University of Groningen View Institution's Website 26 articles published in JoVE Medicine Precision of In Vivo Quantitative Tooth Wear Measurement Using Intra-Oral Scans Hilde Bronkhorst1, Ewald Bronkhorst1, Stanimira Kalaykova1, Wicher van der Meer2, Marie-Charlotte Huysmans1, Bas Loomans1 1Department of Dentistry, Radboud University Medical Center, 2Department of Orthodontics, University Medical Center Groningen, University of Groningen Quantitative wear measurement is a method of increasing importance in measuring tooth wear progression. We here describe a protocol, its precision, and its intra/inter-rater precision for the acquisition and superimposition of repeated in vivo scanned dentitions in patients with moderate to severe wear, reporting on both height and volume measurements. Biology Automated Charting of the Visual Space of Housefly Compound Eyes Maurico Muñoz Arias1, John K. Douglass2,3, Martin F. Wehling2, Doekele G. Stavenga3 1Design Group, Faculty of Science and Engineering, University of Groningen, 2Air Force Research Laboratory, Eglin Air Force Base, 3Surfaces and thin films department, Zernike Institute for Advanced Materials, University of Groningen The protocol here describes the measurement of the spatial organization of the visual axes of housefly eyes, mapped by an automatic device, using the pseudopupil phenomenon and the pupil mechanism of the photoreceptor cells. Neuroscience Electrocorticographic Recording of Cerebral Cortex Areas Manipulated Using an Adeno-Associated Virus Targeting Cofilin in Mice Julien Dufort-Gervais1, Robbert Havekes2, Valérie Mongrain1,3 1Center for Advanced Research in Sleep Medicine, Recherche CIUSSS-NIM, 2GELIFES, University of Groningen, 3Department of Neuroscience, Université de Montréal This article describes a protocol for the manipulation of molecular targets in the cerebral cortex using adeno-associated viruses and for monitoring the effects of this manipulation during wakefulness and sleep using electrocorticographic recordings. Behavior An Inertial Measurement Unit Based Method to Estimate Hip and Knee Joint Kinematics in Team Sport Athletes on the Field Bram J.C. Bastiaansen*1, Erik Wilmes*2, Michel S. Brink1, Cornelis J. de Ruiter2, Geert J.P. Savelsbergh2, Annemarijn Steijlen3, Kaspar M.B. Jansen3, Frans C.T. van der Helm4, Edwin A. Goedhart5, Doris van der Laan6, Riemer J.K. Vegter1, Koen A.P.M. Lemmink1 1Center for Human Movement Sciences, University Medical Center, University of Groningen, 2Department of Human Movement Sciences, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, 3Emerging Materials, Department of Design Engineering, Delft University of Technology, 4Department of Biomechanical Engineering, Delft University of Technology, 5FIFA Medical Center, Royal Netherlands Football Association, 6Royal Dutch Hockey Association Monitoring athletes is essential for improving performance and reducing injury risk in team sports. Current methods to monitor athletes do not include the lower extremities. Attaching multiple inertial measurement units to the lower extremities could improve monitoring athletes in the field. Biology In Situ Monitoring of Transiently Formed Molecular Chaperone Assemblies in Bacteria, Yeast, and Human Cells Niels Alberts*1, Yasith Mathangasinghe*2, Nadinath B. Nillegoda3 1Department of Biomedical Sciences of Cells & Systems, University of Groningen, 2Department of Anatomy, Faculty of Medicine, University of Colombo, 3Australian Regenerative Medicine Institute (ARMI), Monash University Cognate J-domain proteins cooperate with the Hsp70 chaperone to assist in a myriad of biological processes ranging from protein folding to degradation. Here, we describe an in situ proximity ligation assay, which allows the monitoring of these transiently formed chaperone machineries in bacterial, yeast and human cells. Chemistry Light-driven Molecular Motors on Surfaces for Single Molecular Imaging Jiawen Chen1, Jérôme Vachon1, Ben L. Feringa1 1Stratingh Institute for Chemistry, University of Groningen The manuscript describes how to synthesize and graft a molecular motor on surfaces for single molecular imaging. Bioengineering Manufacturing of a Nafion-coated, Reduced Graphene Oxide/Polyaniline Chemiresistive Sensor to Monitor pH in Real-time During Microbial Fermentation Selvaraj Chinnathambi1, Gert-Jan Euverink1 1Products and Processes for Biotechnology, Engineering and Technology Institute Groningen, Faculty of Science and Engineering, University of Groningen Here, we report the protocol for the fabrication of a Nafion-coated, polyaniline-functionalized, electrochemically reduced graphene oxide chemiresistive micro pH sensor. This chemiresistor-based, solid-state micro pH sensor can detect pH changes in real-time during a Lactococcus lactis fermentation process. Bioengineering A Zebrafish Embryo Model for In Vivo Visualization and Intravital Analysis of Biomaterial-associated Staphylococcus aureus Infection Xiaolin Zhang1,2, Leonie de Boer1, Oliver W. Stockhammer1, Dirk W. Grijpma2,3, Herman P. Spaink4, Sebastian A.J. Zaat1 1Department of Medical Microbiology, Amsterdam UMC, 2Technical Medical Center, Department of Biomaterials Science and Technology, University of Twente, 3Department of Biomedical Engineering, W.J. Kolff Institute, University Medical Center Groningen, University of Groningen, 4Institute of Biology, Leiden University The present study describes a zebrafish embryo model for in vivo visualization and intravital analysis of biomaterial-associated infection over time based on fluorescence microscopy. This model is a promising system complementing mammalian animal models such as mouse models for studying biomaterial-associated infections in vivo. Chemistry Extraction of Lignin with High β-O-4 Content by Mild Ethanol Extraction and Its Effect on the Depolymerization Yield Douwe S. Zijlstra1, Alessandra de Santi2, Bert Oldenburger1,2, Johannes de Vries2,3, Katalin Barta2, Peter J. Deuss1 1Department of Chemical Engineering (ENTEG), University of Groningen, 2Stratingh Institute for Chemistry, University of Groningen, 3Leibniz-Insitut f ür Katalyse e.V., Universität Rostock Here, we present a protocol to perform ethanol extraction of lignin from several biomass sources. The effect of the extraction conditions on the lignin yield and β-O-4 content are presented. Selective depolymerization is performed on the obtained lignins to obtain high aromatic monomer products. Behavior An Automated Method to Determine the Performance of Drosophila in Response to Temperature Changes in Space and Time Andrea Soto-Padilla1,2, Rick Ruijsink3, Mark Span4, Hedderik van Rijn*4, Jean-Christophe Billeter*1 1Groningen Institute for Evolutionary Life Sciences, University of Groningen, 2Department of Cell Biology, University of Groningen, University Medical Center Groningen, 3Ruijsink Dynamic Engineering, 4Department of Psychology, University of Groningen Here we present a protocol to automatically determine the locomotor performance of Drosophila at changing temperatures using a programmable temperature-controlled arena that produces fast and accurate temperature changes in time and space. Chemistry Stereolithographic 3D Printing with Renewable Acrylates Vincent S.D. Voet1, Geraldine H.M. Schnelting1, Jin Xu2, Katja Loos2, Rudy Folkersma1, Jan Jager1 1Professorship Sustainable Polymers, NHL Stenden University of Applied Sciences, 2Macromolecular Chemistry and New Polymeric Materials, Zernike Institute for Advanced Materials, University of Groningen A protocol for additive manufacturing with renewable photopolymer resins on a stereolithography apparatus is presented. Biology Plant-Microbe Interaction: Transcriptional Response of Bacillus Mycoides to Potato Root Exudates Yanglei Yi1, Zhibo Li1, Oscar P. Kuipers1 1Department of Molecular Genetics, University of Groningen The goal of the protocol presented here is to study the transcriptomic response of endosphere-isolated Bacillus mycoides to potato root exudates. This method facilitates the identification of important bacterial genes involved in plant-microbe interactions and is in principle applicable to other endophytes and plants, with minor adjustments. Bioengineering Antimicrobial Peptides Produced by Selective Pressure Incorporation of Non-canonical Amino Acids Jessica H. Nickling*1, Tobias Baumann*1, Franz-Josef Schmitt2, Maike Bartholomae3, Oscar P. Kuipers3, Thomas Friedrich2, Nediljko Budisa1 1Department of Biocatalysis, Institute of Chemistry, Technische Universität Berlin, 2Department of Bioenergetics, Institute of Chemistry, Technische Universität Berlin, 3Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Department of Molecular Genetics, University of Groningen The protocol presents the Escherichia coli-based selective pressure incorporation of non-canonical amino acids (ncAAs) into the lactococcal antimicrobial peptide nisin. Its properties can be changed during recombinant expression via substitution with desired ncAAs in defined growth media. Resulting changes in bioactivity are mapped by growth inhibition assays and fluorescence microscopy. Behavior A Method to Test the Effect of Environmental Cues on Mating Behavior in Drosophila melanogaster Jenke A. Gorter1, Jean-Christophe Billeter1 1Groningen Institute for Evolutionary Life Sciences, University of Groningen We demonstrate an assay to analyze the environmental and genetic cues that influence mating behavior in the fruit fly Drosophila melanogaster. Chemistry The Preparation and Properties of Thermo-reversibly Cross-linked Rubber Via Diels-Alder Chemistry Lorenzo Massimo Polgar1,2, Martin van Duin1, Francesco Picchioni1 1Department of Chemical Engineering, University of Groningen, 2Dutch Polymer Institute (DPI) A simple two-step approach involving rubber modification and cross-linking yields fully reworkable, elastic rubber products. Medicine Ex Situ Normothermic Machine Perfusion of Donor Livers Negin Karimian1,2, Alix P.M. Matton1,2, Andrie C. Westerkamp1,2, Laura C. Burlage1,2, Sanna op den Dries1,2, Henri G.D. Leuvenink2, Ton Lisman1,2, Korkut Uygun3, James F. Markmann4, Robert J. Porte1,2 1Section of Hepato-Pancreato-Biliary Surgery and Liver Transplantation, University of Groningen, University Medical Center Groningen, 2Surgical Research Laboratory, Department of Surgery, University of Groningen, University Medical Center Groningen, 3Center of Engineering in Medicine/Surgical Services, Massachusetts General Hospital, Harvard Medical School, and Shriners Burns Hospital, 4Division of Transplantation, Department of Surgery, Massachusetts General Hospital, Harvard Medical School Here we present a protocol describing oxygenated ex situ machine perfusion of donor liver grafts. This article contains a step by step protocol to procure and prepare the liver graft for machine perfusion, prepare the perfusion fluid, prime the perfusion machine and perform oxygenated normothermic machine perfusion of the liver graft. Medicine Functional Human Liver Preservation and Recovery by Means of Subnormothermic Machine Perfusion Bote G. Bruinsma*1, James H. Avruch*2, Pepijn D. Weeder1, Gautham V. Sridharan1, Basak E. Uygun1, Negin G. Karimian1, Robert J. Porte3, James F. Markmann2, Heidi Yeh2, Korkut Uygun1 1Center for Engineering in Medicine, Dept. of Surgery, Massachusetts General Hospital, Harvard Medical School, 2Transplant Center, Dept. of Surgery, Massachusetts General Hospital, Harvard Medical School, 3Section of Hepatobiliary Surgery and Liver Transplantation, Department of Surgery, University Medical Center Groningen, University of Groningen We describe a method of ex vivo machine perfusion of human liver grafts at subnormothermic temperature (21 °C). Biology A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae Muhammad Afzal1,2, Irfan Manzoor1,2, Oscar P. Kuipers1 1Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 2Department of Bioinformatics and Biotechnology, Government College University Faisalabad This manuscript describes the use of state-of-the-art technology provided by DNA-microarrays. Microarrays provide an overview of the transcriptomic changes in bacteria incurred under a specific condition. Moreover, we highlight the ease by which large amounts of data can be analyzed by using convenient in-house developed software packages. Chemistry Gyroid Nickel Nanostructures from Diblock Copolymer Supramolecules Ivana Vukovic1, Sergey Punzhin2, Vincent S. D. Voet1, Zorica Vukovic3, Jeff Th. M. de Hosson2, Gerrit ten Brinke1, Katja Loos1 1Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, 2Materials Science, Zernike Institute for Advanced Materials, University of Groningen, 3ICTM - Center for Catalysis and Chemical Engineering This article describes the preparation of well-ordered nickel nanofoams via electroless metal deposition onto nanoporous templates obtained from self-assembled diblock copolymer based supramolecules. Biology FtsZ Polymerization Assays: Simple Protocols and Considerations Ewa Król1, Dirk-Jan Scheffers1 1Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Polymerization of FtsZ is essential for bacterial cell division. In this report, we detail simple protocols to monitor FtsZ polymerization activity and discuss the influence of buffer composition. The protocols can be used to study the interaction of FtsZ with regulatory proteins or antibacterial drugs that affect FtsZ polymerization. Bioengineering Continuous High-resolution Microscopic Observation of Replicative Aging in Budding Yeast Daphne H. E. W. Huberts1, Georges E. Janssens2, Sung Sik Lee3, Ima Avalos Vizcarra4, Matthias Heinemann1,5 1Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 2Department for the Biology of Ageing, European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, 3Institute of Biochemistry, ETH Zurich, 4Department of Health Sciences and Technology, ETH Zurich, 5Institute of Molecular Systems Biology, ETH Zurich We describe here the operation of a microfluidic device that allows continuous and high-resolution microscopic imaging of single budding yeast cells during their complete replicative and/or chronological lifespan. Behavior The Resident-intruder Paradigm: A Standardized Test for Aggression, Violence and Social Stress Jaap M. Koolhaas1, Caroline M. Coppens1, Sietse F. de Boer1, Bauke Buwalda1, Peter Meerlo1, Paul J.A. Timmermans2 1Department of Behavioral Physiology, Center for Behavior and Neurosciences, University Groningen, 2Radboud University Nijmegen This video shows the resident-intruder paradigm in rats. This test is a standardized method to measure offensive aggression, defensive behavior and violence in a semi-natural setting. The use of the paradigm for social stress experiments is explained as well. Chemistry Fabricating Nanogaps by Nanoskiving Parisa Pourhossein1, Ryan C. Chiechi1 1Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen The fabrication of electrically addressable, high-aspect-ratio (> 1000:1) metal nanowires separated by gaps of single nanometers using either sacrificial layers of aluminum and silver or self-assembled monolayers as templates is described. These nanogap structures are fabricated without a clean room or any photo- or electron-beam lithographic processes by a form of edge lithography known as nanoskiving. Neuroscience Rodent Stereotaxic Surgery and Animal Welfare Outcome Improvements for Behavioral Neuroscience Raquel V. Fornari1, Romy Wichmann1, Piray Atsak1, Erika Atucha1, Areg Barsegyan1, Hassiba Beldjoud1, Fany Messanvi1, Catriene M.A. Thuring2, Benno Roozendaal1 1Department of Neuroscience, Section Anatomy, University Medical Center Groningen, University of Groningen, 2Animal Welfare Office, University of Groningen Stereotaxic surgery on rodents allows for targeted administration of drugs or electrical stimulation and recordings in awake, behaving animals. In this video presentation we will demonstrate recent procedural refinements to this long-standing procedure that successfully improved survival rate and reduced post-surgical weight loss. Immunology and Infection Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae using Automated Time-lapse Microscopy Imke G. de Jong1, Katrin Beilharz1, Oscar P. Kuipers1, Jan- Willem Veening1 1Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen This protocol provides a step-by-step procedure to monitor single cell behavior of different bacteria in time using automated fluorescence time-lapse microscopy. Furthermore, we provide guidelines how to analyze the microscopy images. Biology Isolation of Mouse Salivary Gland Stem Cells Sarah Pringle1,2, Lalitha S. Y. Nanduri1, van der Zwaag Marianne1, van Os Ronald1,2, Rob P. Coppes1,2 1Department of Cell Biology, University Medical Center Groningen, University of Groningen, 2Department of Radiation Oncology, University Medical Center Groningen, University of Groningen An optimized protocol for the isolation of stem cells from the mouse salivary gland is described. The method employs enzymatic and mechanical digestion, and permits isolation of salispheres containing cells with characteristics of stem cells.