“Structure informs function” says Hannah Stuwe, a second year PhD student in Biochemistry and Biophysics (BB), summing up the big picture of her discipline. Hannah works in the lab of Prof. Elisar Barbar, using biophysical techniques to study essential proteins encoded by the SARS-Cov2 virus.

Much attention has been paid to the spike protein of the SARS-Cov2 virion, which is the target of the vaccines developed during the COVID-19 pandemic. Hannah’s research digs into another crucial protein called the nucleocapsid, which plays a role in organizing and packaging the viral genome. Proteins are the primary molecular actors in most biological process, so a detailed structural understanding of the proteins involved could shed light into how the virus disrupts the infected cell. It could also help to develop therapies for people who contract COVID.

The primary analytical technique that Hannah uses is nuclear magnetic resonance (NMR), which probes the atomic nuclei within the protein using magnetic fields. Proteins mainly consist of hydrogen and nitrogen, so these two elements are analyzed separately with different NMR protocols. The resonance information from the individual hydrogen and nitrogen atoms can be combined into a two-dimensional landscape. This gives a rich picture of the protein structure, including how the conformation changes over time and how it interacts with RNAs and other proteins.

Hannah focuses on a short stretch of the nucleocapsid which is intrinsically disordered, meaning that it does not fold to a stable configuration. Instead, the structure of this region varies according to chemical modification by other proteins. When phosphoryl chemical groups are added, the region adopts an open configuration that exposes the viral genome, allowing it to be transcribed by the hijacked cell’s machinery. Without phosphorylation, the structure becomes more compact, possibly making it easier to spread the virion to other cells.

Hannah went to Oregon State for her undergraduate degree in BB and knew her advisor at the time. After graduating in 2019, she worked for a while at an industrial hemp company, working with natural cannabinoid products. Soon after, she felt the call to return to graduate school and accepted a laboratory job and eventually a PhD position with Prof. Barbar. For the rest of her degree, Hannah will analyze the mutations that are continually reshaping the SARS-Cov2 genome.

This is also a special episode because Hannah is in the process of joining the ID team as a host! To hear more about her research before she becomes a regular on the other side of the mic, tune in tonight, April 30^th, at 7pm on 88.7 KBVR.

We are pleased to introduce our upcoming guest, Christopher Cousins, a fourth-year PhD student in the Department of Fisheries and Wildlife, advised by Prof. Tiffany Garcia. Cousins is  researching torrent salamanders, a family of small amphibians endemic to the Pacific Northwest.

The habitat for torrent salamanders stretches from the far north of California up through the Washington coast and includes distinct populations in the Cascade Range and the Oregon Coast Range. Torrent salamanders inhabit cold streams at relatively high altitude — the kind where few or no fish live, leaving the amphibians near or at the top of the local food chain. Such streams can be ephemeral, disappearing at times throughout the year and leaving salamanders vulnerable to desiccation. This problem is only expected to worsen as climate change further upends these water systems. Torrent salamanders are currently candidates for classification under the Endangered Species Act (ESA), the federal law which grants protections to threatened species. Logging presents another danger to salamander habitats, as reduced tree canopy cover can contribute to higher water temperatures. Under the ESA, officials could prohibit logging in buffer zones around small streams, granting salamander habitats the same protection as the larger streams where salmon live.

Chris’s work with salamanders takes many different forms. He has extensive experience in fieldwork, spending six months traveling throughout Oregon and Washington. He has used environmental DNA from water samples to detect torrent salamander populations in various streams. In another project, he collected DNA directly from approximately 150 salamanders. Chris performed both the lab work to process these samples and the bioinformatics analysis to assemble their DNA sequences. This summer, he plans to conduct a detailed survey of the streams of the streams in the H.J. Andrews Experimental Forest. The overarching goal of his PhD is to document the genetic diversity among torrent salamanders and characterize their population structure across the region, which he hopes will help inform the ESA decision-making process.

Chris remembers catching frogs and salamanders as a child – proof of his fascination with amphibians at a young age. His father was in the Navy, so the family moved around repeatedly, but Chris grew up mostly in Japan. Upon moving back to the US, he felt drawn to Oregon and enrolled at Lane community college before transferring to Oregon State to earn his bachelor’s degree as a first-generation college graduate. He remained at OSU for his graduate work due to the community of scientific mentors he had built. To hear more about his journey, what it is like to explore the Mt. St. Helens eruption zone, and what motivates him to work with this threatened species, tune in to KBVR 88.7 FM this this Sunday, Feb 19^th, at 7pm.

This week on Inspiration Dissemination, we are looking forward to chatting with Andrew Carpenter, a postdoctoral fellow working in the lab of Professor Joe Baio in the School of Chemical, Biological, and Environmental Engineering.

Andrew’s research seeks a better understanding of a protein called dysferlin, which plays a critical role in repairing muscle cells.  Muscles undergo constant strain as they expand and contract, leading to tears in the sarcolemmas — thin membranes that surround muscle fibers. Dysferlin is responsible for recruiting vesicles to the site of these tears for a process called vesicle fusion to take place. Andrew likens this mechanism to using a denim patch to fix a hole in jeans, if the patch could become fully absorbed into the fabric in the way that vesicles eventually do into sarcolemmas. Dysferlin is clinically important because certain mutations (dysferlinopathies) to the gene encoding dysferlin lead to a disease called muscular dystrophy. The symptoms of dysferlinopathy typically include muscle weakness and damage to the musculoskeletal system, especially in the limbs.

The general importance of dysferlin to cell repair is well-established, but the molecular details of its mechanism of action are relatively unknown.  Andrew uses an advanced experimental method called sum-frequency spectroscopy to study the protein at high resolution. This procedure uses two lasers — one infrared and one visible green — and points them at the sample of interest. When the lasers hit the sample, a third beam of light is generated at the surface, carrying information about the vibrations of the molecules. Quantum mechanical calculations are used to examine the intensity of this light as a function of frequency. In Andrew’s research, a synthetic lipid monolayer serves as an in-vitro model of the sarcolemma, and he introduces the dysferlin protein either in its healthy form or with various mutations. Then he uses spectroscopy data to infer changes in protein orientation and binding. In the future, he intends to correlate his experiments with data from live cells.

Andrew first discovered his fascination with laser instrumentation as an undergraduate at Linfield University. After that, he obtained a PhD in Chemistry at the University of Oregon, where he used small oil droplets called nano-emulsions to study the oil-water interface. His background in physical chemistry and expertise in the sum-frequency spectroscopy method have enabled him to readily adapt to studying biological lipid interfaces. His research, including a recent publication, is currently supported by the National Science Foundation.

To hear more about Andrew’s research journey and the differences and similarities in being a postdoc and a graduate student, tune in after the Super Bowl this Sunday, February 12^th, at 7pm on 88.7 FM KBVR.

Heat, Hatchlings, and Sea Turtle Survival

A team of researchers makes its way across the beach on this dark night, lighting their way only with starlight and moonlight. It’s high tide on this small island off the coast of Brazil, and the kind of night when green sea turtles love to come ashore to nest. The turtles fall into a trance-like state after wandering around for hours and finally building their nests, and this is when the team approaches. They take a skin sample, place a temperature logger to measure the nest temperature, and tag the turtle with a nail polish marking for future identification. One member of the team is Vic Quennessen (she/they), the subject of our next episode. Vic is a PhD student in the Department of Fisheries, Wildlife, and Conservation Sciences. Quennessen is a computational researcher on the project but helping out on nights like these is part of the job. Vic’s team collaborates with Projeto TAMAR, a Brazilian nonprofit organization that works to preserve and conserve these endangered animals throughout Brazil since the 1980s.

Sea turtles have no sex chromosomes, and their sex is instead determined by the environmental temperature during incubation. Eggs subjected to higher temperatures are more likely to produce female hatchlings. The point at which the sex ratio of eggs approaches 50/50 is around 29 degrees Celsius, but at just one degree higher, some clutches of eggs produce as high as 90% female hatchlings. As temperatures rise due to climate change, this has resulted in a worrying oversupply of female hatchlings.

Sea turtles are difficult to study due to their long and mysterious life cycles. It is believed that they reach reproductive maturity after around twenty-five years, but only females are readily observed because they return to land to build their nests and lay eggs. In contrast, the males stay out at sea for their entire lives. This complicates any effort to ascertain the true population structure. Sea turtles also live a long time, so there is a lag between changes in the hatchling population and the overall population. Finally, hatchlings lack external reproductive organs or other visible sexual characteristics, so the sex ratios must be estimated using temperature as a surrogate.

Vic has always loved the ocean, and they came to OSU looking to help conserve resources that are threatened, such as fish stocks or sea turtles. While attending UMass Dartmouth for their undergraduate degree, they double majored in computational mathematics and marine biology. Initially these felt like separate interests, until a professor suggested that she apply to a NOAA workshop on marine resources and population dynamics. Here she learned that mathematical methods could be a part of rigorous modeling efforts in population biology. After a gap year dedicated to science education, Vic made her way to Oregon State for a Masters in Fisheries Science. Her advisor, Prof. Will White, persuaded her to stay on for a PhD with an opportunity to study her beloved sea turtles.

Quennessen’s research seeks to predict how the green sea turtle population will be affected by their looming sex imbalance. Vic uses data collected from over 3000 hatchlings per season, including nest temperature readings as well as the numbers of nesting females, hatchlings, and captured males. They build a mathematical model to explore possible scenarios for the “mating function”, the unknown relationship between the sex ratio and reproductive success. On the one hand it is easy to imagine that such a mismatch could reduce the number of mating pairs and lead to a rapid population decline. On the other, it is not well understood how many breeding males are required to sustain the population, and adaptations in mating behavior could slow the decline in population long enough for the more optimistic climate mitigation scenarios to take effect. In any case, it will take a lot of international cooperation to conserve these ancient marine creatures – green sea turtles nest on the shores of over 80 countries. Vic’s hope is that a mathematical exploration of this question could help reveal the chances of survival for the green sea turtles and possibly inform these conservation efforts.

To learn more about Vic’s research and their other interests, including science education and working with CGE, the graduate student union at OSU, tune in Sunday, Nov 6th at 7pm PST on KBVR 88.7 FM or online!

Missed the show? Don’t worry, you can download this episode via your podcast player of choice here.