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University of Groningen

29 ARTICLES PUBLISHED IN JoVE

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Immunology and Infection

Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae using Automated Time-lapse Microscopy
Imke G. de Jong 1, Katrin Beilharz 1, Oscar P. Kuipers 1, Jan- Willem Veening 1
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.

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Neuroscience

Rodent Stereotaxic Surgery and Animal Welfare Outcome Improvements for Behavioral Neuroscience
Raquel V. Fornari 1, Romy Wichmann 1, Piray Atsak 1, Erika Atucha 1, Areg Barsegyan 1, Hassiba Beldjoud 1, Fany Messanvi 1, Catriene M.A. Thuring 2, Benno Roozendaal 1
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.

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Bioengineering

Continuous High-resolution Microscopic Observation of Replicative Aging in Budding Yeast
Daphne H. E. W. Huberts 1, Georges E. Janssens 2, Sung Sik Lee 3, Ima Avalos Vizcarra 4, Matthias Heinemann 1,5
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.

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Chemistry

Fabricating Nanogaps by Nanoskiving
Parisa Pourhossein 1, Ryan C. Chiechi 1
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.

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Chemistry

Gyroid Nickel Nanostructures from Diblock Copolymer Supramolecules
Ivana Vukovic 1, Sergey Punzhin 2, Vincent S. D. Voet 1, Zorica Vukovic 3, Jeff Th. M. de Hosson 2, Gerrit ten Brinke 1, Katja Loos 1
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.

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Biology

FtsZ Polymerization Assays: Simple Protocols and Considerations
Ewa Król 1, Dirk-Jan Scheffers 1
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.

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Biology

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae
Muhammad Afzal 1,2, Irfan Manzoor 1,2, Oscar P. Kuipers 1
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.

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Developmental Biology

Development of an Ethanol-induced Fibrotic Liver Model in Zebrafish to Study Progenitor Cell-mediated Hepatocyte Regeneration
Mianbo Huang 1, Jin Xu 1, Chong Hyun Shin 1
1School of Biology, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology

Sustained fibrosis with deposition of excessive extracellular matrix proteins leads to cirrhosis. Alcohol abuse is one of the main causes of severe liver disease. We established an ethanol-induced zebrafish fibrotic liver model to study the mechanisms and strategies of promoting hepatocyte regeneration upon alcohol-induced injury.

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JoVE Core

The Preparation and Properties of Thermo-reversibly Cross-linked Rubber Via Diels-Alder Chemistry
Lorenzo Massimo Polgar 1,2, Martin van Duin 1, Francesco Picchioni 1
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.

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Medicine

Shunt Surgery, Right Heart Catheterization, and Vascular Morphometry in a Rat Model for Flow-induced Pulmonary Arterial Hypertension
Diederik E. van der Feen 1, Michel Weij 2, Annemieke Smit-van Oosten 2, Lysanne M. Jorna 1, Quint A.J. Hagdorn 1, Beatrijs Bartelds 1, Rolf M.F. Berger 1
1Center for Congenital Heart Diseases, Department of Pediatric Cardiology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, 2Research and Development Facility, University Medical Center Groningen, University of Groningen

This protocol describes a surgical procedure to create a model for flow-induced pulmonary arterial hypertension (PAH) in rats and the procedures to analyze the principle hemodynamic and histological end-points in this model.

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Behavior

A Method to Test the Effect of Environmental Cues on Mating Behavior in Drosophila melanogaster
Jenke A. Gorter 1, Jean-Christophe Billeter 1
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.

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Bioengineering

Antimicrobial Peptides Produced by Selective Pressure Incorporation of Non-canonical Amino Acids
Jessica H. Nickling *1, Tobias Baumann *1, Franz-Josef Schmitt 2, Maike Bartholomae 3, Oscar P. Kuipers 3, Thomas Friedrich 2, Nediljko Budisa 1
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.

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Biology

Plant-Microbe Interaction: Transcriptional Response of Bacillus Mycoides to Potato Root Exudates
Yanglei Yi 1, Zhibo Li 1, Oscar P. Kuipers 1
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.

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Chemistry

Stereolithographic 3D Printing with Renewable Acrylates
Vincent S.D. Voet 1, Geraldine H.M. Schnelting 1, Jin Xu 2, Katja Loos 2, Rudy Folkersma 1, Jan Jager 1
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.

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Behavior

An Automated Method to Determine the Performance of Drosophila in Response to Temperature Changes in Space and Time
Andrea Soto-Padilla 1,2, Rick Ruijsink 3, Mark Span 4, 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.

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Bioengineering

Manufacturing of a Nafion-coated, Reduced Graphene Oxide/Polyaniline Chemiresistive Sensor to Monitor pH in Real-time During Microbial Fermentation
Selvaraj Chinnathambi 1, Gert-Jan Euverink 1
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.

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Bioengineering

A Zebrafish Embryo Model for In Vivo Visualization and Intravital Analysis of Biomaterial-associated Staphylococcus aureus Infection
Xiaolin Zhang 1,2, Leonie de Boer 1, Oliver W. Stockhammer 1, Dirk W. Grijpma 2,3, Herman P. Spaink 4, Sebastian A.J. Zaat 1
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.

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JoVE Journal

Extraction of Lignin with High β-O-4 Content by Mild Ethanol Extraction and Its Effect on the Depolymerization Yield
Douwe S. Zijlstra 1, Alessandra de Santi 2, Bert Oldenburger 1,2, Johannes de Vries 2,3, Katalin Barta 2, Peter J. Deuss 1
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.

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Chemistry

Light-driven Molecular Motors on Surfaces for Single Molecular Imaging
Jiawen Chen 1, Jérôme Vachon 1, Ben L. Feringa 1
1Stratingh Institute for Chemistry, University of Groningen

The manuscript describes how to synthesize and graft a molecular motor on surfaces for single molecular imaging.

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Developmental Biology

An Ectopic Chemokine Expression Model for Testing Macrophage Recruitment In Vivo
Yunyun Jiang 1, Jiahao Chen 1, Jin Xu 2
1Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, 2Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology

To test the effect of a chemokine on macrophage recruitment in vivo, the whole mount in situ hybridization was used to detect the ectopic expression of the chemokine, and immunostaining was used to label macrophages. Live imaging was used for real-time observation of macrophage migration.

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Biology

In Situ Monitoring of Transiently Formed Molecular Chaperone Assemblies in Bacteria, Yeast, and Human Cells
Niels Alberts *1, Yasith Mathangasinghe *2, Nadinath B. Nillegoda 3
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.

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Medicine

Quantification of Biventricular Function and Morphology by Cardiac Magnetic Resonance Imaging in Mice with Pulmonary Artery Banding
Anne-Marie C. Koop *1, Quint A.J. Hagdorn *1, Kees (C.) W.A. van de Kolk 2,3, Annemieke van Oosten 2, Michel Weij 2, Herman H.W. Silljé 4, Tineke P. Willems 5, Rolf M.F. Berger 1
1Center for Congenital Heart Diseases, Department of Pediatric Cardiology, University Medical Center Groningen, University of Groningen, 2The Central Animal Facility, University Medical Center Groningen, University of Groningen, 3Gronsai (Groningen Small Animal Imaging Facility), University Medical Center Groningen, University of Groningen, 4Department of Cardiology, University Medical Center Groningen, University of Groningen, 5Department of Radiology, University Medical Center Groningen, University of Groningen

To understand the pathophysiology of right ventricular (RV) adaptation to abnormal loading, experimental models are crucial. However, assessment of RV dimensions and function is complex and challenging. This protocol provides a method to perform cardiac magnetic resonance imaging (CMR) as a noninvasive benchmark procedure in mice subjected to RV pressure load.

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JoVE Core

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. Brink 1, Cornelis J. de Ruiter 2, Geert J.P. Savelsbergh 2, Annemarijn Steijlen 3, Kaspar M.B. Jansen 3, Frans C.T. van der Helm 4, Edwin A. Goedhart 5, Doris van der Laan 6, Riemer J.K. Vegter 1, Koen A.P.M. Lemmink 1
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.

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Neuroscience

Electrocorticographic Recording of Cerebral Cortex Areas Manipulated Using an Adeno-Associated Virus Targeting Cofilin in Mice
Julien Dufort-Gervais 1, Robbert Havekes 2, Valérie Mongrain 1,3
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.

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Bioengineering

Imaging-Guided Bioreactor for Generating Bioengineered Airway Tissue
Mohammad Mir 1, Jiawen Chen 1, Meghan R. Pinezich 1, John D. O’Neill 3, Brandon A. Guenthart 4, Gordana Vunjak-Novakovic 2, Jinho Kim 1
1Department of Biomedical Engineering, Stevens Institute of Technology, 2Department of Biomedical Engineering, Columbia University, 3Department of Cell Biology, State University of New York Downstate Medical Center, 4Department of Cardiothoracic Surgery, Stanford University

The protocol describes an imaging-enabled bioreactor that allows the selective removal of the endogenous epithelium from the rat trachea and homogenous distribution of exogenous cells on the lumen surface, followed by long-term in vitro culture of the cell-tissue construct.

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Biology

Automated Charting of the Visual Space of Housefly Compound Eyes
Maurico Muñoz Arias 1, John K. Douglass 2,3, Martin F. Wehling 2, Doekele G. Stavenga 3
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.

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Medicine

Precision of In Vivo Quantitative Tooth Wear Measurement Using Intra-Oral Scans
Hilde Bronkhorst 1, Ewald Bronkhorst 1, Stanimira Kalaykova 1, Wicher van der Meer 2, Marie-Charlotte Huysmans 1, Bas Loomans 1
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.

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Biochemistry

Construction of Out-of-Equilibrium Metabolic Networks in Nano- and Micrometer-Sized Vesicles
Jelmer Coenradij 1, Eleonora Bailoni 1, Bert Poolman 1
1Department of Biochemistry, University of Groningen

We present a protocol for reconstituting membrane proteins and encapsulating enzymes and other water-soluble components in lipid vesicles of sub-micrometer and micrometer size.

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Engineering

Characterizing Dissipative Elastic Metamaterials Produced by Additive Manufacturing
Sidharth Beniwal 1, Ranjita K. Bose 1, Anastasiia O. Krushynska 1
1Engineering and Technology Institute Groningen (ENTEG), Faculty of Science and Engineering, University of Groningen

Additively manufactured polymers have been widely used for producing elastic metamaterials. The viscoelastic behavior of these polymers at ultrasonic frequencies remains, however, poorly studied. This study reports a protocol to estimate the viscoelastic properties of 3D-printed polymers and show how to use them to analyze the metamaterial dynamics.

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