University of Hamburg View Institution's Website 12 articles published in JoVE Biochemistry Design and Construction of an Experimental Setup to Enhance Mineral Weathering through the Activity of Soil Organisms Tullia Calogiuri1,2, Mathilde Hagens2, Jan Willem Van Groenigen1, Thomas Corbett3, Jens Hartmann4, Rick Hendriksen5, Iris Janssens6, Ivan A. Janssens7, Guillermo Ledesma Dominguez7, Grant Loescher4, Steven Mortier6, Anna Neubeck3, Harun Niron7, Reinaldy P. Poetra4, Lukas Rieder4, Eric Struyf7, Michiel Van Tendeloo8, Tom De Schepper6, Tim Verdonck9, Siegfried E. Vlaeminck8, Sara Vicca7, Alix Vidal1 1Soil Biology Group, Wageningen University & Research, 2Soil Chemistry and Chemical Soil Quality, Wageningen University & Research, 3Department of Earth Sciences, Uppsala University, 4Institute for Geology, Center for Earth System Research and Sustainability, University of Hamburg, 5Tupola, Wageningen University & Research, 6IDLab - Department of Computer Science, University of Antwerp - imec, 7Plants and Ecosystems (PLECO), Biology Department, University of Antwerp, 8Research Group of Sustainable Energy, Air and Water Technology, University of Antwerp, 9Department of Mathematics, University of Antwerp - imec Here we present the construction and operation of an experimental setup to enhance mineral weathering through the activity of soil organisms while concurrently manipulating abiotic variables known to stimulate weathering. Representative results from the functioning of the setup and sample analyses are discussed together with points for improvement. Immunology and Infection Immunofluorescence Imaging of Neutrophil Extracellular Traps in Human and Mouse Tissues Lavinia Schoenfeld1, Birgit Appl1, Laia Pagerols-Raluy1, Annika Heuer3, Konrad Reinshagen1, Michael Boettcher1,2 1Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, 2Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 3Division of Spine Surgery, Department of Trauma and Orthopedic Surgery, University Medical Center Hamburg-Eppendorf (UKE) Neutrophil extracellular traps (NETs) are associated with various diseases, and immunofluorescence is often used for their visualization. However, there are various staining protocols, and, in many cases, only one type of tissue is examined. Here, we establish a generally applicable protocol for staining NETs in mouse and human tissue. Engineering X-ray Beam Induced Current Measurements for Multi-Modal X-ray Microscopy of Solar Cells Christina Ossig1,3, Tara Nietzold2, Bradley West2, Mariana Bertoni2, Gerald Falkenberg1, Christian G. Schroer1,3, Michael E. Stuckelberger1 1Deutsches Elektronen-Synchrotron, 2School of Electrical, Computer and Energy Engineering, Arizona State University, 3Department Physik, Universität Hamburg A setup for X-ray beam induced current measurements at synchrotron beamlines is described. It unveils the nanoscale performance of solar cells and extends the suite of techniques for multi-modal X-ray microscopy. From wiring to signal-to-noise optimization, it is shown how to perform state-of-the-art XBIC measurements at a hard X-ray microprobe. Bioengineering CRISPR/Cas12a Multiplex Genome Editing of Saccharomyces cerevisiae and the Creation of Yeast Pixel Art Klaudia Ciurkot1,2, Brenda Vonk1, Thomas E. Gorochowski3,4, Johannes A. Roubos1, René Verwaal1 1DSM Biotechnology Center, 2Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 3BrisSynBio, University of Bristol, Life Sciences Building, 4School of Biological Sciences, University of Bristol, Life Sciences Building The CRISPR/Cas12a system in combination with a single crRNA array enables efficient multiplex editing of the S. cerevisiae genome at multiple loci simultaneously. This is demonstrated by constructing carotenoid producing yeast strains which are subsequently used to create yeast pixel art. Biochemistry Growing Protein Crystals with Distinct Dimensions Using Automated Crystallization Coupled with In Situ Dynamic Light Scattering Daniela Baitan1,2, Robin Schubert2,3, Arne Meyer1, Karsten Dierks1, Markus Perbandt2,3, Christian Betzel2,3 1Xtal Concepts GmbH, 2Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation c/o DESY, University of Hamburg, 3The Hamburg Center for Ultrafast Imaging, University of Hamburg Here we present a protocol for controlled production of protein microcrystals. The process uses an automated device allowing controlled manipulation of several crystallization parameters. The protein crystallization is carried-out by controlled and automated addition of crystallization solutions while monitoring and investigating the radius distribution of particles in the crystallization droplet. Chemistry Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography Yannig Gicquel*1,2, Robin Schubert*3,4,5, Svetlana Kapis3, Gleb Bourenkov6, Thomas Schneider6, Markus Perbandt3,4, Christian Betzel3,4,5, Henry N. Chapman1,2,4, Michael Heymann1,7 1Center for Free Electron Laser Science, DESY, 2Department of Physics, University of Hamburg, 3Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, 4The Hamburg Center for Ultrafast Imaging, University of Hamburg, 5Integrated Biology Infrastructure Life-Science Facility at the European XFEL (XBI), 6European Molecular Biology Laboratory, EMBL c/o DESY, 7Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry This protocol describes in detail how to fabricate and operate microfluidic devices for X-ray diffraction data collection at room temperature. Additionally, it describes how to monitor protein crystallization by dynamic light scattering and how to process and analyze obtained diffraction data. Biology Phloem Sap Sampling from Brassica napus for 3D-PAGE of Protein and Ribonucleoprotein Complexes Steffen Pahlow1, Anna Ostendorp1, Lena Krüßel1, Julia Kehr1 1Molecular Plant Genetics, Universität Hamburg Here we present a protocol to analyze the protein composition of large native protein:protein and protein:nucleic acid complexes from oilseed rape (B. napus) phloem exudate using a 3D polyacrylamide gel electrophoresis (PAGE) approach combining blue native (BN) with two denaturing PAGEs followed by mass spectrometric identification. Environment Preparation of Authigenic Pyrite from Methane-bearing Sediments for In Situ Sulfur Isotope Analysis Using SIMS Zhiyong Lin1,3, Xiaoming Sun1,2,3,4, Jörn Peckmann5, Yang Lu2,3, Harald Strauss6, Li Xu2,3, Hongfeng Lu7, Barbara M.A. Teichert6 1School of Earth Sciences and Engineering, Sun Yat-sen University, 2School of Marine Sciences, Sun Yat-sen University, 3Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, 4South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, 5Institut für Geologie, Universität Hamburg, 6Institut für Geologie und Paläontologie, Westfälische Wilhelms-Universität Münster, 7Guangzhou Marine Geological Survey Analyses of the sulfur isotopic composition (δ34S) of pyrite from methane-bearing sediments have typically focused on bulk samples. Here, we applied secondary ion mass spectroscopy to analyze the δ34S values of various pyrite generations to understand the diagenetic history of pyritization. Chemistry Synthesis of Indoxyl-glycosides for Detection of Glycosidase Activities Stephan Böttcher1, Joachim Thiem1 1Department of Chemistry, Faculty of Sciences, University of Hamburg Indoxyl glycosides are well-established and widely used tools for enzyme screening and enzyme activity monitoring. Especially for glucose type structures previous syntheses proved to be challenging and low yielding. Our novel approach employs indoxylic acid esters as precious intermediates to yield a considerable number of indoxyl glycosides in good yields. Engineering Spatial Separation of Molecular Conformers and Clusters Daniel Horke1, Sebastian Trippel1, Yuan-Pin Chang1, Stephan Stern1,2, Terry Mullins1, Thomas Kierspel1,3, Jochen Küpper1,2,3 1Center for Free-Electron Laser Science, CFEL, DESY, 2Department of Physics, University of Hamburg, 3The Hamburg Center for Ultrafast Imaging, University of Hamburg We present a technique that allows the spatial separation of different conformers or clusters present in a molecular beam. An electrostatic deflector is used to separate species by their mass-to-dipole moment ratio, leading to the production of gas-phase ensembles of a single conformer or cluster stoichiometry. Medicine Human Internal Mammary Artery (IMA) Transplantation and Stenting: A Human Model to Study the Development of In-Stent Restenosis Xiaoqin Hua1,2, Tobias Deuse1,2, Evangelos D. Michelakis3, Alois Haromy3, Phil S. Tsao4, Lars Maegdefessel4, Reinhold G. Erben5, Claudia Bergow5, Boris B. Behnisch6, Hermann Reichenspurner1,2, Robert C. Robbins7, Sonja Schrepfer1,2,7 1University Heart Center Hamburg, TSI-Lab, Germany, 2Cardiovascular Research Center, University of Hamburg, 3Department of Medicine, Cardiology Division, Pulmonary Hypertension Program, University of Alberta, 4Department of Medicine, Stanford University School of Medicine, 5Department of Biomedical Sciences, Institute of Physiology, Pathophysiology, and Biophysics, University of Veterinary Medicine, Vienna, 6Translumina GmbH, Hechingen, 7Department of Cardiothoracic Surgery, Stanford University School of Medicine This video shows a model to study the development of intimal hyperplasia after stent deployment using a human vessel (IMA) in an immunodeficient rat model. Biology Interview: HIV-1 Proviral DNA Excision Using an Evolved Recombinase Joachim Hauber1 1Department of Cell Biology and Virology, Heinrich-Pette-Institute for Experimental Virology and Immunology, University of Hamburg Current HIV-1 strategies act to suppress the viral life cycle but do not effectively eradicate infection. Here, we demonstrate that an engineered recombinase can efficiently excise integrated HIV-1 proviral DNA from the genome of infected cells.