Team:Valencia UPV/Hardware

Hardware

Index

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  • Weight: 5kg
  • Consume:180W
  • Cost: 767.62€


Introduction

One of the main barriers faced by research is the high cost of the laboratory equipment. To avoid this problem the team Hype-it has designed a set of hardware to make possible working with the technology CRISPR/Cas9 for plant genome editing (and others) at a low price (<1000€). Approximately 7% of what usually costs a set of the same hardware of commercial brands.
For the design of this hardware the designing team has worked with the wet lab team in order to have an effective feedback and give the ideal solutions that better fit the needs of the final user.
The designed hardware not only has proved to be functional but also has been proved to be able to rival professional laboratory equipment.

We have designed:

  • Structure
  • Electroporator.
  • Colorimeter.
  • Centrifuge.
  • Gel electrophoresis unit.
  • Stirrer with temperature control.
  • Phytotron.
  • Thermal cycler.
  • Luminometer.


PartsUnitCOST unit €COST €
Structure1285285
Electroporator157,0757,07
Colorimeter126,226,2
Centrifuge15656
Electrophoresis166,0766,07
Stirrer181,2481,24
Fitotron197,697,6
Thermocycler174,1474,14
Luminometer124,324,3
TOTAL COST767,62



STRUCTURE


  • Weight: 3kg
  • Materials: Aluminium and methacrylate
  • Cost: 285 €


WHAT IS IT FOR IN OUR PROJECT


The aim of the structure is to hold all the devices designed by Hype-it team. Is included a case in order to keep the whole system safe. The lightness of the Labware allows anyone to carry it between different labs.

KEY PARTS OF THIS MACHINE


Aluminium Structure: The main part of the structure is made of aluminium from Mecaduino Brand because it gives the optimal relation stability-weight. For the joining of the profiles it has been used the option of perpendicular joints with hidden tensor.

Power supply: All the equipment designed by us needs a direct current (DC) electricity source. For this purpose we have chosen a 12V 15A (180W) power supply with security for short circuits.


Wire: The power supply is connected to a wire of 16 A that can be removed to store the Labware better.

Screen: Any user who works with this kind of systems needs a way of communication with the labware. To achieve this our proposal is a smart LCD for arduino and 3D printers with button, which allows to easily control all the labware.


Arduino Mega: It will be the “brain” of the labware. It is only needed one Arduino to control all the machines at the same time, reducing in this way the final cost.


External parts (cover): The external parts are made of methacrylate because it is easy to clean and can resist chemical attacks.
We have added holes to refrigerate the inside of the system.

YOU WILL NEED


MATERIALSUNITCOST unit €COST €
Aluminium structure1130130
Power supply +wire+plug11720
Methacrylate parts19090
Screen199
Arduino Mega11616
general wires11212
screen holder177
screws 20xM4200.051
TOTAL COST285


ELECTROPORATOR

  • Working voltage: 0V to 1600V
  • Resolution: 2.5V
  • Time range: 0.5-10.0 ms
  • Price: 57,07€


WHAT IS IT FOR IN OUR PROJECT


The electroporator is a machine which applies an electrical field to cells in order to increase the permeability of the cell membrane. This is used to transform bacteria by introducing new coding DNA, plasmids.

It works by passing through 1500 volts across a special cuvette, where electrocompetent bacteria are introduced.

FUNCTION PRINCIPLE


To produce the high voltage electrical pulse it is necessary a high voltage power supply. The problem is that this type of power supply does not have much power, so it cannot be able to maintain constant the voltage in the cuvette. One solution is the use of a capacitor to accumulate the energy before doing the electroporation. Hence, a MOSFET will be used to control the duration of the pulse.

OUR RESULTS


To test the low-cost electroporator, we transform electrocompetent DH5α E. coli with a plasmid with purple color (BBa_K592009). One petri dish was cultured with bacteria transformed with the low-cost electroporator (left), and the other with bacteria transformed with a professional electroporator as positive control (right).

In the picture it can be seen that colony density is higher with our low-cost electroporator, meaning that the transformation was probably more efficient. This suggests that the electroporator designed works better than the professional electroporator we had in the laboratory.

In order to repeat the experiment and test its reproducibility, we did tried with two more different plasmids. In the first we used a plasmid with dsRed. The transformed cells should express a red protein. As seen in the picture, bacteria were successfully transformed.


The second plasmid has GFP, so colonies should be green under the fluorescence microscope. This third experiment was also successful.



KEY PARTS OF THIS MACHINE

High voltage power supply: this power supply will provide the voltage needed to electroporate. It is based in a DC-DC boost converter and the output voltage can be adjusted between 300V to 1200V. Because the normal voltage for electroporation is 1500V, we will need two of this power supplies connected in serie.


High voltage capacitor: The capacitor will accumulate the energy needed for electroporation. The voltage rating of the capacitor should be greater than 1500V in order to provide a security margin. The value of capacitance can be choosen between 1uF and 8uF, in this range the capacitor will accumulate enough energy and can be charged quickly. We selected a capacitor of 1600V and 1uF.


High voltage MOSFET: The mosfet acts like a switch in the circuit. When the mosfet is in the “off” state, the high voltage source will charge the capacitor. When the mosfet is in the “on” state, the capacitor discharges through the load, producing a negative pulse voltage. The voltage rating of the mosfet selected is 1700V, and the nominal current is 4.9A.


MOSFET: It is also needed a MOSFET to activate and deactivate the high voltage power supply. The input of the power supply is 12V, so we use a mosfet with a 55V and 41 A rating.


Cuvette Holder: The cuvette needs to be connected electrically to the electroporator circuit, so a 3D printed cuvette holder has been designed. This design includes a poka-yoke, so the cuvette will only fit in the correct way. It also has two copper plates to make contact with the electrodes of the cuvette.

ELECTRICAL MODEL OF THE CUVETTE


The cuvette used in this machine is a 1 mm gap electroporation cuvette. Electroporation cuvettes can have different gap sizes. This size will determine the voltage of the electroporation.

This type of cuvette, which contains two parallel plate electrodes, can be modeled as a resistor and a capacitor in parallel.

The value of the resistance can be calculated with the next equation:


Where l is the size of the gap between the plates, sigma is the conductivity of the buffer solution and A is the area of the electrodes.

The value of the capacitance can be calculated this way:


where e_o is the permittivity of free space (8.85 x 10°-12 F/m), e_r is the water dielectric constant, A is the area of the electrode, and d is the gap distance between electrodes.

The resistance has a typical value between 10 ohm and 15 koh. On the other hand, the capacitance is independent of the medium conductivity and it is 35 pF.

CIRCUIT


The circuit that implements the electroporator is the following one:


Q1 is the high voltage mosfet, which will control the charge and discharge of the capacitor C1. The mosfet Q1 is driven with one digital output of the arduino. When Q1 is in “off” state the capacitor will charge through the resistor R4. This resistor is used to limit the current demand to the high voltage source.

The capacitor will take a few seconds to charge, so to be sure that it is fully charged there is a tension divider to measure the actual voltage in the capacitor. This divider is implemented with two resistors R1 and R2, that will reduce voltage of +1500 V to +3 V, so this voltage can be read with an analog input of the Arduino.

Then, when the capacitor is charged to the desired voltage, the mosfet Q1 will change to “on” state so the capacitor will discharge through the cuvette and the mosfet Q1, producing a negative pulse across the cuvette.

The high voltage source needs a +12V input to start working, so a mosfet Q2 is used to control the on/off state of the high voltage source. The mosfet Q2 is controlled by the Arduino with one digital output. This way, it is secure to discharge the capacitor.

FUTURE LINES

In the design we have proposed, the mosfet are connected directly to the arduino. This will reduce the lifetime of both the Arduino and the mosfet. So even though the current design works, it will be good to have a mosfet driver circuit in between the Arduino and the mosfet.


DOWNLOADS


Electroporator Arduino Code

YOU WILL NEED

MATERIALSUNITCOST/unit€COST €
Mosfet N-Channel C2M1000170D15,325,32
Mosfet N-Channel IRFZ44NPBF11,621,62
High voltage DC-DC boost converter 5-12V to 300-1200V29,1718,34
High Voltage Capacitor 1,6kV 1uF18,058,05
PCB17,187,18
Resistor 30k 600mW10,060,06
Resistor 15M 500mW11,321,32
Resistor 22k 3W10,180,18
Cuvette Holder (3D printed)11515
Screw 25XM420,10,2
Nut M440,050,2
Copper plate 5x15mm20,10,2
Total Cost57,07


COLORIMETER

  • This device works for a wavelength of 650 nm.
  • Deviation = 0.007 OD
  • Price: 26,2€

WHAT IS IT FOR IN OUR PROJECT


The aim of the colorimeter is to calculate the concentration of bacteria in the sample. Cell concentration is key in the agroinfiltration process: a low concentration means that few plant cells will be infected, and a high concentration will damage the plant. The optimal range is 1.8-2.2 OD.

FUNCTION PRINCIPLE


The light emitted from the laser goes across the sample in the tube and is sensed by the photodiode in the other side of the tube. This measure is compared to the measure that would be obtained if the light had gone across as if there was any sample. The equation to calculate the optical density is the following one:

OD = - (1/L)*log10(I/Io)

Where :

L = distance the light travels across the sample in centimeters
I = light intensity that goes across the sample
Io = light intensity emitted



OUR RESULTS

We tested the density meter with optical filters. This filters have a fixed range of optical density values between 0.2 OD and 1.5 OD.
In the following graph, it is compared the value of the measured optical density and the real value.


Deviation = 0.007 OD (error bars too small for being watched)

The result is that the lectures of the density meter are virtually identical to the real values. For each value of real OD, we did three measures and the deviation was 0.0007 OD.

In conclusion, this density meter design has proved to be great with high accuracy lectures and extremely low deviation. The specifications of this density meter can be easily compared with a high cost professional density meter.
It should be recalled its low cost, around only 27€.

KEY PARTS OF THIS MACHINE


Tube holder: This part of the machine will hold the tube. It is recommended to have this part covered and black painted, or printed with black PLA or ABS. Our design includes a poka-yoke in order to help the user with the use of the machine.
Laser: The laser will emit the light that will go cross the tube. The wavelength of the laser will determine the wavelength of the measures. The most common to measure optical density in cells is 600 nm. Being necessary to choose a laser around that wavelength, we selected a 650 nm laser. It is important that the light beam generated is in dot shape, this will improve the precision of the lectures. Finally, the power generated by the laser has to be around 3W. With lower power the sensibility can be reduced and with higher values the sensor might get saturated.


Sensor: A photodiode has been selected to measure the light that has gone trough. This type of sensors have a high sensibility and precision. The sensor selected is a TSL235-LF and it converts light into frequency, which can be measured with Arduino.


CIRCUIT


The circuit that implements the colorimeter is the following one:


It is a simple and efficient design. A mosfet is used to drive the laser module and the output of the sensor has to be connected to an Arduino digital pin with interruptions. This is crucial, because the arduino program uses interruptions in order to measure the output frequency of the sensor. The pins which can do interruptions in Arduino Mega are 2, 3, 18, 19, 20 and 21.

DOWNLOADS


Colorimeter Arduino Code

YOU WILL NEED

MATERIALSUNITCOST/unit €COST €
TUBE HOLDER11515
LASER- Red point laser 650nm17,57,5
TSL235R-LF13,13,1
SCREW 25XM440,10,4
NUT M440,050,2
TOTAL COST26.2

CENTRIFUGE

  • Capacity: 6 x 1.5mL Eppendorf tubes
  • Max Speed: 13,000 rpm
  • Max RCF: 8000 g
  • Cost: 56.0 €

WHAT IS IT FOR IN OUR PROJECT


Generally, the purpose of a centrifuge is to separate particles dense particles from low-density substances. Working with bacteria, it is common its use for the extraction of plasmids using special kits, that allow the separation of the plasmidic DNA. This is achieved thanks to a filter that is put in the sample tubes which are centrifuged using specially prepared solutions. The centrifuge is also used in genomic DNA extraction from plant samples. The centrifuge has been designed to reach 13,000 rpm, which is the maximum speed needed for a plasmid extraction.

FUNCTION PRINCIPLE


The centrifuge makes spin at high velocity objects, then the centripetal acceleration will cause denser substances and particles to move outward. In the other hand, substances that are less denser will get displaced to the center. The normal use in the laboratory is to use sample tubes and the goal is to separate substances by its density.

OUR RESULTS


We tested the centrifuge and was able to reach speeds of 13.000 rpm. In the following graph we show the temporal response of the centrifuge by increasing the control action every 10 seconds:

The minimum control action is 1000 and the maximum is 2000. In this graphic we can see that with a control action of 1250 we can get around 8000rpm.

We have done a control that manage to establish the speed of the centrifuge to the desired speed.

KEY PARTS OF THIS MACHINE


Rotor: The rotor is the part of the centrifuge that will be connected to the motor and where the sample tubes will fit. Rotors are normally expensive so a 3D printed rotor has been designed. This design is able to support the forces produced by the spinning.

Motor brushless: The centrifuge has to get high speed and also needs high torque to be able to move the rotor and the sample tubes. A DC brushless motor has this two requirements, and it is also easy to set its speed to a certain value, being very reliable. The technical specifications for this motor are KV and A. KV refers to the rpm constant of the motor - it is the number of revolutions per minute that the motor turn for each 1 volt supplied. A is the maximum current it can demand. This value is directly related to the torque it can produce. Motors with bigger KV tend to have less torque. For the centrifuge a high KV will be needed to reach the a high speed but it is also important not to pick a huge KV value because the motor will not be able to move the rotor. A KV above 1200 means that if you supply the motor with +12V you will get a maximum of 14400 rpm. Finally, a value for A around 25 works perfectly.


ESC(Electronic Control Speed): The ESC will control the power supplied to the brushless motor. This way the speed will be controlled. It is important to match the specifications of the ESC with the specifications of the motor. The most important value is that the max A of the ESC is bigger or at least equal to the A of the motor. This way, the ESC will never burn due to an overcurrent produced by the motor.


Tachometer: The tachometer is an electronical device that counts the revolutions per second the rotor does. There are many types of tachometers but normally they consist of an infrared emitter and an infrared sensor. Every time the rotor spins the beam generated by the emitter will be cut, producing a pulse in the measure of the sensor. This way counting the number of pulsed generated the rpm can be measured with high precision.


CONTROL

To control the speed of the centrifuge we have designed a PI controller to reach the setted speed and have zero error. This way the centrifuge will always spin at the speed it is demanded, independently of the weight of the sample tubes.

CIRCUIT

The circuit that implements the centrifuge is the following one:


The arduino will control the speed of the motor through the ESC, so it will be needed a digital pin. Then the speed is measured with the tachometer and converted into analog electrical pulses. This pulses are readed with a analog input of the Arduino.

FUTURE LINES


There are two different main future lines. One is related with security: it will be necessary to add for the security system an automatic lock and unlock of the cap. The other line addresses the vibration movement. The system will be improved by adding two bearings in the shaft.

DOWNLOADS


Centrifuge Arduino Code

YOU WILL NEED

MATERIALSUNITCOST/unit €COST €
Motor 1400 kV + ESC 30A116,6116,61
Encoder Kit15,115,11
Power Source117,6217,62
Screw 4Mx1540,050,2
Nut 4M40,050,2
Rotor 3D printed11515
Tachometer Module for Arduino11,281,28
TOTAL COST56,0

ELECTROPHORESIS

  • Voltage: 48V
  • Price: 66.07 €
  • #

WHAT IS IT FOR IN OUR PROJECT

  • Electrophoresis is a technique used to separate DNA samples according to its length. It is used to separate a desired DNA fragment or to check if a DNA sample is the expected.

  • FUNCTION PRINCIPLE

  • The DNA is placed in wells of the agarose gel. Then an electrical field is applied. The DNA is affected by the electrical field, and it will start moving through the gel. Shorter DNA fragments will move faster than larger DNA fragments, causing the separation of the DNA by its size.

  • OUR RESULTS

  • We tested the low-cost electrophoresis cuvette and the power supply doing an electrophoresis, using a molecular marker. In the next figure, we can see the obtained electrophoresis in a transilluminator.
  • It can be checked that the separation has correctly been performed.

    • KEY PARTS OF THIS MACHINE

  • Power source: The power source will generate the electrical field needed for the electroporation. The typically voltage of this source is 100V but a different voltage value can be used. The voltage will determine the time will require the electrophoresis to separate the DNA. In our project, a 48V source is used and it takes one and half hour to work. The last parameter is the power, the current generated through the gel is normally around 100 mA so with 25W it will be more than enough.
  • https://static.igem.org/mediawiki/2016/9/91/T--Valencia_UPV--22fuenteGel.png
  • Electroporation cuvette: In this cuvette is where the electroporation will be done. These cuvettes are expensive so a 3D printable model has been designed, including the comb and the gel mold. In addition to the 3D cuvette some electronic parts are also needed, but they are minimal: just two banana connectors and two platinum cover wires. The platinum cover wire is strictly necessary. Other type of wires will oxidize during the electrophoresis. It is critical to make sure that there are not any leaks in the cuvette.
  • UV light: UV light is necessary to make visible the DNA bands. The easiest way to produce UV light is to use a UV torch.

  • CIRCUIT

  • The following circuit implements the eletrofesis power source and cuvette.

  • The +48V power source is connected through a mosfet to the electrophoresis cuvette. This way the we can select to apply voltage or not to the cuvette. The Arduino will control the mosfet so it is possible to set the amount of time you need to apply the voltage.

  • FUTURE LINES

  • The UV torch is a easy way to visualize the result of the electrophoresis, but it is not very handy and the UV light is dangerous. It will be better to have a small transilluminator where the gel can be placed. This way you can avoid to expose yourself to the UV light. There are some DIY (do it yourself) designs on the internet.

  • DOWNLOADS

  • Electrophoreis Arduino Code

  • YOU WILL NEED

  • MATERIALS
    		• UDCOST/unit €COST €
  • Electrophoresis cuvette 3D printed
    		• 13030
  • Power source 48V 25W
    		• 116,516,5
  • Banana male connector
    		• 21,32,6
  • Banana female connector
    		• 21,012,02
  • Platinum coated wire 30 cm
    		• 155
  • UV torch 4W
    		• 19,959,95
  		• Total Cost66,07

  • STIRRER WITH CONTROLLED TEMPERATURE

    • his device can shake the samples with a ratio of 600 r.p.m.
    • The temperature can be setted between 15ºC and 45ºC.
    • Price: 81.24€

    WHAT IS IT FOR IN OUR PROJECT

  • The aim of the stirrer with controlled temperature is to allow the uniform growth of Agrobacterium tumefaciens (28ºC) and Escherichia Coli (37ºC) after they have been transformed and selected from the culture plates. It is also used to distribute the agroinfiltration solution inside the tubes with Agrobacterium before agroinfiltration.

  • FUNCTION PRINCIPLE

  • Bacteria need oxygen as well as different sources of energy, if there is not movement during the growth, they go to the bottom of the tube and have not acces to the nutrients causing small growth.
  • The optimum temperature to grow the bacteria needed to improve a plant variety are between 34 and 39 ºC this is why to have a good bacterial culture is needed to keep the temperature around 34 and 39ºC as mentioned.
  • To carry out this purpose has been designed an orbital stirrer (to get the movement) with a peltier cell on it to keep the temperature.

  • OUR RESULTS

  • We tested the temperature control in the stirrer by setting a temperature reference of 37.0ºC. In the following graphic we can see the response of the system:
  • It took about 150 seconds ( 2 and a half minutes) to reach the desired temperature, in addition the system was able to maintain constant the temperature in the reference value. In conclusion, the control works properly so the stirrer is functional.

  • KEY PARTS OF THIS MACHINE

  • Tubes holder: This part of the machine will hold the tubes and receive the heat from the peltier cell, this is the reason for have a part made of metal due the high heat conductivity.
  • Peltier cell: The difference of tension between the poles, produce a delta of temperature in both surfaces of the peltier. The warm part is used to keep the tubes at 37ºC.

  • LM35: Our temperature sensor: To keep the temperature at 37ºC is needed a feedback from the own system in closed loop, with a Proportional,Integral and Derivative (PID) control.

  • Bearings: The soft movement is got thanks to the bearings.

  • Motor: Nema 17+polulu driver a4988, its function is to shake the tubes with a controlled speed. One of the advantages is the easiness of programming of the driver because it has only 3 ports:step, direction, and on.

  • CIRCUIT

  • The circuit that implements the stirrer is the following one. It realizes three tasks: (1) control the peltier, (2) measure the temperature and (3) drive the stepper motor.

  • The peltier is control through a mosfet by applying a PWM. The resistors R1 and R2 reduce the current demand of the mosfet, protecting the Arduino.
  • The temperature is measured with a LM35 attached to a analog pin of the Arduino.
  • The stepper motor is controlled by the driver a4988. The speed and the direction are controlled by two digital pin of the Arduino.

  • DOWNLOADS

  • Stirrer Arduino Code

  • YOU WILL NEED

  • MATERIALS
    		• UDCOST/unit €COST €
  • 3d printed pieces
    		• 12020
  • nema 17+ driver a4988
    		• 12020
  • Mosfet N-Channel IRFZ44NPBF
    		• 11,621.62
  • PCB
    		• 17,187,18
  • Peltier Cell 110W MCTE1-12712L-S
    		• 118,8418,84
  • LM35
    		• 144
  • Relay +12V 15A
    		• 24,569,12
  • Resistor 4.7k 1/4W
    		• 30,020,06
  • Resistor 100k 1/4W
    		• 30,140,42
  		• TOTAL COST81.24

    PHYTOTRON

    • his device works in a range of temperature of (15 to 30 ºC)
    • Temperature resolution = 1 degree
    • Measures humidity
    • Nett space: 40x80 Cm
    • Consume: 160W
    • Price: 97.6€

  • WHAT IS IT FOR IN OUR PROJECT

  • The use of the phytotron is to grow plants in the optimal conditions, In the particular case of Nicotiana Benthamiana 16 hours periods of light, and 24 ºC.

  • FUNCTION PRINCIPLE

  • To keep the temperature at 24ºC, we have taken peltier modules, even its consume is high. The reason reducing the budget and the size of the hardware we have projected. To bigger scales, peltier cells would be the worst option due to the high consume.
  • The lights chosen are leds because of its ability to emit the wavelength that chlorophyll needs to photosynthesis.

  • As you can see the chlorophyll A and B have different absorption peaks, but these peaks are covered by the different peaks from the LEDs although the chlorophyll peaks and LED peaks are not in the same wavelength.

    • OUR RESULTS

  • The fitotron is capable of monitoring the temperature and the humidity with an one second of sampling time. It has been tested the temperature control and it is able to maintain the temperature constant in 24 degrees.
  • In the following picture you can see the result of the phytotron:

  • KEY PARTS OF THIS MACHINE

  • The “box”: To this purpose we have selected a commercial solution from a known brand.To keep the temperature we have opted by an isolation material used in construction.

  • Peltier cooling system: The purpose of the peltier module is to keep the “box” in the setted temperature.

  • We have added to the “box” 2 peltiers in order to have a lower temperature difference.
  • Q=h*A*T1-T2
  • where Q is the energy we need to remove from the box, h the convection air coefficient, and T1,T2 the temperature of the material and the air, and A is the area of the different sides of the box.
  • h=50
  • A=1 m°2
  • T1-T2=25 ºK
  • Q=50W
  • One peltier cooling system would not be enough because in its 72W are included the fans what makes only a 60W but due the low efficiency of this system 40 W of real refrigeration.This is why we have added an other peltier cooling system.
  • Sensor: We have used a temperature sensor to have the feedback and keep the temperature with a closed loop. The sensor chosen has been the KY-015 DHT11 Temperature Humidity Sensor Module For Arduino. Also, with this sensor we can measure the humidity.

  • The leds: Maybe talk about blue leds is something weird for most of the people, but things change when we talk about cold white light from leds, what is the same. The option selected has been Lexman LED REFLECTORA REGULABLE GU10.

  • Arduino UNO R3: Will manage the control of the whole system.

  • CONTROL

  • The controller is designed as a closed loop PID. Due to the fitotron is a big space, the temperature control gets difficult because all the response in temperature are extremely slow. So we had to be extremely careful in the tuning of the PID.
  • Finally we were able to control the temperature in the range of 15ºC to 35ºC.

  • CIRCUIT

  • The circuit that implements the phytotron is the following one:

  • This circuit realizes several functions: (1) actives the fans of the peltier modules and the fan of ventilation, (2) measures the temperature and humidity and (3) control the power supply to the peltiers cells.
  • The fans always have to be on so they connected directly to the power supply.
  • The sensor DHT11 is attached to a digital pin of the Arduino.
  • The power of the peltiers is controlled by the mosfet Q1 with a PWM. The relays will change the polarity of the peltiers cells, changing its state to cool or to heat. The relay are driven by two mosfet.
  • This machine has his own Arduino and his own power supply due to it will be outside of the structure.

  • FUTURE LINES

  • The main parts to improve in this design are related with 2 different variables, CO2 and humidity.
  • These key factors will make that plants grow in the optimal conditions.

  • DOWNLOADS

  • Phytotron Arduino Code

  • YOU WILL NEED

  • MATERIALS
    		• UDCOST/unit €COST €
  • led white light
    		• 11515
  • Box
    		• 14545
  • TEC1-12706 Thermoelectric PeltierRefrigeration Cooling System Kit Cooler
    		• 212.7825.65
  • KY-015 DHT11 Temperature Humidity Sensor Module For Arduino+ Arduino
    		• 199
  • SCREW 25XM4
    		• 40,10,4
  • NUT M4
    		• 40,050,2
  • white tube
    		• 122
  • power supply
    		• 11717
  • wires
    		• 133
  • Isolating material (spray foam)
    		• 177
  		• TOTAL COST97.6€

  • THERMOCYCLER

    • emperature range: 0 to 100ºC
    • Temperature ramp: 2ºC
    • Temperature max error: +-0.2ºC
    • Price 74.14

  • WHAT IS IT FOR IN OUR PROJECT

  • The thermocycler is a machine commonly used to amplify DNA, but it can be used as well in others reactions affected by temperature.

  • FUNCTION PRINCIPLE

  • The thermocycler has a thermal block where reaction tubes can be introduced in its pierced surface, and it raises and lowers the temperature of the block according to a preprogrammed temperature stages.

  • OUR RESULTS

  • We did a test that consist in generating the temperature cycles needed for a PCR. We obtained very good results, we did manage to get the temperature needed and also the time required. In the following graph we can see the temperature cycles:
  • However the PCR is a very sensitive process so although we have accomplished the temperature and time requirements we did not manage to make the PCR work. This can be caused for multiple factors. The most probable one is that the sensor we have is on the aluminium block so the temperature we measure is slightly different that the temperature inside the reaction tubes. A difference of a few degrees is crucial in a PCR, and can suppose the difference between a working PCR and a non.working PCR.
  • We are currently working in a program to estimate the temperature inside the reaction tubes.

  • KEY PARTS OF THIS MACHINE

  • Thermoblock: The thermoblock is made from aluminium plates. Aluminium was chosen due to its high thermal conductivity and its low thermal inertia. Since reaction tubes are meant to be placed here, it is critical that the tubes make a good contact with the thermoblock to prevent differences between the temperature of the block and the tube.
  • Peltier cell: The peltier will make the temperature variations in the thermoblock. The peltier is a electronical device able to produce heat or cold. On one hand, the peltier is easy to install in the thermoblock and has the ability of cooling. On the other hand, this device consumes a significant amount of power, so it will be necessary to have an electronic power driver which is hard to design. A peltier of at least 100W will be need in order to change the temperature satisfying the specifications. We choose a 150W peltier cell in order to have a security margin in the power specifications.

  • Heat sink: In order to get more efficiency from the peltier cell it will be needed a heat sink. The heat sink will keep one of the faces of the peltier cell to ambient temperature, this way the face that is in contact with the thermoblock will get heated or cooled easily. The heat sink is composed by a fan and an aluminium sink.

  • Temperature sensor: The temperature sensor will be crucial. It has to have a low error, lower than 0.5 ºC, high precision, and also it need to have a fast time response. We choosed the sensor LM35CA.

  • CIRCUIT

  • The circuit design realize three task: (1) lecture of temperature, (2) switch between heating or cooling state and (3) provides regulated power to the peltier.

  • In order to measure the temperature the sensor LM35CA is attach to the analog input of the Arduino
  • There are two relay that will change the way is connected the peltier cell. This way the peltier can be power with positive and negative voltage. The arduino does not have enough power to activate the relays so two channel N mosfet are used to provide the power.
  • A channel N mosfet is used to generate a PWM to regulate the power feeded to the peltier cell. This mosfet is controlled by a digital arduino pin.

  • CONTROL

  • A PID with a regulator has been design in order to control the temperature.This is extremely robust and it secure to get to the reference value of temperature in a low time.
  • However the dynamic response was poorly due to the influence of the ambient temperature. So an ambient temperature pre-alimentation has been designed and it has improve the dynamic response.

  • FUTURE LINES

  • The most difficult part of this machine is the thermoblock, it is hard to make it from aluminium plates. So a improve will consist to do a 3D model and then send it to fabricate in aluminium.
  • An other line,could consist in the improvement of the peltier power what would lead to a better thermal response, this will improve the efficiency of the thermocycler.

  • DOWNLOADS

  • Thermocycler Arduino Code

  • YOU WILL NEED

  • Mosfet N-Channel IRFZ44NPBF
    		• 31,624,86
  • PCB
    		• 17,187,18
  • Peltier Cell 110W MCTE1-12712L-S
    		• 118,8418,84
  • LM35CAH
    		• 116,0416,04
  • Relay +12V 15A
    		• 24,569,12
  • Resistor 4.7k 1/4W
    		• 30,020,06
  • Resistor 100k 1/4W
    		• 30,140,42
  • Power source +12V 250W
    		• 117,6217,62
  		• Total Cost74,14

  • LUMINOMETER

    • avelenght: 400 to 1000nm
    • Price: 24.3€

    WHAT IS IT FOR IN OUR PROJECT

  • The luminometer is designed in order to allow the detection of light produced by the some bioluminescent molecules such as luciferin/luciferase. Our gRNA Testing System enables the determination of the efficiency of a gRNA by observing the mutagenesis with a luminescence reporter.

  • FUNCTION PRINCIPLE

  • The samples emit bioluminescence with a wavelength between 400 and 600 nm. The light signal generated has very low power so a high sensitive sensor is needed. In addition, it is important to reduce external light that can influence the measures.

  • OUR RESULTS

  • With the design we proposed the external light was reduced to minimum values. But the problem was that the sensor chosen was not sensitive enough so we could not measure properly the bioluminescence generated.
  • We did a test with a positive control (35s:Luciferase:Tnos), a negative control (35s:Ga20oxPCR:AEK:Luc:Tnos-XT1) and empty. We did three measures of each sample.

  		• 35s:Luciferase:Tnos35s:Ga20oxPCR:AEK:Luc:Tnos-XT1empty
  • First Measure
    		• 313131
  • Second Measure
    		• 343235
  • Third Measure
    		• 323130

  • The units of this measures are pulses generated by the sensor (the sensor converts light into frequency) in ten seconds. If the sensor is exposed to ambient light a normal value is around 10.000. With the empty sample we prove that the external light is reduced to minimum around 30. However the positive control and the negative control have the same value as the empty sample, meaning that the sensor does not have enough sensibility to differentiate them.
  • The are more expensive (more that 100€) sensors with higher sensibility that will be able to measure the bioluminescence.
  • However, in order to use the testing system is necessary to measure three sample at the same time -negative control, positive control and sample-, that mean it is need to have three sensors. So if we use the expensive sensor will increase to much the final price of the labware and that will affect negatively the accessibility.
  • In conclusion we have tested different types of sensor but it is necessary to research more in order to find a sensor that is sensible enough and is low cost.

  • KEY PARTS OF THIS MACHINE

  • Structure: the structure of the luminometer one of the most important things. In this structure is where the sample tubes and the sensor will be placed. The structure has to be white in order to have a greater sensibility, this way the light will reflect in the inners walls of the structure so more light intensity will reach the sensor. However, if all the structure is white, external light will get across the walls and will reach the sensor, producing interferences in the signal measure. The solution is to cover or paint the external walls.
  • We have designed a 3D model structure that will accomplish all the specifications commented before.
  • Sensor: the sensor will measure the light intensity It is strictly necessary that the sensor works in wavelength from 300 to 600 nm. Moreover it will be also recommended that the sensor only measure in that wavelength, this way noise is reduced. We tested several photodiodes, but anyone could measure the bioluminescence properly. However the sensor TSL235R-LF perform good in terms of noise and stability in measures.

    • CIRCUIT

  • The circuit consist in the connection of the sensors TSL235R-LF to the Arduino Mega.

  • It is important that the sensor can only be attached to digital pins of the arduino which are associated with a interrupt line, because interruptions are needed in order to read the output of the sensors. Pins 18 , 19 and 20 can do interruptions in Arduino Mega. But in Arduino UNO only pins 2 and 3 can be used.

  • FUTURE LINES

  • It is necessary to test different types of sensor in order to find one that is sensitive enough and not expensive. There exist a type of photodiode, the photomultiplier. This type of sensor is high sensitive and is the typical used for luminometers, however the are quite expensive so the might not be the solution.

  • DOWNLOADS

  • Luminometer Arduino Code

  • YOU WILL NEED

  • MATERIALS
    		• UDCOST/unit €COST €
  • 3D printed structure
    		• 11515
  • TSL235R-LF
    		• 33,19,3
  		• Total Cost24,3

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