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Pandemic Closing Opened New Horizon for Undergraduate Researcher

Professor Rachel Martin and Undergraduate TJ Cross
Professor Rachel Martin (left) and TJ Cross (Right)

When the pandemic derailed undergraduate T.J. Cross’s research plans, a Zoom meeting quickly set him on a different track. His flexibility and persistence reaped new skills and the satisfaction of helping in the fight against COVID-19.

As the spring 2020 quarter neared, Cross was set to work with Professor Rachel Martin, who holds joint appointments in the Department of Molecular Biology and Biochemistry and the Department of Chemistry. He would have worked on a project involving beta-gamma crystallins; proteins thought to be responsible for cataract formation. But his plans were sidelined when the laboratory suddenly closed as part of UCI’s campus-wide COVID-19 safety shut down.

Then during a lab Zoom meeting, Professor Martin said she wanted to study emerging mutations in SARS-CoV-2. The focus would be on the main protease (MPro), a protein that enables the virus to replicate inside host cells and is a potential antiviral drug target. Learning more about the protein could help in developing treatments for those suffering from COVID-19.

Cross swung into action, locating and gaining lab access to GISAID, a German influenza database. The database had begun serving as a repository for SARS-CoV-2 genome sequences, including the virus’s emerging variants. He knew the lab’s researchers required the GISAID data to conduct their investigation. By the time Professor Martin brought up the matter in a Slack message two days later, he had already begun manually culling the information for the team to use.

Early on, he forged a close working relationship with MBB graduate student and Martin Lab member Gemma Takahashi. She needed the data to build a phylogenetic “tree” that would reveal the order and pattern of the mutations.

“I was blown away by how eager T.J. was to do things,” Takahashi said. “If you give him something to do, he will do it and take it ten extra steps.”

The volume of information in GISAID quickly swelled as scientists worldwide submitted more genetic sequences. Cross decided to learn to code so he could write

software to speed up his data extraction. Through UCI’s partnership with Coursera, he started taking classes on the Python programming language on top of his already jammed schedule. The ten hours weekly he devoted to the endeavor paid off, enabling him to reduce the sequencing data extraction process from hours to minutes.

His hard work was published in the journal Biochemistry in September, where Cross served as first author, a recognition that Professor Martin says was well-earned.

“I have never seen an undergraduate student jump into research and teach himself what he needed to know,” she said. “Initiative and persistence are crucial in research because it is hard and you need to have the will and determination to keep going.”

Cross, a chemistry major, will head to graduate school after receiving his undergraduate degree; he has been accepted at Caltech and UCLA. Reflecting on his experience in the Martin Lab, he said that “it was difficult starting this project knowing absolutely nothing. I can’t tell you the number of things that failed along the way, but it was worth the struggle. We wanted to get that paper out there and we did. It feels really good to have been part of something that could help people with COVID-19.”

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