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Delft University of Technology

21 ARTICLES PUBLISHED IN JoVE

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Education

A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments
Eva K. Brinkman 1, Kira Schipper 1, Nadine Bongaerts 1, Mathias J. Voges 1, Alessandro Abate 2, S. Aljoscha Wahl 1
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.

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Biology

Application of an In vitro DNA Protection Assay to Visualize Stress Mediation Properties of the Dps Protein
Vlad O. Karas 1, Ilja Westerlaken 1, Anne S. Meyer 1
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.

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Chemistry

Surface Passivation for Single-molecule Protein Studies
Stanley D. Chandradoss 1, Anna C. Haagsma 1, Young Kwang Lee 2, Jae-Ho Hwang 2, Jwa-Min Nam 2, Chirlmin Joo 1
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.

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Environment

Transient Gene Expression in Tobacco using Gibson Assembly and the Gene Gun
Matthew D. Mattozzi 1,2, Mathias J. Voges 1,2,3, Pamela A. Silver 1,2, Jeffrey C. Way 1,2
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.

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Education

Magnetic Tweezers for the Measurement of Twist and Torque
Jan Lipfert 1, Mina Lee 1, Orkide Ordu 1, Jacob W. J. Kerssemakers 1, Nynke H. Dekker 1
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.

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Biology

EPR Monitored Redox Titration of the Cofactors of Saccharomyces cerevisiae Nar1
Peter-Leon Hagedoorn 1, Laura van der Weel 1, Wilfred R. Hagen 1
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.

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Engineering

Fabrication of Low Temperature Carbon Nanotube Vertical Interconnects Compatible with Semiconductor Technology
Sten Vollebregt 1, Ryoichi Ishihara 1
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.

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JoVE Core

Light-driven Enzymatic Decarboxylation
Katharina Köninger 1, Marius Grote 1, Ioannis Zachos 1, Frank Hollmann 2, Robert Kourist 1
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.

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Engineering

Ultrasonic Welding of Thermoplastic Composite Coupons for Mechanical Characterization of Welded Joints through Single Lap Shear Testing
Irene F. Villegas 1, Genevieve Palardy 1
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.

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JoVE Journal

Reconstitution of Basic Mitotic Spindles in Spherical Emulsion Droplets
Mathijs Vleugel 1, Sophie Roth 1, Celebrity F. Groenendijk 1, Marileen Dogterom 1
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.

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Environment

Extraction of Structural Extracellular Polymeric Substances from Aerobic Granular Sludge
Simon Felz 1, Salah Al-Zuhairy 1, Olav Andreas Aarstad 2, Mark C.M. van Loosdrecht 1, Yue Mei Lin 1
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).

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Biochemistry

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions
Markus Götz 1, Philipp Wortmann 1, Sonja Schmid 1,2, Thorsten Hugel 1
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.

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Bioengineering

Three-dimensional Patterning of Engineered Biofilms with a Do-it-yourself Bioprinter
Ewa M. Spiesz *1, Kui Yu *1, Benjamin A.E. Lehner 1, Dominik T. Schmieden 1, Marie-Eve Aubin-Tam 1, Anne S. Meyer 2
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.

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Education

Fabrication and Design of Wood-Based High-Performance Composites
Marion Frey 1,2, Meri Zirkelbach 3, Clemens Dransfeld 4, Eric Faude 1, Etienne Trachsel 1, Mikael Hannus 5, Ingo Burgert 1,2, Tobias Keplinger 1,2
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.

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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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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 Meijlink 1, Ilya Skachkov 1, Antonius F. W. van der Steen 1,2, Nico de Jong 1,2, Klazina Kooiman 1
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.

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Biochemistry

Purification and Quality Control of Recombinant Septin Complexes for Cell-Free Reconstitution
Gerard Castro-Linares 1, Jeffrey den Haan 1, Francois Iv 2, Carla Silva Martins 2, Aurélie Bertin 3, Manos Mavrakis 2, Gijsje H. Koenderink 1
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.

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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 Beber 1,7, Aurélie Di Cicco 1, Bassam Hajj 1, François Iv 2, Manos Mavrakis 2, Gijsje H. Koenderink 3, João T. Cabral 4, Michaël Trichet 5, 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.

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Bioengineering

Quantifying Cytoskeleton Dynamics Using Differential Dynamic Microscopy
Hannah N. Verwei 1, Gloria Lee 2, Gregor Leech 2, Irene Istúriz Petitjean 3, Gijsje H. Koenderink 3, Rae M. Robertson-Anderson 2, Ryan James McGorty 2
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.

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Bioengineering

A Method to Study the Correlation Between Local Collagen Structure and Mechanical Properties of Atherosclerotic Plaque Fibrous Tissue
Hanneke Crielaard 1, Su Guvenir Torun 1, Tamar B. Wissing 1,2, Pablo de Miguel Muñoz 1,3, Gert-Jan Kremers 4, Frank J. H. Gijsen 1,3, Kim Van Der Heiden 1,2, Ali C. Akyildiz 1,3
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.

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Biochemistry

Hybrid Ensemble and Single-molecule Assay to Image the Motion of Fully Reconstituted CMG
Daniel Ramírez Montero 1, Humberto Sánchez 1, Edo van Veen 1, Theo van Laar 1, Belén Solano 1, John F. X. Diffley 2, Nynke H. Dekker 1,3
1Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2Chromosome Replication Laboratory, Francis Crick Institute, 3Department of Physics and Kavli Institute of Nanoscience Discovery, University of Oxford

We report a hybrid ensemble and single-molecule assay to directly image and quantify the motion of fluorescently labeled, fully reconstituted Cdc45/Mcm2-7/GINS (CMG) helicase on linear DNA molecules held in place in an optical trap.

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