Research Spotlight | Dipti Nayak
Gaining Insights into the Past, Present, and Future of Life on Earth
By Kirsten Mickelwait
It’s fair to say that Dipti Nayak’s research is far-reaching in scope. On the one hand, it seeks solutions to our most existential problems, like climate change. On the other, it provides a glimpse into the origins of life itself.
For decades, biologists have referred to a three-branched “tree of life,” founded on molecular phylogenetics and microbial evolution, which traces all life on Earth to one common ancestor. One branch is Eukarya, which includes humans, animals, insects, fishes, birds, plants, and fungi. Another branch is Bacteria, which are well-known microorganisms that both keep us healthy and cause disease. The third branch is Archaea, a distinct group of microbes that are among the most abundant—yet least understood—life forms.
Nayak—an assistant professor of genetics, genomics, evolution, and development—and her lab use genome-editing approaches to study Archaea and their impact on humans and the environment. They use a subset of organisms called methanogens, so named because they generate methane as a by-product of growth.
Released into the atmosphere, methane is far more damaging than carbon dioxide as a greenhouse gas. Methanogens also affect calorie intake, obesity, and cardiovascular health within the human gastrointestinal tract. By growing in environments without oxygen— reminiscent of conditions on early Earth—methanogens can provide insights into the provenance of life.
“Altogether, our goal is to develop methanogens as a model system to gain insights into the biology of Archaea and also to unravel their impact on the past, present, and future of life on Earth,” Nayak says. “We’re a fundamental biology lab, and the motivation for our work is understanding life better. But sometimes we understand something well enough that we can propose a solution for a societal problem. And one particular area where I think our work could have a translational impact is in the arena of climate change.”
In December Nayak, along with postdoc Gray Chadwick and graduate student Gavin Dury, submitted a preprint for review that explores methyl-coenzyme M reductase (MCR), an enzyme that catalyzes the final step of methanogenesis, or methane synthesis. Past studies have provided insights into MCR function in vitro, yet very little is known about how MCR interfaces with the physiology of methanogens in vivo.
“How much of this enzyme does the cell need? And what happens when the cells are deprived of MCR; are they coming up with other ways to survive?” Nayak asks. Using CRISPR genome-editing tools, her lab can manipulate the biology of these organisms. “People have always assumed that these organisms need a lot of MCR to sustain optimal growth but, it turns out, that’s far from the truth. We’re finding some interesting insights that contradict that.”
Nayak’s academic trajectory was hardly traditional. She pursued her bachelor’s and master’s degrees in engineering, hoping to solve important environmental problems. She found, however, that many of the potential solutions she was working on were derived from biological systems. “One of the biggest limitations in engineering is that we don't understand natural systems well enough,” she says. “My decision to study biology was to gain insights that would ultimately solve engineering problems.” She switched fields, earning a master’s and then a PhD in biology. She’s been an assistant professor at MCB since 2019.
Climate solutions and the origins of life aren’t the only areas that interest the Nayak Lab. Her group also runs and participates in five outreach programs to increase community engagement with science and promote equity in pursuing scientific careers.
One such program is Backyard Microbes, developed by postdoc Fernando Medina Ferrer, which gives local high school students hands-on experience in microbiology. The lab group also participates in Pub Science, a monthly speaker series offered at a local pub. In addition, the graduate students are heavily involved in peer mentorship programs, which match prospective graduate students with mentors who guide them through the graduate school application process.
How does Nayak juggle ambitious scientific inquiry with the time commitment of community service? “I’ve just been very fortunate to have recruited such great people in my lab who are not only amazing scientists but also care deeply about science education,” she says.
“At the end of the day, our science is funded by taxpayer dollars. And we owe it to the taxpayers to show what that money is used for, and that it will come back and help society more broadly. It just makes sense.”
Learn more about the Nayak Lab’s research at www.dnayaklab.com.
Banner image: Planktonic cells of the methanogenic archaeon, Methanosarcina acetivorans (Sunnyjoy Dupuis, Nayak Lab)
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