Weizmann Institute of Science View Institution's Website 16 articles published in JoVE Immunology and Infection Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors Tabitha Bucher1, Elena Kartvelishvily2, Ilana Kolodkin-Gal1 1Department of Molecular Genetics, Weizmann Institute of Science, 2Electron Microscopy Unit, Weizmann Institute of Science This study presents the development of reproducible methodologies to study biofilm inhibitors and their effects on Bacillus subtilis multicellularity. Genetics Novel RNA-Binding Proteins Isolation by the RaPID Methodology Nitzan Samra1,2, Yoav Arava1 1Faculty of Biology, Technion - Israel Institute of Technology, 2Department of Biomolecular Sciences, Weizmann Institute of Science RNA-protein interactions lie at the heart of many cellular processes. Here, we describe an in vivo method to isolate specific RNA and identify novel proteins that are associated with it. This could shed new light on how RNAs are regulated in the cell. Biochemistry Mimicking the Function of Signaling Proteins: Toward Artificial Signal Transduction Therapy Ronny Peri-Naor1, Leila Motiei1, David Margulies1 1Department of Organic Chemistry, Weizmann Institute of Science We present guidelines for developing synthetic 'chemical transducers' that can induce communication between naturally unrelated proteins. In addition, detailed protocols are presented for synthesizing and testing a specific 'transducer' that enables a growth factor to activate a detoxifying enzyme and consequently, to regulate the cleavage of an anticancer prodrug. Biology Studying the Supramolecular Organization of Photosynthetic Membranes within Freeze-fractured Leaf Tissues by Cryo-scanning Electron Microscopy Dana Charuvi1,3, Reinat Nevo1, Ifat Kaplan-Ashiri2, Eyal Shimoni2, Ziv Reich1 1Department of Biological Chemistry, Weizmann Institute of Science, 2Department of Chemical Research Support, Weizmann Institute of Science, 3Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Here we describe a procedure for studying freeze-fractured plant tissues. High-pressure frozen leaf samples are freeze-fractured and double-layer coated, yielding well preserved frozen-hydrated samples that are imaged using the cryo-scanning electron microscope at high magnifications with minimal beam damage. Chemistry Water in Oil Emulsions: A New System for Assembling Water-soluble Chlorophyll-binding Proteins with Hydrophobic Pigments Dominika Bednarczyk1, Dror Noy2 1Department of Biological Chemistry, Weizmann Institute of Science, 2Migal-Galilee Research Institute This manuscript describes a simple and high-throughput method for assembling water-soluble proteins with hydrophobic pigments that is based on water-in-oil emulsions. We demonstrate the effectiveness of the method in the assembly of native chlorophylls with four variants of recombinant water-soluble-chlorophyll binding proteins (WSCPs) of Brassica plants expressed in E. coli. Environment Air-sampled Filter Analysis for Endotoxins and DNA Content Naama Lang-Yona1,2, Yinon Mazar1, Michal Pardo1, Yinon Rudich1 1Department of Earth and Planetary Sciences, Weizmann Institute of Science, 2Multiphase Chemistry Department, Max Planck Institute Two complementary analyses of atmospheric biological particles from air sampled filters are described herein: the extraction and detection of endotoxin, and of DNA. Medicine Tracking the Mammary Architectural Features and Detecting Breast Cancer with Magnetic Resonance Diffusion Tensor Imaging Noam Nissan1, Edna Furman-Haran2, Myra Feinberg-Shapiro3, Dov Grobgeld1, Erez Eyal1, Tania Zehavi4, Hadassa Degani1 1Department of Biological Regulation, Weizmann Institute of Science, 2Unit of Biological Services, Weizmann Institute of Science, 3Department of Diagnostic Imaging, Meir Medical Center, 4Pathology Department, Meir Medical Center We describe how to obtain parametric and vector maps of the diffusion tensor of the breast using magnetic resonance imaging. The protocol and final output following imaging processing are tailored for tracking breast architectural features and detecting breast malignancy. Biology Assessing the Secretory Capacity of Pancreatic Acinar Cells Erez Geron1, Eyal D. Schejter1, Ben-Zion Shilo1 1Department of Molecular Genetics, Weizmann Institute of Science Isolated pancreatic acini retain their in vivo morphology and activity and offer powerful ways for monitoring and manipulating secretion. This work demonstrates how acini can be isolated from the mouse pancreas, and how their secretory capacities can be assessed. Neuroscience Generation of Topically Transgenic Rats by In utero Electroporation and In vivo Bioluminescence Screening Sandra Vomund1, Tamar Sapir2, Orly Reiner2, Maria A. de Souza Silva3, Carsten Korth1 1Department of Neuropathology, Medical School Düsseldorf, 2Department of Molecular Genetics, Weizmann Institute for Science, 3Center of Behavioral Neuroscience, University of Düsseldorf Genes can be manipulated during development of the cortex or the hippocampus of the rat via in utero electroporation (IUE) at E16, to enable fast and targeted modifications in neuronal connectivity for later studies of behavior or neuropathology in adult animals. Postnatal in vivo imaging for control of IUE success is performed by bioluminescence of activating co-transfected luciferase. Engineering Bringing the Visible Universe into Focus with Robo-AO Christoph Baranec1,2, Reed Riddle1, Nicholas M. Law3, A.N. Ramaprakash4, Shriharsh P. Tendulkar2, Khanh Bui1, Mahesh P. Burse4, Pravin Chordia4, Hillol K. Das4, Jack T.C. Davis1, Richard G. Dekany1, Mansi M. Kasliwal5, Shrinivas R. Kulkarni1,2, Timothy D. Morton2, Eran O. Ofek6, Sujit Punnadi4 1Caltech Optical Observatories, California Institute of Technology, 2Department of Astronomy, California Institute of Technology, 3Dunlap Institute for Astronomy and Astrophysics, University of Toronto, 4Inter-University Centre for Astronomy & Astrophysics, 5Observatories of the Carnegie Institution for Science, 6Benoziyo Center for Astrophysics, Weizmann Institute of Science Light from astronomical objects must travel through the earth's turbulent atmosphere before it can be imaged by ground-based telescopes. To enable direct imaging at maximum theoretical angular resolution, advanced techniques such as those employed by the Robo-AO adaptive-optics system must be used. Bioengineering High Resolution 3D Imaging of Ex-Vivo Biological Samples by Micro CT Amnon Sharir1, Gregory Ramniceanu2, Vlad Brumfeld3 1Department of Molecular Genetics, Weizmann Institute of Science, 2Department of Biological Regulation, Weizmann Institute of Science, 3Department of Chemical Infrastructure, Weizmann Institute of Science Non-destructive volume visualization can be achieved only by tomographic techniques, of which the most efficient is the x-ray micro computerized tomography ( CT). Biology Dissection and Staining of Drosophila Larval Ovaries Iris Maimon1, Lilach Gilboa1 1Department of Biological Regulation, Weizmann Institute of Science How niches and stem cells form during development is an important question with practical implications. In the Drosophila ovary, germ line stem cells and their somatic niches form during larval development. This video demonstrates how to dissect, stain and mount female gonads from late third instar (LL3) Drosophila larvae. Biology Two-Photon-Based Photoactivation in Live Zebrafish Embryos Niva Russek-Blum*1, Helit Nabel-Rosen*1, Gil Levkowitz1 1Molecular Cell Biology, Weizmann Institute of Science Multiphoton microscopy allows control of low energy photons with deep optical penetration and reduced phototoxicity. We describe the use of this technology for live cell labeling in zebrafish embryos. This protocol can be readily adapted for photo-induction of various light-responsive molecules. Neuroscience Axoplasm Isolation from Rat Sciatic Nerve Ida Rishal1, Meir Rozenbaum1, Mike Fainzilber1 1Department of Biological Chemistry, Weizmann Institute of Science We demonstrate a protocol for axoplasm isolation from adult rat sciatic nerve based on dissection of nerve fascicles and incubation in hypotonic medium to release myelin and lyse non-axonal structures, followed by extraction of the remaining axon-enriched material. Biology T-wave Ion Mobility-mass Spectrometry: Basic Experimental Procedures for Protein Complex Analysis Izhak Michaelevski1, Noam Kirshenbaum1, Michal Sharon1 1Department of Biological Chemistry, Weizmann Institute of Science Ion mobility-mass spectrometry is an emerging gas-phase technology that separates ions, based on their collision cross-section and mass. The method provides three-dimensional information on the overall topology and shape of protein complexes. Here, we outline a basic procedure for instrument setting and optimization, calibration of drift times, and data interpretation. Biology Analyzing Large Protein Complexes by Structural Mass Spectrometry Noam Kirshenbaum1, Izhak Michaelevski1, Michal Sharon1 1Department of Biological Chemistry, Weizmann Institute of Science Mass spectrometry has proven to be a valuable tool for analyzing large protein complexes. This method enables insights into the composition, stoichiometry and overall architecture of multi-subunit assemblies. Here, we describe, step-by-step, how to perform a structural mass spectrometry analysis, and characterize macromolecular structures.