SETAC North America 44th Annual Meeting

This course will cover the fundamentals of key ASTM sediment guidance related to sediment corrective actions, including an overview of the risk-based corrective action framework guidance, analytical guidance, non-aqueous phase liquid mobility/migration evaluations for sediment sites, as well as post-remedy monitoring. Additionally, this course will cover the fundamentals of determining representative background concentrations for sediment sites. At the end of the course, attendees would be familiar with these guidance documents, and have a better understanding of approaches to – and resources for – sediment site assessment, including sediment-specific considerations.

Instructors

Allison D. Geiselbrecht, Floyd | Snider

Geiselbrecht is a marine microbiologist with 20 years of experience coordinating and managing multidisciplinary environmental projects. Her expertise is in the investigation of sediment and water chemistry. Geiselbrecht has worked extensively on projects involving geochemistry of freshwater and marine sediments and has conducted numerous study design, research, and field investigations. She has extensive field sampling experience with sediments and biota.

Eric Litman, NewFields

Eric Litman is an environmental chemist at NewFields with 20 years of experience in the field of applied forensic chemistry. His work at NewFields is focused on the investigation of contaminated sediment sites, with a particular focus on NRD assessments and CERCLA cost allocation cases. Litman has worked in a variety of laboratory settings as both an analytical chemist specializing in hydrocarbon chemistry and as a laboratory manager. His research interests include environmental policy, the history of industrial chemistry, the optimization of analytical techniques and the development of novel methods to measure emerging contaminants.

The analysis of microbial communities is challenging due to their biological and bioinformatic complexity. A variety of culture-based and molecular assay are available, the latter of which especially can generate diverse, noisy data with no one clear “best” analysis method. This is especially true for environmental microbiomes, since common analysis methods are often easiest for human-associated microbiota. This course will provide a brief introduction to microbial community analysis techniques appropriate for both host-associated and free-living microbiomes, based on amplicon and metagenomic sequencing. The day will begin with lecture and discussions around sample collection, extraction, library prep and sequencing. We will then transition to a format of short background lectures followed by several hands-on tutorials. We will cover the processing of data from raw reads through the generation of taxonomic and functional feature tables and the subsequent approaches for data visualization and statistical analysis. This will include both 16S rRNA gene amplicon sequencing (generalizable to 18S and ITS amplicons) as well as a brief introduction to the analysis of shotgun metagenomics. In full the course will leverage both the command line environment as well as tutorials in RStudio.

Instructors

Kelsey Thompson, Harvard T.H. Chan School of Public Health

Kelsey Thompson is a Research Associate in the Huttenhower Laboratory at the Harvard T.H. Chan School of Public Health Department of Biostatistics, an affiliate with the Broad Institute. Her postdoctoral research focuses on elucidating the role of the gut microbiome in autoimmunity and distal inflammation. Kelsey has a Ph.D. in Environmental Toxicology from Texas Tech University and a B.S. in Marine Science from the University of New England. Her dissertation research focused on acid rock drainage and its impact on microbial communities, specifically on changes in the microbial community structures of sediment, water, and fishes exposed downstream of highly contaminated sites.

Joseph Bisesi, University of Florida

Joseph Bisesi, Ph.D., is an assistant professor in the Department of Environmental and Global Health and the Center for Environmental and Human Toxicology at the University of Florida. Bisesi’s research focuses on how emerging contaminants impact the physiology and behavior of aquatic organisms with a specific focus on the gastrointestinal system as a target of contaminants. Much of Bisesi’s work examines the relationship between effects of chemical on gastrointestinal function and the host associated microbiome.

Jeremy Wilkinson, PacBio

Jeremy Wilkinson is the Segment Lead for Microbial Genomics at PacBio. He has a Ph.D. in Environmental Toxicology with a specific focus on microbiome analysis from Texas Tech University, a M.S. in Zoology with a focus on phylogenetics from Oklahoma State University, and a B.S. in Biochemistry and Molecular Biology with a minor in Microbiology from Oklahoma State University. Jeremy came to PacBio ~2 years ago from the Harvard T.H. Chan School of Public Health, where he was the Director of the Microbiome Analysis Core and a Research Scientist in the Department of Biostatistics in the Huttenhower Lab for ~4 years. Before that he was at RTL Genomics (Research and Testing Laboratory), a privately-owned next-generation sequencing laboratory that specializes in microbiome sequencing and analysis, where he worked for ~6 years and was most recently the Director of Operations and Senior Biostatistician after being a wet lab Research Scientist, a Biostatistician, and the Associate Director of Operations.

Chris Martynuk, University of Florida

Christopher Martyniuk studies organismal responses to endocrine disruptors. His academic appointment is at the University of Florida as an Associate Professor at the Center for Environmental and Human Toxicology. Martyniuk is also the Editor-in-Chief of Comparative Biochemistry and Physiology: Genomics and Proteomics. His research group currently utilizes methods in microbiome, transcriptomics, proteomics, and computational biology, to improve mechanistic understanding of exogenous hormonal agents and chemical toxicants.

Data describing the potential adverse effects of chemicals across species is sparse. Therefore, novel strategies are needed to make use of existing data to understand chemical effects across species. An underutilized data source for purposes of species extrapolation is protein sequence and structural information. To capitalize on these data, bioinformatics approaches are being applied to challenges in extrapolating toxicity data/knowledge across the diversity of species. A tool that has been developed to serve this purpose is the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool, that utilizes this data to predict chemical susceptibility across species based on concepts derived from evolutionary biology. The assumption underlying the SeqAPASS tool is that the greater the similarity between the protein target in a sensitive or model organism to other species, the more likely the protein in the other species functions similarly, either binding to a chemical or performing a similar role in a pathway. This knowledge of conservation across species provides a rapid mechanism for understanding how well model organisms serve as surrogates for other untested species and provides a line of evidence for extrapolation of toxicity or pathway data to other species.

Instructors

Carlie LaLone, USEPA

Carlie LaLone is Acting Branch Chief/Research Bioinformatician, in USEPA’s Center for Computational Toxicology and Exposure. Her primary research interest is developing tools for researchers and decision makers to extrapolate biological knowledge from one species to the diversity of species and predict chemical susceptibility to species that could never be tested in the lab. She received her B.S./B.A. degrees from U. MN Duluth and a Ph.D. in genetics from Iowa State. Carlie is the co-founder of the International Consortium to Advance Cross Species Extrapolation in Regulation.

Marissa Jensen, USEPA

Marissa Jensen is a U.S. Environmental Protection Agency Cooperative Agreement Trainee and Ph.D. student at the University of Minnesota-Duluth. Jensen received her master’s degree in Integrated Biosciences from the University of Minnesota-Duluth, where she was advised by Carlie LaLone (USEPA/UMD). Her master’s research focused on broadening the definition of the taxonomic domain of applicability of adverse outcome pathways through bioinformatics approaches. Currently, Jensen is pursuing a Ph.D. at the University of Minnesota-Duluth continuing under the direction of Carlie LaLone. Her research focus includes furthering adverse outcome pathway application and studying effects of pesticides across multiple species. 

Peter Schumann, Oak Ridge Institute for Science and Education

Peter Schumann is currently a research fellow through the Oak Ridge Institute for Science and Education (also known as ORISE) at the Great Lakes Toxicology and Ecology Division within the USEPA. He holds a bachelor’s degree in biochemistry from the University of Wisconsin – Stevens Point and a master’s degree in freshwater science from the University of Wisconsin – Milwaukee. His research interests relate to the application of bioinformatics towards ecotoxicology to improve non-animal-based testing methods.

In response to concerns that certain environmental chemicals might interfere with the endocrine system of humans and wildlife, regulations have been promulgated around the world targeting the evaluation of these types of effects. The purpose of this course is to address key topics related to endocrine system evaluation and regulatory requirements around the world. The course provides basic information on vertebrate endocrine systems, mechanisms of control, and adverse effects. Focus is on the estrogen, androgen, and thyroid systems, although new endocrine system targets will be discussed. Requirements of the ECHA/EFSA Guidance document (2018) and the US EPA’s Endocrine Disruptor Screening Program will be presented. Regulatory needs for pesticides, biocides and industrial chemicals, including the development of guidance and criteria, will be covered. Screens and tests used in these programs are described, including plans to reduce the reliance on animal testing with the use of high throughput in vitro assays, in silico modeling, new approach methods, read-across, and adverse outcome pathways. Use of weight of evidence evaluations in interpreting the data will be covered. Finally, an interactive simulation/game will be staged where groups of participants can engage in a transparent and quantitative weight of evidence evaluation of data.

Instructors

Ellen Mihaich, Environmental and Regulatory Resources

Ellen Mihaich, Ph.D., DABT, owns ER2, an environmental firm in Durham, NC. Among endocrine-related activities, she is a BIAC representative to the OECD Eco-Validation Management Group for endocrine testing and is the scientific coordinator of the Endocrine Policy Forum. She received a B.A. from Wellesley College and M.S. and Ph.D. degrees in environmental toxicology from Duke University, where she holds an adjunct appointment and teaches a graduate course in risk assessment. She is a past-president of SETAC and a SETAC Fellow.

Steve Levine, Bayer CropScience

Steve Levine joined a legacy Bayer CropScience in 2000 following EPA & NIH Fellowships in Ecotoxicology and Toxicology. Levine is a Bayer Distinguished Fellow within Regulatory Sciences and has conducted research on the regulation of endocrine pathways and led testing programs to assess potential interaction with endocrine pathways. Levine has served on international committees developing guidelines for endocrine testing, is actively involved with training programs on pesticide product safety assessments & Chairs CropLife International’s ED Working Group.

Carlie Lalone, USEPA

Carlie LaLone is Acting Branch Chief/Research Bioinformatician, in USEPA’s Center for Computational Toxicology and Exposure. Her primary research interest is developing tools for researchers and decision makers to extrapolate biological knowledge from one species to the diversity of species and predict chemical susceptibility to species that could never be tested in the lab. She received her B.S./B.A. degrees from U. MN Duluth and a Ph.D. in genetics from Iowa State. Carlie is the co-founder of the International Consortium to Advance Cross Species Extrapolation in Regulation.

Bee pollinators play a vital role in ecosystem health and are essential to ensuring food security. With declines of both managed and wild pollinator populations in recent years, regulatory scientists have been challenged to develop and implement better ways to identify and assess risks in order to protect pollinator populations now and in the future. Pesticide Risk Assessment for Pollinators was the topic of a SETAC Pellston Workshop convened in Pensacola, FL, and a regulatory guidance document issued jointly by the U.S. Environmental Protection Agency, Health Canada’s Pest Management Regulatory Agency, and California Department of Pesticide Regulation. This course will cover the components of this tiered risk assessment process for honey bees, bumble bees, and solitary nesting bees, including problem formulations for various chemical use scenarios, effects studies, exposure measurements, risk evaluation procedures, interspecies toxicity extrapolation, and emerging trends. A copy of the SETAC Pellston Workshop report, Pesticide Risk Assessment for Pollinators, will be included in the course materials.

Instructors

Dan Schmehl, Bayer CropScience

Daniel Schmehl, Ph.D., is a Global Pollinator Safety Expert and Science Fellow for Bayer CropScience LP.  Schmehl has a background in honey bee husbandry and environmental toxicology. He joined Bayer in 2015 with expertise in honey bee husbandry, pollinator ecotoxicology, and Varroa management. His primary responsibilities are to conduct environmental risk assessments aimed at reducing non-target effects of pesticides to pollinators and other species. He participates in multiple external research collaborations and working groups aimed at advancing our understanding and methodology for assessing pesticide risks to pollinators.

Max Feken, Syngenta Crop Protection

Max Feken, M.S. is an ecotoxicologist with Syngenta with 20 years of experience in pesticide ecological risk assessments. Prior to joining Syngenta in 2014, Max worked for the Florida Department of Agriculture where he was responsible for evaluating potential impacts of registered pesticides to non-target terrestrial and aquatic organisms including determining risk of pesticides on honey bees and other pollinators. While in Florida, Max assisted in the development of a collaborative effort between citrus growers and beekeepers to identify measures that growers and beekeepers can adopt to protect both crops and honey bee colonies.

Michael Wagman, USEPA

Michael Wagman, M.S., is a Biologist for the USEPA Office of Pesticide Programs, Environmental Fate and Effects Division. Michael has worked in pesticide risk assessment for EPA for the past 8 years and has co-chaired several EPA tech teams including the Terrestrial Biology Tech Team (TBTT) and Plant Tech Team (PTT). He led the development of EPA’s residue strategy for testing neonicotinoid insecticides in agricultural crops and co-authored the Preliminary Bee Risk Assessments for the Registration Review of Clothianidin and Thiamethoxam. Michael has recently worked to improve the characterization of seed treatment exposures in risk assessments.

Carlie Lalone, USEPA

Carlie LaLone is Acting Branch Chief/Research Bioinformatician, in USEPA’s Center for Computational Toxicology and Exposure. Her primary research interest is developing tools for researchers and decision makers to extrapolate biological knowledge from one species to the diversity of species and predict chemical susceptibility to species that could never be tested in the lab. She received her B.S./B.A. degrees from U. MN Duluth and a Ph.D. in genetics from Iowa State. Carlie is the co-founder of the International Consortium to Advance Cross Species Extrapolation in Regulation.

Jeremy Koelmel and John Bowden, experts in non-targeted PFAS analysis and software development, will share their workflow from start to finish for PFAS non-targeted analysis. The workshop will cover all steps of the workflow including sample handling, sample extracting, data-acquisition, data-processing, and validation. The workshop will focus on LC-HRMS/MS approaches, but GC approaches will also be covered. By the end of the course, you should be able to understand all steps in the PFAS non-targeted analysis workflow and have a good understanding of what you need to begin PFAS non-targeted analysis in your laboratory. You will also get hand on experience investigating non-targeted datasets using open-source software approaches, with challenges provided to see how many PFAS molecules you can validate/discover.

Instructors

Jeremy Paul Koelmel, Yale University

Jeremy Koelmel’s research focuses on developing and applying techniques in exposomics. Exposomics covers the interaction between environmental exposures, including from contaminants, diet, and drugs, with biological consequences. Koelmel’s team develops mass spectrometry data-acquisition methodologies and software that more comprehensively cover molecules which are indicative of our exposures and biological response. By increasing coverage and developing high-throughput pipelines in exposomics and related fields, his team aims to increase the ease, utility, harmonization, and adoption of omics approaches. The research, trainings and mentoring during Koelmel’s career are effecting changes in policy and education, informing litigation, and ideally will reduce harmful exposures and their consequences. Through Koelmel’s various capacities as CEO of innovative omics, working closely with Agilent Technologies, and in various research positions at the University of Florida and Yale University, Koelmel has led teams in industry and academia to develop state-of-the-art data-processing and identification software in the fields of metabolomics, lipidomics, per- and polyfluoroalkyl substances (PFAS), and general non-targeted suspect screening. These proprietary and open-source tools (over 12 software developed, most available at innovativeomics.com) are widely used by the scientific community and industry. For PFAS analysis Jeremy Koelmel has led the development of FluoroMatch Suite, the most comprehensive open-source and free software for PFAS non-targeted analysis to date. Koelmel has also provided trainings to many companies and laboratories on PFAS non-targeted analysis as part of his services at Innovative Omics. Koelmel has co-authored 53 articles and book chapters, 5 technical reports, and 12 software to date in the fields of measuring xenobiotics, and detection of biological molecules for clinical and environmental applications. Fourty-eight of his publications were published recently (2017 onwards), and 25 are first author publications. Koelmel has given over 67 academic talks, including 14 invited talks, presenting his work at both public and industrial venues. He has published with numerous undergraduates for which he mentored and they have often taken a lead position in the work (e.g., co-first author).

John A. Bowden, University of Florida

John Bowden's research focuses on employing mass spectrometric methods at the chem/bio interface, with a long-standing interest in endocrine disruption and environmental chemistry. A new drive in the laboratory is focused on studying the interplay between external measures of exposure (e.g., anthropogenic contaminants) and internal measures of exposure (e.g., lipids, hormones), in the context of health and disease. The tools Bowden's group uses to study these relationships are either gas or liquid chromatography and mass spectrometry (employing both targeted and non-targeted workflows). Beyond the implementation of these workflows, a considerable effort in the laboratory also focuses on improving key metrological aspects, including method development and optimization, quantitation, and quality control. Current work primarily employs workflows capable of performing lipidomics, metabolomics, and the measurement of chemicals of emerging concern (e.g., perfluorinated chemicals). Application areas are varied, encompassing environmental sampling, nutritional studies, lab-based models, and both wildlife and human health. Bowden has published 135 publications in the field of mass spectrometry and omics-related methodologies. Just in the last 3 years, he has published over 25 manuscripts on PFAS targeted and non-targeted analysis. These publications focus on discovering PFAS in novel materials, developing PFAS methodologies for mass spectrometry, understanding the health impacts of PFAS using model and non-model organisms, and characterizing PFAS fate and transport in the environment.

Science communication is key to retaining support of the community and nation, both moral and monetary. Communicating science to scientists is vastly different from communicating science to the public. This short course explores the different communication avenues a scientist has available to them in communicating their science and provides practical steps in creating science writing for the public. During the short course, participants will transform their scientific writings into science writing that is accessible to non-scientist readers. Participants will bring a research or white paper with them, translate that into a press release, which they will learn how to edit appropriately for a general audience. That press release will be shortened into a sound bite and finally the sound bite will be converted into a social media post for their preferred platform (Facebook, IG, Twitter, etc). The course will end with a discussion on how the COVID pandemic has challenged science communicators, highlighting examples of good and bad science communication over the last few years. We will also discuss the differences between platforms and discuss the changing social media landscape.

Instructors

Corinna Singleman, Singleman Consulting

Corinna Singleman is a science communicator and founder of Singleman Consulting, a consulting firm whose goal is to increase science understanding between scientists and the public. As a communications consultant, Corinna trains other scientists on how to communicate their science better and helps to create materials for researchers to better share their science. She is an ecotoxicologist who studied the impacts of PCBs on fish in the Hudson River, NY. Corinna has spoken at community events with local stakeholders and with political representatives in Albany, NY and is passionate about science communication. She was a freelance editor for peer-reviewed scientific articles and has taught course modules in scientific writing. Corinna will be leading the first part of this short course training participants in editing and translating their scientific writing for the general public. She will be assisting participants in activities during the second half of the short course focusing on social media.

Laura Langan, Baylor University

Laura Langan is a research scientist (ecotoxicology) at the University of Baylor. She has volunteered her time as a scientist communicator in various roles at both a SETAC regional and international level as well as more locally. Recently in collaboration with colleagues in Europe and Asia, she co-wrote a go to guide to aid her peers with science communication using peer reviewed science communication literature. Laura will be leading the second part of this short course training participants in the use of social media and translating longer writing for the public into the varied styles of different social media platforms. She will be assisting participants in activities during the first half of the short course.