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Technion - Israel Institute of Technology

15 ARTICLES PUBLISHED IN JoVE

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Immunology and Infection

In vitro tRNA Methylation Assay with the Entamoeba histolytica DNA and tRNA Methyltransferase Dnmt2 (Ehmeth) Enzyme
Ayala Tovy 1, Benjamin Hofmann 2, Mark Helm 2, Serge Ankri 1
1Faculty of Medicine, Rappaport Institute, Technion - Israel Institute of Technology, 2The Pharmacy and Biochemistry Institute, Johannes Gutenberg University

This protocol describes the preparation of a synthetic tRNA substrate for the Entamoeba histolytica DNA/tRNA methyltransferase 2 (Dnmt2) homolog Ehmeth and the measure of its methyltransferase activity. This experimental approach can be used for investigating the activity of other Dnmt2 proteins.

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Biology

Preparation of Cell-lines for Conditional Knockdown of Gene Expression and Measurement of the Knockdown Effects on E4orf4-Induced Cell Death
Anna Brestovitsky 1, Rakefet Sharf 1, Tamar Kleinberger 1
1Department of Molecular Microbiology, Faculty of Medicine, Technion - Israel Institute of Technology

Contribution of the ACF chromatin remodeling factor to E4orf4-induced cell death was measured. The protocol includes selection of cell clones in which doxycycline treatment induces conditional knockdown of the ACF subunits Acf1 and SNF2h, and use of the DAPI assay to measure E4orf4-induced cell death in the inducible cell lines.

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Biology

Live Imaging of Apoptotic Cell Clearance during Drosophila Embryogenesis
Boris Shklyar 1, Jeny Shklover 1, Estee Kurant 1
1Department of Anatomy and Cell Biology and the Rappaport Institute for Research in the Medical Sciences, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology

Here we describe an effective method for studying dynamics of apoptotic cell clearance in vivo. This method employs live Drosophila embryos as a powerful model for monitoring phagocytosis of apoptotic cells using specific labeling of apoptotic cells and phagocytes.

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Bioengineering

Optical Detection of E. coli Bacteria by Mesoporous Silicon Biosensors
Naama Massad-Ivanir *1, Giorgi Shtenberg *2, Ester Segal 1,3
1Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 2The Inter-Departmental Program of Biotechnology, Technion - Israel Institute of Technology, 3The Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology

A label-free optical biosensor for rapid bacteria detection is introduced. The biosensor is based on a nanostructured porous Si, which is designed to directly capture the target bacteria cells onto its surface. We use monoclonal antibodies, immobilized onto the porous transducer, as the capture probes. Our studies demonstrate the applicability of these biosensors for the detection of low bacterial concentrations within minutes with no prior sample processing (such as cell lysis).

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Biology

Isolation of mRNAs Associated with Yeast Mitochondria to Study Mechanisms of Localized Translation
Chen Lesnik 1, Yoav Arava 1
1Department of Biology, Technion - Israel Institute of Technology

Many mRNAs encoding mitochondrial proteins are associated with the mitochondria outer membrane. We describe a subcellular fractionation procedure aimed at isolation of yeast mitochondria with its associated mRNAs and ribosomes. This protocol can be applied to cells grown under diverse conditions in order to reveal mechanisms of mRNA localization and localized translation near the mitochondria.

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JoVE Journal

Fabrication and Testing of Microfluidic Optomechanical Oscillators
Kewen Han 1, Kyu Hyun Kim 2, Junhwan Kim 1, Wonsuk Lee 2,3, Jing Liu 3, Xudong Fan 3, Tal Carmon 2, Gaurav Bahl 1
1Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, 2Electrical Engineering and Computer Science, University of Michigan, 3Biomedical Engineering, University of Michigan

Parametric optomechanical excitations have recently been experimentally demonstrated in microfluidic optomechanical resonators by means of optical radiation pressure and stimulated Brillouin scattering. This paper describes the fabrication of these microfluidic resonators along with methodologies for generating and verifying optomechanical oscillations.

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Bioengineering

A Microfluidic Model of Biomimetically Breathing Pulmonary Acinar Airways
Rami Fishler 1, Josué Sznitman 1
1Department of Biomedical Engineering, Technion - Israel Institute of Technology

Soft-lithography was utilized to produce a representative true-scale model of pulmonary alveolated airways that expand and contract periodically, mimicking physiological breathing motion. This platform recreates respiratory acinar flows on a chip, and is anticipated to facilitate experimental investigation of inhaled aerosol dynamics and deposition in the pulmonary acinus.

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Genetics

Novel RNA-Binding Proteins Isolation by the RaPID Methodology
Nitzan Samra 1,2, Yoav Arava 1
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.

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Engineering

Design and Fabrication of an Optical Fiber Made of Water
Mark L. Douvidzon 1, Shai Maayani 2, Leopoldo L. Martin 3, Tal Carmon 4
1Department of Nanoscience and Nanotechnology, Russell Berrie Nanotechnology Institute (RBNI), Technion - Israel Institute of Technology, 2Department of Material Sciences and Engineering, MIT, 3Centro de Tecnologia Nanofotónica, Universitat Politècnica de València, 4Department of Mechanical Engineering, Technion - Israel Institute of Technology

This protocol describes the design and manufacture of a water bridge and its activation as a water fiber. The experiment demonstrates that capillary resonances of the water fiber modulate its optical transmission.

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Bioengineering

Designing Porous Silicon Films as Carriers of Nerve Growth Factor
Michal Rosenberg 1, Neta Zilony 2,3, Orit Shefi 2,3, Ester Segal 1,4
1Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 2Faculty of Engineering, Bar-Ilan University, 3Bar-Ilan Institute of Nanotechnologies and Advanced Materials, 4Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology

Here, we present a protocol to design and fabricate nanostructured porous silicon (PSi) films as degradable carriers for the nerve growth factor (NGF). Neuronal differentiation and outgrowth of PC12 cells and mice dorsal root ganglion (DRG) neurons are characterized upon treatment with the NGF-loaded PSi carriers.

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Bioengineering

Preparing Protein Producing Synthetic Cells using Cell Free Bacterial Extracts, Liposomes and Emulsion Transfer
Omer Adir *1,2, Noga Sharf-Pauker *1,2, Gal Chen *1,3, Maya Kaduri 1, Nitzan Krinsky 1,3, Janna Shainsky-Roitman 1, Jeny Shklover 1, Avi Schroeder 1
1Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, 2The Norman Seiden Multidisciplinary Program for Nanoscience and Nanotechnology, Technion - Israel Institute of Technology, 3The Interdisciplinary Program for Biotechnology, Technion - Israel Institute of Technology

This protocol describes the method, materials, equipment and steps for bottom-up preparation of RNA and protein producing synthetic cells. The inner aqueous compartment of the synthetic cells contained the S30 bacterial lysate encapsulated within a lipid bilayer (i.e., stable liposomes), using a water-in-oil emulsion transfer method.

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Bioengineering

Continuous Measurement of Biological Noise in Escherichia Coli Using Time-lapse Microscopy
Einel A. Chaimovitz *1, Evgeniy Reznik *1, Mouna Habib 1, Netanel Korin 1, Ramez Daniel 1
1Department of Biomedical Engineering, Technion - Israel Institute of Technology

This work presents a microscopy method that allows live imaging of a single cell of Escherichia coli for analysis and quantification of the stochastic behavior of synthetic gene circuits.

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Neuroscience

Optogenetic Activation of Afferent Pathways in Brain Slices and Modulation of Responses by Volatile Anesthetics
Caitlin A. Murphy 1, Aeyal Raz 1,2, Sean M Grady 1, Matthew I Banks 1
1Department of Anesthesiology, University of Wisconsin, 2Department of Anesthesiology, Rambam Health Care Campus, the Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology

Ex vivo brain slices can be used to study the effects of volatile anesthetics on evoked responses to afferent inputs. Optogenetics are employed to independently activate thalamocortical and corticocortical afferents to non-primary neocortex, and synaptic and network responses are modulated with isoflurane.

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Bioengineering

In Vitro 3D Cell-Cultured Arterial Models for Studying Vascular Drug Targeting Under Flow
Maria Khoury 1, Mark Epshtein 1, Netanel Korin 1
1Department of Biomedical Engineering, Technion - IIT

Here, we present a new protocol to study and map the targeted deposition of drug carriers to endothelial cells in fabricated, real-sized, three-dimensional human artery models under physiological flow. The presented method may serve as a new platform for targeting drug carriers within the vascular system.

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Biology

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling
Johannes Venezian 1, Hila Zilberman 1, Ayala Shiber 1
1Faculty of Biology, Technion - Israel Institute of Technology

Co-translational interactions play a crucial role in nascent-chain modifications, targeting, folding, and assembly pathways. Here, we describe Selective Ribosome Profiling, a method for in vivo, direct analysis of these interactions in the model eukaryote Saccharomyces cerevisiae.

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