Forschungszentrum Julich 12 articles published in JoVE Immunology and Infection Confocal Laser Scanning Microscopy-Based Quantitative Analysis of Aspergillus fumigatus Conidia Distribution in Whole-Mount Optically Cleared Mouse Lung Ivan V. Maslov1, Andrey O. Bogorodskiy1, Mariia V. Pavelchenko1, Ilia O. Zykov1, Natalya I. Troyanova2, Valentin I. Borshchevskiy1,3, Marina A. Shevchenko2 1Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 2Department of Immunology, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 3Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich We describe the method for quantitative analysis of the distribution of Aspergillus fumigatus conidia (3 µm in size) in the airways of mice. The method also can be used for the analysis of microparticles and nanoparticle agglomerate distribution in the airways in various pathological condition models. Genetics Application of DNA Fingerprinting using the D1S80 Locus in Lab Classes Meike Siebers*1, Agatha Walla*1,2, Thea Rütjes1, Moritz-Fabian Müller4, Maria von Korff1,2,3 1Institute of Plant Genetics, Heinrich-Heine-University, 2Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 3Max Planck Institute for Plant Breeding Research, 4IBG-1: Biotechnology, Forschungszentrum Jülich GmbH Here we describe a simple protocol to generate DNA fingerprinting profiles by amplifying the VNTR locus D1S80 from epithelial cell DNA. Chemistry Fractionation of Lignocellulosic Biomass using the OrganoCat Process Leonie Schoofs1, Dennis Weidener1, Ulrich Schurr1, Holger Klose1, Philipp M. Grande1 1Institut für Bio- und Geowissenschaften, Pflanzenwissenschaften (IBG-2), Forschungszentrum Jülich OrganoCat is a method for the pretreatment and fractionation of lignocellulose under mild conditions into lignin, fermentable sugars, and cellulose pulp. In a biogenic, biphasic solvent system of water and 2-methyltetrahydrofuran with 2,5-furancarboxylic acid as catalyst, the OrganoCat products are separated in situ for straightforward product recovery. Neuroscience Conducting Hyperscanning Experiments with Functional Near-Infrared Spectroscopy Vanessa Reindl1,2, Kerstin Konrad1,2, Christian Gerloff2,3, Jana A. Kruppa1,2,4, Laura Bell1, Wolfgang Scharke1 1Child Neuropsychology Section, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Medical Faculty, RWTH Aachen University, 2JARA-Brain Institute II, Molecular Neuroscience and Neuroimaging, RWTH Aachen & Research Centre Juelich, 3Lehrstuhl II für Mathematik, RWTH Aachen University, 4Translational Brain Research in Psychiatry and Neurology, Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital Aachen The present protocol describes how to conduct fNIRS hyperscanning experiments and analyze brain-to-brain synchrony. Further, we discuss challenges and possible solutions. Bioengineering Generic Protocol for Optimization of Heterologous Protein Production Using Automated Microbioreactor Technology Johannes Hemmerich*1,2, Lars Freier*1,2, Wolfgang Wiechert1,2,3, Eric von Lieres1,2, Marco Oldiges1,2,4 1IBG-1: Biotechnology, Forschungszentrum Jülich, 2Research Center Jülich, Bioeconomy Science Center (BioSC), 3Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 4Institute for Biotechnology, RWTH Aachen University This manuscript describes a generic approach for tailor-made design of microbial cultivation media. This is enabled by an iterative workflow combining Kriging-based experimental design and microbioreactor technology for sufficient cultivation throughput, which is supported by lab robotics to increase reliability and speed in liquid handling media preparation. Bioengineering Studying Soft-matter and Biological Systems over a Wide Length-scale from Nanometer and Micrometer Sizes at the Small-angle Neutron Diffractometer KWS-2 Aurel Radulescu1, Noemi Kinga Szekely1, Marie-Sousai Appavou1, Vitaliy Pipich1, Thomas Kohnke1, Vladimir Ossovyi1, Simon Staringer1, Gerald J. Schneider2, Matthias Amann3, Bo Zhang-Haagen3, Georg Brandl1, Matthias Drochner4, Ralf Engels4, Romuald Hanslik5, Günter Kemmerling1 1Jülich Centre for Neutron Science Outstation at MLZ, Forschungszentrum Jülich GmbH, 2Department of Chemistry, Louisiana State University, 3Jülich Centre for Neutron Science JCNS-1 & Institute of Complex Systems ICS-1, Forschungszentrum Jülich GmbH, 4Central Institute of Engineering, Electronics and Analytics — Electronic Systems (ZEA-2), Forschungszentrum Jülich GmbH, 5Central Institute of Engineering, Electronics and Analytics — Engineering and Technology (ZEA-1), Forschungszentrum Jülich GmbH Here, we present a protocol to investigate soft matter and biophysical systems over a wide mesoscopic length scale, from nm to µm that involves the use of the KWS-2 SANS diffractometer at high intensities and an adjustable resolution. Engineering Hand Controlled Manipulation of Single Molecules via a Scanning Probe Microscope with a 3D Virtual Reality Interface Philipp Leinen1,2, Matthew F. B. Green1,2, Taner Esat1,2, Christian Wagner1,2, F. Stefan Tautz1,2, Ruslan Temirov1,2 1Peter Grünberg Institut (PGI-3), Forschungszentrum Jülich, 2Fundamentals of Future Information Technology, Jülich Aachen Research Alliance (JARA) We demonstrate the precise manipulation of individual organic molecules on a metal surface with the tip of a scanning probe microscope driven in 3D by the experimenter's hand using a motion capture system and fully immersive virtual reality goggles. Engineering Frequency Mixing Magnetic Detection Scanner for Imaging Magnetic Particles in Planar Samples Hyobong Hong1, Eul-Gyoon Lim2, Jae-chan Jeong1, Jiho Chang1, Sung-Woong Shin2, Hans-Joachim Krause3 1Advanced Vision System Research Section, Electronics & Telecommunication Research Institute (ETRI), 2Intelligent Cognitive Technology Research Department, Electronics & Telecommunication Research Institute (ETRI), 3Peter Grünberg Institute (PGI-8), Forschungszentrum Jülich A scanner for imaging magnetic particles in planar samples was developed using the planar frequency mixing magnetic detection technique. The magnetic intermodulation product response from the nonlinear nonhysteretic magnetization of the particles is recorded upon a two-frequency excitation. It can be used to take 2D images of thin biological samples. Chemistry Functionalization of Single-walled Carbon Nanotubes with Thermo-reversible Block Copolymers and Characterization by Small-angle Neutron Scattering Youngkyu Han1, Suk-kyun Ahn2,3, Zhe Zhang1,4, Gregory S. Smith1, Changwoo Do1 1Biology and Soft Matter Division, Neutron Science Directorate, Oak Ridge National Laboratory, 2Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, 3Department of Polymer Science and Engineering, Pusan National University, 4Jülich Center for Neutron Science, Forschungszentrum Jülich A method for the functionalization of carbon nanotubes with structure-tunable polymeric encapsulation layers and structural characterization using small-angle neutron scattering is presented. Neuroscience Electrophysiological and Morphological Characterization of Neuronal Microcircuits in Acute Brain Slices Using Paired Patch-Clamp Recordings Guanxiao Qi1, Gabriele Radnikow1, Dirk Feldmeyer1,2 1Institute of Neuroscience and Medicine (INM-2), Research Centre Jülich, 2Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, JARA, RWTH Aachen University Patch-clamp recordings and simultaneous intracellular biocytin filling of synaptically coupled neurons in acute brain slices allow a correlated analysis of their structural and functional properties. The aim of this protocol is to describe the essential technical steps of electrophysiological recording from neuronal microcircuits and their subsequent morphological analysis. Engineering Preparation and Friction Force Microscopy Measurements of Immiscible, Opposing Polymer Brushes Sissi de Beer1,2, Edit Kutnyanszky2, Martin H. Müser1,3, G. Julius Vancso2 1Jülich Supercomputing Centre, Forschungszentrum Jülich, 2Materials Science and Technology of Polymer, MESA+ Institute for Nanotechnology, University of Twente, 3Department of Materials Science and Engineering, Universität des Saarlandes The methodology to perform friction force microscopy experiments for contacting brushes is presented: Two polymer brushes that are grafted from (a) substrates and (b) colloidal probes are slid to show that, by using two contacting immiscible brush systems, friction in sliding contacts is reduced compared to miscible brush systems. Bioengineering Microfluidic Picoliter Bioreactor for Microbial Single-cell Analysis: Fabrication, System Setup, and Operation Alexander Gruenberger1, Christopher Probst1, Antonia Heyer1, Wolfgang Wiechert1, Julia Frunzke1, Dietrich Kohlheyer1 1Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Juelich GmbH In this protocol the fabrication, setup and basic operation of a microfluidic picoliter bioreactor (PLBR) for single-cell analysis of prokaryotic microorganisms is introduced. Industrially relevant microorganisms were analyzed as proof of principle allowing insights into growth rate, morphology, and phenotypic heterogeneity over certain time periods, hardly possible with conventional methods.