January 29, 2021
Author: Lindsay Wilson
While only approximately 1 inch long, zebrafish are remarkably similar to humans. Understandably, their size and appearance may cause doubt about how much information they can give us about human health impacts of chemical exposures. To help explain the use of zebrafish and other unique research tools within our Superfund Research Program, we developed two educational infographics for public distribution.
Continue readingNative Americans have a long history of being under-represented in higher education. Currently, only 5% of Native American high school graduates go directly into a four-year college and a small percentage of those major in STEM-related degrees. In an effort to increase participation of Native American students in college programs, and introduce them to biomedical sciences, Oregon State Superfund Research Center holds several activities to bring Native Youth to campus to increase their awareness of opportunities in College and scientific careers.
On May 20, over 20 tribal youth and chaperones came to Oregon State University for a campus tour, student panel and the 41st annual Klatowa Eena Powwow. (Klatowa Eena is Chinook Wawa for ‘Go Beavers.’) SRP trainee Sydelle Harrison, who is part of the Community Engagement Core (CEC), worked with the Research Translation Core, the Training Core and SRP Administration to procure funding and organize the daylong event. For the second year in a row, Sydelle worked with youth organizations to bring students from the Confederated Tribes of the Umatilla Indian Reservation and the Confederated Tribes of Warm Springs.
The 20+ students started at Callahan Hall, where SRP trainee Amelia Allee, (CEC), and University Housing and Dining Services staff took the students through the freshman dormitory, highlighting the shared lounges and kitchenettes, and showing the students a dorm room.
Following the dorm tour, Athletics staff took students on a tour of Reser stadium, including a tour of President Ed Ray’s box, and provided them an opportunity to run on the field. Up next, was the OSU Basketball Center where the students (and chaperones) took to the court. After working up an appetite, the dining halls were next, followed by the Powwow. To finish off the day, SRP trainees hosted a pizza dinner. Here, students had the opportunity to ask trainees questions about college, graduate school and SRP research. Two tribal elders attended, giving the youth their perspective regarding the importance of college. SRP trainees and faculty answered questions about the value of community college, the typical length of a college degree as well as opportunities for distance learning at the OSU satellite campuses. Many thanks to Sydelle Harrison; without her these tours would not be possible. In addition, many thanks to Amber Kramer, Carolyn Poutasse, Alix Robel, Amelia Allee and Drs. Molly Kile, Diana Rohlman, Craig Marcus and Robyn Tanguay for their help.
By Mike Garland and Mitra Geier
This past fall, we traveled to the Pacific Northwest National Laboratory (PNNL) for training in computational analysis of RNA-seq data. During this two-day externship, we worked with PNNL scientists as they walked us through our data and gave us an overview of computational approaches they use to analyze RNA-seq data.
Research Impacts
During the externship we were provided hands-on experience with computational methods under the guidance of experts. Our ultimate goal was to apply what we learned at PNNL to current and future RNA-seq projects.
Our work at PNNL centered around an experiment that compared regenerating vs non-regenerating caudal fins of zebrafish, which is a phenomenon of interest for a variety of applications. The regenerating caudal fin model is a useful toxicological tool for chemical screening, and is well-suited for studying how chemical exposure can lead to changes in molecular signaling events that occur during the wound healing process. Furthermore, regeneration and development share many critical signaling events, making this model useful for interrogating mechanisms of developmental toxicity.
By using a systems approach to understand expression patterns of mRNA and miRNA during regeneration, we can improve our understanding of molecular processes involved in wound healing. This would allow us to be better-informed when making hypotheses about the mechanisms of toxicity following chemical exposure in zebrafish. Given the applicability of this model to developmental toxicology, the results from this experiment will be particularly useful for future directions of SRP Project 3.
Age is a known factor of regenerative ability, and different life stages are frequently used in various toxicological studies. This was incorporated into the experiment using age-based cohorts and we learned methods to compare age-dependent differences in gene expression during regeneration. Drs. Joe Brown and Jason Wendler, both computational biologists at PNNL, trained us over our externship on a variety of methodologies including quality control, read alignment, statistical inference, biological pathway enrichments, and data visualization methods.
Career Impacts
Over the course of the two days, we covered many computational methods involved in RNA-seq data analysis, which will be useful in our other ongoing projects, as well as future work as our careers progress. We are also grateful for the opportunities for professional networking outside of our typical academic circles. We learned quite a bit about the mechanics of working in a national laboratory and how that is different than working for a university. We are appreciative of the time and effort put in by Drs. Brown and Wendler, and we also thank Dr. Katrina Waters who helped organize our trip to PNNL.
Sydelle Harrison was awarded an SRP Externship to work with the Yellowhawk Tribal Health Center (Confederated Tribes of the Umatilla Indian Reservation). The clinic is celebrating 20 years of self-governance this month and preparing to move into a new state of the art facility next year.
Sydelle is working on various special projects to support the Public Health Accreditation process. Her duties include outreach related to the community health assessment. She is also collecting feedback regarding the community health improvement plan.
As a Tribal member and SRP trainee, Sydelle is also working on the clinic’s new strategic plan. She aims to promote integration of environmental health back into the organization as they expand services. This has also proven to be a focal point for many Tribal members in her presentations as they ask what the people and first foods are being exposed to. Between her externship and her role as an SRP trainee, Sydelle is helping connect SRP researchers and tribal commission members and community members to expand capacity environmental health research.
Amber Kramer is a first year Chemistry Graduate student working with Dr. Staci Simonich on SRP Project 5. She is working on identifying oxidation products formed during polycyclic aromatic hydrocarbons (PAH) remediation.
Amber has been selected to work with Dr. Alla Zelenyuk this summerat Pacific Northwest National Laboratory (PNNL) to get hands on experience studying atmospheric reactions of PAHs adsorbed to secondary organic aerosols (SOAs). Many PAHs are on the US Environmental Protection Agency’s (USEPA) priority pollutant list. Amber has been awarded an SRP Trainee Externship Award through the SRP Training Core to support her during this training.
Dr. Zelenyuk’s group at PNNL has done extensive work with SOAs. This externship will provide training and experience for Amber to study PAH adsorption during SOA formation, as well as reactions these PAHs may undergo when exposed to atmospheric species like ozone and hydroxyl radicals. Some oxidation products of PAHs have been show to be more toxic than the original PAH, and this work along with long range transport models, will help identify U.S. populations at risk from exposure to common atmospheric PAH sources.