Author Archives: Grace Deitzler

The Puzzle of Puffy Snout

Puffy snout syndrome: though it has a cute-sounding name, this debilitating condition causes masses on the face of Scombridae fish (a group of fish that includes mackerel and tuna.) Fish afflicted with puffy snout syndrome (PSS) develop excessive collagenous tumor-like growths around the eyes, snout, and mouth. This ultimately leads to visual impairment, difficulty feeding, and eventual death. PSS is surprisingly confined to just fish raised in captivity – those in aquaculture farms or aquariums, for example. Unfortunately, when PSS is identified in aquaculture, the only option is to cull the entire tank — no treatments or cures currently exist.

Left: a mackerel with puffy snout syndrome. Collagenous growths cover the snout and eye. Right: a healthy mackerel. Photos Emily Miller

PSS was first identified in the 1950s, in a fish research center in Honolulu, Hawaii. Since then, there have only been 9 publications in the scientific literature documenting the condition and possible causes, although the fish community has come to the conclusion that PSS is likely a transmittable condition with an infectious agent as the cause. But despite this conclusion, there’s been no success so far in identifying such a cause – tests for parasites, bacterial growth, and viruses have come up empty-handed. That was until a 2021 paper, using high-resolution electron microscopy, found evidence of viral particles in facial tissues taken from Pacific mackerel. Suddenly, there was a lead: could PSS be caused by a virus that we just don’t have a test for yet?

Electron microscopy images showing viral-like particles (red arrows) in facial tissue from Pacific mackerel (Miller et al 2022).

Putting Together the Pieces

To investigate this hypothesis, this week’s guest Savanah Leidholt (a co-author of the 2021 microscopy study) is using an approach for viral detection known as metatranscriptomics. Leidholt, a fourth year PhD candidate in the Microbiology department, sees this complex approach as a sort of puzzle: “Your sample of RNA has, say, 10 giant jigsaw puzzles in it. But the individual puzzles might not be complete, and the pieces might fit into multiple places, so your job is to reassemble the pieces into the puzzles in a way that gives you a better picture of your story.”

Savanah Leidholt, PhD candidate in Rebecca Vega-Thurber’s lab, is looking for evidence of viruses in the tissues of fish with puffy snout syndrome.

RNA, or ribonucleic acid, is a nucleic acid similar to DNA found in all living organisms, But where DNA is like a blueprint – providing the code that makes you, you; RNA is more like the assembly manual. When a gene is expressed (meaning the corresponding protein is manufactured), the double-stranded DNA is unwound and the information is transcribed into a molecule called messenger RNA. This single-stranded mRNA is now a copy of the gene that can be translated into protein. The process of writing an mRNA copy of the DNA blueprint is called transcription, and these mRNA molecules are the target of this metatranscriptomics approach, with the prefix “meta” meaning all of the RNA in a sample (both the fish RNA and the potential viral RNA, in this case) and the suffix “omics” just referring to the fact that this approach happens on a large scale (ALL of the RNA, not just a single gene, is sequenced here!) When mRNA is sequenced in this manner, the researchers can then conclude that the gene it corresponds to was being expressed in the fish at the time the sample was collected.

The process of transcription: making messenger RNA from DNA. Image from Nature Education.

So far, Leidholt has identified some specific genes in fish that tend to be much more abundant in fish from captive settings versus those found in the wild. Could these genes be related to why PSS is only seen in fish in captivity? It’s likely – the genes identified are immune markers, and the upregulation of immune markers is well-known to be associated with chronic stress. Think about a college student during finals week – stress is high after a long semester, maybe they’ve been studying until late in the night and not eating or sleeping well, consuming more alcohol than is recommended. And then suddenly, on the day of the test, they’re stuck in bed with the flu or a cold. The same thing can happen to fish (well, maybe not the part where they take a test!,) especially in captivity – Pacific mackerel, tuna, and other scombrid species susceptible to PSS are fairly large, sometimes swimming hundreds of miles in a single day in the ocean. But in captivity, they are often in very small tanks, constantly swimming in constrained circles. They’re not exposed to the same diversity of other fish, plankton, prey, and landscape as they would be in the wild. “Captivity is a great place to be if you’re a pathogen, but not great if you’re a fish”, says Leidholt.

The results of Leidholt’s study are an exciting step forward in the field of PSS research, as one of the biggest challenges currently facing aquaculture farms and aquariums is that there is no way to screen for PSS in healthy fish before symptoms begin to show. Finding these marker genes that appear in fish that could later on develop PSS means that in the future a test could be developed. If vulnerable fish could be identified and removed from the population before they begin to show symptoms and spread the condition, then it would mean fish farmers no longer have to cull the entire tank when PSS is noticed.

The elusive virus

One of the challenges that remains is going beyond the identification of genes in the fish and beginning to identify viruses in the samples. Viruses, which are small entities made up of a DNA or RNA core and a protective protein coating, are thought to be the most abundant biological entities on the planet Earth – and the smallest in terms of size. They usually get a bit of a bad reputation due to their association with diseases in humans and other animals, but there are also viruses that play important positive roles in their ecosystems – bacteriophages, for example, are viruses that infect bacteria. In humans, bacteriophages can attack and invade pathogenic or antibiotic-resistance bacteria like E. coli or S. aureus (for more information on phages and how they are actually studied as a potential therapy for infections, check out this November 2021 interview with Miriam Lipton!) Across the entire planet there are estimated to be between 10^7 to 10^9 distinct viral species – that’s between 10 million and 10 billion different species. And fish are thought to host more viruses than any other vertebrate species. Because of technological advancements, these viral species have only really been identified very recently, and identification still poses a significant challenge.

As a group, viruses are very diverse, so one of the challenges is finding a reliable way to identify them in a given sample. For bacteria, researchers can use a marker gene called the 16S rRNA gene – this gene is found in every single bacterial cell, making it universal, but it also has a region of variability. This region of variability allows for identification of different strains of bacteria. “Nothing like 16S exists for viruses,” Leidholt says. “Intense sequencing methods have to be used to capture them in a given sample.” The metatranscriptomic methods that Leidholt is using should allow her to capture elusive viruses by taking a scorched earth approach – targeting and sequencing any little bit of RNA in the sample at all, and trying to match up that RNA to a virus. 

To learn more about Savanah’s research on puffy snout syndrome, her journey to Oregon State, and the amazing outreach she’s doing with high school students in the Microbiology Department, tune in to Inspiration Dissemination on Sunday, November 20th at 7 PM Pacific!

Schmitty Thompson wears glasses and a sweater, and smiles at the camera while standing in front of a vast field.

What ice sheets can teach us about ancient ocean shorelines

Around 80,000 years ago, the Earth was in the middle of the late Pleistocene era, and much of Canada and the northern part of the United States was blanketed in ice. The massive Laurentide Ice Sheet covered millions of square miles, and in some places, up to 2 miles thick. Over vast timescales this ice sheet advanced its way across the continent slowly, gouging out what we now know as the Great Lakes, carving the valleys, depositing glacial tills, and transforming the surface geology of much of the southern part of Canada and northern US. Further west, the Cordilleran ice sheet stretched across what is now Alaska, British Columbia, and the northern parts of the Western US, compressing the ground under its massive weight. As these ice sheets depressed the land beneath them, the Earth’s crust bulged outwards, and as the planet warmed and the ice sheets began to melt, the pressure was released, returning the crust underneath to its previous shape. As this happened, ocean water flowed away, resulting in lower sea levels locally, but higher levels across the other side of the planet.

The effects of massive bodies of ice forming, moving, and melting are far from negligible in their impact on the overall geology of the region, the sea level throughout history, and the patterns of a changing climate. Though there are only two ice sheets on the planet today, deducing the ancient patterns and dynamics of ice sheets can help researchers fill the geological record and even make predictions about what the planet might look like in the future. Our guest on Inspiration Dissemination this week is PhD candidate and researcher Schmitty Thompson, of the Department of Geology in CEOAS. Thompson is ultimately trying to answer questions about ice distribution, sea levels, and other unknown parameters that the geologic record is missing during two different ice age warming periods. Their research is very interdisciplinary – Thompson has degrees in both math and geology, and also uses a lot of data science, computer science, and physics in their work. They are using computer modeling to figure out just what the shorelines looked like during this time period around 80,000 years ago. 

Schmitty Thompson, fourth year PhD candidate with Jessica Creveling in the Geology Department.

“I use models because the geologic record is pretty incomplete – the further back you go, the less complete it is. So by matching my models to the existing data, we can then infer more information about what the shoreline was like,” they explain. To do this accurately, Thompson feeds the model what the ice sheets looked like over the course of around 250,000 years. They also need to incorporate other inputs to the model to get an accurate picture – variables such as the composition of the interior of the Earth, the physics of Earth’s interior, and even the ice sheets’ own gravitational pull (ice sheets are so massive they exert a gravitational pull on the water around them!)

Using math to learn about ice

The first equation to describe global changes in sea level was published in 1976, with refining throughout the 90s and early 2000s. Thompson’s model builds on these equations in two versions: one which can run in about 10 minutes on their laptop, and another which can take multiple weeks and must run on a supercomputer. The quicker version uses spherical harmonics as the basis function for the pseudospectral formulation, which is basically a complex function that does math and incorporates coefficient representations of the earth’s radius, meridional wave numbers, variation across north/south and east/west, and a few other variables. The short of it is that it can perform these calculations across a 250k time span relatively quickly, but it makes assumptions about the homogeneity of the earth’s crust and mantle viscosity. Think of it like a gumball: a giant, magma-filled gumball with a smooth outer surface and even layers. So while this method is fast, the assumptions that it makes means the output data is limited in its usefulness. When Thompson needs a more accurate picture, they turn to collaborators who are able to run the models on a supercomputer, and then they work with the model’s outputs.

While the model is useful for filling in gaps in the historical record, Thompson also points out that it has uses in predicting what the future will look like in the context of a changing climate. After testing out these models and seeing how sensitive they are, they could be used by researchers looking at much smaller time scales and more sensitive constraints for current and future predictions. “There are still lots of open questions – if we warm the planet by a few degrees, are we going to collapse a big part of Antarctica or a small part? How much ice will melt?”


To learn more about ice sheets, sea levels, and using computer models to figure out how the shoreline looked thousands of years ago, tune in to Schmitty Thompson’s episode on Inspiration Dissemination this upcoming Sunday evening at 7 PM PST. Catch the show live by streaming on https://kbvrfm.orangemedianetwork.com/, or check out the show later wherever you get your podcasts!

Thompson was also recently featured on Alie Ward’s popular podcast Ologies. You can catch up with all things geology by checking out their episode here.

Warming waters, waning nutrition

Here at Inspiration Dissemination, we are fascinated by the moments of inspiration that lead people to pursue graduate studies. For our next guest, an experience like this came during a boat trip accompanying the National Oceanic and Atmospheric Administration (NOAA) on a research expedition. Becky Smoak, an M.S. student in OSU’s Marine Resource Management program, remembers feeling in awe of the vibrant array of marine life that she saw, including whales, sunfish, and sharks. Growing up on a farm in eastern Washington, Becky had always wanted to be a veterinarian. During her undergraduate studies at Washington State University, she came to feel that the culture of pre-veterinary students was too cutthroat. In search of something more collaborative, she came to Oregon State in summer 2019 for a Research Experience for Undergrads (REU) and was impressed by the support and inclusivity of her research mentors. A couple years later, Becky is now on the cusp of graduation after her time spent studying marine life.

Becky’s graduate work is the continuation of a long-running collaboration between Oregon State and NOAA out of the Hatfield Marine Science Center in Newport. Beginning in 1996 under the direction of Bill Peterson, a team of researchers has monitored oceanic conditions along a route called the Newport Hydrographic, which extends in a straight line eastward from the Oregon Coast and intersects the northern part of the vast Californian Current. The team takes samples of ocean water at fixed points along the route and analyzes the concentrations of plankton and other organisms or compounds of interest. 

Becky Smoak, teaching on the OSU research vessel The Elakha.

The specific biochemicals that Becky studies are Omega-3 fatty acids. In a set of experiments from the 1930s, rats fed with a diet poor in Omega-3 fatty acids eventually died, demonstrating that these compounds are essential to life and are not produced by mammals. Two types of Omega-3 fatty acids, called EPA and DHA, can only be synthesized by phytoplankton, microscopic photosynthetic organisms that live in the ocean. The ability of phytoplankton to produce fatty acids is intimately linked with oceanic temperature. Studies have shown that increases in sea surface temperature and decreases in nutrient availability can decrease the quality of fatty acids in phytoplankton, thus decreasing food availability and quality in the marine environment. Fatty acid levels have downstream effects on the ecosystem, for example on copepods, a type of zooplankton that feeds on phytoplankton. Becky’s team affectionately refers to the copepod colony of the chilly northern Pacific as the “cheeseburger” copepods, in contrast to the “celery” copepods of the southern Pacific colony. The present-day effect of temperature also points to a key ecological challenge, as warming oceans due to climate change could disrupt the supply of this vital nutrient.

In her thesis work, Becky seeks to untangle the contributions of phytoplankton community structure to oceanic Omega-3 fatty acid levels. She uses a set of statistical methodologies called nonmetric multidimensional scaling to uncover correlations in the datasets. A particularly interesting instrument used to collect her data is a flow cytometry robot dubbed ‘Lucy’. Lucy uses advanced imaging to count individual plankton and characterize their sizes. This yields an improvement in accuracy over older monitoring techniques that assumed a fixed size for all plankton. Becky’s goal for finishing her thesis is to create a statistical procedure for predicting fatty acid availability given information on phytoplankton population structure.

To hear more about Becky’s journey to OSU, her experiences as a first-generation college student, and the fascinating role of Omega-3s in marine ecosystems, be sure to tune in this Sunday October 9th at 7pm on KBVR.

This article was written by Joseph Valencia.

Violence and Masculinity in Film

After a long summer hiatus, Inspiration Dissemination is back on the airwaves and your podcast platforms this week! Kicking off our Fall quarter lineup is Andrew Herrera, MA candidate with Jon Lewis in the School of Writing, Literature, and Film here at Oregon State University.

Herrera’s research might sound like a dream come true to some: “I study movies, honestly.”

For Herrera it really is a dream come true – he grew up with a lifelong love of film, inspired by watching movies with his mother as a child, the same movies that she had also grown up with. But it was after seeing Darren Aronofsky’s 2010 hit film Black Swan that he knew that studying film was going to be a career for him. The psychological horror production stars Natalie Portman as a dancer in a production of Swan Lake and follows her descent into madness as she struggles with a rival dancer. Herrera recalls that after seeing the film in theaters he sat in the car for several hours, just thinking about what he’d seen. This was around the time he learned that he could actually study film as an academic pursuit, and ended up writing about Black Swan for a literature class, comparing and contrasting it with The Strange Case of Dr. Jekyll and Mr. Hyde.

Andrew Herrera, MA candidate in SWLF.

He eventually finished his Bachelor’s degree in English Literature here at Oregon State University, and decided to stay and pursue a Master’s in Film Studies. His dissertation is focusing on the themes of three films by acclaimed Danish director Nicolas Winding Refn: Drive, Only God Forgives, and Bronson. Herrera is looking at the three films through the lens of masculinity, gender performativity and violence – all three center around male characters engaged in violent trajectories. Herrera in part argues that the three films present masculinity as a kind of performance or even a very literal costume, in the case of Drive (Ryan Gosling’s character is known for his iconic white jacket which sports a scorpion design, which he is only seen wearing when committing acts of violence.) The removal of weakness and femininity through violence and fighting leads to the rebirth of masculinity in Bronson, and in Only God Forgives features an almost Oedipal-like protagonist (also played by Ryan Gosling) who eventually cuts open the womb of his dead mother in a representation of asserting control over his own masculinity. Herrera is also interested in the intersection of masculinity and queerness in media, and how these themes show up explicitly or implicitly in these three and other films.


To hear more about these movies, the way masculinity is portrayed in film and its cultural impacts, and Herrera’s research, tune in to Inspiration Dissemination this Sunday evening at 7 PM at KBVR 88.7 FM or listen live online at https://kbvrfm.orangemedianetwork.com/. If you missed the live episode don’t forget to check out the podcast, now available wherever you get your podcasts.

From A(lgorithms) to Z(O-1 proteins): A Computer Scientist’s Journey into the Lab

By Grace Deitzler

Improvements in DNA sequencing technology have allowed scientists to dig deeper than ever before into the intricacies of the microbes that inhabit our gut, also called the gut microbiome. Massive amounts of data – on the scale of pentabytes – have been accumulated as labs and institutes across the globe sequence the gut microbiome in an effort to learn more about its inhabitants and how they contribute to human health. But now that we have all of this data (and more accumulating all the time), the challenge becomes making sense of it.

This is a challenge that Christine Tataru, a rising fifth year PhD student in the Department of Microbiology, is tackling head-on. “My research is trying to understand what a ‘healthy’ gut microbiome actually looks like, how it ‘should’ look, and to do so in a way that is integrative,” she explains. 

A woman with long hair in a red and white striped shirt sits at a computer.
Christine Tataru, fifth year PhD student in Maude David’s lab.

An integrative approach looks at all of the processes and relationships that are occurring between all of the trillions of microorganisms in our gut, and the cells within our body. Previous microbiology dogma focused on the behavior and impact of singular species such as pathogens, but as we learn more about microbiomes, this approach becomes limiting. There are a vast number of relationships that can occur between microbes and human cells. And there are many different lenses through which we can look at this system: taking a census of what microbes are present; tracking the genes that are present rather than just the microbes (this tells us about the functions that might be carried out); and what proteins or metabolites are actually present, whether those are created by the bacteria or the host. Each piece of the puzzle allows us a glimpse of the massively complex system that is the gut microbiome.

“It’s difficult for a human brain to keep track of these relationships and sources of variations, so I use computer algorithms to try to get a picture of what is happening, and what that might mean for health.” 

It’s an approach that makes sense for the Stanford-trained computer-scientist-turned-biologist. Christine recalls a deep learning class in college in which a natural language processing algorithm on the whiteboard struck her with inspiration: what if instead of being applied to words, this algorithm could be applied to gut microbiomes? The thought stuck with her and when she came to OSU to pursue her PhD, she already had a clear goal in mind for what she wanted to do.

The natural language processing and interpretation algorithm treats words in a document as discrete entities, and looks for patterns and relationships between words to gain context and “understand” the contents. A computer can’t really understand what words mean linguistically and with the complex nuances that natural language presents, but they are really good at looking for patterns. It can look at what words occur together frequently, what words never occur together, and what words share a ‘social network’ — words that don’t appear together, but appear with the same other words. Christine has developed a way to apply this algorithm to large gut microbiome datasets: using this approach to identify what microbes frequently appear together, which don’t, and which share ‘social networks’. This produces clusters of microbes, or what she refers to as ‘topics’, which can then be interpreted by humans to try to understand how these clusters relate to certain aspects of health. You can read more about this method in her recent PLOS Computational Biology publication here.

It’s quite the challenging undertaking: no one has done this type of approach before, and even when the clusters are generated, we still need to be able to interpret what it means – why is it interesting or important that these microbes occur with each other and also correlate with these genes or metabolites? Biologically, what does it actually mean?

The question of biological meaning prompted Christine to pivot to a more traditional ‘wet lab’ biology approach. “Who gave this computer scientist a pipette,” she jokes. But to be perfectly honest, it makes a lot of sense: who better to investigate the hypotheses that can be generated by computers than the scientist who wrote the code?

Taking the ‘integrative approach’ to the next level, she now works on recapitulating the environment of the gut microbiome on a chip in the lab. The organ-on-a-chip system is a fairly new approach to studying biological mechanisms in a way that better mimics the naturally occurring environment. In Christine’s case, she is using a ‘gut on a chip’, which is made of a thin piece of silicone with input and output channels. The silicone is split by a microporous membrane in such a way that two different kinds of cells can be grown, one on the top layer and one on the bottom. What makes this system unique as compared to traditional cell culture is that the channels and membrane allow for constant flow of growth media, which physically simulates the flow of blood over the cells. It can also mimic peristalsis, which is the stretching and relaxing of intestinal cells that helps push food and nutrients through the digestive tract. It’s a sophisticated system, and one that allows her a high degree of control over the environment. She can use this system to mimic Inflammatory Bowel Disease, and then add in specific microbes or combinations of microbes to see how the gut cells respond, using findings from her algorithm results to inform what kinds of additions might have anti-inflammatory effects.

Christine in a biosafety hood, preparing gut-chips for experiments.

This innovative approach provides Christine another lens through which to view the relationship between the gut microbiome and health. Though she will be finishing her doctorate at the end of the year, the curiosity doesn’t end there – “Broadly, my life goal to some extent has always been to make ways for people to help people.” Whether that’s pipeline and methods development or building the infrastructure to study complex biological relationships, Christine’s innovation-driven approach is sure to lead to huge strides in our understanding of how the tiny living things in our gut influence our health, behavior, and mood.

Tune in at 7 PM this Sunday evening on KBVR 88.7 or stream online to hear more about her research and how she ended up here at OSU!

Spaghetti & Networks: Oodles of Nodes

Picture a bowl of spaghetti and meatballs. There are pristine noodles, drenched in rich tomato sauce, topped with savory meatballs. Now imagine you’re only allowed to eat just one noodle, and one meatball. You’re tasked with finding the very best, the most interesting bite out of this bowl of spaghetti. It might sound absurd, but replace spaghetti with ‘edges’ and meatballs with ‘nodes’ and you’ve got a network.

An image of a network from Nolan’s recent publication. The lines are ‘edges’ and the dots are ‘nodes’.

Computational biologists like our guest this week use networks to uncover meaningful relationships, or the tastiest spaghetti noodle and meatball, between biological entities.
Joining us this week is Nolan Newman, a PhD candidate in the College of Pharmacy under PI Andriy Morgun. Nolan’s research lies at the intersection of math, statistics, computer science, and biology. He’s looking at how networks, such as covariation networks, can be used to look for relationships and correlations between genes, microbes, and other factors from massive datasets which compare thousands or even of biological entities. With datasets this large and complex, it can be difficult to pare down just the important or interesting relationships – like trying to scoop a single bowl of spaghetti from a giant tray at a buffet, and then further narrowing it down to pick just one interesting noodle.

Nolan Newman, PhD candidate


Nolan is further interested in how different statistical thresholds and variables contribute to how the networks ‘look’ when they are changed. If only noodles covered in sauce are considered ‘interesting’, then all of the sauce-less noodles are out of the running. But what if noodles are only considered ‘sauce-covered’ if they are 95% or more covered? Could you be missing out on perfectly delicious, interesting noodles by applying this constraint?


If you’re left scratching your head and a little hungry, fear not. We’ll chat about all things computational biology, networks, making meaning out of chaos, and why hearing loss prompted Nolan to begin a career in science, all on this week’s episode of Inspiration Dissemination. Catch the episode live at 7 PST at 88.7 FM or https://kbvrfm.orangemedianetwork.com/, or catch the podcast after the episode on any podcast platform.

AI that benefits humans and humanity

When you think about artificial intelligence or robots in the everyday household, your first thought might be that it sounds like science fiction – like something out of the 1999 cult classic film “Smart House”. But it’s likely you have some of this technology in your home already – if you own a Google Home, Amazon Alexa, Roomba, smart watch, or even just a smartphone, you’re already plugged into this network of AI in the home. The use of this technology can pose great benefits to its users, spanning from simply asking Google to set an alarm to wake you up the next day, to wearable smart devices that can collect health data such as heart rate. AI is also currently being used to improve assistive technology, or technology that is used to improve the lives of disabled or elderly individuals. However, the rapid explosion in development and popularity of this tech also brings risks to consumers: there isn’t great legislation yet about the privacy of, say, healthcare data collected by such devices. Further, as we discussed with another guest a few weeks ago, there is the issue of coding ethics into AI – how can we as humans program robots in such a way that they learn to operate in an ethical manner? Who defines what that is? And on the human side – how do we ensure that human users of such technology can actually trust them, especially if they will be used in a way that could benefit the user’s health and wellness?

Anna Nickelson, a fourth-year PhD student in Kagan Tumer’s lab in the Collaborative Robotics and Intelligent Systems (CoRIS) Institute in the Department of Mechanical, Industrial and Manufacturing Engineering, joins us this week to discuss her research, which touches on several of these aspects regarding the use of technology as part of healthcare. Also a former Brookings Institute intern, Anna incorporates not just coding of robots but far-reaching policy and legislation goals into her work. Her research is driven by a very high level goal: how do we create AI that benefits humans and humanity?

Anna Nickelson, fourth year PhD student in the Collaborative Robotics and Intelligent Systems Institute.

AI for social good

When we think about how to create technology that is beneficial, Anna says that there are four major considerations in play. First is the creation of the technology itself – the hardware, the software; how technology is coded, how it’s built. The second is technologists and the technology industry – how do we think about and create technologies beyond the capitalist mindset of what will make the most money? Third is considering the general public’s role: what is the best way to educate people about things like privacy, the limitations and benefits of AI, and how to protect themselves from harm? Finally, she says we must also consider policy and legislation surrounding beneficial tech at all levels, from local ordinances to international guidelines. 

Anna’s current research with Dr. Tumer is funded by the NSF AI Institute for Collaborative Assistance and Responsive Interaction for Networked Groups (AI-CARING), an institute through the National Science Foundation that focuses on “personalized, longitudinal, collaborative AI, enabling the development of AI systems that learn personalized models of user behavior…and integrate that knowledge to support people and AIs working together”, as per their website. The institute is a collaboration between five universities, including Oregon State University and OHSU. What this looks like for Anna is lots of code writing and simulations studying how AI systems make trade-offs between different objectives.For this she looks at machine learning for decision making, and how multiple robots or AIs can work together towards a specific task without necessarily having to communicate with each other directly. For this she looks at machine learning for decision making in robots, and how multiple robots or AIs can work together towards a specific task without necessarily having to communicate with each other directly. Each robot or AI may have different considerations that factor into how they accomplish their objective, so part of her goal is to develop a framework for the different individuals to make decisions as part of a group.

With an undergraduate degree in math, a background in project management in the tech industry, engineering and coding skills, and experience working with a think tank in DC on tech-related policy, Anna is uniquely situated to address the major questions about development technology for social good in a way that mitigates risk. She came to graduate school at Oregon State with this interdisciplinary goal in mind. Her personal life goal is to get experience in each sector so she can bring in a wide range of perspectives and ideas. “There are quite a few people working on tech policy right now, but very few people have the breadth of perspective on it from the low level to the high level,” she says. 

If you are interested in hearing more about Anna’s life goals and the intersection of artificial intelligence, healthcare, and policy, join us live at 7 PM on Sunday, May 7th on https://kbvrfm.orangemedianetwork.com/, or after the show wherever you find your podcasts. 

In the face of national anti-trans legislation, local game developer and OSU graduate raises over $400k for trans advocacy groups

Content warning: this article includes mentions of transphobia and suicide.

Rue Dickey found himself feeling helpless and frustrated upon reading the news about the onslaught of anti-transgender legislation sweeping the country this year. In the four months of 2022 alone, nearly 240 anti-LGBTQ bills have been filed in states across the United States. This skyrocketing number is up from around 41 such bills in 2018, and around half of these bills targeting transgender folks specifically. In February 2022, Texas governor Greg Abbott called for teachers and members of the public to report parents of transgender children to authorities, equating providing support and medical care for trans youth to child abuse –  a move that made national headlines.  It’s imperative that we understand the consequences of this wave of horrific and discriminatory legislation: a survey by the Trevor Project found that 42% of LGBTQ youth have seriously considered suicide within the past year alone, and over half of transgender and nonbinary youth have considered suicide.

Rue (they/he) graduated from Oregon State University in 2019, and they are currently the Marketing Coordinator for the Corvallis Community Center. They also develop and create content for TTRPGs, or Tabletop Role Playing Games. TTRPGs are role playing games in which players describe their characters’ actions and adhere to a set of rules and characterizations based on the world setting, and characters work together to achieve a goal or go on an adventure. They often involve improvisation and their choices shape the world around them. Think Dungeons & Dragons – many TTRPGs involve the use of dice rolling to determine the outcomes of certain actions and events.

Rue Dickey, 2019 OSU graduate and Marketing Director for the Corvallis Community Center.

Gaming as a way to crowdfund for a cause

Wanting to do something to help children and transgender people living in Texas, Rue decided to turn his passion for TTRPGs into a fundraiser. The online indie game hosting platform itch.io has been used in the past to create fundraisers for charities by bundling together and selling games. A few of Rue’s friends who run a BIPOC tabletop server have had experience with creating profit-sharing bundles using the platform in the past, so after he consulted them and walked through the steps, he set up a bund?ndraiser, Rue wanted to ensure that the money was going directly to transgender people. “At the time, a lot of the larger media outlets were encouraging people to donate to Equality Texas, which works to get pro-queer legislature through in Texas, but they don’t necessarily help trans folks on an individual level.”  

After tweeting about the fundraiser and soliciting ideas for charities, he landed on two organizations in Texas that are trans-led and focused on transgender individuals: TENT (Transgender Education Network of Texas, a trans-led group that works to combat misinformation on the community level through the corporate level, offering workshops as well as emergency relief funds for trans folks in need) and OLTT (Organización Latina Trans in Texas, a Latina trans woman-led organization focusing on transgender immigrants in Texas, assisting with the legal processes of immigration, name changes, and paperwork.) Both charities serve transgender folks directly in Texas, and you can donate to the organizations by following the links we have included in the article. Both charities were thrilled to learn about the donation – for OLTT, it’s the largest single donation they have ever received, and they will be able to use it to perform needed renovations and expansions at their shelter facilities.

Since the fundraiser ended, Rue has been interviewed by several national news outlets, including NBC, Gizmodo, and The Mary Sue, as well as gaming-centric websites like Polygon, Dicebreaker, and GamesHub. Although they have received some harassment and nasty DMs, Rue says that the support from the community has vastly overshadowed the naysayers. Similarly, he spoke of the overwhelming rush of support from trans folks, queer folks, and allies to the movement in the face of structural legislation that seeks to harm trans people. 

“It restores a bit of my faith in humanity to see that on a structural level, they are trying to get rid of us, but on a community level, there is support – there will always be a place to go and people looking out for you.”

Tune in at 5 PM on Sunday, April 24 for this special episode of Inspiration Dissemination. Stream the show live or listen to this episode wherever you get your podcasts! You can keep up with Rue and their games on twitter and itch.io.

This article was written by Grace Deitzler.

Microbial and biochemical community dynamics in low-oxygen Oregon waters

Much like Oregon’s forests experience wildfire seasons, the waters off the Oregon coast experience what are called “hypoxia seasons”. During these periods, which occur in the summer, northern winds bring nutrient-rich water to the Eastern Current Boundary off the Oregon Coast. While that might sound like a good thing, the upwells bring a bloom of microscopic organisms such as phytoplankton that consume these nutrients and then die off. As they die off, they sink and are then decomposed by marine microorganisms. This process of decomposition removes oxygen from the water, creating what’s called an oxygen minimum zone, or OMZs. These OMZs can span thousands of square miles. While mobile organisms such as fish can escape these areas and relocate, place-bound creatures such as crabs and bottom-dwelling fish can perish in these low oxygen zones. While these hypoxia seasons can occur due to natural phenomena, stratification of the water column due to other factors such as climate change can increase the frequency or severity of these seasons.

2021 was one of the worst years on record for hypoxic waters off the Western coast of the United States. A major contributing factor was the extremely early start to the upwelling triggered by strong winds. Measurements of dissolved oxygen and ocean acidity were high enough to be consistent with conditions that can lead to dead zones, and this is exactly what happened. Massive die-offs of crabs are concerning as the harvesting of Dungeness crab is one of the most lucrative fishing industries in the state. Other species and organisms move into shallower waters, disturbing the delicate balance of the coastal ecosystems. From the smallest microbe to the largest whale, almost every part of the coast can be affected by hypoxia season. 

Our guest this week is Sarah Wolf, a fourth year PhD candidate in the Department of Microbiology here at Oregon State. Sarah, who is co-advised by Dr. Steve Giovannoni and Dr. Francis Chan, studies how microbes operate in these OMZs. Her work centers around microbial physiology and enzyme kinetics, and how these things change over time and in varying oxygen concentrations. To do this, she spent her second year developing a mesocosm, which is a closed environment that allows for the study of a natural environment, which replicates conditions found in low oxygen environments. 

Sarah Wolf, a fourth year PhD Candidate in the department of Microbiology, in her lab

Her experiments involve hauling hundreds of liters of ocean water from the Oregon coast back to her lab in Nash Hall, where she filters and portions it into different jugs hooked up to a controlled gas delivery system which allows her to precisely control the concentration of oxygen in the mesocosm. Over a period of four months Sarah samples the water in these jugs to look at the microbial composition, carbon levels, oxygen respiration rates, cell counts, and other measures of the biological and chemical dynamics occurring in low oxygen. Organic matter can get transformed by different microorganisms that “eat” different pieces through the use of enzymes, but many enzymes which can break down large, complex molecules require oxygen, and in low oxygen conditions, this can be a problem for the breakdown and accumulation of organic matter. This is the kind of phenomenon that Sarah is studying in these mesocosms, which her lab affectionately refers to as the “Data Machine”. 

Sarah’s journey into science has been a little nontraditional. A first generation college student, she started out her education as a political science major at Montana State before moving to the University of the Virgin Islands for a semester abroad. At the time she wasn’t really sure how to get into research or science as a career. During this semester her interest in microbiology was sparked during an environmental science course which led to her first research experience, studying water quality in St. Thomas. This experience resulted in an award-winning poster at a conference, and prompted Sarah to change her major to Microbiology and transfer to California State University Los Angeles. Her second research experience was very different – an internship at NASA’s Jet Propulsion Laboratory studying cleanroom microbiology, which resulted in a publication identifying two novel species of Bacillus isolated from the Kennedy Space Center. Ultimately Sarah’s journey brought her here to Oregon State, which she was drawn to because of its strong marine microbiology research program.

Sarah works on the “Data Machine”

But Sarah’s passion for science doesn’t stop at the lab: during the Covid-19 pandemic, she began creating and teaching lessons for children stuck at home. During this time she taught over 60 kids remotely, with lessons about microbes ranging from marine microbiology to astrobiology and even how to create your own sourdough starter at home. Eventually she compiled these lessons onto her website where parents and teachers alike can download them for use in classrooms and at home. She also began reviewing children’s science books on her Instagram page (@scientist.sarahwolf), and inviting experts in different fields to participate in livestreams about books relating to their topics. A practicing Catholic, she also shares thoughts and resources about religion and science, especially topics surrounding climate science. With around 12k followers, Sarah’s outreach on Instagram has certainly found its audience, and will only continue to grow. 

If you’re curious about microbes in low oxygen conditions, what it’s like to be a science educator and social media influencer, or want to hear more about Sarah’s journey in her own words, tune in at 7 PM on March 13th to catch the live episode at 7 PM PST on 88.7 FM Corvallis, online at https://kbvrfm.orangemedianetwork.com – or you can catch this episode after the show airs wherever you get your podcasts! 

Trusting Your Gut: Lessons in molecular neuroscience and mental health

The bacteria in your gut can talk to your brain.

No, really.

It might sound like science fiction, but you’ve probably heard the phrase ‘gut-brain axis’ used in recent years to describe this phenomenon. What we call the “gut” actually refers to the small and large intestines, where a collection of microorganisms known as the gut microbiome reside. In addition to the microbes that inhabit it, your gut contains around 500 million neurons, which connect to your brain through bidirectional nerves – the biggest of which is the vagus nerve. Bacteria might be able to interact with specialized sensory cells within the gut lining and trigger neuronal firing from the gut to the brain.

Our guest this week is Caroline Hernández, a PhD student in the Maude David Lab in the Department of Microbiology, and she is studying exactly this phenomenon. While the idea that the gut and the brain are connected is not exactly new (ever heard the phrase “a gut feeling” or felt “butterflies” in your gut when you’re nervous?), there still isn’t much known about how exactly this works on a molecular level. This is what Caroline’s work aims to untangle, using an in vitro  (which means outside of a living organism – in this case, cells in a petri dish) approach: if you could grow both the sensory gut cells and neurons in the same petri dish, and then expose them to gut bacteria, what could you observe about their interactions? 

Caroline Hernández in her lab at Oregon State, using a stereo microscope to identify anatomical structures in a mouse before dissecting out a nerve bundle

The answer to this question could tell us a lot about how the gut-brain axis works on a molecular level, and could help researchers understand the mechanisms by which the gut microbiome can possibly modulate behavior, mood, learning, and cognition. This could have important implications down the line for how we conceptualize and potentially treat mood and behavioral disorders. Some mouse studies have already shown that mice treated with the probiotic Lactobacillus rhamnosus display reduced anxiety-like and depressive behaviors, for example – but exactly how this works isn’t really clear.

The challenges of in vitro research

Before these mechanisms can really be untangled, there are several challenges that Caroline is working on solving. The biggest one is just getting the cells to grow at all: Caroline and her team must first carefully extract specific gut sensory tissue and a specific ganglion (which is a blob of neurons) from mice, a delicate process that requires the use of specialized tools and equipment. Once they’ve verified that they have the correct anatomy, the tissues are moved into media, a liquid that contains specialized nutrients to help provide the cells with the growth factors they need to stay alive. Because this is very cutting-edge research, Caroline’s team is among the first in the world to attempt this technique – meaning there is a lot of trial and error and not a great amount of resources out there to help. There have been a number of hurdles along the way, but Caroline is no stranger to meeting challenges head-on and overcoming them with incredible resilience.

From art interactions to microbial interactions

Her journey into science started in a somewhat unexpected way: Caroline began her undergraduate career as a studio art major in community college. Her art was focused on interactivity and she was especially interested in how the person perceiving the art could interact with and explore it. Eventually she decided that while she was quite skilled at it, art was not the career path she wanted to pursue, so she switched into science, where she began her Bachelors of Science in molecular and cellular biology at the University of Illinois in Urbana Champaign. 

During her undergraduate degree, a mental health crisis prompted Caroline to file for a medical withdrawal from her program. The break was much needed and allowed her to focus on taking care of herself and her health before returning to the rigorous and intense program three years later. Caroline is now a strong supporter of mental health resource awareness – in this episode of Inspiration Dissemination she will describe some of the challenges and barriers she faced when returning to finish her degree, and some of the pushback she faced when deciding to pursue a PhD. 

“Not everyone was supportive,” she says. “I didn’t receive great encouragement from some of my advisors.”

Where she did find support and community was in her undergraduate research lab. Her work in this lab on the effects of diet and the microbiome on human health gave her the confidence to pursue graduate school, demonstrating that she was more than capable of engaging in independent research. In particular Caroline recalls her mentor Leila Shinn, a PhD student at the time in that lab, who had a profound impact on her decision to apply to graduate programs.

Tune in on Feb 27th to hear the rest of Caroline’s story and what brought her to Oregon State in particular. You can listen live at 7 PM PST on 88.7 FM Corvallis, online at https://kbvrfm.orangemedianetwork.com, or you can catch the episode after the show airs wherever you get your podcasts. 

If you are an undergraduate student or graduate student at Oregon State University and are experiencing mental health struggles, you’re not alone and there are resources to help. CAPS offers crisis counseling services as well as individual therapy and support and skill-building groups.