Monthly Archives: April 2023

The noxious nucleocapsid

“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 SARS-Cov2 genome is made of RNA wound around nucleocapsids.

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 preparing samples for NMR analysis.

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 30th, at 7pm on 88.7 KBVR.

The opposite of a pest: Bees, wasps and other beneficial bugs

Lots of terrestrial invertebrates have bad reputations. Spiders, bees, flies, wasps, ants. They’re thought of as pests in the garden or they are perceived as threatening, possibly wanting to sting or bite us. I’ll admit it, I’m terrified and grossed out by most invertebrates every time I see one in my house. But this week’s guest may have successfully managed to get me to change my tune…

Scott (left) and his intern/doppelganger Tucker (right) in the field.

Scott Mitchell is a 4th year PhD student in the Department of Fisheries, Wildlife, and Conservation Sciences advised by Dr. Sandy DeBano. His overarching research goal is to understand how different land management practices may impact beneficial invertebrate communities in a variety of managed landscapes. Yes, you read that right: beneficial invertebrates. Because while many invertebrates have a bad rep, they’re actually unsung heroes of the world. They pollinate plants, aerate soil, eat actual pest invertebrates and are prey for many other species. In order to tackle his overarching research goal, Scott is conducting two studies in Oregon; one focuses on native bees while the second looks at non-pollinators such as wasps, spiders, and beetles.

(See captions for images at the end of the blog post)

The first study occurs in the Starkey Experimental Forest and Range which is managed by the US Forest Service. The initial research at Starkey in the 1900s was about how cattle grazing impacts on the land. Since then, many more studies have been undertaken and are ongoing, including about forest management, wildlife, plants, and recreation. For Scott’s study, he is collaborating with the Forest Service to look how bee community composition may differ in a number of experimental treatments that are already ongoing at Starkey. The two treatments that Scott is looking into are thinning (thinned vs unthinned forest) and ungulate density (high vs low). The current hypothesis is that in high ungulate densities, flower booms may be reduced due to high grazing and trampling by many ungulate (specifically elk) individuals, thus reducing the number of available blooms to bees. While in the thinning treatments, Scott is expecting to see more flower blooms available to bees in the thinned sites due to increased access to light and resources because of a reduced tree canopy cover. To accomplish this project, Scott collects bee samples in traps and handnets, as well as data on blooming plants.

(See captions for images at the end of the blog post)

Scott’s second study explores non-pollinator community composition in cherry orchards in the Dalles along the Columbia River Gorge. Agricultural landscapes, such as orchards, are heavily managed to produce and maximize a particular agricultural product. However, growers have options about how they choose to manage their land. So, Scott is working closely with a grower to see how different plants planted underneath orchards can benefit the grower and/or the ecology of the system as a whole. 

To hear more details about both of these projects, as well as Scott’s background and several minutes dedicated solely to raving about wasps, tune in this Sunday, April 23rd live on 88.7 FM or on the live stream. Missed the show? You can listen to the recorded episode on your preferred podcast platform! 

Figure captions

Image 1: This bright green native bee is foraging on flowers for nectar and pollen. It is probably in the genus Osmia.

Image 2: A brightly colored bumblebee foraging on a rose.

Image 3: This is one of the most common bumblebee species in western Oregon – the aptly named yellow-faced bumble bee (Bombus vosnesenskii).

Image 4: Most native bees, like this small mining bee are friendly creatures and will even crawl onto your hands or fingers if you let them. No bees (or human fingers) were harmed in the making of this photo.

Image 5: While Scott doesn’t know what his favorite wasp is, this large furry, friendly bee is his favorite native bee species. It is known as the Pacific digger bee or Anthophora pacifica. This is his favorite bee because they are very agile fliers and fun to watch foraging on flowers. They are a solitary species that lives in the ground.

Image 6: Not only are wasps beautiful, but sometimes the signs they leave behind can be too. This is a gall from a gall forming cynipid wasp. Wasp galls are a growth on plants that occurs when a wasp lays its eggs inside of a leaf or other plant structure.

Image 7: This is a pair of wasps in the family Sphecidae. The wasp on top is a male wasp (males are often smaller than females in wasps and bees) and he is likely guarding a potential mate by hanging onto her back.

Image 8: This is a beautiful bright metallic jewel wasp, probably in the family Chrysididae. This wasp was mentioned in the episode.

Image 9: This sphecid wasp is foraging on nectar on flowers. Many insects, including wasps, use nectar as an energy source in their adult life stage – even if they act as predators when foraging for their young.

Image 10: This is a tiny wasp on a flower. This wasp is around 1.5-3 millimeters long.

Nobody wants to eat bitter cheese

There are many adjectives used to describe the taste of different kinds of cheese: mild, tangy, buttery, nutty, sharp, smoky, I could continue but I won’t. Our preferences between these different characteristics will then drive what cheese we look for in stores and buy. But I would wager that most people (or dare I say anyone?) are rarely looking for a bitter cheese. I had never thought about how cheese could be bitter; probably because it’s something that I’ve never tasted before and that’s because the cheese production industry actively works to prevent cheese from being bitter. Intrigued? Good, because our guest this week researches why and how cheese can become bitter.

Paige in the lab

Paige Benson is a first year Master’s student advised by Dr. David Dallas in the Food Science Department. For her research, Paige is trying to understand how starter cultures affect the bitterness in aged gouda and cheddar cheeses. The cheese-making process begins with ripening milk, during which milk sugar is converted to lactic acid. To ensure that this process isn’t random, cheese makers use starter cultures of bacteria to control the ripening process. The bitterness problems don’t appear until the very end when a cheese is in its aging stage, which can take anywhere from 0-90 days. During this aging process, casein proteins (one of the main proteins in milk and therefore cheese) are being broken down into smaller peptides and it’s during this step that bitterness can arise. Even though this bitter cheese problem has been widely reported for decades (probably centuries), there are many different hypotheses about what causes the bitterness. Some say it might be the concentration of peptides, while others believe it’s a result of the starter culture used, and a third school of thought is that it’s the specific types of peptides. Paige is trying to bring some clarity to this problem by focusing on the bitterness that might be coming from the peptides.

To accomplish this work, Paige will be making lots of mini cheeses from different starter cultures, then aging them and extracting the peptides from the cheese to investigate the peptide profiles through genome sequencing. Scaling down the size of the cheeses will allow Paige to investigate starter cultures in isolation as well as in combination with different strains to see how this may affect peptide profiles, and therefore potentially bitterness.

Some of the mini cheeses Paige makes for her research

Besides Paige’s research in cheese, we will also be discussing her background which also features lots of dairy! As a Minnesotan, Paige grew up surrounded by the best of the best dairy. In fact, her grandparents owned and ran a dairy farm, where Paige spent many of her summers and holidays. Her passion for food science was solidified when she started working as an organic farmer during her senior year of high school and she hasn’t ever looked back. Join us on Sunday, April 16th at 7 pm live on 88.7 FM or on the live stream. Missed the live show? You can listen to the recorded episode on your preferred podcast platform!