Author Archives: Lillian Padgitt-Cobb

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.

Exploring immigrant identity through poetry

As a 2nd year MFA student in the School of Writing, Literature, and Film, Tatiana Dolgushina is writing her history through poetry as a way to understand herself and the country she came from that no longer exists. Born in Soviet Russia, Tatiana and her family fled the country after it collapsed in 1991. Tatiana grew up in South America and came to the US when she was 12, settling in Ohio. She remarks, “so much cultural history of Soviet Russia is influencing who I am today.” Central to her work are ideas of identity formation and childhood displacement. Through writing, she is digging deeper into her experience as an immigrant growing up in multiple countries.

To better understand the root of her identity, Tatiana is reading about the history that led to the dissolution of Soviet Russia. Reading about the history has helped her to understand the events that led to her family’s displacement. She grew up with silence surrounding why they had left, explaining, “Soviet culture is based on a fear of talking about historical events.” She reflects on feeling shame associated with being an immigrant, and in “not belonging to the old place or the new place.” A fractured in-between place. “As a kid, when you’re displaced, you lose so much: language, traditions, and culture.” She further explains, “you seek assimilation as a kid, and either forget these things, or push them away.”

Tatiana explains that poetry is a catalyst for understanding herself and more broadly, for us to understand ourselves as humans. It’s about connecting the dots. Her family doesn’t speak about what transpired. But reading the history, it begins to make sense. “When you’re a kid, you’re focused on survival.” She reflects that she has been trying to compensate for certain things, and is now understanding how and why she is different. She realized, “the older I get, the more I feel it, my immigrant self emerging.” Her experience growing up in multiple countries has contributed to her identity formation, but she admits that she doesn’t have a space to talk about it. “I blend in, but still feel like an outsider. I am not of this culture, and I realize that I really have no home because my home is not a country.”

Tatiana is still trying to figure out what her writing is about, but articulates that writing is a process of not being able to say certain things in the beginning. It’s about writing through the memory and being able to see the things you need to see when you’re ready, peeling away each layer of experience. Approaching the writing process linearly, Tatiana began writing about early memories, then proceeded beyond to older memories, asking, for example, “why did I write about that nightmare I had when I was 4 years old?”

Originally trained as a wildlife biologist, Tatiana decided to change directions after spending time pursuing a Master’s degree. When she initially began the MFA program, she was shocked at the discussion of subjective ideas, which is so different from many areas of scientific discourse. In science, the focus is not so much on identity. But, she explains, “science and art are coming from the same place. It’s about observation, and understanding through observation.”

As a personal goal, Tatiana is working towards publishing a book. It has been something she has wanted to do for many years. “The hope is that a 15 year old immigrant kid in the library will read it and be able to relate to my story.”

Tatiana studies with Dr. Karen Holmberg and will be graduating this Spring. Tune in on Sunday, February 3rd at 7pm on KBVR 88.7 FM to hear more from Tatiana about her thesis work and experience as a graduate student at OSU. You can also stream the show or download our podcast on iTunes!

Exploring the disconnect between humans and the ocean

Unseen associations

We are all connected to the ocean, and organisms living in the ocean are an integral – if often unseen – part of our lives. You might be more connected to the ocean than you think. For example, fertilizer used to grow vegetables is often made from fish, and ingredients derived from fish are often added to processed foods. And amazingly, the ocean produces more than half of the oxygen on the planet, while also being responsible for storing 50 times more carbon dioxide than is found in the atmosphere.

The impact of human activity can be observed in a variety of ways. Run-off from agriculture empties into fragile marine ecosystems, and plastic accumulates in the ocean and cycles back into our food supply, for example. Consequences of human activity disturb a precarious balance that is not fully understood. Within the American mind, there is a fractured connection to the ocean, and it is this disconnect that Samm Newton is studying. As a 3rd year Master’s student in the Environmental Arts and Humanities program in the College of Liberal Arts, she is exploring multiple questions as part of her thesis. What has been the role of science and technology in how we have known the ocean? What has been the relationship between that knowledge and how we have valued and made decisions about marine systems? And, how can scholars approach the study of these relationships in new ways?

Scientific inquiry is a tangled knot: the direction of research is often decided based on narrow criteria

Scientific funding agencies have often determined the direction of research based on the priorities of a moment in time. Some priorities arose from crises, while others might have been derived from a perceived risk to lives in human or animal communities. Other priorities were influenced by what types of technology and datasets were available. Within that structure, it has been difficult for science to be innovative if it doesn’t address a problem that has been classified as relevant by funding authorities. Samm explains further, “we have taken the environment, deconstructed its components, and focused only on certain aspects that we deemed interesting at a given moment, while the rest of the pieces slid into the background.”

Samm studies the ocean using methods traditionally associated with the humanities. She describes her method as an interdisciplinary approach to unpack how we have generated knowledge about the ocean through science. Her approach includes extracting information from scientific history and papers, archives, oral histories, as well as popular literature from sources like National Geographic and the Washington Post.

Different ways to think about our connection with the ocean

How can we encourage people to recognize their connection to the ocean, and direct their attention to how their lives are impacted by ocean issues? Samm indicates how advancements in technology and media have created new ways for people to access scientific knowledge about the ocean. With outlets such as Nautilus live, people can learn about ocean ecosystems by watching videos of organisms living in the sea. They can also interact with scientists in real time (check out this one about a large number of octopus brooding near Monterey Bay, CA. Science videos on the internet have become an engaging and popular way to share knowledge of the ocean and science with a broad audience.

“The ocean is very special to me.”

Samm grew up in the “shadow of the petrochemical industry” in Freeport, Texas, where the sea is brown, and air and water pollution are an everyday reality. Observing these anthropogenic forces impacting her coast and community, and how disconnected people seem to be from the ocean, led her to question the relationship between humans and marine environments. She found that science and technology have played a dominant role in how we have known the ocean—and possibly how we have valued it. Samm also found that methods from the humanities, particularly marine environmental history, as well as science and technology studies, provide a meaningful framework to examine that relationship further.

During her undergrad, Samm studied psychology and behavioral neuroendocrinology, with a focus toward consciousness and philosophy of the mind. She spent 10 years working outside of academia before pursuing a Master’s degree at OSU. Samm credits the Environmental Arts and Humanities program at OSU with providing a flexible framework for people from different backgrounds – including art and science – to decide how they want to study a topic of interest.

After finishing her Master’s degree, Samm plans to pursue a PhD in an interdisciplinary field studying environmental issues. As a graduate student at OSU, Samm has enjoyed working in a “scholarly space, and getting the opportunity to do research.” Beyond grad school, Samm’s goal is to be involved in work that transforms the world, and to contribute to projects that strengthen interdisciplinary associations between diverse, yet interconnected, academic fields.

Check out Samm’s exhibit at Autzen House on the OSU campus:The Need to Know Comes in Waves: Paintings by Samm Newton

On view from Sept. 20th – Dec. 15th, 10 AM – 4 PM at Autzen House (811 SW Jefferson)

Reception Oct. 18th, 4 – 6 PM; mini artist talks at 4:30 and 5:30

Samm will also be the Featured Artist at Hatfield Marine Science Center in Newport, OR in January 2019. Check out this page for more details!

Challenging assumptions about wellness and illness through the lens of Mad Studies

Our entire environment is built upon assumptions about how someone is supposed to move and interact with/in the world. Although disability studies have been around for a long time, in recent years the field has distanced itself from the medical model of disability, in which people with disabilities are viewed as flawed and in need of cure, instead towards a social model of disability. In the social model of disability, an individual in a wheelchair is not the problem; rather, the problem is the building without a ramp and automatic doors. As a 2nd year PhD student of Dr. Patty Duncan in the Women, Gender, and Sexuality Studies Program at OSU, Lzz Johnk pursues questions posed by Mad Studies scholars, such as, what does it mean to think of Mad, neuroqueer, neurodivergent, and mentally disabled people as self-organizing political agents, instead of individuals who society must deal with to maintain order? The core of Lzz’s research consists of applying a genealogical lens to the root of Mad Studies, which is a field examining the lived experiences and culture surrounding individuals identifying as mentally ill, neurodiverse, mentally disabled, and/or Mad. From a white-dominated, Amerocentric perspective, Mad Studies has been around for ~10 years, although the field actually goes back much further, with its roots in the perspectives of people of color, and more specifically, women of color. Lzz explains, “we need to interrogate who gets to decide what constitutes Mad Studies.”

Framing the history of Mad Studies

Examining and interrogating the history of Mad Studies requires understanding the relationships within that history. The location and history of the institution provides framework for the context of the research being done within, as institutions are saturated in the history of the land. Specifically, what does it mean for a white, European settler at a land grant institution such as OSU to be working and researching in a field steeped in the lived experiences of Indigenous people and people of color? Much of the work being done in Mad Studies is limited to the perspectives of cis-masculine individuals and ignores the work of marginalized peoples.

We are all stigmatized to varying extents based on components of our identities, be it national identity, religion, gender, or social class, which is conceptually encompassed by a theory forwarded by Black and other feminists of colour known as intersectionality. The degree to which these stigmas overlap and compound, can effectively result in more acute and damaging marginalization. Historically, people of color and femme and/or gender-deviant people have been hyper-diagnosed as Mad (think of the stereotype of hysteria applied to women). As an example, in considering borderline personality disorder as discussed by writer Susanna Kaysen, Lzz asks, “where is the border-line? Why do women cross that line so often? That line has historically been set and upheld by white settler cis-masculine doctors who determine the boundaries of Madness and wellness. But, the closer you look at the line, the harder it is to define.”

Implementing change

One reason Lzz cites as motivation to return to the academy is to be part of the conversation to make real change in the lives of people identifying as Mad. Changes are being implemented at an unacceptably slow rate. However, Lzz’s research is not directly associated with generating tailored recommendations about health, and explains, “we should be really cautious about the people and institutions making recommendations, by asking what community they are coming from and what their intentions might be. The tendency of entire fields to broad-brush people, and to distill people’s identities into crude stereotypes that get turned against them in moments of vulnerability – as if it is remotely possible to categorize an individual’s whole life experience – is one reason why Mad and disabled people are so stigmatized in our culture.”

Lzz cites the work of Gloria Anzaldúa, a Chicana feminist, as being a critical influence on their wanting to pursue the study of Madness. Anzaldúa wrote and theorized mind-body differences embodying what gets pathologized as Madness or disability. Lzz relates how the work of Anzaldúa exposed them to the concept of navigating overlapping interstitial spaces – or “the space between things, where things don’t fit; falling between, but not quite fitting into binary systems of identity, such as gender.” In this sense, Mad and disabled people are continually finding ourselves in ambiguous terrain.

Why OSU?

Lzz completed their undergrad at Michigan State University in Cultural Anthropology with a certificate in Asian Studies, followed by completion of an MA at Eastern Michigan University in Women and Gender Studies. Lzz felt they could handle doctoral-level work, and also felt strongly that the institution they ended up pursuing a PhD at would need to embrace their Madness. About OSU, Lzz says, “the faculty in my program, in all of their various subfields, are really stellar. Even faculty who don’t necessarily position themselves within Mad Studies are supportive.”

Future directions

Lzz loves teaching and research and would like to pursue these endeavors after graduate school. They also enjoy community work and plan to be involved in outreach to young people who might need support in navigating their neuroqueerness, Madness, and/or mental illness. As someone who has experienced violent pathologization firsthand – fostering a sense of self-hatred instead of acceptance and celebration – Lzz feels that teaching can be one way to disrupt those violences and impact people’s lives in a tangible and meaningful way.

You will not want to miss our interview with Lzz on Sunday, September 16th at 7pm. Listen live on KBVR Corvallis 88.7 FM or stream live. Also, check us out on Apple Podcasts!

Mobility is critical to social and cognitive development in children

Learning to crawl and walk affords children opportunities to explore their world. As such, early childhood mobility is intertwined with other formative childhood milestones, such as motor skill development and learning to negotiate social encounters. Disabled children who may have difficulty reaching mobility milestones, are thus at risk for missing out on opportunities for play and exploration that are critical to cognitive, social, and motor skill development. Samantha Ross, a PhD student in the Kinesiology, Adapted Physical Activity program within the College of Public Health and Human Sciences at Oregon State University, asks the question: how can we support the movement experiences of children with mobility disabilities to ensure they have equitable access to play, exploration and social encounters?

The experience of movement Ride-on cars are modified, child-sized, battery powered vehicles designed to support children with disabilities during play. The ride-on car is equipped with a large button to initiate movement, as well as structural modifications to enhance body support. As part of her research, Samantha observes children with and without disabilities participating in an inclusive play group. She monitors changes in the behavior of individual children, and video analysis helps her to track their distance traveled while using a ride-on car. Factors including whether the child initiated their own movement, if movement included interaction with a peer, or was motivated by a toy, all contribute to a child’s experience of mobility. The ride-on car facilitates the initiation of new relationships among children, noticeably reducing the barrier between children with and without disabilities and promoting equitable play experiences.

For more information about ride-on cars and to watch videos of the cars in action, visit the GoBabyGo website: https://health.oregonstate.edu/gobabygo

The impact of impaired mobility is nuanced Nearly thirty years of research has indicated that young children can benefit from powered mobility devices. However, the field is dominated by the medical perspective of reducing disability. In recent years, a major push from disability groups has emphasized the importance of community and social interactions in enhancing the well-being of children with disabilities. Mobility cannot be distilled down to simply moving from point A to point B, rather the self-perceived experience of movement and how movement facilitates encounters with people and objects is integral to children’s feelings of well-being. It is important for children to feel valued for their contribution. Samantha’s goal is to facilitate a social environment that enhances the well-being and development of children with disabilities, thereby promoting equitable access to a healthy and active childhood.

Following graduate school, Samantha would like to continue her involvement in research at one of the University Centers of Excellence in Developmental Disabilities, representing a partnership between state, federal, academic, and disability communities. Samantha explains, “We need to hear from people with disabilities – we need everyone at the table for the system to work.” These centers provide the interface between policy and research, where priorities are weighed and decisions are made. Often headquartered at medical schools, the centers raise awareness and help train future healthcare professionals. Samantha would love to be involved in this discussion.

Join us on Sunday, August 5th at 7pm on KBVR Corvallis 88.7 FM or stream live to hear more about Samantha’s research. We will discuss other aspects of her research, as well, including her investigation of national surveillance reports, which provide insight about whether children’s service needs are being met, and how to identify children who could benefit from mobility assistive devices.

How do bone cancer cells become resistant to chemotherapy?

Limited treatments for bone cancer Bone cancer is a devastating and poorly understood disease with few available treatment options in humans. The disease disproportionately impacts young adults and children, and treatment still often includes amputation of the affected limb. Relapse within one year is common. Dogs can also spontaneously develop bone cancer, which makes them a suitable model for comparative oncology: insights about disease progression in dogs can yield insights about the disease in humans.

Animal models – one size does not fit all The difficulty of establishing a robust animal model has impeded scientists’ ability to study bone cancer rigorously. For example, although mice are commonly used to study human disease, they do not develop bone cancer spontaneously. Invasive tumor tissue grafts are required to study the disease in mice, which adds confounding variables to the results – it is not necessarily clear if an observed effect is the result of the tumor or the grafting procedure.

Understanding how chemotherapy resistance develops As a 2nd year Master’s student in the College of Veterinary Medicine, Marcus Weinman is working towards understanding how bone cancer tumors adapt and acquire resistance to chemotherapy. He has been developing canine osteosarcoma cell lines to study disease progression, which entails exposing cells to chemotherapy until they become resistant. Using a variety of molecular biology techniques, Marcus investigates how cells acquire resistance, and whether specific molecules or groups of molecules are more active or less active as resistance develops. The goal is to identify possible targets within the cell that might be sensitive to therapeutic intervention.  

Complexity of bone cancer cells Cells contain exosomes – small packages containing a diverse mix of molecules – that participate in signaling and transfer of molecules between cells. These compact cellular packages are being investigated for their role in the development of resistance. These tumor cells are also endocrine tumors – they express hormones normally found in other tissues, such as the brain and the gut – which adds a layer of physiology to the already-complex nature of cancer.

Why cancer research? Originally from Denver, Colorado, Marcus knew he wanted to attend OSU to pursue research opportunities. He completed his undergraduate studies at OSU, and attributes part of his desire to attend OSU to a deep family connection to Corvallis – his grandfather was a professor at OSU!

After completing his Master’s, Marcus plans to attend med school, with the eventual goal of becoming an oncologist, while maintaining his connection to research. He emphasizes how the teaching component of medicine is a motivating factor in his desire to become a physician. As a clinician, he would like to teach patients how to take care of themselves by integrating educational and interpersonal aspects of medicine.

Join us on Sunday, July 29th at 7pm on KBVR Corvallis 88.7 FM or stream live to hear more from Marcus about his research and experience as a graduate student at OSU.

 

Stream ecosystems and a changing climate

Examining the effect of climate change on stream ecosystems

Oak Creek near McDonald Dunn research lab. The salamander and trout in the experiments were collected along this stretch of creek.

As a first year Master’s student in the lab of Ivan Arismendi, Francisco Pickens studies how the changing, warming climate impacts animals inhabiting stream ecosystems. A major component of stream ecosystem health is rainfall. In examining and predicting the effects of climate change on rainfall, it is important to consider not only the amount of rainfall, but also the timing of rainfall. Although a stream may receive a consistent amount of rain, the duration of the rainy season is projected to shrink, leading to higher flows earlier in the year and a shift in the timing of the lowest water depth. Currently, low flow and peak summer temperature are separated by time. With the shortening and early arrival of the rainy season, it is more likely that low flow and peak summer temperature will coincide.

A curious trout in one of the experimental tanks.

Francisco is trying to determine how the convergence of these two events will impact the animals inhabiting streams. This is an important question because the animals found in streams are ectothermic, meaning that they rely on their surrounding environment to regulate their body temperature. Synchronization of the peak summer temperature with the lowest level of water flow could raise the temperature of the water, profoundly impacting the physiology of the animals living in these streams.

 

 

How to study animals in stream ecosystems?

Salamander in its terrestrial stage.

Using a simulated stream environment in a controlled lab setting, Francisco studies how temperature and low water depth impact the physiology and behavior of two abundant stream species – cutthroat trout and the pacific giant salamander. Francisco controls the water temperature and depth, with depth serving as a proxy for stream water level.

Blood glucose level serves as the experimental readout for assessing physiological stress because elevated blood glucose is an indicator of stress. Francisco also studies the animals’ behavior in response to changing conditions. Increased speed, distance traveled, and aggressiveness are all indicators of stress. Francisco analyzes their behavior by tracking their movement through video. Manual frame-by-frame video analysis is time consuming for a single researcher, but lends itself well to automation by computer. Francisco is in the process of implementing a computer vision-based tool to track the animals’ movement automatically.

The crew that assisted in helping collect the animals: From left to right: Chris Flora (undergraduate), Lauren Zatkos (Master’s student), Ivan Arismendi (PI).

Why OSU?

Originally from a small town in Washington state, Francisco grew up in a logging community near the woods. He knew he wanted to pursue a career involving wild animals and fishing, with the opportunity to work outside. Francisco came to OSU’s Department of Fisheries and Wildlife for his undergraduate studies. As an undergrad, Francisco had the opportunity to explore research through the NSF REU program while working on a project related to algae in the lab of Brooke Penaluna. After he finishes his Master’s degree at OSU, Francisco would like to continue working as a data scientist in a federal or state agency.

Tune in on Sunday, June 24th at 7pm PST on KBVR Corvallis 88.7 FM, or listen live at kbvr.com/listen.  Also, check us out on Apple Podcasts!

Ocean sediment cores provide a glimpse into deep time

Theresa on a recent cruise on the Oceanus.
Photo credit: Natasha Christman.

First year CEOAS PhD student Theresa Fritz-Endres investigates how the productivity of the ocean in the equatorial Pacific has changed in the last 20,000 years since the time of the last glacial maximum. This was the last time large ice sheets blanketed much of North America, northern Europe, and Asia. She investigates this change by examining the elemental composition of foraminifera (or ‘forams’ for short) shells obtained from sediment cores extracted from the ocean floor. Forams are single-celled protists with shells, and they serve as a proxy for ocean productivity, or organic matter, because they incorporate the elements that are present in the ocean water into their shells. Foram shell composition provides information about what the composition of the ocean was like at the point in time when the foram was alive. This is an important area of study for learning about the climate of the past, but also for understanding how the changing climate of today might transform ocean productivity. Because live forams can be found in ocean water today, it is possible to assess how the chemistry of seawater is currently being incorporated into their shells. This provides a useful comparison for how ocean chemistry has changed over time. Theresa is trying to answer the question, “was ocean productivity different than it is now?”

Examples of forams. For more pictures and information, visit the blog of Theresa’s PI, Dr. Jennifer Fehrenbacher: http://jenniferfehrenbacher.weebly.com/blog

Why study foram shells?

Foram shells are particularly useful for scientists because they preserve well and are found ubiquitously in ocean sediment, offering a consistent glimpse into the dynamic state of ocean chemistry. While living, forams float in or near the surface of the sea, and after they die, they sink to the bottom of the sea floor. The accumulating foram shells serve as an archive of how ocean conditions have changed, like how tree rings reflect the environmental conditions of the past.

Obtaining and analyzing sediment cores

Obtaining these records requires drilling cores (up to 1000 m!) into deep sea sediments, work that is carried out by an international consortium of scientists aboard large ocean research vessels. These cores span a time frame of 800 million years, which is the oldest continuous record of ocean chemistry. Each slice of the core represents a snapshot of time, with each centimeter spanning 1,000 years of sediment accumulation. Theresa is using cores that reach a depth of a few meters below the surface of the ocean floor. These cores were drilled in the 1980s by a now-retired OSU ship and are housed at OSU.

Theresa on a recent cruise on the Oceanus, deploying a net to collect live forams. Photo credit: Natasha Christman.

The process of core analysis involves sampling a slice of the core, then washing the sediment (kind of like a pour over coffee) and looking at the remainder of larger-sized sediment under a powerful microscope to select foram species. The selected shells undergo elemental analysis using mass spectrometry. Vastly diverse shell shapes and patterns result in different elements and chemistries being incorporated into the shells. Coupled to the mass spectrometer is a laser that ablates through the foram shell, providing a more detailed view of the layers within the shell. This provides a snapshot of ocean conditions for the 4 weeks-or-so that the foram was alive. It also indicates how the foram responded to light changes from day to night.

Theresa is early in her PhD program, and in the next few years plans to do field work on the Oregon coast and on Catalina island off the coast of California. She also plans to undertake culturing experiments to further study the composition of the tiny foram specimens.

Why grad school at OSU?

Theresa completed her undergraduate degree at Queen’s University in Ontario, followed by completion of a Master’s degree at San Francisco State University. She was interested in pursuing paleo and climate studies after transformative classes in her undergrad. In between her undergraduate and Master’s studies she spent a year working at Mt. Evans in Colorado as part of the National Park Service and Student Conservation Association.

Theresa had already met her advisor, Dr. Jennifer Fehrenbacher, while completing her Master’s degree at SF State. Theresa knew she was interested in attending OSU for grad school for several reasons: to work with her advisor, and to have access to the core repository, research ships, and technical equipment available at OSU.

To hear more about Theresa’s research and her experience as a PhD student at OSU, tune in on Sunday, June 10th at 7pm on KBVR Corvallis 88.7 FM, or listen live at kbvr.com/listen.  Also, check us out on Apple Podcasts!

When Fungus is Puzzling: A Glimpse into Natural Products Research

Ninety years ago, a fungal natural product was discovered that rocked the world of medicine: penicillin. Penicillin is still used today, but in the past ninety years, drug and chemical resistance have become a hot topic of concern not only in medicine, but also in agriculture. We are in desperate need of new chemical motifs for use in a wide range of biological applications. One way to find these new compounds is through natural products chemistry. Over 50% of drugs approved in the last ~30 years have been impacted by natural products research, being directly sourced from natural products or inspired by them.

Picture a flask full of microbe juice containing a complex mixture of hundreds or thousands of chemical compounds. Most of these chemicals are not useful to humans – in fact, useful compounds are exceedingly rare. Discovering new natural products, identifying their function, and isolating them from a complex mixture of other chemicals is like solving a puzzle. Donovon Adpressa, a 5th year PhD candidate in Chemistry working in the Sandra Loesgen lab, fortunately loves to solve puzzles.

Nuclear Magnetic Resonance (NMR): an instrument used to elucidate the structure of compounds.

Donovon’s thesis research involves isolating novel compounds from fungi. Novel compounds are identified using a combination of separation and analytical chemistry techniques. Experimentally, fungi can be manipulated into producing compounds they wouldn’t normally produce by altering what they’re fed. Fungi exposed to different treatments are split into groups and compared, to assess what kind of differences are occurring. By knocking out certain genes and analyzing their expression, it’s possible to determine how the compound was made. Once a new structure has been identified and isolated, Donovon moves on to another puzzle: does the structure have bioactivity, and in what setting would it be useful?

Donovon’s interest in chemistry sparked in community college. While planning to study Anthropology, he took a required chemistry course. Not only did he ace it, but he loved the material. The class featured a one-week lecture on organic chemistry and he thought, ‘I’m going to be an organic chemist.’ However, there were no research opportunities at the community college level, and he knew he would need research experience to continue in chemistry.

At Eastern Washington University, Donovon delved into undergraduate research, and got to work on a few different projects combining elements of medicinal and materials chemistry. While still an undergrad, Donovon had the opportunity to present his research at OSU, which provided an opportunity to meet faculty and see Corvallis. It all felt right and fell into place here at OSU.

As a lover of nature and hiking in the pacific northwest, Donovon has always had a soft spot for mycology. It was serendipitous that he ended up in a natural products lab doing exactly what interested him. Donovon’s next step is to work in the pharmaceutical industry, where he will get to solve puzzles for a living!

Tune in at 7pm on Sunday, March 18th to hear more about Donovon’s research and journey through graduate school. Not a local listener? Stream the show live.

Exploring a protein’s turf with TIRF

Investigating Otoferlin

Otoferlin is a protein required for hearing. Mutations in its gene sequence have been linked to hereditary deafness, affecting 360 million people globally, including 32 million children. Recently graduated PhD candidate Nicole Hams has spent the last few years working to characterize the activity of Otoferlin using TIRF microscopy. There are approximately 20,000 protein-coding genes in humans, and many of these proteins are integral to processes occurring in cells at all times. Proteins are encoded by genes, which are comprised of DNA; when mutations in the gene sequence occur, diseases can arise. Mutations in DNA that give rise to disease are the focus of critical biomedical research. “If DNA is the frame of the car, proteins are the engine,” explains Nicole. Studying proteins can provide insight into how diseases begin and progress, with the strategic design of therapies to treat disease founded on our understanding of protein structure and function.

Studying proteins

Proteins are difficult to study because they’re so small: at an average size of ~2 nanometers (0.000000002 meters!), specific tools are required for visualization. Enter TIRF. Total Internal Reflection Fluorescence is a form of microscopy enabling scientists like Nicole to observe proteins tagged with a fluorescent marker. One reason TIRF is so useful is that it permits visualization of samples at the single molecule level. Fluorescently-tagged proteins light up as bright dots against a dark background, indicating that you have your protein.

Another reason why proteins are hard to study is that in many cases, parts of the protein are not soluble in water (especially if part of the protein is embedded in the fatty cell membrane). Trying to purify protein out of a membrane is extremely challenging. Often, it’s more feasible for scientists to study smaller, soluble fragments of the larger protein. Targeted studies using truncated, soluble portions of protein offer valuable information about protein function, but they don’t tell the whole story. “Working with a portion of the protein gives great insight into binding or interaction partners, but some information about the function of the whole protein is lost when you study fragments.” By studying the whole protein, Nicole explains, “we can offer insight into mechanisms that lead to deafness as a result of mutations.”

Challenges and rewards of research

Nicole cites being the first person in her lab to pursue single molecule studies as a meaningful achievement in her graduate career. She became immersed in tinkering with the new TIRF instrument, learning from the ground up how to develop new experiments. Working with cells containing Otoferlin, in a process known as tissue culture, required Nicole to be in lab at unusual hours, often for long periods of time, to make sure that the cells wouldn’t die. “The cells do not wait on you,” she explains, adding, “even if they’re ready at 3am.” Sometimes Nicole worked nights in order to get time on the TIRF. “If you love it, it’s not a sacrifice.”

Why grad school?

As an undergraduate student studying Agricultural Biochemistry at the University of Missouri, Nicole worked in a soybean lab investigating nitrogen fixation, and knew she wanted to pursue research further. She had worked in a lab work since high school, but didn’t realize it was a path she could pursue, instead convinced that she wanted to go to medical school. Nicole’s mom encouraged her to pursue research, because she knew that it was something she enjoyed, and her undergraduate advisor (who completed his post-doc at OSU) suggested that she apply to OSU. She feels lucky to have found an advisor like Colin Johnson, and stresses the importance of finding a mentor who is personally vested in their graduate student’s success.

Besides lab work…

In addition to research, Nicole has been actively involved in outreach to the community, serving as Educational Chair of the local NAACP Chapter. Following completion of her PhD, Nicole intends to continue giving back to the community, by establishing a scholarship program for underrepresented students. Nicole remembers a time when she was told and believed that she wasn’t good enough, and while she was able to overcome this discouraging dialogue, she has observed that many students do not find the necessary support to pursue higher education. Her goal is to reach students who don’t realize they have potential, and provide them with resources for success.

Tune in on December 3rd  at 7pm to 88.7 KBVR Corvallis or stream the show live right here to hear more about Nicole’s journey through graduate school!

Thanks for reading!

You can download Nicole’s iTunes Podcast Episode!

Earlier in the show we discussed current events, specifically how the tax bill moving through the House and Senate impact students. Please see our references and sources for more information.