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 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.

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.

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.

Ivan Titaley
Ivan Titaley

By Ivan Titaley, Project 5 Trainee

Back in April, I was awarded the SRP Trainee Externship Award through OSU’s SRP Training Core to help support my training opportunity at the Pacific Northwest National Laboratory (PNNL) as an Alternate Sponsored Fellow. The aim of this internship was to predict the formation of hydroxy- and oxygenated‑PAHs (OHPAHs and OPAHs, respectively) in the environment using a computational chemistry approach. OPAHs and OHPAHs can be formed from the degradation of PAHs. OPAHs in air samples have been found to be more mutagenic than the unsubstituted PAHs.

To achieve this objective, I used the NWChem software, which is a high performance computational chemistry software developed by PNNL scientists. Through a collaboration set-up by Dr. Dayle Smith (previously in Core C), I spent two months learning how to use NWChem under the supervision of Dr. Kurt Glaesemann.

The Environmental and Molecular Science Laboratory (EMSL) is a national user facility that houses multiple instruments and laboratories. My office was located inside this building at PNNL in Richland, WA.
The Environmental and Molecular Science Laboratory (EMSL) is a national user facility that houses multiple instruments and laboratories. My office was located inside this building at PNNL in Richland, WA.

Using this approach, my goal was to be able to predict which OHPAHs and OPAHs are likely to form in the environment based on their thermodynamic properties, specifically the reaction Gibbs free energy. There were three main areas related to Project 5’s focus where this predictive capability will be helpful. First, the results could assist in explaining why toxicity in remediated soils increased, even after PAHs’ concentrations went down (e.g. Chibwe et al., 2015). Secondly, prior data of OHPAHs found in human urine, (e.g. Motorykin et al., 2015) can be compared with computational results to see if I can formulate a prediction of which OHPAHs are likely to form in human urine. Finally, continuing on prior work that has predicted the formation of NPAHs in ambient air (e.g. Jariyasopit et al., 2013), I could then apply similar approach, but for OHPAHs and OPAHs.

The learning curve during my externship was quite steep. Although I was able to understand how to use NWChem, I also learned that a one-size-fits-all approach was not possible and I would need to tailor my modeling approach to successfully predict formation of OHPAHs and OPAHs. It was during this time that I found out how valuable it was for me to be able to spend time at PNNL. Being in a facility where there were experts in almost every imaginable field, I was able to talk to many experts about issues that I faced. These conversations led me to the field of chemometrics which helped me tailor the computational chemistry approach accordingly. One of the online programs that I found to be useful was XenoSite, which can predict CYP450 inhibition sites on a given compound. This program can potentially be useful when narrowing down potential OHPAHs that might form through bioactivation.

In addition, the myriad instruments and facilities that are available at PNNL have also assisted me greatly during my internship. For example, the NWChem software that I used was connected to the supercomputing facility, which helped speed up the calculation, resulting in faster computational time. Another perk of being in Richland, was that I managed to tour the Hanford B Reactor—coincidentally a couple of days before the anniversary of the atomic bomb being dropped in Japan.

All in all, the externship challenged me to get me out of my comfort zone, but also rewarded me with a new skill and unique

Constance, my "instrument" over the summer. Constance is one of several supercomputers available at PNNL.
Constance, my “instrument” over the summer. Constance is one of several supercomputers available at PNNL.

experience. In a way, the internship at PNNL served as a preview of what may come once I am finished with my Ph.D. More importantly, I found the networking opportunity and exposure to a possible career path while at PNNL to be invaluable. Currently, I am excited to combine the in silico approach that I learned at PNNL with the analytical chemistry approach at the Simonich lab into my research projects. The chemical analysis component will verify how accurate the prediction capabilities are. If this approach is proven to be reliable, I hope that this perspective can offer a different insight in predicting the formation of OHPAHs and OPAHs.