Our student team members this year are Frank D’Agostino, Rahul Subramaniam, Robert Shekoyan, Maya Razmi, Siva Muthupalaniappan and David Cao. Our student team leaders are Zehan Zhou and Aaron Hodges. Our mentors/instructors are Anastasia Ershova and Olivia Young, both graduate students in Dr. William Shih's lab at the Harvard Wyss Institute for Biologically Inspired Engineering and Harvard Medical School. Our primary investigators (PIs) are Dr. Jia Liu at the Harvard John A. Paulson School of Engineering and Applied Sciences (Harvard SEAS), and Dr. Alain Viel in the Molecular and Cellular Biology department of the Harvard Faculty of Arts and Sciences (Harvard FAS).
We would like to thank our amazing mentors, Ms. Ershova and Ms. Young, for readily providing feedback and guidance in finding project design and simulation resources over the course of the project. Additionally, we would like to thank our PIs, Drs. Liu and Viel for providing regular feedback and assistance in choosing and honing a project idea.
Team Structure and Early Work
Our team is an extracurricular club (not a synthetic biology course) that meets on weekends to discuss synthetic biology and conduct research for the iGEM competition. From September 2019 to March 2020, we met once a week on Sundays to learn about the principles of synthetic biology. Our team’s student board members (Zehan Zhou, Aaron Hodges, Teagan Steadman, Ralph Estanboulieh and Joshua Lui) created lectures about synthetic biology and presented a lecture at each regular meeting. We would also like to thank Dr. Melissa Hancock of the Harvard SEAS Active Learning Labs, who gave us basic training in basic synthetic biology wetlab techniques, including PCR and gel electrophoresis.
Project Ideation and Design
Our project ideas were designed from March to June 2020 by the student team members listed above. Drs. Liu and Viel provided regular feedback and guidance in choosing an idea at regular virtual team meetings. Once the student team members had selected a final idea (that would become this year’s project), we reached to and recruited Ms. Ershova and Ms. Young from William Shih’s lab to serve as team mentors for the remainder of the season.
The bulk of our research was conducted virtually from June to September 2020. The student team members conducted all design, programming, modeling and simulation work on their own. Ms. Ershova and Ms. Young organized weekly meetings in which the team shared updates on ongoing work and decided on future steps, and also organized weekly journal club meetings in which student team members took turns presenting literature that pertained to that week’s research topics. Beyond these weekly meetings, Ms. Ershova and Ms. Young also provided regular feedback and troubleshooting assistance for both machine learning and DNA origami over Slack as necessary. We would like to thank the European Centre for Genomic Regulation for providing us with their FoldX computational chemistry suite free of charge, as well as the CanDo and oxDNA teams for allowing us to freely use their simulation webservers.
We would like to thank Harvard SEAS for graciously funding our team’s research this year. We would also like to thank our team coordinator, Ms. Jessa Piaia for coordinating funding with the Harvard SEAS administration and managing our team’s funds.
Our human practices and survey were created and edited by the student team members. Maya Razmi analyzed and presented our survey data. We would like to thank Ms. Alicia McGovern and Ms. Meaghan Pronovost from the Harvard University Committee on the Use of Human Subjects for reviewing our human practices survey. We would also like to thank the 205 individuals who graciously responded to our survey.
Collaboration and Project Presentation
Our student team leaders organized and hosted the virtual NEGEM conference in September 2020. We would like to thank Dr. Pamela Silver from Harvard Medical School for presenting her research on synthetic biology, as well as Dr. Jacob Beal from the iGEM Measurements Committee for giving a talk on obtaining accurate and replicable measurements. We would like to thank our volunteer judges, Dr. Nikki Thadani, Dr. Nikhil Gopalkrishnan, Mr. Chris Wintersinger and Ms. Anastasia Ershova for listening to and providing written feedback on teams’ presentations. We would also like to thank UIUC iGEM, Cornell iGEM, MIT iGEM and Purdue iGEM for attending the NEGEM conference and presenting their work to be judged.
In terms of project presentation and iGEM deliverables, Frank D’Agostino created our Project Promotion Video and Project Description video. We would like to thank Mr. Casey Cann from the Harvard Derek Bok Center for Teaching and Learning for meeting with us and volunteering assistance and feedback in video editing. Our team wiki content and coding as well as the judging form were completed by all of the student team members as well as the student team leaders.
Finally, we would also like to thank Mr. Adam Zewe from Harvard SEAS for interviewing us about our project and publishing an article about our work in the Harvard Inside SEAS newsletter as well as the Harvard Crimson publication.