Attributions PROS by the Stony Brook University 2022 iGEM Team

Attributions

There are so many individuals and organizations who proved crucial in the development of our project, and whose insight and guidance was invaluable throughout the competition cycle. Without their help, our project would not be what it is, and we are extremely grateful for all the patience and support they’ve shown us over the past year. From the very beginning of our project to the very end, they helped us brainstorm, decide on a topic, design experiments, execute our designs, and even raise funds, so that we could properly participate in iGEM. This support came from various individuals, institutions, and organizations. We would like to do our best to thank all of them.

Team Members

Lori Saxena. Lori was one of the co-leads for the 2022 Stony_Brook team. She was responsible for planning and implementing every outreach initiative, including work in integrated human practices, inclusivity, education, entrepreneurship, collaborations/partnerships, and communication. This included sending and responding to emails, meeting with stakeholders, contacting other iGEM teams, interacting with our local campus and greater Long Island community, and leading initiatives such as our scientific journal, podcasts, etc. In particular, she worked to aid in the creation of a research program between Suffolk County Community College and Stony Brook University, with the goal of helping non-traditional students gain access to opportunities within academia. Lori was further involved in mathematical modeling for the project. She was responsible for a large portion of the protein modeling, and helped derive ODE’s, and wrote and ran simulations in MATLAB. She also participated in wet lab experiments for E.coli, particularly experiments regarding transformation and protein expression. Finally, Lori helped contribute to various funding efforts, safety and security, and also wrote a large portion of all wiki content. In addition to writing, she edited and proofread every wiki page to ensure it was ready for publication. Overall, Lori was responsible for helping with analysis, conceptualization, brainstorming, fundraising, public engagement, entrepreneurship, background research, investigation, data curation, project administration, visualization, writing, and safety.

Eva Paruch. Eva was the other co-lead for the 2022 Stony_Brook team. She was responsible for planning and designing all wet lab experiments. This included collecting and writing all protocols and designing primers. She ordered/secured all necessary reagents and lab equipment, and created a detailed wet lab schedule for the team to follow over the course of the project. In order to secure wet lab support, she was responsible for helping the team find and contact advisors, and engaged in frequent communication with them. Eva helped conduct almost every experiment, and trained other members of the team in this regard. She also helped contribute to outreach and fundraising initiatives, and was involved in the design of the team’s scientific journal. In terms of wiki production, Eva helped write and review a portion of the wiki content for Contributions, and Engineering Success. Overall, Eva was responsible for helping with analysis, conceptualization, brainstorming, fundraising, lab maintenance, investigation, public engagement, entrepreneurship, background research, data curation, project administration, visualization, writing, and safety.

Ahmed Rehman. Ahmed was responsible for learning fundamental programming languages for web development, including HTML, CSS, and JavaScript. He created the foundation and layout of the webpages, developed tables, equations, slideshows, and buttons for the wiki, and troubelshooted FLASK pipeline Error 404 on Gitlab through Python. He was in charge of the entire wiki team, keeping them organized, setting tasks for the wiki members, and sending out annual updates as well as training other members of the team on how to transfer wiki content into code. Overall, Ahmed coded all the webpages.. Ahmed also aided significantly in outreach efforts, contributing to collaborations with EmpireGene and URochester, helping fundraise, and being in charge of our team’s TikTok account, which spread awareness of our project using witty videos. He was the main graphic designer/illustrator for the team, and was responsible for designing the logos and apparel. Ahmed also contributed significantly to web lab experiments, assisting with transformation and protein expression, and teaching other members aseptic streak plating. Most importantly, he brought comedic relief to the team. Overall, Ahmed was responsible for conceptualization, investigation, lab maintenance, fundraising, public engagement, background research, software, project administration, and visualization.

Maulik Masaliya. Maulik helped with the overall design of the project, which included doing independent research and talking with professors and advisors. He worked closely with Eva to determine cell lines for protein S expression, design experiments, and collect protocols. In particular, he researched plasmids and cloning techniques best suited for our project, and met with various advisors to discuss these project components. He was also heavily involved in procuring lab equipment and reagents, as well as securing funding. Maulik reached out to multiple biotech and pharmaceutical companies looking for sponsorships and donations, and worked closely with WeSci to build the team’s crowdfunding platform. He was also responsible for conducting wet lab experiments for both SF9 and E.coli. In particular, he was involved in transforming and verifying protein S expression, and troubleshooting and optimizing experiments. Maulik was further involved in the mathematical modeling portion of the project, helping to create simulations to model regulatory gene circuits of SF9 and E. coli vectors. He also aided in outreach efforts by participating in collaboration meetings and contributing to the team’s scientific journal. Maulik was solely responsible for documenting the team’s new parts and contributions in the iGEM registry He also wrote the wiki content for the following pages: Design, Proof of Concept and Parts, and helped write Results, Engineering Success, and Mathematical Modeling. Overall, Maulik was responsible for analysis, conceptualization, investigation, lab maintenance, fundraising, background research, data curation, project administration, writing, and safety.

Ya Jing Chen. Ya Jing was heavily involved in the wet lab and dry lab portions of the project, helping to update the notebooks and conduct experiments. She also aided significantly in the outreach portion of the project, writing our news article, contacting and conducting interviews for the podcast initiative and planning out the episodes, contributing and helping design our scientific journal, and participating in meetings with advisors and stakeholders. She was also responsible for helping to draft iGEM presentations, presenting our project to the greater campus community, and helping create a question panel to introduce EOP students to scientific opportunities on campus, as well as inviting a career advisor, Todd Dickson to tour the lab. Finally, Ya Jing helped proofread some wiki pages, and spent time brainstorming various fundraising ideas. Overall, Ya Jing was responsible for investigation, lab maintenance, fundraising, public engagement, background research, and data curation.

Divleen Singh. Divleen was responsible for researching protein S deficiency in the early phase of the project, and drafting the initial safety form. To learn more about the disorder and our project, she reached out to doctors as well as pharmaceutical companies for their insights on the availability of protein s detection/functionality assays. She was largely involved in the wet lab aspect of the project, including finding/designing protocols for E. coli experiments, and conducting some of the E. coli wet lab experiments (making the recombinant vector through LIC and transformation of cells), and writing and updating the E. coli wet lab notebook. She contributed to outreach efforts by presenting our project to the campus community and interviewing for the podcast initiative. Divleen also contributed to some protein modeling by modeling mutations of protein S on Chimera X. Overall, Divleen was responsible for conceptualization, investigation, background research, data curation, and safety.

Namrata Singh. Nami was largely involved in the outreach aspects of our project, interviewing alumni and professors for the podcast initiative, and reaching out to campus clubs and organizations to spread awareness about iGEM. This included Society for Women Engineers, Society for Asian Scientists and Engineers, the Butterfly Project, and CSTEP. She also aided in collaborations with other teams, particularly EmpireGene during our in-person meeting with them. Finally, Nami aided in developing our supporting entrepreneurship, doing research for this initiative of our project. This included doing a full market analysis and designing an AUTOCAD model of our product. Overall, Nami was responsible for fundraising, public engagement, entrepreneurship, and aided in writing for entrepreneurship.

Maira Riaz. Maira was responsible for researching protein S deficiency in the early phase of the project. To learn more about the disorder and our project, she reached out to doctors as well as pharmaceutical companies for their insights on the availability of protein s detection/functionality assays. She helped secure funding by writing grants. She was involved in performing some of the E. coli wet lab experiments which involved making the recombinant vector through LIC and transformation of cells. She aided in updating the wet lab notebook at times. Maira also participated in various outreach initiatives, including meetings and collaborations, interviewing students and faculty for the podcast, contributing to the scientific journal, and went to various campus and community events, helping to present our project to our community at large. She also helped significantly contribute to the following wiki pages: Safety and Security and Protocols. Overall, Maira was responsible for background research, investigation, lab maintenance, public engagement, data curation, and safety.

Ziyin Zhang. Ziyin was responsible for helping to contact professors and possible advisors at our university. She also proactively took responsibility for contacting multiple universities in China to seek communication and collaboration from their iGEM team. She also assisted with translating materials, both for our team, and as a part of collaborations with other teams. Ziyin drafted instagram posts to promote our team’s work, actively contributed to writing a journal article and translating various articles, and she helped modify and format the web pages on the wiki. Overall, Ziyin was responsible for public engagement and software.

Isam Adnan. Isam was responsible for assisting with coding some of the webpages for the wiki. He also assisted with overall professional development, entrepreneurship goals, and collaborated on numerous different outreach events. In particular, Isam was involved in the journal collaboration, and went to various different clubs and community events. This included meeting with SASA during their pre-conference, attending the in-person meeting with iGEM EmpireGene, meeting with various stakeholders, and actively working to further the outreach goals of the team. Overall, Isam was responsible for public engagement and software.

Honorable Mention

Stephanie Laderwager. Stephanie was initially a member of the team, but since she is a non-traditional undergraduate student seeking her first degree, and due to age requirements for the iGEM competition, was reclassified as an advisor. She was largely responsible for helping in the mathematical modeling section of the project. She collaborated with Lori and Maulik on writing MATLAB scripts, and also created the two mathematical modeling guides which we distributed to other iGEM teams. Stephanie was also heavily involved in all outreach activities. This included helping create the team brochure, designing infographics, creating guides for inclusive research and a streamlined algorithm for diagnosis, and meeting with stakeholders who gave us advice on our project. Stephanie also contributed significantly to entrepreneurship, meeting with industrial stakeholders and companies to get feedback, and emailing various community and national organizations to this extent. Stephanie worked closely with Lori and Dr. Gergen to aid in the creation of a research program between Suffolk County Community College and Stony Brook University, with the goal of helping non-traditional students gain access to opportunities within academia. Finally, Steph helped write up a large portion of the wiki content including pages such as Integrated Human Practices, Mathematical Modeling, Inclusivity, Entrepreneurship, and Diagnostics. Overall, Stephanie was responsible for analysis, public engagement, entrepreneurship, background research, data curation, visualization, and writing.

Principal Investigators

John Peter Gergen, head of Undergraduate Biology at Stony Brook University. We are extremely grateful for all the feedback that Dr. Gergen gave us on our project, and the large amount of time that he invested in meeting with us, discussing our project, and guiding us through the competition. Without his input on wet-lab experiments, aid in securing funding, contacts and connections, the laboratory space he helped secure for us, and his commitment to keeping us on track with deadlines and expectations, we would have been at a loss. Whenever there were any problems, or any confusion (which happened often), he was always quick to respond and lend us a helping hand. We cannot thank Dr. Gergen enough for his diligence in helping us develop and present our project to a global audience.

Gabor Balazsi, Henry Laufer Professor of Physical & Quantitative Biology at Stony Brook University. Dr. Balaszi was always ready to support our project. We are extremely grateful for all the feedback he provided when something was unclear in the lab, discussing the design of our wet lab experiments, and the various levels of support he provided us with. From the very beginning, he was crucial in helping us decide on a project topic and how to best address our chosen issue. We cannot thank him enough for all that he did!

Instructors

Joshua Rest, Associate Professor in the Department of Ecology and Evolution at Stony Brook University. Dr. Rest was instrumental in providing invaluable feedback and suggestions during the spring reading course and when we were developing our project. Without his comments and questions, our project would not be nearly as refined, and we would have been at a deficit in formulating our wet lab plans.

Steven Glynn. Ph.D., Associate Professor in the Department of Biochemistry and Cell Biology at Stony Brook University. Dr. Glynn was instrumental for the design and execution of the wet lab portion of our project. He provided us with many of our protocols, and helped us troubleshoot the wet lab protocols throughout the design cycle. The Glynn lab was also an immense resource and provided us with reagents and materials, helped us design our plasmids, gave us an enormous amount of feedback and guidance on research techniques, and really helped us through every step of the competition.

Advisors and Additional Help

Michael V. Airola, Assistant Professor in the Department of Biochemistry & Cell Biology at Stony Brook University. Dr. Airola helped us significantly in designing our wet lab procedures and better understanding the more technical aspects of our project. He taught us about techniques he commonly uses for protein expression, and advised us on which donor vector to use. His lab also generously donated many supplies including plasmids and cells and demonstrated wet lab techniques to our team.

Mary A. Bernero, Head Curator at Stony Brook University. Dr. Bernero was instrumental for the success of our team, helping us procure reagents, and gain access to lab instruments that were critical to our project. She oriented us between the different laboratories, taught us how to use instruments, and advised us.

Extremely Special Thanks To

AJ Sillato, Masters Student, Glynn Lab. AJ never hesitated to answer our questions and give us advice. He generously offered his time throughout the summer, helped provide us with protocols, reagents, and equipment, and drew upon his experience as a past iGEM team leader to help guide us through the competition, particularly with our wet lab experiments regarding E.coli. From early mornings to late nights, he was always willing to lend a hand and teach us how to do certain procedures and experiments, helped us troubleshoot for our project, checked in on all portions of our project, and even helped give our members pep talks to help boost our morale! Our project, especially the wet lab portion, would not have been possible to accomplish without his guidance. Thank you so much for everything AJ!

Christopher Helenek, Graduate Student in Biomedical Engineering, Balázsi Lab. Chris was on the 2019 Stony Brook iGEM team as the former team leader, never hesitated to answer our questions or give advice, and was very generous with his time. He helped us significantly in the dry lab portion of our project. Specifically, he helped teach us how to use MATLAB and determine what models, parameters and variables were best suited to model in our project. He taught us the very basics, and helped us build on our understanding in order to develop a more complex model. He spent hours every week answering our questions, and stopping by whenever we ran into a problem to help us troubleshoot. From calculus, to MATLAB code, to giving general tips for our team and the competition, Chris was invaluable and instrumental in the success of our project. We cannot thank him enough for all his support and guidance!

Douglas Marr, Molecular and Cellular Biology PhD Student and Graduate Researcher at Stony Brook University. Doug was instrumental in the development and execution of the wet lab portion of our project. He never hesitated to answer our questions and give us advice. He generously offered his time throughout the summer, and helped provide us with protocols, reagents, and equipment, particularly aiding us with our wet lab experiments regarding SF9. He taught us about certain techniques and protocols, and helped us troubleshoot the many many times we ran into issues or had any confusion. We cannot thank Doug enough for all his time and support!

Sponsors and Funding Support

Institutional In-Kind Support of Facilities and Faculty Effort. The Undergraduate Biology Program at Stony Brook University provided the iGEM team access to an instructional laboratory fully equipped for routine Molecular Biology. We had 24/7 card and key access to the room and used it on an essentially full-time basis for the entire summer before transitioning to a smaller space in one of the preparatory rooms in the Biology Learning Laboratories once the fall semester started. The estimated value of this kind of institutional contribution based on quotes received from off-campus providers is $9,200.

This in-kind contribution is not included in the table of commitments and resources provided below but is certainly a significant and invaluable component of the institution’s support of this project. The team was also provided access to SF9 cells from Dr. Michael V. Airola (Biochemistry and Cell Biology) and E. coli bacteria from Dr. Steven Glynn (Biochemistry and Cell Biology) as well as access to a Nanodrop Spectrophotometer from Jessica Seeliger (Pharmacological Sciences).

Throughout the entire year the team has benefited from active guidance and support from an interdisciplinary group of faculty that includes: Gabor Balazsi from the Department of Biomedical Engineering, Peter Gergen and Steven Glynn from the Department of Biochemistry and Cell Biology, and Joshua Rest from the Department of Ecology and Evolution. We do not want to put a dollar value on the in-kind contribution represented by this faculty support, but as is the case for the access to facilities and equipment this is also an invaluable component of Stony Brook University’s support of the iGEM team.

Institutional Direct Financial Support (totaling $41,200). Research Support Request (RSR), from the Office of the Vice-President for Research, totaling $6,000 which was used to cover the cost of lab materials and reagents. There were also stipends that different iGEM team members received from different sources to support their research in the summer of 2022 came to a total of $41,200. The breakdown of support from different sources is as follows:

  1. Participation in the Explorations in STEM Program - 3 full stipends (2 with housing) funded by PSEG ($11,200); 2 full stipends funded by the Biology Program ($10,000).
  2. URECA Biology Alumni Research (U-BAR) award - 1 full stipend cost-shared by URECA ($2,500) and the Biology Program ($2,500)
  3. U-BAR awards - 1 full stipend and 4 half stipends funded by the Biology Program ($15,000)

External Sponsor Commitments and Donations (totaling $25,755)

  1. Dr. Steven Galson, Senior Vice President of Global Regulatory Affairs and Safety at Amgen Inc., $20,000 donation to the iGEM team to register for the competition and participate in the Giant Jamboree. This covered our initial registration fee, Jamboree registration, and partially covered travel and lodging expenses for Jamboree participants.
  2. Snapgene, eleven free copies of software access for an estimated value of $1,555.
  3. Integrated DNA Technologies Inc. (IDT), free oligonucleotides synthesis for up to 20,000 base pairs for an estimated value worth $3,200.
  4. Contract Pharmacal Corp., $1,000 donation
  5. New England Biolabs donated DNA cloning kits and reagents worth $511.
  6. Thermofisher Pharmaceuticals offered us a total of $3,266 in lab supplies, including items that included plasticware and disposables, solutions and reagents, and various different kits.
    • In particular, we communicated with Kate Brice, the Biosciences Account Manager at the NY Life Sciences Solutions for Thermofisher, and Brett Strahin, the Technical Sales Specialist for Cell Biology Delivery and Protein Expression. They were both extremely enthusiastic and generous, and donated a good portion of the supplies required for our project. We cannot thank them enough for the time and resources they devoted to our project!
  7. Crowdfunding on WeSci. WeSci is a crowdfunding platform for scientific research & innovations, with the mission to bolster scientific funding through transparency and accessibility. We created a crowdfunding campaign with them, working to raise a total of $4,588.44, of which our payout was $3,897.62. This money was then committed to helping cover travel and lodging expenses for Jamboree participants. You can see our WeSci Campaign. We want to thank the incredible team at WeSci for their help setting up our campaign..

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Team

The members of the 2022 Stony Brook University iGEM Team

Description

Introduction to our project.

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