Difference between revisions of "Team:Virginia/Attributions"

 
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               <a class="hvr-sweep-to-right" href="https://2020.igem.org/Team:Virginia">Main</a>
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               <a class="hvr-sweep-to-right" href="index.html#abstract">Abstract</a>
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               <a class="hvr-sweep-to-right" href="#">Inspiration</a>
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               <a class="hvr-sweep-to-right" href="https://2020.igem.org/Team:Virginia/Design">Design</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="#">Attributions</a>
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             <div>General Template Page</div>
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             <div>Attributions</div>
 
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           <div class="sectionTitle" id="Section 1">Team</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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                 <li><b>Julia Ball</b>: As our team captain, member of the Human Practices and Wetlab Committees, Julia helped organize our team, communicated with other iGEM teams, advisors, and experts through almost 100 emails, helped fill out safety forms, organized the recruitment for next year’s team, and was the primary point of contact with the iGEM organization overall. Also, Julia wrote the code of ethical conduct, worked on the blog for the iGEM engineering school website, and helped develop the Resource Hub and the Wiki. As part of the DNA subteam of the Wetlab committee, Julia helped design the DNA scaffold procedures and worked in the lab. </li>
 
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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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                <li><b>Collin Marino</b>: As head of the Wetlab committee and member of the Wiki and Entrepreneurship committees, Collin was the member that originally came up with the project idea. As Wetlab lead, he spearheaded the initial planning of experimental procedures and oversaw the procedure development and flow chart design. In addition, Collin wrote and successfully filed the provisional patent, allowing the team to begin sharing our idea with experts and getting their feedback. Also, Collin did the coding for the Wiki and created a template for the pages, which allowed other team members to help add content to the wiki.</li>
 
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                <li><b>Colin Haws</b>: As head of the Modeling committee and member of the Wetlab committee, Colin focused on leading the modeling efforts to describe the efficiency of the Manifold system. More specifically he worked on the promotor calculator and the reaction kinetics models. In Wetlab, Colin helped in the collection and assembly of BMC parts, both in the lab and virtually, and worked on the BMC procedures in the lab with Veronica.</li>
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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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                <li><b>Dev Patel</b>: As head of the Human Practices Committee and member of the Wetlab, Wiki, and Modeling, Dev worked on writing the code of ethical conduct and most of the Wiki write-up for the Human Practices committee. In Modeling, Dev worked with Pietro to develop the NetLogo model to show substrate movement in BMCs. In addition, in Wetlab, Dev helped research collect and write the procedures for the Enzyme subteam, inputting those into Benchling, along with any sequences.</li>
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                <li><b>Jacob Polzin</b>: As head of the Wiki committee and member of the Modeling and Wetlab committees, Jacob was the one that proposed our circuit contain operon elements with unique promoter/enhancer/RBS to curtail metabolic overload while maintaining the right product ratio. He also proposed we add GFP to one of the Pdu proteins so that we could verify formation. In addition, as Wiki Lead, Jacob kept everyone motivated and focused on building quality content cooperatively. For Modeling, he focused on helping determine the required concentration outputs along with the means of achieving that ratio with promoter and RBS sequence manipulation.</li>
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                <li><b>Pietro Revelli</b>: As Chief Financial Officer, co-head of then Entrepreneurship Committee and member of the Wetlab and Modeling, Pietro worked on the market analysis of resveratrol, applied to countless grants and made the budget for the team. In addition, on the Modeling team, Pietro worked on the Cobra Toolbox in Python and Matlab and was the one who pointed out the importance of the ACS and ACC in the resveratrol pathway. </li>
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                <li><b>Aparna Kola</b>: As co-head of the Entrepreneurship Committee and a member of the Modeling and Human Practices Committee, Aparna worked to conduct industry research, and network with the stakeholders in the local community while organizing discussions regarding IP protection and patentability. In addition, she worked on the promoter calculator, flux balance analysis, and pore diffusion models. As part of HP, she helped to author the Code of Ethical conduct, organize the virtual Resource Hub, and worked on the blog for the iGEM engineering school website.</li>
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                <li><b>Sophia Link</b>: As a member of the Wetlab and Wiki committees, Sophia worked on the design of the DNA scaffold and helped with the writeup and organization of Reverse transcriptase assembly Wetlab procedures. In addition, Sophia created most (if not all) of Manifold's graphics, including the one on our home page and the design of the flowcharts that can be seen on the experiments page.  </li>
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                <li><b>Veronica Gutierrez</b>: As a member of the Wetlab, Wiki, and Entrepreneurship committees, Veronica helped research and write procedures regarding the construction of the BMC, aided in the overall structure and organization of the wiki and helped collect details on current or pending patents. In the lab, Veronica worked with Colin Haws to go through the different procedures pertaining to BMC formation and analyze the results. </li>
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                <li><b>Apekchha Pradhan</b>: As a member of the Wetlab, Entrepreneurship, and Wiki committees, Apekchha was in charge of forming the sequences and parts for the 4Cl and STS enzymes in the resveratrol pathway. She worked with Peitro and Jacob in the lab, following the protocols for their enzyme sub-team. She also took part in helping build the Wiki and got to be more familiar with web design and HTML/CSS. </li>
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                <li><b>Edward (Eddie) Micklovic</b>: As part of the Human Practices committee, Eddie spearheaded the Virginia iGEM podcast series “Mick and Mates”, filming and editing the videos and sound. In addition, Eddie helped work on the code of ethical conduct and did the voice-over for our team's promotional video. </li>
 
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                    <li><b>Dr. Keith Kozminski</b>: As our team's head advisor, Professor Kozminski aided in nearly every aspect of team and project development. In the spring, he was the teacher of the class the gave us the foundation of synthetic biology and where we first developed our project idea. Throughout the summer and the fall, Professor Kozminski was always available for advice or suggestions on device design, experimental protocol development, intellectual property advice, general iGEM questions, and much more. The entire team is incredibly grateful for all of his help and guidance. </li>
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                  <li><b> Dr. Jason Papin</b>: Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.</li>
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                    <li><b>Ms. Kathryn Christopher</b>: From helping set up the laboratory to collecting and providing us with common reagents, Ms. Christopher was central to our team’s transition from virtual development to in-person experimentation. She sorted through available reagents and helped set up the lab for our team to be able to come into the lab and hit the ground running. Furthermore, she was available throughout the fall if we needed any extra glassware, tools, or reagents. The Virginia iGEM team is very thankful and appreciates Ms. Christopher’s work and availability throughout our time in the lab and the months leading up to it.</li>
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                    <li><b>Dr. Cheryl Kerfeld</b>: We begin by cold-emailing Dr. Cheryl Kerfeld, a renowned researcher out of UCLA and Michigan State with a long history of experimenting with BMCs. Dr. Kerfeld agreed to talk about her cutting-edge BMC research, even explaining her current work on customizable BMC shells, and also gave feedback on our initial project ideas. She immediately took to our concepts, and she afforded us the endorsement of a researcher who's worked with BMCs for decades. She gave us multiple contacts for other top BMC researchers, as well as a better understanding of her field of work, all of which better helped us move forward.</li>
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                    <li><b>Dr. Martin Warren</b>: We also reached out to Professor Martin Warren at the University of Kent in the UK after reading a paper of his. What began as a chance email became a continued dialogue about the initial paper of interest, as well as his pertinent work with BMCs. He also agreed to share a plasmid described in his paper, which provided us with the sequence, the ability to partially replicate his findings, and a much faster route to creating our final device. </li>
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                  <li><b>Dr. Laura Fontenas</b>: One protocol that no one on our team had previously performed is qPCR. This led to our advisor connecting us to Dr. Laura Fontenas, a research associate at UVA. She was happy to share her qPCR protocol, recommendations, steps for designing primers, and any other advice we may need during our lab work.</li>
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                  <li><b>Dr. George McArthur</b>: Further into the summer, we reached out to Dr. McArthur, the founder of the Virginia iGEM Team, Director of Genetic Design-Build at Arzeda, and new Head of Product at Ansa Biotechnologies, Inc. We did a short presentation for him on the Wetlab component of our project, and he gave us advice on next steps for the project: get funding, find other ways to market the device (ie. expand its applications) and figure out how to get data without having normal access to our lab (outsource to Teselagen/Honeybee/Culture Biosciences). </li>
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                  <li><b>Dr. Stacey Joe Criswell</b>: Dr. Criswell, who works at the University of Virginia’s Advanced Microscopy Facility, was happy to help us with our TEM images of our BMCs. We are especially thankful for her patience and flexibility.</li></div>
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                  <li><b>Dr. Deborah Roach</b>: We would like to thank Dr. Roach, the Chair of Biology at the Univeristy of Virginia, who provided the laboratory space and the funds to help run the lab.</li></div>
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                    <li><b>Dr. Anthony Spano</b>: Dr. Spano, a Research Assistant Professor of Biology at the Univeristy of Virginia, graciously provided us with the BL21(DE3) <i>E. coli</i> cells that were used throughout our experiments. </li></div>
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                <li><b>Dr. Dorothy Schafer</b>: We would also like to extend a huge thank you to Dr. Schafer for donating various restriction enzymes, chemicals, lab supplies, the PCR machine, and much more. </li></div>
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          <div class="sectionTitle" id="Section 4">Human Practices Advising and Support</div>
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                  <li><b>Dr. Lois Shepherd</b>: Early on, we reached out to Dr. Shepherd, a UVA Bioethicist, to gain insights into the pharmaceutical manufacturing industry. We were looking for information on good practice and the stipulations required to go beyond the typical legal and safety confined. She advised us to assess how we can actually benefit society despite the restrictions of patent monopolies, and suggested we write a Code of Ethical Conduct to organize our findings. She stressed important questions regarding what we wanted to accomplish with our project, who it would affect, and how we could balance benefits, risks, and harms. Dr. Shepherd then pointed us to Professor Riley, a fellow UVA Bioethicist, for ethical advice more specific to synthetic biology. </li>
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                  <li><b>Professor Mimi Riley</b>: Now armed with the relevant questions and our tentative answers, we reached out to Professor Riley, a professor of law, PHS, and public policy at UVA, and the chair of UVA's Embryonic Stem Cell Research Oversight Committee, as well as a  legal advisor to the Health Sciences Institutional Review Board. In our first meetings, we asked general questions regarding synthetic biology society, and our conversations gradually shifted to discussing the current social movements occurring in the country, and if we have a role as a research team to take a stance on such issues. We spoke intensely about our capability to positively and directly impact our community as a team of researchers, and we learned the true difficulty of going beyond merely making a statement and moving on. Through this, Professor Riley encouraged us to think internally first and to detail our own responsibilities and actions before blindly charging into the public eye. She further endorsed the idea of a COEC, as a means to debate and understand our values as a team and how they affect the work we put out into society. Professor Riley later reviewed our COEC gave us direct advice on individual statements and sections, and how to finalize this document for others to adapt and improve.</li>
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                    <li><b>Ryan Taylor</b>: Ryan Taylor is the former captain of the 2018 Virginia iGem Team and an ongoing resource in developing our 2D ABM and helping us to understand and troubleshoot our MatLab models.</li>
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          <div class="sectionTitle" id="Section 7"> Entrepreneurship, Legal and/or Business Advising and Support</div>
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                    <li><b>Dr. Mark Kester</b>: Dr. Kester is a longtime iGEM supporter and was a valuable early advisor in our intellectual property efforts. Dr. Kester provided us with information regarding past iGEM entrepreneurship efforts and the focus of our project, and the types of market evaluations we would need to project in order to build out the scope of our potential device.</li>
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                  </div>
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                <div class="paragraph">
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                    <li><b>Nathan Evans</b>: Long before the establishment of a proper Entrepreneurship committee, we were still interested in protecting our device and intellectual property. We began early by speaking to Nathan Evans, a patent lawyer in the Charlottesville area who offered us a no-cost meeting to discuss the process of filing and how to protect ourselves from losing claim to our device. Mr. Evans detailed our path forward and the time structure that we would be subject to in our patent filing process. It was a great first step in us understanding the weight of our ideas and how to properly handle them.</li>
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                  </div>
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                <div class="paragraph">
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                    <li><b>David Vance</b>: Following our consultation with Nathan Evans, we sought out a conversation with David Vance, another local patent attorney with whom we further asked our intellectual property questions. Mr. Vance gave us further credence in the steps we would take in order to protect and develop our IP, while also detailing to us how our idea would interact and be a part of our university.</li>
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                  </div>
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                  <li><b>Rahul Keshap</b>: To learn about proper company development, we reached out to Rahul Keshap, a lecturer in the UVA law school who shared his insight into starting a company. He broke down each of our team's individual claims to the idea, and how we could best move forward in forming a company. This conversation led us to form the basis of our Entrepreneurship committee, a committee that explores our own finances and structure in order to potentially grow our device beyond the scope of a project.</li>
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                  <li><b>UVA Licensing and Ventures Group</b>: We also had a meeting with UVA LVG to discuss how UVA’s investment in our project might be exchanged for partial ownership, and, more generally, how our university supports the entrepreneurial efforts of its students. We had many team discussions about the pros and cons of appealing to different resources and how it might affect the course of our project, and talking to UVA LVG (among other connections in the Charlottesville community) gave us a better idea of the effects of our final decision.</li>
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                  <li><b>Dr. Nikki Hastings and Dr. Paul Sartori</b>: Later on, we spoke to Dr. Nikki Hastings, CEO of Cville BioHub, and Dr. Paul Sartori, Cville BioHub's first Entrepreneur-in-Residence a cville collective of biological startups working to build their companies in the local incubator. Dr. Hastings offered us her resources, but we were much more interested in their business model and the other companies under the banner of Cville BioHub. </li>
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                    <li><b>Ian Burbulis</b></li>
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                    <li><b>Josaih Zoyner</b></li>
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                  <li><b>Hank Greely</b></li>
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                    <li><b>Dylan Culfogienis</b></li>
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Latest revision as of 05:28, 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:
Attributions
Team
  • Julia Ball: As our team captain, member of the Human Practices and Wetlab Committees, Julia helped organize our team, communicated with other iGEM teams, advisors, and experts through almost 100 emails, helped fill out safety forms, organized the recruitment for next year’s team, and was the primary point of contact with the iGEM organization overall. Also, Julia wrote the code of ethical conduct, worked on the blog for the iGEM engineering school website, and helped develop the Resource Hub and the Wiki. As part of the DNA subteam of the Wetlab committee, Julia helped design the DNA scaffold procedures and worked in the lab.
  • Collin Marino: As head of the Wetlab committee and member of the Wiki and Entrepreneurship committees, Collin was the member that originally came up with the project idea. As Wetlab lead, he spearheaded the initial planning of experimental procedures and oversaw the procedure development and flow chart design. In addition, Collin wrote and successfully filed the provisional patent, allowing the team to begin sharing our idea with experts and getting their feedback. Also, Collin did the coding for the Wiki and created a template for the pages, which allowed other team members to help add content to the wiki.
  • Colin Haws: As head of the Modeling committee and member of the Wetlab committee, Colin focused on leading the modeling efforts to describe the efficiency of the Manifold system. More specifically he worked on the promotor calculator and the reaction kinetics models. In Wetlab, Colin helped in the collection and assembly of BMC parts, both in the lab and virtually, and worked on the BMC procedures in the lab with Veronica.
  • Dev Patel: As head of the Human Practices Committee and member of the Wetlab, Wiki, and Modeling, Dev worked on writing the code of ethical conduct and most of the Wiki write-up for the Human Practices committee. In Modeling, Dev worked with Pietro to develop the NetLogo model to show substrate movement in BMCs. In addition, in Wetlab, Dev helped research collect and write the procedures for the Enzyme subteam, inputting those into Benchling, along with any sequences.
  • Jacob Polzin: As head of the Wiki committee and member of the Modeling and Wetlab committees, Jacob was the one that proposed our circuit contain operon elements with unique promoter/enhancer/RBS to curtail metabolic overload while maintaining the right product ratio. He also proposed we add GFP to one of the Pdu proteins so that we could verify formation. In addition, as Wiki Lead, Jacob kept everyone motivated and focused on building quality content cooperatively. For Modeling, he focused on helping determine the required concentration outputs along with the means of achieving that ratio with promoter and RBS sequence manipulation.
  • Pietro Revelli: As Chief Financial Officer, co-head of then Entrepreneurship Committee and member of the Wetlab and Modeling, Pietro worked on the market analysis of resveratrol, applied to countless grants and made the budget for the team. In addition, on the Modeling team, Pietro worked on the Cobra Toolbox in Python and Matlab and was the one who pointed out the importance of the ACS and ACC in the resveratrol pathway.
  • Aparna Kola: As co-head of the Entrepreneurship Committee and a member of the Modeling and Human Practices Committee, Aparna worked to conduct industry research, and network with the stakeholders in the local community while organizing discussions regarding IP protection and patentability. In addition, she worked on the promoter calculator, flux balance analysis, and pore diffusion models. As part of HP, she helped to author the Code of Ethical conduct, organize the virtual Resource Hub, and worked on the blog for the iGEM engineering school website.
  • Sophia Link: As a member of the Wetlab and Wiki committees, Sophia worked on the design of the DNA scaffold and helped with the writeup and organization of Reverse transcriptase assembly Wetlab procedures. In addition, Sophia created most (if not all) of Manifold's graphics, including the one on our home page and the design of the flowcharts that can be seen on the experiments page.
  • Veronica Gutierrez: As a member of the Wetlab, Wiki, and Entrepreneurship committees, Veronica helped research and write procedures regarding the construction of the BMC, aided in the overall structure and organization of the wiki and helped collect details on current or pending patents. In the lab, Veronica worked with Colin Haws to go through the different procedures pertaining to BMC formation and analyze the results.
  • Apekchha Pradhan: As a member of the Wetlab, Entrepreneurship, and Wiki committees, Apekchha was in charge of forming the sequences and parts for the 4Cl and STS enzymes in the resveratrol pathway. She worked with Peitro and Jacob in the lab, following the protocols for their enzyme sub-team. She also took part in helping build the Wiki and got to be more familiar with web design and HTML/CSS.
  • Edward (Eddie) Micklovic: As part of the Human Practices committee, Eddie spearheaded the Virginia iGEM podcast series “Mick and Mates”, filming and editing the videos and sound. In addition, Eddie helped work on the code of ethical conduct and did the voice-over for our team's promotional video.
    • Advisors
  • Dr. Keith Kozminski: As our team's head advisor, Professor Kozminski aided in nearly every aspect of team and project development. In the spring, he was the teacher of the class the gave us the foundation of synthetic biology and where we first developed our project idea. Throughout the summer and the fall, Professor Kozminski was always available for advice or suggestions on device design, experimental protocol development, intellectual property advice, general iGEM questions, and much more. The entire team is incredibly grateful for all of his help and guidance.
  • Dr. Jason Papin: Dr. Papin is our iGEM sponsor and the backbone of our modeling efforts. After the formulation of our device, our talks with Dr. Papin helped us to understand the questions we need to answer and therefore the models we need to create in order to answer such questions. Dr. Papin also shared with us his own research labs resources to help us understand our models and create better outputs for presentation.
    • Wetlab Advising and Support
  • Ms. Kathryn Christopher: From helping set up the laboratory to collecting and providing us with common reagents, Ms. Christopher was central to our team’s transition from virtual development to in-person experimentation. She sorted through available reagents and helped set up the lab for our team to be able to come into the lab and hit the ground running. Furthermore, she was available throughout the fall if we needed any extra glassware, tools, or reagents. The Virginia iGEM team is very thankful and appreciates Ms. Christopher’s work and availability throughout our time in the lab and the months leading up to it.
  • Dr. Cheryl Kerfeld: We begin by cold-emailing Dr. Cheryl Kerfeld, a renowned researcher out of UCLA and Michigan State with a long history of experimenting with BMCs. Dr. Kerfeld agreed to talk about her cutting-edge BMC research, even explaining her current work on customizable BMC shells, and also gave feedback on our initial project ideas. She immediately took to our concepts, and she afforded us the endorsement of a researcher who's worked with BMCs for decades. She gave us multiple contacts for other top BMC researchers, as well as a better understanding of her field of work, all of which better helped us move forward.
  • Dr. Martin Warren: We also reached out to Professor Martin Warren at the University of Kent in the UK after reading a paper of his. What began as a chance email became a continued dialogue about the initial paper of interest, as well as his pertinent work with BMCs. He also agreed to share a plasmid described in his paper, which provided us with the sequence, the ability to partially replicate his findings, and a much faster route to creating our final device.
  • Dr. Laura Fontenas: One protocol that no one on our team had previously performed is qPCR. This led to our advisor connecting us to Dr. Laura Fontenas, a research associate at UVA. She was happy to share her qPCR protocol, recommendations, steps for designing primers, and any other advice we may need during our lab work.
  • Dr. George McArthur: Further into the summer, we reached out to Dr. McArthur, the founder of the Virginia iGEM Team, Director of Genetic Design-Build at Arzeda, and new Head of Product at Ansa Biotechnologies, Inc. We did a short presentation for him on the Wetlab component of our project, and he gave us advice on next steps for the project: get funding, find other ways to market the device (ie. expand its applications) and figure out how to get data without having normal access to our lab (outsource to Teselagen/Honeybee/Culture Biosciences).
  • Dr. Stacey Joe Criswell: Dr. Criswell, who works at the University of Virginia’s Advanced Microscopy Facility, was happy to help us with our TEM images of our BMCs. We are especially thankful for her patience and flexibility.
  • Dr. Deborah Roach: We would like to thank Dr. Roach, the Chair of Biology at the Univeristy of Virginia, who provided the laboratory space and the funds to help run the lab.
  • Dr. Anthony Spano: Dr. Spano, a Research Assistant Professor of Biology at the Univeristy of Virginia, graciously provided us with the BL21(DE3) E. coli cells that were used throughout our experiments.
  • Dr. Dorothy Schafer: We would also like to extend a huge thank you to Dr. Schafer for donating various restriction enzymes, chemicals, lab supplies, the PCR machine, and much more.
    • Human Practices Advising and Support
  • Dr. Lois Shepherd: Early on, we reached out to Dr. Shepherd, a UVA Bioethicist, to gain insights into the pharmaceutical manufacturing industry. We were looking for information on good practice and the stipulations required to go beyond the typical legal and safety confined. She advised us to assess how we can actually benefit society despite the restrictions of patent monopolies, and suggested we write a Code of Ethical Conduct to organize our findings. She stressed important questions regarding what we wanted to accomplish with our project, who it would affect, and how we could balance benefits, risks, and harms. Dr. Shepherd then pointed us to Professor Riley, a fellow UVA Bioethicist, for ethical advice more specific to synthetic biology.
  • Professor Mimi Riley: Now armed with the relevant questions and our tentative answers, we reached out to Professor Riley, a professor of law, PHS, and public policy at UVA, and the chair of UVA's Embryonic Stem Cell Research Oversight Committee, as well as a legal advisor to the Health Sciences Institutional Review Board. In our first meetings, we asked general questions regarding synthetic biology society, and our conversations gradually shifted to discussing the current social movements occurring in the country, and if we have a role as a research team to take a stance on such issues. We spoke intensely about our capability to positively and directly impact our community as a team of researchers, and we learned the true difficulty of going beyond merely making a statement and moving on. Through this, Professor Riley encouraged us to think internally first and to detail our own responsibilities and actions before blindly charging into the public eye. She further endorsed the idea of a COEC, as a means to debate and understand our values as a team and how they affect the work we put out into society. Professor Riley later reviewed our COEC gave us direct advice on individual statements and sections, and how to finalize this document for others to adapt and improve.
    • Modeling Advising and Support
  • Ryan Taylor: Ryan Taylor is the former captain of the 2018 Virginia iGem Team and an ongoing resource in developing our 2D ABM and helping us to understand and troubleshoot our MatLab models.
    • Entrepreneurship, Legal and/or Business Advising and Support
  • Dr. Mark Kester: Dr. Kester is a longtime iGEM supporter and was a valuable early advisor in our intellectual property efforts. Dr. Kester provided us with information regarding past iGEM entrepreneurship efforts and the focus of our project, and the types of market evaluations we would need to project in order to build out the scope of our potential device.
  • Nathan Evans: Long before the establishment of a proper Entrepreneurship committee, we were still interested in protecting our device and intellectual property. We began early by speaking to Nathan Evans, a patent lawyer in the Charlottesville area who offered us a no-cost meeting to discuss the process of filing and how to protect ourselves from losing claim to our device. Mr. Evans detailed our path forward and the time structure that we would be subject to in our patent filing process. It was a great first step in us understanding the weight of our ideas and how to properly handle them.
  • David Vance: Following our consultation with Nathan Evans, we sought out a conversation with David Vance, another local patent attorney with whom we further asked our intellectual property questions. Mr. Vance gave us further credence in the steps we would take in order to protect and develop our IP, while also detailing to us how our idea would interact and be a part of our university.
  • Rahul Keshap: To learn about proper company development, we reached out to Rahul Keshap, a lecturer in the UVA law school who shared his insight into starting a company. He broke down each of our team's individual claims to the idea, and how we could best move forward in forming a company. This conversation led us to form the basis of our Entrepreneurship committee, a committee that explores our own finances and structure in order to potentially grow our device beyond the scope of a project.
  • UVA Licensing and Ventures Group: We also had a meeting with UVA LVG to discuss how UVA’s investment in our project might be exchanged for partial ownership, and, more generally, how our university supports the entrepreneurial efforts of its students. We had many team discussions about the pros and cons of appealing to different resources and how it might affect the course of our project, and talking to UVA LVG (among other connections in the Charlottesville community) gave us a better idea of the effects of our final decision.
  • Dr. Nikki Hastings and Dr. Paul Sartori: Later on, we spoke to Dr. Nikki Hastings, CEO of Cville BioHub, and Dr. Paul Sartori, Cville BioHub's first Entrepreneur-in-Residence a cville collective of biological startups working to build their companies in the local incubator. Dr. Hastings offered us her resources, but we were much more interested in their business model and the other companies under the banner of Cville BioHub.
    • And a special thanks to...
  • Ian Burbulis
  • Josaih Zoyner
  • Hank Greely
  • Dylan Culfogienis
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