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Wright GD, Thompson KA, Reis Y, Bischof J, Hockberger PE, Itano MS, Yen L, Adelodun ST, Bialy N, Brown CM, Chaabane L, Chew TL, Chitty AI, Cordelières FP, De Niz M, Ellenberg J, Engelbrecht L, Fabian-Morales E, Fazeli E, Fernandez-Rodriguez J, Ferrando-May E, Fletcher G, Galloway GJ, Guerrero A, Guimarães JM, Jacobs CA, Jayasinghe S, Kable E, Kitten GT, Komoto S, Ma X, Marques JA, Millis BA, Miranda K, JohnO'Toole P, Olatunji SY, Paina F, Pollak CN, Prats C, Pylvänäinen JW, Rahmoon MA, Reiche MA, Riches JD, Rossi AH, Salamero J, Thiriet C, Terjung S, Vasconcelos ADS, Keppler A. Recognising the importance and impact of Imaging Scientists: Global guidelines for establishing career paths within core facilities. J Microsc 2024. [PMID: 38691400 DOI: 10.1111/jmi.13307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 05/03/2024]
Abstract
In the dynamic landscape of scientific research, imaging core facilities are vital hubs propelling collaboration and innovation at the technology development and dissemination frontier. Here, we present a collaborative effort led by Global BioImaging (GBI), introducing international recommendations geared towards elevating the careers of Imaging Scientists in core facilities. Despite the critical role of Imaging Scientists in modern research ecosystems, challenges persist in recognising their value, aligning performance metrics and providing avenues for career progression and job security. The challenges encompass a mismatch between classic academic career paths and service-oriented roles, resulting in a lack of understanding regarding the value and impact of Imaging Scientists and core facilities and how to evaluate them properly. They further include challenges around sustainability, dedicated training opportunities and the recruitment and retention of talent. Structured across these interrelated sections, the recommendations within this publication aim to propose globally applicable solutions to navigate these challenges. These recommendations apply equally to colleagues working in other core facilities and research institutions through which access to technologies is facilitated and supported. This publication emphasises the pivotal role of Imaging Scientists in advancing research programs and presents a blueprint for fostering their career progression within institutions all around the world.
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Affiliation(s)
- Graham D Wright
- Research Support Centre, Agency for Science, Technology & Research (A*STAR), Singapore, Singapore
| | - Kerry A Thompson
- Anatomy Imaging and Microscopy Facility, School of Medicine, College of Medicine, Nursing and Health Science, University of Galway, Galway, Ireland
| | - Yara Reis
- Global BioImaging, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Johanna Bischof
- Euro-BioImaging Bio-Hub, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Michelle S Itano
- Neuroscience Center, Department of Cell Biology & Physiology, Carolina Institute of Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Lisa Yen
- Microscopy Australia, The University of Sydney, Sydney, Australia
| | - Stephen Taiye Adelodun
- Department of Anatomy, Ben Carson College of Health and Medical Sciences, Babcock University, Ilisan Remo, Ogun State, Nigeria
| | - Nikki Bialy
- BioImaging North America, Morgridge Institute of Research, Madison, USA
| | - Claire M Brown
- Advanced BioImaging Facility, Department of Physiology, McGill University, Montreal, Canada
| | - Linda Chaabane
- Euro-BioImaging Med-Hub, IBB-CNR, Italian Council of Research (CNR), Turin, Italy
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, USA
| | - Andrew I Chitty
- OHSU University Shared Resources, Oregon Health and Science University, Portland, USA
| | - Fabrice P Cordelières
- France BioImaging INBS, Bordeaux Imaging Center (UAR3420), Centre National de la Recherche Scientifique (CNRS), Bordeaux, France
| | - Mariana De Niz
- Department of Cell and Developmental Biology, Center for Advanced Microscopy, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Lize Engelbrecht
- Central Analytical Facilities Microscopy Unit, Stellenbosch University, Stellenbosch, South Africa
| | - Eunice Fabian-Morales
- Genetics Department, Harvard Medical School, Boston, USA
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Elnaz Fazeli
- Biomedicum Imaging Unit, Faculty of Medicine and HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - Elisa Ferrando-May
- Department of Enabling Technology, German Cancer Research Center, Heidelberg, Germany
| | | | - Graham John Galloway
- Herston Imaging Research Facility, The University of Queensland, Queensland, Australia
| | - Adan Guerrero
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jander Matos Guimarães
- Multi-user Center for Analysis of Biomedical Phenomena, State University of Amazonas (CMABio-UEA), Manaus, Brazil
| | - Caron A Jacobs
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Sachintha Jayasinghe
- Office of the Pro Vice-Chancellor (Research Infrastructure), The University of Queensland, Brisbane, Australia
- Office of the Pro Vice-Chancellor (Research Infrastructure), Queensland University of Technology, Brisbane, Australia
| | - Eleanor Kable
- Sydney Microscopy and Microanalysis, Microscopy Australia, University of Sydney, Sydney, Australia
| | - Gregory T Kitten
- Center of Microscopy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Shinya Komoto
- Imaging Core Facility, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
- Optics and Imaging Facility, National Institute for Basic Biology (NIBB), Okazaki, Japan
| | - Xiaoxiao Ma
- Research Support Centre, Agency for Science, Technology & Research (A*STAR), Singapore, Singapore
| | - Jéssica Araújo Marques
- Multi-user Center for Analysis of Biomedical Phenomena, State University of Amazonas (CMABio-UEA), Manaus, Brazil
| | - Bryan A Millis
- Department of Biomedical Engineering, Vanderbilt Biophotonics Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Kildare Miranda
- National Center for Structural Biology and Bioimaging and Biophysics Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Sunday Yinka Olatunji
- Department of Anatomy, Adventist School of Medicine of East Central Africa, Adventist University of Central Africa, Kigali, Rwanda
| | - Federica Paina
- Government Relations, LyondellBasell Industries N.V., Brussels, Belgium
| | - Cora Noemi Pollak
- Instituto de Investigación en Biomedicina de Buenos Aires - CONICET, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Clara Prats
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Mai Atef Rahmoon
- Advanced Imaging Center, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, USA
| | - Michael A Reiche
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - James Douglas Riches
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Australia
| | - Andres Hugo Rossi
- Servicio de Microscopía y Bioimagenes, Fundación Instituto Leloir - CONICET, Buenos Aires, Argentina
| | - Jean Salamero
- CNRS-Institut Curie, France BioImaging INBS, Paris, France
| | - Caroline Thiriet
- France BioImaging INBS, Bordeaux Imaging Center (UAR3420), Centre National de la Recherche Scientifique (CNRS), Bordeaux, France
| | - Stefan Terjung
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Antje Keppler
- Global BioImaging, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Euro-BioImaging Bio-Hub, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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2
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Renaud O, Aulner N, Salles A, Halidi N, Brunstein M, Mallet A, Aumayr K, Terjung S, Levy D, Lippens S, Verbavatz JM, Heuser T, Santarella-Mellwig R, Tinevez JY, Woller T, Botzki A, Cawthorne C, Munck S. Staying on track - Keeping things running in a high-end scientific imaging core facility. J Microsc 2024. [PMID: 38656474 DOI: 10.1111/jmi.13304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/19/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Modern life science research is a collaborative effort. Few research groups can single-handedly support the necessary equipment, expertise and personnel needed for the ever-expanding portfolio of technologies that are required across multiple disciplines in today's life science endeavours. Thus, research institutes are increasingly setting up scientific core facilities to provide access and specialised support for cutting-edge technologies. Maintaining the momentum needed to carry out leading research while ensuring high-quality daily operations is an ongoing challenge, regardless of the resources allocated to establish such facilities. Here, we outline and discuss the range of activities required to keep things running once a scientific imaging core facility has been established. These include managing a wide range of equipment and users, handling repairs and service contracts, planning for equipment upgrades, renewals, or decommissioning, and continuously upskilling while balancing innovation and consolidation.
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Affiliation(s)
- Oliver Renaud
- Cell and Tissue Imaging Platform (PICT-IBiSA, France-BioImaging), Institut Curie, Université PSL, Sorbonne Université, CNRS, Inserm, Paris, France
| | - Nathalie Aulner
- Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT), Institut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Paris, France
| | - Audrey Salles
- Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT), Institut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Paris, France
| | - Nadia Halidi
- Advanced Light Microscopy Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Maia Brunstein
- Bioimaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, Université Paris Cité, Inserm, Institut de l'Audition, Paris, France
| | - Adeline Mallet
- Centre de Ressources et Recherches Technologiques (UBI, C2RT), Institut Pasteur, Université Paris Cité, Ultrastructural BioImaging, Paris, France
| | - Karin Aumayr
- BioOptics Facility, Research Institute of Molecular Pathology (IMP) Campus-Vienna-Biocenter 1, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences (GMI), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Stefan Terjung
- Advanced Light Microscopy Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Daniel Levy
- Cell and Tissue Imaging Platform (PICT-IBiSA, France-BioImaging), Institut Curie, Université PSL, Sorbonne Université, CNRS, Inserm, Paris, France
| | | | - Jean-Marc Verbavatz
- Institut Jacques Monod (Imagoseine), Université Paris Cité, CNRS, Paris, France
| | - Thomas Heuser
- Vienna Biocenter Core Facilities GmbH (VBCF), Wien, Austria
| | | | - Jean-Yves Tinevez
- Image Analysis Hub, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Tatiana Woller
- VIB Technology Training, Data Core, VIB BioImaging Core, VIB, Ghent, Belgium
- Neuroscience Department, KU Leuven, Leuven, Belgium
| | | | - Christopher Cawthorne
- Department of Imaging and Pathology, Nuclear Medicine and Molecular Imaging, KU Leuven, Leuven, Belgium
| | - Sebastian Munck
- Neuroscience Department, KU Leuven, Leuven, Belgium
- VIB BioImaging Core, VIB, Leuven, Belgium
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3
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Nelson G, Boehm U, Bagley S, Bajcsy P, Bischof J, Brown CM, Dauphin A, Dobbie IM, Eriksson JE, Faklaris O, Fernandez-Rodriguez J, Ferrand A, Gelman L, Gheisari A, Hartmann H, Kukat C, Laude A, Mitkovski M, Munck S, North AJ, Rasse TM, Resch-Genger U, Schuetz LC, Seitz A, Strambio-De-Castillia C, Swedlow JR, Alexopoulos I, Aumayr K, Avilov S, Bakker GJ, Bammann RR, Bassi A, Beckert H, Beer S, Belyaev Y, Bierwagen J, Birngruber KA, Bosch M, Breitlow J, Cameron LA, Chalfoun J, Chambers JJ, Chen CL, Conde-Sousa E, Corbett AD, Cordelieres FP, Nery ED, Dietzel R, Eismann F, Fazeli E, Felscher A, Fried H, Gaudreault N, Goh WI, Guilbert T, Hadleigh R, Hemmerich P, Holst GA, Itano MS, Jaffe CB, Jambor HK, Jarvis SC, Keppler A, Kirchenbuechler D, Kirchner M, Kobayashi N, Krens G, Kunis S, Lacoste J, Marcello M, Martins GG, Metcalf DJ, Mitchell CA, Moore J, Mueller T, Nelson MS, Ogg S, Onami S, Palmer AL, Paul-Gilloteaux P, Pimentel JA, Plantard L, Podder S, Rexhepaj E, Royon A, Saari MA, Schapman D, Schoonderwoert V, Schroth-Diez B, Schwartz S, Shaw M, Spitaler M, Stoeckl MT, Sudar D, Teillon J, Terjung S, Thuenauer R, Wilms CD, Wright GD, Nitschke R. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. J Microsc 2021; 284:56-73. [PMID: 34214188 PMCID: PMC10388377 DOI: 10.1111/jmi.13041] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/16/2021] [Indexed: 11/27/2022]
Abstract
A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
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Affiliation(s)
- Glyn Nelson
- Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Ulrike Boehm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Steve Bagley
- Visualisation, Irradiation & Analysis, Cancer Research UK Manchester Institute, Alderley Park, Macclesfield, UK
| | - Peter Bajcsy
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | | | - Claire M Brown
- Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada
| | - Aurélien Dauphin
- Unité Génétique et Biologie du Développement U934, PICT-IBiSA, Institut Curie/Inserm/CNRS/PSL Research University, Paris, France
| | - Ian M Dobbie
- Department of Biochemistry, University of Oxford, Oxford, Oxon, UK
| | - John E Eriksson
- Turku Bioscience Centre, Euro-Bioimaging ERIC, Turku, Finland
| | | | | | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Laurent Gelman
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ali Gheisari
- Light Microscopy Facility, CMCB Technology Platform, TU Dresden, Dresden, Germany
| | - Hella Hartmann
- Light Microscopy Facility, CMCB Technology Platform, TU Dresden, Dresden, Germany
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Alex Laude
- Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Miso Mitkovski
- Light Microscopy Facility, Max Planck Institute of Experimental Medicine, Goettingen, Germany
| | - Sebastian Munck
- VIB BioImaging Core & VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department for Neuroscience, Leuven, Flanders, Belgium
| | | | - Tobias M Rasse
- Scientific Service Group Microscopy, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ute Resch-Genger
- Division Biophotonics, Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Lucas C Schuetz
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
| | - Arne Seitz
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Vaud, Switzerland
| | | | - Jason R Swedlow
- Divisions of Computational Biology and Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ioannis Alexopoulos
- General Instrumentation - Light Microscopy Facility, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Karin Aumayr
- BioOptics Facility, IMP - Research Institute of Molecular Pathology, Vienna, Austria
| | - Sergiy Avilov
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gert-Jan Bakker
- Department of Cell Biology (route 283), Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Andrea Bassi
- Dipartimento di Fisica, Politecnico di Milano, Milan, Italy
| | - Hannes Beckert
- Microscopy Core Facility, Medizinische Fakultät, Universität Bonn, Bonn, Germany
| | | | - Yury Belyaev
- Microscopy Imaging Center, University of Bern, Bern, Switzerland
| | | | | | - Manel Bosch
- Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | | | - Lisa A Cameron
- Light Microscopy Core Facility, Department of Biology, Duke University, Durham, North Carolina, USA
| | - Joe Chalfoun
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - James J Chambers
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | | | - Eduardo Conde-Sousa
- i3S - Instituto de InvestigaÇão e InovaÇão em Saúde, Universidade do Porto, Porto, Portugal.,INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | | | | | - Elaine Del Nery
- BioPhenics High-Content Screening Laboratory (PICT-IBiSA), Translational Research Department, Institut Curie - PSL Research University, Paris, France
| | - Ralf Dietzel
- Omicron-Laserage Laserprodukte GmbH, Rodgau, Germany
| | | | | | | | - Hans Fried
- Light Microscope Facility, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Wah Ing Goh
- A*STAR Microscopy Platform, Research Support Centre, Agency for Science, Technology and Research, Singapore, Singapore
| | - Thomas Guilbert
- Institut Cochin, INSERM (U1016), CNRS (UMR 8104), Université de Paris (UMR-S1016), Paris, France
| | | | - Peter Hemmerich
- Core Facility Imaging, Leibniz Institute on Aging, Jena, Germany
| | | | - Michelle S Itano
- Neuroscience Microscopy Core, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Helena K Jambor
- Mildred-Scheel Nachwuchszentrum, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Stuart C Jarvis
- Prior Scientific Instruments Limited, Cambridge, Cambridgeshire, UK
| | - Antje Keppler
- EMBL Heidelberg, Global BioImaging, Heidelberg, Germany
| | | | - Marcel Kirchner
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Gabriel Krens
- Bioimaging Facility, Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Susanne Kunis
- University Osnabrueck, Biology/Chemistry, Osnabrueck, Germany
| | | | - Marco Marcello
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, Merseyside, UK
| | - Gabriel G Martins
- Instituto Gulbenkian de Ciencia & Faculdade de Ciencias, University of Lisboa, Oeiras, Portugal
| | | | - Claire A Mitchell
- Warwick Medical School, University of Warwick, Coventry, West Midlands, UK
| | - Joshua Moore
- Divisions of Computational Biology and Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tobias Mueller
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Vienna, Austria
| | | | - Stephen Ogg
- Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | | | - Perrine Paul-Gilloteaux
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, F-44000 Nantes, France
| | - Jaime A Pimentel
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Laure Plantard
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Santosh Podder
- Microscopy Facility, Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India
| | | | | | - Markku A Saari
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Damien Schapman
- UNIROUEN, INSERM, PRIMACEN, Normandie University, Rouen, France
| | | | - Britta Schroth-Diez
- Light Microscopy Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Michael Shaw
- National Physical Laboratory, Teddington, Middlesex, UK
| | - Martin Spitaler
- Imaging Facility, Max Planck Institute of Biochemistry, Martinsried, Munich, Germany
| | | | - Damir Sudar
- Quantitative Imaging Systems, Portland, Oregon, USA
| | - Jeremie Teillon
- Bordeaux Imaging Center, Université de Bordeaux, Bordeaux, Gironde, France
| | - Stefan Terjung
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
| | - Roland Thuenauer
- Technology Platform Microscopy and Image Analysis, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Graham D Wright
- A*STAR Microscopy Platform, Research Support Centre, Agency for Science, Technology and Research, Singapore, Singapore
| | - Roland Nitschke
- Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany
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4
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Dietzel S, Ferrando-May E, Fried H, Kukat C, Naumann A, Nitschke R, Pasierbek P, Peychl J, Rasse TM, Schroth-Diez B, Stöckl MT, Terjung S, Thuenauer R, Tulok S, Weidtkamp-Peters S. A Joint Action in Times of Pandemic: The German BioImaging Recommendations for Operating Imaging Core Facilities During the SARS-Cov-2 Emergency. Cytometry A 2020; 97:882-886. [PMID: 32583531 PMCID: PMC7361206 DOI: 10.1002/cyto.a.24178] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/18/2022]
Abstract
Operating shared resource laboratories (SRLs) in times of pandemic is a challenge for research institutions. In a multiuser, high‐turnover working space, the transmission of infectious agents is difficult to control. To address this challenge, imaging core facility managers being members of German BioImaging discussed how shared microscopes could be operated with minimal risk of spreading SARS‐CoV‐2 between users and staff. Here, we describe the resulting guidelines and explain their rationale, with a focus on separating users in space and time, protective face masks, and keeping surfaces virus‐free. These recommendations may prove useful for other types of SRLs. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Steffen Dietzel
- Core Facility Bioimaging at the Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Großhaderner Straße 9, 82152, Germany
| | - Elisa Ferrando-May
- Bioimaging Center, University of Konstanz, Konstanz, Universitätsstrasse 10, 78464, Germany
| | - Hans Fried
- German Center for Neurodegenerative Diseases (DZNE), Light Microscopy Facility, Bonn, Venusberg-Campus 1, Gebäude 99, 53127, Germany
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Joseph-Stelzmann-Str. 9b, 50931, Germany
| | - Angela Naumann
- Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Habsburgerstr. 49, 79104, Germany
| | - Roland Nitschke
- Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Habsburgerstr. 49, 79104, Germany
| | - Pawel Pasierbek
- Biooptics Core Facility, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Dr. Bohr-Gasse 3, 1030, Austria
| | - Jan Peychl
- Light Microscopy Facility (LMF) Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Dresden, Pfotenhauerstrasse 108, 01307, Germany
| | - Tobias Manuel Rasse
- Scientific Service Group Microscopy, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Ludwigstraße 43, 61231, Germany
| | - Britta Schroth-Diez
- Light Microscopy Facility (LMF) Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Dresden, Pfotenhauerstrasse 108, 01307, Germany
| | - Martin Thomas Stöckl
- Bioimaging Center, University of Konstanz, Konstanz, Universitätsstrasse 10, 78464, Germany
| | - Stefan Terjung
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Meyerhofstraße 1, 69117, Germany
| | - Roland Thuenauer
- Advanced Light and Fluorescence Microscopy Facility, Centre for Structural Systems Biology (CSSB), Hamburg, Germany and Department of Biology, University of Hamburg, Hamburg, Germany
| | - Silke Tulok
- Technische Universität Dresden, Faculty of Medicine Carl Gustav Carus, Core Facility Cellular Imaging, Dresden, Fetscherstrasse 74, 01307, Germany
| | - Stefanie Weidtkamp-Peters
- Center for Advanced Imaging, Heinrich-Heine University Duesseldorf, Duesseldorf, Universitätsstr. 1, 40225, Germany
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- GerBI-GMB, c/o University of Konstanz, Konstanz, Universitätsstrasse 10, 78464, Germany
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5
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Kumar V, Fleming T, Terjung S, Gorzelanny C, Gebhardt C, Agrawal R, Mall MA, Ranzinger J, Zeier M, Madhusudhan T, Ranjan S, Isermann B, Liesz A, Deshpande D, Häring HU, Biswas SK, Reynolds PR, Hammes HP, Peperkok R, Angel P, Herzig S, Nawroth PP. Homeostatic nuclear RAGE-ATM interaction is essential for efficient DNA repair. Nucleic Acids Res 2017; 45:10595-10613. [PMID: 28977635 PMCID: PMC5737477 DOI: 10.1093/nar/gkx705] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 08/02/2017] [Indexed: 12/12/2022] Open
Abstract
The integrity of genome is a prerequisite for healthy life. Indeed, defects in DNA repair have been associated with several human diseases, including tissue-fibrosis, neurodegeneration and cancer. Despite decades of extensive research, the spatio-mechanical processes of double-strand break (DSB)-repair, especially the auxiliary factor(s) that can stimulate accurate and timely repair, have remained elusive. Here, we report an ATM-kinase dependent, unforeseen function of the nuclear isoform of the Receptor for Advanced Glycation End-products (nRAGE) in DSB-repair. RAGE is phosphorylated at Serine376 and Serine389 by the ATM kinase and is recruited to the site of DNA-DSBs via an early DNA damage response. nRAGE preferentially co-localized with the MRE11 nuclease subunit of the MRN complex and orchestrates its nucleolytic activity to the ATR kinase signaling. This promotes efficient RPA2S4-S8 and CHK1S345 phosphorylation and thereby prevents cellular senescence, IPF and carcinoma formation. Accordingly, loss of RAGE causatively linked to perpetual DSBs signaling, cellular senescence and fibrosis. Importantly, in a mouse model of idiopathic pulmonary fibrosis (RAGE−/−), reconstitution of RAGE efficiently restored DSB-repair and reversed pathological anomalies. Collectively, this study identifies nRAGE as a master regulator of DSB-repair, the absence of which orchestrates persistent DSB signaling to senescence, tissue-fibrosis and oncogenesis.
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Affiliation(s)
- Varun Kumar
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz-Zentrum, München, Germany
| | - Thomas Fleming
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz-Zentrum, München, Germany
| | - Stefan Terjung
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
| | - Christian Gorzelanny
- Experimental Dermatology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Christoffer Gebhardt
- Division of Dermatooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Signal Transduction and Growth Control DKFZ DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raman Agrawal
- Department of Translational Pulmonology, Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, INF 156, Heidelberg, Germany
| | - Marcus A Mall
- Department of Translational Pulmonology, Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, INF 156, Heidelberg, Germany
| | - Julia Ranzinger
- Department of Nephrology, University of Heidelberg, Heidelberg, INF 410, Heidelberg, Germany
| | - Martin Zeier
- Department of Nephrology, University of Heidelberg, Heidelberg, INF 410, Heidelberg, Germany
| | - Thati Madhusudhan
- Institute of Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke-University, Magdeburg, Germany
| | - Satish Ranjan
- Institute of Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke-University, Magdeburg, Germany
| | - Berend Isermann
- Institute of Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke-University, Magdeburg, Germany
| | - Arthur Liesz
- Institute for Stroke and Dementia Research (ISD) University Hospital München, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Divija Deshpande
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Hans-Ulrich Häring
- German Center for Diabetes Research (DZD), Helmholtz-Zentrum, München, Germany.,Department of Internal Medicine, University of Tübingen, Tübingen, Germany
| | - Subrata K Biswas
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Shahbag, Dhaka 1000, Bangladesh
| | - Paul R Reynolds
- Department of Physiology and Developmental Biology, Brigham Young University, 3054 Life Sciences Building, Provo, UT 84602, USA
| | - Hans-Peter Hammes
- 5th Medical Department, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Rainer Peperkok
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
| | - Peter Angel
- Division of Signal Transduction and Growth Control DKFZ DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan Herzig
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz-Zentrum, München, Germany.,Institute for Diabetes and Cancer, Helmholtz Center Munich, Neuherberg, Germany.,Joint Heidelberg-IDC Translational Diabetes Program, Helmholtz-Zentrum, München, Germany
| | - Peter P Nawroth
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany.,German Center for Diabetes Research (DZD), Helmholtz-Zentrum, München, Germany.,Joint Heidelberg-IDC Translational Diabetes Program, Helmholtz-Zentrum, München, Germany
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6
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Terjung S, Geldmacher J, Brato S, Teschler H, Götze J, Weinreich G. A novel device for the detection ofsleep disordered breathingand periodic limb movement. Pneumologie 2017. [DOI: 10.1055/s-0037-1598513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- S Terjung
- Departement of Pneumology, Ruhrlandklinik, Westdeutsches Lungenzentrum Essen; Faculty of Physics, Technical University Dortmund
| | | | - S Brato
- Swg Sportwerk GmbH und Co KG
| | | | | | - G Weinreich
- Abteilung für Pneumologie, Ruhrlandklinik, Westdeutsches Lungenzentrum, Universitätsklinikum Essen
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7
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Abstract
Laser-mediated dissection methods have been used for many years to micro-irradiate biological samples, but recent technological progress has rendered this technique more precise, powerful, and easy to use. Today pulsed lasers can be operated with diffraction limited, sub-micrometer precision to ablate intracellular structures. Here, we discuss laser nanosurgery setups and the instrumentation in our laboratory. We describe how to use this technique to ablate cytoskeletal elements in living cells. We also show how this technique can be used in multicellular organisms, to micropuncture and/or ablate cells of interest and finally how to monitor a successful laser nanosurgery.
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Affiliation(s)
| | - Paolo Ronchi
- Cell Biology and Cell Biophysics Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Electron Microscopy Core Facility, EMBL Heidelberg, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Sevi Durdu
- Cell Biology and Cell Biophysics Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Stefan Terjung
- Advanced Light Microscopy Facility, EMBL Heidelberg, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Rainer Pepperkok
- Cell Biology and Cell Biophysics Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117, Heidelberg, Germany. .,Advanced Light Microscopy Facility, EMBL Heidelberg, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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8
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Ferrando-May E, Hartmann H, Reymann J, Ansari N, Utz N, Fried HU, Kukat C, Peychl J, Liebig C, Terjung S, Laketa V, Sporbert A, Weidtkamp-Peters S, Schauss A, Zuschratter W, Avilov S. Advanced light microscopy core facilities: Balancing service, science and career. Microsc Res Tech 2016; 79:463-79. [PMID: 27040755 PMCID: PMC5071710 DOI: 10.1002/jemt.22648] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 02/13/2016] [Indexed: 11/08/2022]
Abstract
Core Facilities (CF) for advanced light microscopy (ALM) have become indispensable support units for research in the life sciences. Their organizational structure and technical characteristics are quite diverse, although the tasks they pursue and the services they offer are similar. Therefore, throughout Europe, scientists from ALM-CFs are forming networks to promote interactions and discuss best practice models. Here, we present recommendations for ALM-CF operations elaborated by the workgroups of the German network of ALM-CFs, German Bio-Imaging (GerBI). We address technical aspects of CF planning and instrument maintainance, give advice on the organization and management of an ALM-CF, propose a scheme for the training of CF users, and provide an overview of current resources for image processing and analysis. Further, we elaborate on the new challenges and opportunities for professional development and careers created by CFs. While some information specifically refers to the German academic system, most of the content of this article is of general interest for CFs in the life sciences. Microsc. Res. Tech. 79:463-479, 2016. © 2016 THE AUTHORS MICROSCOPY RESEARCH AND TECHNIQUE PUBLISHED BY WILEY PERIODICALS, INC.
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Affiliation(s)
- Elisa Ferrando-May
- Department of Biology, University of Konstanz, Bioimaging Center, Universitätsstrasse 10, Konstanz, 78464, Germany
| | - Hella Hartmann
- Technical University Dresden, Center for Regenerative Therapies, Light Microscopy Facility, Fetscherstraße 105, Dresden, 01307, Germany
| | - Jürgen Reymann
- Heidelberg University, BioQuant, ViroQuant-CellNetworks RNAi Screening Facility, Im Neuenheimer Feld 267, & Heidelberg Center for Human Bioinformatics, IPMB, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - Nariman Ansari
- Goethe University Frankfurt am Main, Buchmann Institute for Molecular Life Sciences, Physical Biology Group, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Nadine Utz
- Department of Biology, University of Konstanz, Bioimaging Center, Universitätsstrasse 10, Konstanz, 78464, Germany
| | - Hans-Ulrich Fried
- Deutsches Zentrum für Neurodegenerative Erkrankungen, Core Facility and Services, Light Microscopy Facility, Ludwig-Erhard-Allee 2, Bonn, 53175, Germany
| | - Christian Kukat
- Max Planck Institute for Biology of Ageing, FACS & Imaging Core Facility, Joseph-Stelzmann-Str. 9b, Köln, 50931, Köln, Germany
| | - Jan Peychl
- Max Planck Institute for Molecular Cell Biology and Genetics, Light Microscopy Facility, Pfotenhauerstr. 108, Dresden, 01307, Germany
| | - Christian Liebig
- Max Planck Institute for Developmental Biology, Light Microscopy Facility, Spemannstrasse 35, Tübingen, 72076, Germany
| | - Stefan Terjung
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Meyerhofstr. 1, Heidelberg, 69117, Germany
| | - Vibor Laketa
- Department of Infectious Diseases, German Center for Infection Research, Im Neuenheimer Feld 345, Heidelberg, 69120, Germany
| | - Anje Sporbert
- Max Delbrück Center for Molecular Medicine Berlin, Advanced Light Microscopy Technology Platform, Robert-Rössle-Str. 10, Berlin, 13125, Germany
| | - Stefanie Weidtkamp-Peters
- Heinrich Heine Universität Düsseldorf, Center for Advanced Imaging, Universitätsstr. 1, Düsseldorf, 40225, Germany
| | - Astrid Schauss
- University of Cologne, CECAD Imaging Facility, Joseph-Stelzmann Strasse 26, Köln, 50931, Germany
| | - Werner Zuschratter
- Leibniz Institute for Neurobiology, Electron & Laser Scanning Microscopy, Brenneckestrasse 6, Magdeburg, 39118, Germany
| | - Sergiy Avilov
- Max-Planck Institute for Immunobiology and Epigenetics, Imaging Facility, Stübeweg 51, Freiburg, 79108, Germany
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9
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Terjung S, Wang Y, Armitstead J, Bateman P, Richards G, Teschler H, Weinreich G. Validation of the S9 AutoSet APAP device for the apnea-hypopnea index detection in OSA patients. Pneumologie 2016. [DOI: 10.1055/s-0036-1571962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Terjung S, Wang Y, Werther S, Zaffaroni A, Teschler H, Weinreich G. Validierung von SleepMinder® zur Erfassung der Schlafqualität bei Patienten mit OSAS. Somnologie 2016. [DOI: 10.1007/s11818-016-0043-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Weinreich G, Terjung S, Wang Y, Werther S, Zaffaroni A, Teschler H. Validierung von SleepMinder® als Screeninggerät für die obstruktive Schlafapnoe. Somnologie 2014. [DOI: 10.1007/s11818-014-0690-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Abstract
Laser-mediated nanosurgery has become popular in the last decade because of the previously unexplored possibility of ablating biological material inside living cells with sub-micrometer precision. A number of publications have shown the potential applications of this technique, ranging from the dissection of sub-cellular structures to surgical ablations of whole cells or tissues in model systems such as Drosophila melanogaster or Danio rerio . In parallel, the recent development of micropatterning techniques has given cell biologists the possibility to shape cells and reproducibly organize the intracellular space. The integration of these two techniques has only recently started yet their combination has proven to be very interesting. The aim of this review is to present recent applications of laser nanosurgery in cell biology and to discuss the possible developments of this approach, particularly in combination with micropattern-mediated endomembrane organization.
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Affiliation(s)
- Paolo Ronchi
- Cell Biology and Biophysics Unit , European Molecular Biology Laboratory-EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
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13
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Seitz A, Terjung S, Zimmermann T, Pepperkok R. Quantifying the influence of yellow fluorescent protein photoconversion on acceptor photobleaching-based fluorescence resonance energy transfer measurements. J Biomed Opt 2012; 17:011010. [PMID: 22352644 DOI: 10.1117/1.jbo.17.1.011010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Fluorescence resonance energy transfer (FRET) efficiency measurements based on acceptor photobleaching of yellow fluorescent protein (YFP) are affected by the fact that bleaching of YFP produces a fluorescent species that is detectable in cyan fluorescent protein (CFP) image channels. The presented quantitative measurement of this conversion makes it possible to correct the obtained FRET signal to increase the accuracy of intensity based CFP/YFP FRET measurements. The described method can additionally be used to compare samples with very different fluorescence levels.
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Affiliation(s)
- Arne Seitz
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Meyerhofstr 1, 69117 Heidelberg, Germany.
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14
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Terjung S, Walter T, Seitz A, Neumann B, Pepperkok R, Ellenberg J. High-throughput microscopy using live mammalian cells. Cold Spring Harb Protoc 2010; 2010:pdb.top84. [PMID: 20679389 DOI: 10.1101/pdb.top84] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Nagel KA, Kastenholz B, Jahnke S, van Dusschoten D, Aach T, Mühlich M, Truhn D, Scharr H, Terjung S, Walter A, Schurr U. Temperature responses of roots: impact on growth, root system architecture and implications for phenotyping. Funct Plant Biol 2009; 36:947-959. [PMID: 32688706 DOI: 10.1071/fp09184] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 09/11/2009] [Indexed: 05/02/2023]
Abstract
Root phenotyping is a challenging task, mainly because of the hidden nature of this organ. Only recently, imaging technologies have become available that allow us to elucidate the dynamic establishment of root structure and function in the soil. In root tips, optical analysis of the relative elemental growth rates in root expansion zones of hydroponically-grown plants revealed that it is the maximum intensity of cellular growth processes rather than the length of the root growth zone that control the acclimation to dynamic changes in temperature. Acclimation of entire root systems was studied at high throughput in agar-filled Petri dishes. In the present study, optical analysis of root system architecture showed that low temperature induced smaller branching angles between primary and lateral roots, which caused a reduction in the volume that roots access at lower temperature. Simulation of temperature gradients similar to natural soil conditions led to differential responses in basal and apical parts of the root system, and significantly affected the entire root system. These results were supported by first data on the response of root structure and carbon transport to different root zone temperatures. These data were acquired by combined magnetic resonance imaging (MRI) and positron emission tomography (PET). They indicate acclimation of root structure and geometry to temperature and preferential accumulation of carbon near the root tip at low root zone temperatures. Overall, this study demonstrated the value of combining different phenotyping technologies that analyse processes at different spatial and temporal scales. Only such an integrated approach allows us to connect differences between genotypes obtained in artificial high throughput conditions with specific characteristics relevant for field performance. Thus, novel routes may be opened up for improved plant breeding as well as for mechanistic understanding of root structure and function.
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Affiliation(s)
- Kerstin A Nagel
- Institute of Chemistry and Dynamics of the Geosphere ICG-3: Phytosphere, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bernd Kastenholz
- Institute of Chemistry and Dynamics of the Geosphere ICG-3: Phytosphere, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Siegfried Jahnke
- Institute of Chemistry and Dynamics of the Geosphere ICG-3: Phytosphere, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Dagmar van Dusschoten
- Institute of Chemistry and Dynamics of the Geosphere ICG-3: Phytosphere, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Til Aach
- Lehrstuhl für Bildverarbeitung, RWTH Aachen University, 52056 Aachen, Germany
| | - Matthias Mühlich
- Lehrstuhl für Bildverarbeitung, RWTH Aachen University, 52056 Aachen, Germany
| | - Daniel Truhn
- Lehrstuhl für Bildverarbeitung, RWTH Aachen University, 52056 Aachen, Germany
| | - Hanno Scharr
- Institute of Chemistry and Dynamics of the Geosphere ICG-3: Phytosphere, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stefan Terjung
- Institute of Chemistry and Dynamics of the Geosphere ICG-3: Phytosphere, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Achim Walter
- Institute of Chemistry and Dynamics of the Geosphere ICG-3: Phytosphere, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ulrich Schurr
- Institute of Chemistry and Dynamics of the Geosphere ICG-3: Phytosphere, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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16
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Tournaviti S, Pietro ES, Terjung S, Schafmeier T, Wegehingel S, Ritzerfeld J, Schulz J, Smith DF, Pepperkok R, Nickel W. Reversible phosphorylation as a molecular switch to regulate plasma membrane targeting of acylated SH4 domain proteins. Traffic 2009; 10:1047-60. [PMID: 19453972 DOI: 10.1111/j.1600-0854.2009.00921.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Acylated SH4 domains represent N-terminal targeting signals that anchor peripheral membrane proteins such as Src kinases in the inner leaflet of plasma membranes. Here we provide evidence for a novel regulatory mechanism that may control the levels of SH4 proteins being associated with plasma membranes. Using a fusion protein of the SH4 domain of Leishmania HASPB and GFP as a model system, we demonstrate that threonine 6 is a substrate for phosphorylation. Substitution of threonine 6 by glutamate (to mimic a phosphothreonine residue) resulted in a dramatic redistribution from plasma membranes to intracellular sites with a particular accumulation in a perinuclear region. As shown by both pharmacological inhibition and RNAi-mediated down-regulation of the threonine/ serine-specific phosphatases PP1 and PP2A, recycling back to the plasma membrane required dephosphorylation of threonine 6. We provide evidence that a cycle of phosphorylation and dephosphorylation may also be involved in intracellular targeting of other SH4 proteins such as the Src kinase Yes.
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17
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Tournaviti S, San Pietro E, Terjung S, Schafmeier T, Wegehingel S, Ritzerfeld J, Schulz J, Smith DF, Pepperkok R, Nickel W. Reversible Phosphorylation as a Molecular Switch to Regulate Plasma Membrane Targeting of Acylated SH4 Domain Proteins. Traffic 2009. [DOI: 10.1111/j.1600-0854.2009.0921.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Terjung S, Schulte JH, Schlierf S, Schramm A, Eggert A, Meyer HE, Stühler K. Proteomics of neuroblastoma master regulators. Klin Padiatr 2009. [DOI: 10.1055/s-0029-1222691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Tournaviti S, Hannemann S, Terjung S, Kitzing TM, Stegmayer C, Ritzerfeld J, Walther P, Grosse R, Nickel W, Fackler OT. SH4-domain-induced plasma membrane dynamization promotes bleb-associated cell motility. J Cell Sci 2008; 120:3820-9. [PMID: 17959630 DOI: 10.1242/jcs.011130] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
SH4 domains provide bipartite membrane-targeting signals for oncogenic Src family kinases. Here we report the induction of non-apoptotic plasma membrane (PM) blebbing as a novel and conserved activity of SH4 domains derived from the prototypic Src kinases Src, Fyn, Yes and Lck as well as the HASPB protein of Leishmania parasites. SH4-domain-induced blebbing is highly dynamic, with bleb formation and collapse displaying distinct kinetics. These reorganizations of the PM are controlled by Rho but not Rac or Cdc42 GTPase signalling pathways. SH4-induced membrane blebbing requires the membrane association of the SH4 domain, is regulated by the activities of Rock kinase and myosin II ATPase, and depends on the integrity of F-actin as well as microtubules. Endogenous Src kinase activity is crucial for PM blebbing in SH4-domain-expressing cells, active Src and Rock kinases are enriched in SH4-domain-induced PM blebs, and PM blebbing correlates with enhanced cell invasion in 3D matrices. These results establish a novel link between SH4 domains, Src activity and Rho signalling, and implicate SH4-domain-mediated PM dynamization as a mechanism that influences invasiveness of cells transformed by SH4-domain-containing oncoproteins.
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Affiliation(s)
- Stella Tournaviti
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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20
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Abstract
We have compared the distribution of endogenous heterochromatin protein 1 (HP1) proteins (α, β and γ) in different epithelial lines, pluripotent stem cells and embryonic fibroblasts. In parallel, we have interrogated assembly and dynamics of newly expressed HP1-GFP proteins in cells lacking both HP1α and HP1β alleles, blocked at the G1-S boundary, or cultured in the presence of HDAC and HAT inhibitors. The results reveal a range of cell type and differentiation state-specific patterns that do not correlate with `fast' or `slow' subunit exchange in heterochromatin. Furthermore, our observations show that targeting of HP1γ to heterochromatic sites depends on HP1α and H1β and that, on an architectural level, HP1α is the most polymorphic variant of the HP1 family. These data provide evidence for HP1 plasticity under shifting microenvironmental conditions and offer a new conceptual framework for understanding chromatin dynamics at the molecular level.
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Affiliation(s)
- George K Dialynas
- The Stem Cell and Chromatin Group, Laboratory of Biology, The University of Ioannina, School of Medicine and The Institute of Biomedical Research (FORTH/BRI), 45 110 Ioannina, Greece
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21
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Dialynas GK, Makatsori D, Kourmouli N, Theodoropoulos PA, McLean K, Terjung S, Singh PB, Georgatos SD. Methylation-independent Binding to Histone H3 and Cell Cycle-dependent Incorporation of HP1β into Heterochromatin. J Biol Chem 2006; 281:14350-60. [PMID: 16547356 DOI: 10.1074/jbc.m600558200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have examined HP1beta-chromatin interactions in different molecular contexts in vitro and in vivo. Employing purified components we show that HP1beta exhibits selective, stoichiometric, and salt-resistant binding to recombinant histone H3, associating primarily with the helical "histone fold" domain. Furthermore, using "bulk" nucleosomes released by MNase digestion, S-phase extracts, and fragments of peripheral heterochromatin, we demonstrate that HP1beta associates more tightly with destabilized or disrupted nucleosomes (H3/H4 subcomplexes) than with intact particles. Western blotting and mass spectrometry data indicate that HP1beta-selected H3/H4 particles and subparticles possess a complex pattern of posttranslational modifications but are not particularly enriched in me3K9-H3. Consistent with these results, mapping of HP1beta and me3K9-H3 sites in vivo reveals overlapping, yet spatially distinct patterns, while transient transfection assays with synchronized cells show that stable incorporation of HP1beta-gfp into heterochromatin requires passage through the S-phase. The data amassed challenge the dogma that me3K9H3 is necessary and sufficient for HP1 binding and unveil a new mode of HP1-chromatin interactions.
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Affiliation(s)
- George K Dialynas
- Stem Cell and Chromatin Group, Laboratory of Biology, The University of Ioannina, School of Medicine and Ioannina Biomedical Research Institute/Foundation for Research and Technology, 45 110 Ioannina, Greece
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22
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Abstract
In this chapter we describe automated imaging methods used to measure the transport of an established membrane transport marker from the endoplasmic reticulum to the plasma membrane. The method is fast and significantly robust to be applied in systematic studies on a large scale such as genome-wide screening projects. We further describe the use of software macros and plugins in Image J that allow the quantification of the kinetics of membrane transport intermediates in fluorescence microscopy time-lapse sequences.
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Affiliation(s)
- Rainer Pepperkok
- Cell Biology and Cell Biophysics Program, European Molecular Biology Laboratory, Heidelberg, Germany
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Walter A, Spies H, Terjung S, Küsters R, Kirchgessner N, Schurr U. Spatio-temporal dynamics of expansion growth in roots: automatic quantification of diurnal course and temperature response by digital image sequence processing. J Exp Bot 2002; 53:689-98. [PMID: 11886889 DOI: 10.1093/jexbot/53.369.689] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A newly developed technique based on image sequence analysis allows automatic and precise quantification of the dynamics of the growth velocity of the root tip, the distribution of expansion growth rates along the entire growth zone and the oscillation frequencies of the root tip during growth without the need of artificial landmarks. These three major parameters characterizing expansion growth of primary roots can be analysed over several days with high spatial (20 microm) and temporal resolution (several minutes) as the camera follows the growing root by an image-controlled root tracking device. In combination with a rhizotron set up for hydroponic plant cultivation the impact of rapid changes of environmental factors can be assessed. First applications of this new system proved the absence of diurnal variation of root growth in Zea mays under constant temperature conditions. The distribution profile of relative elemental growth rate (REGR) showed two maxima under constant and varying growth conditions. Lateral oscillatory movements of growing root tips were present even under constant environmental conditions. Dynamic changes in velocity- and REGR-distribution within 1 h could be quantified after a step change in temperature from 21 degrees C to 26 degrees C. Most prominent growth responses were found in the zone of maximal root elongation.
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Affiliation(s)
- A Walter
- Biosphere 2 Center, Columbia University, Oracle, AZ 85623, USA
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