Difference between revisions of "Team:NUS Singapore-A/Hardware/CoJar"
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| − | <h1>Fermentation Chamber | + | <h1>Fermentation Chamber</h1> |
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<p>The fermentation chamber contains the bacterial culture. It also comes with a cover designed to include a means of illuminating the chamber’s contents. </p> | <p>The fermentation chamber contains the bacterial culture. It also comes with a cover designed to include a means of illuminating the chamber’s contents. </p> | ||
| − | + | <h2>Design - Innovation!</h2> | |
| − | + | ||
| − | <h2>Design</h2> | + | |
<p>We selected components of the fermentation chamber based on whether they were easily obtainable and modifiable. This was because it was difficult to fabricate a cylindrical, watertight chamber using conventional methods of prototyping such as laser cutting and 3D printing. Rather than spend time attempting to manufacture a suitable container from scratch, we looked to modifying existing commercial, easily obtainable products. This also makes it easier for others to make their own bioreactor based on our work.</p> | <p>We selected components of the fermentation chamber based on whether they were easily obtainable and modifiable. This was because it was difficult to fabricate a cylindrical, watertight chamber using conventional methods of prototyping such as laser cutting and 3D printing. Rather than spend time attempting to manufacture a suitable container from scratch, we looked to modifying existing commercial, easily obtainable products. This also makes it easier for others to make their own bioreactor based on our work.</p> | ||
<br> | <br> | ||
| − | < | + | <button class="accordion">CONTAINER</button> |
| + | <div class="panel"> | ||
<p>We decided on a suitable working volume for our bioreactor based on literature review<sup>[1]</sup>. Possible working volumes suitable for the laboratory ranged from 0.5 L to 2 L. After discussion, we decided that 0.5 L would be a manageable volume. We hypothesized that this volume was sufficient for us to demonstrate proof-of-concept. It is also more portable.</p> | <p>We decided on a suitable working volume for our bioreactor based on literature review<sup>[1]</sup>. Possible working volumes suitable for the laboratory ranged from 0.5 L to 2 L. After discussion, we decided that 0.5 L would be a manageable volume. We hypothesized that this volume was sufficient for us to demonstrate proof-of-concept. It is also more portable.</p> | ||
<p>A bail jar from IKEA was repurposed for this. Discarding the original glass cover, we retained the rubber ring and two-part wire clasp.</p> | <p>A bail jar from IKEA was repurposed for this. Discarding the original glass cover, we retained the rubber ring and two-part wire clasp.</p> | ||
| − | < | + | <button class="accordion-closer">CLOSE</button> |
| + | </div> | ||
| − | < | + | <button class="accordion">COVER</button> |
| + | <div class="panel"> | ||
<p>We opted not to use the original cover because we knew we would have to perforate it to accommodate tubing. Drilling would generate many points of failure. For example, the glass cover might shatter from the stress, it is challenging to control the accuracy of our drilling, and drilling may not be able to provide the required precision.</p> | <p>We opted not to use the original cover because we knew we would have to perforate it to accommodate tubing. Drilling would generate many points of failure. For example, the glass cover might shatter from the stress, it is challenging to control the accuracy of our drilling, and drilling may not be able to provide the required precision.</p> | ||
| − | <p>We thus retrofitted our own lasercut Plexiglass cover. This allowed us greater flexibility to explore potential sensing modules and components we intended to add to our system. Considered, but eventually discarded, were modules like a pH meter, as we decided to focus on other metrics to indicate cell stress (See <a href="https://2018.igem.org/Team:NUS_Singapore-A/Design#SRM">Design: Stress Reporter</a>). Eventually, we decided to have 4 small holes, through which acrylic/glass tubes with outer diameters of 6 mm should be inserted, and 2 large holes, to each fit a test tube (Figure 1).</p> | + | <p>We thus retrofitted our own lasercut Plexiglass cover. This allowed us greater flexibility to explore potential sensing modules and components we intended to add to our system. Considered, but eventually discarded, were modules like a pH meter, as we decided to focus on other metrics to indicate cell stress (See <a href="https://2018.igem.org/Team:NUS_Singapore-A/Design#SRM"><i>Design: Stress Reporter</i></a>). Eventually, we decided to have 4 small holes, through which acrylic/glass tubes with outer diameters of 6 mm should be inserted, and 2 large holes, to each fit a test tube (Figure 1).</p> |
<br> | <br> | ||
| − | <figure class="figures"> | + | <figure class="figures" style="width: 40%;"> |
<img src="https://static.igem.org/mediawiki/2018/9/97/T--NUS_Singapore-A--CoJar_Fig1.png"> | <img src="https://static.igem.org/mediawiki/2018/9/97/T--NUS_Singapore-A--CoJar_Fig1.png"> | ||
| − | <figcaption>Figure 1. Top view of lasercut cover, showing the locations of apertures for acrylic tubes and test tubes.</figcaption> | + | <figcaption><b>Figure 1</b>. Top view of lasercut cover, showing the locations of apertures for acrylic tubes and test tubes.</figcaption> |
</figure> | </figure> | ||
<br> | <br> | ||
<p>For the acrylic tubes, 2 tubes would be connected to a peristaltic pump, one to an air pump, and the last one to a length of silicone tubing so that new media can be introduced. The test tubes act as containers for LEDs, allowing them to suffuse the culture with light (Figure 2).</p> | <p>For the acrylic tubes, 2 tubes would be connected to a peristaltic pump, one to an air pump, and the last one to a length of silicone tubing so that new media can be introduced. The test tubes act as containers for LEDs, allowing them to suffuse the culture with light (Figure 2).</p> | ||
<br> | <br> | ||
| − | <figure class="figures"> | + | <figure class="figures" style="width: 40%;"> |
<img src="https://static.igem.org/mediawiki/2018/a/a3/T--NUS_Singapore-A--Hardware_Bioreactor_filenameclash_White.png"> | <img src="https://static.igem.org/mediawiki/2018/a/a3/T--NUS_Singapore-A--Hardware_Bioreactor_filenameclash_White.png"> | ||
| − | <figcaption>Figure 2. Section view of fermentation chamber, showing how test tubes can provide an illumination solution. Also included is an example of how an acrylic tube may be inserted into the cover. Tubing and wiring have been omitted for clarity.</figcaption> | + | <figcaption><b>Figure 2</b>. Section view of fermentation chamber, showing how test tubes can provide an illumination solution. Also included is an example of how an acrylic tube may be inserted into the cover. Tubing and wiring have been omitted for clarity.</figcaption> |
</figure> | </figure> | ||
| − | < | + | <button class="accordion-closer">CLOSE</button> |
| − | < | + | </div> |
| − | <p>The ambient temperature of where our bioreactor would be located was too cold to be conducive for growing bacteria. Another problem we faced was the magnetic stirrer limiting the depth to which the test tubes could be sunken and thus the light penetration. We had a eureka moment when we realized that both problems could be solved by placing Light Wait into a shaking incubator as shown in <a href="https://2018.igem.org/Team:NUS_Singapore-A/Hardware#LWPD">Light Wait: Product Demonstration</a>.</p> | + | |
| − | < | + | <button class="accordion">STIRRING MECHANISM</button> |
| + | <div class="panel"> | ||
| + | <p>The ambient temperature of where our bioreactor would be located was too cold to be conducive for growing bacteria. Another problem we faced was the magnetic stirrer limiting the depth to which the test tubes could be sunken and thus the light penetration. We had a eureka moment when we realized that both problems could be solved by placing Light Wait into a shaking incubator as shown in <a href="https://2018.igem.org/Team:NUS_Singapore-A/Hardware#LWPD"><i>Light Wait: Product Demonstration</i></a>.</p> | ||
| + | <button class="accordion-closer">CLOSE</button> | ||
| + | </div> | ||
| + | |||
<h2>Construction</h2> | <h2>Construction</h2> | ||
| − | <p>Do you like cookies? Do you like jars? Your answer doesn’t matter. Make our | + | <p>Do you like cookies? Do you like jars? Your answer doesn’t matter. Make our fermentation chamber anyway! Batteries and bacteria not included.</p> |
<br> | <br> | ||
| − | < | + | <button class="accordion">BILL OF MATERIALS</button> |
| + | <div class="panel"> | ||
<br> | <br> | ||
<ul> | <ul> | ||
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</ul> | </ul> | ||
<br> | <br> | ||
| + | <button class="accordion-closer">CLOSE</button> | ||
| + | </div> | ||
| − | < | + | <button class="accordion">STRUCTURAL ASSEMBLY</button> |
| + | <div class="panel"> | ||
<br> | <br> | ||
| − | <figure class="figures"> | + | <figure class="figures" style="width: 70%;"> |
<img src="https://static.igem.org/mediawiki/2018/c/c6/T--NUS_Singapore-A--CoJar_Fig3.gif"> | <img src="https://static.igem.org/mediawiki/2018/c/c6/T--NUS_Singapore-A--CoJar_Fig3.gif"> | ||
| − | <figcaption>Figure 3. Fermentation Chamber assembly.</figcaption> | + | <figcaption><b>Figure 3</b>. Fermentation Chamber assembly.</figcaption> |
</figure> | </figure> | ||
<br> | <br> | ||
| + | <button class="accordion-closer">CLOSE</button> | ||
| + | </div> | ||
| + | <br> | ||
<p>Files for lasercutting are available in SLDPRT and SLDASM format so that you may easily modify its dimensions to fit your jar (please find your own). You may download them all as a ZIP file <a href="https://static.igem.org/mediawiki/2018/5/52/T--NUS_Singapore-A--Hardware_Fermentation_Chamber_Cover.zip"><u>here</u></a>.</p> | <p>Files for lasercutting are available in SLDPRT and SLDASM format so that you may easily modify its dimensions to fit your jar (please find your own). You may download them all as a ZIP file <a href="https://static.igem.org/mediawiki/2018/5/52/T--NUS_Singapore-A--Hardware_Fermentation_Chamber_Cover.zip"><u>here</u></a>.</p> | ||
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<div class="reference"> | <div class="reference"> | ||
[1] Zhao, E. M., Zhang, Y., Mehl, J., Park, H., Lalwani, M. A., Toettcher, J. E., & Avalos, J. L. (2018). Optogenetic regulation of engineered cellular metabolism for microbial chemical production. <i>Nature, 555(7698)</i>, 683–687. http://doi.org/10.1038/nature26141 | [1] Zhao, E. M., Zhang, Y., Mehl, J., Park, H., Lalwani, M. A., Toettcher, J. E., & Avalos, J. L. (2018). Optogenetic regulation of engineered cellular metabolism for microbial chemical production. <i>Nature, 555(7698)</i>, 683–687. http://doi.org/10.1038/nature26141 | ||
| + | </div> | ||
</div> | </div> | ||
<br> | <br> | ||
Latest revision as of 23:58, 17 October 2018
Fermentation Chamber
The fermentation chamber contains the bacterial culture. It also comes with a cover designed to include a means of illuminating the chamber’s contents.
Design - Innovation!
We selected components of the fermentation chamber based on whether they were easily obtainable and modifiable. This was because it was difficult to fabricate a cylindrical, watertight chamber using conventional methods of prototyping such as laser cutting and 3D printing. Rather than spend time attempting to manufacture a suitable container from scratch, we looked to modifying existing commercial, easily obtainable products. This also makes it easier for others to make their own bioreactor based on our work.
We decided on a suitable working volume for our bioreactor based on literature review[1]. Possible working volumes suitable for the laboratory ranged from 0.5 L to 2 L. After discussion, we decided that 0.5 L would be a manageable volume. We hypothesized that this volume was sufficient for us to demonstrate proof-of-concept. It is also more portable.
A bail jar from IKEA was repurposed for this. Discarding the original glass cover, we retained the rubber ring and two-part wire clasp.
We opted not to use the original cover because we knew we would have to perforate it to accommodate tubing. Drilling would generate many points of failure. For example, the glass cover might shatter from the stress, it is challenging to control the accuracy of our drilling, and drilling may not be able to provide the required precision.
We thus retrofitted our own lasercut Plexiglass cover. This allowed us greater flexibility to explore potential sensing modules and components we intended to add to our system. Considered, but eventually discarded, were modules like a pH meter, as we decided to focus on other metrics to indicate cell stress (See Design: Stress Reporter). Eventually, we decided to have 4 small holes, through which acrylic/glass tubes with outer diameters of 6 mm should be inserted, and 2 large holes, to each fit a test tube (Figure 1).
For the acrylic tubes, 2 tubes would be connected to a peristaltic pump, one to an air pump, and the last one to a length of silicone tubing so that new media can be introduced. The test tubes act as containers for LEDs, allowing them to suffuse the culture with light (Figure 2).
The ambient temperature of where our bioreactor would be located was too cold to be conducive for growing bacteria. Another problem we faced was the magnetic stirrer limiting the depth to which the test tubes could be sunken and thus the light penetration. We had a eureka moment when we realized that both problems could be solved by placing Light Wait into a shaking incubator as shown in Light Wait: Product Demonstration.
Construction
Do you like cookies? Do you like jars? Your answer doesn’t matter. Make our fermentation chamber anyway! Batteries and bacteria not included.
- 180 x 100 x 5 mm acrylic sheet x 1
- Arduino Uno x 1
- 472 nm LED x 16
- LED driver x 1
- 2 kΩ resistor x 1
- 0.1 uF ceramic capacitor x 1
- 4.7uF electrolytic capacitor x 1
- 28-pin IC socket x 1
- Test tube x 2
- AC Adapter x 1
Files for lasercutting are available in SLDPRT and SLDASM format so that you may easily modify its dimensions to fit your jar (please find your own). You may download them all as a ZIP file here.
References
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