U.S. Department of Agriculture View Institution's Website 19 articles published in JoVE Environment In Situ Soil Moisture Sensors in Undisturbed Soils Todd G. Caldwell1, Michael H. Cosh2, Steven R. Evett3, Nathan Edwards4, Heather Hofman5, Bradley G. Illston6, Tilden Meyers7, Marina Skumanich8, Kent Sutcliffe9 1Nevada Water Science Center, U.S. Geological Survey, 2Agricultural Research Service, Hydrology and Remote Sensing Lab., U.S. Department of Agriculture, 3Agricultural Research Service, Conservation and Production Research Lab., U.S. Department of Agriculture, 4South Dakota State University, 5National Water and Climate Center, U.S. Department of Agriculture, 6University of Oklahoma, 7Air Resources Lab, National Oceanic and Atmospheric Administration, 8National Integrated Drought Information System, National Oceanic and Atmospheric Administration, 9Snow Survey Staff, U.S. Department of Agriculture The determination of soil water content is a critical mission requirement for many state and federal agencies. This protocol synthesizes multi-agency efforts to measure soil water content using buried in situ sensors. Immunology and Infection Collection and Processing of Lymph Nodes from Large Animals for RNA Analysis: Preparing for Lymph Node Transcriptomic Studies of Large Animal Species Catherine E. Vrentas1, Paola M. Boggiatto1, Robert G. Schaut1, Steven C. Olsen1 1National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture This protocol provides an overview of procedures for the isolation of RNA for the transcriptomic profiling of lymph node tissues from large animals, including steps in the identification and excision of lymph nodes from livestock and wildlife, sampling approaches to provide consistency across multiple animals, and considerations plus representative results for the post-collection preservation and processing for RNA analysis. Environment Double-stranded RNA Oral Delivery Methods to Induce RNA Interference in Phloem and Plant-sap-feeding Hemipteran Insects Saikat Kumar B. Ghosh1, Wayne B. Hunter2, Alexis L. Park1, Dawn E. Gundersen-Rindal1 1Invasive Insect Biocontrol and Behavior Laboratory, Agricultural Research Service, United States Department of Agriculture, 2Horticultural Research Laboratory, Agricultural Research Service, United States Department of Agriculture This article demonstrates novel techniques developed for oral delivery of double-stranded RNA (dsRNA) through the vascular tissues of plants for RNA interference (RNAi) in phloem sap feeding insects. Environment The Hawaii Protocol for Scientific Monitoring of Coffee Berry Borer: a Model for Coffee Agroecosystems Worldwide Melissa Anne Johnson1,2, Robert Hollingsworth2, Samuel Fortna2,3, Luis F. Aristizábal4, Nicholas C. Manoukis2 1Oak Ridge Institute for Science and Education, 2Daniel K. Inouye US Pacific Basin Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service, 3College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, 4Independent Consultant on CBB Management Comprehensive monitoring of coffee berry borer and host plant dynamics is essential for aggregating landscape-level data to improve management of this invasive pest. Here, we present a protocol for scientific monitoring of coffee berry borer movement, infestation, mortality, coffee plant phenology, weather, and farm management via a mobile electronic data recording application. Bioengineering Efficient Generation and Editing of Feeder-free IPSCs from Human Pancreatic Cells Using the CRISPR-Cas9 System Anjali Nandal1,2, Barbara Mallon3, Bhanu P. Telugu1,2,4 1Department of Animal and Avian Sciences, University of Maryland, 2Animal Bioscience and Biotechnology Laboratory, ARS, USDA, 3NIH Stem Cell Unit, Bethesda, National Institutes of Health, 4RenOVAte Biosciences Inc This protocol describes in detail the generation of footprint-free induced pluripotent stem cells (iPSCs) from human pancreatic cells in feeder-free conditions, followed by editing using CRISPR/Cas9 ribonucleoproteins and characterization of the modified single-cell clones. Environment Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health Shawn A. Steffan1,2, Prarthana S. Dharampal2, Luis Diaz-Garcia3,4, Cameron R. Currie5, Juan Zalapa1,3, Chris Todd Hittinger6,7,8 1Vegetable Crop Research Unit, USDA-ARS, 2Department of Entomology, University of Wisconsin-Madison, 3Department of Horticulture, University of Wisconsin-Madison, 4Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, 5Department of Bacteriology, University of Wisconsin-Madison, 6Laboratory of Genetics, Genome Center of Wisconsin, 7DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 8J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison Microbial consortia within bumble bee hives enrich and preserve pollen for bee larvae. Using next generation sequencing, along with laboratory and field-based experiments, this manuscript describes protocols used to test the hypothesis that fungicide residues alter the pollen microbiome, and colony demographics, ultimately leading to colony loss. Environment Continuous Instream Monitoring of Nutrients and Sediment in Agricultural Watersheds Niroj Aryal1,2, Michele L. Reba2 1Oak Ridge Institute of Science and Education (ORISE), 2Delta Water Management Research Unit, United States Department of Agriculture, Agriculture Research Unit USDA-ARS With the advancement of technology and the rise in end-user expectations, the need and use of higher temporal resolution data for pollutant load estimation has increased. This protocol describes a method for continuous in situ water quality monitoring to obtain higher temporal resolution data for informed water resource management decisions. Environment Measuring and Mapping Patterns of Soil Erosion and Deposition Related to Soil Carbonate Concentrations Under Agricultural Management Robert H. Erskine1, Lucretia A. Sherrod1, Timothy R. Green1 1Water Management and System Research Unit, Center for Agricultural Resources Research, USDA Agricultural Research Service (ARS) Spatial patterns of soil erosion and deposition can be inferred from differences in ground elevation mapped at appropriate time increments. Such changes in elevation are related to changes in near-surface soil carbonates. Repeatable methods for field and laboratory measurements of these quantities and data analysis methods are described here. Chemistry Green and Low-cost Production of Thermally Stable and Carboxylated Cellulose Nanocrystals and Nanofibrils Using Highly Recyclable Dicarboxylic Acids Huiyang Bian1,3, Liheng Chen2,3, Ruibin Wang2,3, Junyong Zhu3 1Jiangsu Provincial Key Lab of Pulp and Paper Science and Technology, Nanjing Forestry University, 2State Key Lab of Pulp and Paper Engineering, South China University of Technology, 3Forest Products Laboratory, U.S. Forest Service, U.S. Department of Agriculture Here we demonstrate a novel method for green and sustainable productions of highly thermally stable and carboxylated cellulose nanocrystals (CNC) and nanofibrils (CNF) using highly recyclable solid dicarboxylic acids. Immunology and Infection Procedures for Identifying Infectious Prions After Passage Through the Digestive System of an Avian Species Justin W Fischer1, Tracy A Nichols1, Gregory E Phillips1, Kurt C VerCauteren1 1Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, USDA Scavengers have potential to translocate infectious transmissible spongiform encephalopathy prions in their feces to disease-free areas. We detail methods used to determine if mouse-adapted scrapie prions remain infectious after passage though the digestive tract of American crows (Corvus brachyrhynchos), a common consumer of dead animals. Bioengineering Establishing Fungal Entomopathogens as Endophytes: Towards Endophytic Biological Control Soroush Parsa1, Viviana Ortiz1, Fernando E. Vega2 1Entomology, International Center for Tropical Agriculture (CIAT), Cali, Colombia, 2Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, USA This protocol demonstrates two inoculation methods to introduce the fungal entomopathogen Beauveria bassiana as an endophyte in the common bean (Phaseolus vulgaris), in preparation for subsequent evaluations of endophytic biological control. Biology Using High Resolution Computed Tomography to Visualize the Three Dimensional Structure and Function of Plant Vasculature Andrew J. McElrone1,2, Brendan Choat3, Dilworth Y. Parkinson4, Alastair A. MacDowell4, Craig R. Brodersen5 1U.S. Department of Agriculture, 2Department of Viticulture and Enology, University of California - Davis, 3Hawkesbury Institute for the Environment, University of Western Sydney, 4Advanced Light Source, Lawrence Berkeley National Lab, 5Citrus Research & Education Center, University of Florida High resolution x-ray computed tomography (HRCT) is a non-destructive diagnostic imaging technique that can be used to study the structure and function of plant vasculature in 3D. We demonstrate how HRCT facilitates exploration of xylem networks across a wide range of plant tissues and species. Immunology and Infection Analysis of the Solvent Accessibility of Cysteine Residues on Maize rayado fino virus Virus-like Particles Produced in Nicotiana benthamiana Plants and Cross-linking of Peptides to VLPs Angela Natilla1,2, Rosemarie W. Hammond1,2 1Plant Sciences Institute, Agricultural Research Service, United States Department of Agriculture, 2Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture A method to analyze the solvent accessibility of the thiol group of cysteine residues of Maize rayado fino virus (MRFV)-virus-like particles (VLPs) followed by a peptide cross-linking reaction is described. The method takes advantage of the availability of several chemical groups on the surface of the VLPs that can be targets for specific reactions. Biology Electroantennographic Bioassay as a Screening Tool for Host Plant Volatiles John J. Beck1, Douglas M. Light1, Wai S. Gee1 1Plant Mycotoxin Research, U.S. Department of Agriculture, Agricultural Research Service A method to rapidly screen host plant volatiles by measurement of the electrophysiological response of adult navel orangeworm (Amyelois transitella) antennae to single components and blends via electroantennographic analysis is demonstrated. Immunology and Infection Glass Wool Filters for Concentrating Waterborne Viruses and Agricultural Zoonotic Pathogens Hana T. Millen1, Jordan C. Gonnering1, Ryan K. Berg2, Susan K. Spencer3, William E. Jokela3, John M. Pearce4, Jackson S. Borchardt1, Mark A. Borchardt3 1Wisconsin Water Science Center, United States Geological Survey, 2University of Wisconsin – Madison, 3Agricultural Research Service, United States Department of Agriculture, 4Alaska Science Center, United States Geological Survey Glass wool filters have been used to concentrate waterborne viruses by a number of research groups around the world. Here we show a simple approach for constructing glass wool filters and demonstrate the filters are also effective in concentrating waterborne viral, bacterial and protozoan pathogens. Biology A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica Leland J. Cseke1, Sharon M. Talley2 1Department of Biological Sciences, The University of Alabama, Huntsville, 2USDA-APHIS-PPQ, Center for Plant Health Science and Technology We provide a cost-effective and rapid molecular genotyping protocol that employs variety-specific PCR primers that target DNA sequence differences within the chloroplast trnL-F spacer region to differentiate between varieties of Imperata cylindrica (cogongrass) that cannot be distinguished by morphology alone. These varieties include the federally listed noxious weed, cogongrass and closely-related, wide-spread ornamental variety, I. cylindrica var. koenigii (Japanese blood grass). Biology An Optimized Protocol for Rearing Fopius arisanus, a Parasitoid of Tephritid Fruit Flies Nicholas Manoukis1, Scott Geib1, Danny Seo1, Michael McKenney1, Roger Vargas1, Eric Jang1 1Agricultural Research Service, US Dept. of Agriculture, US Pacific Basin Agricultural Research Center Fopius arisanus is an egg-larval parasitoid of Tephritid fruit flies that is successfully used in biological control of these important tropical pests. We describe here an optimized protocol for rearing F. arisanus on a small scale using readily available materials. 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 Biology Gibberella zeae Ascospore Production and Collection for Microarray Experiments. Matias Pasquali1,2, Corby Kistler3 1Cereal Disease Laboratory, USDA, 2University of Minnesota/ Agroinnova, University of Torino, 3Cereal Disease Laboratory, University of Minnesota To study the developmental processes of ascospores in Gibberella zeae, a procedure for collection under sterile conditions is filmed in order to generate the highest level of information for protocol description. This should facilitate the reproducibility of the experiment, a crucial aspect when full genome expression profile tests are implemented.
