UCSC’s 2023 iGEM team grabs fourth consecutive gold medal and nomination for best software tool at international competition

November 29, 2023

By Emily Cerf

A team of UC Santa Cruz students won a gold medal at the 2023 International Genetically Engineered Machine (iGEM) Grand Jamboree, marking their fourth consecutive year of bringing home the prize, and were nominated as best software tool for the first time. The annual iGEM competition brings together student teams from around the world to present synthetic biology projects that aim to address 21st century societal challenges.

The 2023 UCSC iGEM team’s project, called the Toxic Algal Bloom Interference (TABI), centered on addressing harmful algal blooms in local Watsonville’s Pinto Lake, creating a solution that could also be applied globally to similar environmental problems.

The competition was the culmination of months of dedication to the project, which included brainstorming, fundraising, building a project website, software development, local outreach, research, and, of course, wet lab work. Students on the iGEM team take four courses and dedicate a summer to working around 40 hours a week in the lab, gaining deep experience and a passion for research and developing a tight-knit community. The 14 UCSC students on the iGEM team and one iGEM intern from Hartnell College traveled to Paris, France with their advisor, Baskin Engineering Associate Teaching Professor, David Bernick and Teaching Assistant Gia Balius.

Presenting in Paris

This year’s iGEM competition was the second in-person Jamboree after the pandemic, giving the students the opportunity to connect and bond with other students enthusiastic about synthetic biology from around the world who have also gone through the rigorous iGEM process. The UCSC iGEM team was in the iGEM Jamboree “project village” with the theme of bioremediation, meaning they mostly interfaced with other groups working in similar areas.

“You go through the project with just your team members, and you don’t realize how much else is out there, what other people are doing, that they’re going through the same path with you,” said Nikita Rajesh, a biomolecular engineering student on the iGEM team. “It feels very approachable because it’s peer to peer and they’ve been through this experience, too. You already have the connection going in. So within like five minutes, you’ve made a new friend.”

The Jamboree also provides opportunities to network with representatives from industry and government who also attend the competition and are often interested in transforming the ideas presented into startups.

“Something that people don’t really know is that the field of synthetic biology grows from iGEM,” Bernick said. “Not only are students getting trained in this field, it’s also throwing new ideas out there. All of the topic areas are attempting to in some way address some of the most critical problems that exist, and so everything that is being invented is something that is intended to make a big difference in the world.”

For the first time in ten years of iGEM history at UCSC, the team was nominated for best software tool, a recognition for teams whose projects did not purely focus on software itself but rather as a complementary component of the project.

“It excited us because there’s a very small number of teams that get nominated for the software awards,” said Varun Kodur, a molecular, cell, and developmental Biology student and co-captain of the 2023 iGEM team. “Getting a gold for iGEM is something that we’ve been thankfully able to do with our team for the past four years, but this is the first time we got a nomination in software.”

Addressing algal blooms

The 2023 UCSC iGEM team focused their project on toxic algal blooms at Watsonville’s Pinto Lake, which has been used for community recreation and is home to more than 130 bird species. With this project, the iGEM team became the first group of researchers to consider synthetic biology as an intervention strategy at Pinto Lake.

“Watsonville is a low-income community surrounded by agriculture. The project directly impacts not only people who can relate to these communities – I myself come from a community like that — but it also brings about this recognition that these are communities that are providing our food but are living in a state where they don’t necessarily have the socioeconomic mobility to bring about change themselves,” said Danny Cruz, a biomolecular engineering student on the iGEM team. “We are giving back to that community, and being able to provide something after they’ve provided so much for us for so long.”

Pinto Lake has seen toxic algal blooms for the past four decades due to high levels of phosphates in agricultural runoff. Similar algal blooms are found in bodies of water around the globe, becoming more toxic and pervasive due to warming temperatures from climate change. Exposure to these algal blooms can be extremely harmful to humans and animals, potentially causing severe sickness and death.

While other efforts to remove the toxic blooms revolve around killing off all the algae in the environment, the iGEM team’s approach targets the harmful genes of the specific bacteria responsible for the algal blooms, called Microcystis aeruginosa, creating a non-invasive, long-term solution to preserve biodiversity, ecosystem balance, and public health. Their approach uses synthetic biology to disrupt the toxic genes within the bacteria that causes the algal blooms.

The team set out to solve this with a plasmid, an extrachromosomal DNA molecule, but determined that they needed a way to evade the bacteria’s native immunity in order for a plasmid to be able to efficiently transform the cell and target the harmful elements.

However, Microcystis aeruginosa is not a model organism, meaning it is not commonly studied in the lab and therefore lacks an existing body of scientific research on the specifics of its genome, which made it harder to find out how to get past that native immunity. They realized other scientists studying other non-model species would likely face similar barriers, presenting a laborious and time-consuming challenge for the field of synthetic biology.

“We knew we wanted our project to contribute to the community meaningfully, not just demonstrate engineering success in a lab,” said Jordan Nichols, a neuroscience and biomolecular engineering student and iGEM team co-captain. “We decided to tackle the problem of scale before we implemented an engineering solution, and to do that we developed this software that pretty generically makes engineering non-model species much easier.”

This led them to their solution: a software tool called Chameleon which helps identify how plasmids can be designed to best evade the bacterial immunity of their target. It does this by running a statistical analysis to determine which elements, called motifs, of the plasmid are most likely to be targeted by the immune system and then removes those motifs without changing the function of the plasmid.

Chameleon expands on Stealth, software developed by Bernick which is available for licensing. Stealth runs the statistical analysis of determining problematic motifs in a plasmid to more holistically avoid the target bacteria’s native immunity. In building Chameleon, the iGEM team focused on efficiency, simplicity, and accessibility throughout their software design.

With this software, they were able to better engineer their plasmid to disrupt toxin production without detection by the bacteria. They hope other scientists will be empowered to use Chameleon to come up with solutions to toxic blooms in their community. While the team spread the word about their tool at the iGEM Jamboree, they also hope to expand its reach into the wider synthetic biology community.

“We’re trying to catalyze the adoption of this by making it easier for more people to use, lower the bar of entry, and put it in the hands of other people,” said James Larbalestier, a molecular, cell, and developmental Biology student and iGEM team member.

In the meantime, the iGEM team is actively excited about carrying forward their project now that the Jamboree is over. They want to continue to test their idea for disrupting toxin production in the lab. They are hoping to publish a scientific paper on their work through an iGEM collection within the Frontiers family of journals. They also want to further develop their software, to make it easier to use and more effective.

Beyond this, the 2023 iGEM team collaborated with UC Berkeley to help the school set up a iGEM team to compete in the Jamboree in future years. Although Berkeley does have an iGEM team already, they do not currently send students to the competition.

The complete 2023 UCSC iGEM team includes: Gia Balius, Srikar Bevara, Danny Cruz, Blanca Davila Gil, Tyler Gaw, Ashlyn Huynh, Allison Jaballas, Varun Kodur, James Larbalestier, Daniel Li, Zokhira Mukhammadyunusova, Jordan Nichols, Nikita Rajesh, Julia Saltz, and Katie Warren.