Bar-Ilan University View Institution's Website 19 articles published in JoVE Biochemistry Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology Yana Lerner*1, Surya Sukumaran*1, Mei-Sze Chua2, Samuel K. So2, Nir Qvit1 1The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, 2Asian Liver Center, Department of Surgery, Stanford University School of Medicine Field-effect biosensing (FEB) is a label-free technique for detecting biomolecular interactions. It measures the electric current through the graphene biosensor to which the binding targets are immobilized. The FEB technology was used to evaluate biomolecular interactions between Hsp90 and Cdc37 and a strong interaction between the two proteins was detected. Biology Measuring Cell-Edge Protrusion Dynamics during Spreading using Live-Cell Microscopy Nikola Lukic*1, Trishna Saha*1, Stefanie Lapetina1, Michal Gendler1, Gilad Lehmann1, Anthony J. Koleske2,3, Hava Gil-Henn1 1The Azrieli Faculty of Medicine, Bar-Ilan University, 2Department of Molecular Biophysics and Biochemistry, Yale University, 3Department of Neuroscience, Yale University This protocol aims to measure the dynamic parameters (protrusions, retractions, ruffles) of protrusions at the edge of spreading cells. Bioengineering Fabrication of Magnetic Platforms for Micron-Scale Organization of Interconnected Neurons Ganit Indech1,4, Reut Plen2,4, Dafna Levenberg2,4, Naor Vardi1,4, Michal Marcus2,4, Alejandra Smith2,4, Shlomo Margel3,4, Orit Shefi2,4, Amos Sharoni1,4 1Department of Physics, Bar-Ilan University, 2Faculty of Engineering, Bar-Ilan University, 3Department of chemistry, Bar-Ilan University, 4The Institutes of Nanotechnology & Advanced Materials, Bar-Ilan University This work presents a bottom-up approach to the engineering of local magnetic forces for control of neuronal organization. Neuron-like cells loaded with magnetic nanoparticles (MNPs) are plated atop and controlled by a micro-patterned platform with perpendicular magnetization. Also described are magnetic characterization, MNP cellular uptake, cell viability, and statistical analysis. Immunology and Infection An Intestinal Gut Organ Culture System for Analyzing Host-Microbiota Interactions Shalhevet Azriel*1,2, Hadar Bootz*1,2, Alon Shemesh*1,2, Sivan Amidror1,2, Nissan Yissachar1,2 1The Goodman Faculty of Life Sciences, Bar-Ilan University, 2Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University This article presents a unique method for analyzing host-microbiome interactions using a novel gut organ culture system for ex vivo experiments. Behavior Generating Acute and Chronic Experimental Models of Motor Tic Expression in Rats Esther Vinner*1, Katya Belelovsky*1, Izhar Bar-Gad1 1The Leslie & Susan Goldschmied (Gonda) Multidisciplinary Brain Research Center, Bar-Ilan University We present protocols for generating acute and chronic experimental models of tic expression in freely behaving rats. The models are based on striatal cannula implantation and subsequent GABAA antagonist application. The acute model uses transient injections whereas the chronic model utilizes prolonged infusions via a subcutaneous implanted mini-osmotic pump. Cancer Research Detection of Cell-Free DNA in Blood Plasma Samples of Cancer Patients Vikrant Palande1, Dorith Raviv Shay1, MILANA Frenkel-Morgenstern1,2,3 1Cancer Genomics and BioComputing of Complex Diseases laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, 2The Data Science Institute, Bar-Ilan University, 3The Dangoor Centre For Personalized Medicine, Bar-Ilan University In this paper we present a detailed protocol for non-invasive liquid biopsy technique, including blood collection, plasma and buffy coat separation, cfDNA and germline DNA extraction, quantification of cfDNA or germline DNA, and cfDNA fragment enrichment analysis. Bioengineering Designing Porous Silicon Films as Carriers of Nerve Growth Factor Michal Rosenberg1, Neta Zilony2,3, Orit Shefi2,3, Ester Segal1,4 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. Cancer Research Analysis of Cancer Cell Invasion and Anti-metastatic Drug Screening Using Hydrogel Micro-chamber Array (HMCA)-based Plates Orit Ravid-Hermesh1, Naomi Zurgil1, Yana Shafran1, Elena Afrimzon1, Maria Sobolev1, Yaron Hakuk1, Zehavit Bar-On Eizig1, Mordechai Deutsch1 1Physics Department, Bar-Ilan University A HMCA-based imaging plate is presented for invasion assay performance. This plate facilitates the formation of three-dimensional (3D) tumor spheroids and the measurement of cancer cell invasion into the extracellular matrix (ECM). The invasion assay quantification is achieved by semi-automatic analysis. Genetics Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq Ivana Grbesa1, Miriam Tannenbaum1, Avital Sarusi-Portuguez1, Michal Schwartz1, Ofir Hakim1 1The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University Assay for Transposase-Accessible Chromatin coupled with high-throughput sequencing (ATAC-seq) is a genome-wide method to uncover accessible chromatin. This is a step-by-step ATAC-seq protocol, from molecular to the final computational analysis, optimized for human lymphocytes (Th1/Th2). This protocol can be adopted by researchers without prior experience in next-generation sequencing methods. Engineering Scanning SQUID Study of Vortex Manipulation by Local Contact Eylon Persky1, Anna Kremen1, Shai Wissberg1, Yishai Shperber1, Beena Kalisky1 1Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University We present a protocol for manipulation of individual vortices in thin superconducting films, using local mechanical contact. The method does not include applying current, magnetic field or additional fabrication steps. Neuroscience A Simple Way to Measure Alterations in Reward-seeking Behavior Using Drosophila melanogaster Shir Zer1, Julia Ryvkin1, Harel J. Wilner1, Hila Zak1, Anat Shmueli1, Galit Shohat-Ophir1 1The Mina & Everard Goodman Faculty of Life Sciences, The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University We describe a protocol for inducing rewarding and nonrewarding experiences in fruit flies (Drosophila melanogaster) using voluntary ethanol consumption as a measure for changes in reward states. Chemistry Folding and Characterization of a Bio-responsive Robot from DNA Origami Yaniv Amir1, Almogit Abu-Horowitz1, Ido Bachelet1 1Faculty of Life Sciences and the Institute for Nanotechnology & Advanced Materials, Bar-Ilan University DNA origami is a powerful method for fabricating precise nanoscale objects by programming the self-assembly of DNA molecules. Here we describe a protocol for the folding of a bio-responsive robot from DNA origami, its purification and negative staining for transmission electron microscopic imaging (TEM). Chemistry Exploring the Radical Nature of a Carbon Surface by Electron Paramagnetic Resonance and a Calibrated Gas Flow Uri Green1,2, Yulia Shenberger3, Zeev Aizenshtat1, Haim Cohen2,4, Sharon Ruthstein3 1Chemistry Institute, The Hebrew University of Jerusalem, 2Biological Chemistry Department, Ariel University, 3Chemistry Department, Faculty of Exact Science, Bar Ilan University, 4Chemistry Department, Ben-Gurion University Stable radicals that are present in carbon substrates interact with paramagnetic oxygen through a Heisenberg spin exchange. This interaction can be significantly reduced under STP conditions by flowing a diamagnetic gas over the carbon system. This manuscript describes a simple method to characterize the nature of those radicals. Engineering Time Multiplexing Super Resolving Technique for Imaging from a Moving Platform Asaf Ilovitsh1, Shlomo Zach2, Zeev Zalevsky1 1Faculty of Engineering, Bar-Ilan University, 210 Nachum Street, Kfar Saba, Israel A method for overcoming the optical diffraction limit is presented. The method includes a two-step process: optical phase retrieval using iterative Gerchberg-Saxton algorithm, and imaging system shifting followed by repetition of the first step. A synthetically increased lens aperture is generated along the direction of movement, yielding higher imaging resolution. Bioengineering Designing a Bio-responsive Robot from DNA Origami Eldad Ben-Ishay1, Almogit Abu-Horowitz1, Ido Bachelet1 1Faculty of Life Sciences and the Institute for Nanotechnology & Advanced Materials, Bar-Ilan University DNA origami is a powerful method for fabricating precise nanoscale objects by programming the self-assembly of DNA molecules. Here, we describe how DNA origami can be utilized to design a robotic robot capable of sensing biological cues and responding by shape shifting, subsequently relayed to a desired effect. Immunology and Infection The Synergistic Effect of Visible Light and Gentamycin on Pseudomona aeruginosa Microorganisms Yana Reznick1, Ehud Banin2, Anat Lipovsky3, Rachel Lubart3, Pazit Polak4, Zeev Zalevsky4 1Department of Physics, Bar-Ilan University, 2The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 3Department of Chemistry, Bar-Ilan University, 4Faculty of Engineering, Bar-Ilan University We show that a developed biomedical device involving continuous or pulsed visible laser based treatment that is combined with antibiotic treatment (gentamycin), results in a statistically significant synergistic effect leading to a reduction in the viability of P. aeruginosa PAO1, by 8 log's compared to antibiotic treatment alone. Immunology and Infection Real-time Live Imaging of T-cell Signaling Complex Formation Elad Noy*1, Maor H. Pauker*1, Mira Barda-Saad1 1The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University We describe a live-cell imaging method that provides insight into protein dynamics during the T-cell activation process. We demonstrate the combined usage of the T-cell spreading assay, confocal microscopy and imaging analysis to yield quantitative results to follow signaling complex formation throughout T-cell activation. Bioengineering High-throughput Protein Expression Generator Using a Microfluidic Platform Yair Glick*1, Dorit Avrahami*1, Efrat Michaely1, Doron Gerber1 1The Mina & Everard Goodman Faculty of Life Sciences, The Nanotechnology Institute, Bar-Ilan University We present a microfluidic approach for the expression of protein arrays. The device consists of thousands of reaction chambers controlled by micro-mechanical valves. The microfluidic device is mated to a microarray-printed gene library. These genes are then transcribed and translated on-chip, resulting in a protein array ready for experimental use. Biology Measuring the Kinetics of mRNA Transcription in Single Living Cells Yehuda Brody1, Yaron Shav-Tal1 1The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University RNA polymerase II transcriptional kinetics are measured on specific genes in living cells. mRNAs transcribed from the gene of interest are fluorescently tagged and using Fluorescence Recovery After Photobleaching (FRAP) the in vivo kinetics of transcriptional elongation are obtained.