Team
Collin Marino: As our Team Captain, member of the Wetlab Committee, Modeling Committee, and Wiki Committee, Collin served as the driving force behind our team. He organized our team, communicated with other iGEM teams, advisors, and experts, and worked dilligently to advance our project through part design and educating team members on correct wetlab practices. Furthermore, he introduced sophisticated computational models into our project that further pushed our project towards a more feasible solution. As if those weren't enough, Collin was one of the lead programmers who wrote much of the main wiki pages and even built a template for others to work from. Overall, without Collin and the sacrifices he made, our team would not be where we are today. We thank him for his role as a leader.
Christopher Nguyen: As head of the Human Practices Committee and member of the Wetlab and Wiki Committees, Chris spearheaded the development of our I4A framework in hopes of connecting our research to the broader world. His dedication to serving those in need and building a responsible, socially good and ethical project motivated him to spread our research to new communities, including leading scientists, stakeholders, ethicists and even clinic patients over the course of the year. Using the knowledge he obtained through integrated human practices, Chris adapted our project's focus and detailed the accounts of our journey by writing the Human Practices Wiki page. If that weren't enough, Chris wrote a proposal to the iGEM Headquarters detailing a plan on how to make the 2021 Giant Jamboree more equitable, inclusive and diverse in spite of the challenges of the COVID-19 pandemic. This caught the attention of the iGEM community and even iGEM president Randy Rettberg, which was partially adopted into the competition. (He also was the team drone operator.)
Maria Lyons: As head of the WetLab Committee and member of the Wiki Committee, Maria lead the Wetlab Commitee to engineer a working Manifold device. Sacrificing most of her free time and much of her sleep, she worked dilligently to overcome and troubleshoot the challenges we faced, while inspiring our team members to push through the grueling and lab-intensive year. Maria leads by example, inspiring others to be as knowledgable, hardworking and supportive as her. She led the charge in organizing, designing, and preparing the team for the weekly wetlab tasks, while educating wetlab members on correct procedures. Furthermore, she helped condense our results into a more manageable reading experience on our Wiki in hopes of inspiring future iGEM teams to advance synthetic biology research.
Rahul Andurkar: As head of the Wiki committee, Rahul (or Randy) always has a smile on his face. He kept focused towards the Wiki deadline and helped push our Wiki to completion by coding many pages, such as the Human Practices and Experiments Page. Randy is a first year student with a bright future and most importantly, we're all grateful for the continual snacks he brought to meetings. Thanks Randy!
Victor Jian:
As head of the Modeling committee and member of the Wetlab committee, Victor was dedicated to lab work and proved to be determined to conquer gromacs (a molecular dynamics package designed for simulations of proteins). He was always the first to dive headfirst into solving a problem and was a great resource in the planning and enactment of our experiments through modeling and wetlab.
David Bass: As Chief Financial Officer and member of the Wetlab Committee, Wiki Committee, and Modeling team, David was the responsible mentor the team needed to navigate the logistical and legal waters of running the team. On the modeling committee, he worked to bring AlphaFold, an artificial intelligence program developed by Google, to the University of Virginia to aid our project and future projects. On the Wiki committee, he spearheaded many tasks such as the modeling page and collaborations page, all while continuing to push full steam ahead in our lab work.
Robby Phillips: As co-lead of Wiki committee and member of the Wetlab and Human Practices committees, Robby worked to create many of the animations and figures you see on the Wiki. He helped code many of the Wiki pages as well as edit and film the promotional video and any Instagram content for the team. He worked diligently in wetlab to create or test parts for our project all while teaching the team basic level web-development.
Nikki Akula: As a member of the Wetlab and Human Practices committees, Nikki worked to create instructional videos of our wetlab. She directed, filmed, and edited these instructional wetlab videos, so that future iGEM teams could follow in our footsteps and repeat our lab techniques and protocols. Nikki worked diligently in the lab and was a problem solving machine for our team. She helped write our Community Suggestions letter and ran our team's Instagram and did it all with a smile.
Annie An: As a member of the Wetlab and Wiki Committees, Annie worked in many avenues of our project. From the writing up of important team documents to helping write the description page of our Wiki, Annie could do it all. She found most of her work revolving around the lab. She also spearheaded the recruitment of next year's team, organizing the interviews of over 30 candidates and creating a standardized selection process. Annie's sacrifices to make sure we completed lab tasks, were prepared for presentations, and willingness to help in anyway she could will always be remembered.
Allison Kumar: As a member of the Wetlab and Wiki committees, Allison was instrumental in the completion of our project through her dedication in the lab. She was the first to say yes to any assignment and could always be relied upon to perform any lab task. She spearheaded the push for Western Blots in our lab and created the flow charts explaining our project mechanistically on the experiments Wiki page.
Joel Valliath: As part of the Wetlab and Wiki committees, Joel was ready for lab everyday and helped push our team over the line in the end. Joel could always make us laugh and had an uncanny ability to get genes sequenced. Joel's sacrifices to complete our results page by the deadline will always be remembered.
Advisors
Dr. Keith Kozminski: As our team's head advisor and Professor in Biology and Cell Biology, Professor Kozminski aided in nearly every aspect of team and project development. In the spring, he taught the class the gave us the foundation of synthetic biology. 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, a Professor of Biomedical Engineering, 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 his own research lab's 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, the department's teaching lab coordinator/preparator, 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 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.
Ms. Jacqueline Parker: Ms. Parker took over much of UVA's lab supply management in the fall, and devoted a lot of her time to supplying the iGEM team with all the reagents, agar plates, and materials we needed. We appreciate her constant availability, all-hours email answers, good humor and helpful advice. Her willingness to work around the last-minute scheduling of bacteria was key to the success of our project, and we treasure the sacrifices she made to help us with the project. Without her contributions, our team could never have gotten as far as it did.
Dr. Bryan Berger: Our discussion with Dr. Berger, an Associate Professor of Chemical Engineering at the University of Virginia, was incredibly helpful in framing Manifold within the context of the biotechnology industry. We discovered that alongside the pharmaceutical industry, the chemical manufacturing industry at large faces several problems that stem from current manufacturing practices, including plant synthesis and chemical synthesis. These problems included supply shortages, poor product quality, low chemical yields, excess chemical waste, slow chemical discovery, or lengthy manufacturing steps to name a few. Because of the overwhelming amount of problems facing the entire chemical manufacturing industry, Dr. Berger shared that these problems were all a result of current manufacturing practices.
Dr. Ann Meyer: During the Mid-Atlantic Meetup at William and Mary, Team Virginia had the unique opportunity to talk to Dr. Meyer, an Associate Professor of Biology at the University of Rochester, about materials production and how upcoming synthetic biology platforms aimed at manufacturing industrial materials like the 2015 TU DELFT’s Project Biolinker could innovate the industry. To our surprise, we learned that the future of materials manufacturing wasn’t focused on improving current manufacturing practices, rather was focused around discovering new methods that introduced novel properties to existing material or entirely discovering new materials.
Dr. Mark Kester: In our countless discussions with Dr. Kester, a Professor of Pharmacology and the Director of the NanoSTAR Institute of the University of Virginia, Team Virginia realized that the pharmaceutical manufacturing industry was split between maintaining current manufacturing practices like plant synthesis and chemical synthesis, while also trying to integrate new technologies like biosynthetic manufacturing. He was a great help to the team with legal advice as well.
Dr. Martin Warren: From our hours long conversation with Dr. Warren, a Professor of Biochemistry at the University of Kent, we learned that although PDU bacterial microcompartments and carboxysomes were largely similar in function (encasing reactions that have toxic or volatile intermediates), carboxysomes differed from PDU bacterial microcompartments in two key respects. First, carboxysomes are composed of anywhere between 12-15 different polypeptides, whereas PDU bacterial microcompartments are composed of strictly 14 different polypeptides. Second, carboxysomes have a significantly smaller ratio of pentameric protein to hexamers than PDU bacterial microcompartments, meaning more simply, that transport across carboxysome pores is essentially insignificant compared to transport across pores in PDU bacterial microcompartments.
Dr. Mark Kester: Dr. Kester is the Professor of Pharmacology and the Director of the NanoSTAR Institute of the University of Virginia. 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. With the help of Dr. Kester, our team determined the economic impact of Manifold and was thus able to label our project a responsible, socially good and ethical solution.
Alex Zorychta, MBA: Our team first met with Alex Zorychta, the Head of Products for Zealot Interactive consumer electronics. Alex is a long-time mentor for University of Virginia undergraduates in creativity, during one of his public speaking events hosted by the nanoSTAR Institute. From this opportunity, our team had the amazing opportunity of talking more about the creative problem solving process and how our team could best use it.
Dr. David Vance: Our team met with Dr. David Vance, the President of Vance Intellectual Property, PC. Mr. Vance gave us further credence in the steps we would take in order to protect and develop our intellectual property, while also detailing to us how our idea would interact and be a part of our university.
Dr. Ruoshi Sun: From our initial hands-on-experience with I-Tasser, the modeling committee faced a serious problem of routine crashes as a result of not having enough graphic processing unit to support the graphic intensive process of modeling. Although we came to Dr. Sun, an experienced computational scientist, to learn more about how to apply I-Tasser to support wet-lab research, Dr. Sun introduced us to the UVA supercomputer called Rivanna that expedited our ability to model complex biological systems. Rivanna allowed our modeling team to improve and accelerate all of our computing processes.
Dr. Todd O. Yeates: Team Virginia consulted Dr. Todd O. Yeates, a Professor of Biochemistry from UCLA. With Dr. Yeate's critical interpretation, our team decided to retest the model with and without pduK. As a result, we ended with the same conclusion that pduK sometimes was needed to facilitate folding of the PDU bacterial microcompartment and other times it wasn’t. This led the modeling committee to present their findings in our weekly meeting, where our team unanimously agreed that we needed to keep pduK in our plasmid construct, such that we ensure the protein shell always folds even at the expense of precious base pairs in our plasmid construct.
Dr. Peter Kasson: From the advice of Dr. Kasson, an Associate Professor of Molecular Physiology and Biomedical Engineering at the University of Virginia, we began exploring how to implement molecular dynamic simulations into our PDE model. As a result, this led us to meet with Dr. Kasson throughout our iGEM experience, where we eventually agreed that we should follow an “umbrella sampling” to find the permeability of pduA and then use that data in our PDE model to predict how resveratrol should interact with pduA. Overall, this led us to create a model that we would later be used to communicate our project to stakeholders..
University of Virginia School of Engineering and Applied Sciences
: With guidance from the University of Virginia School of Engineering and Applied Sciences , we recognized designing bioreactors was no easy feat and required almost an entirely new project on its own. Yet, from our realization that this bioreactor designs like the continuous stirred-tank reactors with cell recycling capabilities existed, we became highly intrigued by the possibility of combining this similar concept with a future Manifold design. We asked, “Instead of only separating the cellular content, could we design a bioreactor that could recycle our cellular waste back into our reactor? Could we use that cellular waste to help with cell growth or could we use it to reduce the energy consumption of our bioreactor? Could we recycle our cells (the major waste produced of Manifold) to assist with further iterations of product synthesis?” Our visit left us even more intrigued about bioreactor design.
Dr. W. Bernard Carlson: After meeting with Dr. Carlson, a Professor of Science, Technology, and Society and the Director of Engineering Business Programs at the University of Virginia, our team needed to identify the ethical concerns related to Manifold before crafting our implementation strategy. At this point, it became a great priority for our team to learn more about ethical perspectives and how to apply their reasonings to Manifold’s implementation. After learning that the 2017 Technion-Israel Team developed an introductory guide to ethics, we carefully reviewed their work to understand synthetic biology through an ethical framework.
Dr. Lois Shepherd: After talking with Dr. Shepherd, an Associate Professor of Public Health and Professor of Law at the University of Virginia, our team was overjoyed to learn that implementing Manifold was an ethical decision as long as it was directed at being socially good and improving end-user lives. But before meeting with the University of Virginia Licensing and Ventures Group to ideate an implementation strategy that helped both patients and pharmaceutical companies, we still wanted to meet with other experts to discuss the other facets of Manifold’s social impact. This included learning more about the environmental impact and economic impact. At this point of the project, our integrated human practices journey identified a problem, modified and improved our a solution, showed that Manifold was a responsible, socially good, and ethical project, but we still needed to understand to what extent our project could help society.
Dr. Scott Doney: Our conversation with Dr. Doney, a Professor in Enviromental Change at UVA, reaffirmed our commitment towards bringing an end to environmental pollution caused by chemical synthesis. Although we knew in principle that industrial biosynthesis could reduce global carbon emissions, we never realized the larger contribution of biosynthesis. We weren’t just building Manifold to reduce carbon emissions or stop chemical waste from ending up in bodies of waters. We were building Manifold to entirely modernize the chemical manufacturing industry into a sustainable and environmentally solution that could bring an end to human-driven droughts, storms, heat waves, rising sea levels, environmental degradation, melting glaciers and so many other effects of climate change. After our conversation with Dr. Doney, we would later modify our implementation approach such that it emphasized our team’s mission towards environmental protection.
Marc Oettinger, MBA: From our conversation with licensing manager Marc Oettinger, our team learned so much about the process of turning a scientific concept into a real-world product. Although we learned that entrepreneurship had the ability to take our project to the next level, our direction for Manifold as an open, synthetic biology platform ultimately resulted in our team looking elsewhere for assistance. Nevertheless, Marc Oettinger introduced the converstaion of entrepreneurship, which inevitably resulted in us applying for a full patent.
nanoSTAR Institute: With the help of the nanoSTAR Institute, our team met with them throughout the start of the fall semester to ideate an implementation approach for Manifold. We agreed that the best way to ensure that our conditions were met (stakeholders follow our terms of service and that all savings made from Manifold go directly to the end-user) was through applying for a full patent. This would allow us to write up a terms-of-service agreement, that would allow us to control exactly how our technology would be implemented in the real-world. Using the provisional patent filed by the 2020 Virginia iGEM Team, we set out to file a full patent with the redesigned Manifold.
And a special thanks to...
