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.

Native 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 Robert 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.

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.