Difference between revisions of "Team:Calgary/Bioreactor"

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           <a href="#overview">Overview</a>
 
           <a href="#overview">Overview</a>
<br>
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        <br>
           <a href="#project-design">Project Designs</a>
+
           <a href="#understanding-the-problem">Understanding The Problem</a>
<br>
+
        <br>
           <a href="#part-design">Part Design</a>
+
           <a href="#research-and-ideate">Research And Ideate</a>
<br>
+
        <br>
           <a href="#experimental-design">Experimental Design</a>
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           <a href="#design-solutions">Design Solutions</a>
<br>
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        <br>
           <a href="#future-directions">Future Directions</a>
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           <a href="#expected-results-and-troubleshooting">Create: Expected Results And Troubleshooting</a>
 +
        <br>
 +
        <a href="#testing">Testing</a>
 +
        <br>
 +
        <a href="#future-directions">Future Directions</a>
 +
        <br>
 +
        <a href="#references">References</a>
 
         </div>
 
         </div>
  
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<img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/5/55/T--Calgary--bioreactorpipeline.png" />
 
<img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/5/55/T--Calgary--bioreactorpipeline.png" />
 
<br>
 
<br>
         <h4>Need for a bioreactor</h4>
+
         <h4>Bringing Oviita to the community</h4>
         <p>
+
         <p>The aim of our project is to supply communities experiencing vitamin A deficiency with our product, Oviita, to
Add stuff here </p>
+
        provide them with a sustainable source of nutrients. For this to happen we will need to culture the  yeast at the
 +
        local community level. Therefore, we needed to develop a bioreactor capable of accomplishing this task in suboptimal
 +
        conditions while also being sensitive to the available resources in these areas.
 +
        </p>
  
 
<video autoplay muted controls id="myVideo" style="width: 100%;">
 
<video autoplay muted controls id="myVideo" style="width: 100%;">
               <source src="https://static.igem.org/mediawiki/2020/f/f7/T--Calgary--testmovie.mov" type="video/mp4">
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               <source src="https://static.igem.org/mediawiki/2020/9/9b/T--Calgary--Bioreactor_video.mp4" type="video/mp4">
 
             </video>
 
             </video>
  
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<br>
 
<br>
 
<hr>
 
<hr>
<div class = "project-design" id="project-design">
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<div class = "understanding-the-problem" id="understanding-the-problem">
         <h2>PROJECT DESIGN</h2>
+
         <h2>UNDERSTANDING THE PROBLEM</h2>
 
         <h4>What do the people need? </h4>
 
         <h4>What do the people need? </h4>
 
         <p>
 
         <p>
          In order to provide a sustainable, community-based solution, we plan
+
        We couldn’t just draft a design at our desk and expect it to be successful in various locations across the world.
          to genetically modify <i>Rhodosporidium toruloides</i>, an oleaginous
+
        First, we needed to design a laboratory bioreactor that could give us data regarding variables required to support
          yeast that naturally produces beta-carotene and lipids, to be more
+
        growth to later assist in determining the required conditions for real-world application and design predictions.
          robust and resource-efficient. By modifying the yeast to produce
+
        <br>
          cellulase, it can then use common agricultural waste products as an
+
        <br>
          energy source for synthesizing its oil. It can then be eaten as a
+
        When speaking with Dr. Charles Mather, a nutritional anthropologist at the University of Calgary, he mentioned that
          vitamin A supplement. The yeast strain, while naturally safe and
+
        his experience of working in developing nations suggested that locals are much more knowledgeable about how to use their
          non-pathogenic, will also be genetically modified to include a kill
+
        resources than we are.  Therefore, the Field Adaptable Bioreactor needs to be as simple and flexible as possible to allow
          switch for bio-containment, and optimized for oil production.
+
        for our end-user construction using the varied resources they may have on hand. By supplying communities with the required
         </p>
+
        growing conditions, as well as design suggestions, they are able to efficiently determine the best design that fits their needs.  
<img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/e/e7/T--Calgary--bioreactorworkflow.png">
+
        This avoids the all-too-common engineering fallacy of designing a product that isn’t built around local, real-world conditions.
<br>
+
         <br>
<p>
+
       
          In order to provide a sustainable, community-based solution, we plan
+
        <img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/e/e7/T--Calgary--bioreactorworkflow.png">
          to genetically modify <i>Rhodosporidium toruloides</i>, an oleaginous
+
 
          yeast that naturally produces beta-carotene and lipids, to be more
+
          robust and resource-efficient. By modifying the yeast to produce
+
          cellulase, it can then use common agricultural waste products as an
+
          energy source for synthesizing its oil. It can then be eaten as a
+
          vitamin A supplement. The yeast strain, while naturally safe and
+
          non-pathogenic, will also be genetically modified to include a kill
+
          switch for bio-containment, and optimized for oil production.
+
 
         </p>
 
         </p>
 
  
 
</div>
 
</div>
<br>
 
 
<hr>
 
<hr>
<div class = "part-design" id="part-design">
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<div class = "research-and-ideate" id="research-and-ideate">
         <h2>PART DESIGN</h2>
+
         <h2>RESEARCH AND IDEATE</h2>
         <h4>Thoughtful design of genetic constructs</h4>
+
         <h4>Finding Constraints</h4>
 
         <p>
 
         <p>
          In order to provide a sustainable, community-based solution, we plan
+
        First we needed some data to inform the design of our lab reactor. We then constructed growth models based on literature and
          to genetically modify <i>Rhodosporidium toruloides</i>, an oleaginous
+
        conducted metabolic flux analysis. From that we were able to calculate growth rates and growth with different substrates. Our
          yeast that naturally produces beta-carotene and lipids, to be more
+
        calculations with a 50L bioreactor, we should be able to produce enough yeast for a group of 20 people. However, after meeting
          robust and resource-efficient. By modifying the yeast to produce
+
        with ******* we concluded that the calculations assumed unconstrained growth and we needed to identify some constraints to improve accuracy.
          cellulase, it can then use common agricultural waste products as an
+
        <br>
          energy source for synthesizing its oil. It can then be eaten as a
+
        <br>
          vitamin A supplement. The yeast strain, while naturally safe and
+
        To add to that knowledge, we began experimenting with the yeast in the lab. It was unknown whether or not the yeast would settle or remain
          non-pathogenic, will also be genetically modified to include a kill
+
        suspended, and if it settled, how long that would take. This Information had a large effect on the bioreactor design and tests showed the
          switch for bio-containment, and optimized for oil production.
+
        yeast settling <12 hours which meant we could use a simpler design since we wouldn’t have to filter the yeast out. Other tests included,
 +
        temperature sensitivity and the solutions change in pH during growth.
 +
        <br>
 +
        <video autoplay muted controls id="myVideo" style="width: 100%;">
 +
            <source src="https://static.igem.org/mediawiki/2020/a/a0/T--Calgary--yeast-settling-video.mp4" type="video/mp4">
 +
        </video>
 +
        <br>
 +
        From that, we could start our design on the lab reactor.
 +
 
 +
        </p>
 +
        <h4>Obtaining More Data</h4>
 +
        <p>
 +
        We have made a significant effort to apply Occam’s Razor to all of our designs to promote simplicity in bioreactor construction and to ensure
 +
        that our product can reach as many people as possible.
 +
        <br>
 +
        <br>
 +
        In doing so, our research suggested that the lowest cost and simplest bioreactor design for cultivating our yeast was an airlift bioreactor.  
 +
        An airlift bioreactor uses the buoyancy of bubbles to push the water in the center of the container up and create a convection current that
 +
        can continually mix the solution, creating a uniform distribution of yeast cells within their growth medium. When compared with a stirred bioreactor,  
 +
        the airlift reactor produced nearly equal production rates with less moving parts (Braga, 2015, 55-62).
 +
    <img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/2/29/T--Calgary--airlift-vs-stir-reactor.png">
 +
        Therefore, with those levels of production with an airlift reactor, we have room to account for inefficiencies without harming our end goal of sustainable production.
 
         </p>
 
         </p>
  
        <!--Here's the bioreactor equations image. Please move to wherever Bioreactor Modelling section is. Thanks!-->
 
        <img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/a/a3/T--Calgary--bioreactor_modelling.png">
 
 
</div>
 
</div>
<br>
 
 
<hr>
 
<hr>
<div class = "experimental-design" id="experimental-design">
+
<div class = "design-solutions" id="design-solutions">
         <h2>EXPERIMENTAL DESIGN</h2> </div>
+
         <h2>DESIGN SOLUTIONS</h2> </div>
         <h4>Thoughtful design of experiments</h4>
+
         <h4>Lab Adaptable Bioreactor:</h4>
 +
        <br>
 +
    <img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/3/31/T--Calgary--lab-bioreactor-cad.jpeg">   
 +
        <p style="font-size: 110%; font-weight:bold;">PHYSICAL DESIGN</p>
 +
 
 
         <p>
 
         <p>
          In order to provide a sustainable, community-based solution, we plan
+
        To produce accurate models and projections, we will need accurate data. At the same time, we need our Lab Adaptable Bioreactor to resemble conditions
          to genetically modify <i>Rhodosporidium toruloides</i>, an oleaginous
+
        in the field and therefore should be of relatively similar scale. Given our initial estimations, a 40L bucket should be able to produce enough yeast for a
          yeast that naturally produces beta-carotene and lipids, to be more
+
        small group of people and therefore would suffice. Removing as much yeast with as little water possible was a significant challenge to overcome. Yeast
          robust and resource-efficient. By modifying the yeast to produce
+
        are single celled fungi ranging between fungi, 5~10 μm in size. Centrifugal separation would leave us with too much water and typical micron filters would
          cellulase, it can then use common agricultural waste products as an
+
        get clogged and become quickly ineffective. Fortunately, we found a stainless steel, 1 micron, 4 layer mesh filter that won’t clog as easily and can be  
          energy source for synthesizing its oil. It can then be eaten as a
+
        cleaned in an autoclave.  
          vitamin A supplement. The yeast strain, while naturally safe and
+
        <br>
          non-pathogenic, will also be genetically modified to include a kill
+
        <img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/9/99/T--Calgary--micron_filter.jpeg">
          switch for bio-containment, and optimized for oil production.
+
 
         </p>
 
         </p>
<!--ACCORDION -->
 
  
<div class="accordion" id="accordionExample">
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        <p style="font-size: 110%; font-weight:bold;">ELECTRICAL DESIGN</p>
  <div class="card">
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        <br>
    <div class="card-header" id="headingOne">
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         <img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/8/88/T--Calgary--bioreactor-wiring-diagram.png">
      <h2 class="mb-0">
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        <p>
         <button class="btn btn-link" type="button" data-toggle="collapse" data-target="#collapseOne" aria-expanded="true" aria-controls="collapseOne">
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        The data we needed to collect is the growth conditions against diffused oxygenation levels, pH, temperature, the corresponding growth rates, settling rates
          Experiment 1
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        and anything else that may require design considerations.
         </button>
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         <br>
      </h2>
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        <br>
    </div>
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        To achieve this we have the Gravity: Analog Dissolved Oxygen Sensor for determining the oxygenation rates in the solution because the yeast is an obligate aerobe
 +
        meaning it requires oxygen to grow. Literature has shown substantial growth with 9L/min of air being pumped into the solution and therefore we are using a
 +
        commercial air pump for aquariums that is capable of delivering a maximum 50L/min of air (Braga, 2015, 55-62). From that, we will be able to determine
 +
        the minimal amount of oxygenation needed for growth and find a range of values to be able to predict the growth for that specific range.
 +
        <br>
 +
        <br>
 +
        To monitor pH, we are using the Gravity: Analog pH Meter Pro. This way we can continuously monitor the pH as it might change with cellular respiration.
 +
        Our concern is that the yeast will convert the oxygen into CO2 and that CO2 in the solution will lower the pH to a point where the yeast will no longer
 +
        be able to sustain life. Fortunately, our yeast can thrive at a pH of 4.5 so some acidification is ok. (Timoumi, 2016)
 +
        <br>
 +
        <br>
 +
        In order to maintain or simulate the temperatures or temperature fluctuations of the locations we intend on distributing our yeast, the bioreactor
 +
        will have an aquarium heating element and a DS18B20 digital thermometer.
 +
        <br>
 +
        <br>
 +
        Each of the components is controlled with an Arduino inside a 3D printed box with all of the data being saved  to the Geekstory micro SD module
 +
        as comma separated values in a text file. This text file can then be used to create a graph using the data. In addition, a DS3231 time module will
 +
        timestamp the data to ensure an accurate interpretation of the data.
 +
        </p>
  
    <div id="collapseOne" class="collapse show" aria-labelledby="headingOne" data-parent="#accordionExample">
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         <p style="font-size: 110%; font-weight:bold;">SAFETY</p>
      <div class="card-body">
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         Since some of the electrical components are using an AC current, safety is a major concern. To address these concerns, we made sure to include the following:
         Anim pariatur cliche reprehenderit, enim eiusmod high life accusamus terry richardson ad squid. 3 wolf moon officia aute, non cupidatat skateboard dolor brunch. Food truck quinoa nesciunt laborum eiusmod. Brunch 3 wolf moon tempor, sunt aliqua put a bird on it squid single-origin coffee nulla assumenda shoreditch et. Nihil anim keffiyeh helvetica, craft beer labore wes anderson cred nesciunt sapiente ea proident. Ad vegan excepteur butcher vice lomo. Leggings occaecat craft beer farm-to-table, raw denim aesthetic synth nesciunt you probably haven't heard of them accusamus labore sustainable VHS.
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         <br>
      </div>
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         -Wire joints are sealed and hidden underneath the components
    </div>
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         -Use of 16AWG wire
  </div>
+
         -15 Amp Fuse
  <div class="card">
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         -The bioreactor is grounded in case the heating element fails
    <div class="card-header" id="headingTwo">
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      <h2 class="mb-0">
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        <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseTwo" aria-expanded="false" aria-controls="collapseTwo">
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          Experiment 2
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        </button>
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      </h2>
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    </div>
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    <div id="collapseTwo" class="collapse" aria-labelledby="headingTwo" data-parent="#accordionExample">
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      <div class="card-body">
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         Anim pariatur cliche reprehenderit, enim eiusmod high life accusamus terry richardson ad squid. 3 wolf moon officia aute, non cupidatat skateboard dolor brunch. Food truck quinoa nesciunt laborum eiusmod. Brunch 3 wolf moon tempor, sunt aliqua put a bird on it squid single-origin coffee nulla assumenda shoreditch et. Nihil anim keffiyeh helvetica, craft beer labore wes anderson cred nesciunt sapiente ea proident. Ad vegan excepteur butcher vice lomo. Leggings occaecat craft beer farm-to-table, raw denim aesthetic synth nesciunt you probably haven't heard of them accusamus labore sustainable VHS.
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      </div>
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    </div>
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  </div>
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    <div class="card-header" id="headingThree">
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      <h2 class="mb-0">
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         <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseThree" aria-expanded="false" aria-controls="collapseThree">
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          Experiment 3
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         </button>
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      </h2>
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    </div>
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    <div id="collapseThree" class="collapse" aria-labelledby="headingThree" data-parent="#accordionExample">
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      <div class="card-body">
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         Anim pariatur cliche reprehenderit, enim eiusmod high life accusamus terry richardson ad squid. 3 wolf moon officia aute, non cupidatat skateboard dolor brunch. Food truck quinoa nesciunt laborum eiusmod. Brunch 3 wolf moon tempor, sunt aliqua put a bird on it squid single-origin coffee nulla assumenda shoreditch et. Nihil anim keffiyeh helvetica, craft beer labore wes anderson cred nesciunt sapiente ea proident. Ad vegan excepteur butcher vice lomo. Leggings occaecat craft beer farm-to-table, raw denim aesthetic synth nesciunt you probably haven't heard of them accusamus labore sustainable VHS.
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      </div>
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    </div>
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      <h2 class="mb-0">
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          Experiment 4
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         </button>
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      </h2>
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        Anim pariatur cliche reprehenderit, enim eiusmod high life accusamus terry richardson ad squid. 3 wolf moon officia aute, non cupidatat skateboard dolor brunch. Food truck quinoa nesciunt laborum eiusmod. Brunch 3 wolf moon tempor, sunt aliqua put a bird on it squid single-origin coffee nulla assumenda shoreditch et. Nihil anim keffiyeh helvetica, craft beer labore wes anderson cred nesciunt sapiente ea proident. Ad vegan excepteur butcher vice lomo. Leggings occaecat craft beer farm-to-table, raw denim aesthetic synth nesciunt you probably haven't heard of them accusamus labore sustainable VHS.
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      </div>
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    </div>
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  </div>
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 +
        <img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/b/ba/T--Calgary--bioreactor-parts-list.png">
  
 +
        <h4>Field Adaptable Bioreactor:</h4>
 +
        <br>
 +
        <img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/9/9b/T--Calgary--field-bioreactor-cad.jpeg">
 +
  <p>   
 +
        A general design for a field reactor includes two tanks; one tank will act as the main culturing tank and the second tank will be the collection tank.
 +
        Once the main tank has reached the desired levels of yeast production, users will drain 75% of the solution into the collection tank.
 +
        In the collection tank, the yeast will have time to settle to the bottom. A drain located just above the height of the settled yeast can then
 +
        drain most of the water leaving the yeast behind. To minimize the modifications/parts required, a simple siphon can be constructed. (see photos)
 +
        The remaining water could then be evaporated by placing a fire under the collection container making the yeast easier to collect, store and consume.
 +
        The fire would also be able to sanitize the collection tank to ensure nothing harmful begins to culture.
 +
        <img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/a/a2/T--Calgary--bottle_syphon.png">
  
 +
        </p>
 +
</div>
 +
<hr>
 +
<div class = "expected-results-and-troubleshooting" id="expected-results-and-troubleshooting">
 +
        <h2>CREATE: EXPECTED RESULTS AND TROUBLESHOOTING</h2> </div>
 +
        <h4>Thoughtful design of experiments</h4>
 +
        <p>
 +
        Bioreactor modelling is an essential step to determining a bioreactor’s performance in any given condition. With the current public health
 +
        situation making in-person collaboration much harder, it has become more important for the team to use information gathered from mathematical
 +
        models and previous experimental data. Optimal growth conditions for microorganisms like Yarrowia lipolytica are often complex and these make it
 +
        difficult to design and scale up a bioreactor (Nauha, 1970). While it is not the most accurate method of finding out the parameters for the
 +
        bioreactor, it gives the team an idea of what to expect when the actual testing is done.
 +
        <br>
 +
        <div class="row">
 +
        <div class="col-4"><img class="img-fluid"src="https://static.igem.org/mediawiki/2020/2/23/T--Calgary--cell_density_yarrawai_yeast.jpeg"> </div>
 +
        <div class="col-4"><img class="img-fluid"src="https://static.igem.org/mediawiki/2020/9/94/T--Calgary--yarrawai_rate_of_change.jpeg"> </div>
  
 +
        <br>
 +
        The value for the yeast’s growth rate was taken from literature (Workman et al, 2013). In order to determine the cell density at a given
 +
        point in time, the model uses the growth rate equation (Carlsson, 2009). The rate of change in beta carotene, on the other hand, is
 +
        modelled from the rate of change in biomass equation (derived from mass balance equation).  The rate of change in oxygen consumption
 +
        uses the same function except it has a downward trend. It is important to note that these models were made with the assumption that the
 +
        yeast culture follows an unconstrained growth pattern. The model does not take into consideration which substrate is the limiting factor in the growth of the culture.
 +
      <br>
 +
        <img class="img-fluid"style="width:100%;"src="https://static.igem.org/mediawiki/2020/a/a3/T--Calgary--bioreactor_modelling.png">
  
 +
       
 +
        </p>
 +
 +
</div>
 +
<hr>
 +
<div class = "testing" id="testing">
 +
        <h2>DESIGN SOLUTIONS</h2> </div>
 +
        <h4>Thoughtful design of experiments</h4>
 +
        <p>
 +
        With the LAB built, we were able to run a test as a proof of concept. After finding literature to support sucrose as a viable feedstock we felt
 +
        comfortable using it for this test (Lazar, 2013, 1273). The literature used a ratio of 50g of sugar per litre of water. To reduce the amount of
 +
        sugar used, we put 1kg of sugar in 20L of water.
 +
        <br>
 +
        Future Testing
 +
 +
        </p>
  
</div> <!--Everything above this is in the ACCORDION. So copy and paste a new experiment above here. -->
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</div>  
 
<hr>
 
<hr>
 
<div class = "Future Directions" id="future-directions">
 
<div class = "Future Directions" id="future-directions">
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         <h4>Next Steps</h4>
 
         <h4>Next Steps</h4>
 
         <p>
 
         <p>
          In order to provide a sustainable, community-based solution, we plan
+
        Snubber module and high power relay
          to genetically modify <i>Rhodosporidium toruloides</i>, an oleaginous
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          yeast that naturally produces beta-carotene and lipids, to be more
+
          robust and resource-efficient. By modifying the yeast to produce
+
          cellulase, it can then use common agricultural waste products as an
+
          energy source for synthesizing its oil. It can then be eaten as a
+
          vitamin A supplement. The yeast strain, while naturally safe and
+
          non-pathogenic, will also be genetically modified to include a kill
+
          switch for bio-containment, and optimized for oil production.
+
 
         </p>
 
         </p>
 
</div>
 
</div>
<br>
 
 
<hr>
 
<hr>
 
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<div class = "references" id="references">
 
+
        <h2>REFERENCES</h2> </div>
 +
        <p>
 +
        Braga, A. (2015). Aroma production by Yarrowia lipolytica in airlift and stirred tank bioreactors: Differences in yeast metabolism and morphology.
 +
        Biochemical Engineering Journal, 93(January), 55-62. https://www.sciencedirect.com/science/article/abs/pii/S1369703X14002460
 +
        <br>
 +
        <br>
 +
        Lazar, Z. (2013). Optimized invertase expression and secretion cassette for improving Yarrowia lipolytica growth on sucrose for industrial applications.
 +
        Journal of Industrial Microbiology & Biotechnology, 40(09), 1273–1283. https://link.springer.com/article/10.1007/s10295-013-1323-1
 +
        <br>
 +
        <br>
 +
        Timoumi, A. (2016, October 11). Dynamic behavior of Yarrowia lipolytica in response to pH perturbations: dependence of the stress response on the culture mode.
 +
        Springer Link. https://link.springer.com/article/10.1007/s00253-016-7856-2
 +
        <br>
 +
        <br>
 +
        1. Nauha, E. (1970, January 01). Modeling of bioreactors. Retrieved October 22, 2020, from https://research.aalto.fi/en/publications/modeling-of-bioreactors
 +
        <br>
 +
        <br>
 +
        2. Workman, M., Holt, P., & Thykaer, J. (2013). Comparing cellular performance of Yarrowia lipolytica during growth on glucose and glycerol in submerged cultivations.
 +
        AMB Express, 3(1), 58. doi:10.1186/2191-0855-3-58
 +
        <br>
 +
        <br>
 +
        3. Carlsson, B. (2009). An introduction to modeling of bioreactors. Retrieved 2020, from http://www.it.uu.se/edu/course/homepage/modynsyst/vt09/Lecture/DynSystBior2009.pdf
 +
        </p>
  
  

Revision as of 14:35, 27 October 2020



OVERVIEW


Bringing Oviita to the community

The aim of our project is to supply communities experiencing vitamin A deficiency with our product, Oviita, to provide them with a sustainable source of nutrients. For this to happen we will need to culture the yeast at the local community level. Therefore, we needed to develop a bioreactor capable of accomplishing this task in suboptimal conditions while also being sensitive to the available resources in these areas.



UNDERSTANDING THE PROBLEM

What do the people need?

We couldn’t just draft a design at our desk and expect it to be successful in various locations across the world. First, we needed to design a laboratory bioreactor that could give us data regarding variables required to support growth to later assist in determining the required conditions for real-world application and design predictions.

When speaking with Dr. Charles Mather, a nutritional anthropologist at the University of Calgary, he mentioned that his experience of working in developing nations suggested that locals are much more knowledgeable about how to use their resources than we are. Therefore, the Field Adaptable Bioreactor needs to be as simple and flexible as possible to allow for our end-user construction using the varied resources they may have on hand. By supplying communities with the required growing conditions, as well as design suggestions, they are able to efficiently determine the best design that fits their needs. This avoids the all-too-common engineering fallacy of designing a product that isn’t built around local, real-world conditions.


RESEARCH AND IDEATE

Finding Constraints

First we needed some data to inform the design of our lab reactor. We then constructed growth models based on literature and conducted metabolic flux analysis. From that we were able to calculate growth rates and growth with different substrates. Our calculations with a 50L bioreactor, we should be able to produce enough yeast for a group of 20 people. However, after meeting with ******* we concluded that the calculations assumed unconstrained growth and we needed to identify some constraints to improve accuracy.

To add to that knowledge, we began experimenting with the yeast in the lab. It was unknown whether or not the yeast would settle or remain suspended, and if it settled, how long that would take. This Information had a large effect on the bioreactor design and tests showed the yeast settling <12 hours which meant we could use a simpler design since we wouldn’t have to filter the yeast out. Other tests included, temperature sensitivity and the solutions change in pH during growth.

From that, we could start our design on the lab reactor.

Obtaining More Data

We have made a significant effort to apply Occam’s Razor to all of our designs to promote simplicity in bioreactor construction and to ensure that our product can reach as many people as possible.

In doing so, our research suggested that the lowest cost and simplest bioreactor design for cultivating our yeast was an airlift bioreactor. An airlift bioreactor uses the buoyancy of bubbles to push the water in the center of the container up and create a convection current that can continually mix the solution, creating a uniform distribution of yeast cells within their growth medium. When compared with a stirred bioreactor, the airlift reactor produced nearly equal production rates with less moving parts (Braga, 2015, 55-62). Therefore, with those levels of production with an airlift reactor, we have room to account for inefficiencies without harming our end goal of sustainable production.


DESIGN SOLUTIONS

Lab Adaptable Bioreactor:


PHYSICAL DESIGN

To produce accurate models and projections, we will need accurate data. At the same time, we need our Lab Adaptable Bioreactor to resemble conditions in the field and therefore should be of relatively similar scale. Given our initial estimations, a 40L bucket should be able to produce enough yeast for a small group of people and therefore would suffice. Removing as much yeast with as little water possible was a significant challenge to overcome. Yeast are single celled fungi ranging between fungi, 5~10 μm in size. Centrifugal separation would leave us with too much water and typical micron filters would get clogged and become quickly ineffective. Fortunately, we found a stainless steel, 1 micron, 4 layer mesh filter that won’t clog as easily and can be cleaned in an autoclave.

ELECTRICAL DESIGN


The data we needed to collect is the growth conditions against diffused oxygenation levels, pH, temperature, the corresponding growth rates, settling rates and anything else that may require design considerations.

To achieve this we have the Gravity: Analog Dissolved Oxygen Sensor for determining the oxygenation rates in the solution because the yeast is an obligate aerobe meaning it requires oxygen to grow. Literature has shown substantial growth with 9L/min of air being pumped into the solution and therefore we are using a commercial air pump for aquariums that is capable of delivering a maximum 50L/min of air (Braga, 2015, 55-62). From that, we will be able to determine the minimal amount of oxygenation needed for growth and find a range of values to be able to predict the growth for that specific range.

To monitor pH, we are using the Gravity: Analog pH Meter Pro. This way we can continuously monitor the pH as it might change with cellular respiration. Our concern is that the yeast will convert the oxygen into CO2 and that CO2 in the solution will lower the pH to a point where the yeast will no longer be able to sustain life. Fortunately, our yeast can thrive at a pH of 4.5 so some acidification is ok. (Timoumi, 2016)

In order to maintain or simulate the temperatures or temperature fluctuations of the locations we intend on distributing our yeast, the bioreactor will have an aquarium heating element and a DS18B20 digital thermometer.

Each of the components is controlled with an Arduino inside a 3D printed box with all of the data being saved to the Geekstory micro SD module as comma separated values in a text file. This text file can then be used to create a graph using the data. In addition, a DS3231 time module will timestamp the data to ensure an accurate interpretation of the data.

SAFETY

Since some of the electrical components are using an AC current, safety is a major concern. To address these concerns, we made sure to include the following:
-Wire joints are sealed and hidden underneath the components -Use of 16AWG wire -15 Amp Fuse -The bioreactor is grounded in case the heating element fails

Field Adaptable Bioreactor:


A general design for a field reactor includes two tanks; one tank will act as the main culturing tank and the second tank will be the collection tank. Once the main tank has reached the desired levels of yeast production, users will drain 75% of the solution into the collection tank. In the collection tank, the yeast will have time to settle to the bottom. A drain located just above the height of the settled yeast can then drain most of the water leaving the yeast behind. To minimize the modifications/parts required, a simple siphon can be constructed. (see photos) The remaining water could then be evaporated by placing a fire under the collection container making the yeast easier to collect, store and consume. The fire would also be able to sanitize the collection tank to ensure nothing harmful begins to culture.


CREATE: EXPECTED RESULTS AND TROUBLESHOOTING

Thoughtful design of experiments

Bioreactor modelling is an essential step to determining a bioreactor’s performance in any given condition. With the current public health situation making in-person collaboration much harder, it has become more important for the team to use information gathered from mathematical models and previous experimental data. Optimal growth conditions for microorganisms like Yarrowia lipolytica are often complex and these make it difficult to design and scale up a bioreactor (Nauha, 1970). While it is not the most accurate method of finding out the parameters for the bioreactor, it gives the team an idea of what to expect when the actual testing is done.


The value for the yeast’s growth rate was taken from literature (Workman et al, 2013). In order to determine the cell density at a given point in time, the model uses the growth rate equation (Carlsson, 2009). The rate of change in beta carotene, on the other hand, is modelled from the rate of change in biomass equation (derived from mass balance equation). The rate of change in oxygen consumption uses the same function except it has a downward trend. It is important to note that these models were made with the assumption that the yeast culture follows an unconstrained growth pattern. The model does not take into consideration which substrate is the limiting factor in the growth of the culture.


DESIGN SOLUTIONS

Thoughtful design of experiments

With the LAB built, we were able to run a test as a proof of concept. After finding literature to support sucrose as a viable feedstock we felt comfortable using it for this test (Lazar, 2013, 1273). The literature used a ratio of 50g of sugar per litre of water. To reduce the amount of sugar used, we put 1kg of sugar in 20L of water.
Future Testing


FUTURE DIRECTIONS

Next Steps

Snubber module and high power relay


REFERENCES

Braga, A. (2015). Aroma production by Yarrowia lipolytica in airlift and stirred tank bioreactors: Differences in yeast metabolism and morphology. Biochemical Engineering Journal, 93(January), 55-62. https://www.sciencedirect.com/science/article/abs/pii/S1369703X14002460

Lazar, Z. (2013). Optimized invertase expression and secretion cassette for improving Yarrowia lipolytica growth on sucrose for industrial applications. Journal of Industrial Microbiology & Biotechnology, 40(09), 1273–1283. https://link.springer.com/article/10.1007/s10295-013-1323-1

Timoumi, A. (2016, October 11). Dynamic behavior of Yarrowia lipolytica in response to pH perturbations: dependence of the stress response on the culture mode. Springer Link. https://link.springer.com/article/10.1007/s00253-016-7856-2

1. Nauha, E. (1970, January 01). Modeling of bioreactors. Retrieved October 22, 2020, from https://research.aalto.fi/en/publications/modeling-of-bioreactors

2. Workman, M., Holt, P., & Thykaer, J. (2013). Comparing cellular performance of Yarrowia lipolytica during growth on glucose and glycerol in submerged cultivations. AMB Express, 3(1), 58. doi:10.1186/2191-0855-3-58

3. Carlsson, B. (2009). An introduction to modeling of bioreactors. Retrieved 2020, from http://www.it.uu.se/edu/course/homepage/modynsyst/vt09/Lecture/DynSystBior2009.pdf