# Team:Aachen/OD/F device

(Difference between revisions)
 Revision as of 11:05, 11 October 2014 (view source)Mjoppich (Talk | contribs) (→Development)← Older edit Latest revision as of 03:48, 18 October 2014 (view source)Pdemling (Talk | contribs) (→Achievements) (167 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 in general. Often the qeustion is, how many cells are in a suspension. The OD can give you a hint. + 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. - Commercial 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. + 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 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. + 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. - 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. +
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- First, 3 ml have been consideres, and an optimal height of 1.5 cm from ground has been determined as optimal. +
- Indeed, this works quite well for the large cuvettes, but unfortunately delivers random1 results on semi-micro cuvettes. + - We could determine that the cause of this problem originates from refractions on the sample surface in the cuvette, as this coincedences with the measurement height. + - 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. + {{Team:Aachen/BlockSeparator}} - 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. + [[File:Aachen_14-10-10_ODF_Button_ipo.png|right|150px]] - The final cuvette holder design is rendered below in a stl-file: + == 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 OD{{sub|600}} measurement. -
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+ - + - Once the cuvette holder has been finished, finding good filters was a tough challenge. The overall goal has been to choose easily available parts, which are also inexpensive. So choosing Schott glasses as filters unfortunately could not be considered. + 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. - Filters, as used for illumination of theatres, seemed to be ideal. + - However, despite testing a lot of filters, no ideal filter could be found. The selection of filters here represents our best efforts to choose  the most suitable filter. + - Especially for the fluorescence measurements of GFP this has been a big problem. + - [http://parts.igem.org/Part:BBa_E0040 GFPmut3b] has a peak excitation at 501nm and a peak emission at 511nm - too close for our low-cost filters. Instead we choose to excite at around 485nm, try to avoid and response lower than 500nm. However, no filter with these strict properties could be found. + Further details about selecting filters, code, a construction manual and evaluation can be found [http://2014.igem.org/Team:Aachen/Notebook/Engineering/ODF here]. - Finally, using the dark greenish Twickenham Green filter only little amounts of sub-500nm-light gets through, reducing any bias from this significantly. Unfortunately the transmission rate of this filter is still quite bad at 20% for the target emission wavelength. + - Also for the OD measurement 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/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}} - +
- == Combined Device == +
+ {{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.