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Technical University of Denmark

17 ARTICLES PUBLISHED IN JoVE

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Biology

A Protocol for Computer-Based Protein Structure and Function Prediction
Ambrish Roy 1,2, Dong Xu 1, Jonathan Poisson 1, Yang Zhang 1,2
1Center for Computational Medicine and Bioinformatics, University of Michigan , 2Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas

Guidelines for computer based structural and functional characterization of protein using the I-TASSER pipeline is described. Starting from query protein sequence, 3D models are generated using multiple threading alignments and iterative structural assembly simulations. Functional inferences are thereafter drawn based on matches to proteins with known structure and functions.

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Biology

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Henrik D. Møller 1, Rasmus K. Bojsen 2, Chris Tachibana 3, Lance Parsons 4, David Botstein 5, Birgitte Regenberg 1
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.

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JoVE Core

Noninvasive Sampling of Mucosal Lining Fluid for the Quantification of In Vivo Upper Airway Immune-mediator Levels
Helene M. Wolsk 1, Bo L. Chawes 1, Jonathan Thorsen 1, Jakob Stokholm 1, Klaus Bønnelykke 1, Susanne Brix 2, Hans Bisgaard 1
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.

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JoVE Core

Treatment with Vancomycin Loaded Calcium Sulphate and Autogenous Bone in an Improved Rabbit Model of Bone Infection
Yang Zhang *1, Lifeng Shen *2, Ping'er Wang 3, Weixing Xi 4, Zhongming Yu 1, Xiaowen Huang 1, Xuping Wang 1, Dan Shou 1
1Department of Medicine, Zhejiang Academy of Traditional Chinese Medicine, 2Department of Orthopaedic Surgery, Tongde Hospital of Zhejiang Province, 3Institute of Orthopaedics and Traumatology, First Affiliated Hospital of Zhejiang Chinese Medical University, 4Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province

This study presents an improved rabbit model infected with Staphylococcus aureus by blocking the same amount of bacteria in bone marrow. Vancomycin loaded calcium sulphate and autogenous bone are used for antibiotic and bone repair treatment. The protocol could be helpful for studying bone infection and regeneration.

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JoVE Journal

Experimental Procedure for Laboratory Studies of In Situ Burning : Flammability and Burning Efficiency of Crude Oil
Laurens van Gelderen 1, Grunde Jomaas 1,2
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.

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Engineering

A Soft Tooling Process Chain for Injection Molding of a 3D Component with Micro Pillars
Yang Zhang 1, David Bue Pedersen 1, Michael Mischkot 1, Matteo Calaon 1, Federico Baruffi 1, Guido Tosello 1
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.

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Neuroscience

Cochlear Implant Surgery and Electrically-evoked Auditory Brainstem Response Recordings in C57BL/6 Mice
Charlotte Amalie Navntoft 1,2, Jeremy Marozeau 1, Tania Rinaldi Barkat 2
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.

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Chemistry

Tuning Oxide Properties by Oxygen Vacancy Control During Growth and Annealing
Tristan Steegemans *1, Shinhee Yun *1, Carlos N. Lobato 1, Eric Brand 1, Yunzhong Chen 2, Felix Trier 1, Dennis V. Christensen 1
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.

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Cancer Research

Three-Dimensional Bone Extracellular Matrix Model for Osteosarcoma
Yu Zhang 1, Yupeng Yao 1, Yan Zhang 1
1MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University

The bone extracellular matrix (BEM) model for osteosarcoma (OS) is well established and shown here. It can be used as a suitable scaffold for mimicking primary tumor growth in vitro and providing an ideal model for studying the histologic and cytogenic heterogeneity of OS.

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Biology

Assessing Mineral Availability in Fish Feeds using Complementary Methods Demonstrated with the Example of Zinc in Atlantic Salmon
Marta S. Silva 1,2, Thea Stewart 4, Heidi Amlund 1,3, Jens J. Sloth 1,3, Pedro Araujo 1, Erik-Jan Lock 1, Christer Hogstrand 4, Robin Ørnsrud 1, Rune Waagbø 1,2, Antony Jesu Prabhu 1
1Institute of Marine Research, 2Department of Biological Sciences, University of Bergen, 3National Food Institute, Technical University of Denmark, 4Metal metabolism group, Nutritional Sciences Division, King's College London

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. 

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Bioengineering

A Quantitative Fluorescence Microscopy-based Single Liposome Assay for Detecting the Compositional Inhomogeneity Between Individual Liposomes
Rasmus Münter 1,3, Thomas Lars Andresen 1,2,3, Jannik Bruun Larsen 1,2,3
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.

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Environment

A Small-Scale Setup for Algal Toxicity Testing of Nanomaterials and Other Difficult Substances
Lars Michael Skjolding 1, Susanne Kruse 1, Sara Nørgaard Sørensen 1, Rune Hjorth 1, Anders Baun 1
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.

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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 Sørensen 1, Moises Espindola Rodriguez 1, Marcial Fernández Castro 1, Ashwin Nambi 1, Luise Theil Kuhn 1, Jens Wenzel Andreasen 1
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.

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Medicine

Aggravation of Myocardial Ischemia upon Particulate Matter Exposure in Atherosclerosis Animal Model
Yuanmin Yang *1, Shuoqiu Deng *1, Shuiqing Qu 1, Yu Zhang 1, Zhongyuan Zheng 1, Lina Chen 1, Yujie Li 1
1China Academy of Chinese Medical Sciences

This protocol describes a composite animal model with exposure to particulate matter (PM) that aggravates myocardial ischemia with atherosclerosis.

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Medicine

Binocular Dynamic Visual Acuity in Eyeglass-Corrected Myopic Patients
Yuexin Wang *1, Yining Guo *1, Shanshan Wei 2, Yifei Yuan 1, Tingyi Wu 1, Yu Zhang 1, Yueguo Chen 1, Xuemin Li 1
1Department of Ophthalmology, Beijing Key Laboratory of Restoration of Damaged Ocular Nerves, Peking University Third Hospital, 2Beijing Tongren Eye Center, Beijing Tongren Hospital

The present research demonstrates a method to accurately examine dynamic visual acuity (DVA) in myopic subjects with eyeglass correction. Further analysis indicated that the closer the refraction state to emmetropia, the better the eyeglass-corrected binocular DVA is at both 40 and 80 degrees per second.

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Developmental Biology

Generation of a Mouse Artificial Decidualization Model with Ovariectomy for Endometrial Decidualization Research
Yang Zhang *1,2,3, Zhe Zhang *1,2,3, Nannan Kang 1,2,3, Xiaoqiang Sheng 1,2,3
1Center for Reproductive Medicine and Obstetrics and Gynecology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, 2State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 3Center for Molecular Reproductive Medicine, Nanjing University

Here, we describe the method of generating an artificial decidualization model using the ovariectomized mouse, a classic endometrial decidualization experiment in the research field of endometrial decidualization.

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Bioengineering

Microgel-Extracellular Matrix Composite Support for the Embedded 3D Printing of Human Neural Constructs
Janko Kajtez 1, Carmen Radeke 2, Johan Ulrik Lind 2, Jenny Emnéus 3
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.

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