Difference between revisions of "Team:Virginia/Awards"

 
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      <div class="menulogo">MANIFOLD</div>
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            <a class="active mainitem" href="#home">HOME</a>
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              <a class="hvr-sweep-to-right" href="index.html#">Main</a>
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              <a class="hvr-sweep-to-right" href="index.html#abstract">Abstract</a>
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            <a class="mainitem" href="#project">PROJECT</a>
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              <a class="hvr-sweep-to-right" href="#">Inspiration</a>
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            <a class="mainitem" href="#parts">PARTS</a>
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              <a class="hvr-sweep-to-right" href="#">New Parts</a>
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            <a class="mainitem" href="#outreach">OUTREACH</a>
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              <a class="hvr-sweep-to-right" href="#">Human Practices</a>
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              <a class="hvr-sweep-to-right" href="https://2020.igem.org/Team:Virginia/Members">Members</a>
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            <a class="mainitem" href="#awards">AWARDS</a>
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              <a class="hvr-sweep-to-right" href="#">Awards</a>
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              <a class="hvr-sweep-to-right" href="#">Medals</a>
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            <a class="mainitem" href="#about">RESOURCES</a>
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              <a class="hvr-sweep-to-right" href="#">Papers</a>
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              <a class="hvr-sweep-to-right" href="#">Nucleic Acids</a>
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            Index:
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            <div>General Template Page</div>
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          <div class="sectionTitle" id="Section 1">Section 1</div>
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                The lack of a versatile and reliable way to improve metabolic flux channeling, pathway orthogonality, and product yields is a major impediment to the expanded utilization of biosynthesis for the production of drugs and industrially valuable chemicals. Manifold, a platform technology that addresses this problem, consists of <div class="dict">bacterial microcompartments<span><img src="https://upload.wikimedia.org/wikipedia/commons/thumb/2/25/Carboxysome_and_bacterial_microcompartments.jpg/800px-Carboxysome_and_bacterial_microcompartments.jpg"/>Bacterial microcompartments (BMCs) are organelle-like structures, consisting of a protein shell that encloses enzymes and other proteins. BMCs are typically about 40–200 nanometers in diameter and are entirely made of proteins. The shell functions like a membrane, as it is selectively permeable.</span></div> (BMCs) with encapsulated dsDNA scaffolds <div class="ref">[1]<span>Elbaz, J., Yin, P., &amp; Voigt, C. A. (2016). Genetic encoding of DNA nanostructures and their self-assembly in living bacteria. Nature communications, 7(1), 1-11.</span></div> that sequester and spatially organize, at fixed concentrations, biosynthetic enzymes presented as zinc-finger fusion proteins. Here we deliver the designs for an E. coli cell capable of synthesizing resveratrol using the Manifold platform. The Manifold platform will help lower costs and expand the applications of chemical biosynthesis. The lack of a versatile and reliable way to improve metabolic flux channeling, pathway orthogonality, and product yields is a major impediment to the expanded utilization of biosynthesis for the production of drugs and industrially valuable chemicals. Manifold, a platform technology that addresses this problem, consists of bacterial microcompartments (BMCs) with encapsulated dsDNA scaffolds that sequester and spatially organize, at fixed concentrations, biosynthetic enzymes presented as zinc-finger fusion proteins. Here we deliver the designs for an E. coli cell capable of synthesizing resveratrol using the Manifold platform. The Manifold platform will help lower costs and expand the applications of chemical biosynthesis.
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              The invention consists of a protein shell comprising one or more proteins, one or more nucleic acid scaffolds of which there can be multiple copies, anabolic and/or catabolic enzymes specific to the desired biosynthesis pathway each containing a nucleic acid binding domain, recognition sequences for the utilized nucleic acid binding domains, nucleic acid spacers, and a linkage between the nucleic acid scaffolds and the protein shell. The protein shell (10) can take the form of any closed or open surface that comprises one or more repeating protein units (12). Examples of valid shells include bacterial microcompartments such as the Pdu, Eut, and carboxysome microcompartments, as well as modified,  but not necessarily closed, surfaces composed of mutated versions of these microcompartment shell proteins. The nucleic acid scaffolds (18) comprise multiple recognition sequences (22) and spacers (32) and can be made from any form of nucleic acid, including: deoxyribonucleic acid, ribonucleic acid, and synthetic nucleic acids such as xeno nucleic acids and peptide nucleic acids among others. These scaffolds are attached to the protein shell. The pathway enzymes are biological proteins whose exact sequences are dependent on the given use case of the invention, but which all contain a nucleic acid binding domain either internal to their structure, or at their N or C terminus.
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              <b>Fig 1.</b> Figure taken from iGEM Tainan 2019 for demo purposes. Notice how the figure is much longer than it is wide, and two images are coupled together to achive this. Try to do that as well so it looks good.
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              Additionally, protein linkers are usually present between this nucleic acid binding domain and the enzyme structure to prevent inhibition of enzyme activity. However the exact linker(s) used,  if any, is(are) also dependent on the specific use case of the invention. These pathway enzymes are attached to the nucleic acid scaffolds via their nucleic acid binding domains. The nucleic acid recognition sequences (22) are unique or semi-unique sequences of nucleic acid monomers on the nucleic acid scaffolds to which the utilized nucleic acid binding domains have some degree of molecular complementarity. These nucleic recognition sequences comprise most of the scaffold and mark the locations to which the DNA binding domains of the pathway enzymes attach to the scaffolds. The nucleic acid spacers (32) are relatively short sequences of nucleic acid monomers that are also present on the nucleic acid scaffolds, between the recognition sequences. The linkage between the nucleic acid scaffolds (18) and protein shell (10) provides a means by which the nucleic acid scaffolds are bound to the protein shell through direct or multi-molecule complementarity. This linkage is found between the nucleic acid scaffolds and the protein shell. One example is through the addition of a nucleic acid binding domain (24) to one or more of the shell proteins forming a nucleic acid binding domain, shell protein fusion (14). Like the pathway enzymes, this nucleic acid binding-domain can be either internal to the shell protein structure or at its N or C terminus, where the exact placement depends on the shell protein being utilized. Alternatively, one or more intermediate proteins can be used to adhere the nucleic acid scaffolds to the shell, where the region of the protein interacting with the shell binds the shell via protein-protein complementarity (28) with a given shell protein, and the region of the protein interacting with the nucleic acid scaffold binds another recognition sequence on the nucleic acid scaffold through another nucleic acid binding domain (30). This forms a shell protein binding, nucleic acid domain fusion (26).<br/><br/><br/>
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           <div class="sectionTitle" id="Section 1">Section 1</div>
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           <div class="sectionTitle" id="Section 1">Bronze Medal Requirements</div>
 
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             <h3>Deliverables
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                The lack of a versatile and reliable way to improve metabolic flux channeling, pathway orthogonality, and product yields is a major impediment to the expanded utilization of biosynthesis for the production of drugs and industrially valuable chemicals. Manifold, a platform technology that addresses this problem, consists of <div class="dict">bacterial microcompartments<span><img src="https://upload.wikimedia.org/wikipedia/commons/thumb/2/25/Carboxysome_and_bacterial_microcompartments.jpg/800px-Carboxysome_and_bacterial_microcompartments.jpg"/>Bacterial microcompartments (BMCs) are organelle-like structures, consisting of a protein shell that encloses enzymes and other proteins. BMCs are typically about 40–200 nanometers in diameter and are entirely made of proteins. The shell functions like a membrane, as it is selectively permeable.</span></div> (BMCs) with encapsulated dsDNA scaffolds <div class="ref">[1]<span>Elbaz, J., Yin, P., &amp; Voigt, C. A. (2016). Genetic encoding of DNA nanostructures and their self-assembly in living bacteria. Nature communications, 7(1), 1-11.</span></div> that sequester and spatially organize, at fixed concentrations, biosynthetic enzymes presented as zinc-finger fusion proteins. Here we deliver the designs for an E. coli cell capable of synthesizing resveratrol using the Manifold platform. The Manifold platform will help lower costs and expand the applications of chemical biosynthesis. The lack of a versatile and reliable way to improve metabolic flux channeling, pathway orthogonality, and product yields is a major impediment to the expanded utilization of biosynthesis for the production of drugs and industrially valuable chemicals. Manifold, a platform technology that addresses this problem, consists of bacterial microcompartments (BMCs) with encapsulated dsDNA scaffolds that sequester and spatially organize, at fixed concentrations, biosynthetic enzymes presented as zinc-finger fusion proteins. Here we deliver the designs for an E. coli cell capable of synthesizing resveratrol using the Manifold platform. The Manifold platform will help lower costs and expand the applications of chemical biosynthesis.
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              1. Wiki - You're on it! The Wiki will be updated with results from the competition after the Wiki Thaw on November 25th. Thanks for visiting!<br/>2. Poster - Our poster can be found on the <a href="https://2020.igem.org/Team:Virginia/Poster">Poster Page</a><br/>3. Presentation Video - This video is still forthcoming<br/>4. Project Promotion Video - Find this video on the <a href="https://2020.igem.org/Team:Virginia">Main Page</a><br/>5. Judging Form - The form is completed and available for Judges to view as of October 28th.
 +
            <h3>Attributions
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 +
          The <a href="https://2020.igem.org/Team:Virginia/Attributions">Attributions Page</a> gives credit for all contributions to Manifold. Thank you to everyone who made this project possible!
 +
            <h3>Project Description
 +
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 +
              To learn more about our project, please visit the <a href="https://2020.igem.org/Team:Virginia/Description">Project Description Page</a>.
 +
            <h3>Contribution
 +
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              We are proud to present iGEM's Resource Hub on our <a href="https://2020.igem.org/Team:Virginia/Contribution">Contributions Page</a>. This Hub will soon be available on the iGEM site to share the resources we found with as many future teams as possible.<br/><br/>
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          <div class="sectionTitle" id="Section 2">Silver Medal Requirements</div>
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            <h3>Engineering Success
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              Check out our <a href="https://2020.igem.org/Team:Virginia/Engineering">Engineering Page</a> to see how we followed the engineering design cycle to develop the best version of Manifold by taking into account input from our models, realizing we need to recycle malonyl-coA, designing and re-designing our scaffolds, and planning new ways to test the efficacy of our device.
 +
            <h3>Collaboration
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              The <a href="https://2020.igem.org/Team:Virginia/Collaborations">Collaborations Page</a> talks about our close work with the Univeristy of Chicago iGEM Team as well as a far-reaching, informative project we call the Resource Hub.
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            <h3>Human Practices
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              Read about the many brilliant experts who gave input on our project, as well as the deliverables those interactions inspired, on the <a href="https://2020.igem.org/Team:Virginia/Human_Practices">Human Practices Page</a>.
 +
            <h3>Proposed Implementation
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              How will Manifold even work in the real world? What applications of the device are possible in the future? What will the positive impact of Manifold have on the field of synbio and the world of pharmaceuticals? All of your questions are answered on the <a href="https://2020.igem.org/Team:Virginia/Implementation">Implementation Page</a>.<br/><br/>
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          <div class="sectionTitle" id="Section 3">Gold Medal Requirements</div>
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            <h3>Integrated Human Practices
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              From pondering ethics to building models to continually improving design, Human Practices was deeply incorporated into every aspect of Manifold. Take a look at our <a href="https://2020.igem.org/Team:Virginia/Human_Practices">Human Practices Page</a> for a more in-depth description of all the ways IHP impacted our project.
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            <h3>Project Modeling
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              We developed a complex network based on 7 main models and a mountain of literature behind them, all of which is detailed on our <a href="https://2020.igem.org/Team:Virginia/Model">Modeling Page</a>.
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            <h3>Excellence in Another Area: Entrepreneurship
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              Starting with the creation of a stand-alone Entrepreneurship committee, we dove into market research, consultations with experts, and planning the future of Manifold. All available on the <a href="https://2020.igem.org/Team:Virginia/Entrepreneurship">Entrepreneurship Page</a>.<br/><br/>
 
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              The invention consists of a protein shell comprising one or more proteins, one or more nucleic acid scaffolds of which there can be multiple copies, anabolic and/or catabolic enzymes specific to the desired biosynthesis pathway each containing a nucleic acid binding domain, recognition sequences for the utilized nucleic acid binding domains, nucleic acid spacers, and a linkage between the nucleic acid scaffolds and the protein shell. The protein shell (10) can take the form of any closed or open surface that comprises one or more repeating protein units (12). Examples of valid shells include bacterial microcompartments such as the Pdu, Eut, and carboxysome microcompartments, as well as modified,  but not necessarily closed, surfaces composed of mutated versions of these microcompartment shell proteins. The nucleic acid scaffolds (18) comprise multiple recognition sequences (22) and spacers (32) and can be made from any form of nucleic acid, including: deoxyribonucleic acid, ribonucleic acid, and synthetic nucleic acids such as xeno nucleic acids and peptide nucleic acids among others. These scaffolds are attached to the protein shell. The pathway enzymes are biological proteins whose exact sequences are dependent on the given use case of the invention, but which all contain a nucleic acid binding domain either internal to their structure, or at their N or C terminus.  
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             <div class="paragraph">IHP efforts this year have resulted in three diverse deliverables. We collaborated with other teams to create a Resource Hub, currently available <a href="https://2020.igem.org/Team:Virginia/Contribution">here</a>, which will soon be available on the iGEM Foundation site, and will share websites, software, databases, and other ways to assist teams working online. We also reached out to dozens of researchers, bioethicists, and industry leaders to discuss what place social movements have in science, had internal group discussions about how societal influence may cause bias and how to be aware of that bias, and our conclusions as a team were compiled into our <a href="https://2020.igem.org/Team:Virginia/Public_engagement">Code of Ethical Conduct</a>. We put special consideration into making this document adaptable for other teams and inclusive to the ethical beliefs of different societies, pursuing iGEM’s overall goal of international collaboration. Lastly, speaking with experts helped refine the design of our device, which is now patent-pending as a foundational advance in metabolic engineering.<br/>
 
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             <div class="paragraph">Without summer access to lab space, a large emphasis of the project was put on experimental planning and computational/mathematical modeling. <b>We built out an <a href="https://2020.igem.org/Team:Virginia/Model">extensive modeling pipeline</a> to best inform DNA scaffold design and metabolic flux through the BMC.</b> We developed a promoter model based on our cell kinetics models and evidence from literature to optimize our 14 parts to be used in experimental design. We also successfully investigated the spatial constraints presented by substrate molecules on BMC pore diffusion. Literature-based insight that malonyl-CoA was a limiting factor in the resveratrol metabolic pathway led us to model the diffusion of various substrates through the pore both spatially through PyMol, and metabolically using a custom-built pore-diffusion Matlab model. These models were pivotal in redefining our BMC substrate, and introducing a second scaffold to our inner BMC architecture.<br/>
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              <b>Fig 1.</b> Figure taken from iGEM Tainan 2019 for demo purposes. Notice how the figure is much longer than it is wide, and two images are coupled together to achive this. Try to do that as well so it looks good.
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            <h3>Best Supporting Entrepreneurship
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              Additionally, protein linkers are usually present between this nucleic acid binding domain and the enzyme structure to prevent inhibition of enzyme activity. However the exact linker(s) used,  if any, is(are) also dependent on the specific use case of the invention. These pathway enzymes are attached to the nucleic acid scaffolds via their nucleic acid binding domains. The nucleic acid recognition sequences (22) are unique or semi-unique sequences of nucleic acid monomers on the nucleic acid scaffolds to which the utilized nucleic acid binding domains have some degree of molecular complementarity. These nucleic recognition sequences comprise most of the scaffold and mark the locations to which the DNA binding domains of the pathway enzymes attach to the scaffolds. The nucleic acid spacers (32) are relatively short sequences of nucleic acid monomers that are also present on the nucleic acid scaffolds, between the recognition sequences. The linkage between the nucleic acid scaffolds (18) and protein shell (10) provides a means by which the nucleic acid scaffolds are bound to the protein shell through direct or multi-molecule complementarity. This linkage is found between the nucleic acid scaffolds and the protein shell. One example is through the addition of a nucleic acid binding domain (24) to one or more of the shell proteins forming a nucleic acid binding domain, shell protein fusion (14). Like the pathway enzymes, this nucleic acid binding-domain can be either internal to the shell protein structure or at its N or C terminus, where the exact placement depends on the shell protein being utilized. Alternatively, one or more intermediate proteins can be used to adhere the nucleic acid scaffolds to the shell, where the region of the protein interacting with the shell binds the shell via protein-protein complementarity (28) with a given shell protein, and the region of the protein interacting with the nucleic acid scaffold binds another recognition sequence on the nucleic acid scaffold through another nucleic acid binding domain (30). This forms a shell protein binding, nucleic acid domain fusion (26).<br/><br/><br/>
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             <div class="paragraph">Starting with extensive industry and market research, <b>we were able to calculate the theoretical improvement our device would provide to resveratrol manufacturers.</b> We also reached out to patent lawyers to discuss the importance of preventing prior art disclosure, and attended Cville BioHub meetings to look at future steps for our team. <b>It was clear we needed a <a href="https://2020.igem.org/Team:Virginia/Entrepreneurship">provisional patent</a>, so in August, we successfully filed one.</b> We were then able to review our device plans with experts from around the world who work with the same technology. We also talked to the CEO of one of the largest resveratrol distributors in North America, who confirmed the need for a cheaper, sustainable alternative. Finally, we talked to George McArthur, founder of Virginia iGEM and biotech expert, who pointed us to a company that helps startups test their devices in large-scale bioreactors and monitor the results in real time. <br/><br/><br/>
 
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Latest revision as of 05:37, 18 December 2020

Manifold

HOME
Main Abstract
PROJECT
Description Design Experiments Results Modeling Engineering Implementation Notebook Safety
PARTS
Parts
OUTREACH
Human Practices Public Engagement Collaborations Contributions Entrepreneurship
TEAM
Members Attributions
AWARDS
Awards Medals
RESOURCES
Sources Nucleic Acids Protocols
Index:
Awards
Bronze Medal Requirements

Deliverables

1. Wiki - You're on it! The Wiki will be updated with results from the competition after the Wiki Thaw on November 25th. Thanks for visiting!
2. Poster - Our poster can be found on the Poster Page
3. Presentation Video - This video is still forthcoming
4. Project Promotion Video - Find this video on the Main Page
5. Judging Form - The form is completed and available for Judges to view as of October 28th.

Attributions

The Attributions Page gives credit for all contributions to Manifold. Thank you to everyone who made this project possible!

Project Description

To learn more about our project, please visit the Project Description Page.

Contribution

We are proud to present iGEM's Resource Hub on our Contributions Page. This Hub will soon be available on the iGEM site to share the resources we found with as many future teams as possible.

Silver Medal Requirements

Engineering Success

Check out our Engineering Page to see how we followed the engineering design cycle to develop the best version of Manifold by taking into account input from our models, realizing we need to recycle malonyl-coA, designing and re-designing our scaffolds, and planning new ways to test the efficacy of our device.

Collaboration

The Collaborations Page talks about our close work with the Univeristy of Chicago iGEM Team as well as a far-reaching, informative project we call the Resource Hub.

Human Practices

Read about the many brilliant experts who gave input on our project, as well as the deliverables those interactions inspired, on the Human Practices Page.

Proposed Implementation

How will Manifold even work in the real world? What applications of the device are possible in the future? What will the positive impact of Manifold have on the field of synbio and the world of pharmaceuticals? All of your questions are answered on the Implementation Page.

Gold Medal Requirements

Integrated Human Practices

From pondering ethics to building models to continually improving design, Human Practices was deeply incorporated into every aspect of Manifold. Take a look at our Human Practices Page for a more in-depth description of all the ways IHP impacted our project.

Project Modeling

We developed a complex network based on 7 main models and a mountain of literature behind them, all of which is detailed on our Modeling Page.

Excellence in Another Area: Entrepreneurship

Starting with the creation of a stand-alone Entrepreneurship committee, we dove into market research, consultations with experts, and planning the future of Manifold. All available on the Entrepreneurship Page.

Special Awards

Best Integrated Human Practices

IHP efforts this year have resulted in three diverse deliverables. We collaborated with other teams to create a Resource Hub, currently available here, which will soon be available on the iGEM Foundation site, and will share websites, software, databases, and other ways to assist teams working online. We also reached out to dozens of researchers, bioethicists, and industry leaders to discuss what place social movements have in science, had internal group discussions about how societal influence may cause bias and how to be aware of that bias, and our conclusions as a team were compiled into our Code of Ethical Conduct. We put special consideration into making this document adaptable for other teams and inclusive to the ethical beliefs of different societies, pursuing iGEM’s overall goal of international collaboration. Lastly, speaking with experts helped refine the design of our device, which is now patent-pending as a foundational advance in metabolic engineering.

Best Model

Without summer access to lab space, a large emphasis of the project was put on experimental planning and computational/mathematical modeling. We built out an extensive modeling pipeline to best inform DNA scaffold design and metabolic flux through the BMC. We developed a promoter model based on our cell kinetics models and evidence from literature to optimize our 14 parts to be used in experimental design. We also successfully investigated the spatial constraints presented by substrate molecules on BMC pore diffusion. Literature-based insight that malonyl-CoA was a limiting factor in the resveratrol metabolic pathway led us to model the diffusion of various substrates through the pore both spatially through PyMol, and metabolically using a custom-built pore-diffusion Matlab model. These models were pivotal in redefining our BMC substrate, and introducing a second scaffold to our inner BMC architecture.

Best Supporting Entrepreneurship

Starting with extensive industry and market research, we were able to calculate the theoretical improvement our device would provide to resveratrol manufacturers. We also reached out to patent lawyers to discuss the importance of preventing prior art disclosure, and attended Cville BioHub meetings to look at future steps for our team. It was clear we needed a provisional patent, so in August, we successfully filed one. We were then able to review our device plans with experts from around the world who work with the same technology. We also talked to the CEO of one of the largest resveratrol distributors in North America, who confirmed the need for a cheaper, sustainable alternative. Finally, we talked to George McArthur, founder of Virginia iGEM and biotech expert, who pointed us to a company that helps startups test their devices in large-scale bioreactors and monitor the results in real time.


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