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Attributions

Principal Investigators

We would like to thank Dr. Margaret Saha for her fierce support of iGEM at William & Mary! Despite the closure of the university in March, the inability to conduct any lab work, and challenging financial issues faced by the university, she ensured that iGEM at W&M would happen this year! Her expertise and guidance throughout this unprecedented iGEM season, and her always being one Zoom call away, made iGEM possible this year.

We would like to thank Dr. Eric Bradley for his support of our team since 2014.

We are so grateful for the modeling expertise of Dr. Mainak Patel, who has supported our iGEM team over the past three years. This year’s model would not be possible without his input!

Funding

We would like to thank Vice Provost Dennis Manos, who has championed William & Mary iGEM since its inception in 2014. The financial support of Vice Provost Manos (Vice Provost for Research and Graduate/Professional Studies), Dean Maria Donoghue Velleca (Dean of the Faculty of Arts and Sciences), Dean Teresa Longo (Dean for Interdisciplinary Studies and Director of the Charles Center), and Dr. Dan Cristol (Director, 1693 Program, Undergraduate Research) made our participation in iGEM possible during this unprecedented time. We are extremely grateful.

Consults

We would like to thank Dr. Jennifer Stevens, Chair of the Protection of Human Subjects Committee at William & Mary. Her guidance in revising and submitting our PHSC protocol made our work in integrated human practices possible.

We are thankful to Dr. Mark Forsyth for his support and microbiology expertise.

Dr. Dana Wilner’s bioinformatics guidance was invaluable for modeling recombination events.

Researchers

We would like to thank Dr. Jeong Lee, Dr. Tohru Dairi, Dr. Arnold Driessen, and Dr. James Shelhamer for patiently answering our questions regarding their publications. We are grateful to them for expanding our knowledge of fatty acids, protein secretion, and inflammation.

For our integrated human practices this year, we consulted experts in drug development, probiotics, and the nasopharyngeal microbiome for guidance on how to make our probiotic design as safe, accessible, and effective as possible.

We would like to thank the following medical professionals and academic experts for participating in our interviews. We would especially like to thank K.M. for courageously caring for patients with COVID-19.

Medical Professionals

Dr. James Shelhamer
Dr. Cecilia Mikita
Dr. Anders Cervin
Dr. Alan Shikani
Dr. Ronald Turner
Dr. Matthias Kramer
Nurse K.M.

Drug, Probiotic, and Microbiome Experts

Dr. Rachel Lappan
Lydia Mapstone
Karolyn Gale
Dr. Shen Xiaokun

Team

Beteel Abu-ageel

As a co-captain, I worked with the modeling team to create a list of parameters for our “inside the body” model and contributed several parameters based on this list. I conducted a literature review on bacterial sensors for human cytokines for the sensing portion of our “smart” circuit and researched the range of cytokine concentrations found in nasal fluid after viral infection. I also helped to write the scripts and storyboards for the TikTok videos and created the whiteboard drawings for them. In addition, I interviewed Dr. Lappan and Dr. Turner as part of our integrated human practices and helped to review and write content for our wiki.

Avery Bradley

This season, I worked on developing the team's TikTok account. I helped to write the script for the TikTok videos, specifically the viral recombination video, and I promoted these videos on various social media platforms. Further, I collaborated with Purdue University, Ohio State University, Cornell University, University of Maryland, and Michigan State University to create a YouTube video series which covers basic information about synthetic biology. Within this collaboration, I wrote the script for the promoter video. Within our own team, I helped to research various viral recombination computer programs, looked into ways to create a machine learning program to predict future locations of viral recombination, and assisted in coding the wiki. Furthermore, I wrote the parts page summary of OmpA and researched the protocol for differentiating the polyunsaturated fatty acid chains and for determining viral titer.

Matt Dennen

I extensively researched cellular methods of fatty acid recognition and import, especially: FakA and FakB3, FabT, FadL and FadD, DesT, and FapR. FadR, DesK and DesR, FarR and FarE, ToxT, Bm3R1, and FabR were also explored to a notable degree. I assisted in searching for mechanisms for recognition of cytokines. I authored a detailed entry on FadD for the parts page and I am doing the same for protocols on PUFA quantification and genome incorporation. I found many parameter values necessary for the modeling of both our circuit and the body. I contributed to our outreach project called "Modeling for the Masses" with the goal of explaining COVID-19 epidemiological models to people of all backgrounds who may be confused by the information presented, what it means, and where it came from. We researched many prominent or interesting models and produced an educational video series on our findings. I presented our circuit at the Mid-Atlantic Meetup we hosted this summer. I am contributing to coding the wiki.

Riya Garg

This season, I researched the mechanisms that cause the switch between the production of inflammatory and anti-inflammatory metabolites of arachidonic acid in the body, looked into cytokine sensors, and the secretion mechanisms of eukaryotic proteins from prokaryotes. Additionally, I wrote the FabH parts page as part of our contribution to the parts registry and researched the protocols for quantifying proteins in the periplasm of gram negative and gram positive bacteria. I also made some contributions to the parameters for our inside the body model and helped code the wiki. I was also one of four presenters for our project at the Mid-Atlantic Meetup our team hosted. As part of our outreach this year, I helped create and publicize an educational TikTok series. Lastly, I compiled our project promotion videos, which we did in 5 languages, and voiced over the Hindi version of the video.

Min Guo

This year I helped to research papers about computer programs that detect viral recombination and helped compare different programs that detect viral recombination. I worked on finding a possible bacteria chassis that we can base our model on. I worked on research for cytokine-sensing proteins in bacteria, examined species and quantity of bacteria in the nasopharyngeal microbiome, and analyzed possible probiotic candidates. I focused on contributing the sensor part of the circuit. I did work on finding a possible signal transduction system in bacteria to help our circuit. I also contributed parameters for our “inside the body” model. I made some contributions to the iGEM OprF parts page. I wrote protocols for testing cytokine sensors.

Josh Hughes

This year, my introductory year to iGEM, I dipped my toes into the waters of viral recombination and bioinformatics. I have worked to identify prevailing issues and limitations in the field of identifying recombination breakpoints through bioinformatic computer programs. I have suggested solutions to these issues and used simulated viral genomes to not only assess the current performance of the widely used program RDP but to also tune the parameters inside of RDP. In terms of modeling, I have worked with Hantao, Wei, and Julia in creating our mathematical models and have given invaluable insights in terms of the foundational equations, mathematical representations of biological processes, and concerns of how our model may deviate from the biology. Additionally, I presented our groups research multiple times to age groups varying from 5th graders to graduate students and professors. Finally, I had the opportunity to translate and dub a dense scientific script into my second language, French.

Adam Oliver

This year marks my third year as part of William & Mary’s iGEM team, and my second time as co-captain. First, I helped to identify antiviral bioactive lipids that could be produced in a prokaryotic host. Then, I conducted the literature review of existing nasopharyngeal probiotics, and identified species of bacteria that would likely serve as good chassis organisms for use as a nasopharyngeal probiotic. Additionally, I was responsible for overseeing the literature review and production needed to create our Modeling for the Masses video series. I also worked closely with the rest of the team to help find and evaluate the parts needed to construct our PUFA producing circuits. Next, I helped to find and verify the parameters needed for our inside the body model. Finally, I provided feedback and guidance for the circuit design and inside the body model.

Julia Urban

This iGEM season, I returned to William & Mary’s iGEM team for my third year as a member and my second year as a co-captain. I identified polyunsaturated fatty acids (PUFAs) as candidates for a broad-spectrum antiviral therapy after reviewing literature regarding membrane rearrangement by positive-strand RNA viruses. Afterwards, I designed systems for the synthesis of export of PUFAs in bacterial chasses, and constructed ordinary differential equations to model this process according to Michaelis-Menten kinetics. To develop the “smart” aspect of the probiotic, I guided the team in developing a high-pass filter for distinguishing excess inflammation from basal inflammation. I interviewed five medical doctors, an ICU nurse, a probiotic specialist, and a COVID vaccine manufacturer for guidance on design, implementation, safety, and accessibility. Finally, I communicated our project through Wiki pages I wrote and presentations and graphics I designed.

Wei Wang

This iGEM season, I reviewed literature of a variety of viral recombination prediction programs to summarize their current state. Additionally, I built a complicated intra-host model to predict the feasibility of using AA and DHA to prohibit viral infection after implementation in the nasal cavity. I built the ordinary differential equations and coded them in python. In order to account for the spatial factor, I also built and coded a 10 by 10 grid model where diffusions are considered and viral particles initially follow uniform, gradient, or random distribution. I varied the parameters including initial probiotic number, replenishing interval and sensitivity of sensor to find the range where PUFA had a significant effect on viral load. The range helped us to determine the feasibility and indicated further adjustments we may need. Together with Josh and Hantao, we gave a presentation in a biomath seminar. In addition, Hantao and I made and recorded the Chinese translation of the promotion video.

Hantao Yu

I researched various viral recombination computer programs and looked into ways to create a machine learning program to predict future locations of viral recombination. I helped develop models for AA and DHA export, and helped to build and improve the intrahost model to predict the feasibility of AA and DHA in prohibiting viral infection after implementation in the nasal cavity. Collaborating with Wei, I made and recorded the Chinese translation of our team’s promotion video. With math team members, I made two presentations for our project and one in future.

Team:William and Mary/Attributions