Team:William and Mary/Medal Requirements
Fulfillment of Medal Requirements
Competition Results
At the virtual Giant Jamboree, we were awarded Best Model, Best Therapeutics Project, and a gold medal. Additionally, we received nominations for Best Integrated Human Practices and Best Poster. Congratulations to all teams that competed in iGEM this year!
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Bronze Medal
We registered for iGEM, had a great iGEM season (despite the pandemic and not having access to wetlab), and will attend the Virtual Giant Jamboree.
Competition Deliverables: We have completed the Wiki, Poster, Presentation video, Project Promotion video, and Judging Form.
Attributions: We have detailed our attributions on our Attributions page.
Project Description: We have detailed our project motivation, inspiration, goals, and impacts of COVID-19 on our Project Description page.
Contribution: For Contribution, we have added extensive, new characterization (from existing literature) of the FadD, FadL, FabH, OprF, and OmpA parts on the Registry of Standard Biological Parts. We also contributed multiple systems for PUFA synthesis and export in bacteria, and created pages detailing troubleshooting for circuit design of novel systems and troubleshooting our modeling. Additionally, we performed an in-depth analysis of the current state of recombination detection programs and shared with future researchers advice on how to optimize the performance of Recombination Detection Program version 4 (RDPv4), allowing synthetic biologists to build sensors for emerging pathogens.
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Silver Medal
Engineering Success: We have demonstrated engineering success by describing in detail the iterative design, build, test cycle for our project. We extensively detailed how we would design our experiments, evaluate the outcome, deal with unexpected results, plan further steps, and repeat the process.
Collaboration: We collaborated with multiple iGEM teams by collaborating to create a video series with Purdue, participating in a podcast with Pittsburgh, and contributing to an informative video about synthetic biology with TU Delft. Additionally, we held a virtual MidAtlantic Meetup and hosted six iGEM teams.
Human Practices: Our team engaged in extensive Human Practices, interviewing stakeholders and experts that guided, informed, and changed the design and direction of our project on multiple levels.
Proposed Implementation: We presented a proposal for the implementation of our project, detailing each aspect of the form of probiotic administration and associated safety elements, including how it would be tested if it were to be implemented in the real world.
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Gold Medal
Integrated Human Practices: We conducted in depth interview sessions with ten experts and stakeholders, including Dr. James Shelhamer, Dr. Anders Cervin, Dr. Matthias Kramer, Dr. Cecilia Mikita, Dr. Ronald B. Turner, Dr. Alan H. Shikani, Dr. Shen Xiaokun, Dr. Rachel Lappan, Lydia Mapstone, and Ms. Karolyn Gale as part of our integrated human practices. We demonstrate how they informed our project and how our project direction changed (often dramatically) based on their input; and how our activities altered the design of our project.
Project Modeling: We employed extensive and iterative mathematical modeling to test the feasibility of our probiotic improvement upon the design. Our model allowed us to implement the design - test cycle to continually improve the design. We created a Model page detailing every aspect of our model including its assumptions, data, parameters, and results.
Proof of Concept: Given that we did not have wet lab access, we demonstrated Proof of Concept for our project and created a proof of concept page using mathematical modeling.
Partnership: We collaborated with Purdue iGEM on a crash course YouTube video series to achieve our mutual objectives of introducing high school students to molecular biology and synthetic biology concepts. We communicated back and forth via email and Slack to collaboratively develop a video on promoters.
Science Communications: We participated in Science Communications through several pre-pandemic in person public events (high school students and teachers) and several virtual public engagement events from March onwards (workshops for middle school students, sessions with prospective STEM majors from underrepresented backgrounds). We also created educational Synthetic Biology materials in the form of two educational video series. Our TikTok video series educates on synthetic biology and its various applications. Our “Modeling for the Masses” video series describes various COVID-19 models and provides explanations for their contradictory predictions.
Excellence in another Area: We exhibited Excellence in Another Area through a critical in depth analysis of the current state of recombination detection programs and shared with future researchers not only our struggles in identifying recombination, but also advice on how to optimize the performance of Recombination Detection Program version 4. Recombination can result in novel phenotypic expression which is why the research conducted by our team can be used as a pivotal tool for future synthetic biologists to create sensors for detecting emerging pathogens with pandemic potential.
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Special Prizes
Education: This year we have reached out and engaged with both local communities and the general public. To engage with local communities, we presented our project, and held two way conversations about synthetic biology with students from low income socioeconomic backgrounds and / or those who are underrepresented in STEM. To engage with the general public we created a video series on TikTok, introducing our project and providing an overview of how synthetic biologists are working to counter COVID-19. Our 1-minute videos can reach and engage a broad audience by demonstrating the ability of synthetic biology to directly affect their lives. In total, our videos have reached over 300 views on TikTok. Additionally, we have created another series of videos for our Modeling For The Masses project, which explains to a general audience how COVID-19 models work, and why their predictions were so contradictory, especially in the early stages of the pandemic.
Integrated Human Practices: From start to finish, human practices informed every aspect of our project, including circuit design, probiotic safety, proposed administration and implementation, and therapeutic accessibility. In an interactive cycle our interview sessions guided and continually changed the design and direction of our project. We interviewed six medical doctors, including ENT’s, allergists & immunologists, a pulmonologist, and a pediatrician specializing in infectious disease. Their feedback was instrumental in helping us to select safe probiotic chasses, design our smart, inflammation-regulating circuits, and develop our probiotic administration plan. To learn more about drug regulations and accessibility, we consulted a drug developer who is currently testing an antiviral therapy for SARS-CoV-2, as well as a vaccine and plasma manufacturing expert. Finally, we interviewed microbiology expert Rachel Lappan, PhD., and iGEM alumna Lydia Mapstone, cofounder and CEO of breastmilk probiotic company BoobyBiome, for their expertise on microbiology. Ms. Mapstone provided additional guidance on probiotic manufacturing, regulation, and accessibility. Together, our interviewees critically informed and frequently changed the direction of our project in its design, safety precautions, and proposed administration and distribution.
Model: The overarching goal of our project was to design a “smart” broad spectrum antiviral nasal probiotic and to investigate its feasibility and improvement through iterative and extensive mathematical modeling. To model the effect of a PUFA producing probiotic on viral load we have: modeled the synthesis and export of PUFA from our bacterial chasses; adapted the target cell limited model in order to represent viral infection inside the nose; incorporated the antiviral effects of both DHA and AA; modeled the production of cytokines inside of the nose along with the pro/anti-inflammatory effects of DHA and AA on cytokine production; added a sensor which responds to specific levels of TNF-α and IFN-ˠ by promoting DHA and repressing AA production; incorporated stochasticity; and converted our system of equations into a grid in which the spatial dynamics and heterogeneity of the nose were incorporated along with the diffusion of each element across the nasal cavity. Above all, our model informed our probiotic design throughout the project and suggested approaches in which our probiotic design could be adapted to better decrease viral titer during infection.