Author Archives: Lisa Hildebrand

Poopy predators: Assessing carnivore diet and population dynamics via non-invasive genetics

Getting to the bottom of what top predators in an ecosystem are eating is critical to understand how they may be influencing dynamics in the entire system and food web. But how do you figure out what a predator is eating if it’s hard to catch and collar or watch continuously? Easy, you use their poop! Ellen Dymit, a 4^th year graduate student in the Department of Fisheries, Wildlife, and Conservation Sciences advised by Dr. Taal Levi, is our guest on the show this week and she is a poop-tracker extraordinaire!

For her PhD research, Ellen uses primarily non-invasive genetic methods to study large carnivores in two projects in Alaska and Central America. While the systems and carnivores she studies for these two projects are pretty different, the techniques she uses to analyze the collected scats are the same. The Alaska project is focused on determining what different wolf populations and packs across coastal Alaska are consuming, whether individuals are specialized in their feeding habits, and how large the populations are. The Central America project, which is based out of Guatemala, looks at a whole host of predators, including jaguars, pumas, and ocelots, to gain a better understand of the food web dynamics in the ecosystem.

One of Ellen’s extremely remote field camps in Alaska

Both of these projects involve some unique challenges in the field that Ellen has had to learn to tackle. DNA can deteriorate pretty quickly, especially in warm Guatemalan temperatures, which is problematic when you’re trying to analyze it. Yet, Ellen’s lab has perfected methods over the last few years to work with neotropical samples. Ellen’s Alaska field work is incredibly remote as it’s just Ellen and one field technician roaming the Alaskan tundra in search of wolf scat. Accessing her field sites involves being flown in on a small fixed wing plane, where they are extremely space and weight-limited. Therefore, every single piece of gear needs to be weighed to ensure that the pilot has enough fuel to get to the site and back. As a result, Ellen isn’t able to collect the entire scat samples that she finds but can only take a small, representative sample.

Ellen’s incredibly adventurous field work is followed by months spent in the lab processing her precious scat samples. So far, her results have revealed some pretty interesting differences in diet of wolf packs and populations across three field sites in Alaska. The Guatemalan project, which occurs in collaboration with the Wildlife Conservation Society Guatemala, is one of the first to analyze a large sample size of ocelot scats and the first to attempt DNA metabarcoding of samples collected in the neotropics.

To hear more details about both of these projects, as well as Ellen’s background and some bad-a$$ stories from her Alaskan field work, tune in this Sunday, October 15^th 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!

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 4^th 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 23^rd 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 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 16^th 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!

What to do with all the whey?

You probably already know that skim milk and buttermilk are byproducts of cheese-making. But did you know that whey is another major byproduct of the cheese-making process? Maybe you did. Well, did you know that for each 1 kg of cheese obtained, there are about 9 kg of whey produced as a byproduct?! What in the world is done with all of that whey? And what even is whey? In this week’s episode, Food Science Master’s student Alyssa Thibodeau tells us all about it!

Whey is the liquid that remains after milk has been curdled and strained to produce cheese (both soft and hard cheeses) and yoghurt. Whey is mainly water but it also has lots of proteins and fats, as well as some vitamins, minerals, and a little bit of lactose. There are two types of whey: acid-whey (byproduct of yoghurt and soft cheese production) and sweet-whey (byproduct of hard cheese production). Most people are probably familiar with whey protein, which is isolated from whey. The whey protein isolates are only a small component of the liquid though and unfortunately the process of isolating the proteins is very energy inefficient. So, it is not the most efficient or effective way of using the huge quantities of whey produced. This is where Alyssa comes in. Alyssa’s research at OSU is focused on trying to develop a whey-beverage. Because of the small amounts of lactose that are in whey, yeast can be used to ferment the lactose, creating ethanol. This ethanol can then be converted by bacteria to acetic acid. Does this process sound a little familiar? It is! A similar process is involved when making kombucha and the end-product in Alyssa’s mind isn’t too far off of kombucha. She envisions creating an organic, acid-based or vinegar-type beverage from whey.

Morphology of yeast species *Brettanomyces anomalus* which Alyssa is planning on using for her whey-beverage.

How does one get into creating the potentially next-level kombucha? Alyssa’s route to graduate school has been backwards, one that most students don’t get to experience. While the majority of students get a degree, get a job and then start a family, Alyssa started a family, got a job, and then went to graduate school. On top of being a single mother in graduate school, she is also a first-gen student and Hispanic. To quote Alyssa: “It makes me proud every day that I am able to go back to school as a single mom. In the past, this would have maybe been too hard to do or wouldn’t have been possible for older generations but our generations are progressing and people are making decisions for themselves.”.

Intrigued by Alyssa’s research and personal journey? You can hear all about it on Sunday, January 29^th at 7 pm on https://kbvrfm.orangemedianetwork.com/. Missed the live show? You can listen to the recorded episode on your preferred podcast platform!

LGBTQ+ health disparities and the impact of stress

Correlation does not equal causation. This phrase gets mentioned a lot in science. In part, because many scientists can fall into the trap of assuming that correlation equals causation. Proof that this phrase is true can be found in ice cream and sharks. Monthly ice cream sales and shark attacks are highly correlated in the United States each year. Does that mean eating lots of ice cream causes sharks to attack more people? No. The likely reason for this correlation is that more people eat ice cream and get in the ocean during the summer months when it’s warmer outside, which explain why the two are correlated. But, one does not cause the other. Correlation does not equal causation.

To date, much of the research that has been conducted on LGBTQ+ health has been correlational. Our guest this week, Kalina Fahey, hopes that her dissertation project will play a part in changing this paradigm as she is trying to get more at causation. Kalina is a 5^th year PhD candidate in the School of Psychological Science working with her advisors Drs. Anita Cservenka and Sarah Dermody. Her research broadly investigates LGBTQ+ health disparities and how stress impacts health in LGBTQ+ groups. She is also interested in understanding ways in which spiritual and/or religious identities can influence stress, and thereby, health. To do this, Kalina is employing a number of methods, including undertaking a systematic review to synthesize the existing research on substance use in transgender youth, analyzing large-scale publicly available datasets to look at how religious and spiritual identity relates to health outcomes, and finally developing a safe experiment to look at how specific forms of stress impact substance use-related behaviors in real time.

Most of Kalina’s time at the moment is being spent on the experimental portion of her research as part of her dissertation. For this study, Kalina is adapting the personalized guided induction stress paradigm, with the aim of safely eliciting minor stress responses in a laboratory setting. The experiment involves one virtual study visit and two in-person sessions. During the first visit, participants are asked to describe a minority-induced stressful event that occurred recently, as well as a description of a moment or situation that is soothing or calming. After this session, Kalina and her team develop two meditative scripts – one each to recreate the two events or moments described by the participant. When the participant comes back for their in-person sessions, they listen to one of two different meditative scripts and are asked a series of questions regarding their stress levels. Kalina and her team also are collecting saliva and heart rate readings to look at physiological stress levels. This project is still looking for participants. If you are a sexual-minority woman who drinks alcohol, consider checking out the following website to learn more about the study: https://oregonstate.qualtrics.com/jfe/form/SV_8e443Lq10lgyX66?fbclid=IwAR3XOdECIOvCbx1xn3QA5rrCtHfSezZrR5Ppkpnd9sx1SsicZRQnfYHAqb8. Kalina hopes to continue experiment-based research on LGBTQ+ health disparities in the future as she sees the lack of experimental studies to be a major gap in better understanding, and thereby supporting, the LGBTQ+ community.

Interested in learning more about Kalina’s research, the results, and her background? Listen live on Sunday, January 15, 2023 at 7 PM on 88.7 KBVR FM. Missed the live show? You can download the episode on our Podcast Pages! Also, check out her other work here or finder her on Twitter @faheypsych

“Creepy” Beer

Happy Halloween from the ID team! This week we’re chatting about a popular halloweekend beverage: Beer and a “creepy” phenomenon seen in a west coast favorite, IPAs. Hop creep may not mean that there are creepy crawlies in your beer, but it may lead to exploding cans or a beer that’s all trick and no treat. To find out more, we are talking with Cade Jobe on his work on hops maturity and its impact on understanding this spooky problem facing the beer industry.

*Cade Jobe, a 1st year masters student in FST*

Cade is a 1^st year masters student in the Department of Food Science and Technology at OSU, where he works under the advisement of Dr. Tom Shellhammer. In the “Beer”, or “Hops”, lab there are a wide variety of projects on the various components of beer, in addition to offering resources to the brewing industry by running standard analytical measurements on hops. Cade moved to Oregon in pursuit of joining the Hop Lab, after falling in love with home-brewing and embarking upon a career shift from law to food science. While his master’s work is going to be more focused on the impact of wildfire-smoke on hops, his post-baccalaureate work focused on hop maturity, in particular the Citra hop variety.

How does one study the impact of hop maturity? Cade worked with a hop grower in Yakima, Washington to harvest hops from 3 fields at 7 different time points during the hop picking season. These dried samples were then sent back to Corvallis where they underwent standard hop chemical analysis, sensory analysis, and enzymatic analysis.

This is all great, but how does it help me drink beer? From the chemical analysis, there are standard components that are measured to give an overall hop quality measure to know if it is going to produce the desired result. From sensory analysis, they can see what aromas are associated with the different maturity levels of the hops and what aromas they would impart in beer. Spoiler: late season hops might identify if you are a vampire! And finally, going back to the exploding beer cans, the enzymatic analysis shows the potential of hop creep occurring so that brewers can mitigate the problem.

Want to learn more about the science behind beer and more on Cade’s research into hops? Tune in Sunday, October 30^th, 2022 at 7 PM on KBVR 88.7FM (https://kbvrfm.orangemedianetwork.com) or wherever you get your podcasts!

Also, if you’re interested in learning more about the wide-world of brewing, check out Cade on the “BruLab” podcast.

This blog post was written by Jenna Fryer and posted by Lisa Hildebrand.

Stressed out corals

Coral reef ecosystems offer a multitude of benefits, ranging from coastline protection from storms and erosion to a source of food through fishing or harvest. In fact, it is estimated that over half a billion people depend on reefs for food, income, and/or protection. However, coral reefs face many threats in our rapidly changing world. Climate change and nutrient input due to run-off from land are two stressors that can affect coral health. How exactly do these stressors impact corals? This week’s guest Alex Vompe is trying to figure that out!

Alex is a 4^th year PhD candidate in the Department of Microbiology at OSU, where he is co-advised by Dr. Becky Vega-Thurber and Dr. Tom Sharpton. The goal of Alex’s research is to understand how coral microbe communities change over time and across various sources of stress. While the microbial communities of different coral species can differ, typically under normal, non-stressed conditions, they look quite similar. However, once exposed to a stressor, changes start to arise in the microbial community between different coral species, which can have different outcomes for the coral host. This pattern has been coined the ‘Anna Karenina principle’ whereby all happy corals are alike, however as soon as things start to go wrong, corals suffer differently.

Alex is testing how this Anna Karenina principle plays out for three different coral species (Acropora retusa, Pocillopora verrucosa [also known as cauliflower coral], Porites lobata [also known as lobe coral]) in the tropical Pacific Ocean. The stressors that Alex is investigating are reduction in herbivory and introduction of fertilizer. A big source of stress for reefs is when fish populations are low, which results in a lack of grazing by fish on macroalgae. In extreme situations, macroalgae can overgrow a coral reef completely and outcompete it for light and resources. Fertilizers contain a whole host of nutrients with the intent of increasing plant growth and production on land. However, these fertilizers run-off from land into aquatic ecosystems which can often be problematic for aquatic flora and fauna.

How is Alex testing the effects of these stressors on the corals? He is achieving this both in-situ and in the lab. Alex and his lab conduct field work on coral reefs off the island of Moorea in French Polynesia. Here, they have set up experimental apparatus in the ocean on coral reefs (via scuba diving!) to simulate the effects of reduced herbivory and fertilizer introduction. This field work is conducted three times a year. When not under the water surface, Alex sets up aquaria experiments on land in Moorea using coral fragments, which he has been able to grow in order to investigate the microbial communities more closely. These samples then get processed in the lab at OSU for genomic analysis and Alex uses bioinformatics to investigate the coral microbiome dynamics.

Curious to know more about Alex’s research? Listen live on Sunday, October 23, 2022 at 7 PM on KBVR 88.7FM. Missed the live show? You can download the episode on our Podcast Pages! Also, feel free to follow Alex on Twitter (@AVompe) and Instagram (@vompedomp) to learn more about him and his research.

The non-Ghostbusting Venkman: a virus that “eats” marine bacteria

Have you ever considered that a virus that eats bacteria could potentially have an effect on global carbon cycling? No? Me neither. Yet, our guest this week, Dr. Holger Buchholz, a postdoctoral researcher at OSU, taught me just that! Holger, who works with Drs. Kimberly Halsey and Stephen Giovannoni in OSU’s Department of Microbiology, is trying to understand how a bacteriophage (a bacteria-eating virus), called Venkman, impacts the metabolism of marine bacterial strains in a clade called OM43.

Bacteria that are part of the OM43 clade are methylotrophs, in other words, these bacteria eat methanol, a type of volatile organic compound. It is thought that the methanol that the OM43 bacteria consume are a by-product of photosynthesis by algae. In fact, OM43 bacteria are more abundant in coastal waters and are particularly associated with phytoplankton (algae) blooms. While this relationship has been shown in the marine environment before, there are still a lot of unknowns surrounding the exact dynamics. For example, how much methanol do the algae produce and how much of this methanol do the OM43 bacteria in turn consume? Is methanol in the ocean a sink or a source for methanol in the atmosphere? Given that methanol is a carbon compound, these processes likely affect global carbon cycles in some way. We just do not know how much yet. And methanol is just one of many different Volatile Organic Carbon (VOC) compounds that scientists think are important in the marine ecosystem, and they are probably consumed by bacteria too!

Depiction of the carbon cycle within the marine food web. DOM means Dissolved Organic Material, POM stands for Particulate Organic Material. This refers to all the things that are bound within cells that gets released when for example viruses destroy cells.

All of this gets even more complicated by the fact that a bacteriophage, by the name of Venkman, infects the OM43 bacteria. If you are a fan of Ghostbusters and your mind is conjuring the image of Bill Murray in tan coveralls at the sound of the name Venkman, then you are actually not at all wrong. During his PhD, which he conducted at the University of Exeter, part of Holger’s research was to isolate the bacteriophage that consumes OM43 bacteria (which he successfully did). As a result, Holger and his advisor (Dr. Ben Temperton, who is a big Ghostbusters fan) were able to name the bacteriophage and called it Venkman. Holger’s current work at OSU is to try and figure out how the Venkman bacteriophage affects the metabolism of methanol in OM43 bacteria and the viral influence on methanol production in algae. Does the virus increase the bacteria’s methanol metabolism? Decrease it? Or does nothing happen at all? At this point, Holger is not entirely sure what he is going to find, but whatever the answer, there would be an effect on the amount of carbon in the oceans, which is why this work is being conducted.

Holger is currently in the process of setting up experiments to answer these questions. He has been at OSU since February 2022 and has funding to conduct this work for three years from the Simons Foundation. Join us live on Sunday at 7 pm PST on 88.7 KBVR FM or https://kbvrfm.orangemedianetwork.com/ to hear more about Holger’s research and how a chance encounter with a marine biologist in Australia set him on his current career path! Can’t make it live, catch the podcast after the episode on your preferred podcast platform!

The rigamarole of RNA, ribosomes, and machine learning

Basic biology and computer science is probably not an intuitive pairing to think of, when we think of pairs of scientific disciplines. Not as intuitive as say biology and chemistry (often referred to as biochem). However, for Joseph Valencia, a third year PhD student at OSU, the bridge between these two disciplines is a view of life at the molecular scale as a computational process in which cells store, transmit, and interpret the information necessary for survival.

Think back to your 9^th or 10^th grade biology class content and you will (probably? maybe?) vaguely remember learning about DNA, RNA, proteins, and ribosomes, and much more. In case your memory is a little foggy, here is a short (and very simplified) recap of the basic biology. DNA is the information storage component of cells. RNA, which is the focus of Joseph’s research, is the messenger that carries information from DNA to control the synthesis of proteins. This process is called translation and ribosomes are required to carry out this process. Ribosomes are complex molecular machines and many of them can also be found in each of our cells. Their job is to interpret the RNA. The way this works is that they attach themselves to the RNA, they take the transcript of information that the RNA contains, interpret it and produce a protein. The proteins fold into a specific 3D shape and the shape determines the protein’s function. What do proteins do? Basically control everything in our bodies! Proteins make enzymes which control everything from muscle repair to eye twitching. The amazing thing about this process is that it is not specific to humans, but is a fundamental part of basic biology that occurs in basically every living thing!

An open reading frame (ORF) is a stretch of nucleotides beginning with a start codon and ending with a stop codon. Ribosomes bind to RNA transcripts and translate certain ORFs into proteins. The Kozak sequence (bottom right, from Wikipedia) depicts the nucleotides that commonly occur around the start codons of translated ORFs.

So now that you are refreshed on your high school biology, let us tie all of these ‘basics’ to what Joseph does for his research. Joseph’s research focuses on RNA, which can be broken down into two main groups: messenger RNA (mRNA) and non-coding RNA. mRNA is what ends up turning into a protein following the translation by a ribosome, whereas with long non-coding RNA, the ribosome decides not to turn it into a protein. While we are able to distinguish between the two types of RNA, we do not fully understand how a ribosome decides to turn one RNA (aka mRNA) into a protein, and not another (aka long non-coding RNA). That’s where Joseph and computer science come in – Joseph is building a machine learning model to try and better understand this ribosomal decision-making process.

Machine learning, a field within artificial intelligence, can be defined as any approach that creates an algorithm or model by using data rather than programmer specified rules. Lots of data. Modern machine learning models tend to keep learning and improving when more data is fed to them. While there are many different types of machine-learning approaches, Joseph is interested in one called natural language processing . You are probably pretty familiar with an example of natural language processing at work – Google Translate! The model that Joseph is building is in fact not too dissimilar from Google Translate, or at least the idea behind it; except that instead of taking English and translating it into Spanish, Joseph’s model is taking RNA and translating (or not translating) it into a protein. In Joseph’s own words, “We’re going through this whole rigamarole [aka his PhD] to understand how the ins [RNA & ribosomes] create the outs [proteins].”.

A high-level diagram of Joseph’s deep learning model architecture.

But it is not as easy as it sounds. There are a lot of complexities to the work because the thing that makes machine learning so powerful is that the exact complexities that gives these models the power that they have, also makes it hard to interpret why the model is doing what it is doing. Even a highly performing machine learning model may not capture the exact biological rules that govern translation, but successfully interpreting its learned patterns can help in formulating testable hypotheses about this fundamental life process.

To hear more about how Joseph is building this model, how it is going, and what brought him to OSU, listen to the podcast episode! Also, you can check out Joseph’s personal website to learn more about him & his work!

Imaging nuclear fallout with a camera and a scintillating crystal

Our guest this week, Dr. Ari Foley, is a recent (July 2021) OSU graduate from the School of Nuclear Science and Engineering. For her PhD research, she developed a rapid imaging method for post-detonation nuclear forensics. While methods to do this work already exist, a lot of them are time- and material-intensive. Therefore, the goal of Ari’s work was to develop a method that could inform optimized destructive analysis of samples after a detonation event of a nuclear weapon, with a particular focus on reducing the amount of imaging time required. Not only was Ari able to accomplish this task but the system she developed is able to take an image of the spatial distribution of radiation omitted from an object in the same exposure as taking a traditional photograph of the object being analyzed (see Image below). How in the world did Ari do this? Read below for a short synopsis or even better listen to the episode here!

A core component of Ari’s system was an electron-magnifying charged couple device, also known as an EMCCD. The CCD part of that is essentially a normal camera but the EM part magnifies the signal collected from whatever the camera is pointed at. Ari rigged an inorganic scintillation crystal to the EMCCD, which sits in a 3D-printed holder just in front of the camera. The purpose of the crystal is that once it is held in close proximity to radioactive fallout material from a detonation, the radiation interacts with the crystal, which leads to the emission of light. This light is proportional to the amount of energy that is imparted within the crystal. The EM part of the EMCCD kicks in as the image is taken as it allows for a high intensity image to be made that magnifies the light emitted from the crystal interacting with the radiation. This process needs to occur in light tight box, however it is mobile, meaning that it can easily be taken into the field and directly be used at a nuclear detonation site to measure the intensity of radiation of fallout material.

Ari spent the last three years of her PhD time in Idaho at the Idaho National Laboratory (INL), which is one of the leading nuclear research labs in the USA and has close ties with OSU. In fact, Ari was one of two students in the inaugural class of INL Graduate Fellows, which enabled her to conduct this work while working full-time at the lab. However, Ari’s career may have gone down a very different path because she had always wanted to be an Arts student or pursue a career in human rights. However, during a summer school experience during her high school years, Ari attended a class on Indigenous Peoples and the United Nations. During this class, the students took a trip to the United Nations General Assembly Building in New York, which hosts a statue from Hiroshima, Nagasaki. The statue is of a woman holding a lamb, which from the front, looks completely normal. However, when you walk around to the back of the statue, the statue is completed charred and scarred – a consequence of the atomic bomb. The same class presented case studies of radiation contamination on tribal reservations in the USA. Seeing and learning these things really riled Ari up at the time because while she had been interested by radiation in chemistry class, she was suddenly confronted by the fact that radiation contamination were actual ongoing world issues.

Listen to the podcast episode here to learn more about the nitty-gritty of how Ari developed her nuclear forensic system, how she prevented from getting radiation in the lab, and her road to OSU!

Inspiration Dissemination

Inspiring Stories From Oregon State Graduate Students on 88.7 KBVR FM