United States Department of Agriculture-Agricultural Research Service 4 articles published in JoVE Chemistry Identification of Antibacterial Immunity Proteins in Escherichia coli using MALDI-TOF-TOF-MS/MS and Top-Down Proteomic Analysis Clifton K. Fagerquist1, Ernesto Rojas1 1Produce Safety & Microbiology, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture Here we present a protocol for the rapid identification of proteins produced by genomically sequenced pathogenic bacteria using MALDI-TOF-TOF tandem mass spectrometry and top-down proteomic analysis with software developed in-house. Metastable protein ions fragment because of the aspartic acid effect and this specificity is exploited for protein identification. Environment A Protocol for Collecting and Constructing Soil Core Lysimeters Louis S. Saporito1, Ray B. Bryant1, Peter J. A. Kleinman1 1Pasture Systems and Watershed Management Research Unit, USDA - Agricultural Research Service A detailed method for extraction and assembly of intact soil core lysimeters and their use for study of leachate and associated loss of nutrients from surface applied poultry litter is demonstrated. Environment RNAi-mediated Control of Aflatoxins in Peanut: Method to Analyze Mycotoxin Production and Transgene Expression in the Peanut/Aspergillus Pathosystem Renée S. Arias1, Phat M. Dang1, Victor S. Sobolev1 1National Peanut Research Laboratory, United States Department of Agriculture, Agricultural Research Service We demonstrate a method for the analysis of aflatoxins and transgene expression in peanut seeds that contain RNA-interference signals for silencing aflatoxin-synthesis genes in the fungus Aspergillus flavus. RNAi-mediated control of mycotoxins in plants has not been reported previously. Environment Surface Renewal: An Advanced Micrometeorological Method for Measuring and Processing Field-Scale Energy Flux Density Data Andrew J. McElrone1,2, Thomas M. Shapland2, Arturo Calderon2,3, Li Fitzmaurice4,5, 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.
