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/

 

 

Environmental planning in an age of human-animal interactions

Many people enjoy their time visiting wildlands whether it means hiking, birding, or searching for exotic mushrooms, but as more people visit the outdoors there are more and more layers of expected uses for a single patch of forest. Since a 1960 Congressional act, National Forests have been designated multi-use which includes managing the land for “outdoor recreation, range, timber, watershed, and wildlife and fish purposes.” Hikers and bird-enthusiasts may have overlapping expectations of calm and serenity when stepping foot on the trailhead, but that’s a far cry from what a mountain biker wants out of a trail system where speed and steepness are prioritized. Additionally, there are demands for timber production vital to rural community survival and finding recreational areas for hunting and fishing. With all these expected uses, there is no doubt there will be conflicts. The vexing questions that simmer for land managers is understanding where on the landscape federal dollars can be utilized for maximum public good.

The way we’ve approached that question has changed over time. In the past, these management decisions were answered with a pure ecological understanding of the area such as: which soils can support mushrooms growth, or what trees species can support a bird species of interest. Making decisions completely within the ecological framework could miss the fact that the local community prioritizes river access because of its strength as a tourism hub for whitewater rafting, for example. Instead of spending money on a bird exploration trail they may prioritize the repair of a boat ramp or a wildfire prevention treatment around a heavily used section of river that is susceptible to summer fires. The latter two options are likely to have much stronger public support, gain local advocates in the process and, in the long run, make it possible to expand the range of successful recreational programs. Those ideas are examples of an idea where the ecology of the land and the social factors are taken into account to better focus management decisions in a process called Human Ecology Mapping.

Jackie Delie and brother, Anthony Delie, exploring the Great Bear Rainforest, British Columbia Canada

If we can take into account the ecological factors of the area that bracket what is physically possible on the land and better understand the priorities of the local community, then land managers can make more informed decisions that are less likely to result in user conflicts and are more likely to create long-term positive impacts on the relationships humans have with the land. Our guest is Jackie Delie a Masters student in the Department of Fisheries and Wildlife who is using the Human Ecology Mapping technique in a more visceral relationship: human and black bear interactions in Oregon. Jackie is advised by Dr. Kelly Biedenweg, a social scientist, who previously had another student exploring social spatial data for sustainable management in the Hood Canal between Oregon and Washington. This study suggested that this is a method that can yield positive results across a variety of user groups.

Black bear sighting on the river bank in the Great Bear Rainforest, British Columbia Canada

Furry and curious or big and scary? Your immediate thoughts about black bears is likely related to your previous experiences with them. If you’ve seen bears napping in the sun from behind a glass enclosure at a zoo, you probably think they’re gentle giants. If you’re chasing bears out of your backyard while they scatter trash across your front lawn every week, you probably have different feelings. You may expect the more you are exposed to bears the more you know about them; however, what kind of exposure is critical to your feeling about bears. If you’re a hunter or hiker, you likely have very positive experiences with bears compared to a homeowner nestled in the wildland urban interface but does not recreate in the forest. Jackie is leveraging the spatial GPS data of black bears killed over the past decade, as reported from the Oregon Department of Fisheries and Wildlife, and examining how the cluster of those points relate to how people use the landscape and their experiences and values.

Jackie Delie checking on camera trap cameras in black bear habitat on the urban-wildlife fringe in King County, Washington

This is the first study of its kind that looks at the human dimensions of human and black bear interactions in Oregon, as Oregon is one of the few places that mandate GPS points be recorded for black bear kills. Jackie collected in-person interviews at 18 different trailheads throughout Oregon asking participants a variety of questions. One of them is to physically draw where in Oregon they use the landscape and for what use –  hiking, hunting, rafting, or another activity.  Using both spatial and social datasets she may begin to elucidate not only where there are overlapping user areas, but how those areas may influence the human perceptions of black bears in the environment. The larger goal of Jackie’s project is to help inform the management plan through the Oregon Department Fish and Wildlife so they can make better decisions on where to prioritize resources on the landscape to better understand why human opinions differ about black bears.

Jackie Delie conducting research in the Panama rainforest on the behavior of mantled howler monkeys (Alouatta palliata) or you can say solo research time in the Panama rainforest

Merging two (somewhat) disparate fields of science is rare for a graduate degree, but knowing Jackie’s road to graduate school makes it seem rather natural. She conducted her undergraduate degree in Switzerland doing countless endeavors from Australia to Kenya learning about new foods, cultures, and sciences. After many travels and internships, she knew she wanted to purse graduate school. It was almost one year from the first time Jackie contacted her advisor until she became a student here at Oregon State.

Be sure to listen to the interview Sunday 7PM, either on the radio 88.7KBVR FM or live-stream, to learn how a holistic approach to land management can ensure a more successful project outcome, and how Jackie traveled the world and ended up back in the Pacific Northwest, an area she calls home.

Dr. Biedenweg Research Website

Jackie Delie’s Website

 

Zebrafish sentinels: studying the effects of cadmium on biology and behavior

Cadmium exposure is on the rise

There’s a good chance you might have touched cadmium today. A heavy metal semi-conductor used in industrial manufacturing, cadmium is found in batteries and in some types of solar panels. Fertilizers and soil also contain cadmium because it is present in small levels in the Earth’s crust. The amount of cadmium in the environment is increasing because of improper disposal of cell phone batteries, contaminating groundwater and soil. This is a problem that impacts people all over the world, particularly in developing countries.

Plants take up cadmium from the soil, which is how exposure through food can occur. Leafy greens like spinach and lettuce can contain high levels of cadmium. From the soil, cadmium can leach into groundwater, contaminating the water supply. Cadmium is also found in a variety of other foods, including chocolate, grains and shellfish, as well as drinking water.

Cadmium has a long half-life, reaching decades, which means that any cadmium you are exposed to will persist in your body for a long time. Once in the body, cadmium ends up in the eyes or can displace minerals with similar chemical properties, such as zinc, copper, iron, and calcium. Displacement can cause grave effects related to the metabolism of those minerals. Cadmium accumulation in the eyes is linked to age-related macular degeneration, and for people in the military and children, elevated cadmium is linked to psychosocial and neurological disorders.

Read more about cadmium in the food supply:



Using zebrafish to study the effects of cadmium

Delia Shelton, a National Science Foundation post-doctoral fellow in the Department of Environmental and Molecular Toxicology, uses zebrafish to investigate how cadmium exposure in an individual affects the behavior of the group. Exposing a few individuals to cadmium changes how the group interacts and modifies their response to novel stimuli and environmental landmarks, such as plants. For example, poor vision in a leader might lead a group closer to predators, resulting in the group being more vulnerable to predation.

Zebrafish

As part of her post-doctoral research, Delia is asking questions about animal behavior in groups: how does a zebrafish become a leader, how do sick zebrafish influence group behavior, and what are the traits of individuals occupying different social roles? These specific questions are born from larger inquiries about what factors lead to individual animals wielding inordinately large influence on a group’s social dynamic. Can we engineer groups that are resilient to anthropogenic influences on the environment and climate change?

Zebrafish

Zebrafish are commonly used in biomedical research because they share greater than 75% similarity with the human genome. Because zebrafish are closely related to humans, we can learn about human biology by studying biological processes in zebrafish. Zebrafish act as a monitoring system for studying the effects of compounds and pollution on development. It is possible to manipulate their vision, olfactory system, level of gene expression, size, and aggression level to study the effects of pollutants, drugs, or diseases. As an added benefit, zebrafish are small and adapt easily to lab conditions. Interestingly, zebrafish are transparent, so they are great for imaging. Zebrafish have the phenomenal ability to regenerate their fins, heart and brain. What has Delia found? Zebrafish exposed to cadmium are bolder and tend to be attracted more to novel stimuli, and they have heightened aggression.

Read more about zebrafish:

ZFIN- Zebrafish Information Network – https://zfin.org/
Zebrafish International Research Center in Eugene Or – http://zebrafish.org/home/guide.php



What led Delia to study cadmium toxicity in zebrafish?

As a child, Delia was fascinated by animals and wanted to understand why they do the things they do. As an undergrad, she enjoyed research and pursued internships at Merck pharmaceutical, a zoo consortium, and Indiana University where she worked with Siamese fighting fish. She became intrigued by social behavior, social roles, and leadership. Delia studied the effects of cadmium in grad school at Indiana University, and decided to delve into this area of research further.

Delia began her post-doctoral work after she finished her PhD in 2016. She was awarded an NSF Postdoctoral Fellowship to complete a tri-institute collaboration: Oregon State University, Leibniz Institute for Freshwater Ecology and Inland Fisheries in Berlin, Germany, and University of Windsor in Windsor, Ontario. She selected the advisors she wanted to work with by visiting labs and interviewing past students. She wanted to find advisors she would work well with and who would help her to accomplish her goals. Delia also outlined specific goals heading into her post-doc about what she wanted to accomplish: publish papers, identify collaborators, expand her funding portfolio, learn about research institutes, and figure out if she wanted to stay in academia.

Research commercialization and future endeavors

During her time at OSU, Delia developed a novel assay to screen multiple aspects of vision, and saw an opportunity to explore commercialization of the assay. She was awarded a grant through the NSF Innovation Corps and has worked closely with OSU Accelerator to pursue commercialization of her assay. Delia is now wrapping up her post-doc, and in the fall, she will begin a tenure track faculty position at University of Tennessee in the Department of Psychology, where she will be directing her lab, Environmental Psychology Innovation Center (E.P.I.C) and teaching! She is actively recruiting graduate students, postdocs, and other ethnusiatic individuals to join her at EPIC.

Please join us tonight as we speak with Delia about her research and navigation of the transition from PhD student to post-doc and onwards to faculty. We will be talking to her about her experience applying for the NSF Postdoctoral Fellowship, how she selected the labs she wanted to join as a post-doc, and her experience working and traveling in India to collect zebrafish samples.

Tune in to KBVR Corvallis 88.7 FM or stream the show live on Sunday, April 7th at 7 PM. You can also listen to the episode on our podcast.

Magnet blocks, connect the dots, and the world of modern mathematics

At the Mathematical Sciences Research Institute in Berkely, CA with the Klein quartic sculpture. Photo by Charles Camacho

Charles Camacho, a sixth-year PhD student in the Department of Mathematics at Oregon State University, spends a lot of time thinking about shapes. He describes his research as such: “I study the symmetries of abstract mathematical surfaces made from gluing triangles together.”

Charles explaining his thesis research at the Latinx in the Mathematical Sciences conference at UCLA. Photo by Farida Saleh from the Daily Bruin.

Charles works in a branch of mathematics called topology. Topologists think about shapes and surfaces. There’s a joke among mathematicians that a topologist is someone who can’t tell the difference between a coffee cup and a donut, and there’s some truth to that. It’s not that they can’t see a difference, but that they look past the difference to see the core similarity: both are solid objects punctured with a single hole. Topology as a formal area of mathematics is fairly recent (early 20th century). Topology’s roots go much further back, though, through the streets of Königsberg in the 1700s and to the geometry of the ancient Greeks.

Königsberg bridge problem
There’s a famous puzzle that originated in  Königsberg, Prussia in the 1700s (Königsberg is now Kaliningrad, Russia). The puzzle didn’t originate among mathematicians—but my understanding is that it’s mainly mathematicians that think about the puzzle now. Back then, there were seven bridges crossing the river Preger.

The Bridges of Königsberg (illustration by Leonard Euler, 1736).

The puzzle is this: Is it possible to cross each one of the seven bridges exactly once? (Go on, try it!) In his description of the problem and its solution, Euler said “it neither required the determination of quantities, nor did calculation with quantities help towards its solution.” He was interested in solving this superficially trivial problem because he couldn’t see a way for algebra, counting, or geometry to solve it. This goes against most people’s conception of mathematics—can it really be a math problem if you don’t fill a chalkboard with calculations?

The fact that no one yet had found a way to cross all the bridges without a repeat did not prove that it could not be done. To do that, and thus solve the problem for good, Euler had the insight to try and reduce the problem to its core. Reframing the Königsberg Bridges problem (elements of image from Wikimedia Commons, composited graphic by Daniel Watkins)
Knowing the layout of the city and all of its streets is irrelevant, so we can simplify to a map of just bridges. But even knowing that there is a river and land doesn’t really matter. All we really need is to know is represented in the network on the right (what mathematicians today call a graph). Euler’s solution was this: “If there are more than two regions with an odd number of bridges leading into them, then it can safely be stated that there is no such crossing.” It didn’t matter where the bridges were, it just mattered how many of the possible paths led to each landmass.

With collaborators at a summer research workshop on graph theory. Photo copyright American Mathematical Society

Being a mathematician, Euler wasn’t satisfied just stating a solution to the Königsberg problem. He went further, and generalized: he came up with rules and a solution that would work for any city with any number of bridges. All you have to do is look at the crossings, and note whether there’s an odd number of ways to get there, or an even number of ways. Euler’s method was developed by later mathematicians into graph theory, a branch of mathematics focusing on sets of points and the paths connecting them. Graph theory has a reputation for having many problems that are simple to state, but incredibly difficult to solve conclusively. In this sense, graph theory has a lot in common with geometric toy blocks.

Platonic solids
Charles has a set of magnetic toys in familiar shapes: triangles, squares, pentagons. These shapes are known as regular polygons, which just means that they are shapes composed of straight lines, each of which has the same length. Playing with these, one can hardly help but to arrange them into three-dimensional shapes. Playing with the triangles, you can quickly form a triangular pyramid: a tetrahedron. With six squares, a cube. With eight triangles, an octahedron. And with twelve pentagons, a dodecahedron. Surprisingly, there are only five shapes that can be made this way! Why is this the case? And must this always be the case?

The Platonic Solids: Tetrahedron, Cube, Octahedron, Dodecahedron, Icosahedron. Image copyright Daniel Watkins.

You might notice some other interesting things about these shapes. If you turn a cube while holding the middle of a side, you will see that it looks the same after each turn. It has rotational symmetry. Each of these shapes has multiple axis of symmetry. They can be rotated holding them in different ways and still show symmetry.

As a mathematician, Charles thinks about ways to generalize these ideas. We know that the five Platonic shapes are the only solids that can be formed from regular polygons, but what shapes could be formed if you used slightly different definitions? What if, for example, you used arcs of a circle to form the lines? What can we say about different kinds of surfaces? These shapes are defined on flat planes, like a piece of paper, but we know of lots of other surfaces, like the world we live on, that aren’t perfectly flat.  What kind of symmetry do polygons in these geometries show? “Specifically, I wanted to know all the ways that such surfaces can be rotated a given number of times. I generalized previous research on counting symmetries and discovered a formula describing the number of these rotational symmetries,” Charles said.

A topological representation of a four-holed surface with a twelve-fold rotational symmetry (blue arrows indicate which edges are to be glued to make the surface. Graphic copyright Charles Camacho

Tune in to KBVR Corvallis 88.7 FM on Sunday March, 10 at 7 PM to hear more about Charles’s research, his inspirations, and his path to research in mathematics. Stream the show live or catch this episode as a podcast.

Being the Multilingual, Racialized “Other” in an English Dominated Linguistic Landscape

Jason at the whiteboard

Consider the language and messages you process each day. As you navigate your daily routine, what language do you hear and see most frequently? For folks living in the Corvallis, Oregon, the answer is probably English. In the last month, how many times, when, and where have you been exposed to spoken words or even signs in another language? For those of us on the Oregon State University campus, you could easily overhear or may participate in a conversation in Spanish, Chinese, or Arabic in the Memorial Union or Valley Library. How does the “linguistic landscape” (written or spoken words you encounter in life) affect you? What do you feel and how do you react to hearing a language you don’t understand? Have you been told that you don’t speak English well enough?

Shenanigans in Portland with Pat

Jason Sarkozi-Forfinski, a PhD student in Anthropology, wants to gain insight into the linguistic landscape students at Oregon State University are exposed to and their actions and feelings about about it, especially for students from non-English speaking countries. Jason’s research involves interviewing students and community members about their experiences in the US such as:

  • How do Thai-speaking folks fair when practicing English with a non-American accent?
  • How does a (white) American- English speaker from Roseburg regard different accents?
  • How do Mandarin speakers from Malaysia react to others speaking English with different accents?
  • How does an Arabic speaker from the Gulf region perceive their own accent?
  • How comfortable do Japanese speakers feel speaking a language other than English in the US?
  • How is all of this connected to the institutionalized tool of racism?

Jason has found that folks have preferences or biases about their linguistic landscape. Oregon State recruits both students from around the world and a large multilingual community of more local students. His respondents have reported being discouraged from speaking in a non-English language or facing negative social and professional consequences for speaking other languages or English with a non-(white)American accent. Could a preference for English with a (white) American accent perpetuate division? Or even bigoted practices?

Jason’s current research developed from years of conversations with friends and colleagues about being multilingual in the US. He began exploring language in his undergraduate education where he majored in Spanish and also studied Portuguese. He also studied English in Miami,

Grilled cheese on a school bus in Portland with Veronica (left) and husband, Nick.

Florida, and worked to understand how non-English languages influences local English. Before coming to OSU for his PhD, Jason has worked as a Spanish and English instructor in the US, Spain, Japan, and China.

Tune in to KBVR Corvallis 88.7 FM on Sunday March, 10 at 7 PM to hear more about Jason’s research and his path to graduate school. Stream the show live or catch this episode as a podcast.

Clarification [See Podcast at 25:45]: Asking someone to change their accent, according to Lippi-Green a linguistic who wrote “Speaking with an Accent,” is like asking someone to change their height. It’s doable (with lots of surgery) but would require a lot of intervention. The point here is that it’s not realistic to ask someone to work on their accent. It’s also rather demeaning.