U.S. Environmental Protection Agency View Institution's Website 11 articles published in JoVE Genetics Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation Sara M. F. Vliet1, Monique Hazemi2, Donovan Blatz2, Marissa Jensen3, Sally Mayasich4, Thomas R. Transue5, Cody Simmons5, Audrey Wilkinson5, Carlie A. LaLone6 1Office of Research and Development, Center for Computational Toxicology and Exposure, Scientific Computing and Data Curation Division, U.S. Environmental Protection Agency, 2Oak Ridge Institute for Science and Education, 3Swenson College of Science and Engineering, Department of Biology, University of Minnesota Duluth, 4University of Wisconsin-Madison Aquatic Sciences Center, 5General Dynamics Information Technology, Research Triangle Park, 6Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, U.S. Environmental Protection Agency Here, we present a protocol to utilize the latest version of the US Environmental Protection Agency Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool. This protocol demonstrates the application of the online tool to rapidly analyze protein conservation and provide customizable and easily interpretable predictions of chemical susceptibility across species. Engineering Determining Viral Disinfection Efficacy of Hot Water Laundering Anne Mikelonis*1, John Archer*1, Barbara Wyrzykowska-Ceradini2, Eric Morris3, Jonathan Sawyer2, Timothy Chamberlain2, Ahmed Abdel-Hady2, Mariela Monge4, Abderrahmane Touati2 1Office of Research and Development, Center for Environmental Solutions and Emergency Response, Homeland Security and Materials Management Division, U.S. Environmental Protection Agency, 2Jacobs Technology Inc., 3Science Systems and Applications Inc., 4CSS Inc. In response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, a laboratory protocol was developed to test the viral disinfection efficacy of hot water laundering of cloth face coverings, cotton scrubs, and denim pants. The Phi6 virus (bacteriophage) was used as the organism to test disinfection efficacy. Environment Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow James McCord1, Mark Strynar2 1Oak Ridge Institute for Science and Education, National Exposure Research Laboratory, U.S. Environmental Protection Agency, 2National Exposure Research Laboratory, U.S. Environmental Protection Agency Here, we present a protocol for the sequential targeted quantification and non-targeted analysis of fluorinated compounds in water by mass spectrometry. This methodology provides quantitative levels of known fluorochemical compounds and identifies unknown chemicals in related samples with semi-quantitative estimates of their abundance. Biology Procedure and Key Optimization Strategies for an Automated Capillary Electrophoretic-based Immunoassay Method Gail M Nelson1, Jenna M Guynn2, Brian N Chorley1 1National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, 2Oak Ridge Institute for Science and Education at U.S. Environmental Protection Agency A capillary-based immunoassay using a commercial platform to measure target proteins from total protein preparations is demonstrated. In addition, assay parameters of exposure time, protein concentration, and antibody dilution are optimized for a cell culture model system. Immunology and Infection Developing a Salivary Antibody Multiplex Immunoassay to Measure Human Exposure to Environmental Pathogens Swinburne A. J. Augustine1, Tarsha N. Eason2, Kaneatra J. Simmons1, Clarissa L. Curioso3, Shannon M. Griffin1, Malini K. D. Ramudit1, Trevor R. Plunkett4 1National Exposure Research Laboratory, U.S. Environmental Protection Agency, 2National Risk Management Research Laboratory, U.S. Environmental Protection Agency, 3Oak Ridge Institute for Science and Education, 4Department of Biological Sciences, McMicken College of Arts and Sciences, University of Cincinnati In the current climate of scarce resources, new technologies are emerging that allow researchers to conduct studies cheaper, faster and with more precision. Here we describe the development of a bead-based salivary antibody multiplex immunoassay to measure human exposure to multiple environmental pathogens simultaneously. Environment EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. II. Total Culturable Virus Assay G. Shay Fout1, Jennifer L. Cashdollar1 1National Exposure Research Laboratory, U.S. Environmental Protection Agency Here we present a procedure to measure total culturable viruses using the Buffalo Green Monkey kidney cell line. The procedure provides a standardized tool for measuring the occurrence of infectious viruses in environmental and drinking waters. Environment EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. Part III. Virus Detection by RT-qPCR G. Shay Fout1, Jennifer L. Cashdollar1, Shannon M. Griffin1, Nichole E. Brinkman1, Eunice A. Varughese1, Sandhya U. Parshionikar2 1National Exposure Research Laboratory, U.S. Environmental Protection Agency, 2Technical Services Center, Office of Ground Water and Drinking Water, U.S. Environmental Protection Agency Here we present a procedure to quantify enterovirus and norovirus in environmental and drinking waters using reverse transcription-quantitative PCR. Mean virus recovery from groundwater with this standardized procedure from EPA Method 1615 was 20% for poliovirus and 30% for murine norovirus. Environment EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. I. Collection of Virus Samples G. Shay Fout1, Jennifer L. Cashdollar1, Eunice A. Varughese1, Sandhya U. Parshionikar2, Ann C. Grimm1 1National Exposure Research Laboratory, U.S Environmental Protection Agency, 2Technical Support Center, Office of Ground Water and Drinking Water, U.S Environmental Protection Agency EPA Method 1615 uses an electropositive filter to concentrate enteroviruses and noroviruses in environmental and drinking waters. This manuscript describes the procedure for collecting samples for Method 1615 analyses. Environment A Small Volume Procedure for Viral Concentration from Water Brian R. McMinn1, Asja Korajkic1 1U.S. EPA An approach was developed for identifying optimal viral concentration conditions for small volume water samples using spikes of human adenovirus. The techniques described here are used to identify concentration parameters for other viral targets, and applied to large-scale viral concentration experimentation. Immunology and Infection A Modified EPA Method 1623 that Uses Tangential Flow Hollow-fiber Ultrafiltration and Heat Dissociation Steps to Detect Waterborne Cryptosporidium and Giardia spp. Eric R. Rhodes1, Leah Fohl Villegas2, Nancy J. Shaw2, Carrie Miller3, Eric N. Villegas1 1National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency, 2Shaw Environmental & Infrastructure, 3Office of Ground Water and Drinking Water, US Environmental Protection Agency This protocol describes the use of a tangential flow hollow-fiber ultrafiltration sample concentration system and a heat dissociation as alternative steps for the detection of waterborne Cryptosporidium and Giardia species using EPA Method 1623. Immunology and Infection Obtaining Highly Purified Toxoplasma gondii Oocysts by a Discontinuous Cesium Chloride Gradient Sarah E. Staggs1, Mary Jean See2, J P. Dubey3, Eric N. Villegas2,4 1Dynamac, Inc., 2Department of Biological Sciences, University of Cincinnati, McMicken College of Arts and Science, 3Animal Parasitic Disease Laboratory, Agricultural Research Service, U.S. Department of Agriculture, 4National Exposure Research Laboratory, US Environmental Protection Agency This study describes the development of a modified CsCl method that easily purifies T. gondii oocysts from feces of infected cats that are suitable for molecular biological and tissue culture manipulation
