Internship Projects at EPA and NIST
Below is a list of past EPA and NIST Projects that students have worked on.
1. Building cell models to identify chemical targets important in cancer
Description of project: Transcript profiling which measures global gene expression changes in response to chemical exposure is a robust, data-rich approach to chemical toxicity screening. However, a major challenge when using transcript profiling is linking gene expression changes to molecular and cellular effects important in chemical toxicity. Our lab has recently made significant progress in developing computational approaches that allow prediction of the activation or inhibition of specific transcription factors in rodents and humans important in endocrine disruption and cancer. There are a number of transcription factor- and pathway-focused projects open for students to participate in, and they include those which involve construction and characterization of cell lines knocked out for specific genes using Crispr-Cas9 that can be used to help interpret predictions from transcript profiling data bases. The student will learn how to construct knockout cell lines using as an example a set of transcription factors important in cancer. The student will learn how to construct vectors used to express the Cas9 enzyme and the guide RNA, how to transfect the plasmids into mammalian cells, how to select for the plasmid, how to determine the percentage of the cell population that is knocked out, and how to use the set of cell lines to identify chemicals that work through specific factors.
Special skills the intern should have: A background in the basics of molecular biology, experience in cell culture techniques and cloning, and an understanding of the biology behind Crispr-Cas9 methods would be very useful but are not required.
Contact: Chris Corton, ORD/National Health and Environmental Effects Laboratory in Research Triangle Park, NC; 919 541 0092, corton.chris@epa.gov
2. Identification of molecular targets of chemicals in complex mixtures using transcript profiling
Description of the project: Transcript profiling which measures global gene expression changes in response to chemical exposure is a robust, data-rich approach to chemical toxicity screening; however, a major challenge when using transcript profiling is linking gene expression changes to molecular and cellular effects important in chemical toxicity. Our lab has recently made significant progress in developing computational approaches that allow prediction of the activation or inhibition of specific transcription factors in rodents and humans important in endocrine disruption and cancer. There are a number of transcription factor- and pathway-focused projects open for students to participate in, and they include those which involve understanding the health risks of exposure to contaminated water. The student will apply a number of techniques to use gene expression profiling to identify molecular targets modulated by mixtures of chemicals in water in human cells and to link those effects to adverse outcomes in animals and people. The student will learn how to culture human cells, expose the cells to chemicals or chemical mixtures, to interpret the resulting transcript profiles for identification of molecular targets using a number of bioinformatic techniques, perform dose-response modeling, and to make linkages to health effects through perturbation of networks of adverse outcome pathways.
Special skills the intern should have: Experience in cell culture techniques and transcript profiling, and experience with R would be very useful but are not required.
Contact: Chris Corton, ORD/National Health and Environmental Effects Laboratory in Research Triangle Park, NC; 919 541 0092, corton.chris@epa.gov
3. Speciation Data Improvements
An important foundation of EPA’s Air Quality Management Policy are the emissions used in Air Quality Models. EPA develops and uses the SPECIATE database for obtaining source category-specific chemical composition data for organic gases and particulate matter (PM). These chemical composition data are called speciation profiles, and they are used to generate speciated emissions from volatile organic compounds (VOC) and PM emissions collected in EPA’s National Emissions Inventory (NEI). Efforts to update and use SPECIATE is a multi-office EPA effort and is coordinated by a SPECIATE work group (SWG) consisting of experts from the EPA’s Office of Air and Radiation (OAR) and Office of Research and Development (ORD). The EPA SWG strives to improve the speciation profiles in SPECIATE and ensure that the most appropriate speciation profiles are being used for VOC and PM in air quality modeling. A detailed assessment to prioritize speciation profile improvements for air quality modeling has been completed and has resulted in a journal article accepted for publication in Atmospheric Environment. The next step of this work, which could also result in a peer-reviewed publication and conference presentations, is to address the highest priority profile needs by identifying candidate profiles from the SPECIATE database, the literature and/or current EPA test programs.
The intern will review the SPECIATE needs assessment journal article to identify the priority speciation profiles for improvement, which inventory sources are assigned to those profiles, and determine if there are any new profiles that can be used instead. In addition to searching through the SPECIATE database, the intern will conduct literature searches and coordinate with ORD research teams to find data to add to SPECIATE. The intern will present candidate profile replacements for further quality review and decision by the SWG, document the SWG decisions, and help make the updates in the SPECIATE and the mapping of speciation profiles to the NEI source categories. The intern will track the quantity of emissions for which improved speciation profiles were identified. The results of the research will be documented and presented at appropriate emissions and/or modeling related research conferences and prepared for a publication. Successful applicants will have experience in using spreadsheets to organize and manipulate data. The intern should be a fast learner with a technical background and an interest in air quality, emissions, and/or chemical pollutants in the environment.
POC: Madeleine Strum, Office of Air and Radiation/Office of Air Quality Planning and Standards in Research Triangle Park, NC; 919 541 2383, strum.madeleine@epa.gov
4. Measurement-Model Fusion Mapping of Total (Wet + Dry) Deposition
Goal: Update methodology for merging existing monitoring data (ambient concentrations and wet deposition fluxes) with model results from the Community Multiscale Model (CMAQ) to provide total deposition gridded surfaces. The total deposition maps are used to assess changes in nitrogen and sulfur deposition due to emission reduction programs, develop ecosystem effects models for terrestrial and aquatic ecosystems, and improve our understanding of atmospheric deposition in a changing climate. The total deposition maps are also used to link ecosystem response with air quality under the current NO2, SO2, PM secondary NAAQS review. The processes and scripts used to create the maps need to be updated to provide increased flexibility in data inputs (new model runs, varying measurement sample periods) and outputs (grids, data visualization web tools).
Skills Needed: Proficient in Python, Arc GIS; Atmospheric Science/Chemistry background helpful, but not required
POC: Richard Haeuber, Ph.D., Office of Air and Radiation/Office of Atmospheric Programs in Washington, DC, 202 343 9250, haeuber.richard@epa.gov
5-9. PFAS Treatment Opportunities
Per-and polyfluoroalkyl substances (PFAS) are fluorinated aliphatic substances with unique properties, such as being hydrophobic, lipophobic, and extremely stable due to the strength of the C-F bond. These properties led to their extensive use as surface active agents in products like stain repellants and fire-fighting foams. Currently, EPA has an extensive program ranging from analytics, health effects, exposure, and treatment. There is an opportunity for a student(s) to work collaboratively with EPA’s staff who are working on treating PFAS in drinking waters and contaminated sites. Below is a short description of the work. The student will work with a team of EPA researchers in Cincinnati, OH along with our collaborators in the Office of Water (Washington, DC), Department of Defense (San Antonio, TX and Dayton, OH), and numerous communities such as Wilmington, NC; Plainfield, MI; and Horsham, PA. It is acknowledged that this work is too broad for one student. The goal is to allow for the student/advisor/mentor to select the ideal subsection(s) of work based on the student’s interest and technical background.
This multiple components of the work on the treatment of PFAS include:
- Update the EPA’s Drinking Water Treatability Database (TDB) with recent literature. This will entail searching the recent literature for papers dealing with the treatment of PFAS, and condensing the results and conclusions to be incorporated in the TDB. Search EPA TDB.
- Work with EPA researchers on modeling GAC and anion exchange data obtained from numerous sources. This would involve model development and would require a student familiar with Python or R programing languages.
- 3) Work with EPA’s Work Breakdown Structure (WBS) Cost Models by including recent data and generating costs from pilot- and full-scale results from data gathered from numerous sources such as EPA, DOD, and communities. This can be in conjunction with an effort at the Air Force Institute of Technology (AFIT) that is attempting to merge EPA and DOD cost models. This will require a student to be familiar with Excel programing and with some engineering background. Search: EPA WBS
- Work with an EPA project with Calgon Carbon and Evoqua on evaluating the fate of PFAS in granular activated carbon reactivation (GAC) systems that will be reactivating spend GAC from community/remediation systems. This will involve coordinating with additional researchers from Research Triangle Park, NC. This would require a student to be familiar with system operations in general, and the ability to travel to Pennsylvania.
- Track and summarize EPA’s PFAS management programs (drinking water, site remediation, landfills, biosolids, etc.). This will involve collecting data from numerous sites across the country where EPA is studying/evaluating/responding to contaminated sites. The student will summarize the issues involved and EPA’s response. Compare actions and results across sites and prepare communication pieces for internal and external audiences. This will involve working with engineers and scientists in Cincinnati, RTP, Regional offices, communities, DOD, etc. Also, this will involve working with communication specialists in Cincinnati, OH and Washington, DC.
POC: Thomas Speth, ORD/National Risk Management Research Laboratory in Cincinnati, OH; 513 569 7208, speth.thomas@epa.gov
10. Resource Inventory of Uncertainty/Variability Tools and Guidance
EPA’s Risk Assessment Forum (RAF) Uncertainty and Variability Technical Panel was tasked with reviewing EPA’s needs in addressing uncertainty and variability in risk assessments used to inform decisions under various regulatory programs. Among the key challenges faced by risk assessors, decision makers and communicators are how to assess, address and communicate uncertainty in Agency products. Among the actions taken by the RAF Technical Panel was the development of a Resource Inventory – an annotated inventory of currently available resources regarding uncertainty and variability both within and outside of EPA. The panel concluded there are numerous existing resources developed by EPA and other organizations at the national and international level that provide a range of guidance and tools to support enhanced treatment of uncertainty and variability. The Technical Panel proposed that a Resource Inventory would be extremely valuable to risk assessors. Since the development of the Resource Inventory in early 2016, the Technical Panel recognized the need to review and update the Inventory to ensure that all entries are current, easily accessible, and organized in a manner that the user can easily locate information. The Inventory may also need to be updated to reflect additional resources that have been developed since 2016. Therefore, we request the intern review each of the current entries in the inventory to make sure that the references are current, links to the materials are still valid, descriptions are adequate and complete, and conduct a literature review to see if additional resources have been developed in the past few years. The intern will benefit from the experience of reviewing, curating and identifying the range of resources addressing uncertainty and also characterizing information gaps.
The successful candidate will have strong quantitative and communication skills and demonstrate motivation to see a project to completion. The benefits from this internship will be a greater understanding of the challenges facing a science-based regulatory agency and the utility of mathematics and statistical tools in the regulatory environment.
POC: Michael Broder, ORD/Office of the Science Advisor in Washington, DC; 202 564 3393, broder.michael@epa.gov
11. Applying Systematic Review to Risk Assessments
As part of Office of Research and Development, the National Center for Environmental Assessment (NCEA) is a leader in conducting the human health and ecological risk assessment to support the EPA program offices and regional offices as well as other stakeholders to support the decision making. Through evaluating a large body of complex scientific information for hazard identification and dose response, NCEA provides a strong scientific foundation for the regulatory decision making in protecting the human health and the environment based on reviewed publicly available scientific literature. As part of systematic review, a large body of literature is assessed in a transparent and reproducible manner through a set of criteria to identify the relevant studies from those that are not critical in the risk assessment. Systematic review is an advanced methodological approach but can be a resource intensive exercise especially for the large size of the database that contain many health endpoints to be evaluated. As part of systematic review, evidence mapping becomes a popular tool that helps to focus on the research assessment priorities and needs for the decision makers. It allows an assessor to systematize and visualize the complex scientific information in a user-friendly manner to help understand the database and to address specific questions that the decision makers may have. It also allows an assessor to identify data gaps for guiding future research. As a summer intern, the student would be able to learn the latest tool(s) used in systematic review and apply them to help advance the assessment needs for high profile chemicals.
Students should have taken biology, environmental science, or public health courses. Students should be proficient in Microsoft office software and have interest to learn systematic review tools.
POC: Santhini Ramasamy, ORD/National Center for Environmental Assessment in Washington, DC; 202 564 8328, Ramasamy.santhini@epa.gov
12. Evidence Synthesis Applied to Phosphorous in U.S. Lakes
Effective environmental management and policy decisions typically depend on the integration of large bodies of evidence gleaned from existing research and knowledge. Cohesively and transparently presenting this evidence to decision-makers and other stakeholders is a critical challenge in applied environmental sciences. Evidence syntheses must be detailed enough to adequately represent the complexity of environmental issues (and the myriad scientific findings relevant to those issues), yet simple enough to quickly convey (and provide support for) bottom-line messages. This project will explore different methods and tools for integrating and visualizing evidence derived from multiple sources (e.g., literature-based evidence, raw data analyses, data inventories, and empirical modeling), as part of a larger project examining phosphorus trends in US lakes.
Suggested skills for this project include a strong interest in data visualization and communication, a willingness to actively seek out novel visualization examples and possibilities, and the ability to become familiar with the technologies (i.e., software, programming code) powering the most promising options.
POC: Kate Schofield, ORD/National Center for Environmental Assessment in Washington, DC; 202 564 2640, schofield.kate@epa.gov
13-14. PFAS Screening of NIST Environmental Reference Materials
Environmental management and policy decisions are strengthened by the availability of suitable reference materials to underpin the analysis of environmental samples. The goal of these efforts is to screen existing NIST environmental reference materials (e.g. sludge, drinking water, house dust, sediments) for per- and polyfluoroalkyl substances (PFAS) with high resolution mass spectrometry. One project will focus primarily on the collection of high-resolution mass spectra for the identification of common PFAS and the other project will be more data focused to create consensus mass spectra of common per- and polyfluoroalkyl substances (PFAS) from existing and newly created data. This opportunity is suitable for up to two interns. Together these efforts will both expand NIST’s offering of PFAS standards to the wider research community and will contribute reference PFAS spectra to mass spectral databases.
Suggested skills for these projects include previous chemistry lab experience which involved sample extraction and analysis by mass spectrometry, organic chemistry, and beginner level R programming for the lab-based project. A general understanding of beginner to intermediate level R programming experience and a solid background in statistics with some Bayesian experience is preferred for the data project.
POC: Benjamin Place, MML/National Institute of Standards and Technology in Gaithersburg, MD; 301-975-3941, benjamin.place@nist.gov
15-16. Elemental Analysis of Seafood (Salmon and Shrimp) Reference Materials and Samples
With over 90% of the seafood imported into United States, it is critical for industry professionals to have access to suitable reference materials to ensure the quality and safety of our seafood. The focus of these projects is to strengthen efforts to provide evidence on the authenticity and traceability of salmon and shrimp. This opportunity is suitable for up to two interns. Interested candidates will perform broad elemental analysis (e.g. Cd, Ca, Cu, Mg, P, K, Se, Na, Zn, Pb) on farm raised and wild caught salmon and shrimp to establish within and between group variations. Measurements will be made on two new NIST reference materials and commercial samples.
Suggested skills for these projects include experience with inductively coupled plasma mass spectrometry (ICP-MS), previous chemistry lab experience which includes sample extraction and sample analysis and beginner level R programming.
POC: Lee Yu, MML/National Institute of Standards and Technology in Gaithersburg, MD; 301-975-4127, lee.yu@nist.gov