Difference between revisions of "Team:Bielefeld-CeBiTec/Hardware"

Line 69: Line 69:
 
The task of scavenging metal ions from MD poses a great challenge to conventional cultivation strategies. Not only is the MD toxic to cells due to its elevated concentrations of sodium chloride and heavy metal ions like iron and copper. The shear amount of MD which has to be processed poses a problem in its own right. We tackle the toxic effects of heavy metals by our <a href="https://2018.igem.org/Team:Bielefeld-CeBiTec/Toxicity_Theory">approach</a> on anti-oxidants and anti-toxic measures leading to an improved cell viability.</br>
 
The task of scavenging metal ions from MD poses a great challenge to conventional cultivation strategies. Not only is the MD toxic to cells due to its elevated concentrations of sodium chloride and heavy metal ions like iron and copper. The shear amount of MD which has to be processed poses a problem in its own right. We tackle the toxic effects of heavy metals by our <a href="https://2018.igem.org/Team:Bielefeld-CeBiTec/Toxicity_Theory">approach</a> on anti-oxidants and anti-toxic measures leading to an improved cell viability.</br>
 
To solve the problem of the large MD volume that has to be processed and, after our first assessment indicated that cultivating cells in such a large volume would be difficult and further complicate downstream processing (e.g. filtering of the biomass), we decided to construct a suitable hardware. Therefore, we designed a prototype for a customized cross-flow bioreactor adapted to the task of filtering large quantities of MD. The system comprises two core units: A reaction chamber for containing the cells (“reactor unit”) and a larger reservoir area providing mining drainage (“reservoir unit”) (figure 1).</br>
 
To solve the problem of the large MD volume that has to be processed and, after our first assessment indicated that cultivating cells in such a large volume would be difficult and further complicate downstream processing (e.g. filtering of the biomass), we decided to construct a suitable hardware. Therefore, we designed a prototype for a customized cross-flow bioreactor adapted to the task of filtering large quantities of MD. The system comprises two core units: A reaction chamber for containing the cells (“reactor unit”) and a larger reservoir area providing mining drainage (“reservoir unit”) (figure 1).</br>
−
Bild des Prototypen einfügen
+
<figure role="group">
 +
                      <img class="figure hundred" src="https://static.igem.org/mediawiki/2018/d/db/T--Bielefeld-CeBiTec--jr--Bioreactor.png">
 +
                      <figcaption>
 +
                          <b>Figure 1:</b> Prototype of the first bioreactor.
 +
                      </figcaption>
 +
                  </figure></br>
 
The core units are connected by silicon tubes. The reactor unit is charged with genetically engineered <i>Escherichia coli</i> cells able to scavenge metal ions from the MD. Homogeneity is guaranteed by usage of a stir bar simulating a stirrer. The high concentration of bacterial cells is maintained by applying a filter membrane system to each port, preventing any living organism from the MD to contaminate the reaction unit or the <i>E. coli</i> cells to leave the reactor unit. Possible blocking of the membrane system because of filter cake could simply be prevented by reversing the flow direction. This is enabled by using a peristaltic pump with reversible pumping direction per tube. After the desired incubation time of the cells with the substrate medium, the cells in the reactor unit can be harvested by usage of the other two ports to the reactor unit.</br>
 
The core units are connected by silicon tubes. The reactor unit is charged with genetically engineered <i>Escherichia coli</i> cells able to scavenge metal ions from the MD. Homogeneity is guaranteed by usage of a stir bar simulating a stirrer. The high concentration of bacterial cells is maintained by applying a filter membrane system to each port, preventing any living organism from the MD to contaminate the reaction unit or the <i>E. coli</i> cells to leave the reactor unit. Possible blocking of the membrane system because of filter cake could simply be prevented by reversing the flow direction. This is enabled by using a peristaltic pump with reversible pumping direction per tube. After the desired incubation time of the cells with the substrate medium, the cells in the reactor unit can be harvested by usage of the other two ports to the reactor unit.</br>
 
However, after performing several tests we concluded that this prototype does not work the way it is intended to. Due to the speed of cells plugging the membrane filter system, it was not be possible to cycle the whole content of the reservoir unit through the system. The substrate medium was pumped in the reverse direction. However, since this event occurred rather quickly, only a small quantity of the MD was used for the incubation, leading to an incomplete process and limiting the yield. Therefore, we came up with a new design for the improvement of the desired cross-flow bioreactor. The basic design is maintained while substantial changes have been introduced to the reactor unit, in particular the filter membrane system.</br>
 
However, after performing several tests we concluded that this prototype does not work the way it is intended to. Due to the speed of cells plugging the membrane filter system, it was not be possible to cycle the whole content of the reservoir unit through the system. The substrate medium was pumped in the reverse direction. However, since this event occurred rather quickly, only a small quantity of the MD was used for the incubation, leading to an incomplete process and limiting the yield. Therefore, we came up with a new design for the improvement of the desired cross-flow bioreactor. The basic design is maintained while substantial changes have been introduced to the reactor unit, in particular the filter membrane system.</br>
−
Bild des neuen Reaktors einfügen
+
<figure role="group">
 +
                      <img class="figure hundred" src="https://static.igem.org/mediawiki/2018/6/6c/T--Bielefeld-CeBiTec--jr--Bioreactor2.png">
 +
                      <figcaption>
 +
                          <b>Figure 2</b> Screenshot of the model on the improved bioreactor with adjustments for a settler system, a double jacket for isothermal cultivation and adjustments of the form to enable easier oxygenation.ments for a settler system, a double jacket for isothermal cultivation and adjustments of the form to enable easier oxygenation. The model was created using FreeCAD.
 +
                    </figcaption>
 +
                  </figure></br>
 
The filter system has been replaced by a favorable settler. This system is not only more cost-efficient in comparison to an expensive filter membrane system, it also enables the easy performable return of cells to the reactor unit without the risk of forming a filter cake. Cells leaving the reactor unit are intercepted by the settler based on the phenomenon of sedimentation. A glass hopper serves as a settler. If the cells sediment to the ground of the hopper, pressure is applied using a common syringe to pump sterile air into the settler system. The pressure applied by the syringe forces the accumulated biomass back into the reactor unit allowing to maximize the yield. Furthermore, an increase in nanoparticle formation was <a href="https://2018.igem.org/Team:Bielefeld-CeBiTec/Model">modeled</a> by applying the van't Hoff equation. Therefore, the temperature of the reactor unit was adjusted to 37 °C using a double jacket plugged to a thermostat. Previously, the process occurred at room temperature. However, since <i>E. coli</i> exhibits the greatest activity at 37 °C, it is favorable to adjust the temperature to its needs. Control over the temperature is essential for process optimization. A conical form of the reactor unit improves the oxygenation of the culture. The whole system can be autoclaved.</br>
 
The filter system has been replaced by a favorable settler. This system is not only more cost-efficient in comparison to an expensive filter membrane system, it also enables the easy performable return of cells to the reactor unit without the risk of forming a filter cake. Cells leaving the reactor unit are intercepted by the settler based on the phenomenon of sedimentation. A glass hopper serves as a settler. If the cells sediment to the ground of the hopper, pressure is applied using a common syringe to pump sterile air into the settler system. The pressure applied by the syringe forces the accumulated biomass back into the reactor unit allowing to maximize the yield. Furthermore, an increase in nanoparticle formation was <a href="https://2018.igem.org/Team:Bielefeld-CeBiTec/Model">modeled</a> by applying the van't Hoff equation. Therefore, the temperature of the reactor unit was adjusted to 37 °C using a double jacket plugged to a thermostat. Previously, the process occurred at room temperature. However, since <i>E. coli</i> exhibits the greatest activity at 37 °C, it is favorable to adjust the temperature to its needs. Control over the temperature is essential for process optimization. A conical form of the reactor unit improves the oxygenation of the culture. The whole system can be autoclaved.</br>
 
In order to promote the thought of open source and public accessibility we provide the scientific community with a construction plan for 3D printing both reactor units using the freeware FreeCAD. The production takes approximately eight hours using a 3D printer. Since the favored printing material polylactic acid (PLA) costs around 0.5 USD per cm<sup>3</sup>, reconstructing the reactor unit is cheap. Several components of the system can be produced using PLA although using glass is possible as well. Cell retainment in the reactor unit saves time and reduces costs as working procedures to separate the cells from the medium become no longer necessary. Silicon tubes can be acquired for 0.88 USD per meter, peristaltic pumps for less than 177 USD, yielding a total cost of less than 360 USD for the complete reactor.
 
In order to promote the thought of open source and public accessibility we provide the scientific community with a construction plan for 3D printing both reactor units using the freeware FreeCAD. The production takes approximately eight hours using a 3D printer. Since the favored printing material polylactic acid (PLA) costs around 0.5 USD per cm<sup>3</sup>, reconstructing the reactor unit is cheap. Several components of the system can be produced using PLA although using glass is possible as well. Cell retainment in the reactor unit saves time and reduces costs as working procedures to separate the cells from the medium become no longer necessary. Silicon tubes can be acquired for 0.88 USD per meter, peristaltic pumps for less than 177 USD, yielding a total cost of less than 360 USD for the complete reactor.

Revision as of 22:11, 17 October 2018

Hardware

Printing Electronics

Printing electronics is a recent development whereby metal nanoparticles are mixed with organic solvents to form an ink that can be deposited in thin layers on various surfaces with inkjet printers or other printing techniques.

Design of a Cross-flow Bioreactor

We designed a cross-flow bioreactor perfectly adapted to filtering heavy metals out of mining drainage (MD) using genetically engineered Escherichia coli. Bacteria are retained in a reaction chamber while a large volume gets pumped through the chamber. The cells take up the heavy metals leading to an intracellular accumulation. The application was improved by user feedback and modeling and is now easy to run. It can easily be reconstructed by using the building plans we offer in our wiki. Furthermore, our device tackles the difficulty of applying GMOs to extract valuables out of large volumes and enables the safe application of GMOs outside the laboratory.
The task of scavenging metal ions from MD poses a great challenge to conventional cultivation strategies. Not only is the MD toxic to cells due to its elevated concentrations of sodium chloride and heavy metal ions like iron and copper. The shear amount of MD which has to be processed poses a problem in its own right. We tackle the toxic effects of heavy metals by our approach on anti-oxidants and anti-toxic measures leading to an improved cell viability.
To solve the problem of the large MD volume that has to be processed and, after our first assessment indicated that cultivating cells in such a large volume would be difficult and further complicate downstream processing (e.g. filtering of the biomass), we decided to construct a suitable hardware. Therefore, we designed a prototype for a customized cross-flow bioreactor adapted to the task of filtering large quantities of MD. The system comprises two core units: A reaction chamber for containing the cells (“reactor unit”) and a larger reservoir area providing mining drainage (“reservoir unit”) (figure 1).
Figure 1: Prototype of the first bioreactor.

The core units are connected by silicon tubes. The reactor unit is charged with genetically engineered Escherichia coli cells able to scavenge metal ions from the MD. Homogeneity is guaranteed by usage of a stir bar simulating a stirrer. The high concentration of bacterial cells is maintained by applying a filter membrane system to each port, preventing any living organism from the MD to contaminate the reaction unit or the E. coli cells to leave the reactor unit. Possible blocking of the membrane system because of filter cake could simply be prevented by reversing the flow direction. This is enabled by using a peristaltic pump with reversible pumping direction per tube. After the desired incubation time of the cells with the substrate medium, the cells in the reactor unit can be harvested by usage of the other two ports to the reactor unit.
However, after performing several tests we concluded that this prototype does not work the way it is intended to. Due to the speed of cells plugging the membrane filter system, it was not be possible to cycle the whole content of the reservoir unit through the system. The substrate medium was pumped in the reverse direction. However, since this event occurred rather quickly, only a small quantity of the MD was used for the incubation, leading to an incomplete process and limiting the yield. Therefore, we came up with a new design for the improvement of the desired cross-flow bioreactor. The basic design is maintained while substantial changes have been introduced to the reactor unit, in particular the filter membrane system.
Figure 2 Screenshot of the model on the improved bioreactor with adjustments for a settler system, a double jacket for isothermal cultivation and adjustments of the form to enable easier oxygenation.ments for a settler system, a double jacket for isothermal cultivation and adjustments of the form to enable easier oxygenation. The model was created using FreeCAD.

The filter system has been replaced by a favorable settler. This system is not only more cost-efficient in comparison to an expensive filter membrane system, it also enables the easy performable return of cells to the reactor unit without the risk of forming a filter cake. Cells leaving the reactor unit are intercepted by the settler based on the phenomenon of sedimentation. A glass hopper serves as a settler. If the cells sediment to the ground of the hopper, pressure is applied using a common syringe to pump sterile air into the settler system. The pressure applied by the syringe forces the accumulated biomass back into the reactor unit allowing to maximize the yield. Furthermore, an increase in nanoparticle formation was modeled by applying the van't Hoff equation. Therefore, the temperature of the reactor unit was adjusted to 37 °C using a double jacket plugged to a thermostat. Previously, the process occurred at room temperature. However, since E. coli exhibits the greatest activity at 37 °C, it is favorable to adjust the temperature to its needs. Control over the temperature is essential for process optimization. A conical form of the reactor unit improves the oxygenation of the culture. The whole system can be autoclaved.
In order to promote the thought of open source and public accessibility we provide the scientific community with a construction plan for 3D printing both reactor units using the freeware FreeCAD. The production takes approximately eight hours using a 3D printer. Since the favored printing material polylactic acid (PLA) costs around 0.5 USD per cm3, reconstructing the reactor unit is cheap. Several components of the system can be produced using PLA although using glass is possible as well. Cell retainment in the reactor unit saves time and reduces costs as working procedures to separate the cells from the medium become no longer necessary. Silicon tubes can be acquired for 0.88 USD per meter, peristaltic pumps for less than 177 USD, yielding a total cost of less than 360 USD for the complete reactor.
Raut, N. C., & Al-Shamery, K. (2018). Inkjet printing metals on flexible materials for plastic and paper electronics. Journal of Materials Chemistry C, 6(7), 1618-1641.