Difference between revisions of "Team:NUS Singapore-A/shadow/Hardware"
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| − | <h1> | + | <h1>Ontroduction</h1> |
| − | <p>Our team developed two sets of hardware to address problems in synthetic biology.<br> | + | <p>Our team developed two sets of hardware to address problems in synthetic biology.</p> |
| − | The first problem is that while | + | <br> |
| − | The second problem is that so far, while Zhao et al. have increased yield of isobutanol from yeast by using a blue light repressible system in a simple bioreactor, they did not optimize the duration or intensity of blue light, and shone blue light periodically. Dynamic regulation is a good method for optimization. Argeitis et. al developed automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth. However after examining his method, we found that while his feedback control system was closed-loop, his physical system was not. Measurement samples were discarded as waste. This is not advantageous to biomanufacturing as this will lead to much product being wasted, lowering effective yield. To solve this, we combined the insights and design features from these two systems to create Light Wait, a closed-system, closed-loop photobioreactor | + | <p> |
| − | </p> | + | The first problem is that while there is a rapidly-growing interest in using optogenetics for biomanufacturing, development of custom tools to support the research of optogenetic circuits is insufficient to meet user needs<sup>[2]</sup>.</p> |
| − | + | <br> | |
| + | <p>An example of the most current hardware tools available is a modified Tecan microplate reader, which provides controlled illumination on top of its usual measurement capabilities<sup>[3]</sup>. Such an approach is costly and requires specialized knowledge of the microplate reader model. <i>Tabor et al.</i> constructed an open-source light exposure tool for a 24-well plate<sup>[4]</sup>. Based on literature review it seems that tools have been developed only for well plates. However there are certain reasons why researchers would like to choose petri dishes and erlenmeyer flasks over well plates when studying optogenetic circuits. | ||
| + | </p> | ||
| + | <br> | ||
| + | <figure class="figures"> | ||
| + | <img src="#" alt="Graphic of scaling-up process"> | ||
| + | <figcaption><b>Figure 1</b> : blah blah</figcaption> | ||
| + | </figure> | ||
| + | <br> | ||
| + | <p> | ||
| + | We needed to use these when developing our biomanufacturing process. We thus created <i>PDF-LA!</i> to empower optogenetic researchers. | ||
| + | </p> | ||
| + | <br> | ||
| + | <figure class="figures"> | ||
| + | <img src="#" alt="picture"> | ||
| + | <figcaption><b>Figure 2</b> : blah blah 2</figcaption> | ||
| + | </figure> | ||
| + | <br> | ||
| + | <p> | ||
| + | We validated this using modelling and characterization of our own blue-light repressible circuits. See our Modelling page <a href="#">here</a>. | ||
| + | </p> | ||
| + | <br> | ||
| + | <p> | ||
| + | The second problem is that so far, while <i>Zhao et al</i>. have increased yield of isobutanol from yeast by using a blue light repressible system in a simple bioreactor as compared to traditional methods, showing the potential of optogenetics in biomanufacturing<sup>[5]</sup>, they did not optimize the duration or intensity of blue light, and shone blue light periodically. Dynamic regulation is a good method for optimization, because prioritization of growth and production can be achieved simultaneously. <i>Argeitis et. al</i> developed automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth<sup>[6]</sup>. So far this is the most recent and sophisticated feedback system for optogenetics. However after examining his method, we found that while his feedback control system was closed-loop, his physical system was not. Measurement samples were discarded as waste. This is not advantageous to biomanufacturing, as this will lead to much product being wasted, lowering effective yield. We should not take this approach, especially when there is no issue with introducing the samples back into the bioreactor. To solve this, we combined the insights and design features from these two systems to create <i>Light Wait</i>, a closed-system, closed-loop photobioreactor. | ||
| + | </p> | ||
<h2>Optogenetics</h2> | <h2>Optogenetics</h2> | ||
| − | <p>The use of optogenetics in synthetic biology requires hardwares to control on and off, intensity of light. We designed and built light inducible or repressible hardware for the use in laboratory. Devices used to induce gene expression through light is developed. Devices range from small volume of 12 well plate to larger volume of bioreactor.</p><br> | + | <p>The use of optogenetics in synthetic biology requires hardwares to control on and off, intensity of light. We designed and built light inducible or repressible hardware for the use in laboratory. Devices used to induce gene expression through light is developed. Devices range from small volume of 12 well plate to larger volume of bioreactor.</p> |
| + | <br> | ||
| + | <figure class="figures"> | ||
| + | <img src="#" alt="picture"> | ||
| + | <figcaption><b>Figure 3</b> : blah blah 3</figcaption> | ||
| + | </figure> | ||
| + | <br> | ||
| + | <p> | ||
| + | We validated this through hardware testing. Read more <a href="#">here</a>. | ||
| + | </p> | ||
| + | <br> | ||
| + | <hr> | ||
| + | <br> | ||
| + | |||
<h1>Methodology</h1> | <h1>Methodology</h1> | ||
<p>IN progress.</p><br> | <p>IN progress.</p><br> | ||
Revision as of 09:59, 12 October 2018
Ontroduction
Our team developed two sets of hardware to address problems in synthetic biology.
The first problem is that while there is a rapidly-growing interest in using optogenetics for biomanufacturing, development of custom tools to support the research of optogenetic circuits is insufficient to meet user needs[2].
An example of the most current hardware tools available is a modified Tecan microplate reader, which provides controlled illumination on top of its usual measurement capabilities[3]. Such an approach is costly and requires specialized knowledge of the microplate reader model. Tabor et al. constructed an open-source light exposure tool for a 24-well plate[4]. Based on literature review it seems that tools have been developed only for well plates. However there are certain reasons why researchers would like to choose petri dishes and erlenmeyer flasks over well plates when studying optogenetic circuits.
We needed to use these when developing our biomanufacturing process. We thus created PDF-LA! to empower optogenetic researchers.
We validated this using modelling and characterization of our own blue-light repressible circuits. See our Modelling page here.
The second problem is that so far, while Zhao et al. have increased yield of isobutanol from yeast by using a blue light repressible system in a simple bioreactor as compared to traditional methods, showing the potential of optogenetics in biomanufacturing[5], they did not optimize the duration or intensity of blue light, and shone blue light periodically. Dynamic regulation is a good method for optimization, because prioritization of growth and production can be achieved simultaneously. Argeitis et. al developed automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth[6]. So far this is the most recent and sophisticated feedback system for optogenetics. However after examining his method, we found that while his feedback control system was closed-loop, his physical system was not. Measurement samples were discarded as waste. This is not advantageous to biomanufacturing, as this will lead to much product being wasted, lowering effective yield. We should not take this approach, especially when there is no issue with introducing the samples back into the bioreactor. To solve this, we combined the insights and design features from these two systems to create Light Wait, a closed-system, closed-loop photobioreactor.
Optogenetics
The use of optogenetics in synthetic biology requires hardwares to control on and off, intensity of light. We designed and built light inducible or repressible hardware for the use in laboratory. Devices used to induce gene expression through light is developed. Devices range from small volume of 12 well plate to larger volume of bioreactor.
We validated this through hardware testing. Read more here.
Methodology
IN progress.
12 Well Plate LED System
IN progress.
Petri Dish/Flask LED System
IN progress.
Small Bioreactor LED System
IN progress.
Industrial Scale Bioreactor
IN progress.
Bio-production
It’s important to have automation in bioproduction especially in industrial level. We designed a small bioreactor system which incorporated optical density (OD) and fluorescence sensors to control the metabolic behaviours in E. coli.
Automated Control through feedbacks
IN progress.
OD/F sensor
IN progress.
Pump
IN progress.
HEAR OUR STORY
We’re using synthetic biology to change the way the world thinks and functions.
We’re a little disruptive, dangerous and maybe a tad too bold. But the world needs some shaking up every now and then, and we think we’re just the right people for that.
Together we’re going to engineer biology and create something awesome.
CONTACT US
nusigem@gmail.com21 Lower Kent Ridge Rd, Singapore 119077