Difference between revisions of "Team:Calgary/Results"

(Prototype team page)
 
 
(34 intermediate revisions by 6 users not shown)
Line 1: Line 1:
−
{{IGEM_TopBar}}
+
{{Calgary/Imposter-Navbar-No-Logo}}
−
{{Calgary}}
+
<!--
−
<html>
+
    Final Colours:
 +
    menu bar (red-brown): #882916
 +
    progress bar (light orange-yellow): #FFA600
 +
    light blue: #0197AE
 +
    dark blue: #1E6273
 +
    dark orange: #FF7700
 +
    light red: #FBF6F3
 +
    light yellow: #F1C23F (jumbotron h1)
 +
-->
 +
<!-- INSTRUCTIONS for adding more sections
 +
 
 +
1. copy and paste the following code above the message at end of code (message says CONTENT):
  
−
<div class="column full_size">
+
<div class = "NAME" id="NAME">
−
<h1>Results</h1>
+
        <h2>NAME</h2>
−
<p>You can describe the results of your project and your future plans here. </p>
+
        <h4>HEADER</h4>
 +
        <p>
 +
          PASTE IN TEXT HERE
 +
        </p>
 
</div>
 
</div>
 +
<br>
 +
<hr>
  
 +
2. Where it says NAME, type in name of section. This has to be the SAME thing you type in for every place it says NAME. for the NAME after the id, you cannot include spaces between words, so use dashes instead, also don't use capitals. (Ex. NAME of section is "Future Directions", so i would paste that in where ever it says NAME. for the NAME after the id, I would type in "future-directions".) Also type in desired HEADER and text where it says PASTE IN TEXT HERE.
  
−
<div class="column third_size" >
+
3. Now we have to add the section to the sidebar menu. For this, go through the code and find the part where it says SIDEBAR. where it says "replace-title" paste in the NAME you put in after the id (Ex. I would paste in "future-directions".) Where it says "Title" paste in the NAME of the section.
  
−
<h3>What should this page contain?</h3>
+
4. Now go to the part of the code where it says "References section of page slightly above the header". In the line of code after that, add in #NAME after a comma after the last one that is there before the curly brackets. (Ex. I would paste in #future-directions after the last item in that line of code after a comma.)
−
<ul>
+
−
<li> Clearly and objectively describe the results of your work.</li>
+
−
<li> Future plans for the project. </li>
+
−
<li> Considerations for replicating the experiments. </li>
+
−
</ul>
+
−
</div>
+
  
 +
5. I've included the example in the code so you can follow along.That's all. You're all done!! :D If you need help just ask! 
 +
-->
 +
<!-- INSTRUCTIONS for adding more experiment sections to accordion:
  
 +
1. copy and paste the following above the message showing where to paste (it says ACCORDION in the message):
  
 +
<div class="card">
 +
    <div class="card-header" id="headingREPLACE">
 +
      <h2 class="mb-0">
 +
        <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseREPLACE" aria-expanded="false" aria-controls="collapseREPLACE">
 +
          EXPERIMENT
 +
        </button>
 +
      </h2>
 +
    </div>
 +
    <div id="collapseREPLACE" class="collapse" aria-labelledby="headingREPLACE" data-parent="#accordionExample">
 +
      <div class="card-body">
 +
        PASTE IN TEXT HERE.
 +
      </div>
 +
    </div>
 +
  </div>
  
−
<div class="column two_thirds_size" >
+
2. Every place where it says REPLACE in the code, type in the next highest numerical number. (Ex. if I am putting in a new experiment I would copy and paste the code above, and type in "Five" where REPLACE is because the last number used in the code was "Four".) The main thing is that whatever you type in for REPLACE has to only be present there and nowhere else in the code!!!!
−
<h3>Describe what your results mean </h3>
+
−
<ul>
+
−
<li> Interpretation of the results obtained during your project. Don't just show a plot/figure/graph/other, tell us what you think the data means. This is an important part of your project that the judges will look for. </li>
+
−
<li> Show data, but remember <b>all measurement and characterization data must also be on the Part's Main Page on the <a href="http://parts.igem.org/Main_Page">Registry</a>.</b> Otherwise these data will not be in consideration for any medals or part awards! </li>
+
−
<li> Consider including an analysis summary section to discuss what your results mean. Judges like to read what you think your data means, beyond all the data you have acquired during your project. </li>
+
−
</ul>
+
−
</div>
+
  
 +
3. You can now copy and paste in your text from your protocol where it says PASTE IN TEXT HERE. And paste in the name of your experiment where it says EXPERIMENT.
  
−
<div class="clear extra_space"></div>
+
-->
 +
<html>
 +
  <head>
 +
<!-- LINKS THE SIDEBAR CSS SHEET BECAUSE THIS PAGE USES A SIDEBAR -->
 +
    <link
 +
      rel="stylesheet"
 +
      type="text/css"    href="https://2020.igem.org/Template:Calgary/Imposter-Sidebar-2-Style?action=raw&ctype=text/css"
 +
    />
  
 +
<link href="https://fonts.googleapis.com/css2?family=Public+Sans:wght@500;600;700&display=swap" rel="stylesheet">
  
 +
<link
 +
      rel="stylesheet"
 +
      type="text/css"
 +
      href="https://2020.igem.org/Template:Calgary/Imposter-Content-Style?action=raw&ctype=text/css"
 +
    />
 +
   
 +
   
 +
    <script src="https://2020.igem.org/Template:Calgary/DynamicSizeModelPage?action=raw&ctype=text/javascript"></script>
 +
    <style>
  
−
<div class="column two_thirds_size" >
+
/* The banner image */
−
<h3> Project Achievements </h3>
+
.banner-image {
 +
  /* Use "linear-gradient" to add a darken background effect to the image (photographer.jpg). This will make the text easier to read */
 +
  background-image: linear-gradient(to bottom, rgba(0,0,0,0.5) 0%,rgba(0,0,0,0.5) 100%), url("https://static.igem.org/mediawiki/2020/e/e1/T--Calgary--results.jpg");
 +
  background-position: 0px -200px;
 +
}
  
−
<p>You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.</p>
 
  
−
<ul>
+
/*header font size for tablet*/
−
<li>A list of linked bullet points of the successful results during your project</li>
+
@media(max-width: 768px){
−
<li>A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.</li>
+
  .resp h1{
−
</ul>
+
    font-size:55px!important;
 +
  }}
 +
 
 +
/*header font size for mobile*/
 +
@media (max-width:525px){
 +
  .resp h1{
 +
    font-size:50px!important;
 +
  }}
 +
 
 +
@media (max-width: 767px) {
 +
 
 +
.banner-image {
 +
  background-position: center;
 +
}
 +
}
 +
 
 +
 
 +
 
 +
 
 +
 
 +
/* Fixing the top content under the navbar */
 +
      .banner-image {
 +
        position: relative;
 +
      }
 +
 
 +
 
 +
 
 +
 
 +
 
 +
/* References section of page slightly above the header */
 +
#project-design, #part-design, #experimental-design, #future-directions {
 +
    padding-top: 50px;
 +
    margin-top: -50px;
 +
}
 +
 
 +
 
 +
 
 +
 
 +
/* Accordion styling */
 +
.btn {color:#882916;}
 +
 
 +
    </style>
 +
  </head>
 +
 
 +
  <body style="background-color: #FFFFFF;" ;>
 +
    <div class="container-fluid">
 +
 
 +
 
 +
<!-- SIDEBAR -->
 +
        <div class="sidenav" id="sidenav">
 +
          <a href="https://2020.igem.org/Team:Calgary"
 +
            ><img
 +
              src="https://static.igem.org/mediawiki/2020/c/c1/T--Calgary--whitelogo.jpg"
 +
              style="height: 150px; width: auto; padding-top:20px; position:relative; left:-20px;"
 +
          /></a>
 +
 
 +
          <a href="#project-design">Overview</a>
 +
<br>
 +
          <a href="#part-design">Engineering Success</a>
 +
<br>
 +
          <a href="#experimental-design">Human Practices</a>
 +
<br>
 +
          <a href="#implementation">Proposed Implementation</a>
 +
<br>
 +
          <a href="#engagement>Engagement</a>
 +
<br>
 +
          <a href="#parts">Parts</a>
 +
<br>
 +
          <a href="#modelling">Modelling, Software, and Measurement</a>
 +
<br>
 +
         
 +
        </div>
 +
 
 +
 
 +
 
 +
 
 +
<div class="main">
 +
      <!-- HEADER/BANNER -->
 +
      <div class="banner-image">
 +
        <div class="banner-text resp">
 +
          <h1 style="font-family: 'Public Sans', sans-serif; font-weight: 600;">RESULTS</h1>
 +
             
 +
        </div>
 +
      </div>
 +
     
 +
      <!-- BODY -->
 +
      <div class="intro-body">
 +
<div class = "project-design" id="project-design">
 +
        <h2>OVERVIEW</h2>
 +
        <p>
 +
        The following page describes the summarized results of our work in each of our subprojects. Please visit the corresponding links to the subproject specific pages to get more details on the background information and our methods. </p>
  
 
</div>
 
</div>
 +
<br>
 +
<hr>
 +
<div class = "part-design" id="part-design">
 +
        <h2>ENGINEERING SUCCESS</h2>
 +
        <h4>Cellulase Integration</h4>
 +
<a href="Cellulase_Engineering"><p style="font-size: 80%; font-weight: bold; color:#0197AE;">Go to Cellulase page </p></a>
 +
        <p>
 +
Our cellulase integration system makes Oviita sustainable and accessible to VAD communities. This year our goals were to design our cellulase parts and make sure they were suited for function in <span style="font-style:italic">Y. lipolytica</span> and do preliminary testing with commercial cellulose and cellulase to prove the functionality of our idea before we moved forward with genetic engineering. </p>
  
 +
<p>Overall, this year we were able to: </p>
  
 +
&#10004;&nbsp; Select, model, and optimize our cellulase proteins for function in <span style="font-style: italic;class="italic">Y. lipolytica</span> <br>
  
−
<div class="column third_size" >
+
&#10004;&nbsp;Contribute 20 parts to the iGEM registry <br>
−
<div class="highlight decoration_A_full">
+
 
−
<h3>Inspiration</h3>
+
&#10004;&nbsp;Extensively plan all of our experiments for the next year <br>
−
<p>See how other teams presented their results.</p>
+
 
 +
&#10004;&nbsp;Determine minimum amount of glucose concentration required to maintain <span style="font-style:italic">Y. lipolytica</span> <br>
 +
 
 +
&#10004;&nbsp;Determine approximately how much cellulase enzyme is required to reach that minimum glucose concentration <br>
 +
 
 +
&#10004;&nbsp;Verify that <span style="font-style:italic">Y. lipolytica</span> can grow on crude (and pure) cellulose when cellulases are present<br>
 +
<br>
 +
 
 +
 
 +
        </p>
 +
        <h4>Biocontainment</h4>
 +
<a href="Biocontainment_Engineering"><p style="font-size: 80%; font-weight: bold; color:#0197AE;">Go to Biocontainment page </p></a>
 +
        <p>
 +
       
 +
We developed a sustainable and affordable biosafety system where two yeast strains will be co-cultured together in a syntrophic community. These strains will each be auxotrophic for a molecule the other strain has been modified to overproduce. This ensures that the two strains are co-dependent, reducing the chances of environmental escape. The organism can only proliferate if both strains are present in sufficient quantities to support each other’s growth. Ultimately, this novel method of co-dependent auxotrophy provides an easily implementable biocontainment strategy to prevent the escape of genetically engineered organisms.</p>
 +
<p>This season specifically, we developed a proof of concept for our co-culturing system using a pair of already engineered <span style="font-style:italic">S. cerevisiae</span> strains. We are happy to say that by the end of this season, we accomplished quite a bit:</p>
 +
 
 +
<p>&#10004;&nbsp;We successfully characterised a proof of concept for our biocontainment system using a pair of already engineered <span style="font-style:italic">S. cerevisiae</span> strains:</p>
 
<ul>
 
<ul>
−
<li><a href="https://2014.igem.org/Team:TU_Darmstadt/Results/Pathway">2014 TU Darmstadt </a></li>
+
<li>Characterised the strains in terms of auxotrophy and amino acid overproduction </li>
−
<li><a href="https://2014.igem.org/Team:Imperial/Results">2014 Imperial </a></li>
+
<li>Created a viable co-culture demonstrating the ability of the strains to survive using the amino acid released by each of the complementary strains </li>
−
<li><a href="https://2014.igem.org/Team:Paris_Bettencourt/Results">2014 Paris Bettencourt </a></li>
+
<li>Demonstrated the inability of the yeast to survive in environmental conditions outside of the expected growth vessel conditions </li>
−
</ul>
+
</ul> <br>
−
</div>
+
<p>&#10004;&nbsp;We designed and submitted a total of eight parts to the <a href="Parts">parts registry</a> that allow for the engineering of <span style="font-style:italic">Y. lipolytica</span> to create complementary overproducing, auxotrophic strains.</p>
 +
<br>
 +
 +
 +
 
 +
        <h4>Thymol Production</h4>
 +
<a href="Thymol_Engineering"><p style="font-size: 80%; font-weight: bold; color:#0197AE;">Go to Thymol page </p></a>
 +
          <p>
 +
       
 +
We developed a system where our supplemental yeast can produce thymol, an anthelmintic compound, which can serve as a temporary measure in between rounds of mass-deworming. This will allow the perforated intestines of parasite-infected children to heal and maximize vitamin A and micronutrient absorption. </p>
 +
 
 +
<p>This year in particular, we were able to do the following: </p>
 +
<p>&#10004;&nbsp;Identified promoter and gene sequences for thymol production in <span style="font-style:italic">Y. lipolytica</span></p>
 +
 
 +
<br>
 +
<p>&#10004;&nbsp;Collected our reagents and C. elegans for testing </p>
 +
<br>
 +
 
 +
<p>&#10004;&nbsp;Extensively planned all of our experiments and made troubleshooting plans </p>
 +
<br>
 
</div>
 
</div>
 +
<br>
 +
<hr>
 +
<div class = "experimental-design" id="experimental-design">
 +
        <h2>HUMAN PRACTICES</h2>
 +
        <h4>Creating a human-centred project</h4>
 +
<a href="Human_Practices"><p style="font-size: 80%; font-weight: bold; color:#0197AE;">Go to Human Practices page </p></a>
 +
        <p>
 +
          By following our HP pipeline, we were able to inform our design with help from experts in the community from start to finish, at every step in the project. We were careful to consult those with experience in every aspect of our project, from anthropologists, to NGOs, to medical doctors, to local health workers living in our target communities, and everything in between. By accessing a broad spectrum of viewpoints and experiences, we were able to consider the complex issue of Vitamin A deficiency holistiaclly, and create Oviita to address it from every angle we could. That direction by the community became the foundations of not only the Vitamin A production itself, but cellulases to ensure long-term financial sustainability, thymol production to address parasitic inhibition of vitamin absorption, Randall Cell to improve VAD diagnosis and public health data, and our plans for future implementation.
 +
        </p>
 +
 +
</div>
 +
<br>
 +
<hr>
 +
<div class = "implementation" id="implementation">
 +
        <h2>PROPOSED IMPLEMENTATION</h2>
 +
        <h4>Bioreactor</h4>
 +
<a href="Bioreactor"><p style="font-size: 80%; font-weight: bold; color:#0197AE;">Go to Bioreactor page </p></a>
 +
        <p>
 +
          With the help our our HP contacts, we have been able to make extensive plans for where, how, and by whom our project can best be implemented in order to maximize consumer acceptance of Oviita. This has meant minimizing cost and inconvenience, and maximizing accessibility and integration. By designing the FAB bioreactor with a flexible but effective design, it can now be adapted by communities to utilize the varying resources they have available. We have been able to recieve feedback from community members in VAD regions that these plans seem accessible and feasible within their local areas, and would be readily adopted. We also considered the taste of our product and ability to be incorporated into local diets. We were able to determine common regional dishes, with some aditional help from HP team members with family in affected regions of South Asia, and plan how Oviita could be incorporated into meals. To further increase economic viability, we developed plans and partnerships for the development of locally-led microenterprises forr the production and sale of yeast. Finally, we ensured using literature review that we could be confident of the safety of our product for future use.
 +
        </p>
 +
 +
</div>
 +
<br>
 +
<hr>
 +
<div class = "engagement" id="engagement">
 +
        <h2>ENGAGEMENT</h2>
 +
        <h4>Education</h4>
 +
<a href="Education"><p style="font-size: 80%; font-weight: bold; color:#0197AE;">Go to Education page </p></a>
 +
        <p>
 +
          We successfully developed and executed an introductory synthetic biology course at the undergraduate level--the only synthetic biology-specific course offered at our institution. This has helped bring more attention to the field of synthetic biology to faculty members and students alike. Our course included a variety of assignments, laboratory experiments, and group work to train new iGEM members for the season. Furthermore, we dedicated ourselves to helping iGEM teams by providing mentorship on human practices and team organization. We also developed a branding style guide that we implemented in our own project this season, which promotes scientific communication to general audiences. You can learn more <a href="Education">here</a>.
 +
        </p>
 +
        <h4>Collaborations</h4>
 +
<a href="Collaborations"><p style="font-size: 80%; font-weight: bold; color:#0197AE;">Go to Collaboration page </p></a>
 +
        <p>
 +
          iGEM Calgary is all about cooperation, and that can be seen from the list of collaborations we did this year. Our King’s College London collaboration provided us with the tools to develop iGAM 2.0, one of our smaller software projects, and iGEM Toulouse graciously provided us with constructs that could be implemented into the Oviita yeast in the future. Our attendance at friendly meet-ups and competitions, such as cGEM and Concordia’s Mini-Jamboree, lead to us revisiting and refining many aspects of our project, and really taking the judge’s critiques to mind. They also gave us good ideas for how we could improve JulyGEM, the online iGEM meet-up we held at the end of July. JulyGEM also led to us getting to know other teams and their projects relatively early in the iGEM season. Our education collaborations lead to more feedback on our MDSC507 synthetic biology course, giving us more direction for future editions, and helped us develop friendships with iGEM teams worldwide. As the saying goes, sharing is caring!
 +
        </p>
 +
 +
</div>
 +
<br>
 +
<hr>
 +
<div class = "parts" id="parts">
 +
        <h2>PARTS</h2>
 +
        <h4>Characterize</h4>
 +
<a href="Characterize"><p style="font-size: 80%; font-weight: bold; color:#0197AE;">Go to Parts Characterization page </p></a>
 +
        <p>
 +
          We added new literature-review characterization to <a href="BBa_K2117000">BBa_K2117000</a> from the iGEM registry and also made plans to experimentally characterize this part when we have further lab access. Furthermore, we have contributed the first engineered cellulases for <span style="font-style:italic">Y. lipolytica</span> to the iGEM registry <a href="BBa_K3629013">(BBa_K3629013</a> and <a href="BBa_K3629016">BBa_K3629016)</a> and discussed our in-silico characterization and future experimental plans.
 +
        </p>
 +
 +
</div>
 +
<br>
 +
<hr>
 +
<div class = "modelling" id="modelling">
 +
        <h2>MODELLING, SOFTWARE, AND MEASUREMENT</h2>
 +
        <h4>Bellatrix</h4>
 +
<a href="Bellatrix"><p style="font-size: 80%; font-weight: bold; color:#0197AE;">Go to Bellatrix page </p></a>
 +
        <p>
 +
The ultimate underdog story, though Bellatrix was never an underdog. It started as a quest to break free from the PDB standard into a format that provided more relational information. This crusade ultimately ballooned out of our expectations and finished with a beautiful piece of software, a manuscript, and has inspired many to reread the Harry Potter series.
 +
        </p>
 +
        <h4>Protein Modelling</h4>
 +
<a href="Model"><p style="font-size: 80%; font-weight: bold; color:#0197AE;">Go to Modelling page </p></a>
 +
        <p>
 +
Jacques Vaché once said, "Nature is only another chimera.". This hits a little too close to home for our modelling team. Over the summer, we worked to improve, and then subsequently prove these improvements were not structurally detrimental to our two modified cellulases. The improvements took the form of literature review on what optimal chimeric protein could be made from the available components. This resulted in our two cellulases, dubbed Penny and SEGI-8 to be generated and verified in silico.
 +
        </p>
 +
        <h4>GausHaus</h4>
 +
<a href="GausHaus"><p style="font-size: 80%; font-weight: bold; color:#0197AE;">Go to GausHaus page </p></a>
 +
        <p>
 +
GausHaus was not like the other software sitting by the beach enjoying sparkling cider; it put in the work.  GausHaus spent the summer confusing and terrorizing our statistician with sprinkles of success amongst an ocean of setbacks. Once it clicked though, we were off to the races with GausHaus coming through whenever called upon. This resulted in it being instrumental to our protein modelling, allowing the quantification of SEGI-8s dynamics along all three axes. It then also served as a software contribution to the iGEM community. And just when we thought it was done, it hit us. GausHaus' quantification of protein dynamics is an ideal measurement for teams during this renaissance of computational biology brought on by COVID-19. All in all we fought, we loved, and we demolished some molecular dynamics. What more could you ask for?
 +
        </p>
 +
<h4>THE LITTLE GUYS - PERIPHERY SOFTWARE</h4>
 +
<a href="Software"><p style="font-size: 80%; font-weight: bold; color:#0197AE;">Go to Software page </p></a>
 +
        <p>
 +
Not everyone can be a quarterback. This was apparent for our team this summer as we focused on our top two software: Bellatrix and GausHaus. Despite our focus, we found small software projects developing in the periphery. These projects include Sticks, iGAM 2.0, and our Hardware necessitated software. The Hardware Software was incredibly important to our bioreactor and Randles Cell Testing Device. iGAM 2.0 became a meaningful collaboration/development path with the KCL iGEM team. And Sticks homoured our gristled statistician with its cute GIFs. Overall Oviita benefited from these projects just as much as the ones we planned for.
 +
</p>
 +
 +
</div>
 +
<br>
 +
<hr>
 +
 +
 +
 +
  
  
Line 66: Line 326:
  
  
 +
          </div> <!-- add in new section of CONTENT above this -->
 +
      </div>
 +
    </div>
 +
  </body>
 
</html>
 
</html>
 +
{{Calgary/Imposter-Footer}}

Latest revision as of 03:57, 28 October 2020



OVERVIEW

The following page describes the summarized results of our work in each of our subprojects. Please visit the corresponding links to the subproject specific pages to get more details on the background information and our methods.


ENGINEERING SUCCESS

Cellulase Integration

Go to Cellulase page

Our cellulase integration system makes Oviita sustainable and accessible to VAD communities. This year our goals were to design our cellulase parts and make sure they were suited for function in Y. lipolytica and do preliminary testing with commercial cellulose and cellulase to prove the functionality of our idea before we moved forward with genetic engineering.

Overall, this year we were able to:

✔  Select, model, and optimize our cellulase proteins for function in Y. lipolytica
✔ Contribute 20 parts to the iGEM registry
✔ Extensively plan all of our experiments for the next year
✔ Determine minimum amount of glucose concentration required to maintain Y. lipolytica
✔ Determine approximately how much cellulase enzyme is required to reach that minimum glucose concentration
✔ Verify that Y. lipolytica can grow on crude (and pure) cellulose when cellulases are present

Biocontainment

Go to Biocontainment page

We developed a sustainable and affordable biosafety system where two yeast strains will be co-cultured together in a syntrophic community. These strains will each be auxotrophic for a molecule the other strain has been modified to overproduce. This ensures that the two strains are co-dependent, reducing the chances of environmental escape. The organism can only proliferate if both strains are present in sufficient quantities to support each other’s growth. Ultimately, this novel method of co-dependent auxotrophy provides an easily implementable biocontainment strategy to prevent the escape of genetically engineered organisms.

This season specifically, we developed a proof of concept for our co-culturing system using a pair of already engineered S. cerevisiae strains. We are happy to say that by the end of this season, we accomplished quite a bit:

✔ We successfully characterised a proof of concept for our biocontainment system using a pair of already engineered S. cerevisiae strains:

  • Characterised the strains in terms of auxotrophy and amino acid overproduction
  • Created a viable co-culture demonstrating the ability of the strains to survive using the amino acid released by each of the complementary strains
  • Demonstrated the inability of the yeast to survive in environmental conditions outside of the expected growth vessel conditions

✔ We designed and submitted a total of eight parts to the parts registry that allow for the engineering of Y. lipolytica to create complementary overproducing, auxotrophic strains.


Thymol Production

Go to Thymol page

We developed a system where our supplemental yeast can produce thymol, an anthelmintic compound, which can serve as a temporary measure in between rounds of mass-deworming. This will allow the perforated intestines of parasite-infected children to heal and maximize vitamin A and micronutrient absorption.

This year in particular, we were able to do the following:

✔ Identified promoter and gene sequences for thymol production in Y. lipolytica


✔ Collected our reagents and C. elegans for testing


✔ Extensively planned all of our experiments and made troubleshooting plans



HUMAN PRACTICES

Creating a human-centred project

Go to Human Practices page

By following our HP pipeline, we were able to inform our design with help from experts in the community from start to finish, at every step in the project. We were careful to consult those with experience in every aspect of our project, from anthropologists, to NGOs, to medical doctors, to local health workers living in our target communities, and everything in between. By accessing a broad spectrum of viewpoints and experiences, we were able to consider the complex issue of Vitamin A deficiency holistiaclly, and create Oviita to address it from every angle we could. That direction by the community became the foundations of not only the Vitamin A production itself, but cellulases to ensure long-term financial sustainability, thymol production to address parasitic inhibition of vitamin absorption, Randall Cell to improve VAD diagnosis and public health data, and our plans for future implementation.


PROPOSED IMPLEMENTATION

Bioreactor

Go to Bioreactor page

With the help our our HP contacts, we have been able to make extensive plans for where, how, and by whom our project can best be implemented in order to maximize consumer acceptance of Oviita. This has meant minimizing cost and inconvenience, and maximizing accessibility and integration. By designing the FAB bioreactor with a flexible but effective design, it can now be adapted by communities to utilize the varying resources they have available. We have been able to recieve feedback from community members in VAD regions that these plans seem accessible and feasible within their local areas, and would be readily adopted. We also considered the taste of our product and ability to be incorporated into local diets. We were able to determine common regional dishes, with some aditional help from HP team members with family in affected regions of South Asia, and plan how Oviita could be incorporated into meals. To further increase economic viability, we developed plans and partnerships for the development of locally-led microenterprises forr the production and sale of yeast. Finally, we ensured using literature review that we could be confident of the safety of our product for future use.



PARTS

Characterize

Go to Parts Characterization page

We added new literature-review characterization to BBa_K2117000 from the iGEM registry and also made plans to experimentally characterize this part when we have further lab access. Furthermore, we have contributed the first engineered cellulases for Y. lipolytica to the iGEM registry (BBa_K3629013 and BBa_K3629016) and discussed our in-silico characterization and future experimental plans.


MODELLING, SOFTWARE, AND MEASUREMENT

Bellatrix

Go to Bellatrix page

The ultimate underdog story, though Bellatrix was never an underdog. It started as a quest to break free from the PDB standard into a format that provided more relational information. This crusade ultimately ballooned out of our expectations and finished with a beautiful piece of software, a manuscript, and has inspired many to reread the Harry Potter series.

Protein Modelling

Go to Modelling page

Jacques Vaché once said, "Nature is only another chimera.". This hits a little too close to home for our modelling team. Over the summer, we worked to improve, and then subsequently prove these improvements were not structurally detrimental to our two modified cellulases. The improvements took the form of literature review on what optimal chimeric protein could be made from the available components. This resulted in our two cellulases, dubbed Penny and SEGI-8 to be generated and verified in silico.

GausHaus

Go to GausHaus page

GausHaus was not like the other software sitting by the beach enjoying sparkling cider; it put in the work. GausHaus spent the summer confusing and terrorizing our statistician with sprinkles of success amongst an ocean of setbacks. Once it clicked though, we were off to the races with GausHaus coming through whenever called upon. This resulted in it being instrumental to our protein modelling, allowing the quantification of SEGI-8s dynamics along all three axes. It then also served as a software contribution to the iGEM community. And just when we thought it was done, it hit us. GausHaus' quantification of protein dynamics is an ideal measurement for teams during this renaissance of computational biology brought on by COVID-19. All in all we fought, we loved, and we demolished some molecular dynamics. What more could you ask for?

THE LITTLE GUYS - PERIPHERY SOFTWARE

Go to Software page

Not everyone can be a quarterback. This was apparent for our team this summer as we focused on our top two software: Bellatrix and GausHaus. Despite our focus, we found small software projects developing in the periphery. These projects include Sticks, iGAM 2.0, and our Hardware necessitated software. The Hardware Software was incredibly important to our bioreactor and Randles Cell Testing Device. iGAM 2.0 became a meaningful collaboration/development path with the KCL iGEM team. And Sticks homoured our gristled statistician with its cute GIFs. Overall Oviita benefited from these projects just as much as the ones we planned for.