The Research Translation Core, represented by Dr. Diana Rohlman, was invited to attend and present at the 14th summit of the Northwest Toxic Communities Coalition. Dr. Rohlman’s talk highlighted the innovative tools, methodologies and approaches used by the Superfund Research Program at Oregon State. One of the presented case studies highlighted the work being done at the Portland Harbor Superfund site. More information  can be found here.

Excerpted from the event summary: “Dr. Diana Rohlman kicked off the day with an introduction to research being done by the Oregon State University Superfund Research Program. Her talk emphasized the complexity of pinning down risks from manmade chemicals like Polycyclic Aromatic Hydrocarbons (which are chemicals released from burning substances or during oil spills and also used in consumer goods like air fresheners) when environments like Portland Harbor are contaminated differently over time and when the effects of a given chemical often depend on which other chemicals are present or on the specific sensitivity of the exposed individual. She also pointed out that bioremediation can be problematic because chemicals are sometimes broken down into even more toxic metabolites. This means that bioremediation may sometimes successfully eliminate one compound from an environment only to replace it with something even more toxic.” Read the full article here.

Hurricane Harvey and hazardous exposures

Following a disaster, we tend to be worried about finding food and shelter, reuniting with families and pets, and cleaning up the damage left behind. We don’t tend to think about toxic chemical exposures. With Hurricane Harvey, it’s a different story.

Harvey flooded at least 13 Superfund sites flooded. Millions of pounds of hazardous chemicals were released. In addition, small explosions and chemical spills were reported. The New York Times created maps showing  the magnitude of the disaster. For example, this image from the New York Times shows flooded or damaged Superfund sites, in orange.

Only days after Harvey, OSU SRP researchers partnered with Texas A&M, University of Texas – Houston, and Baylor College of Medicine. The goal of the partnership is to place personal samplers on individuals living in and near hurricane-damaged areas. The passive sampling wristband is the perfect tool.  It doesn’t need batteries or the internet. Additionally, the wristband can detect over 1,500 different chemicals.

Disaster Research Response

Oregon State University has been preparing for disaster research for several years. This year, Oregon State received their first ‘Disaster IRB.’ This allows Oregon State researchers to deploy quickly, with appropriate controls in place to ensure participants are safe and their information is confidential. SRP investigators Drs. Kim Anderson and Rohlman worked carefully with the Oregon State Institutional Review Board to develop this IRB.

The Superfund Research Program is supporting this response effort. In the image below, SRP trainees are preparing wristbands for a September 20th deployment. We hope to enroll several hundred individuals. The results of this study will help us better understand the potentially toxic chemical exposures that could result following natural disasters.

Mary Leonard, PhD
PhD: Chemistry, Oregon State University, 2017
Research focus: transport, transformation and remediation of environmental contaminants.

Mary joined the Simonich laboratory this spring as a post-doctoral research associate. Before beginning her graduate degree, Mary worked in government and industry as an analytical chemist. Mary will be working in the Superfund Research Program to identify certain polycyclic aromatic hydrocarbons in water.

Polycyclic aromatic hydrocarbons (PAHs) are environmental contaminants generated by the incomplete combustion of organic compounds, such as those found in fossil fuels and cigarette smoke.
See this infographic to learn more.

Several PAHs are known to cause human health effects, such as cancer, heart disease and respiratory disease. Humans are mostly exposed to PAHs through air, water and food. New research is showing that PAHs can be transformed into different types of chemicals. When this happens, the ‘new’ PAH may be more toxic than the first one. For example, some PAHs can be transformed when exposed to high heat.

Mary’s project will look at known PAHs and their transformation products in environmental water systems. As these new PAHs have a different chemical structure, much of her work will include developing techniques for the detection and identification of these chemicals. For a more complete summary of Mary’s work, please review this technical abstract.

Mary obtained her doctorate in chemistry at Oregon State University in early 2017. Her area of concentration is analytical chemistry, and she is interested in the transport, transformation, and remediation of environmental contaminants. Prior to her graduate studies, she worked in both government and industry performing analysis of small molecules in biological matrices. Mary joined the Simonich laboratory this spring as a post-doctoral research associate. One of her first contributions to the Superfund Research Program will be the development of a high performance liquid chromatography-mass spectrometry (HPLC-MS) method for analysis of hydroxylated polycyclic aromatic hydrocarbons (OHPAHs) in aqueous systems.


Polycyclic aromatic hydrocarbons (PAHs) are environmental contaminants generated by the incomplete combustion of organic compounds, such as those found in fossil fuels and cigarette smoke. Several PAHs have been identified as mutagens or probable carcinogens, and chronic exposure to these compounds is associated with increased risk of developing lung cancer and peripheral arterial disease. PAHs are metabolized by mammals and some microbes to form hydroxylated PAHs, or OHPAHs. Some OHPAHs are more carcinogenic than their parent compounds, because they can cause oxidative damage to DNA, resulting in cell mutations. Microbial transformation of PAHs to OHPAHs should thus be considered when evaluating the effectiveness of bioremediation strategies. Gas chromatography (GC) is typically used for separation of parent PAHs in complex environmental matrices. Following separation on a GC column, the PAHs can be detected and quantified by mass spectrometry (MS). However, analysis of OHPAHs by GC-MS is not as straightforward. OHPAHs must be chemically modified, or derivatized, prior to separation by GC. Derivatization increases sample processing time, and it can complicate identification and quantification of target compounds. Reverse phase high performance liquid chromatography-mass spectrometry (HPLC-MS) circumvents the need for derivatization. OHPAHs can be separated and quantified by HPLC-MS without modification, resulting in shorter analysis times and improved separation.

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.