New Method of Mapping Proteins Offers Undergraduate Students New Opportunities

By Lorena Anderson

November 7, 2024

Zebra fish make good test subjects for mapping proteins.

Research on cell development has led not only to a more efficient way to map proteins in living cells but also tapped into the research capabilities of UC Merced undergraduate students and brought about a new learning opportunity that could shape their futures.

Researchers know a protein's function is intimately tied to its location in a cell. By mapping its location, they can better understand how its function - and the cell's biology - changes over time.

Department of Molecular and Cell Biology professors Stephanie Woo and Stefan Materna, both Health Sciences Research Institute members, have established a more efficient and reliable way of labeling proteins to see their location in cells and how that location changes under different conditions.

And they can do it in a living, vertebrate organism.

"We can track protein location as the animal develops and ages, and we can compare protein location in cells of different organs," Woo said. "This is important because we can watch cells during different phases of life such as embryonic development or the progression of a disease."

A paper about their study is available in the journal Developmental Biology. Notably, half of the paper's authors are UC Merced undergraduate students - including co-lead author German Paniagua.

This level of undergraduate involvement is unusual. While many UC Merced undergraduates participate in research, not many are asked to contribute to writing scientific papers. Being asked to do so indicates how deeply involved they were with this project.

The students on the research team learned about fluorescent proteins, which are standard components of the modern biologist's toolkit, Woo said. The glowing proteins can be added to molecules that label the whole cell or specific parts of a cell.

Despite their widespread use, there are challenges to working with fluorescent proteins, she said. For example, it can be difficult to achieve the right expression level - not too much, not too little. It's also hard to label a specific cell or tissue type.

To address these problems, the Woo and Materna labs' method uses a split fluorescent protein technique in which the fluorescent protein mNeonGreen is split into two pieces.

"On its own, each piece is not fluorescent; fluorescence is only produced if both pieces are present at the same time in the same cell," Gloria Ligunas, a Ph.D. student in the Quantitative and Systems Biology program, said. "We tested this approach in zebrafish, using CRISPR/Cas gene editing technology. We added the smaller piece to specific target proteins, such as keratin, while the larger piece was expressed in specific tissues, such as the heart or the brain. This approach lets us study how a particular protein is localized in a specific tissue, which provides clues for function."

The faculty members used their experiences on this project to develop a new undergraduate lab course called BIO 118: Gene Editing Research Lab. In it, students learn to use CRISPR/Cas-based gene editing, a cutting-edge method to make precise changes to a cell's DNA, which the researchers used to add the split fluorescent protein tag to the proteins under study.

"As a Course-based Undergraduate Research Experience, the class provides students with an authentic research experience. CUREs have been shown to improve student outcomes and retention, especially for first-generation and historically underrepresented students," Woo said.

The BIO 118 students also receive hands-on training in genetics and molecular biology techniques that can be applied to future careers in research and biotechnology.

"BIO 118 is currently offered every fall semester," she said. "It is open to all UC Merced undergraduate students who fulfill the pre-requisites, and it satisfies lab requirements for the biological sciences major."