Human Practices

A

A stands for “Adaptability.” Although our current project is focused on oil degradation through Alcanivorax borkumensis, we hope to adapt our project’s results to other pressing issues, beginning with the degradation of plastics with Alcan. Furthermore, as we continued to meet with various subject matter experts, our project adapted with the feedback given to us.

L

L stands for “Large Perspective.” Outside of addressing Delaware’s oil spills, we hope to apply our project’s results to a larger perspective. Every year, thousands of oil spills occur in U.S. waters alone and even more occur worldwide. From damaging the physical structures of fur and feathers to incapacitation, oil spills are a real threat to environments and ecosystems around the world. Through our project, we strive to address both a local and global issue.

C

C stands for “Collaboration.” Throughout the season, we spoke with various subject-matter experts to discuss both the technical and social sides of our project. By speaking with them, we gained much insight into how we can improve the scientific aspect (such as Christopher Saul helping us with Alcanivorax conjugation) and how we can ensure that our project will benefit society (such as Dr. Sherri Mason giving us the idea to test our project in a wastewater treatment plant). Meeting with subject matter experts helped us understand how vital it was to consider all aspects of our project’s, including its social, environmental, and economic implications. To help gain engagement within our community, we worked towards creating fun and unique experiences such as an iGEM workshop where we discussed synthetic biology and its applications to fellow high school students, which is crucial for lifting the stigma against it.

A

A stands for “Ambition.” Though this is only our second year competing in iGEM, and our team is made mostly of new members without iGEM or even lab experience, we always strived to learn as much as we could from our PIs, the subject-matter experts we reached out to, and each other, ultimately creating and sharing a project with our community.

N

N stands for “Novelty.” Though there already exist ways to clean up oil spills, they all have flaws. Therefore, we decided to take a synthetic biology approach to the problem, specifically using A. borkumensis. There hasn’t been research conducted to identify the specific protein in A. borkumensis responsible for oil degradation. Additionally, there hasn’t been research to develop a way to engineer A. borkumensis which could be utilized to increase the production of relevant enzymes, and our project hopes to address this.

Our Team's Human Practices Interviews

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Interview with Ross Klauer (3 / 31)

Dr. Ross Klauer, recent PhD graduate from the University of Delaware - March 31, 2025

Dr. Klauer is a researcher studying the mealworm gut microbiome’s ability to degrade plastics, whose work inspired our exploration of Alcanivorax borkumensis for oil degradation when we first began this project. He shared his approach to studying plastic degradation in the context of his research. During our conversation, he explained the multi-step process of alkane (carbon chains) degradation, where the first step involves oxidizing a carbon-carbon bond to make the alkane more chemically accessible in the next steps to come. He suggested we focus on this first step of degradation, as this step often limits overall degradation efficiency. As a result, we decided to focus on identifying candidate proteins from Alcanivorax borkumensis that may be part of this first step of degradation.

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Interview with Kristi Lieske (7 / 10)

Kristi Lieske, the Ocean Planner at the Delaware Department of Natural Resources and Environmental Control (DNREC) – July 10th, 2025

Ms. Lieske is the Ocean Planner at the Delaware Department of Natural Resources and Environmental Control (DNREC) and offered us valuable insight on the substantial economic and environmental impact oil spills have on Delaware’s coastal businesses. Since the main goal of our project is to combat oil spills, we knew Ms. Lieske would be able to help us explore the local impact our project could have. Delaware is home to many native species, specifically coastal birds and horseshoe crabs, whose habitats would be heavily impacted by the oil in the ocean. We also learned about the sizable coastal industries of Delaware; our state, specifically Sussex County, relies heavily on recreation and tourism, where oil spills can result in approximately $150 million in detrimental losses. By implementing our research with Alcanivorax Borkumensis in real-world scenarios, we’d be directly supporting those who face the impacts of oil spills the most. Through conversations with Ms. Lieske, we were able to determine the definite benefits our research would provide to our community, an essential part of the lives of animals and Delawareans.

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Intreview with Dr. Sherri Mason (7 / 18)

Dr. Sherri Mason, professor of chemistry at the State University of New York at Fredonia - July 18, 2025.

Dr. Sherri Mason is an expert in microplastics where she helped put out ideas for human practices. We originally didn’t have any ideas for testing our bacteria and Dr. Mason recommended a waste water treatment plant where everything can be “condensed” so our bacteria would be put out in a controlled environment. Dr. Mason also confirmed our hypothesis that our bacteria would also be able to degrade the hydrocarbon chains within plastic.

We interviewed Dr. Mason to gain insight on our idea about degradation of plastics with Alcanivorax. Her response confirmed our hypothesis that it is very possible for Alcanivorax to degrade plastics by eating the hydrocarbon chains within the plastic. Also, her insight directed us to look for areas of a controlled environment, such as waste water treatment plants, where we could be able to experiment our bacteria for human practices.

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Interview with Christopher Saul (5 / 5)

Mr. Christopher Saul, PhD student at the University of Delaware - May 5, 2025

Mr. Saul is currently a PhD student at the University of Delaware working in the Blenner Lab. He works with Alcanivorax as part of his plastic degradation study. He gave us an overview of possible methods to insert a genetic toolbox (ex., plasmid) into Alcanvorax Borkumensis. This included conjugation and transformation strategies. For instance, for our suicide vector, he proposed we use either a transpose system, a CRISPR system, a CasT (cas and transposon) system, or a λ red phage system. His input directly impacted our project as we decided to use a transpose system, which would randomly insert our GFP gene into the chromosomal DNA of the A. borkumensis. Furthermore, he advised we add lysine to the media when doing the conjugation method, as the E.coli used for conjugation doesn’t have the machinery capable of synthesizing lysine. By implementing his feedback into our project, we were successfully able to implement both conjugation (of our suicide vector) and transformation (of our broad range) within our project.

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Interview with Dr. Vance Jaeger (8 / 15)

Core Learnings

We learned that CHARMM-GUI offered a more precise way of setting up files for Molecular Dynamics simulations, prior to using GROMACs. Furthermore, we obtained clarification to questions relating to why certain features exist in molecular dynamics workflows, such as the presence of Periodic Boundary Conditions in simulation. Lastly, we were able to obtain advice on optimal simulation parameters, such as the necessary simulation runtime and tips to decrease the execution time.

Implementation

We were able to implement this advice into our workflow by taking into account the recommended simulation parameters and utilizing CHARMM-GUI in our molecular dynamics simulation workflow.

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Interview with Ms. Margit Olson (10 / 1)

Ms. Margit Olson, Science Teacher at the Charter School of Wilmington - October 1, 2025

With Ms. Olson being an environmental science teacher to many students and the former iGEM moderator, she was an obvious person to reach out to. She has provided crucial insight into how many communities may be impacted negatively through our project. She explained how our project may cause leftover oils and microplastics to pollute sensitive environments and ecosystems. Furthermore, certain communities like Coastal or Brackish such as Delaware may be impacted through the potential pollution caused. Places like Western Pennsylvania that have high levels of methane, mixed with the oil may cause fires. In addition, it is important that the project is first tested in a controlled environment rather than the ocean as it may lead to severe environmental harm. Ms. Olson’s advice has shown how pollution, specifically oil pollution, may cause drastic harm, especially towards sensitive groups. It is crucial that the project is first tested in a controlled environment to ensure that there is no further impact from the aftermath of the project. Her advice also brings insight on how it is important for the public to understand the harm that oil pollution has on different communities. Through her guidance, she has helped us understand the potential long term impact our project has and how it is crucial to minimize it.

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