The bacteria living inside us and what they have to say about autism

Trillions of bacterial cells are living within us and they’re controlling your brain activity.

Grace Deitzler is a 2nd year PhD student in microbiology working in Dr. Maude David’s lab on the gut-microbiome and its relation to autism spectrum disorder.

The gut-microbiome is the total population of bacteria living within our digestive tract. These bacteria are critical for digestive health, but also for our immune system and mental health. For example, we harbor bacteria capable of digesting plant fibres we otherwise could not digest. And if you’ve been told that probiotics are good for you, that’s because probiotics can change the gut microbiome in a positive way, allowing for increased bacterial diversity associate with improved health. These bacteria communicate with each other through chemical signaling but also communicate with us. Tryptophan, for example, is an amino acid produced through bacteria metabolism and is a precursor for serotonin, a brain-signaling chemical which causes feelings of happiness.

When the gut communicates with the brain, we call this, the “gut-brain axis”. Grace’s work narrows in on the gut-brain axis and more specifically, how one bacterial species in particular impacts autism spectrum disorder. To further complicate things, the gut-microbiome helps to regulate estrogen levels, and we also know that autism is a disorder found primarily in biological males. Which leads Grace to one of her biggest questions: are the bacteria involved in endocrine system regulation in women, also that responsible for this variation we see. Grace uses a mouse model to elucidate underlying mechanisms at play.

Step one is to feed the mice bacteria that have been found in elevated amounts in people with autism spectrum disorder than in neurotypical peers. These bacteria will colonize in the gut, and mice will go through several behavioral tests to determine if they are exhibiting more behaviors associated with autism. Grace performs three types of tests with the mice: one to test inclination to form repetitive behaviors, one to test anxiety, and one to test social behaviors. One test is a marble-burying test, in which a mouse more inclined to form repetitive behaviors will bury more marbles.

After behavioral testing is complete, the mice are sacrificed and different regions of the gut are taken to look for presence of bacterium. Tissues taken from the mice are used to look for transcriptional markers. The transcriptome is collected for both the mouse and the bacteria present, or the sum total of all genes that are read and converted to RNA. RNA are able to be isolated and sequenced using distinctive markers such as a “poly-A tail”. After this data is collected, Grace can finally move to the computational side of her work which involves combining biological and biochemical data with her behavioral studies.

In addition to her work on autism spectrum disorder, Grace also has a side project working in a honey bee lab, looking at the gut microbiome of honey bees in response to probiotics on the market for beekeepers. But Grace is one very busy bee herself because in addition to her lab work, she’s also involved with an art-science club called “seminarium”. The club is filled with scientists interested in art and artists interested in science. Grace is a painter primarily but is also working on ink illustration. The focus of this group is that art and science are complimentary, not at odds. The group has produced some collaborative projects, including a performance for a lab studying a parasite that effects salmon. The group put together a collage of interpretations of the parasites and had a performance in which one member played piano while someone else drew the parasite live.

Grace moved to Oregon from St. Louis Missouri. She completed her undergraduate degree in biological sciences with minors in chemistry and psychology at a small engineering college, Missouri University of Science and Technology, where she was a radio DJ! Grace first became involved in research during a summer internship in a microbiology lab at Washington University. There she studied the vaginal microbiome and how it effects pregnancy outcomes. Grace went back to this lab for the next couple summers and produced 4 publications! Ultimately, Grace graduated college early after they offered her a full time research position where she worked for a year and a half as a research tech. Through this experience, Grace came to realize that medical school was not her path, canceled her scheduled MCAT and signed up for GRE. Grace looked for schools in the PNW because she knew she wanted to live there, got an interview at OSU, loved it, and here we are!

Join us at 7 pm on Sunday, August 11th, 2019, to hear more about Grace’s research and her journey to OSU. Stream the show live on KBVR Corvallis 88.7FM or check out the episode as a podcast after a few weeks.

Language is a barrier to diversity and inclusion in natural resources research

Language usage in natural resources research

As a 3rd year Master’s student in the Department of Forest Ecosystems & Society, Jasmine Brown is investigating diversity and inclusion in the field of natural resources. Her research has consisted of examining how language usage reinforces barriers to inclusion. For example, the usage of terms such as ‘women or minorities’ fails to capture identities that exist at the intersection of both categories. Efforts to include members of marginalized groups still fall short, as current language usage does not include people whose identities intersect multiple categories. As a Black woman working in forestry, Jasmine’s understanding and lived experience of the forestry profession is acutely different from the typical experience of a White male. Through her research, Jasmine is examining what it means to be a Black woman in forestry. Although the demographics of who is contributing to natural resources research is slowly changing, language usage in the field has remained somewhat static. Conventional language used in natural resources is not connected to the historical trauma associated with forest spaces and requires change moving forward.

Jasmine attending the Society of American Foresters 2018 National Convention in Portland as a part of their Diversity Scholars Program.

How Jasmine gathered the data

At the beginning of her project, Jasmine found that language used in natural resources research is ambiguous. She explains how in medical science, “a kneecap refers to a specific body part, and leaves no room for interpretation. However, in natural resources, the term ‘diversity,’ for example, might have multiple meanings depending on the context. It might refer to habitat diversity, biodiversity, and wildlife diversity in addition to diversity of social identities such as race, ethnicity, and gender”. Despite being excited to learn about how diversity and inclusion is discussed in natural resources, Jasmine struggled to find a comprehensive body of text to base her work on. So she ended up having to compile the sources on her own. While conducting a systematic review, she was able to develop targeted search terms to evaluate existing research about diversity and inclusion of researchers in natural resources. A systematic review is comparable to a literature review, and is a method typically used in medical and social science to collect and evaluate published research using specific criteria. The advantage of a systematic review is that it provides a method to systematically and methodically identify relevant literature.

Jasmine talking about her research while dressed in her forestry uniform at a Science Communication Event

To compile a body of literature for her systematic review, Jasmine looked for signifiers, or markers, of diversity in natural resources, such as ‘underrepresented, women, females, minorities.’ Researchers told Jasmine she would have difficulty locating articles on diversity in natural resources, but Jasmine found over 260 articles! The literature she found is a combination of published sources, including scientific journals, and unpublished sources, including magazines, presentations, conference papers, theses, and technical reports. 

By evaluating the body of literature, she has identified which research methods are most popular for investigating diversity and inclusion in natural resources. Jasmine unearthed program evaluations by practitioners in the field, consisting of a summary of their successful implementation of diversity and inclusion programs. Methods used by practitioners in the field tended to be different than methods employed by scientific researchers. She observed that the scientific methods used by natural resources researchers have changed considerably over time. She also indicated that editorials about diversity and inclusion are abundant. Although authors may be highly educated researchers, the methods used to derive conclusions in editorial pieces are casual and less rigorous than in other standardized science disciplines. 

Jasmine further investigated the institutions where authors were working, and found that the top two categories were government and academia. Then, she investigated what titles were held by the authors. Over time, position titles have become more difficult to classify. Early in the field of forestry, a researcher might be known as, ‘forester.’ Today, however, position titles are more complex and reflect hierarchical changes to the academic system. An academic title might consist of multiple categories, such as, ‘assistant professor of forestry in the department of agriculture.’ 

While authors are adept at identifying barriers to diversification, the application of ideas to increase diversity and inclusion is lagging behind. Much more work is required to improve implementation of ideas that will increase diversity and inclusion in natural resources. 

A plan for action

Jasmine is looking forward to presenting her body of work to the larger community. She intends to present her work at the 35th Minorities in Agriculture, Natural Resources and Related Sciences (MANRRS) Conference. She also intends to publish at least 1 of 2 articles from her thesis. Her dataset of more than 260 articles will be made public after her graduation. Her hope is that other researchers trying to locate published articles about diversity and inclusion in natural resources will be able to access the information she has compiled and won’t need to spend over eight months searching for it themselves. She has recognized that the interest and need for writing about diversity and inclusion is increasing, and hopes to move the field, and the language it is built upon, forward. 

Why did Jasmine want to study this topic?

As a senior undergraduate student studying forestry, Jasmine stepped out of her comfort zone and took several sociology classes about sustainability. These courses served as an illuminating accompaniment to her forestry degree, where she was introduced to forests as living ecosystems. Previously, from a forestry perspective, she was accustomed to thinking about trees in terms of their quantitative measurements and economic benefit to society. It was during this time that she became curious about how language is wielded in the forestry discipline. 

Jasmine has been working with the U.S. Forest Service for close to four years. In this environment, she recognized the importance of having difficult conversations, and it is these conversations that pushed her towards grad school for a Master’s degree. Jasmine chose OSU’s Forestry & Ecosystem because of the flexibility of the program and its relevance to her specific interests concerning the ‘human dimension’ of natural resources. She hoped to pursue research at the intersection of race, gender, and ethnicity, in part, because her identity is a part of everything she does. With this in mind, her Ethnic Studies graduate minor was a perfect fit. Jasmine has assembled an interdisciplinary team with faculty from forestry, wildlife, ethnic studies and a research librarian. She has two advisors: Brenda McComb from Forestry and Dana Sanchez from Fisheries and Wildlife. She pitched her research idea about the use of language in natural resources to her advisors, and they expressed excitement about its novelty and potential for impact. 

Jasmine in front of the Student Experience Center after participating in the 4th Social Justice Tour of Corvallis

Future direction

Jasmine’s realization that her identity as a Black woman has been a barrier does make her feel more invested in and passionate about her research. The feedback and pushback she has received during her Master’s research has informed her desire to continue in academia. Now, she identifies as both a forester and a social scientist. After completing her degree, Jasmine will pursue a PhD in a related discipline, where she will continue to drive change surrounding language usage in natural resources research. Jasmine hopes to continue inspiring youth of color to become natural resource professionals. 

Jasmine’s research has made her realize how important is it to consider previous scientific texts as data. Considering how many articles she’s been able to find, she places value on looking at the big picture. While it may not be easy to try evaluating criteria that have surely changed over time, Jasmine gladly accepts the challenge. As a budding researcher, her Master’s degree has taught her that there is much to be learned from previous trends when it comes to scientific standards and language use regarding diversity and inclusion in natural resources. 

Join us at 7 pm on Sunday, August 4th, 2019, to hear more about Jasmine’s research and her experience as a Master’s student at OSU. Stream the show live on KBVR Corvallis 88.7FM or check out the episode as a podcast after a few weeks.

Are Microplastics the New Fish Food?

Geologists have considered an entirely new geologic era as a result of the impact humans are having on the planet. Some plastic material in our oceans near Hawaii along are hot magma vents and is being cemented together with sand, shells, fishing nets and forming never before existing material — Plastiglomerates. This new rock is a geologic marker providing evidence of our impact that will last centuries. Although rocks seem inert, that same plastic material floating around our oceans is constantly being eaten, purposefully and accidentally, by ocean creatures from as small as plankton to as large as whales and we’re just beginning to understand the ubiquity of microplastics in our oceans and food webs that humans depend on.  

Our guest this evening is Katherine Lasdin, a Masters student in the Fisheries and Wildlife Department, and she has to go through extraordinary steps in her lab to measure the quantity and accumulation of plastics in fish. Her work focuses on the area off the coast of Oregon, where she is collecting black rockfish near Oregon Marine Reserves and far away from those protected areas. These Marine Reserves are “living laboratory” zones that do not allow any fishing or development so that long-term monitoring and research can occur to better understand natural ecosystems. Due to the protected nature of these zones, fish may be able to live longer lives compared to fish who are not accessing this reserve. The paradox is whether fish leading longer lives could also allow them to bioaccumulate more plastics in their system compared to fish outside these reserves. But why would fish be eating plastics in the first place? 

These are the locations of Oregon’s Marine Reserves. The sampling for juveniles and adult black rockfish is occurring at Cape Foulweather which is between the Cascade head and Otter Rock Reserves. PC:
Black rockfish are a common fish off the Oregon coast and due to their abundance it’s a great study species for this research.

Plastic bottles, straws, and fishing equipment all eventually degrade into smaller pieces. Either through photodegradation from the sun rays, by wave action physically ripping holes in bottles, or abrasion with rocks as they churn on our beaches. The bottle that was once your laundry detergent  is now a million tiny fragments, some you can see but many you cannot. And they’re not just in our oceans either. As the plastics degrade into even tinier pieces, they can become small enough that, just like dust off a farm field, these microplastics can become airborne where we breathe them in! Microplastics are as large as 5mm (about the height of a pencil eraser) and they are hoping to find them as small as 45 micrometers (about the width of a human hair). To a juvenile fish their first few meals is critical to their survival and growth, but with such a variety of sizes and colors of plastics floating in the water column it’s often mistaken for food and ingested. In addition to the plastic pieces we can see with our eyes there is a background level of plastics even in the air we breathe that we can’t see, but they could show up in our analytical observations so Katherine has a unique system to keep everything clean. 

In order to quantify the amount of plastics in fish, you have to digest some of the fish guts. PC: Katherine Lasdin

Katherine is co-advised by Dr. Susanne Brander who’s lab studies microplastics in marine ecosystems. In order to keep plastics out of their samples, they need to carefully monitor the air flow in the lab. A HEPA filtration laminar flow hood blows purified air towards samples they’re working with in the lab and pushes that clean air out into the rest of the lab. There is a multi-staged glassware washing procedure requiring multiple ethanol rinses, soap wash, deionized water rinses, a chemical solvents rinse, another ethanol, and a final combustion of the glass in a furnace at 350°C for 12-hours to get rid of any last bit of contamination. And everyday that someone in Dr. Brander’s lab works in the building they know exactly what they’re wearing; not to look cool, but to minimize any polyester clothing and maximize cotton clothing so there is even less daily contamination of plastic fibers. These steps are taken because plastics are everywhere, and Katherine is determined to find out just big the problem may be for Oregon’s fish.  

Katherine Lasdin working in the laminar flow hood that blows purified air towards the samples in Dr. Brander’s lab. PC: Cheyenne Pozar

Be sure to listen to the interview Sunday 7PM, either on the radio 88.7KBVR FM or live-stream, to learn how Katherine is conducting her research off the coast of Oregon to better understand our ocean ecosystems in the age of humans.

Listen to the podcast episode!

On this episode at the 16:00 mark we described how every time you wash clothing you will loose some microfibers; and how a different student was looking at this material under microscopes. That person is Sam Athey, a PhD student at the University of Toronto who also studies microplastics.

Perceptions of trust

Imagine a final exam for a college course with hundreds of students. The proctor, a teacher’s assistant who has not interacted with any of the students before, is walking up and down the rows. She sees motion out of the corner of her eye. A small piece of paper is on the floor, covered in tiny print–answers to questions on the exam. She asks the student in the nearest desk, if the paper is his. Should the proctor believe him?

Most of the decisions we make in day-to-day life are unconscious. We don’t make up lists of pros and cons and consult experts when we have to decide what shoe should I tie first, what foot should enter my car first, or whether to I turn on the blinker 5 seconds or 10 seconds before turning. Having to weigh the pros and cons and carefully consider the consequences of every action would be exhausting, and could even be dangerous.

Zoe Alley, PhD Candidate in Psychology at Oregon State

Deciding whether to trust a stranger, however, is not at all inconsequential. Our brains unconsciously process faces to make decisions such as whether a person is, for example, aggressive, or whether they should be trusted. Zoe Alley, a PhD candidate in Psychology at Oregon State, has spent the last three years studying how facial trustworthiness impacts adolescents and new adults.

“People around the world, from many different cultures, from many different ethnicities, tend to hone in on the same facial characteristics when deciding who they want to trust,” Zoe said. Within the first few seconds of seeing a person’s face for the first time, your brain makes judgments of that person’s aggressiveness and trustworthiness (among other traits.) These snap judgements are often inaccurate, but have appeared consistently enough in participants in psychological studies that it is thought by some to be an evolved trait. Nineteenth and early twentieth century scientists went so far as to provide expert witness at trials, describing “typical” features of criminals. Although this view is no longer considered scientific, the human tendency to attempt to draw conclusions from appearances has been measured, with often concerning results.

As Zoe explains it, it is not clear that we have control over how our brain processes faces. And conscious attempts to address these biases can lead to over-correction, which is also undesirable.

Zoe speaking at GradX 2019 at Oregon State University. The faces shown are the Oosterhof-Todorov faces: computer-generated representations of a trustworthy and an untrustworthy face.

However, knowing how the human mind makes judgments is important. “It can help us make decisions about the structure of our society,” says Zoe. She points out some troubling findings looking at the justice system and elections. A 2004 study found that among a random sample of prison inmates, after controlling for race, people with more “Afrocentric” features received harsher sentences. A study from 2007 showed people contenders for Senate and governor’s races in the US and asked them to choose the more competent candidate, making sure that participants didn’t recognize either candidate. The winner of the race was selected 72% and 68% percent of the time, respectively — a far greater success rate than expected by chance.

Zoe’s own work focuses on how people are affected by facial traits such as trustworthiness, aggressiveness, dominance, and exploitativeness. The data comes from a long running longitudinal study of about 200 boys in Oregon that started in the 1980s. Participants in the study were interviewed about once a year from adolescence into adulthood, with a special focus on understanding antisocial and deviant behaviors such as underage substance use and criminal behavior. Along with interviews, photographs of the participants were taken. However, these photographs had not yet been incorporated in any of the many studies based on the data set.

Processing the data was an enormous task. She analyzed facial structure development across 35 years of data for 200 participants. Each photo had to be considered individually, and to protect privacy she had to drive an hour to a secure facility to do the work. “I’m interested in seeing how facial characteristics develop across time, and how these characteristics alter people’s experience,” says Zoe. “Are people who look less trustworthy more likely to associate with deviant peers?”

Hear more about Zoe’s research findings and personal story this Sunday, June 9, 2019 at 7 pm on KBVR Corvallis 88.7FM. Stream the show live or catch the episode as a podcast in the coming weeks.

You can also watch Zoe’s GradX presentation here.

Micro structures and macro support

Our guest this week, Shauna Otto from the Department of Biochemistry and Biophysics, is a member of the lab of Dr. Colin Johnson. The focus of the Johnson lab is a group of proteins called ferlins. The ferlin family of proteins have many different functions, and many are involved in the fusion of vesicles to cell membranes in a process called, “exocytosis.” Another example is the protein otoferlin which fuses vesicles carrying neurotransmitters to the cell membrane of neurons in the inner ear that play a crucial role in hearing. See more about otoferlin from past guests from the Johnson lab, Murugesh Padmanarayana and Nicole Hams.

Shauna loading a sample for Cobalt-60 irradiation at the Notre Dame Radiation Laboratory.

Shauna studies dysferlin, another ferlin protein, which helps mend membrane tears in muscle cells. Mutations in the dysferlin gene lead to Muscular Dystrophy II. Through her work, Shauna has characterized portions or “domains” of the large dysferlin protein via Nuclear Magnetic Resonance (NMR). NMR is a process by which the magnetic field around the nuclei of atoms in a protein domain are excited, and by recording the magnitude of that disruption, Shauna can learn the structure of the domain. Her focus domain putatively binds other proteins that join dysferlin in a protein complex that initiates muscle cell membrane repair. However, the mechanism by which dysferlin bind repair proteins is unclear. Through her explorations with dysferlin, Shauna has found that an increase in Calcium leads to the stabilization of the dysferlin domains that might initiate repair. Right now, it is unclear if this stabilization initiates muscle cell repair, but if it does the next question is how and when such stabilization occurs.

Shauna and husband (Kris Hill) backpacking in Yosemite

Shauna’s academic journey was wrought with hardship, and we are grateful to her for being willing to share her story with us on air. Shauna started undergraduate with an interest in marine biology, but found that college is cost prohibitive. After a two year break, she went back to University of California Long Beach to major in Chemical Engineering, but finally landed on biochemistry. She had a knack for chemistry and loved solving complex puzzles in cellular biology through the lens of protein interactions and biochemical pathways. She began undergraduate research, but her work took a turn as she struggled with homelessness. Homelessness is a growing problem for college students, and has prompted bills targeting the problem of home insecurity for students in California and Washington. However, for Shauna, homelessness was not discussed among fellow students and officials when she attended school. Rather, instead of resources to alleviate her financial hardship, she was met with policy allowances such as permission to sleep in her research lab.

Shauna and her daughter in a bookshop.

Since beginning her PhD at OSU, Shauna has found support here on campus from mentors and her department who have listened and replied with support in the form of University Resources and Services to help her succeed academically, financially, and in personal wellness. Given her past, Shauna now knows the questions to ask about support when seeking the next job, and she is a resource for undergraduates and graduate students who are going through similar life experience.

Hear more about Shauna’s research and personal story this Sunday June 2, 2019 at 7 pm on KBVR Corvallis 88.7FM. Stream the show live or catch the episode as a podcast in the coming weeks.

If a fault moves at the bottom of the ocean, can anyone hear it?

A few hundred miles off the coast of Oregon, and under several miles of sea water, lies the Blanco Transform Fault. It is between the Juan de Fuca and the Gorda tectonic ridges. Ocean transform faults such as this one connect seafloor ridges and are where volcanic activity creates new oceanic crust. This fault is more seismically active than many faults on land, generating over 1,600 earthquakes in a single year (between 2012 and 2013). Did you feel anything then?

Location and tectonic setting of the Blanco Transform Fault.

Vaclav Kuna, a doctoral candidate in seismology in the College of Earth, Ocean and Atmospheric Sciences working with Dr. John Nabelek, is studying this fault—how it slips and how it moves, and whether its motion is seismic (involving an earthquake) or aseismic (slow movement without an earthquake). A collection of movements is called a seismic swarm. The hypothesis is that prior to large, seismic motions, there are small, aseismic motions. Through his research, Vaclav hopes to decipher what occurs in a swarm, and discover if there is a pattern in the fault’s motions.

The model Vaclav is working to develop of the mode of slip of the Blanco Transform Fault. We believe that slow (non-seismic) creep occurs at depth in the fault beneath the Moho and loads the shallower part of the fault. The slip at depth most likely triggers the big earthquakes, that are preceded by foreshocks associated with creep.

This is different than predicting earthquakes. As a seismologist, Vaclav is trying to understand and report on the behavior of a fault, not predict when a certain magnitude earthquake will occur. However, other researchers can use findings like Vaclav’s to create prediction models which are necessary for earthquake damage mitigation and increasing public safety during and after earthquake events.

To look for patterns in the fault’s motions, Vaclav analyzes a year’s worth of data from seismometers and pressure gauges that were deployed from a ship to the fault at the ocean floor several years ago. The seismometers measure the velocity of a fault’s movement in three directions (two horizontal and one vertical), and the pressure gauges act as microphones capturing sound waves. The data can be decomposed into a series of many waves (like sine or cosine waves). Vaclav can track these waves in the sensors deployed along this fault and determine the variability of motion in both time and space. After the sensors are finished collecting the data, a remote control turns on an electrical circuit, that triggers a corrosion reaction and severs a wire holding a large weight that is keeping the sensors at the ocean floor—which seems like something taken right out of a spy movie.

Deployment of ocean bottom seimometers (yellow packets) at the Blanco Transform Fault. Every packet includes a 3-component seismometer and a differential pressure gauge (which acts as a microphone).

So why would a researcher monitor a fault that is miles underwater when there are faults on land? Ocean transform faults are less complex than faults on land, making them desirable to study in order to answer fundamental questions about fault behavior. In addition, they are extremely seismically active and generate earthquakes more frequently than faults on land. However, ocean transform faults are evidently more difficult to observe, and because the process of planning for and conducting fieldwork is time-intensive, most of the data Vaclav uses were gathered before he was enrolled at OSU. In turn, Vaclav helps deploy sensors and gather data for future students to analyze at a number of different faults around the world.

Vaclav at a station deployment at the Kazbegi mountain, Georgia (Caucasus mountain range).

Vaclav did his Bachelor’s and Master’s degrees in Geophysics in Prague, Czech Republic. He was motivated to study Geophysics because there is a lot that is unknown about how the Earth’s tectonic plates move, and many people living near these faults. In his spare time, Vaclav likes swimming, running, skiing and kayaking. After completing his PhD, Vaclav wants to find a job working towards hazard-related mitigation to help people who are vulnerable to the damages caused by earthquake hazards.

A bird’s eye view: hindsight and foresight from long term bird surveys

The Hermit Warbler is a songbird that lives its life in two areas of the world. It spends its breeding season (late May-early July) in the coniferous forests of the Pacific Northwest (PNW) and migrates to Central America for the winter. Due to the long journey from the Central America to the PNW, it is dependent on food resources being available throughout its journey and when it arrives to breed. The environmental conditions across its range are tightly linked to habitat resources, and unfavorable climatic conditions, such as those becoming less frequent due to climate change, can negatively affect bird populations. Changes in bird populations are not always easy to notice, especially with small songbirds that live high in tree canopies. Studying birds for one or a few years may not be enough to signal the change in their well-being.

A Hermit Warbler singing on a lichen-covered branch in the forest canopy. Male Hermit Warblers will defend their territories ferociously against other males during the breeding season. H.J. Andrews Experimental Forest, May 2017.

Fortunately, long term data sets are becoming more available thanks to long term study programs. For example, the Willamette National Forest in Oregon is home to H. J. Andrews Experimental Forest (the Andrews). Designated by the USDA Forest Service Pacific Northwest Research Station, the Andrews forest hosts many forest research projects and has been monitored since 1948. In 1980, it was became one of the National Science Foundation’s Long Term Ecological Research sites ensuring that it will remain a resource for scientists for years to come. Bird surveys at the Andrews began 11 years ago, and researchers at Oregon State University are beginning to draw connections between changing climate and bird communities in relation to the forest’s structure and compositions.

H.J. Andrews Experimental Forest, where long-term bird study is launched in 2009 by Drs. Matt Betts and Sarah Frey. The forest sits on the moist foothills of western Cascades in Willamette National Forest.

One of these researchers, Hankyu Kim PhD student in the Department of Forest Ecosystems and Society, is using this data to study the Hermit Warbler and other bird species at the Andrews. Hankyu is interested in how and why bird communities are changing over time. With 11 years of bird observations and extensive temperature data, he is attempting to estimate how population of birds persist in the forests. To begin approximating how current climate effects birds, we need to have an idea about bird communities in the past. Past conditions can help us explore how birds might respond to future climate scenarios. Without the effort of many researchers before him to monitor birds, his investigation would be impossible.

Bird surveys are conducted via point counts. Researchers stand at a point count station for 10 minutes and count all bird species they see and hear. Listen to a hermit warbler and some other background birdsongs recorded at H.J Andrews in June 2017.

Hankyu realized the importance of long-term data after reviewing the 45-years of wintering waterbird surveys collected by the Birdwatching Club at Seoul National University, Korea during his time as an undergrad. The group took annual trips to the major Rivers and Coastal Areas, and in just a couple decades the members of the club had recorded declines and disappearances of some species that were once common and widespread. This finding inspired Hankyu to pursue graduate school to study unnoticed or uncharismatic species that are in danger of decline. Every species plays a critical role in the ecosystem, even if that role has not yet been discovered.

Tune in on Sunday May, 19 at 7 pm to hear more about Hankyu Kim’s research with birds. Not a local listener? Stream the show live or catch up when the podcast episode is released.

Want more about the Hermit Warblers in Oregon? Check out this video of Oregon Field Guide featuring Hankyu and some of his colleagues from Oregon State University.

This time, it actually is rocket science: computational tools for modeling combustion

A.J. Fillo is in his final year of his PhD in Mechanical Engineering in the School of Mechanical, Industrial, and Manufacturing Engineering, within the College of Engineering. Working with Dr. Kyle Niemeyer. A.J. is studying combustion, or how things burn; specifically, A.J. is working to better understand how the microscopic motion of molecules impacts the type of combustion that we use in jet engines.

From A.J.’s masters work, and an photo-art series A.J. did on combustion, Turbulent, premixed jet fuel air Bunsen burner with a fuel rich jet fuel air flame. Fuel is commercially available ‘Jet-A.’ Photo shot at 1/8000 second shutter speed and aperture of f/2.8

            To understand combustion, first it’s helpful to understand energy.  If you drop a ball at the top of a hill, it will roll to the bottom, if you place a tea bag into a hot glass of water, the flavors will move through the water until you have tea. Both of these processes take something from its high energy state, to a more stable lower energy state. In our tea cup, molecular diffusion is what moves that energy around. Diffusion is the process of molecules becoming evenly dispersed by moving from high to low concentration and happens at very small scales, and affects everything around us including the combustion that we use in jet engines.

Diffusion is only part of the story though.  In fluid mechanics, the study of how gasses and liquids move around, diffusion controls the smallest aspects of motion but what processes control motion on a larger scale? To answer that A.J. used the example of an airplane wing. In physics class, many of us have seen a drawing or a demonstration of an airplane wing with smooth streaks of air flow over it, we call those smooth air streaks streamlines.  These smooth streamlines represent something called laminar flow, which is very smooth and predictable, but fluid flows are rarely predictable, usually they are swirly, changing, and chaotic.  These chaotic flows are called turbulence and exist all around us, they cause planes to bounce around when we fly through rough air, they drive the little vortex tornado the forms when our sink drains, and they can even impact the motion, structure, and chemistry of a jet fuel flame.

2D slice of a 3D simulation results for a turbulent, premixed, n-heptane air flame looking at flame temperature. Flow is from left to right.

Both turbulence and diffusion work to move energy around in combustion, but we don’t yet have a firm understanding of how these two different processes interact to control the combustion we use to propel us through the air.

Turns out, flames are hard to study because as you can imagine, anything you would use to measure a flame, does not want to be in a flame; measurement tools like thermocouples and pressure transducers can melt, or even combust themselves.  But there is another tool at our disposal.  We can use super computers to simulate how combustion is happening in jet engines and even use it to study how turbulence and diffusion interact, or how molecules are moving around during combustion.

From A.J.’s masters work, and an photo-art series A.J. did on combustion, Turbulent, premixed jet fuel air Bunsen burner with a fuel lean jet fuel air flame. Fuel is commercially available ‘Jet-A.’ Photo shot at 1/8000 second shutter speed and aperture of f/2.8

A.J.’s research focuses on developing computational tools to look at these effects. The sum total of reactions happening during jet fuel combustion are large and complex, meaning that the equations are not easy to solve, and trying to do so can take thousands of computer cores for several days. By developing a more efficient computer algorithm to look at these reactions we can make these simulations faster, more efficient, and less expensive.

In reality, Jet fuel is a mixture of hundreds of different chemicals, so to simplify things, A.J. uses fuels like hydrogen (H2), n-heptane (H3C(CH2)5CH3), and toluene (C6H5CH3) as representative fuels. Although a single, simpler compound, even as simple as just hydrogen, has hundreds of chemical reactions and dozens of different radical molecules that form during its combustion. To get around the limitation of computer memory and speed up how quickly his simulations run, A.J. created an algorithm to optimize how the computer handles the math to make sure things run as smoothly as possible.  You can think of it a bit like going to the DMV, usually the line takes forever because people are rarely ready with their paper work in hand when they get to the front of the line, instead people must get out of line, get more paper work, and start over.  Using this analogy, A.J.’s algorithm works to make sure everyone in line arrive with their paper work completed, ready to hand off, and let the next person through. This reduces dramatically reduced the amount of computer memory needed to solve these combustion simulations and speeds up the math.

3D simulation results for a turbulent, premixed, hydrogen air flame looking at peak flame temperature colored by chemical composition. Flow is from back to front

A.J. became interested in mechanical engineering because of his love of magic. A.J. started his academic journey at the University of Missouri Columbia as a journalism major but transferred to OSU for the engineering program. A.J. has always loved performing, which is why science outreach has been such a large part of his graduate school experience. Partnered with the Corvallis Public Library, A.J. hosts LIB LAB, a hands-on multimedia educational YouTube series focused on STEAM (science, technology, engineering, arts, and mathematics) education, which he previously talked about on our GRADx event.

A.J. standing with the Oregon State University Drumline in OSU’s Reser Stadium while filming an episode of his YouTube show LIB LAB about vortex smoke rings.

To find out more about A.J.s research, outreach, and journey to grad school, join us on Sunday, May 12 at 7 PM on KBVR Corvallis 88.7 FM or stream live.

 

Improving hurricane prediction models using GPS data

GPS satellites orbiting the Earth

Exploiting a flaw in the system

GPS was originally designed for positioning, navigation, and timing (PNT) applications which measures the transmitted time of the radio signals from a satellite in the space to a receiver on the ground. But this story is not about improving GPS accuracy in navigation applications, rather it is a clever use of the GPS signal delay to collect data for monitoring the atmosphere for use in weather event predictions.

The transmitted GPS signal contains not only the range information, which is the primary factor of interest, but also error sources, such as atmospheric delay including tropospheric delay. The delay in GPS signals reaching Earth-based receivers due to the presence of water vapor is nearly proportional to the quantity of water vapor integrated along the signal path.

GPS is capable of seamless monitoring of the moisture in the atmosphere with high temporal and spatial resolution. Excellent GPS data availability enables unique opportunities for data analysis and experimental studies in GPS-meteorology.

This week’s guest, Hoda Tahami, is a third year PhD student in Dr. Jihye Park’s geomatics research group in the Department of Civil and Construction Engineering. Using geomatics – the science of gathering, storing, processing, and delivering spatially referenced information – Hoda is working to improve weather models for hurricane prediction.

GPS Meteorology: Estimating vertically integrated atmospheric water vapor, or perceptible water, from Global Positioning System (GPS) radio signals collected by a regional network of ground-based geodetic GPS receiver.

Using GPS signal data for hurricane prediction

Data from Hurricane Matthew that hit Florida in 2016 has been used to explore the idea of using GPS data to predict the path and intensity of hurricanes. “I found a clear correlation between [signal delay] and other atmospheric variables, like temperature, precipitation, and water vapor,” says Hoda. This information can be used for weather models, which rely on quality observational data. Weather models are computer programs that apply physics to observations to make predictions. The set of observations forming the starting point for the model simulation are called the initial conditions. Hoda hopes that this new set of data can be used as an initial condition for existing atmospheric models.

This new set of GPS-based data provides an increase in temporal and spatial resolution. While many satellite data sources provided data every few hours or even just once or twice a day, Hoda explains, “The time scale in my data is in seconds. We average it to five minutes, then use it to make one to twenty-four hour predictions.” This new set of data can be used to complement existing data sets – each with their own caveats – used by agencies like the National Hurricane Service, National Oceanic and Atmospheric Administration (NOAA), and the National Weather Service.

More information about the proposed model can be found at: https://www.ion.org/publications/abstract.cfm?articleID=15074

Hoda Tahami with her poster at the Graduate Research Showcase at Oregon State University

Finding a love for geospatial research

Hoda began her career in civil engineering with a bachelor’s degree at K. N. Toosi University of Technology in Tehran, Iran. This was Hoda’s first experience with geospatial data and geographic information systems (GIS), which piqued her interest and led her to pursue a Master’s degree specializing in GIS. Due to the state-of-the-art geospatial research resources available, Hoda chose to pursue her doctorate degree at Oregon State.

Join us on Sunday, May 5 at 7 PM on KBVR Corvallis 88.7 FM or stream live to learn more about Hoda’s geospatial research and journey to graduate school.

Repair, don’t replace: developing a new treatment for lower back pain

Chances are that you, or someone you know, has had lower back pain get in the way of daily life. For some people it is merely an inconvenience, but for many, it is debilitating. In the United States, over 70% of adults suffer from back pain at some time during their lives. Lower back pain is the second-most common reason for missed work, after the common cold. Lost productivity due to lower back pain is estimated to be over $30 billion dollars annually.

Out of the myriad causes of lower back pain, one of the most common is degeneration of the intervertebral disk. The intervertebral disk is like a shock absorber between bones in the spine. As people age, wear-and-tear on these disks leads to damage: essentially only children have intervertebral disks without any signs of deterioration. By middle age, lower back pain is sometimes bad enough that people resort to invasive surgeries.

Ward presenting his research at the Graduate Research Showcase, 2019.

Ward Shalash, a first-year PhD student studying bioengineering with Dr. Morgan Giers, is working to find a better way to treat deteriorated intervertebral disks. Currently, the primary method for treating severe back pain caused by a deteriorated intervertebral disk is to either replace the disk with an artificial disk, or to remove the disk and fuse the neighboring vertebra. Although these methods are effective in relieving pain, patients often need to have the procedure redone after ten years. In addition, particularly for the method where vertebra are fused, patients experience loss of flexibility. In 2003 a new method, cell replacement therapy, was demonstrated on a rabbit. This treatment involves collecting mesenchymal stem cells from a patient (generally from fat cells), and injecting them into the gel-like material in the center of the intervertebral disk. Ideally, this process allows the disk to be restored in place. While this treatment has been applied with some success to human patients, the procedure is not yet standardized or tested well enough for FDA approval in the US. In particular it isn’t yet clear how to determine the number of cells to inject for best results.

This is where Ward’s research comes in. “The goal is to develop a method so that doctors can know whether cell replacement therapy will work for patients or not,” said Ward. An intervertebral disk consists of three main parts: the nucleous puplosus, a jelly-like substance in the center; the anulus fibrosus, stiff, fibrous walls around the jelly center; and cartilage endplates above and below.

Cross-section of an intervertebral disk. As the disk deteriorates, the gel-like nucleus pulposus leaks into the fibers of the anulus fibrosus.

Cells require a supply of nutrients to survive; as there is no blood flow into the disk, cells inside rely on water seeping through the cartilage endplates. Dissolved in the water are nutrients such as glucose and oxygen which are vital for cell survival.

Ward uses a combination of MRI imaging and mathematical modeling to study the flow of water through the intervertebral disk. From this information, he hopes to find a method doctors can use to determine the number of stem cells to inject. Ward hopes that the ability to algorithmically predict the success of treatment this way would cut down the cost of clinical trials.

Ward’s parents at the commencement ceremony in 2018. As a first-generation college student Ward mentions that his family’s support was important for him to continue his education towards a PhD degree.

Ward first came to Oregon as an exchange student from Israel. After finishing an associate’s degree at Portland Community College, he came to Oregon State to study bioengineering. He has a dream of a world where people don’t have to worry about injuries. One of his concerns is making sure that progress in bioengineering is ethical.  For example, says Ward, “How do you make sure that it’s accessible for all kinds of people?”

Along with his academic pursuits, Ward enjoys the outdoors, playing the oud, and volunteering. To hear more about Ward’s story and his science, tune in this Sunday at 7PM (PST). You can stream the show live online, or listen to the interview live on the air at 88.7 KBVR FM, Corvallis. If you miss the broadcast, you can also listen to the episode on our podcast soon after the broadcast.

In the background is Mt. Broken Top in the Deschutes Basin. Despite common belief that PhD degrees are scary and stressful, Ward believes that there is always time for adventures!

 

References:
Summary of stem cell treatment for back pain: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3347696/
Discussion of current strategies for treatment of lower back pain: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5651638/