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ETH Zürich

14 ARTICLES PUBLISHED IN JoVE

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Biology

Chemotactic Response of Marine Micro-Organisms to Micro-Scale Nutrient Layers
Justin R. Seymour 1, Marcos 1, Roman Stocker 1
1Environmental Microfluidics Group, MIT - Massachusetts Institute of Technology

The fabrication of microfluidic channels and their implementation in experiments for studying the chemotactic foraging behaviour of marine microbes within a patchy nutrient seascape and the swimming behaviour of bacteria within shear flow are described.

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Biology

Studies of Bacterial Chemotaxis Using Microfluidics - Interview
Roman Stocker 1
1Environmental Microfluidics Group, MIT - Massachusetts Institute of Technology

Studies of Bacterial Chemotaxis Using Microfluidics - Interview

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Immunology and Infection

Imaging InlC Secretion to Investigate Cellular Infection by the Bacterial Pathogen Listeria monocytogenes
Andreas Kühbacher 1,2,3, Edith Gouin 1,2,3, Jason Mercer 4, Mario Emmenlauer 5, Christoph Dehio 5, Pascale Cossart 1,2,3, Javier Pizarro-Cerdá 1,2,3
1Unité des Interactions Bactéries Cellules, Pasteur Institute, 2INSERM U604, 3Institut National de la Recherche Agronomique (INRA), USC2020, 4Institute of Biochemistry, ETH Zürich, 5Focal Area Infection Biology, Biozentrum, University of Basel

Listeria monocytogenes is a Gram positive bacterial pathogen frequently used as a major model for the study of intracellular parasitism. Imaging late L. monocytogenes infection stages within the context of small-interfering RNA screens allows for the global study of cellular pathways required for bacterial infection of target host cells.

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Biology

Open-source Single-particle Analysis for Super-resolution Microscopy with VirusMapper
Robert D. M. Gray 1,2, Jason Mercer 1, Ricardo Henriques 1,3
1MRC Laboratory for Molecular Cell Biology, University College London, 2Centre for Mathematics and Physics in Life Sciences and Experimental Biology (CoMPLEX), University College London, 3Department of Cell and Developmental Biology, University College London

This manuscript uses the Fiji-based open-source software package VirusMapper to apply single-particle analysis to super-resolution microscopy images in order to generate precise models of nanoscale structure.

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Behavior

A Networked Desktop Virtual Reality Setup for Decision Science and Navigation Experiments with Multiple Participants
Hantao Zhao 1, Tyler Thrash 1,2,3, Stefan Wehrli 4, Christoph Hölscher 1, Mubbasir Kapadia 5, Jascha Grübel 1, Raphael P. Weibel 1, Victor R. Schinazi 1
1Chair of Cognitive Science, ETH Zürich, 2Digital Society Initiative, University of Zürich, 3Department of Geography, University of Zürich, 4Decision Science Laboratory, ETH Zürich, 5Computer Science Department, Rutgers University

This paper describes a method for conducting multi-user experiments on decision-making and navigation using a networked computer laboratory.

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Behavior

Virtual Reality Experiments with Physiological Measures
Raphael P. Weibel 1, Jascha Grübel 1, Hantao Zhao 1, Tyler Thrash 1,2,3, Dario Meloni 1, Christoph Hölscher 1, Victor R. Schinazi 1
1Chair of Cognitive Science, ETH Zürich, 2Geographic Information Visualization and Analysis, University of Zürich, 3Digital Society Initiative, University of Zürich

Virtual reality (VR) experiments can be difficult to implement and require meticulous planning. This protocol describes a method for the design and implementation of VR experiments that collect physiological data from human participants. The Experiments in Virtual Environments (EVE) framework is employed to accelerate this process.

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Chemistry

Improving High Viscosity Extrusion of Microcrystals for Time-resolved Serial Femtosecond Crystallography at X-ray Lasers
Daniel James 1, Tobias Weinert 1, Petr Skopintsev 1, Antonia Furrer 1, Dardan Gashi 1,2, Tomoyuki Tanaka 3,4, Eriko Nango 3,4, Przemyslaw Nogly 1,5, Joerg Standfuss 1
1Division of Biology and Chemistry - Laboratory for Biomolecular Research, Paul Scherrer Institut, 2Photon Science Division - SwissFEL, Paul Scherrer Institut, 3RIKEN SPring-8 Center, 4Department of Cell Biology, Graduate School of Medicine, Kyoto University, 5Department of Biology, ETH Zürich

The success of a time-resolved serial femtosecond crystallography experiment is dependent on efficient sample delivery. Here, we describe protocols to optimize the extrusion of bacteriorhodopsin microcrystals from a high viscosity micro-extrusion injector. The methodology relies on sample homogenization with a novel three-way coupler and visualization with a high-speed camera.

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Bioengineering

Generating Controlled, Dynamic Chemical Landscapes to Study Microbial Behavior
Francesco Carrara 1, Douglas R. Brumley 2, Andrew M. Hein 3, Yutaka Yawata 4,5, M. Mehdi Salek 1, Kang Soo Lee 1, Elzbieta Sliwerska 1, Simon A. Levin 6, Roman Stocker 1
1Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, 2School of Mathematics and Statistics, University of Melbourne, 3Institute of Marine Sciences, University of California, Santa Cruz, 4Faculty of Life and Environmental Sciences, University of Tsukuba, 5Microbiology Research Center for Sustainability, University of Tsukuba, 6Department of Ecology and Evolutionary Biology, Princeton University

A protocol for the generation of dynamic chemical landscapes by photolysis within microfluidic and millifluidic setups is presented. This methodology is suitable to study diverse biological processes, including the motile behavior, nutrient uptake, or adaptation to chemicals of microorganisms, both at the single cell and population level.

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Biochemistry

Strategic Screening and Characterization of the Visual GPCR-mini-G Protein Signaling Complex for Successful Crystallization
Filip Pamula 1,2, Jonas Mühle 1, Alain Blanc 3, Rony Nehmé 4, Patricia C. Edwards 4, Christopher G. Tate 4, Ching-Ju Tsai 1
1Laboratory of Biomolecular Research, Paul Scherrer Institute, 2Department of Biology, ETH Zürich, 3Center for Radiopharmaceutical Sciences, Paul Scherrer Institute, 4Laboratory of Molecular Biology, Medical Research Council

This report describes screening of different detergents for preparing the visual GPCR, rhodopsin, and its complex with mini-Go. Biochemical methods characterizing the quality of the complex at different stages during purification are demonstrated. This protocol can be generalized to other membrane protein complexes for their future structural studies.

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Environment

In Situ Chemotaxis Assay to Examine Microbial Behavior in Aquatic Ecosystems
Estelle E. Clerc 1, Jean-Baptiste Raina 2, Bennett S. Lambert 3, Justin Seymour 2, Roman Stocker 1
1Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 2Climate Change Cluster, University of Technology Sydney, 3School of Oceanography, University of Washington

Presented here is the protocol for an in situ chemotaxis assay, a recently developed microfluidic device that enables studies of microbial behavior directly in the environment.

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Engineering

Patterning of Microorganisms and Microparticles through Sequential Capillarity-assisted Assembly
Roberto Pioli 1, Roman Stocker 1, Lucio Isa 2, Eleonora Secchi 1
1Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 2Department of Materials, ETH Zurich

We present a technology that uses capillarity-assisted assembly in a microfluidic platform to pattern micro-sized objects suspended in a liquid, such as bacteria and colloids, into prescribed arrays on a polydimethylsiloxane substrate.

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Bioengineering

Experimental and Data Analysis Workflow for Soft Matter Nanoindentation
Giuseppe Ciccone 1, Mariana Azevedo Gonzalez Oliva 1, Nelda Antonovaite 2, Ines Lüchtefeld 3, Manuel Salmeron-Sanchez 1, Massimo Vassalli 1
1Centre for the Cellular Microenvironment, James Watt School of Engineering, University of Glasgow, 2Optics 11 life, 3Laboratory of Biosensors and Bioelectronics, ETH Zürich

The protocol presents a complete workflow for soft material nanoindentation experiments, including hydrogels and cells. First, the experimental steps to acquire force spectroscopy data are detailed; then, the analysis of such data is detailed through a newly developed open-source Python software, which is free to download from GitHub.

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Environment

A Microfluidic Platform to Study Bioclogging in Porous Media
Dorothee L. Kurz 1,2, Eleonora Secchi 1, Roman Stocker 1, Joaquin Jimenez-Martinez 1,2
1Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, 2Department Water Resources and Drinking Water, Swiss Federal Institute of Aquatic Science and Technology

The present protocol describes a microfluidic platform to study biofilm development in quasi-2D porous media by combining high-resolution microscopy imaging with simultaneous pressure difference measurements. The platform quantifies the influence of pore size and fluid flow rates in porous media on bioclogging.

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Immunology and Infection

Microfluidic Approach to Resolve Simultaneous and Sequential Cytokine Secretion of Individual Polyfunctional Cells
Aline Linder *1, Kevin Portmann *1, Luca Johannes Schlotheuber 1, Alessandro Streuli 1, Wiona Sophie Glänzer 1, Klaus Eyer 1,2, Ines Lüchtefeld 1,3
1Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 2Department of Biomedicine, Aarhus University, 3Laboratory for Tumor and Stem Cell Dynamics, Institute of Molecular Health Sciences, Department of Biology, ETH Zürich

The protocol describes an advanced microfluidic platform to quantitatively measure cytokine secretion dynamics of individual human peripheral blood mononuclear cells. The platform measures up to three cytokines in parallel (IL-6, TNFα, and IL-1β) for each individual cell stimulated with lipopolysaccharide as an example.

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