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U.S. Geological Survey

7 ARTICLES PUBLISHED IN JoVE

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Biology

A New Clarification Method to Visualize Biliary Degeneration During Liver Metamorphosis in Sea Lamprey (Petromyzon marinus)
Yu-Wen Chung-Davidson 1, Peter J. Davidson 1, Anne M. Scott 1, Erin J. Walaszczyk 1, Cory O. Brant 1, Tyler Buchinger 1, Nicholas S. Johnson 2, Weiming Li 1
1Department of Fisheries & Wildlife, Michigan State University, 2Hammond Bay Biological Station, Great Lakes Science Center, U.S. Geological Survey

Sea lamprey lose the gall bladder and bile ducts during metamorphosis, a process similar to human biliary atresia. A new fixation and clarification method (CLARITY) was modified to visualize the entire biliary tree using laser scanning confocal microscopy. This method provides a powerful tool to study biliary degeneration.

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Environment

Methods of Soil Resampling to Monitor Changes in the Chemical Concentrations of Forest Soils
Gregory B. Lawrence 1, Ivan J. Fernandez 2, Paul W. Hazlett 3, Scott W. Bailey 4, Donald S. Ross 5, Thomas R. Villars 6, Angelica Quintana 7, Rock Ouimet 8, Michael R. McHale 1, Chris E. Johnson 9, Russell D. Briggs 10, Robert A. Colter 11, Jason Siemion 1, Olivia L. Bartlett 12, Olga Vargas 13, Michael R. Antidormi 1, Mary M. Koppers 9
1New York Water Science Center, U.S. Geological Survey, 2School of Forest Resources, University of Maine, 3Natural Resources Canada, Canadian Forest Service, 4Northern Research Station, U.S. Forest Service, 5Department of Plant and Soil Science, University of Vermont, 6Ottauquechee NRCD, USDA Natural Resources Conservation Service, 7Green Mountain National Forest, U.S. Forest Service, 8Direction de la Recherche Forestière, Ministère du Québec, 9Department of Civil and Environmental Engineering, Syracuse University, 10Division of Environmental Science, SUNY College of Environmental Science and Forestry, 11White Mountain National Forest, U.S. Forest Service, 12Natural Resources and Earth System Sciences, University of New Hampshire, 13Greenwich, NY Field Office, USDA Natural Resources Conservation Service

Repeated soil sampling has recently been shown to be an effective way to monitor forest soil change over years and decades. To support its use, a protocol is presented that synthesizes the latest information on soil resampling methods to aid in the design and implementation of successful soil monitoring programs.

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Environment

Necropsy-based Wild Fish Health Assessment
Vicki S. Blazer 1, Heather L. Walsh 2, Ryan P. Braham 1, Cheyenne Smith 2
1National Fish Health Research Laboratory, Leetown Science Center, U.S. Geological Survey, 2School of Natural Resources, West Virginia University

The health of wild fishes can be used as an indicator of aquatic ecosystem health. Necropsy-based fish health assessments provide documentation of visible lesions or abnormalities, data used to calculate condition indices as well as the opportunity to collect tissues for microscopic evaluation, gene expression and other more in-depth analyses.

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JoVE Journal

Manufacturing Simple and Inexpensive Soil Surface Temperature and Gravimetric Water Content Sensors
Armin Howell 1, Colin Tucker 1, Edmund E. Grote 1, Maik Veste 2,3, Jayne Belnap 1, Gerhard Kast 4, Bettina Weber 5,6, Sasha C. Reed 1
1Southwest Biological Science Center, U.S. Geological Survey, 2Centre for Energy Technology Brandenburg, 3Institute of Environmental Sciences, Brandenburg University of Technology Cottbus-Senftenberg, 4Umweltanalytische Produkte GmbH, 5Institute of Plant Sciences, University of Graz, 6Multiphase Chemistry Department, Max Planck Institute for Chemistry

Accurately measuring temperature and water content of the upper 5 mm of the soil surface can improve our understanding of environmental controls on biological, chemical, and physical processes. Here we describe a protocol for manufacturing, calibrating, and conducting measurements with soil surface temperature and moisture sensors.

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Environment

Capture of Environmental DNA (eDNA) from Water Samples by Flocculation
William B. Schill 1
1Leetown Science Center, U.S. Geological Survey

Environmental DNA (eDNA) is typically captured from water samples using alcohol precipitation, filtration, or flocculation. Presented here is an alternative protocol that uses lanthanum chloride to enable collection of dissolved and particulate-bound nucleic acids from water samples containing eukaryotic cells, prokaryotic cells, and virus.

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Environment

Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications
Katy E. Klymus *1, Dannise V. Ruiz Ramos *1, Nathan L. Thompson *1, Catherine A. Richter *1
1Columbia Environmental Research Center, U.S. Geological Survey

Environmental DNA assays require rigorous design, testing, optimization and validation before the collection of field data can begin. Here, we present a protocol to take users through each step of designing a species-specific, probe-based qPCR assay for the detection and quantification of a target species DNA from environmental samples.

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Environment

In Situ Soil Moisture Sensors in Undisturbed Soils
Todd G. Caldwell 1, Michael H. Cosh 2, Steven R. Evett 3, Nathan Edwards 4, Heather Hofman 5, Bradley G. Illston 6, Tilden Meyers 7, Marina Skumanich 8, Kent Sutcliffe 9
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.

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