Difference between revisions of "Arsenic Prototype 4.0"

Revision as of 11:11, 8 January 2016

Principles

The Arsenic prototype v4.0 is the Winter School 2016 kit version of prototype 3.0.

The basis of the prototype remains the same - the bioreporter, a GMO bacteria expressing eGFP (Green Fluorescent Protein) is incubated with a water sample, where the fluorescence is detected optically and can be quantified in order to measure the concentration of Arsenic in the water

• A vial containing the water sample we want to test is positioned on a socket through which a fluorescent excitation LED (blue 488nm for eGFP) passes.
• GFP absorbs this blue light (λ=475 nm) and emits green light (λ=504 nm) which is detected by a photosensor on which the light is concentrated with the help of two lenses that avoid loss of intensity
• A long-pass filter allow only the signal eGFP fluorescence to reach the photosensor

Moreover, a red LED was added to measure the transmittance, which can be converted into turbidity. The measurement of turbidity will allow us to normalize our results.

• A red LED is placed in-line with the photosensor

We use an arduino to take the measurements, and we have a liquid crystal display (LCD) to read out the numbers.
With these measures, compared against a standard curve of water containing known arsenic concentrations, one can determine the concentration of arsenic in the sample and so know if the water is drinkable or not.

In summary, the most current version consists of:

   lasercut chassis
   blue LED for eGFP fluorescence excitation at 90 degrees from detector
   red LED for transmittance measurements in line with detector
   vial holder matching the vial approved by the Swiss authorities
   light to frequency detector
   a filter to block excitation light
   LCD screen read out
   based on the arduino

Materials

• Plastic Lens Biconvex (Knight Opticals)
• 510nm long pass acrylic filter (Knight Opticals)

You can find the bill of materials here:

Step by Step Buildling

Laser Cutting the Inner Scaffold Pieces

at chez hackuarium neighboring @make space of univercité - laser cutter model: Keyland KQG-1060 120W CO2 laser cutter

With these parameters, the 3mm thickness pieces take 5 min to cut, and the 2mm thickness pieces take min.

Results

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  high-density fiberboard (HDF)

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  medium-density fiberboard (MDF)

Assembling the Electronics

There are four PCBs for:

1. Blue LED (for the eGFP excitation)
2. LCD screen
3. Red LED (for the transmittance)
4. Light to frequency meter (to detect the light)

Each of the PCBs except the LCD screen PCB are fixed onto the lasercut fiber boards using M3 screws.

Soldering and Mounting

Blue LED

Soldering the pieces:

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  1. the super bright blue surface mount LED (SMD) piece is manually soldered onto the "backside" of the PCB

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  2. on the "front side" of the PCB, first solder the resistor

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  3. clip the legs of the resistor from the back

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  4. solder the other components (the connectors for the Red LED and the light to frequency meter)

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  6. the other MOSFET is soldered into place (redo picture!)

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  7. to place the ribbon cable connector, first apply solder on one pad on the PCB

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  8. solder the first foot of the ribbon cable connector, then proceed with the rest

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  9. all except the resistor for the super bright LED is soldered

10. ready for mounting

Now mounting onto the particle board:

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  1. M3 screws are placed

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  2. 2 washers are placed onto the screws before the PCB

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  3. the SMD Blue LED should face the particle board, and the PCB is bolted in

LCD screen

This LCD screen / arduino shield will connect to the blue LED PCB with a ribbon cable

Soldering the pieces:

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  1. solder resistor 1 on the logo side

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  2. place the pins longer pins on the logo side

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  3. solder from the other side by first anchoring one pin per piece - these pins go into the arduino

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  4. solder the ribbon cable plug

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  5. back to the logo side, place the potentiometer on the left, two small buttons on the right and solder into place from the back

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  6. solder the pins onto the LCD screen

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  7. LCD screen with view of the pins from the back

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  8. view of the back with the big button soldered in

9. done soldering

Red LED

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  1. first mount the red LED - short leg = negative

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  2. next, the pins, long pins same side as the LED

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  3. ready to mount on the board

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  4. mounted, view from the PCB side

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  5. mounted, view from the LED side

light to frequency meter

• LFD 1.JPG

  1. place the legs of the light to frequency detector (LFD) in the PCB without bending or soldering

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  2. use the particle board to align the 'eye' of the LFD

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  3. solder the LFD and the long pins same side as the LFD

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  4. back of the soldered PCB aligned with the particle board

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  5. place a washer to account of the LFD thickness

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  6. mounted, view from the PCB side

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  7. mounted, view from the LFD side

Final Assembly

Finally, the Red LED and light to frequency meter will be plugged into the Blue LED board with connectors.

Then the LCD screen is plugged into the Blue LED board with a ribbon cable.

The LCD screen board is ready to be mounted on the arduino.

We are now ready to test it out.

Testing the Electronics

Uploading the arduino code

If you have not done so already, download the arduino open software.
The firmware is in our github repository for the FluoMeter.

Reading the measurements

First test the firmware and the hardware without sample.

• When you push the start button, does the blue LED go on?
• Do you see the measurement on the LCD screen?
• Do you then see the red LED go on?

Then try it with sample with fluorescence

• Do you see changes in the measurement?

Now we are ready for the actual bacterial samples.

Transmittance and absorbance

What we actually measure with the red LEDis the transmittance - how much of the red LED light goes through the sample and reaches the other side.
Absorbance (optical density) is then calculated.
A = - log10 T
where T = (Red LED captured by the light to frequency meter with sample / with buffers (no bacteria))

Making the Outer Housing

What we have built so far leaves the samples exposed to ambient light.
So we need to make outer housing that can mount the LCD screen, house the battery, enclose the scaffold inside, and have easy access to put the samples in and out while keeping the light and optics dark.

Links other References