University of Massachusetts Amherst 10 articles published in JoVE Chemistry Covalent Labeling with Diethylpyrocarbonate for Studying Protein Higher-Order Structure by Mass Spectrometry Zachary J. Kirsch1, Blaise G. Arden1, Richard W. Vachet*1,2, Patanachai Limpikirati*3 1Department of Chemistry, University of Massachusetts Amherst, 2Molecular and Cellular Biology Program, University of Massachusetts Amherst, 3Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University The experimental procedures for performing diethylpyrocarbonate-based covalent labeling with mass spectrometric detection are described. Diethylpyrocarbonate is simply mixed with the protein or protein complex of interest, leading to the modification of solvent accessible amino acid residues. The modified residues can be identified after proteolytic digestion and liquid chromatography/mass spectrometry analysis. Neuroscience Measuring Neural Mechanisms Underlying Sleep-Dependent Memory Consolidation During Naps in Early Childhood Tamara Allard*1, Tracy Riggins*1, Arcadia Ewell1, Benjamin Weinberg1, Sanna Lokhandwala2, Rebecca M. C. Spencer2,3 1Department of Psychology, University of Maryland, 2Department of Psychological and Brain Sciences, University of Massachusetts, 3Neuroscience and Behavior, University of Massachusetts This protocol describes methods used to examine neural mechanisms underlying sleep-dependent memory consolidation during naps in early childhood. It includes procedures for examining the effect of sleep on behavioral memory performance, as well as the application and recording of both polysomnography and actigraphy. Chemistry Reactive Vapor Deposition of Conjugated Polymer Films on Arbitrary Substrates Nongyi Cheng1,2, Trisha L. Andrew2,3 1Department of Chemistry, University of Wisconsin-Madison, 2Department of Chemistry, University of Massachusetts Amherst, 3Department of Polymer Science and Engineering, University of Massachusetts Amherst This paper presents a protocol for reactive vapor deposition of poly(3,4-ethylenedioxythiophene), poly(3,4-propylenedioxythiophene), and poly(thieno[3,2-b]thiophene) films on glass slides and rough substrates, such as textiles and paper. Genetics Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms Blake L. Joyce1,2, Asher K. Haug-Baltzell3, Jonathan P. Hulvey4, Fiona McCarthy5, Upendra Kumar Devisetty1,6, Eric Lyons1,2,3 1BIO5 Institute, University of Arizona, 2The School of Plant Sciences, University of Arizona, 3Genetics GIDP, University of Arizona, 4Biology Department, University of Massachusetts Amherst, 5School of Animal and Comparative Biomedical Sciences, University of Arizona, 6CyVerse, University of Arizona This protocol outlines a comparative de novo transcriptome assembly and annotation workflow for novice bioinformaticians. The workflow is available for free entirely through CyVerse and connected by the Data Store. Command line and graphical user interfaces are used, but all code needed is available to copy and paste. Engineering Printing Fabrication of Bulk Heterojunction Solar Cells and In Situ Morphology Characterization Feng Liu1, Sunzida Ferdous2, Xianjian Wan1, Chenhui Zhu3, Eric Schaible3, Alexander Hexemer3, Cheng Wang3, Thomas P. Russell1,2 1Materials Sciences Division, Lawrence Berkeley National Laboratory, 2Department of Polymer Science and Engineering, University of Massachusetts, Amherst, 3Advanced Light Source, Lawrence Berkeley National Laboratory Here, we present a protocol to fabricate organic thin film solar cells using a mini-slot die coater and related in-line structure characterizations using synchrotron scattering techniques. Environment Kinematic History of a Salient-recess Junction Explored through a Combined Approach of Field Data and Analog Sandbox Modeling Zeshan Ismat*1, Kevin Toeneboehn*2 1Department of Earth and Environmental Science, Franklin and Marshall College, 2Department of Geosciences, University of Massachusetts, Amherst Kinematic histories of fold-thrust belts are typically based on careful examinations of high-grade metamorphic rocks within a salient. We provide a novel method of understanding fold-thrust belts by examining salient-recess junctions. We analyze the oft-ignored upper crustal rocks using a combined approach of detailed fault analysis with experimental sandbox modeling. Chemistry A Filter-based Surface Enhanced Raman Spectroscopic Assay for Rapid Detection of Chemical Contaminants Siyue Gao1, Jessica Glasser1, Lili He1 1Department of Food Science, University of Massachusetts Amherst A procedure for fabrication and performing the filter-based surface enhanced Raman spectroscopic (SERS) assay for the detection of chemical contaminants (i.e., pesticide ferbam and antibiotic ampicillin) is presented. Biology Generating a "Humanized" Drosophila S2 Cell Line Sensitive to Pharmacological Inhibition of Kinesin-5 Anna A. Ye1, Thomas J. Maresca1 1Molecular and Cellular Biology Graduate Group, Biology Department, University of Massachusetts, Amherst This protocol describes how to generate a Drosophila S2 cell line that is sensitive to small molecule inhibitors of kinesin-5. The use of these cells in a cell-based error correction assay is also outlined. Biology Extraction and Analysis of Cortisol from Human and Monkey Hair Jerrold Meyer1,2, Melinda Novak1,2, Amanda Hamel2, Kendra Rosenberg1 1Department of Psychology, University of Massachusetts, Amherst, 2Neuroscience and Behavior Program, University of Massachusetts, Amherst Cortisol (CORT) accumulates in the growing hair shaft of humans and nonhuman primates. We describe methods for extracting and analyzing hair CORT with high precision and sensitivity. Measurement of hair CORT is particularly well-suited for assessing chronic stress over periods of weeks to months. Biology Large-scale Gene Knockdown in C. elegans Using dsRNA Feeding Libraries to Generate Robust Loss-of-function Phenotypes Kathryn N. Maher1, Mary Catanese2, Daniel L. Chase3 1Molecular and Cellular Biology Program, University of Massachusetts, Amherst, 2Neuroscience and Behavior Program, University of Massachusetts, Amherst, 3Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst While dsRNA feeding in C. elegans is a powerful tool to assess gene function, current protocols for large scale feeding screens result in variable knockdown efficiencies. We describe an improved protocol for performing large scale RNAi feeding screens that results in highly efficacious and reproducible knockdown of gene expression.