Difference between revisions of "Team:Bielefeld-CeBiTec/Design"
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<div class="The problem"> | <div class="The problem"> | ||
<h2> The problem</h2> | <h2> The problem</h2> | ||
| − | <p> We | + | <p> We planned to design a convenient test strip using fluorescence as an output signal. Green fluorescent protein (GFP) is one of the most frequently used reporter proteins and it has already been used in numerous iGEM projects. Detecting fluorescence outside the lab sounded impractical to us and so we had to find an easy way to analyze the output. |
</div> | </div> | ||
| Line 33: | Line 33: | ||
<div class="col-md-5"> | <div class="col-md-5"> | ||
| − | <p>In the beginning of our project, we | + | <p>In the beginning of our project, we tried to photograph fluorescence with a smartphone. We got a filter from light engineering by the women cultural center Bielefeld e.V. ("Frauenkulturzentrum Bielefeld e.V.") and put it in front of a smartphone. |
| − | In the | + | In the figure below, we took a picture with this filter from purified GFP, sfGFP lysate and lysate without sfGFP. You can see different colors and a different brightnesses in the picture. In our first impression we thought it's worth to try some other filters, to find the perfect filter or filter combination for sfGFP imaging with almost no background signal. </p> |
</div> | </div> | ||
| Line 54: | Line 54: | ||
<figure style="float:left; margin-right:20px ; width: 300px"> | <figure style="float:left; margin-right:20px ; width: 300px"> | ||
| − | <a href="https://static.igem.org/mediawiki/2015/d/da/Bielefeld-CeBiTec_first_filtertests.png" data-lightbox="detection" data-title=" | + | <a href="https://static.igem.org/mediawiki/2015/d/da/Bielefeld-CeBiTec_first_filtertests.png" data-lightbox="detection" data-title=" First filter test. It was executed to get an indication wheather or not two filters are sufficient for a fluorescence imaging. We used one filter in front of the flash and the same one in front of the camera. In the picture you can see purified GFP, sfGFP lysate and the lysate of a non induced sfGFP culture."><img src="https://static.igem.org/mediawiki/2015/d/da/Bielefeld-CeBiTec_first_filtertests.png" ></a> |
| − | <figcaption> | + | <figcaption> First filter test. It was executed to get an indication wheather or not two filters are sufficient for a fluorescence imaging. We used one filter in front of the flash and the same one in front of the camera. In the picture you can see purified GFP, sfGFP lysate and the lysate of a non induced sfGFP culture. |
</figcaption> | </figcaption> | ||
</figure> | </figure> | ||
| Line 62: | Line 62: | ||
<div class="col-md-4"> | <div class="col-md-4"> | ||
| − | <p> Therefore we bought a lee color filter catalog | + | <p> Therefore we bought a lee color filter catalog. We made a preselection of the filters. This was possible, because we had access to the light transmitting spectra of almost every filter. With this preselection we began to test the different filter combinations. </p> |
| − | <p> The next step was to create a dark environment. Therefore we did handicrafts to design a black carton. Now it was possible to take photos under defined conditions and constant dark background. </p> | + | <p> The next step was to create a dark environment. Therefore we did handicrafts to design a black carton. Now it was possible to take photos under defined conditions and with a constant dark background. </p> |
| Line 79: | Line 79: | ||
<figure style="margin:auto; width: 200px"> | <figure style="margin:auto; width: 200px"> | ||
| − | <a href="https://static.igem.org/mediawiki/2015/1/11/Bielefeld-CeBiTec_black_box.png" data-lightbox="detection" data-title=" The black carton: | + | <a href="https://static.igem.org/mediawiki/2015/1/11/Bielefeld-CeBiTec_black_box.png" data-lightbox="detection" data-title=" The black carton: It was designed to take photos under same conditions"><img src="https://static.igem.org/mediawiki/2015/1/11/Bielefeld-CeBiTec_black_box.png" ></a> |
<figcaption> The black box: tinkered to take photos under same conditions | <figcaption> The black box: tinkered to take photos under same conditions | ||
</figcaption> | </figcaption> | ||
| Line 92: | Line 92: | ||
<div class="The filter combinations"> | <div class="The filter combinations"> | ||
<h2> The filter combinations </h2> | <h2> The filter combinations </h2> | ||
| − | <p> The essential requirements for taking comparable photos are | + | <p> The essential requirements for taking comparable photos are achieved. Now we had to find the ideal filter combination. We made a lot of photos with the preselected Filters. We tested every combinition of 5 filters for emission with 12 filters for extinction. After analyzing the photos with the image processing software Fiji, the optimal filter combination found was tokyo blue (071) in front of the flash and twickenham green (736) in front of the camera. </p> |
</div> | </div> | ||
| Line 100: | Line 100: | ||
<div class="col-md-6 text-center" style="margin-bottom: 20px"> | <div class="col-md-6 text-center" style="margin-bottom: 20px"> | ||
<figure style="margin:auto; width: 400px"> | <figure style="margin:auto; width: 400px"> | ||
| − | <a href="https://static.igem.org/mediawiki/2015/5/57/Bielefeld-CeBiTec_optimal_filtercombination.png " data-lightbox="detection" data-title="Test of different filtercombinations. On the top there is the picture without any filters. In the middle the picture was taken with fluorescence green in front of the camera and deep blue in front of the flash. The bottom photo was taken with the optimal | + | <a href="https://static.igem.org/mediawiki/2015/5/57/Bielefeld-CeBiTec_optimal_filtercombination.png " data-lightbox="detection" data-title="Test of different filtercombinations. On the top there is the picture without any filters. In the middle the picture was taken with fluorescence green (219) in front of the camera and deep blue (120) in front of the flash. The bottom photo was taken with the optimal filter combinition of tokyo blue (71) in front of the flash and twickenham green (736) in front of the camera."><img src="https://static.igem.org/mediawiki/2015/5/57/Bielefeld-CeBiTec_optimal_filtercombination.png" ></a> |
| − | <figcaption> Test of different | + | <figcaption> Test of different filtercombinations. On the top there is the picture without any filters. In the middle the picture was taken with fluorescence green (219) in front of the camera and deep blue (120) in front of the flash. The bottom photo was taken with the optimal filter combinition of tokyo blue (71) in front of the flash and twickenham green (736) in front of the camera |
</figcaption> | </figcaption> | ||
</figure> | </figure> | ||
| Line 108: | Line 108: | ||
<div class="col-md-6 text-center" style="margin-bottom: 20px"> | <div class="col-md-6 text-center" style="margin-bottom: 20px"> | ||
<figure style="margin:auto; width: 400px"> | <figure style="margin:auto; width: 400px"> | ||
| − | <a href="https://static.igem.org/mediawiki/2015/e/e9/Bielefeld-CeBiTec_optimal_filtercombination_mRFP.png" data-lightbox="detection" data-title="Test of different filtercombinations to photograph mRFP. On the top the picture is taken without any filters. | + | <a href="https://static.igem.org/mediawiki/2015/e/e9/Bielefeld-CeBiTec_optimal_filtercombination_mRFP.png" data-lightbox="detection" data-title="Test of different filtercombinations to photograph mRFP. On the top the picture is taken without any filters. The picture in the middle was taken with light red in front of the camera and dark yellow green in front of the flash. The bottom photo was taken with the optimal filter combinition twickenham green in front of the flash and light red in front of the camera."><img src="https://static.igem.org/mediawiki/2015/e/e9/Bielefeld-CeBiTec_optimal_filtercombination_mRFP.png" ></a> |
| − | <figcaption> Test of different filtercombinations to photograph mRFP. On the top the picture is taken without any filters. | + | <figcaption> Test of different filtercombinations to photograph mRFP. On the top the picture is taken without any filters. The picture in the middle was taken with light red in front of the camera and dark yellow green in front of the flash. The bottom photo was taken with the optimal filter combinition twickenham green in front of the flash and light red in front of the camera |
</figcaption> | </figcaption> | ||
</figure> | </figure> | ||
| Line 118: | Line 118: | ||
<br> | <br> | ||
| − | <p> As you can see in the | + | <p> As you can see in the pictures above it is really important to choose the right filters to get a high fluorescence signal and a low background signal. But is it only possible to photograph sfGFP and GFP? To find out, we took photos of the monomeric red fluorescent protein (mRFP) lysate, as well. For this protein we determined Twickenham green (736) in front of the flash and light red (182) in front of the camera to act as the optimal filter combination. </p> |
</div> | </div> | ||
<div class="Does fluorescence photography work on Paper?"> | <div class="Does fluorescence photography work on Paper?"> | ||
| − | <h2> Does fluorescence photography work on | + | <h2> Does fluorescence photography work on paper? </h2> |
| − | <p> | + | <p> We showed that fluorescence imaging of liquids in quite high amounts is possible with our approach. But does it also work with small volumes and on paper? To assess this we took normal laboratory filter papers. (MN 827 B from Macherey and Nagel, C 350 L and FN3 from Munktell and a laboratory filter paper from Merck), put the lysates on the paper and took photos with our filter systems. Exemplary the results of the laboratory filter paper from Merck are shown in the figure below. The other filter papers showed the same results. As it can be seen see, it is possible to photograph volumes of 5 µl purified GFP up to a concentration of 17,5 mmol/L. </p> |
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<div class="col-md-6 text-center" style="margin-bottom: 20px"> | <div class="col-md-6 text-center" style="margin-bottom: 20px"> | ||
<figure style="margin:auto; width: 350px"> | <figure style="margin:auto; width: 350px"> | ||
| − | <a href="https://static.igem.org/mediawiki/2015/d/d7/Bielefeld-CeBiTec_test_on_paper.png" data-lightbox=" | + | <a href="https://static.igem.org/mediawiki/2015/d/d7/Bielefeld-CeBiTec_test_on_paper.png" data-lightbox="Detection" data-title="We added 5 µL of lysate to the paper disc and photographed it with the different filter combinations. In the first row dilution seriesof purified GFP were added to the paper discs. In the second row sfGFP lysate were added, in the third row mRFP lysate was used and in the last row lysat without sfGFP and mRFP were added to the paper discs. The top photo was taken without any filter. As you can see, there is no fluorescence visible. The picture in the middle was taken with the filter combination for sfGFP. In this picture you can see two glowing paper discs in the first and in the second row. In the bottom picture the mRFP filters were used. Three paper discs of the third row are red. So it's possible to detect the mRFP lysate up to a 1:10 dilution."><img src="https://static.igem.org/mediawiki/2015/d/d7/Bielefeld-CeBiTec_test_on_paper.png" ></a> |
| − | <figcaption> We added | + | <figcaption> Detection" data-title="We added 5 µL of lysate to the paper disc and photographed it with the different filter combinations. In the first row dilution seriesof purified GFP were added to the paper discs. In the second row sfGFP lysate were added, in the third row mRFP lysate was used and in the last row lysat without sfGFP and mRFP were added to the paper discs. The top photo was taken without any filter. As you can see, there is no fluorescence visible. The picture in the middle was taken with the filter combination for sfGFP. In this picture you can see two glowing paper discs in the first and in the second row. In the bottom picture the mRFP filters were used. Three paper discs of the third row are red. So it's possible to detect the mRFP lysate up to a 1:10 dilution. |
</figcaption> | </figcaption> | ||
</figure> | </figure> | ||
| Line 142: | Line 142: | ||
<br> | <br> | ||
<br> | <br> | ||
| − | <p> Now we wanted to find out if it is possible to photograph the fluorescence from a <a href="#paperCFPS">CFPS on Paper | + | <p> Now we wanted to find out if it is possible to photograph the fluorescence from a<a href="#paperCFPS">Cell-Free Protein Synthesis (CFPS) on Paper</a>. After a CFPS run on paper, we took the paper discs and took the photo shown below. </p> |
<br> | <br> | ||
| − | <figure style="margin:auto; width: | + | <figure style="margin:auto; width: 300px"> |
| − | <a href="https://static.igem.org/mediawiki/2015/9/99/Bielefeld-CeBiTec_CFPS_on_Paper.png" data-lightbox="detection" data-title="We took the paper | + | <a href="https://static.igem.org/mediawiki/2015/9/99/Bielefeld-CeBiTec_CFPS_on_Paper.png" data-lightbox="detection" data-title="Photo of the CFPS run on paper. We took the paper discs of paper from the <a href="#paperCFPS">Cell-Free Protein Synthesis (CFPS) on Paper<CFPS></a> experiment on paper, took a photo and it worked, hence we can take a photo of the sfGFP generated in a CFPS experiment. In the first row you can see purified GFP, a dilution of the GFP and sfGFP lysat. We used this row for comparison. In the second row is the negativ control. We need the negativ control to visualize the |
| − | <figcaption> We took the | + | self-fluorescence of the cell extract. In the third row are the paper discs where our self made extract were added for the CFPS. In the last row you can see the paper disc with the commercial cell extract for CFPS."><img src="https://static.igem.org/mediawiki/2015/9/99/Bielefeld-CeBiTec_CFPS_on_Paper.png "><img src="https://static.igem.org/mediawiki/2015/9/99/Bielefeld-CeBiTec_CFPS_on_Paper.png" ></a> |
| + | <figcaption> Photo of the CFPS run on paper. We took the paper discs of paper from the <a href="#paperCFPS">Cell-Free Protein Synthesis (CFPS) on Paper<CFPS></a> experiment on paper, took a photo and it worked, hence we can take a photo of the sfGFP generated in a CFPS experiment. In the first row you can see purified GFP, a dilution of the GFP and sfGFP lysat. We used this row for comparison. In the second row is the negativ control. We need the negativ control to visualize the | ||
| + | self-fluorescence of the cell extract. In the third row are the paper discs where our self made extract were added for the CFPS. In the last row you can see the paper disc with the commercial cell extract for CFPS. | ||
</figcaption> | </figcaption> | ||
</figure> | </figure> | ||
| + | |||
</div> | </div> | ||
Revision as of 20:06, 18 September 2015
Output Signal processing
A Prototyp for easy fluorescence detection
The problem
We planned to design a convenient test strip using fluorescence as an output signal. Green fluorescent protein (GFP) is one of the most frequently used reporter proteins and it has already been used in numerous iGEM projects. Detecting fluorescence outside the lab sounded impractical to us and so we had to find an easy way to analyze the output.
The first steps
Before testing we decided to measure the extinction and emission spectra from sfGFP as a basis to choose the most promising filter combination and to have a look if the smartphone flash really excites sfGFP.
In the beginning of our project, we tried to photograph fluorescence with a smartphone. We got a filter from light engineering by the women cultural center Bielefeld e.V. ("Frauenkulturzentrum Bielefeld e.V.") and put it in front of a smartphone. In the figure below, we took a picture with this filter from purified GFP, sfGFP lysate and lysate without sfGFP. You can see different colors and a different brightnesses in the picture. In our first impression we thought it's worth to try some other filters, to find the perfect filter or filter combination for sfGFP imaging with almost no background signal.
Therefore we bought a lee color filter catalog. We made a preselection of the filters. This was possible, because we had access to the light transmitting spectra of almost every filter. With this preselection we began to test the different filter combinations.
The next step was to create a dark environment. Therefore we did handicrafts to design a black carton. Now it was possible to take photos under defined conditions and with a constant dark background.
The filter combinations
The essential requirements for taking comparable photos are achieved. Now we had to find the ideal filter combination. We made a lot of photos with the preselected Filters. We tested every combinition of 5 filters for emission with 12 filters for extinction. After analyzing the photos with the image processing software Fiji, the optimal filter combination found was tokyo blue (071) in front of the flash and twickenham green (736) in front of the camera.
As you can see in the pictures above it is really important to choose the right filters to get a high fluorescence signal and a low background signal. But is it only possible to photograph sfGFP and GFP? To find out, we took photos of the monomeric red fluorescent protein (mRFP) lysate, as well. For this protein we determined Twickenham green (736) in front of the flash and light red (182) in front of the camera to act as the optimal filter combination.
Does fluorescence photography work on paper?
We showed that fluorescence imaging of liquids in quite high amounts is possible with our approach. But does it also work with small volumes and on paper? To assess this we took normal laboratory filter papers. (MN 827 B from Macherey and Nagel, C 350 L and FN3 from Munktell and a laboratory filter paper from Merck), put the lysates on the paper and took photos with our filter systems. Exemplary the results of the laboratory filter paper from Merck are shown in the figure below. The other filter papers showed the same results. As it can be seen see, it is possible to photograph volumes of 5 µl purified GFP up to a concentration of 17,5 mmol/L.
Now we wanted to find out if it is possible to photograph the fluorescence from aCell-Free Protein Synthesis (CFPS) on Paper. After a CFPS run on paper, we took the paper discs and took the photo shown below.
The App
Now it's possible to photograph fluorescence, but sometimes it's difficult to see the differences. And analyzing the pictures with the image processing software Fiji requires know-how of the user. On the one hand for the program and on the other hand for interpreting the results. We solved this problem with a smartphone App. We coded the App with Android Studio 1.2.2 and can be installed on smartphones on Android 4.2 (Jelly bean) and later. The App determines the median of the greenvalue of a area of pixels in the sensorspot and compares it to the pixels of the negative control (the not induced sensor). If the ratio of a sample and the negative control is above a certain theshold (10%), valid biosensor signal is detected. Additionally it is checked whether the value for the positive control (drop of sfGFP) is above a certain value, thereby confirming the functionality of the biosensor. Furthermore the App displays specific information regarding the different heavymetals and date rape drugs to inform the user. You can download it by clicking on the button below. You need to unzip the file on your phone, since one cannot upload .apk files. Alternatively download it here and delete the fileextension ".txt".
The 3D print
Ok, the fluorescence detections works fine, but it is not really practical to take the photo. The filter have to be in the exact right position directly in front of the camera and the flash. Also it has to be quite dark for high quality pictures. Therefore we designed a black case and realized it with a 3D printer. Marco Radukic designed the case in exact accordance with our guidline. The top can be changed specificly for the smartphone you use. The test stripe can be placed on the push loading drawer and inserted into the box. So it is quite easy to use. You just have to put the smartphone on the top, insert the test strip and take the photo. To download the model for the 3D printing click here.
