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Forschungszentrum Jülich

13 ARTICLES PUBLISHED IN JoVE

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Bioengineering

Microfluidic Picoliter Bioreactor for Microbial Single-cell Analysis: Fabrication, System Setup, and Operation
Alexander Gruenberger 1, Christopher Probst 1, Antonia Heyer 1, Wolfgang Wiechert 1, Julia Frunzke 1, Dietrich Kohlheyer 1
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.

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Engineering

Preparation and Friction Force Microscopy Measurements of Immiscible, Opposing Polymer Brushes
Sissi de Beer 1,2, Edit Kutnyanszky 2, Martin H. Müser 1,3, G. Julius Vancso 2
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.

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Engineering

Frequency Mixing Magnetic Detection Scanner for Imaging Magnetic Particles in Planar Samples
Hyobong Hong 1, Eul-Gyoon Lim 2, Jae-chan Jeong 1, Jiho Chang 1, Sung-Woong Shin 2, Hans-Joachim Krause 3
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.

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Chemistry

Functionalization of Single-walled Carbon Nanotubes with Thermo-reversible Block Copolymers and Characterization by Small-angle Neutron Scattering
Youngkyu Han 1, Suk-kyun Ahn 2,3, Zhe Zhang 1,4, Gregory S. Smith 1, Changwoo Do 1
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.

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Engineering

Hand Controlled Manipulation of Single Molecules via a Scanning Probe Microscope with a 3D Virtual Reality Interface
Philipp Leinen 1,2, Matthew F. B. Green 1,2, Taner Esat 1,2, Christian Wagner 1,2, F. Stefan Tautz 1,2, Ruslan Temirov 1,2
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.

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Bioengineering

Generic Protocol for Optimization of Heterologous Protein Production Using Automated Microbioreactor Technology
Johannes Hemmerich *1,2, Lars Freier *1,2, Wolfgang Wiechert 1,2,3, Eric von Lieres 1,2, Marco Oldiges 1,2,4
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.

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Engineering

Magnetic Field Mapping using Off-Axis Electron Holography in the Transmission Electron Microscope
Fengshan Zheng 1, András Kovács 1, Thibaud Denneulin 1, Jan Caron 1, Teresa Weßels 1, Rafal E. Dunin-Borkowski 1
1Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich

Guidelines are presented for recording and interpreting off-axis electron holograms to provide quantitative images of magnetic fields in nanoscale materials and devices in the transmission electron microscope.

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Immunology and Infection

Confocal Laser Scanning Microscopy-Based Quantitative Analysis of Aspergillus fumigatus Conidia Distribution in Whole-Mount Optically Cleared Mouse Lung
Ivan V. Maslov 1, Andrey O. Bogorodskiy 1, Mariia V. Pavelchenko 1, Ilia O. Zykov 1, Natalya I. Troyanova 2, Valentin I. Borshchevskiy 1,3, Marina A. Shevchenko 2
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.

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Neuroscience

Imaging Mitochondrial Ca2+ Uptake in Astrocytes and Neurons using Genetically Encoded Ca2+ Indicators (GECIs)
Nannan Zhang 1, Zhe Zhang 1,2, Ilker Ozden 2, Shinghua Ding 1,2
1Dalton Cardiovascular Research Center, University of Missouri-Columbia, 2Department of Biomedical, Biological and Chemical Engineering, University of Missouri-Columbia

This proctocol aims to provide a method for in vitro and in vivo mitochondrial Ca2+ imaging in astrocytes and neurons.

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Medicine

Robot-assisted Total Mesorectal Excision and Lateral Pelvic Lymph Node Dissection for Locally Advanced Middle-low Rectal Cancer
Chenhao Hu *1,2,3, Zhe Zhang *1,2,3, Lei Zhang 1,2,3, Ruihan Liu 2,3, Jun Yan 1,2,3, Qi Sun 1,2,3, Guanghui Wang 1, Junjun She 1,2,3
1Department of General Surgery, The First Affiliated Hospital of Xian Jiaotong University, 2Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xian Jiao tong University, 3Department of High Talent, The First Affiliated Hospital of Xian Jiaotong University

The robotic technique described herein aims to detail a stepwise approach to robot-assisted total mesorectal excision and lateral pelvic lymph node dissection for locally advanced (T3/T4) rectal cancer located below the peritoneal reflection.

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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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Chemistry

Screening of Coatings for an All-Solid-State Battery Using In Situ Transmission Electron Microscopy
Shibarata Basak 1,2, Junbeom Park 1, Janghyun Jo 2, Osmane Camara 1, Amir H. Tavabi 2, Hermann Tempel 1, Hans Kungl 1, Chandramohan George 3, Rafal E. Dunin-Borkowski 2, Joachim Mayer 2,4, Rüdiger-A. Eichel 1,5
1Institute of Energy and Climate Research - Fundamental Electrochemistry (IEK-9), Forschungszentrum Jülich GmbH, 2Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Forschungszentrum Jülich GmbH, 3Dyson School of Design Engineering, Imperial College London, 4Central Facility for Electron Microscopy (GFE), RWTH Aachen University, 5Institute of Physical Chemistry, RWTH Aachen University

Utilizing the volume change of Si nanoparticles during (de)lithiation, the present protocol describes a screening method of potential coatings for all-solid-state batteries using in situ transmission electron microscopy.

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Biochemistry

NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins
Tobias Stief 1,2, Katharina Vormann 1,2, Nils-Alexander Lakomek 1,2
1Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, 2Institute of Physical Biology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf

Nuclear magnetic resonance (NMR) spectroscopy can characterize structural protein dynamics in a residue-specific manner. We provide a hands-on protocol for recording NMR 15N R1 and R2 relaxation and {1H}-15N heteronuclear Overhauser effect (hetNOE) experiments, sensitive to the picoseconds to nanoseconds timescale.

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