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United States Department of Agriculture-Agricultural Research Service

4 ARTICLES PUBLISHED IN JoVE

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JoVE Journal

Using High Resolution Computed Tomography to Visualize the Three Dimensional Structure and Function of Plant Vasculature
Andrew J. McElrone 1,2, Brendan Choat 3, Dilworth Y. Parkinson 4, Alastair A. MacDowell 4, Craig R. Brodersen 5
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.

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JoVE Journal

Surface Renewal: An Advanced Micrometeorological Method for Measuring and Processing Field-Scale Energy Flux Density Data
Andrew J. McElrone 1,2, Thomas M. Shapland 2, Arturo Calderon 2,3, Li Fitzmaurice 4,5, Kyaw Tha Paw U 4, Richard L. Snyder 4
1Crops Pathology and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, 2Department of Viticulture & Enology, University of California, Davis, 3Faculty of Agricultural Sciences, University of Chile, 4Atmospheric Science, University of California, Davis, 5URS Corporation Australia Pty. Ltd.

Surface renewal is a micrometeorological method that is being used increasingly to determine energy fluxes, but its technical complexity makes it inaccessible to a broad audience. We describe the steps needed to set up and calibrate a surface renewal field station, to acquire and process data, and to correctly interpret results.

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Genetics

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
Marisa E. Miller *1,2, Katie L. Liberatore *1,3, Shahryar F. Kianian 1,3
1Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, 2Department of Horticultural Science, University of Minnesota, 3Department of Plant Pathology, University of Minnesota

The comparison and optimization of two plant organellar DNA enrichment methods are presented: traditional differential centrifugation and fractionation of the total gDNA based on methylation status. We assess the resulting DNA quantity and quality, demonstrate performance in short-read next-generation sequencing, and discuss the potential for use in long-read single-molecule sequencing.

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Environment

The Hawaii Protocol for Scientific Monitoring of Coffee Berry Borer: a Model for Coffee Agroecosystems Worldwide
Melissa Anne Johnson 1,2, Robert Hollingsworth 2, Samuel Fortna 2,3, Luis F. Aristizábal 4, Nicholas C. Manoukis 2
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.

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