Tag Archives: Oregon State University

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 9^th 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.

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!

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!

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 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.

Red, Red, (smoky) Wine

Did you know humans have the ability to “taste” through smelling? Well we do, and it is through a process called retronasal olfaction. This fancy sounding term is just some of the ways that food scientists, such as our guest speaker this week, recent M.S. graduate and soon to be Ph.D. student, Jenna Fryer studies how flavors, or tastes through smell, are understood and what impact external factors have on them. Specifically, Fryer looks at the ways fires affect the flavors of wine, a particularly timely area of research due to the recent wave of devastating wildfires in Oregon.

Having always been interested in food science, Fryer examines the ways smoke penetrates wine grapes. She does this by studying the ways people taste the smoke and how they can best rid the smokiness in their mouths, because spoiler, it has a pretty negative impact on the flavor. This research has forced her to develop novel ways to explain and standardize certain flavors, such as ashiness and mixed berry, as well as learn what compounds are the best palate cleansers. She will continue this research with her Ph.D. where she plans to figure out what compounds make that smoky flavor, and how best to predict which wines will taste like smoke in the future.

Through this work, Fryer has made some fascinating discoveries, such as how many people can actually detect the smoke flavor (because not everyone can), how best to create an ashy flavor (hint, it has to do with a restaurant in the UK and leeks), why red wine is more affected by smoke than white wines, and what the difference is between flavor and taste.

Tune in live at 7pm on Sunday April 24th or listen to this episode anywhere you get your podcasts to learn about Fryer’s research!

And, if you are interested in being a part of a future wine study (and who wouldn’t want to get paid to taste wine), click on this link to sign up!

I, Roboethicist

This week we have Colin Shea-Blymyer, a PhD student from OSU’s new AI program in the departments of Electrical Engineering and Computer Science, joining us to talk about coding computer ethics. Advancements in artificial intelligence (AI) are exploding, and while many of us are excited for a world where our Roomba’s evolve into Rosie’s (á la The Jetsons) – some of these technological advancements require grappling with ethical dilemmas. Determining how these AI technologies should make their decisions is a question that simply can’t be answered, and is best left to be debated by the spirits of John Stewart Mill and Immanual Kant. However, as a society, we are in dire need of a way to communicate ethics in a language that machines can understand – and this is exactly what Colin is developing.

Making An Impact: why coding computer ethics matters

A lot of AI is developed through machine learning – a process where software becomes more accurate without being explicitly told to do so. One example of this is through image recognition softwares. By feeding these algorithms with more and more photos of a cat – it will get better at recognizing what is and isn’t a cat. However, these algorithms are not perfect. How will the program treat a stuffed animal of a cat? How will it categorize the image of a cat on a t-shirt? When the stakes are low, like in image recognition, these errors may not matter as much. But for some technology being correct most of the time isn’t sufficient. We would simply not accept a pace-maker that operates correctly most of the time, or a plane that doesn’t crash into the mountains with just 95% certainty. Technologies that require a higher precision for safety also require a different approach to developing that software, and many applications of AI will require high safety standards – such as with self-driving cars or nursing robots. This means society is in need of a language to communicate with the AI in a way that it can understand ethics precisely, and with 100% accuracy.
The Trolley Problem is a famous ethical dilemma that asks: if you are driving a trolley and see that it is going to hit and kill five pedestrians, but you could pull a lever to reroute the trolley to instead hit and kill one pedestrian – would you do it? While it seems obvious that we want our self-driving cars to not hit pedestrians, what is less obvious is what the car should do when it doesn’t have a choice but to hit and kill a pedestrian or to drive off a cliff killing the driver. Although Colin isn’t tackling the impossible feat of solving these ethical dilemmas, he is developing the language we need to communicate ethics to AI with the accuracy that we can’t achieve from machine learning. So who does decide how these robots will respond to ethical quandaries? While not part of Colin’s research, he believes this is best left answered by the communities the technologies will serve.

Colin doing a logical proof on a whiteboard with a 1/10 scale autonomous vehicle in the foreground.

The ArchIve: a (brief) history of AI

AI had its first wave in the 70’s, when it was thought that logic systems (a way of communicating directly with computers) would run AI. They also created perceptrons which try to mimic a neuron in a brain to put data into binary classes, but more importantly, has a very cool name. Perceptron! It sounds like a Spider-Man villain. However, logic and perceptrons turned out to not be particularly effective. There are a seemingly infinite number of possibilities and variables in the world, making it challenging to create a comprehensive code. Further, when AI has an incomprehensive code, it has the potential to enter a world it doesn’t know could even exist – and then it EXPLODES! Kind of. It enters a state known as the Principle of Explosion, where everything becomes true and chaos ensues. These challenges with using logic to develop AI led to the first “AI winter”. A highly relatable moment in history given the number of times I stop working and take a nap because a problem is too challenging.

The second wave of AI blew up in the 80’s/90’s with the development of machine learning methods and in the mid-2000’s it really took off due to software that can handle matrix conversions rapidly. (And if that doesn’t mean anything to you, that’s okay. Just know that it basically means speedy complicated math could be achieved via computers). Additionally, high computational power means revisiting the first methods of the 70’s, and could string perceptrons together to form a neural network – moving from binary categorization to complex recognition.

A bIography: Colin’s road to coding computer ethics

During his undergrad at Virginia Tech studying computer science, Colin ran into an ArachnId that left him bitten by a philosophy bug. This led to one of many philosophical dilemmas he’d enjoy grappling with: whether to focus his studies on computer science or philosophy? And after reading I, Robot answered that question with a “yes”, finding a kindred spirit in the robopsychologist in the novel. This led to a future of combining computer science with philosophy and ethics: from his Master’s program where he weaved computer science into his philosophy lab’s research to his current project developing a language to communicate ethics to machines with his advisor Hassam Abbas. However, throughout his journey, Colin has become less of a robopsychologist and more of a roboethicist.

Want more information on coding computer ethics? Us too. Be sure to listen live on Sunday, April 17th at 7PM on 88.7FM, or download the podcast if you missed it. Want to stay up to date with the world of roboethics? Find more from Colin at https://web.engr.oregonstate.edu/~sheablyc/.

Colin Shea-Blymyer: PhD student of computer science and artificial intelligence at Oregon State University

This post was written by Bryan Lynn.

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.

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.