Team:Grenoble-EMSE-LSU/Project/Monitoring/Cell2Machine

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<h1>Cell to Machine Communication</h1>
<h1>Cell to Machine Communication</h1>
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<p>To create a means of communication from cell to machine, we chose the red fluorescence protein KillerRed as a reporter protein. The first condition that our device needs to fulfill is to record light intensity. Then it needs to generate fluorescence thanks to a light source and a couple of excitation and emission filters. Firstly we will explain the choice of <a href="#Component">the different components</a>, then the several experiences we did to find the most accurate parameters for each part of the device – <a href="#Photodiode">the photodiode</a>, <a href="#Arduino">Arduino</a> and <a href="#Optic">the optic</a>.</p>
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<p>To create a means of communication from cell to machine, we chose the red fluorescence protein KillerRed as a reporter protein. The first condition that our device needs to fulfill is to record light intensity. Then it needs to generate fluorescence thanks to a light source and a couple of excitation and emission filters. First we will explain how we chose<a href="#Component">the different components</a>, then the experiments we did to find the most accurate parameters for each part of the device – <a href="#Photodiode">the photodiode</a>, <a href="#Arduino">Arduino</a> and <a href="#Optic">the optical components</a>.</p>
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<h2 id="Component">The components</h2>
<h2 id="Component">The components</h2>
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<p>To record light intensity, we were inspired by the E. glometer of the               Cambridge team of iGEM 2010.<br>
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<p>To record light intensity, we were inspired by the E. glometer of the Cambridge team of iGEM 2010.<br>
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                                         <p align="center", style="margin:40px"><img src="https://static.igem.org/mediawiki/2013/a/a7/Eglometer.png" alt="The Eglometer" width="500px" /></p>
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                                         <p align="center"><img src="https://static.igem.org/mediawiki/2013/a/a7/Eglometer.png" alt="The Eglometer" width="500px" /></p>
                                         <p id="legend"><strong><em>The E. glometer of Cambrige team (iGEM 2010)</em></strong><br>
                                         <p id="legend"><strong><em>The E. glometer of Cambrige team (iGEM 2010)</em></strong><br>
                                         Device built by Cambrige team in 2010 to measure the light intensity of their LuxBrick<br>
                                         Device built by Cambrige team in 2010 to measure the light intensity of their LuxBrick<br>
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We use quite the same photodiode (TSL230RD) – same as the TSL230RP-LF but in surface mounted device (SMD) – and an Arduino Uno. Arduino is a single-board microcontroller created to make electronics more accessible. The main asset of the photodiode is that the output can be either a pulse train or a square wave (50% duty cycle) with frequency directly proportional to light intensity. Since we are using a microcontroller, it is easy to calculate a frequency with the digital input of the microchip thanks to high or low level and we will have a better resolution because low frequencies are easier to measure than low voltages. For the optic part we use a domestic LED lamp and a cube filter from a microscope with excitation and emission filters and an adjustable lens. A domestic LED lamp was chosen to allow us not to buy several high-power LEDS and built a card with a heat sink. This lamp illuminate with 520 lumens in a cone of 40° under 12V and 6W. The low voltage was chosen as a safety condition and the small angle to avoid losing to much light. The excitation filter is a green interferential filter to excite the red fluorescent protein and the red emission filter is only a colored filter to collect all the red light in order to have a more efficient measure. In the cube there is also a dichroic mirror that reflects all the green light and transmits all the red light. This mirror enables us to separate completely the photodiode from the light source.
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We use a similar photodiode (TSL230RD) – the same as the TSL230RP-LF but as a surface mounted device (SMD) – and an Arduino Uno. Arduino is a single-board microcontroller created to make electronics more accessible. The main asset of the photodiode is that the output can be either a pulse train or a square wave (50% duty cycle) with its frequency directly proportional to light intensity. Since we are using a microcontroller, it is easy to calculate the frequency with the digital input of the microchip thanks to high or low level detection and we will have a better resolution because low frequencies are easier to measure than low voltages at low light levels. For the optical part we use a LED lamp and a cube filter from a fluorescence microscope with excitation and emission filters and an adjustable lens. The LED lamp was chosen so that e didn't have to buy high-power LEDS and build a card with heat sinks. This lamp illuminates with 520 lumens in a 40° cone under 12V and 6W. The low voltage was chosen as a safety measure and the small angle to avoid losing too much light. The excitation filter is a green interferential filter to excite the red fluorescent protein and the red emission filter is only a colored filter to collect all the red light in order to have a more precise measure. In the cube there is also a dichroic mirror that reflects all the green light and transmits all the red light. This mirror enables us to separate the photodiode from the light source completely.
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<h2 id="Photodiode">The photodiode</h2>
<h2 id="Photodiode">The photodiode</h2>
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<p>Before measuring with the photodiode, we need to know if the photodiode works as indicated in the datasheet. The photodiode was plug on a 5V stabilized power supply.</br></p>
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<p>Before measuring with the photodiode, we need to know if the photodiode works as indicated in the datasheet. The photodiode was plugged in on a 5V stabilized power supply.</br></p>
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                                         <p align="center"><img src="https://static.igem.org/mediawiki/2013/5/5f/IGEMerworkphotodiode.png" alt="memberworkingonphotodiode" width="500px"></p>
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                                         <p align="center", style="margin:20px"><img src="https://static.igem.org/mediawiki/2013/5/5f/IGEMerworkphotodiode.png" alt="memberworkingonphotodiode" width="500px"></p>
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                                        <p id="legend"><strong><em>A member of the team working on the photodiode</em></strong></br></p>
                                         <p>For the same amount of light, we measure the frequency at the output of the photodiode for a pulse train or a square wave (50% duty cycle). According to the datasheet, when using a pulse train the linear relation between the frequency and the irrandiance is given by 1kHz=1µW/cm². When using a square wave (50% duty cycle) it is 1kHz=2µW/cm². This is what we can see on the figure #.
                                         <p>For the same amount of light, we measure the frequency at the output of the photodiode for a pulse train or a square wave (50% duty cycle). According to the datasheet, when using a pulse train the linear relation between the frequency and the irrandiance is given by 1kHz=1µW/cm². When using a square wave (50% duty cycle) it is 1kHz=2µW/cm². This is what we can see on the figure #.
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                                         <p align="center"><img src="https://static.igem.org/mediawiki/2013/5/51/Oscilloscope.png" alt="Oscillogram" width="650px" /></p>
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                                         <p align="center"><img src="https://static.igem.org/mediawiki/2013/5/51/Oscilloscope.png" alt="Oscillogramm" width="650px" /></p>
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                                        <p id="legend"><strong><em>Oscillograms showing the two different mode of the photodiode.</em></strong></br>The first oscillogramm shows the pulse train mode and the second the 50% duty cycle mode</br></p>
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                                         <p>Since this frequency will be calculated by the Arduino controller, it may cause some trouble to the program to use a pulse train because the duration of the pulse is always 500ns and can be missed by the controller. The square wave (50% duty cycle) seems to be a better solution because of the 50% duty cycle. It means that the pulse duration depend on the frequency. Its duration is equal to 1/2f and since the light intensity we want to measure will be low this type of signal can be easily detected by Arduino.</p>
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                                         <p></br>Since this frequency will be calculated by the Arduino controller, it may cause some trouble to the program to use a pulse train because the duration of the pulse is always 500ns and can be missed by the controller. The square wave (50% duty cycle) seems to be a better solution because of the 50% duty cycle. It means that the pulse duration depend on the frequency. Its duration is equal to 1/2f and since the light intensity we want to measure will be low this type of signal can be easily detected by Arduino.</p>
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Latest revision as of 20:13, 16 September 2013

Grenoble-EMSE-LSU, iGEM


Grenoble-EMSE-LSU, iGEM

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