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Informational Interview on Microplastics and Possible Solutions - 2/11
Dr. Jeffrey Farner
Assistant Professor in the Department of Civil and Environmental Engineering at the FAMU-FSU College of Engineering
Why?
Dr. Farner has done extensive research on microplastics, how they develop from larger plastics through environmental weathering and UV exposure, and how they interact with the environment. He has tested the following qualities of microplastics: surface chemistry, the effect of UV weathering on morphology, and self-interactions via aggregation.
How has this affected our project?
We gained valuable insight into the concerns of micro and nano-plastics, and the dangers of toxic chemical properties being leached from microplastics. We then brought the information back to our engineering team, thus influencing the first round of our design to consider the different reactive points on different microplastics.
Modeling Discussion: High-Affinity Plastic-Binding Peptides - 2/11
Michael T. Bergman
PhD candidate in the Chemical and Biomolecular Engineering Department at North Carolina State University
Why?
To gain an introductory understanding of modeling and the possibility of peptides with a high binding affinity for plastics and microplastics.
How has this affected our project?
Our modeling team was given the opportunity to ask questions regarding the binding affinity of prospective peptides to microplastics. Additionally, recommendations were given to research meta-dynamics, enhanced sampling, umbrella sampling, and Molecular Dynamics Simulation setups.
About Plastic Alternatives - 2/12
Dr. Hoyong Chung
Associate Professor in the Department of Chemical & Biomedical Engineering at the FAMU-FSU College of Engineering
Why?
At this point, early on in our design cycle, we were still exploring the possibility of creating an alternative to plastic that can be biodegradable and made from sustainable sources, and wanted to gather as much knowledge as we could from an expert in the field of plastic alternatives.
How has this affected our project?
Dr. Chung provided a critical overview of current sustainable plastic alternatives, highlighting key drawbacks such as durability challenges and the high costs associated with their implementation and improvement. Our team was also informed to explore a theory: that the true environmental threat may be the pollutants that adsorb onto the surface of microplastics, rather than the particles themselves. Lastly, we were inspired to find our innovation point and to continue exploring the problem of microplastics.
Microplastics within the Human Body - 2/19
Dr. David A. Davis
Research Associate Professor at the University of Miami Brain Endowment Bank
Why?
Dr. Davis has devoted his scientific career to exploring the relationship between toxins in the environment and their potential role in causing neurodegenerative diseases. He shared many insights into the role of plastics within our bodies and the potential negative health implications associated.
How has this affected our project?
Our team learned about the presence of plastic within the brain and olfactory bulb, as well as the limited research currently available on their impact. This interview with Dr. Davis gave insight into toxins from algal blooms binding to plastics, reinforced the urgency of our work, and strengthened our team's commitment to a human-health-focused solution. Finally, his emphasis on public education, reducing single-use plastics, and policy change directly influenced our education and outreach.
Understanding Microplastics within the Ecosystem - 2/27
Dr. Mariana Fuentes
Associate Professor at the Department of Earth, Ocean and Atmospheric Science at Florida State University
Why?
The purpose of this interview was to gain expert insight into the ecological and human health impacts of microplastics while gaining perspective on the importance of outreach to the public. We aimed to ensure our project is grounded in real-world challenges and to gain a holistic understanding of the many aspects affected by microplastics.
How has this affected our project?
Dr. Fuentes reinforced the importance of investigating the long-term indirect ecological impacts of having microplastics enter our environments and subsequently enter our bodies. The discussion with Dr. Fuentes directly helped our team refine our outreach and education materials as animal and ecosystem health has a direct cascading effect toward human health.
Discussing Design Timeline and Enzymes with iGEM Stockholm Alumni – 2/28
Ulysse Castet
Doctoral Student in computational design of enzymes and pathways for sustainable industrial bioprocesses at KTH Royal Institute of Technology
Why?
The purpose of this interview with Ulysse was to discuss the design expectations and timeline for a project regarding microplastics with an experienced member of a past iGEM team.
How has this affected our project?
Ulysse gave many helpful insights into the timeline of a design project and realistic expectations to look forward to regarding time constraints and functionality of an iGEM project. Additionally, he suggested different enzymes and what he would have done differently for a microplastic detection solution.
Understanding the Challenge of Microplastic Pollution in Florida – 2/28
Kayla O'Brien
Ph.D. Student in Geosciences at FAU in the Charles E. Schmidt College of Science
Why?
As a Florida-based team, we consulted a local researcher specializing in the prevalence and characteristics (type, color, shape, size) of microplastics within our state's coastal environments. We asked for her feedback on our preliminary project design, particularly in the context of our research into the correlations between environmental pollutants and human health.
How has this affected our project?
This interview provided us with clearer guidance on the issues that microplastic pollution poses in the environment, particularly in our local mangrove and beach environments. We now have a clearer understanding of the variables we will need to keep in mind to ensure our solution makes a positive and measurable impact.
Meeting with Former FSU iGEM Team Member - 3/1
Vicenzo DeVito
2023 FSU iGEM Mathematical Modeling Team Lead, 2024 and 2025 FSU iGEM Mentor
Why?
Vicenzo modeled the changing concentration of the compound Trimethylamine (TMA) as it is being converted to trimethylamine N-oxide (TMAO) while it passes through the digestive system for the 2023 FSU iGEM team. We spoke with Vicenzo to ask for advice and guidance on modeling and engineering at the start of our project cycle.
How has this affected our project?
Vicenzo showed the Modeling team the basics behind AlphaFold and AutoDock Vina, so that we could utilize these resources to model our peptides of interest and their plastic binding affinity. He also assisted us with our timeline and organization, helping us stay on track.
Research Methods Regarding the Prevalence and Identification of Microplastics in Lungs – 3/5
Alberto Chaves
Microplastics lab Research Assistant and Chemical Engineering student at the University of South Florida
Why?
We met with Mr. Chaves to discuss the issues his research lab encountered while studying microplastics within the human body. We also discussed various methods to measure different “types” of microplastics.
How has this affected our project?
With this interview, it was brought to our attention the lack of regimented resources and concise data regarding microplastics research in humans. We learned ways to lower our risk of sample contamination, literature review, and standards to detect and differentiate through different types of microplastics.
Design Idea #1 Professional Feedback - 3/14
Dr. Nick Cogan
Biomathematician and Associate Professor in the Department of Mathematics at Florida State University
Why?
Our original high-level design centered around genetically engineering macrophages in Peyer’s patches to express PETases for degrading phagocytosed microplastics. Considering Dr. Cogan’s background in biomathematics, we sought out his input on modeling microplastic interactions with macrophages.
How has this affected our project?
Dr. Cogan advised our modeling team on ways to mathematically model microplastic interactions with macrophages.
Exploring PETase, the Hydrolase Family, and Immune Cell Engineering - 4/10
Dr. Wen Zhu
Assistant Professor in the Department of Chemistry and Biochemistry at Florida State University; former Research Scientist at Astex Pharmaceuticals researching enzyme catalysis
Why?
To learn more about an expert's perspective on the Hydrolase enzyme family, which is the family of our enzyme of interest at the time, PETase. We asked questions regarding the safety and possible repercussions of PETase within the human body. Dr. Zhu was also a previous faculty advisor for microplastics research, specifically for a student studying the FAST-PETase enzyme, and its potential abilities degrading microplastics, specifically polypropylene.
How has this affected our project?
At this time, we were still on track to engineer immune cells to combat microplastics in the body. This interview introduced us to the vastly complicated world of immune cells and how many variables we would need to monitor when utilizing hydrolase enzymes. After this interview, we explored different immune cells with different viable pH ranges and researched whether our PETase enzyme would be able to survive inside the cell.
Finding the Right Delivery Method for Our Therapeutic – 4/10
Dr. Jingjiao Guan
Associate Professor of Chemical and Biomedical Engineering at FAMU-FSU College of Engineering
Why?
Dr. Guan’s research has illuminated our understanding of the macrophage’s inner mechanisms. Considering this, we wanted to discuss our macrophage-based design with him to better understand the immunocyte and methods of engineering it.
How has this affected our project?
It provided insight into the complex mechanisms involved in phagocytosis, specifically pertaining to how it’s initiated and phagolysosome formation. Ultimately, this interview led us to pursue alternative designs because of the potential challenges of transfecting macrophages with our vector, as well as the complexity required to express enzymes in the phagolysosome.
How Immune Cells React to Microplastics – 4/11
Dr. Nienke Vrisekoop
Associate Professor at the Center of Translational Immunology at the University Medical Center Utrecht
Why?
Dr. Vrisekoop is part of an organization called POLYRISK that conducts research on the risks of microparticles and nanoparticles within the human body, specifically regarding plastics. She had recently presented her findings at a Plastic Summit regarding her research on how macrophages in rat models interact with microplastics.
How has this affected our project?
This interview further informed us of the research that was occurring within the field of immunology regarding microplastics interacting with macrophages. We aim for this interview to affect our educational segment of Human Practices, as well as guide our research on how the human body reacts to microplastics it interacts with.
Methods of Measuring Microplastics within the Lab – 4/13
Dr. Jamel Ali
Associate Professor of Chemical & Biomedical Engineering (CBE) and Materials Science & Engineering (MSE) at FAMU-FSU College of Engineering
Why?
The purpose of this interview was to discuss lab techniques that accurately measure the degradation of microplastics to assist our team’s lab protocol.
How has this affected our project?
Dr. Ali recommended Scanning Electron Microscopy and Nanoparticle Tracking Analysis as methods of measurement for our project. Additionally, he gave the team advice on which lab spaces we should reach out to collaborate with, instruments we may need, and other researchers we should reach out to know more about lab proceedings, modeling human environments, and our topic in general.
Learning About Lipid Nanoparticles with Macrophages for Project Consideration - 4/14
Dr. Stephen Lenhert
Associate Professor in the Department of Biological Science at Florida State University
Why?
Dr. Lenhert is an expert in lipid nanotechnology. We consulted with him to understand the key parameters for designing and using lipid nanoparticles (LNPs) for our potential microplastic degradation design regarding utilizing macrophages.
How has this affected our project?
We learned about critical design parameters (charge, size, dosage), effective methods for measuring transfection efficiency, and received advice on experimental design. Dr. Lenhert’s key recommendation was to first use a commercial kit (e.g., Lipofectamine) to establish a baseline and validate our assay before developing a custom LNP formulation if we were to go about this design choice.
Build Lab Protocol Meeting #1 – 5/21
Michael Taylor
Founding Engineer for Cypher, an AI-powered software platform for scientists, and 2018 FSU iGEM team member
Why?
Michael is a past FSU iGEM team member that is passionate about iGEM and helping the scientific community find new and better ways to generate protocols, create data-rich widgets, and improve interactive experimental planning.
How has this affected our project?
Michael was an amazing resource for our build lab team in helping us design our lab protocols and guide the 2025 FSU iGEM team in lab work. In this meeting he gave us a tour of Cypher, his AI protocol website, and detailed how to build a protocol using AI tools. Additionally, he suggested various resources for building an assay.
Build Lab Protocol Meeting #2 #3 #4 - 6/18, 6/22, 7/1
Michael Taylor
Founding Engineer for Cypher, an AI-powered software platform for scientists, and 2018 FSU iGEM team member
Why?
The purpose of these meetings was to discuss the difficulty of proving expression on the surface of E. Coli and which lab protocols would be appropriate for our project.
How has this affected our project?
Michael suggested using time or dose dependency to demonstrate a relationship. He also introduced protein quantification using plate reader assays. Moreover, we established the idea that a copper/nickel bead can be used to bind to the peptide with a His-tag. Although this idea was not used, it was included in one of our many lab protocol drafts, documented in the Engineering tab. He suggested using three steps for a plastic assay: isolating proteins, denaturing proteins, and plastic quantification. Furthermore, he explained how green fluorescent protein can be utilized to determine binding, as we wanted to find a way to measure the binding of our peptide to the microplastic.
From Idea to Experiment: A Conversation with Dr. Farner – 7/7
Dr. Jeffrey Farner
Assistant Professor in the Department of Civil and Environmental Engineering at the FAMU-FSU College of Engineering
Why?
We met with Dr. Farner back in February to gain a baseline understanding of microplastics and gain feedback on our potential design solutions. After 3 months of design iterations, 18 interviews with experts, and numerous changes to our protocols, our team was ready to test our microplastic aggregation idea within the lab.
How has this affected our project?
Meeting with Dr. Farner in July to discuss microplastic detection and ask questions about lab work was a full-circle moment for our team, highlighting just how far our project had come since those first early conversations. We discussed different variables to consider in the solution (temperature, salinity, pH) and their biological relevance. Dr. Farner suggested a method to determine an optimal ratio of plastic: a peptide in the solution that will produce identifiable results. Additionally, he suggested running a control to confirm steady fluorescence absorbance of the plastic before running the assay. All considerations were taken back to our build team and reviewed before our final lab protocol meetings.
Final Build Lab Protocol Meeting #5 – 7/12
Michael Taylor
Founding Engineer for Cypher, an AI-powered software platform for scientists, and 2018 FSU iGEM team member
Why?
To review our official build lab protocol and the flow of our assay from start to finish with an expert in the field of protocol generation.
How has this affected our project?
He introduced different laboratory techniques that could measure a change in plastic concentration. We reviewed how the assay should flow from start to finish, including the initial transformation of the plasmids. He provided an overview of how gas chromatography, mass spectroscopy, liquid chromatography, and UV Vis would take place in the lab and how to locate a source on campus. Additonally, Michael analyzed and critiqued our proposed buffer solution to use in the assay and explained the reasoning for using certain substances for the buffer. We received guidance on how many conditions to measure the assay in and how many samples to run, taking into account how many peptides and controls we were utilizing. Organizational techniques for running the assays with numerous samples were also discussed.
Modeling Advice and Reaffirming Peptide Binding – 7/16
Dr. Bhargav Karamched
Assistant Professor at Florida State University in the Department of Mathematics and the Institute of Molecular Biophysics
Why?
The purpose of the meeting was to receive guidance on the kinetic ODE and to find out how we can model the combined binding effect of our engineered E. coli surface peptides to microplastics. To develop a new math model to include the interaction of the human gastrointestinal environment.
How has this affected our project?
This meeting helped us improve our kinetic model that treats peptide-plastic events as independent and models the changes in concentration of free peptide, plastic, and peptide-plastic complex. We were able to improve our understanding of the kinetic/concentration model, refining its accuracy by incorporating polystyrene-specific rate constants. In contrast, the Markov-State model considers multiple peptides displayed on the surface of E. coli, assessing both the number of plastic particles bound and the probability distribution of the number of peptides bound.
Choosing Polystyrene, and Advice on Assay Development – 7/21
Dr. Jeffrey Farner
Assistant Professor in the Department of Civil and Environmental Engineering at the FAMU-FSU College of Engineering
Why?
Our team decided to pivot from PET microplastics due to market availability and financial constraints. Since Dr. Farner has been familiar with our project from the very beginning and his academic research interests specialize in microplastics, we asked his advice on which microplastic to tackle instead.
How has this affected our project?
This was our third meeting with Dr. Farner. He advised us to go with Polystyrene (PS) instead of Polyethylene Terephthalate (PET), to lean towards a filtration assay rather than centrifuging, and had us consider the benefits of adding fluorescence to our assay.
Tour of Laboratory Workspace and Safety Procedures - 7/23
Dr. Stephen Arce
Teaching Faculty in the Department of Chemical & Biomedical Engineering at the FAMU-FSU College of Engineering
Why?
Our build lab team met with Dr. Arce to discuss the laboratory workspace we would be working in and familiarize ourselves with the equipment. Additionally, we discussed safety procedures and potential hazards in the lab, recognizing their location and how harmful they are.
How has this affected our project?
This preparation was essential for our team to gain a clear understanding of the laboratory space and equipment we will be using, which has helped us plan more realistically for our experimental work. Our build team also learned essential laboratory techniques and practices that not only assisted us in testing our experimental design, but they also gained valuable hands-on experience in the lab.
Reviewing Kinetic Models - 8/1
Bhargav Karamched
Assistant Professor at Florida State University in the Department of Mathematics and the Institute of Molecular Biophysics
Why?
To review our work in developing a quantitative model of E. coli dynamics within the intestine, incorporating key parameters such as flow rate, adhesion, and detachment, the rate of E. coli adhering to and detaching from the intestinal walls.
How has this affected our project?
This meeting helps us develop a new set of ODEs which describe the changing concentrations of free E. coli, Microplastic, and E. coli microplastic complex as it passes through different segments of the gastrointestinal track. This model also incorporates interaction in the gastrointestinal environment including intestinal flow rate and E. coli adhesion to detachment from the intestinal wall.
Discussion about Developing a Therapeutic - 8/29
Dr. Judith Cornely
Associate Program Director, Pediatric Physician DO at Broward Health (Doctor of Osteopathic Medicine)
Why?
We met with Dr. Cornely to discuss about our proposed therapeutic, and how we should consider our methods of delivery as we keep both the publics interest and our goal for our design in mind.
How has this affected our project?
This interview gave us insight on how our therapeutic should be developed for intake. We agreed that oral intake would be the most optimal and accessible for transport and use, rather than patches or injections. We also spoke on how doctors view potentially helpful therapeutics, and how, despite their lack of ability to prescribe supplements/therapeutics, they can offer advice to us, the developers, so we can better design our therapeutic for public consumption, keeping public preference and safety in mind.
About our Probiotic on the Market - 9/23
May Jingyan Wang