Research Now - Spring 2025
Microbes in Mouth Reflect Lifestyle Choices
Lifestyle can shape the composition of the beneficial bacteria and other microorganisms within the mouth, according to a new study led by Penn State biologists.
The researchers studied the oral microbiomes of people from groups with a variety of subsistence strategies. These included foragers, subsistence farmers that recently settled, agriculturalists that have relied on farming for several centuries, and industrialists. They also asked questions about diet, education, medical practices, and other behaviors.
“In this study, we comprehensively investigated the oral microbiome of individuals across a range of lifestyles from the same country, Nepal,” said Erica Ryu, graduate student in biology.
The researchers found that the composition of species within the oral microbiome was related to subsistence strategy. Additionally, the presence of several species of microbes were related to specific lifestyle factors, including smoking, the prominent type of grains in an individual’s diet, and consumption of a plant called nettle.
“Whenever you make a shift—whether it’s to a different diet or different location or different culture—the microbiome can change too, and it’s important to understand to what extent and how quickly these changes occur,” said Emily Davenport, assistant professor of biology. “Continuing to investigate how oral microbiomes vary across the globe will help improve our understanding of what exactly shapes the microbiome and how that impacts human health.”
Read more about patterns in oral microbiota.
What Happens When Neutron Stars Collide?
When stars collapse, they can leave behind incredibly dense but relatively small remnants called neutron stars. If two stars collapse in close proximity, the leftover binary neutron stars spiral in and eventually collide. To better understand what happens in those first moments after a collision, Penn State astrophysicists created simulations, requiring massive amounts of computing power, that model the merger of binary neutron stars and all of the associated physics.
The simulations showed for the first time that hot neutrinos—tiny, essentially massless particles that rarely interact with other matter—that are created during the collision can be briefly trapped at the interface of the merging stars and remain out of equilibrium with the stars’ cold cores for two to three milliseconds. During this time, the simulations show that the neutrinos can weakly interact with the matter of the stars, helping to drive the particles back toward equilibrium.
“These extreme events stretch the bounds of our understanding of physics and studying them allows us to learn new things,” said David Radice, assistant professor of physics and of astronomy and astrophysics.
The researchers explained that the precise physical interactions that occur during these mergers can impact the types of signals they emit that could be observed on Earth.
“These simulations play a crucial role allowing us to get insight into these extreme events while informing future experiments and observations.” said Pedro Luis Espino, postdoctoral researcher at Penn State and the University of California, Berkeley.
Read more about neutron star collisions.
Genomic Pioneers Collaborate to Access the Inaccessible
A new experimental method allows researchers to dissect how certain proteins, called pioneer factors, can bind to selective regions of the genome that are inaccessible to other DNA-binding proteins.
“All of the cells of an organism contain the same genome, but not all cells are the same,” said Lu Bai, professor of biochemistry and molecular biology and of physics. “Different cell types are different because of the set of genes that they express. Gene expression is regulated by transcription factors that bind to the DNA at specific short sequence motifs that are found across the genome. But only a very small portion of these sequence motifs are actually used at any one time in a cell, and we are interested in how this specificity is determined.”
The new method, named ChIP-ISO or Chromatin Immunoprecipitation with Integrated Synthetic Oligonucleotides, allows the testing of thousands of sequence variants of binding motifs in a single experiment. With this technique, the researchers can begin to identify features of the motifs that allow specialized transcriptions factors called pioneer factors to access typically inaccessible genomic regions and open them up for additional access. The technique also allows the researchers to parse out how the pioneer factors work together with other cofactor proteins, which could inform which motifs are bound in which specific cells.
“The combination of ChIP-ISO’s ability to test thousands of customized DNA sequences with machine learning-based analyses is a very powerful way to gain insight into gene regulatory systems,” said Shaun Mahony, associate professor of biochemistry and molecular biology.
Read more about pioneer factors.
Microplastics Impact Cloud Formation, Likely Affecting Weather and Climate
Microplastics, tiny pieces of plastic smaller than five millimeters, that are found in the atmosphere could be affecting weather and climate, according to new research led by Penn State scientists. They found that microplastics act as ice nucleating particles, microscopic aerosols that facilitate the formation of ice crystals in clouds. This means that microplastics could impact precipitation patterns, weather forecasting, climate modeling, and even aviation safety by influencing how atmospheric ice crystals form clouds.
The research team, led by Miriam Freedman, professor of chemistry, studied the freezing activity of four different types of microplastics in the lab, suspending the plastics in small droplets of water and slowly cooling them to observe how the microplastics affected ice formation. They found that microplastics can trigger water droplets to freeze at warmer temperatures—5 to 10 degrees warmer than droplets without microplastics.
What this discovery means for weather and climate is not entirely clear, the researchers said, but it suggests that microplastics are likely already making an impact.
“We can think about this on many different levels, not just in terms of more powerful storms but also through changes in light scattering, which could have a much larger impact on our climate,” said Heidi Busse, a graduate student at Penn State. “We know the full life cycle of these plastic items we use every day could be changing the physical and optical properties of the Earth’s clouds and, therefore, changing the climate in some way, but we still have a lot to learn about exactly what they are doing.”
Read more about microplastics.
Potential New Target for Early Treatment of Alzheimer's Disease
A class of proteins that regulates cell repair and enhances cell growth-signaling systems could be a promising new target for the treatment of Alzheimer's and other neurodegenerative diseases, according to a new study led by researchers at Penn State.
“Strategies to treat Alzheimer's disease to date have largely focused on pathological changes prominent in the late stages of the disease,” said Scott Selleck, professor of biochemistry and molecular biology. “We are interested in understanding the earliest cellular changes that are found not only in Alzheimer's but shared across other neurodegenerative diseases, including Parkinson's and amyotrophic lateral sclerosis (ALS).”
Roughly 6.9 million Americans over the age of 65 are estimated to be living with Alzheimer’s disease, according to the Alzheimer’s Association. Despite its widespread impact, there is no agreed-upon biological cause or mechanism for the disease. Cell-signaling molecules called heparan sulfate–modified proteins have been implicated in the development of Alzheimer’s, but their specific role has remained unclear, Selleck said.
The researchers showed that these proteins regulate cellular processes known to be affected in several neurodegenerative diseases, including a cell-repair process called autophagy. Additionally, they demonstrated that disrupting these proteins rescues neuron loss and reverses cellular changes associated with neurodegenerative diseases.
“These findings suggest a promising target for future treatments that could rescue the earliest abnormalities that occur in many neurodegenerative diseases,” Selleck said.
Read more about potential treatment target.
New Planet in Kepler-51 System Discovered Using James Webb Space Telescope
Kepler-51, an unusual planetary system with three known ultralow-density “super-puff” planets, has at least one more planet, according to new research led by researchers from Penn State and Osaka University.
Super-puff planets have very low mass and low density, almost like cotton candy. To help explain how these rare and unusual planets form, the research team set out to study Kepler-51d, the third planet in the system, with NASA’s James Webb Space Telescope. But they almost missed their chance when the planet unexpectedly passed in front of its star two hours earlier than models predicted.
The team’s models predicted that Kepler-51d would pass in front of its star—or transit— around 2:00 a.m. (EDT) in June 2023, but the transit began two hours earlier than expected. Although the gravitational tug of planets may cause planets to transit early or late, these transit timing variations are usually on the scale of minutes and can be accounted for by astronomer’s models. A two-hour difference was puzzling, the researchers said.
After scrutinizing new and archival data from a variety of space- and Earth-based telescopes and running many new models, the researchers found that the best explanation is the presence of a fourth planet.
“If trying to explain how three super puffs formed in one system wasn’t challenging enough, now we have to explain a fourth planet,” said Jessica Libby-Roberts, Center for Exoplanets and Habitable Worlds Postdoctoral Fellow. “Continuing to look at transit timing variations might help us discover additional planets and might aid in our search for planets that could potentially support life.”
Read more about Kepler-51e.