Yeshiva University View Institution's Website 10 articles published in JoVE Chemistry A Microfluidic Approach for the Study of Ice and Clathrate Hydrate Crystallization Ran Drori1,2, Yitzhar Shalom1,2 1Department of Chemistry and Biochemistry, Yeshiva University, 2Department of Physics, Katz School of Science and Health, Yeshiva University The present protocol describes the crystallization of microscopic ice crystals and clathrate hydrates in microfluidic devices, enabling liquid exchange around the formed crystals. This provides unparalleled possibilities to examine the crystallization process and binding mechanisms of the inhibitors. Biology Reverse Yeast Two-hybrid System to Identify Mammalian Nuclear Receptor Residues that Interact with Ligands and/or Antagonists Hao Li*1, Wei Dou*2, Emil Padikkala1, Sridhar Mani1 1Department of Genetics, Albert Einstein College of Medicine, 2Shanghai Key Laboratory of Complex Prescription and MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine Ketoconazole binds to and antagonizes Pregnane X Receptor (PXR) activation. Yeast high throughput screens of PXR mutants define a unique region for ketoconazole binding. This yeast-based genetic method discovers novel nuclear receptor interactions with ligands that associate with surface binding sites. Biology Telomere Length and Telomerase Activity; A Yin and Yang of Cell Senescence Mary Derasmo Axelrad1, Temuri Budagov1, Gil Atzmon1,2,3 1Department of Medicine, Albert Einstein College of Medicine, 2Diabetes Research and Training Center, Albert Einstein College of Medicine, 3Department of Genetics, Albert Einstein College of Medicine An accurate, short, sophisticated and cheap method is described that assesses telomere length in multiple tissues and species using qRT-PCR. In addition, we will describe a simple assay to assess telomerase activity as a complementary backbone test for telomere length. Neuroscience Wholemount Immunohistochemistry for Revealing Complex Brain Topography Joshua J. White1, Stacey L. Reeber1, Richard Hawkes2, Roy V. Sillitoe1 1Department of Neuroscience, Albert Einstein College of Medicine, Yeshiva University, 2Department of Cell Biology and Anatomy and the Hotchkiss Brain Institute, Faculty of Medicine, University of Calgary Neural circuits are topographically organized into functional compartments with specific molecular profiles. Here, we provide the practical and technical steps for revealing global brain topography using a versatile wholemount immunohistochemical staining approach. We demonstrate the utility of the method using the well-understood cytoarchitecture and circuitry of cerebellum. Neuroscience Revealing Neural Circuit Topography in Multi-Color Stacey L. Reeber1, Samrawit A. Gebre1, Nika Filatova1, Roy V. Sillitoe1 1Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Yeshiva University We provide a practical guide for delivering tracers in vivo and use the spinocerebellar pathway as a model system to demonstrate essential steps for successful neuronal circuit analysis in mice. We describe in detail our versatile tracing protocol that exploits wheat germ agglutinin (WGA) conjugated to Alexa fluorophores. Biology Monitoring Equilibrium Changes in RNA Structure by 'Peroxidative' and 'Oxidative' Hydroxyl Radical Footprinting Ravichandra Bachu*1, Frances-Camille S. Padlan*2, Sara Rouhanifard2, Michael Brenowitz2, Jörg C. Schlatterer2 1Department of Chemistry, Hunter College, 2Department of Biochemistry, Albert Einstein College of Medicine This protocol describes how to quantify the Mg(II)-dependent formation of RNA tertiary structure by two methods of hydroxyl radical footprinting. Biology Preparation of Adult Drosophila Eyes for Thin Sectioning and Microscopic Analysis Andreas Jenny1 1Department of Developmental and Molecular Biology, Albert Einstein College of Medicine A standard approach to prepare adult Drosophila eyes for semi-thin sectioning and light microscopic analysis is presented here. The protocol can be used for gross morphological analysis of eye defects, or with the indicated adjustments can be used to determine genetic requirements of genes in specific cell types of the eye (e.g. clonal analysis of photoreceptors) or for electron microscopic analysis. Biology Imaging Glycans in Zebrafish Embryos by Metabolic Labeling and Bioorthogonal Click Chemistry Hao Jiang1, Lei Feng1, David Soriano del Amo1, Ronald D. Seidel III2, Florence Marlow3, Peng Wu1 1Department of Biochemistry, Albert Einstein College of Medicine, Yeshiva University, 2Macromolecular Therapeutics Development Facility, Albert Einstein College of Medicine, Yeshiva University, 3Developmental and Molecular Biology, Albert Einstein College of Medicine, Yeshiva University A click-chemistry based method that allows for the rapid, noninvasive, and robust labeling of alkyne-tagged glycans in zebrafish embryos is described. Fucosylated glycans in the enveloping layer of zebrafish embryos in the late gastrulation stage were imaged in this study. Immunology and Infection Passive Administration of Monoclonal Antibodies Against H. capsulatum and Others Fungal Pathogens Allan J. Guimarães1, Luis R. Martinez1, Joshua D. Nosanchuk1 1Department of Microbiology and Immunology, Albert Einstein College of Medicine C57BL/6 mice have been used to study Hc pathogenesis and provide the best model. We are exploring the potential benefits of humoral immunity against this fungus and generated several mAbs [to histone H2B and a heat shock protein 60kDa] that we tested for their protective efficacy after intraperitoneal administration. Biology Dendra2 Photoswitching through the Mammary Imaging Window Bojana Gligorijevic1,2, Dmitriy Kedrin1, Jeffrey E Segall1, John Condeelis1,2, Jacco van Rheenen1,2,3 1Department of Anatomy and Structural Biology, Albert Einstein College of Medicine - Yeshiva University, 2Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine - Yeshiva University, 3Hubrecht Institute-KNAW and University Medical Center Utrecht Intravital photoswitching and tracking of Dendra2-labeled tumor cells through the Mammary Imaging Window is a technique which allows us to image the metastatic behavior of tumor cells in chosen tumor microenvironments over a timescale of days.