Team:Valencia UPV/Hardware
- 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.
DOWNLOADS
General Case Assembly
Layout Assembly
CAD 3D models
All sketches
| Parts | Unit | COST/unit € | COST € |
|---|---|---|---|
| Structure | 1 | 285 | 285 |
| Electroporator | 1 | 57,07 | 57,07 |
| Colorimeter | 1 | 26,2 | 26,2 |
| Centrifuge | 1 | 56 | 56 |
| Electrophoresis | 1 | 66,07 | 66,07 |
| Stirrer | 1 | 81,24 | 81,24 |
| Fitotron | 1 | 97,6 | 97,6 |
| Thermocycler | 1 | 74,14 | 74,14 |
| Luminometer | 1 | 24,3 | 24,3 |
| TOTAL COST | 767,62€ |
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.
DOWNLOADS
Case Short Pilar
Case Long Down
Case Short Up
Aluminum Structure Assembly
Case Bottom Assembly
YOU WILL NEED
| MATERIALS | UNIT | COST/unit € | COST € |
|---|---|---|---|
| Aluminium structure | 1 | 130 | 130 |
| Power supply +wire+plug | 1 | 17 | 20 |
| Methacrylate parts | 1 | 90 | 90 |
| Screen | 1 | 9 | 9 |
| Arduino Mega | 1 | 16 | 16l |
| general wires | 1 | 12 | 12 |
| screen holder | 1 | 7 | 7 |
| screws 20xM4 | 20 | 0.05 | 1 |
| TOTAL COST | 285€ |
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
Electroporator Cuvette Holder
Electroporator
Assembly[Electroporator Assembly path:
https://static.igem.org/mediawiki/2016/3/3a/T--Valencia_UPV--11plano.pdf
YOU WILL NEED
| MATERIALS | UNIT | COST/unit€ | COST € |
|---|---|---|---|
| Mosfet N-Channel C2M1000170D | 1 | 5,32 | 5,32 |
| Mosfet N-Channel IRFZ44NPBF | 1 | 1,62 | 1,62 |
| High voltage DC-DC boost converter 5-12V to 300-1200V | 2 | 9,17 | 18,34 |
| High Voltage Capacitor 1,6kV 1uF | 1 | 8,05 | 8,05 |
| PCB | 1 | 7,18 | 7,18 |
| Resistor 30k 600mW | 1 | 0,06 | 0,06 |
| Resistor 15M 500mW | 1 | 1,32 | 1,32 |
| Resistor 22k 3W | 1 | 0,18 | 0,18 |
| Cuvette Holder (3D printed) | 1 | 15 | 15 |
| Screw 25XM4 | 2 | 0,1 | 0,2 |
| Nut M4 | 4 | 0,05 | 0,2 |
| Copper plate 5x15mm | 2 | 0,1 | 0,2 |
| Total Cost | 57,07€ |
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.
YOU WILL NEED
| MATERIALS | UNIT | COST/unit € | COST € |
|---|---|---|---|
| TUBE HOLDER | 1 | 15 | 15 |
| LASER- Red point laser 650nm | 1 | 7,5 | 7,5 |
| TSL235R-LF | 1 | 3,1 | 3,1 |
| SCREW 25XM4 | 4 | 0,1 | 0,4 |
| NUT M4 | 4 | 0,05 | 0,2 |
| TOTAL COST | 26.2€ |
CENTRIFUGE
https://static.igem.org/mediawiki/2016/e/ee/T--Valencia_UPV--8centrifuga.jpg
- 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
YOU WILL NEED
| MATERIALS | UNIT | COST/unit € | COST € |
|---|---|---|---|
| Motor 1400 kV + ESC 30A | 1 | 16,61 | 16,61 |
| Encoder Kit | 1 | 5,11 | 5,11 |
| Power Source | 1 | 17,62 | 17,62 |
| Screw 4Mx15 | 4 | 0,05 | 0,2 |
| Nut 4M | 4 | 0,05 | 0,2 |
| Rotor 3D printed | 1 | 15 | 15 |
| Tachometer Module for Arduino | 1 | 1,28 | 1,28 |
| TOTAL COST | 56,0€ |
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
YOU WILL NEED
| MATERIALS | UD | COST/unit € | COST € |
|---|---|---|---|
| Electrophoresis cuvette 3D printed | 1 | 30 | 30 |
| Power source 48V 25W | 1 | 16,5 | 16,5 |
| Banana male connector | 2 | 1,3 | 2,6 |
| Banana female connector | 2 | 1,01 | 2,02 |
| Platinum coated wire 30 cm | 1 | 5 | 5 |
| UV torch 4W | 1 | 9,95 | 9,95 |
| Total Cost | 66,07€ |
STIRRER WITH CONTROLLED TEMPERATURE
- This 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.
YOU WILL NEED
| MATERIALS | UD | COST/unit € | COST € |
|---|---|---|---|
| 3d printed pieces | 1 | 20 | 20 |
| nema 17+ driver a4988 | 1 | 20 | 20 |
| Mosfet N-Channel IRFZ44NPBF | 1 | 1,62 | 1.62 |
| PCB | 1 | 7,18 | 7,18 |
| Peltier Cell 110W MCTE1-12712L-S | 1 | 18,84 | 18,84 |
| LM35 | 1 | 4 | 4 |
| Relay +12V 15A | 2 | 4,56 | 9,12 |
| Resistor 4.7k 1/4W | 3 | 0,02 | 0,06 |
| Resistor 100k 1/4W | 3 | 0,14 | 0,42 |
| TOTAL COST | 81.24€ |
PHYTOTRON
- This 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
YOU WILL NEED
| MATERIALS | UD | COST/unit € | COST € |
|---|---|---|---|
| led white light | 1 | 15 | 15 |
| Box | 1 | 45 | 45 |
| TEC1-12706 Thermoelectric PeltierRefrigeration Cooling System Kit Cooler | 2 | 12.78 | 25.65 |
| KY-015 DHT11 Temperature Humidity Sensor Module For Arduino+ Arduino | 1 | 9 | 9 |
| SCREW 25XM4 | 4 | 0,1 | 0,4 |
| NUT M4 | 4 | 0,05 | 0,2 |
| white tube | 1 | 2 | 2 |
| power supply | 1 | 17 | 17 |
| wires | 1 | 3 | 3 |
| Isolating material (spray foam) | 1 | 7 | 7 |
| TOTAL COST | 97.6€ |
THERMOCYCLER
- Temperature 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.
YOU WILL NEED
| Mosfet N-Channel IRFZ44NPBF | 3 | 1,62 | 4,86 |
|---|---|---|---|
| PCB | 1 | 7,18 | 7,18 |
| Peltier Cell 110W MCTE1-12712L-S | 1 | 18,84 | 18,84 |
| LM35CAH | 1 | 16,04 | 16,04 |
| Relay +12V 15A | 2 | 4,56 | 9,12 |
| Resistor 4.7k 1/4W | 3 | 0,02 | 0,06 |
| Resistor 100k 1/4W | 3 | 0,14 | 0,42 |
| Power source +12V 250W | 1 | 17,62 | 17,62 |
| Total Cost | 74,14€ |
LUMINOMETER
- Wavelenght: 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:Tnos | 35s:Ga20oxPCR:AEK:Luc:Tnos-XT1 | empty tube | |
|---|---|---|---|
| First Measure | 31 | 31 | 31 |
| Second Measure | 34 | 32 | 35 |
| Third Measure | 32 | 31 | 30 |
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
YOU WILL NEED
| MATERIALS | UD | COST/unit € | COST € |
|---|---|---|---|
| 3D printed structure | 1 | 15 | 15 |
| TSL235R-LF | 3 | 3,1 | 9,3 |
| Total Cost | 24,3€ |
