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.

Project 3 Update

by Jamie Minick odeq-report

The McCormick and Baxter Superfund Site is located on the Willamette River in Portland, Oregon and has PAH contaminated soils and sediments from historical creosote operations. As part of an Oregon Department of Environmental Quality (ODEQ) ten year study to assess the effectiveness of the sediment cap, passive sampling devices from Kim Anderson’s lab were deployed by U.S. EPA Region 10 divers in both sediment and water at the site. Included in this study was a newly designed passive sampling sediment probe which allowed for deployment in the rocky armoring of the sediment cap. Based on data from this study, the ODEQ reported that the sediment cap appears to be effective in meeting its remedial objectives.  The full results of the study, used to inform ODEQ regulatory decision making, is available here (, beginning on page 20.

FullSizeRenderSydelle 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.

Working with the RTC, SRP trainee Sydelle Harrison coordinated a campus visit for students from the Confederated Tribes of the Warm Springs Reservation and the Confederated Tribes of the Umatilla Indian Reservation (CTUIR) on May 13-14. Students went on a campus tour, ate lunch at the Eena Haws Native American Longhouse Annual Salmon Bake, and met with Dr. Rohlman (CEC, RTC) to learn about recent tribal-university collaborations (more information available here). The tour culminated in a hands-on lab activity wherein students learned how to isolate DNA from strawberries as a proxy for understanding how SRP investigators can learn underlying genetic determinants of disease by analyzing DNA. This event was a collaborative effort between the Research Translation Core, Training Core, Administrative Core and Community Engagement Core.

Me headshotAmber 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.