Difference between revisions of "Team:Aachen/Lab/Bioreactor/Hardware"

(Continous OD Device)
(Stirrer)
 
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=Overview=
 
=Overview=
One of the vital elements of a Do-It-Yourself bioreactor is the hardware design which should be feasible as well as reliable. The most important point to be kept in mind while constructing a bioreactor is the sterility. At every step of the development of the bioreactor, we have fulfilled this criteria.   
+
One of the vital elements of a Do-It-Yourself bioreactor is the hardware design which should be feasible as well as reliable. The most important point to be kept in mind while constructing a bioreactor is the sterility. At every step of the development of the bioreactor, we have fulfilled these criteria.   
  
 
{{Team:Aachen/ReadMore|title=Construction Manuals|link=/Team:Aachen/Notebook/Construction_Manuals|picture=rmConstruction|url=/wiki/images/1/15/Aachen_tile_Lab_Bioreactor_Hardware_construction_manuals.JPG}}
 
{{Team:Aachen/ReadMore|title=Construction Manuals|link=/Team:Aachen/Notebook/Construction_Manuals|picture=rmConstruction|url=/wiki/images/1/15/Aachen_tile_Lab_Bioreactor_Hardware_construction_manuals.JPG}}
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==Principle==
 
==Principle==
For our bioreactor, we need a peristaltic pump and it is necessary to use sterile tubings which requires the pumps to be assembled and disassembled in minimum possible time. Hence the pumps were built with different layers and a 3D structure that could be partly disassembled to position the tube. ??The tube was pressed between the 3D structure and the walls thereby generated the required pressure to pump the liquid from one side to another.??
+
For our bioreactor, we need a peristaltic pump and it is necessary to use sterile tubings which requires the pumps to be assembled and disassembled in minimum possible time. Hence the pumps were built with different layers and a 3D structure that could be partly disassembled to position the tube. The tube was pressed between the 3D structure and the walls thereby generated the required pressure to pump the liquid from one side to another.
  
 
A detailed construction manual is available at '''[[Team:Aachen/Notebook/Construction_Manuals/Pumps|pumps]]'''.
 
A detailed construction manual is available at '''[[Team:Aachen/Notebook/Construction_Manuals/Pumps|pumps]]'''.
  
 
=Stirrer=
 
=Stirrer=
{{Team:Aachen/Figure|Aachen_Reactor_Vortex.JPG|title=The vortex inside the reactor creator by our stirrer|subtitle=The stirring range is between 200 rpm and 1200 rpm|size=medium}}
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{{Team:Aachen/Figure|Aachen_Reactor_Vortex.JPG|title=The vortex inside the reactor created by our stirrer|subtitle=The stirring range is between 200 rpm and 1400 rpm|size=medium}}
  
 
We use a DC motor and a 3D printed structure holding 4 magnets as our stirrer. The Voltage to the circuit is controlled using Analog output values thus controlling the speed of the stirrer. The magnets are placed in such a way so that half of the structure is north and the other half is south. This increases the area of magnetism thus holding the stirrer firmly into its magnetic pull.
 
We use a DC motor and a 3D printed structure holding 4 magnets as our stirrer. The Voltage to the circuit is controlled using Analog output values thus controlling the speed of the stirrer. The magnets are placed in such a way so that half of the structure is north and the other half is south. This increases the area of magnetism thus holding the stirrer firmly into its magnetic pull.
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=Continous OD Device=
 
=Continous OD Device=
The
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How can we find out if there is really bacteria growing in our reactor? The common way is doing OD measurements. But if there is only 10 ml of reactor volume, every measurement would disturb the conditions drastically and thereby influence the experiment itself. Therefore, we are required to take minimum possible sample volume.
How can we find out if there is really bacteria growing in our reactor? The common way is doing OD measurements. But if there is only 10 ml of reactor volume, every measurement would disturb the conditions drastically and thereby influence the experiment itself.
+
  
 
{{Team:Aachen/Figure|Aachen_ODCloseup.jpg|title=Optical Density Measurement device|subtitle=As shown the transmitter and receiver are placed opposite sides of the tube|size=large}}
 
{{Team:Aachen/Figure|Aachen_ODCloseup.jpg|title=Optical Density Measurement device|subtitle=As shown the transmitter and receiver are placed opposite sides of the tube|size=large}}
  
  
It is most important that the samples are taken sterile. Furthermore the OD should be measured automatically so that the experiment can run without the need of a person taking samples. Finally the device to measure to OD has to be cheap and easy to assemble while having a precision to compete with commercial spectrometers.  
+
It is also important that the samples are taken in a sterile manner. Furthermore the OD should be measured automatically so that the experiment can run without the need of a person taking samples. Finally the device to measure to OD has to be cheap and easy to assemble while having a precision to compete with commercial spectrometers.  
  
  
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Light with a wavelength of 605 nm is emitted by a LED and shines through the medium. On the other side we have a phototransister to measure the intensity of the light reaching through the sample, therefore we use a TSL 235 R, a special transitor converting light to frequency.  
+
Light having wavelength 605 nm is emitted by a LED and is emitted in the medium. On the opposite side, we have a phototransistor to measure the intensity of the light reaching it, through the sample.  
We have developed on iGEM Aachen 2014 OD device measurement principle to get live data, and built using optimum materials, along with use of calibration file to get as precise value as possible.
+
We have developed on iGEM Aachen 2014 OD device measurement principle to get live data, and built a device using optimum materials, along with use of calibration file to get as precise values as possible.
 +
 
 +
To obtain the cell concentration in the medium, a special transistor that converts light to frequency, TSL 235R<ref>http://www.ti.com/lit/ds/symlink/tsl235.pdf</ref>, is used.  
  
 
To keep the whole measurement sterile, the medium with the bacteria flows through silicon tubes and a transparent glass structure through the device without getting in contact with the surrounding air, while the device itself is mounted around this tube.
 
To keep the whole measurement sterile, the medium with the bacteria flows through silicon tubes and a transparent glass structure through the device without getting in contact with the surrounding air, while the device itself is mounted around this tube.
 
  
 
A detailed construction manual is available at '''[[Team:Aachen/Notebook/Construction_Manuals/Biomass_Sensor|biomass sensor]]'''.
 
A detailed construction manual is available at '''[[Team:Aachen/Notebook/Construction_Manuals/Biomass_Sensor|biomass sensor]]'''.
  
  
 
+
To test if our continuous OD device can also be used to monitor batch fermentations, we set up a simple batch culture. We used a preculture of ''Eschererichia&nbsp;coli'' BL21 Gold (DE3) with plasmid pSB1KRDP in M9 medium with 40&nbsp;mM glucose that was grown in a stirred flask. A pump was used to cycle the culture from the vessel through the continuous OD sensor and back into the vessel. This setup was far from being perfect from a bioprocess perspective, but the goal of this experiment was testing the OD sensor and not the generation of biologically relevant samples.
To test if our continuous OD device can also be used to monitor batch fermentations, we set up a simple batch culture. We used a preculture of #RP1O# and M9 medium with 40 mM glucose that was grown in a stirred flask. The continuous OD sensor was attached right above the flask and a pump was used to cycle culture from the vessel through the sensor and back into the vessel. This setup was far away from perfect from a bioprocess perspective, but the goal of this experiment was testing the OD sensor and not the generation of biologically relevant samples.
+
  
 
{{Team:Aachen/Figure|Aachen_OnlineOD.png|title=Growth Curve Recorded with our Online OD Unit|subtitle=The growth rate is smoothed with a moving average over 150 data points.|size=large}}
 
{{Team:Aachen/Figure|Aachen_OnlineOD.png|title=Growth Curve Recorded with our Online OD Unit|subtitle=The growth rate is smoothed with a moving average over 150 data points.|size=large}}
 +
 +
As shown in the figure above, our DIY online OD sensor capable of recording growth curves at a very high resolution. By building multiple sensor units it is certainly possible to increase the throughput and data quality of strain characterization experiments.
  
 
=Assembly=
 
=Assembly=
The assembly of the bioreactor electronics was the biggest challenge that we faced. Each device had a pin protocol which was maintained and tagged to the controling firmware. The assembled final firmware had to be checked and rechecked to compromise between each of the seperated devices. Finally we came up with idea of not using delays and using counters in our firmware to make it look easy and compatible to all components.
+
The assembly of the bioreactor electronics was the biggest challenge that we faced. Each device had a defined pin protocol which was required to be maintained and tagged to the controlling firmware.  
  
=Outlook=
 
  
Since in the current version of our project all digital ports of the Arduino Uno are in use, for future designs it will be necessary to change to a bigger controller, for example an Arduino Mega.
+
=Outlook=
  
 +
Since the current version of our project uses all digital ports of the Arduino Uno, it will be necessary to change to a bigger controller, for example an Arduino Mega, for future designs.
  
Then it will be possible to include further analysis units. We allready took some steps towards an offgas analysis with CO{{sub|2}} and O{{sub|2}} sensors, and CH{{sub|X}} analysis would be interesting for many experiments. An integration of these components would be very easy. Even more we cooperated with a local community lab, the Technik Garage, who developed a pumping and heating system for the water bath for us. To include this in the whole system had given us much more parameters to control the experiment.
 
  
 +
Then it will be possible to include further analysis units. We already took some steps towards an offgas analysis with CO{{sub|2}} and O{{sub|2}} sensors, and CH{{sub|X}} analysis could be interesting for various other experiments. An integration of these components would be easy. Furthermore we cooperated with a community lab, the Technik Garage, who developed a pumping and heating system for the water bath for us. To include this in the whole system had given us many more parameters to control the experiment.
  
Biological experiments often run far more than a week. It can be very time-consuming to have a look at the experiment al the time. Therefore it would be comfortable to control your experiments via a local net or even the Internet. Imagine lying on a meadow in summer with a cool drink at hand and checking the OD instead of going to the lab every time.
 
  
 +
Biological experiments often run for more than a week. It is time-consuming to monitor the experiment all the time. It would be the most convenient to control your experiments via a local net or even the Internet. Imagine lying on a meadow in summer with a cool drink in your hand and while you check the OD instead of visiting the lab just to take a sample.
  
It is obvious that there are many challenges to work on with even more opportunities. Hence the modularity and open source features of our system serve as a platform for future developments.  
+
As the number of opportunities increase, so do the challenges. Hence the modularity and open source features of our system serve as a platform for future development.  
  
 
=References=
 
=References=

Latest revision as of 15:58, 5 October 2015


Overview

One of the vital elements of a Do-It-Yourself bioreactor is the hardware design which should be feasible as well as reliable. The most important point to be kept in mind while constructing a bioreactor is the sterility. At every step of the development of the bioreactor, we have fulfilled these criteria.

Key Achievements

  • design and characterization of DIY peristaltic pumps with a dynamic range of 0.5-1400 ml/h
  • development of a semi-continuous OD measurement unit
  • calibrated magnetic stirring from 100-1400 rpm
  • integrated circuit for controlling three pumps and stirring
  • designed DIY constructions to hold circuit, pumps and bioreactor setup
  • parallelization of multiple reactor control units
  • characterization of DIY chemostat bioreactors

Pumps

We built upon a design from thingyverse [1] that uses a 4-wired NEMA 17 stepper motor with 1.8 °/step to construct a peristaltic pump. The original design however did not fit our requirement of sterile assembly, because the tubing was pushed through a hole in a 3D-printed structure. Using Autodesk Inventor, we designed a different structure to accomodate rapid prototyping and sterile assembly.

Aachen PumpConstruct7.jpg
DIY Pump
Fully Assembled Pump in Motion.

Principle

For our bioreactor, we need a peristaltic pump and it is necessary to use sterile tubings which requires the pumps to be assembled and disassembled in minimum possible time. Hence the pumps were built with different layers and a 3D structure that could be partly disassembled to position the tube. The tube was pressed between the 3D structure and the walls thereby generated the required pressure to pump the liquid from one side to another.

A detailed construction manual is available at pumps.

Stirrer

Aachen Reactor Vortex.JPG
The vortex inside the reactor created by our stirrer
The stirring range is between 200 rpm and 1400 rpm

We use a DC motor and a 3D printed structure holding 4 magnets as our stirrer. The Voltage to the circuit is controlled using Analog output values thus controlling the speed of the stirrer. The magnets are placed in such a way so that half of the structure is north and the other half is south. This increases the area of magnetism thus holding the stirrer firmly into its magnetic pull. Contruction Manual can be found on stirrer.

Continous OD Device

How can we find out if there is really bacteria growing in our reactor? The common way is doing OD measurements. But if there is only 10 ml of reactor volume, every measurement would disturb the conditions drastically and thereby influence the experiment itself. Therefore, we are required to take minimum possible sample volume.

Aachen ODCloseup.jpg
Optical Density Measurement device
As shown the transmitter and receiver are placed opposite sides of the tube


It is also important that the samples are taken in a sterile manner. Furthermore the OD should be measured automatically so that the experiment can run without the need of a person taking samples. Finally the device to measure to OD has to be cheap and easy to assemble while having a precision to compete with commercial spectrometers.


Measurement Principle

Light having wavelength 605 nm is emitted by a LED and is emitted in the medium. On the opposite side, we have a phototransistor to measure the intensity of the light reaching it, through the sample. We have developed on iGEM Aachen 2014 OD device measurement principle to get live data, and built a device using optimum materials, along with use of calibration file to get as precise values as possible.

To obtain the cell concentration in the medium, a special transistor that converts light to frequency, TSL 235R[2], is used.

To keep the whole measurement sterile, the medium with the bacteria flows through silicon tubes and a transparent glass structure through the device without getting in contact with the surrounding air, while the device itself is mounted around this tube.

A detailed construction manual is available at biomass sensor.


To test if our continuous OD device can also be used to monitor batch fermentations, we set up a simple batch culture. We used a preculture of Eschererichia coli BL21 Gold (DE3) with plasmid pSB1KRDP in M9 medium with 40 mM glucose that was grown in a stirred flask. A pump was used to cycle the culture from the vessel through the continuous OD sensor and back into the vessel. This setup was far from being perfect from a bioprocess perspective, but the goal of this experiment was testing the OD sensor and not the generation of biologically relevant samples.

Aachen OnlineOD.png
Growth Curve Recorded with our Online OD Unit
The growth rate is smoothed with a moving average over 150 data points.

As shown in the figure above, our DIY online OD sensor capable of recording growth curves at a very high resolution. By building multiple sensor units it is certainly possible to increase the throughput and data quality of strain characterization experiments.

Assembly

The assembly of the bioreactor electronics was the biggest challenge that we faced. Each device had a defined pin protocol which was required to be maintained and tagged to the controlling firmware.


Outlook

Since the current version of our project uses all digital ports of the Arduino Uno, it will be necessary to change to a bigger controller, for example an Arduino Mega, for future designs.


Then it will be possible to include further analysis units. We already took some steps towards an offgas analysis with CO2 and O2 sensors, and CHX analysis could be interesting for various other experiments. An integration of these components would be easy. Furthermore we cooperated with a community lab, the Technik Garage, who developed a pumping and heating system for the water bath for us. To include this in the whole system had given us many more parameters to control the experiment.


Biological experiments often run for more than a week. It is time-consuming to monitor the experiment all the time. It would be the most convenient to control your experiments via a local net or even the Internet. Imagine lying on a meadow in summer with a cool drink in your hand and while you check the OD instead of visiting the lab just to take a sample.

As the number of opportunities increase, so do the challenges. Hence the modularity and open source features of our system serve as a platform for future development.

References

  1. http://www.thingiverse.com/thing:642192
  2. http://www.ti.com/lit/ds/symlink/tsl235.pdf