talk | contribs) (→Linearity)← Older edit Latest revision as of 03:48, 18 October 2014 (view source)Pdemling (Talk | contribs) (→Achievements) (94 intermediate revisions not shown) Line 1: Line 1: __NOTOC__ __NOTOC__ + {{CSS/Main}} + {{Team:Aachen/Stylesheet}} {{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 [http://2010.igem.org/Team:Cambridge 2010 iGEM Cambridge] team actually built 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 to, for example, assess linearity of the measurement. +
- + - The final cuvette holder design was rendered in a stl-file shown below: + - + - + -
+ - +
- === Light filters === - Once the cuvette holder was finished, '''finding good filters was a tough challenge'''. A main goal throughout our project has been to choose easily available parts which are also inexpensive. Thus choosing Schott glasses as filters unfortunately could not be considered. Instead, filters used for illumination of theaters seemed to be ideal solution. - - Especially for the fluorescence measurements of GFP finding the right filter has been a big problem. [http://parts.igem.org/Part:BBa_E0040 GFPmut3b] has a peak excitation at 501 nm and a peak emission at 511 nm - too close together for our low-cost filters to block the excitation light but transmit the emitted light. Thus, we chose to excite at around 485 nm reduce false positive results below 500 nm. However, no adequate filter for these settings could be found. - Eventually, using the dark greenish Twickenham Green filter only little amounts of light shorter than 500 nm got through, reducing any bias from excitation illumination significantly. Unfortunately, the transmission rate of this filter is quite bad, 20 % only, for the target emission wavelength of 511 nm. - - For the OD measurement, too, we had similar problems. The solution to this problem is presented in the F device section. - - - 1. Quite a good random number generator from a computer-scientific perspective! - - -
- {{Team:Aachen/FigureFlex|Aachen_odf_schemes.png|title=Setup of the measuring unit|subtitle=On the left, the setup of a classical spectrophotometer is depicted. The setup around the cuvette holder of our device is shown on the right.|width=400px}} -
- - == Combined Device == - - Even though evaluation of the measurements have been performed in two separate device, it is fairly well possible to put everything into one casing. - All you need to do is choosing another lid, and connect a second light to frequency sensor to your Arduino. - Right at the bottom we present you the differences in wiring things up. {{Team:Aachen/BlockSeparator}} {{Team:Aachen/BlockSeparator}} - = OD device = + [[File:Aachen_14-10-10_ODF_Button_ipo.png|right|150px]] + == Measuring Principle == + - {{Team:Aachen/Figure|Aachen 14-10-09 Flowsheet OD-device ipo.png|title=How to use our OD/F device|subtitle=XXX|width=1000px}} + 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 OD{{sub|600}} 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 [http://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF here]. - == DIY: How to Build Your Own OD Device== +
+ {{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 ODdevice Steckplatine.png|align=center|title=Breadboard of our OD device|subtitle=To build your own OD device, connect the parts as shown in this diagram.|width=900px}} +
+ {{Team:Aachen/Figure|Aachen_ODF_7.JPG|title=The combined OD/F Device for optical density and fluorescence measurement.|subtitle= |width=650px}} +

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.