Delft University of Technology View Institution's Website 23 articles published in JoVE Bioengineering A Method to Study the Correlation Between Local Collagen Structure and Mechanical Properties of Atherosclerotic Plaque Fibrous Tissue Hanneke Crielaard1, Su Guvenir Torun1, Tamar B. Wissing1,2, Pablo de Miguel Muñoz1,3, Gert-Jan Kremers4, Frank J. H. Gijsen1,3, Kim Van Der Heiden1,2, Ali C. Akyildiz1,3 1Department of Biomedical Engineering, Erasmus Medical Center, 2Department of Biomedical Engineering, Eindhoven University of Technology, 3Department of Biomechanical Engineering, Delft University of Technology, 4Erasmus Optical Imaging Center, Erasmus Medical Center We have developed a mechano-imaging pipeline to study the heterogeneous structural and mechanical atherosclerotic plaque properties. This pipeline enables correlation of the local predominant angle and dispersion of collagen fiber orientation, the rupture behavior, and the strain fingerprints of the fibrous plaque tissue. Biology Bottom-Up In Vitro Methods to Assay the Ultrastructural Organization, Membrane Reshaping, and Curvature Sensitivity Behavior of Septins Brieuc Chauvin*1, Koyomi Nakazawa*1, Alexandre Beber1,7, Aurélie Di Cicco1, Bassam Hajj1, François Iv2, Manos Mavrakis2, Gijsje H. Koenderink3, João T. Cabral4, Michaël Trichet5, Stéphanie Mangenot*6, Aurélie Bertin*1 1Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, 2Institut Fresnel, CNRS UMR7249, Aix Marseille Univ, Centrale Marseille, 3Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 4Department of Chemical Engineering, Imperial College London, 5Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Service de microscopie électronique (IBPS-SME), 6Laboratoire Matière et Systèmes Complexes (MSC), Université Paris Cité, 7Institute of Biotechnology, Czech Academy of Sciences, BIOCEV Septins are cytoskeletal proteins. They interact with lipid membranes and can sense but also generate membrane curvature at the micron scale. We describe in this protocol bottom-up in vitro methodologies for analyzing membrane deformations, curvature-sensitive septin binding, and septin filament ultrastructure. Biochemistry Purification and Quality Control of Recombinant Septin Complexes for Cell-Free Reconstitution Gerard Castro-Linares1, Jeffrey den Haan1, Francois Iv2, Carla Silva Martins2, Aurélie Bertin3, Manos Mavrakis2, Gijsje H. Koenderink1 1Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2Institut Fresnel, CNRS UMR7249, Aix Marseille Univ, Centrale Marseille, 3Institut Curie, Université PSL, Sorbonne Université In vitro reconstitution of cytoskeletal proteins is a vital tool to understand the basic functional properties of these proteins. The present paper describes a protocol to purify and assess the quality of recombinant septin complexes, which play a central role in cell division and migration. Bioengineering Quantifying Cytoskeleton Dynamics Using Differential Dynamic Microscopy Hannah N. Verwei1, Gloria Lee2, Gregor Leech2, Irene Istúriz Petitjean3, Gijsje H. Koenderink3, Rae M. Robertson-Anderson2, Ryan James McGorty2 1Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 2Department of Physics and Biophysics, University of San Diego, 3Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology Differential dynamic microscopy (DDM) combines features of dynamic light scattering and microscopy. Here, the process of using DDM to characterize reconstituted cytoskeleton networks by quantifying the subdiffusive and caged dynamics of particles in vimentin networks and the ballistic motion of active myosin-driven actin-microtubule composites is presented. Bioengineering The Preparation of Chicken Ex Ovo Embryos and Chorioallantoic Membrane Vessels as In Vivo Model for Contrast-Enhanced Ultrasound Imaging and Microbubble-Mediated Drug Delivery Studies Bram Meijlink1, Ilya Skachkov1, Antonius F. W. van der Steen1,2, Nico de Jong1,2, Klazina Kooiman1 1Department of Biomedical Engineering, Thoraxcenter, Erasmus MC University Medical Center Rotterdam, 2Laboratory of Acoustical Wavefield Imaging, Faculty of Applied Sciences, Delft University of Technology This protocol describes three methods on how to obtain and use 5 to 8-day old chicken embryos and their chorioallantoic membrane (CAM) as an in vivo model to study contrast-enhanced ultrasound imaging and microbubble-mediated drug delivery. 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. Medicine Determining and Controlling External Power Output During Regular Handrim Wheelchair Propulsion Rick de Klerk1, Riemer J. K. Vegter1, Marika T. Leving1, Sonja de Groot1,2, DirkJan H. E. J. Veeger3,4, Lucas H. V. van der Woude1,5 1Center for Human Movement Sciences, University Medical Center Groningen, 2Amsterdam Rehabilitation Research Center Reade, Amsterdam, 3Research Institute MOVE, Faculty of Behavioral and Human Movement Sciences, VU University, 43M, Delft University of Technology, Delft, 5Center for Rehabilitation, University Medical Center Groningen Accurate and standardized assessment of external power output is crucial in the evaluation of physiological, biomechanical, and perceived stress, strain, and capacity in manual wheelchair propulsion. The current article presents various methods to determine and control power output during wheelchair propulsion studies in the laboratory and beyond. Engineering Fabrication and Design of Wood-Based High-Performance Composites Marion Frey1,2, Meri Zirkelbach3, Clemens Dransfeld4, Eric Faude1, Etienne Trachsel1, Mikael Hannus5, Ingo Burgert1,2, Tobias Keplinger1,2 1Wood Materials Science, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 2Cellulose & Wood Materials, Functional Materials, EMPA, 3Design and Arts, Lucerne University of Applied Sciences and Arts, 4Aerospace Manufacturing Technologies, Aerospace Engineering, Delft University of Technology, 5Stora Enso Oyj Delignified densified wood represents a new promising lightweight, high-performance and bio-based material with great potential to partially substitute natural fiber reinforced- or glass fiber reinforced composites in the future. We here present two versatile fabrication routes and demonstrate the possibility to create complex composite parts. Bioengineering Three-dimensional Patterning of Engineered Biofilms with a Do-it-yourself Bioprinter Ewa M. Spiesz*1, Kui Yu*1, Benjamin A.E. Lehner1, Dominik T. Schmieden1, Marie-Eve Aubin-Tam1, Anne S. Meyer2 1Department of Bionanoscience & Kavli Institute of Nanoscience, Delft University of Technology, 2Department of Biology, University of Rochester This article describes a method of transforming a low-cost commercial 3D printer into a bacterial 3D printer that can facilitate printing of patterned biofilms. All necessary aspects of preparing the bioprinter and bio-ink are described, as well as verification methods to assess the formation of biofilms. Biochemistry Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions Markus Götz1, Philipp Wortmann1, Sonja Schmid1,2, Thorsten Hugel1 1Institute of Physical Chemistry, University of Freiburg, 2Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology Here, we present a protocol to obtain three-color smFRET data and its analysis with a 3D ensemble Hidden Markov Model. With this approach, scientists can extract kinetic information from complex protein systems, including cooperativity or correlated interactions. Chemistry Laser-heating and Radiance Spectrometry for the Study of Nuclear Materials in Conditions Simulating a Nuclear Power Plant Accident Dario Manara1, Luca Soldi1,2,4, Sara Mastromarino1,3,5, Kostantinos Boboridis1, Davide Robba1, Luka Vlahovic1, Rudy Konings1 1European Commission, Joint Research Centre, 2Energy Department, Politecnico di Milano, 3Department of Chemical Physics, Sapienza - Università di Roma, 4CEA Saclay, 5TU Delft We present experiments in which real nuclear fuel, cladding, and containment materials are laser heated to temperatures beyond 3,000 K while their behavior is studied by radiance spectroscopy and thermal analysis. These experiments simulate, on a laboratory scale, the formation of a lava-phase following a nuclear reactor core meltdown. Bioengineering An Experimental and Finite Element Protocol to Investigate the Transport of Neutral and Charged Solutes across Articular Cartilage Vahid Arbabi*1,2, Behdad Pouran*1,2, Amir. A. Zadpoor1, Harrie Weinans1,2,3 1Department of Biomechanical Engineering, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology (TU Delft), 2Department of Orthopedics, UMC Utrecht, 3Department of Rheumatology, UMC Utrecht We propose a protocol to investigate the transport of charged and uncharged molecules across articular cartilage with the aid of recently developed experimental and numerical methods. Environment Extraction of Structural Extracellular Polymeric Substances from Aerobic Granular Sludge Simon Felz1, Salah Al-Zuhairy1, Olav Andreas Aarstad2, Mark C.M. van Loosdrecht1, Yue Mei Lin1 1Department of Biotechnology, Delft University of Technology, 2Department of Biotechnology, Norwegian Biopolymer Laboratory (NOBIPOL), Norwegian University of Science and Technology The protocol provides a methodology to solubilize aerobic granular sludge in order to extract alginate-like extracellular polymers (ALE). Biology Reconstitution of Basic Mitotic Spindles in Spherical Emulsion Droplets Mathijs Vleugel1, Sophie Roth1, Celebrity F. Groenendijk1, Marileen Dogterom1 1Department of Bionanoscience, Delft University of Technology The assembly and positioning of the mitotic spindle depend on the combined forces generated by microtubule dynamics, motor proteins and cross-linkers. Here we present our recently developed methods in which the geometrical confinement of spherical emulsion droplets is used for the bottom-up reconstitution of basic mitotic spindles. Chemistry Light-driven Enzymatic Decarboxylation Katharina Köninger1, Marius Grote1, Ioannis Zachos1, Frank Hollmann2, Robert Kourist1 1Faculty of Biology and Biotechnology, Ruhr Universität Bochum, 2Biology and Biotechnology, Delft University of Technology We describe a protocol for the light-catalyzed generation of hydrogen peroxide — a cofactor for oxidative transformations. Engineering Ultrasonic Welding of Thermoplastic Composite Coupons for Mechanical Characterization of Welded Joints through Single Lap Shear Testing Irene F. Villegas1, Genevieve Palardy1 1Structural Integrity and Composites, Delft University of Technology A straightforward procedure for ultrasonic welding of thermoplastic composite coupons for basic mechanical testing is described. Key characteristics of this ultrasonic welding process are the use of flat energy directors for simplified process preparation and the use of process data for the fast definition of optimum processing conditions. Engineering Fabrication of Low Temperature Carbon Nanotube Vertical Interconnects Compatible with Semiconductor Technology Sten Vollebregt1, Ryoichi Ishihara1 1Department of Microelectronics, Delft University of Technology A method for the growth of low temperature vertically-aligned carbon nanotubes, and the subsequent fabrication of vertical interconnect electrical test structures using semiconductor fabrication is presented. Biology EPR Monitored Redox Titration of the Cofactors of Saccharomyces cerevisiae Nar1 Peter-Leon Hagedoorn1, Laura van der Weel1, Wilfred R. Hagen1 1Department of Biotechnology, Delft University of Technology The goal of this protocol is to use electron paramagnetic resonance (EPR) monitored redox titrations to identify different cofactors of Saccharomyces cerevisiae Nar1. Redox titrations offer a very robust way to obtain midpoint potentials of different redox active cofactors in enzymes and proteins. Bioengineering Magnetic Tweezers for the Measurement of Twist and Torque Jan Lipfert1, Mina Lee1, Orkide Ordu1, Jacob W. J. Kerssemakers1, Nynke H. Dekker1 1Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology Magnetic tweezers, a powerful single-molecule manipulation technique, can be adapted for the direct measurements of the twist (using a configuration called freely-orbiting magnetic tweezers) and torque (using a configuration termed magnetic torque tweezers) in biological macromolecules. Guidelines for performing such measurements are given, including applications to the study of DNA and associated nucleo-protein filaments. Chemistry Surface Passivation for Single-molecule Protein Studies Stanley D. Chandradoss1, Anna C. Haagsma1, Young Kwang Lee2, Jae-Ho Hwang2, Jwa-Min Nam2, Chirlmin Joo1 1Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2Department of Chemistry, Seoul National University We describe a method for passivating a glass surface using polyethylene glycol (PEG). This protocol covers surface cleaning, surface functionalization, and PEG coating. We introduce a new strategy for treating the surface with PEG molecules over two rounds, which yields superior quality of passivation compared to existing methods. Environment Transient Gene Expression in Tobacco using Gibson Assembly and the Gene Gun Matthew D. Mattozzi1,2, Mathias J. Voges1,2,3, Pamela A. Silver1,2, Jeffrey C. Way1,2 1Synthetic Biology Platform, Wyss Institute for Biologically Inspired Engineering, Harvard University, 2Department of Systems Biology, Harvard Medical School, 3Department of Biotechnology, Delft University of Technology This work describes a novel method for selectively targeting subcellular organelles in plants, assayed using the BioRad Gene Gun. Biology Application of an In vitro DNA Protection Assay to Visualize Stress Mediation Properties of the Dps Protein Vlad O. Karas1, Ilja Westerlaken1, Anne S. Meyer1 1Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology The DNA-binding protein from starved cells (Dps) plays a crucial role in combating bacterial stress. This article discusses the purification of E. coli Dps and the protocol for an in vitro assay demonstrating Dps-mediated protection of DNA from degradation by reactive oxygen species. Bioengineering A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments Eva K. Brinkman1, Kira Schipper1, Nadine Bongaerts1, Mathias J. Voges1, Alessandro Abate2, S. Aljoscha Wahl1 1Department of Biotechnology, Delft University of Technology, 2Delft Center for Systems and Control, Delft University of Technology A sustainable auto regulating bacterial system for the remediation of oil pollutions was designed using standard interchangeable DNA parts (BioBricks). An engineered E. coli strain was used to degrade alkanes via β-oxidation in toxic aqueous environments. The respective enzymes from different species showed alkane degradation activity. Additionally, an increased tolerance to n-hexane was achieved by introducing genes from alkane-tolerant bacteria.