Scientist At Work: Jim Pesavento on Unlocking Algae’s Sustainability Potential—and the Students Helping Him Do It

“At Work” is a series that highlights Saint Mary’s faculty and staff at work in the world. Artists, writers, scholars, scientists—we sit down and dive deep into their latest projects.

Here’s one way that Jim Pesavento, Biology professor and department chair, embodies his profession: When you meet, he might not be able to shake your hand. On a crisp morning in January, Pesavento arrives in Brousseau Hall’s sunny atrium and introduces himself, apologetically waggling his gloved fingers. “You wanted ‘scientist at work,” he says. “Figured I’d give that to you.”

Back in his lab, he shows me the work in question: algae colonies, growing on Petri plates arrayed across the counter. He points to a few samples on the left, explaining that his graduate students had “disrupted” the alga’s genes using CRISPR, the groundbreaking gene-editing technology. It’s the kind of experiential learning that first made Pesavento “fall in love with the lab” himself,  he says. 

As a high school student, he was originally drawn to computer engineering himself. He lacked the test scores to get into most programs. But at the University of Illinois, he learned he could apply for another major and switch to engineering. So he put down “biochemistry” (largely inspired, he admits, by Nicholas Cage’s “studly biochemist” character in the 1996 film The Rock.) Once he got a taste of labwork in molecular biology and biochemistry though, he never looked back.

Pesavento went on to earn his PhD in Biophysics and Computational Biology from the University of Illinois and was a postdoctoral scholar at the University of California, Berkeley, before joining Saint Mary’s in 2012. As a researcher, his expertise is in protein biochemistry, specifically focused on the makeup—and modification—of the microalgae Chlamydomonas reinhardtii. He understands that may sound, well, molecular in scale. But, as he explains, microscopic things can have global ramifications. 

What first drew you to Saint Mary’s?

I was a bench scientist without much teaching experience, coming off a four-year postdoc at UC Berkeley. Fortunately, Vidya Chandrasekaran hired me to teach two Biology 201 laboratory courses. Soon, I was teaching molecular biology, loving what I was doing—and getting better each year.

Part of it was the students’ passion. I had never experienced that sixteen-to-one classroom ratio, but it really gives the students space to thrive. I also got to really see what research does for them. To say it's transformative is not doing it justice. They get bit by the lab bug, I like to say.

Speaking of lab work, you recently co-authored an article on research you conducted with an SMC student. Can you explain that project a bit?

What’s exciting to undergraduates now, above most things, is sustainability. As scientists, they look at the data, see that human activity is changing the planet, and want to do something about it. So when I started thinking about sustainability projects that align with my area of expertise, I immediately thought of algae. 

One attractive thing about algae is that they’re a potential source of sustainable biofuels. Some strains of algae—like the one I study, Chlamydomonas—store energy in lipids, or naturally occurring oils. With fossil fuels, you extract them from the earth, burn them up, and pump carbon into the atmosphere. But with algae, those natural oils were made by photosynthesis, so it’s completely circular. In theory, then, if you can find the genes that produce lipids, you can tweak them to produce more, essentially creating massive amounts of renewable biofuel.

Before we get there, though, we have to figure out how to optimize their genes. In algae, DNA isn't just flopping around naked. It’s actually tightly bound in these little compartments, and they’re hard to access. In my research, I look at histones—the proteins that bind DNA and are partly responsible for controlling how accessible it is. So I thought, If we can understand how these histones work, could we open up the DNA influencing lipid production? Surprisingly, little is known about the histones in Chlamydomonas or how they control gene expression.

“It’s an exciting time at Saint Mary’s,” Jim Pesavento says. With great opportunities in the School of Science, “Our faculty is committed to giving students hands-on experiences with modern, cutting-edge instruments and authentic research.”

Where does mass spectrometry fit into all of this? 

Mass spectrometry is a technique that measures the mass of things, helping you assemble a proteoform: a rendering of a protein with its modifications, sequence, and everything. From there, you can often understand what it does. Of course, I'm never looking at one protein; I'm looking at hundreds of thousands. As a result, mass spectrometry gives me extremely complex data sets. 

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What I'm looking for is often very specific, needle-in-a-haystack stuff, and that analysis is time-intensive. I realized, OK, I have all these algae questions, and I need the right software to answer them. So I reached out to Udayan Das, chair of the Computer Science department. I said, “Hey, I have a software project. Do you have a student you’d want to co-mentor who might be interested in further developing this?” He connected me with Megan Bindra ’23, a CS student who is now a successful software engineer. She was immediately interested in the project, and we started working in the summer of 2022. 

What Megan improved upon was pretty incredible. All the work I had to do before—putting all the data in Excel, graphing it—this program does in one fell swoop. In fact, with Megan’s additions to the program, analysis time shrank from months to minutes. 

There’s a reason, when Megan presented her poster at a mass spectrometry conference in 2023, she always had a semi-circle of scientists gathered around her, asking her questions. They knew how big a deal this tool was!

And through this tool, you made a new discovery?

Using the data analysis from Megan’s software, I was able to pinpoint something new during mitosis, the cell division cycle, of Chlamydomonas. Looking at how the cell changed over time, an unanticipated histone protein form jumped out at me. We went back to manually verify it and saw that, yes, a specific histone form was missing a mark that was always assumed to be present. 

Why does that matter? Because it has never been observed before. It could be nothing—or it could be the key to harnessing lipid production. But it’s something we need to understand if we’re going to harness these genes to create fuel. And Megan’s tool is already opening the door to greater understanding.

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Your work really exemplifies how cross-disciplinary—and cutting-edge—research at Saint Mary’s is.

It’s an exciting time at Saint Mary’s; I see myself as part of a new guard. About 10 years ago, there was a huge wave of new, younger faculty members in the School of Science—including myself—who came to campus intent on being more active researchers and grant writers. Not to pat myself on the back too much, but in 2019 I won a National Science Foundation award for half a million dollars. What does that do? It allows me to consistently mentor four or five undergraduates and take them to conferences each year. I get to spend money on apparati and experiments my classes might not access otherwise. 

That helps my research develop—but ultimately, the money goes toward the students. And that's just one instance. Professor Chandrasekaran—who also heads Saint Mary’s Professional Science Master’s in Biotechnology Program—recently led an effort to secure a $350,000 confocal microscope. Having one of those at a college our size is unheard of! But she got enough talented faculty members to co-write a grant proposal to fund this instrument from the National Science Foundation. Eventually, the NSF said, “Let’s do it.” Now that microscope is used in classes, research, and publications. 

That’s the culture in the School of Science now. Our faculty is committed to giving students hands-on experiences with modern, cutting-edge instruments and authentic research.  

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There are so many ways for Gaels to get those experiences in the lab and elsewhere. You’re currently teaching a Jan Term class called “Hands-on STEM Exploration for the Science Inspired.”

The Jan Term class is actually the outcome of another NSF grant proposal, successfully driven by Marianne Rosario, in Physics. The goal of the class is to support first-year students, offering them a cross-disciplinary scientific experience that is 99% hands-on.

This year, my students are researching local newt populations. Week one, they were out in the field as ecologists, finding newts in a nearby pond and taking samples. The next week, they were molecular biologists and biochemists, looking at their samples under a microscope, cracking open the cells, and extracting the DNA. And then they’re computer scientists, comparing databases and developing a simple script to analyze their data. 

My hope is that all this sparks something for these first-year students. Maybe they love tromping around in a pond, or looking at differences in DNA sequences, or writing code using the programming language Python. I firmly believe that if you establish the passion first, the hard work will follow. Science majors know they have to work hard. Hopefully, I’m showing them why: Soon, they’ll get to do all these fun things.

(This interview has been edited and condensed for clarity.)

Hayden Royster is Staff Writer at the Office of Marketing and Communications for Saint Mary's College. Write him.