Technical University of Denmark 11 articles published in JoVE Chemistry Tuning Oxide Properties by Oxygen Vacancy Control During Growth and Annealing Tristan Steegemans*1, Shinhee Yun*1, Carlos N. Lobato1, Eric Brand1, Yunzhong Chen2, Felix Trier1, Dennis V. Christensen1 1Department of Energy Conversion and Storage, Technical University of Denmark, 2Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences Oxide materials show many exotic properties that can be controlled by tuning the oxygen content. Here, we demonstrate the tuning of oxygen content in oxides by varying the pulsed laser deposition parameters and by performing postannealing. As an example, electronic properties of SrTiO3-based heterostructures are tuned by growth modifications and annealing. Bioengineering Microgel-Extracellular Matrix Composite Support for the Embedded 3D Printing of Human Neural Constructs Janko Kajtez1, Carmen Radeke2, Johan Ulrik Lind2, Jenny Emnéus3 1Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2Department of Health Technology (DTU Health Tech), Technical University of Denmark, 3Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark This work describes a protocol for the freeform embedded 3D printing of neural stem cells inside self-healing annealable particle-extracellular matrix composites. The protocol enables the programmable patterning of interconnected human neural tissue constructs with high fidelity. Biology Assessing Mineral Availability in Fish Feeds using Complementary Methods Demonstrated with the Example of Zinc in Atlantic Salmon Marta S. Silva1,2, Thea Stewart4, Heidi Amlund1,3, Jens J. Sloth1,3, Pedro Araujo1, Erik-Jan Lock1, Christer Hogstrand4, Robin Ørnsrud1, Rune Waagbø1,2, Antony Jesu Prabhu1 1Institute of Marine Research, 2Department of Biological Sciences, University of Bergen, 3National Food Institute, Technical University of Denmark, 4 This article explains in detail a systematic approach to assess micro-mineral availability in Atlantic salmon. The methodology includes tools and models with increasing biological complexity: (1) chemical speciation analysis, (2) in vitro solubility, (3) uptake studies in cell lines, and (4) in vivo fish studies. Chemistry In situ Grazing Incidence Small Angle X-ray Scattering on Roll-To-Roll Coating of Organic Solar Cells with Laboratory X-ray Instrumentation Michael Korning Sørensen1, Moises Espindola Rodriguez1, Marcial Fernández Castro1, Ashwin Nambi1, Luise Theil Kuhn1, Jens Wenzel Andreasen1 1Department of Energy Conversion and Storage, Technical University of Denmark This paper is a demonstration and a guideline to perform and analyze in-house (with a laboratory X-ray instrument) in situ GISAXS experiments of drying inks on roll-to-roll slot-die coated, non-fullerene organic photovoltaics. Environment A Small-Scale Setup for Algal Toxicity Testing of Nanomaterials and Other Difficult Substances Lars Michael Skjolding1, Susanne Kruse1, Sara Nørgaard Sørensen1, Rune Hjorth1, Anders Baun1 1Department of Environmental Engineering, Technical University of Denmark We demonstrate algal toxicity testing for difficult substances (e.g., colored substances or nanomaterials) using a setup illuminated vertically with an LED. Bioengineering A Quantitative Fluorescence Microscopy-based Single Liposome Assay for Detecting the Compositional Inhomogeneity Between Individual Liposomes Rasmus Münter1,3, Thomas Lars Andresen1,2,3, Jannik Bruun Larsen1,2,3 1Center for Nanomedicine and Theranostics, Technical University of Denmark, 2Center for Intestinal Absorption and Transport of Biopharmaceuticals, Technical University of Denmark, 3Department of Health Technology, Technical University of Denmark This protocol describes the fabrication of liposomes and how these can be immobilized on a surface and imaged individually in a massive parallel manner using fluorescence microscopy. This allows for the quantification of the size and compositional inhomogeneity between single liposomes of the population. Neuroscience Cochlear Implant Surgery and Electrically-evoked Auditory Brainstem Response Recordings in C57BL/6 Mice Charlotte Amalie Navntoft1,2, Jeremy Marozeau1, Tania Rinaldi Barkat2 1Hearing Systems Group, Department of Electrical Engineering, Technical University of Denmark, 2Brain and Sound Lab, Department of Biomedicine, Basel University Animal models of cochlear implants can advance knowledge of the technological bases of treating permanent sensorineural hearing loss with electrical stimulation. This study presents a surgical protocol for acute deafening and cochlear implantation of an electrode array in mice as well as the functional assessment with auditory brainstem response. Engineering A Soft Tooling Process Chain for Injection Molding of a 3D Component with Micro Pillars Yang Zhang1, David Bue Pedersen1, Michael Mischkot1, Matteo Calaon1, Federico Baruffi1, Guido Tosello1 1Department of Mechanical Engineering, Technical University of Denmark A protocol for fabricating injection molding inserts for complex geometry with micro features on surfaces employing Additive Manufacturing (AM) is presented. Engineering Experimental Procedure for Laboratory Studies of In Situ Burning : Flammability and Burning Efficiency of Crude Oil Laurens van Gelderen1, Grunde Jomaas1,2 1Department of Civil Engineering, Technical University of Denmark, 2School of Engineering, BRE Centre for Fire Safety Engineering, University of Edinburgh Here, we present a protocol to simultaneously study the flammability and burning efficiency of fresh and weathered crude oil under conditions that simulate in situ burning operations on the sea. Immunology and Infection Noninvasive Sampling of Mucosal Lining Fluid for the Quantification of In Vivo Upper Airway Immune-mediator Levels Helene M. Wolsk1, Bo L. Chawes1, Jonathan Thorsen1, Jakob Stokholm1, Klaus Bønnelykke1, Susanne Brix2, Hans Bisgaard1 1Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, 2Department of Biotechnology and Biomedicine, Technical University of Denmark This protocol describes a noninvasive technique for the sampling of undisturbed mucosal lining fluid from the upper airways. It can be used to perform the quantification of in vivo levels of protein mediators, such as cytokines and chemokines, in subjects of all ages. Biology Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells Henrik D. Møller1, Rasmus K. Bojsen2, Chris Tachibana3, Lance Parsons4, David Botstein5, Birgitte Regenberg1 1Department of Biology, University of Copenhagen, 2National Veterinary Institute, Technical University of Denmark, 3Group Health Research Institute, 4Lewis-Sigler Institute for Integrative Genomics, Princeton University, 5Calico Life Sciences LLC This paper presents a sensitive method called Circle-Seq for purifying extrachromosomal circular DNA (eccDNA). The method encompasses column purification, removal of remaining linear chromosomal DNA, rolling-circle amplification and high-throughput sequencing. Circle-Seq is applicable to genome-scale screening of eukaryotic eccDNA and studying genome instability and copy-number variation.