Difference between revisions of "Team:Calgary/Contribution"

 
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           /></a>
 
           /></a>
  
−
          <a href="#project-design">Branding Style Guide</a>
+
           <a href="#part-characterization">Part Characterization</a>
−
<br>
+
−
           <a href="#part-design">Educational Tools</a>
+
 
<br>
 
<br>
 
           <a href="#experimental-design">Part Collection</a>
 
           <a href="#experimental-design">Part Collection</a>
 
<br>
 
<br>
−
           <a href="#part-characterization">Part Characterization</a>
+
          <a href="#project-design">Branding Style Guide</a>
 +
<br>
 +
           <a href="#part-design">Educational Tools</a>
 
<br>
 
<br>
 
           <a href="#future">Complementary Auxotrophy System</a>
 
           <a href="#future">Complementary Auxotrophy System</a>
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<br>
 
<br>
 
           <a href="#gaus-haus">GausHaus</a>
 
           <a href="#gaus-haus">GausHaus</a>
−
<br>
 
−
          <a href="#protocols">Protocols</a>
 
 
         </div>
 
         </div>
  
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       <!-- BODY -->
 
       <!-- BODY -->
 
       <div class="intro-body">
 
       <div class="intro-body">
 +
<div class = "Part Characterization" id="part-characterization">
 +
        <h2>PART CHARACTERIZATION</h2>
 +
        <h4>Characterizing a <span style="font-style: italic;"class="italic">Y. lipolytica </span> promoter</h4>
 +
        <p>
 +
          <span style="font-style: italic;class="italic">Yarrowia lipolytica </span> is a promising new chassis that has a variety of applications in the field of biotechnology. This chassis, however, has not been well established in the iGEM community. As such important molecular elements such as strong constitutive promoters have not been well identified in the iGEM registry for use in this chassis. The development of strong promoter elements is necessary to allow for synthetic biology applications in the chassis as heterologous protein expression often requires a strong constitutive promoter.  In an effort to facilitate the use of this promising chassis in the iGEM community, we have characterized the <span style="font-style: italic;"class="italic">Y. lipolytica </span> native TEF1 promoter <a href="http://parts.igem.org/Part:BBa_K2117000">BBa_K2117000</a> using the information found in the literature. We have identified the basal expression level of the native promoter and methods for improving its expression.
 +
        </p>
 +
 +
<p> Furthermore, we have created experimental plans to characterize the activity of this promoter based on growth phase. This experiment is uses a standard GFP reporter where expression and thereby promoter activity cane quantified by fluorescence. Particularly Oviita, the growth of <span style="font-style: italic;class="italic">Y. lipolytica </span> needs to be monitored closely; therefore, if growth phase has an impact on promoter activity and protein expression levels this would be important information to inform our project.</p>
 +
 +
<p> Learn more on our <a href="Characterize">characterization page. </a>
 +
</div>
 +
<br>
 +
<hr>
 +
 +
<div class = "experimental-design" id="experimental-design">
 +
        <h2>PART COLLECTION</h2>
 +
        <h4>Creating meaningful parts for the iGEM community</h4>
 +
 +
<p> For <span style="font-style: italic;class="italic">Y. lipolytica</span>to be
 +
established further in the iGEM community, a greater breadth of molecular tools need to become available. Therefore, we developed and are contributing a <a href="https://2020.igem.org/Team:Calgary/Part_Collection"> <span style="font-style: italic;class="italic">Y. lipolytica </span> part collection</a>to the iGEM registry. This collection includes a number of essential basic parts such as strong constitutive promoters, a terminator, a signal peptide, antibiotic resistance genes, reporter genes, and amino acid synthesis genes. Together these parts make <span style="font-style: italic;class="italic">Y. lipolytica</span> a more usable chassis as these are essential molecular biology parts. Furthermore, we are introducing cellulase coding sequences that have been optimized for <span style="font-style: italic;class="italic">Y. lipolytica</span>. These are the first engineered cellulases of their kind specifically designed for <span style="font-style: italic;class="italic">Y. lipolytica</span>. By introducing cellulase genes to the <span style="font-style: italic;class="italic">Y. lipolytica</span> genome, this chassis will be less expensive and more sustainable to grow. </p>
 +
 +
<p> Aside from individual parts to assemble genetic constructs, we are also providing fully functional constructs with these coding sequences for high expression in <span style="font-style: italic;class="italic">Y. lipolytica</span>. The constructs can be attached to each other as well, making larger gene cassettes using <a href="BBa_K3629015">BBa_K3629015</a> as a destination vector. After assembly, the larger plasmid can be linearized using NotI and transformed into the <span style="font-style: italic;class="italic">Y. lipolytica</span> genome.  </p>
 +
 +
<p> Furthermore, our expression constructs include multiple unique Gibson homology sequences for modular assembly, learn more on our <a href="Part_Collection">part collection</a> page.</p>
 +
 +
</div>
 +
<br>
 +
<hr>
 +
 
<div class = "project-design" id="project-design">
 
<div class = "project-design" id="project-design">
 
         <h2>BRANDING STYLE GUIDE</h2>
 
         <h2>BRANDING STYLE GUIDE</h2>
 
         <h4>How do you create a brand for your project?</h4>
 
         <h4>How do you create a brand for your project?</h4>
 
         <p>
 
         <p>
−
           A branding style guide espouses the face, personality, and values of your project and defines its visual and voice identity. In other words, your branding style guide shapes how you present your project to the world, and how the world sees your project. Creating a branding style guide is an iterative process that begins with first understanding the values and personality of your project and of your target audiences. We understand that this can be a daunting task, so we used our own experience to develop a comprehensive branding style guide template. This guide can be downloaded as a pdf below and provides a scaffold for future iGEM teams looking to finesse their brand. Enjoy!
+
           A branding style guide espouses the face, personality, and values of your project and defines its visual and voice identity. In other words, your branding style guide shapes how you present your project to the world, and how the world sees your project. Creating a branding style guide is an iterative process that begins with first understanding the values and personality of your project and of your target audiences. We understand that this can be a daunting task, so we used our own experience in creating the <a href= "Branding"> Oviita Brand</a> to develop a comprehensive branding style guide template. This guide can be downloaded as a pdf below and provides a scaffold for future iGEM teams looking to finesse their brand. Enjoy!
 
         </p>
 
         </p>
 
         <p>
 
         <p>
−
         <b>Downloadable Branding Style Guide (pdf):</b> INSERT
+
         <b>Click here: <a href="https://static.igem.org/mediawiki/2020/b/b7/T--Calgary--BrandingStyleGuide.pdf">Branding Style Guide How-to</a></b>
−
        </p>
+
</p>
−
 
+
−
 
+
−
 
+
  
  
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         <h4>Promoting synthetic biology education and more</h4>
 
         <h4>Promoting synthetic biology education and more</h4>
 
         <p>
 
         <p>
−
           In order to provide a sustainable, community-based solution, we plan
+
           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. You can learn more <a href="Education">here</a>.  
−
          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>
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<hr>
 
<hr>
  
−
<div class = "experimental-design" id="experimental-design">
 
−
        <h2>PART COLLECTION</h2>
 
−
        <h4>Creating meaningful parts for the iGEM community</h4>
 
  
−
<p><span style="font-style: italic;class="italic">Y. lipolytica</span>
 
−
is a new promising chassis in molecular biology and needs to be established further in the iGEM community. To this aim, we have developed and are contributing a <a href="https://2020.igem.org/Team:Calgary/Part_Collection"> <span style="font-style: italic;class="italic">Y. lipolytica</span> part collection</a> to the iGEM registry. This collection includes a number of essential basic parts such as strong constitutive promoters, a terminator, a signal peptide, antibiotic resistance genes, reporter genes, and amino acid synthesis genes. Together these parts make <span style="font-style: italic;class="italic">Y. lipolytica</span> a more usable chassis as these are essential molecular biology parts. Furthermore, we are introducing cellulase coding sequences that have been optimized for <span style="font-style: italic;class="italic">Y. lipolytica</span>. By introducing the cellulase genes to the <span style="font-style: italic;class="italic">Y. lipolytica</span> genome, this chassis will be less expensive and more sustainable to grow. </p>
 
−
 
−
<p> Aside from individual parts to assemble genetic constructs, we are also providing fully functional constructs with these coding sequences for high expression in <span style="font-style: italic;class="italic">Y. lipolytica</span>. The constructs can be attached to each other as well into larger gene cassettes using BBa_K3629012 or BBa_K3629028 as a destination vector. After assembly, the larger plasmid can be linearized using NotI and transformed into the <span style="font-style: italic;class="italic">Y. lipolytica</span> genome.  </p>
 
−
 
−
<p> Furthermore our expression constructs include multiple unique Gibson homology sequences for modular assembly, learn more on our part collection page.</p>
 
−
 
−
</div>
 
−
<br>
 
−
<hr>
 
  
 
<div class = "future" id="future">
 
<div class = "future" id="future">
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         <h4>Co-culture biocontainment system</h4>
 
         <h4>Co-culture biocontainment system</h4>
 
         <p>
 
         <p>
−
          In order to provide a sustainable, community-based solution, we plan
+
Synthetic biology is an emerging field, providing solutions to agricultural, environmental, and healthcare problems through the manipulation and repurposing of biological systems. As synthetic biology grows in popularity, so does the need for effective biocontainment strategies that prevent the introduction of non-native organisms into the environment. Current containment strategies used in the industry revolve around the use of auxotrophic microorganisms. Such methods, however, are unsustainable as a constant supplementation of metabolites is required to keep the organism alive. This especially is a problem for biological systems that are designed for use in private spaces, such as households. To ensure that more synthetic biology solutions can be implemented outside of the laboratory, we developed a novel biocontainment strategy using a co-culture system of microorganisms. Our system uses two strains of yeast, cultured together in a syntrophic community. Each yeast strain will be auxotrophic for the molecule the other strain overproduces, resulting in the strains being mandated to stay together in order to survive. We built upon the robustness of an auxotrophy system to create a stable and sustainable solution to biosafety.  
−
          to genetically modify <i>Rhodosporidium toruloides</i>, an oleaginous
+
</p>
−
          yeast that naturally produces beta-carotene and lipids, to be more
+
 
−
          robust and resource-efficient. By modifying the yeast to produce
+
<p>
−
          cellulase, it can then use common agricultural waste products as an
+
Learn more on our <a href="https://2020.igem.org/Team:Calgary/Biocontainment_Engineering">biocontainment page</a>
−
          energy source for synthesizing its oil. It can then be eaten as a
+
</p>
−
          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>
+
 
</div>
 
</div>
 
<br>
 
<br>
Line 240: Line 246:
 
         <h4>Creating a protein library</h4>
 
         <h4>Creating a protein library</h4>
 
         <p>
 
         <p>
−
          In order to provide a sustainable, community-based solution, we plan
+
<a href="Bellatrix">Bellatrix</a> was made to help develop a method for iGEM teams to decompose structure files from the PDB format into usable relational matrices known as Star Files. This program is in Python and is open source to give teams the maximal amount of flexibility and utility.
−
          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>
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<div class = "GausHaus" id="gaus-haus">
 
<div class = "GausHaus" id="gaus-haus">
 
         <h2>GAUSHAUS</h2>
 
         <h2>GAUSHAUS</h2>
−
         <h4>Andrew pls halp</h4>
+
         <h4>Measuring Wonderland</h4>
−
        <p>
+
−
          In order to provide a sustainable, community-based solution, we plan
+
−
          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>
+
−
</div>
+
−
<br>
+
−
<hr>
+
−
<div class = "protocols" id="protocols">
+
−
        <h2>Protocols</h2>
+
−
        <h4>Contributing yeast protocols</h4>
+
 
         <p>
 
         <p>
−
          In order to provide a sustainable, community-based solution, we plan
+
The <a href="GausHaus">GausHaus</a> measuring software was developed to quantify the dynamics of proteins. It was successful, and we look forward to seeing this metric used by iGEM teams in future years. With a little sleuthing on the <a href="https://github.com/iGEMCalgary">iGEM Calgary Github</a> you may notice a large work in progress file. This is GausHaus' future, a promise to the iGEM community that this software will grow and develop to meet their needs, and help grow their possibilities in synthetic biology. GausHaus will be more than just a wonderful measurement.
−
          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>

Latest revision as of 03:09, 28 October 2020



PART CHARACTERIZATION

Characterizing a Y. lipolytica promoter

Yarrowia lipolytica is a promising new chassis that has a variety of applications in the field of biotechnology. This chassis, however, has not been well established in the iGEM community. As such important molecular elements such as strong constitutive promoters have not been well identified in the iGEM registry for use in this chassis. The development of strong promoter elements is necessary to allow for synthetic biology applications in the chassis as heterologous protein expression often requires a strong constitutive promoter. In an effort to facilitate the use of this promising chassis in the iGEM community, we have characterized the Y. lipolytica native TEF1 promoter BBa_K2117000 using the information found in the literature. We have identified the basal expression level of the native promoter and methods for improving its expression.

Furthermore, we have created experimental plans to characterize the activity of this promoter based on growth phase. This experiment is uses a standard GFP reporter where expression and thereby promoter activity cane quantified by fluorescence. Particularly Oviita, the growth of Y. lipolytica needs to be monitored closely; therefore, if growth phase has an impact on promoter activity and protein expression levels this would be important information to inform our project.

Learn more on our characterization page.


PART COLLECTION

Creating meaningful parts for the iGEM community

For Y. lipolyticato be established further in the iGEM community, a greater breadth of molecular tools need to become available. Therefore, we developed and are contributing a Y. lipolytica part collectionto the iGEM registry. This collection includes a number of essential basic parts such as strong constitutive promoters, a terminator, a signal peptide, antibiotic resistance genes, reporter genes, and amino acid synthesis genes. Together these parts make Y. lipolytica a more usable chassis as these are essential molecular biology parts. Furthermore, we are introducing cellulase coding sequences that have been optimized for Y. lipolytica. These are the first engineered cellulases of their kind specifically designed for Y. lipolytica. By introducing cellulase genes to the Y. lipolytica genome, this chassis will be less expensive and more sustainable to grow.

Aside from individual parts to assemble genetic constructs, we are also providing fully functional constructs with these coding sequences for high expression in Y. lipolytica. The constructs can be attached to each other as well, making larger gene cassettes using BBa_K3629015 as a destination vector. After assembly, the larger plasmid can be linearized using NotI and transformed into the Y. lipolytica genome.

Furthermore, our expression constructs include multiple unique Gibson homology sequences for modular assembly, learn more on our part collection page.


BRANDING STYLE GUIDE

How do you create a brand for your project?

A branding style guide espouses the face, personality, and values of your project and defines its visual and voice identity. In other words, your branding style guide shapes how you present your project to the world, and how the world sees your project. Creating a branding style guide is an iterative process that begins with first understanding the values and personality of your project and of your target audiences. We understand that this can be a daunting task, so we used our own experience in creating the Oviita Brand to develop a comprehensive branding style guide template. This guide can be downloaded as a pdf below and provides a scaffold for future iGEM teams looking to finesse their brand. Enjoy!

Click here: Branding Style Guide How-to


EDUCATIONAL TOOLS

Promoting synthetic biology education and more

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. You can learn more here.


COMPLEMENTARY AUXOTROPHY SYSTEM

Co-culture biocontainment system

Synthetic biology is an emerging field, providing solutions to agricultural, environmental, and healthcare problems through the manipulation and repurposing of biological systems. As synthetic biology grows in popularity, so does the need for effective biocontainment strategies that prevent the introduction of non-native organisms into the environment. Current containment strategies used in the industry revolve around the use of auxotrophic microorganisms. Such methods, however, are unsustainable as a constant supplementation of metabolites is required to keep the organism alive. This especially is a problem for biological systems that are designed for use in private spaces, such as households. To ensure that more synthetic biology solutions can be implemented outside of the laboratory, we developed a novel biocontainment strategy using a co-culture system of microorganisms. Our system uses two strains of yeast, cultured together in a syntrophic community. Each yeast strain will be auxotrophic for the molecule the other strain overproduces, resulting in the strains being mandated to stay together in order to survive. We built upon the robustness of an auxotrophy system to create a stable and sustainable solution to biosafety.

Learn more on our biocontainment page


BELLATRIX

Creating a protein library

Bellatrix was made to help develop a method for iGEM teams to decompose structure files from the PDB format into usable relational matrices known as Star Files. This program is in Python and is open source to give teams the maximal amount of flexibility and utility.


GAUSHAUS

Measuring Wonderland

The GausHaus measuring software was developed to quantify the dynamics of proteins. It was successful, and we look forward to seeing this metric used by iGEM teams in future years. With a little sleuthing on the iGEM Calgary Github you may notice a large work in progress file. This is GausHaus' future, a promise to the iGEM community that this software will grow and develop to meet their needs, and help grow their possibilities in synthetic biology. GausHaus will be more than just a wonderful measurement.