United States Department of Agriculture-Agricultural Research Service

4 ARTICLES PUBLISHED IN JoVE

JoVE Journal

Using High Resolution Computed Tomography to Visualize the Three Dimensional Structure and Function of Plant Vasculature

Andrew J. McElrone^1,2, 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.

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. Shapland², Arturo Calderon^2,3, Li Fitzmaurice^4,5, Kyaw Tha Paw U⁴, Richard L. Snyder⁴

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.

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.

Environment

The Hawaii Protocol for Scientific Monitoring of Coffee Berry Borer: a Model for Coffee Agroecosystems Worldwide

Melissa Anne Johnson^1,2, Robert Hollingsworth², Samuel Fortna^2,3, 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.