1
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Gruber FS, Richardson A, Johnston ZC, Myles R, Norcross NR, Day DP, Georgiou I, Sesma-Sanz L, Wilson C, Read KD, Martins da Silva S, Barratt CLR, Gilbert IH, Swedlow JR. Sperm Toolbox-A selection of small molecules to study human spermatozoa. PLoS One 2024; 19:e0297666. [PMID: 38377053 PMCID: PMC10878532 DOI: 10.1371/journal.pone.0297666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/11/2024] [Indexed: 02/22/2024] Open
Abstract
Male contraceptive options and infertility treatments are limited, and almost all innovation has been limited to updates to medically assisted reproduction protocols and methods. To accelerate the development of drugs that can either improve or inhibit fertility, we established a small molecule library as a toolbox for assay development and screening campaigns using human spermatozoa. We have profiled all compounds in the Sperm Toolbox in several automated high-throughput assays that measure stimulation or inhibition of sperm motility or the acrosome reaction. We have assayed motility under non-capacitating and capacitating conditions to distinguish between pathways operating under these different physiological states. We also assayed cell viability to ensure any effects on sperm function are specific. A key advantage of our studies is that all compounds are assayed together in the same experimental conditions, which allows quantitative comparisons of their effects in complementary functional assays. We have combined the resulting datasets to generate fingerprints of the Sperm Toolbox compounds on sperm function. The data are included in an on-line R-based app for convenient querying.
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Affiliation(s)
- Franz S. Gruber
- Divisions of Computational Biology and Molecular, Cell and Developmental Biology, and National Phenotypic Screening Centre, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Anthony Richardson
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Zoe C. Johnston
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Rachel Myles
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Neil R. Norcross
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - David P. Day
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Irene Georgiou
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Laura Sesma-Sanz
- Divisions of Computational Biology and Molecular, Cell and Developmental Biology, and National Phenotypic Screening Centre, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Caroline Wilson
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Kevin D. Read
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sarah Martins da Silva
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Christopher L. R. Barratt
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Ian H. Gilbert
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jason R. Swedlow
- Divisions of Computational Biology and Molecular, Cell and Developmental Biology, and National Phenotypic Screening Centre, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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2
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Wittner R, Holub P, Mascia C, Frexia F, Müller H, Plass M, Allocca C, Betsou F, Burdett T, Cancio I, Chapman A, Chapman M, Courtot M, Curcin V, Eder J, Elliot M, Exter K, Goble C, Golebiewski M, Kisler B, Kremer A, Leo S, Lin‐Gibson S, Marsano A, Mattavelli M, Moore J, Nakae H, Perseil I, Salman A, Sluka J, Soiland‐Reyes S, Strambio‐De‐Castillia C, Sussman M, Swedlow JR, Zatloukal K, Geiger J. Toward a common standard for data and specimen provenance in life sciences. Learn Health Syst 2024; 8:e10365. [PMID: 38249839 PMCID: PMC10797572 DOI: 10.1002/lrh2.10365] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 01/23/2024] Open
Abstract
Open and practical exchange, dissemination, and reuse of specimens and data have become a fundamental requirement for life sciences research. The quality of the data obtained and thus the findings and knowledge derived is thus significantly influenced by the quality of the samples, the experimental methods, and the data analysis. Therefore, a comprehensive and precise documentation of the pre-analytical conditions, the analytical procedures, and the data processing are essential to be able to assess the validity of the research results. With the increasing importance of the exchange, reuse, and sharing of data and samples, procedures are required that enable cross-organizational documentation, traceability, and non-repudiation. At present, this information on the provenance of samples and data is mostly either sparse, incomplete, or incoherent. Since there is no uniform framework, this information is usually only provided within the organization and not interoperably. At the same time, the collection and sharing of biological and environmental specimens increasingly require definition and documentation of benefit sharing and compliance to regulatory requirements rather than consideration of pure scientific needs. In this publication, we present an ongoing standardization effort to provide trustworthy machine-actionable documentation of the data lineage and specimens. We would like to invite experts from the biotechnology and biomedical fields to further contribute to the standard.
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Affiliation(s)
- Rudolf Wittner
- BBMRI‐ERICGrazAustria
- Institute of Computer Science & Faculty of InformaticsMasaryk UniversityBrnoCzechia
| | - Petr Holub
- BBMRI‐ERICGrazAustria
- Institute of Computer Science & Faculty of InformaticsMasaryk UniversityBrnoCzechia
| | - Cecilia Mascia
- CRS4—Center for Advanced StudiesResearch and Development in SardiniaPulaItaly
| | - Francesca Frexia
- CRS4—Center for Advanced StudiesResearch and Development in SardiniaPulaItaly
| | | | | | - Clare Allocca
- National Institute of Standards and TechnologyGaithersburgMarylandUSA
| | - Fay Betsou
- Biological Resource Center of Institut Pasteur (CRBIP)ParisFrance
| | - Tony Burdett
- EMBL's European Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Ibon Cancio
- Plentzia Marine Station (PiE‐UPV/EHU)University of the Basque Country, EMBRC‐SpainBilbaoSpain
| | | | | | | | | | | | - Mark Elliot
- Department of Social Statistics, School of Social SciencesUniversity of ManchesterManchesterUK
| | - Katrina Exter
- Flanders Marine Institute (VLIZ), EMBRC‐BelgiumOstendBelgium
| | - Carole Goble
- Department of Computer ScienceUniversity of ManchesterManchesterUK
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS gGmbH)HeidelbergGermany
| | | | | | - Simone Leo
- CRS4—Center for Advanced StudiesResearch and Development in SardiniaPulaItaly
| | | | - Anna Marsano
- Department of BiomedicineUniversity of BaselBaselSwitzerland
| | - Marco Mattavelli
- SCI‐STI‐MMÉcole Politechnique Fédérale de LausanneLausanneSwitzerland
| | - Josh Moore
- Centre for Gene Regulation and Expression and Division of Computational Biology, School of Life SciencesUniversity of DundeeDundeeUK
- German BioImaging–Gesellschaft für Mikroskopie und Bildanalyse e.V.KonstanzGermany
| | - Hiroki Nakae
- Japan bio‐Measurement and Analysis ConsortiumTokyoJapan
| | - Isabelle Perseil
- INSERM–Institut National de la Sante et de la Recherche MedicaleParisFrance
| | - Ayat Salman
- Standards Council of CanadaOttawaOntarioCanada
- Canadian Primary Care Sentinel Surveillance Network (CPCSSN) Department of Family MedicineQueen's UniversityKingstonOntarioCanada
| | - James Sluka
- Biocomplexity InstituteIndiana UniversityBloomingtonIndianaUSA
| | - Stian Soiland‐Reyes
- Department of Computer ScienceUniversity of ManchesterManchesterUK
- Informatics InstituteUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Michael Sussman
- US Department of AgricultureWashingtonDistrict of ColumbiaUSA
| | - Jason R. Swedlow
- Centre for Gene Regulation and Expression and Division of Computational Biology, School of Life SciencesUniversity of DundeeDundeeUK
| | | | - Jörg Geiger
- Interdisciplinary Bank of Biomaterials and Data Würzburg (ibdw)WürzburgGermany
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3
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Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Casas Moreno X, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Küpcü Yoldaş A, Kyoda K, le Tournoulx de la Villegeorges A, Li T, Liberali P, Lindner D, Linkert M, Lüthi J, Maitin-Shepard J, Manz T, Marconato L, McCormick M, Lange M, Mohamed K, Moore W, Norlin N, Ouyang W, Özdemir B, Palla G, Pape C, Pelkmans L, Pietzsch T, Preibisch S, Prete M, Rzepka N, Samee S, Schaub N, Sidky H, Solak AC, Stirling DR, Striebel J, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR. OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochem Cell Biol 2023; 160:223-251. [PMID: 37428210 PMCID: PMC10492740 DOI: 10.1007/s00418-023-02209-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 07/11/2023]
Abstract
A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself-OME-Zarr-along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain-the file format that underlies so many personal, institutional, and global data management and analysis tasks.
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Affiliation(s)
- Josh Moore
- German BioImaging-Gesellschaft für Mikroskopie und Bildanalyse e.V., Constance, Germany.
| | | | - Sébastien Besson
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - John Bogovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Eva M Brown
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Jean-Marie Burel
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Xavier Casas Moreno
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | | | - David Gault
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | | | - Ilan Gold
- Harvard Medical School, Boston, MA, USA
| | | | - Matthew Hartley
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK
| | - Dave Horsfall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Mark Kittisopikul
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Gabor Kovacs
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Aybüke Küpcü Yoldaş
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK
| | - Koji Kyoda
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Tong Li
- Wellcome Sanger Institute, Hinxton, UK
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland
| | - Dominik Lindner
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | | | - Joel Lüthi
- Friedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland
| | | | | | - Luca Marconato
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | | | - Khaled Mohamed
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - William Moore
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Nils Norlin
- Department of Experimental Medical Science & Lund Bioimaging Centre, Lund University, Lund, Sweden
| | - Wei Ouyang
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Giovanni Palla
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Tobias Pietzsch
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Stephan Preibisch
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | | | | | - Nicholas Schaub
- Information Technology Branch, National Center for Advancing Translational Science, National Institutes of Health, Bethesda, USA
| | | | | | | | | | | | | | - Isaac Virshup
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Petr Walczysko
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | | | - Erin Weisbart
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Frances Wong
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Kevin A Yamauchi
- Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland
| | | | - Beth A Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Nathan Hotaling
- Information Technology Branch, National Center for Advancing Translational Science, National Institutes of Health, Bethesda, USA
| | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Oliver Stegle
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jason R Swedlow
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
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4
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Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Moreno XC, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Yoldaş AK, Kyoda K, de la Villegeorges ALT, Li T, Liberali P, Lindner D, Linkert M, Lüthi J, Maitin-Shepard J, Manz T, Marconato L, McCormick M, Lange M, Mohamed K, Moore W, Norlin N, Ouyang W, Özdemir B, Palla G, Pape C, Pelkmans L, Pietzsch T, Preibisch S, Prete M, Rzepka N, Samee S, Schaub N, Sidky H, Solak AC, Stirling DR, Striebel J, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR. OME-Zarr: a cloud-optimized bioimaging file format with international community support. bioRxiv 2023:2023.02.17.528834. [PMID: 36865282 PMCID: PMC9980008 DOI: 10.1101/2023.02.17.528834] [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] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself -- OME-Zarr -- along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.
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Affiliation(s)
- Josh Moore
- German BioImaging – Gesellschaft für Mikroskopie und Bildanalyse e.V., Konstanz, Germany
| | | | - Sébastien Besson
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - John Bogovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Eva M. Brown
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Jean-Marie Burel
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Xavier Casas Moreno
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | | | - David Gault
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | | | - Ilan Gold
- Harvard Medical School, Boston, MA, USA
| | | | - Matthew Hartley
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK
| | - Dave Horsfall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Mark Kittisopikul
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Gabor Kovacs
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Aybüke Küpcü Yoldaş
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK
| | - Koji Kyoda
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Tong Li
- Wellcome Sanger Institute, Hinxton, UK
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland
| | - Dominik Lindner
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | | | - Joel Lüthi
- Friedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland
| | | | | | - Luca Marconato
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | | | - Merlin Lange
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Khaled Mohamed
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - William Moore
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Nils Norlin
- Department of Experimental Medical Science & Lund Bioimaging Centre, Lund University, Lund, Sweden
| | - Wei Ouyang
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Giovanni Palla
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Tobias Pietzsch
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Stephan Preibisch
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | | | | | - Nicholas Schaub
- Information Technology Branch, National Center for Advancing Translational Science, National Institutes of Health
| | | | | | | | | | | | | | - Isaac Virshup
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Petr Walczysko
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | | | - Erin Weisbart
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Frances Wong
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Kevin A. Yamauchi
- Department of Biosystems Science and Engineering, ETH Zürich, Switzerland
| | | | - Beth A. Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Nathan Hotaling
- Information Technology Branch, National Center for Advancing Translational Science, National Institutes of Health
| | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Loic A. Royer
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Oliver Stegle
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Fabian J. Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jason R. Swedlow
- Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
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5
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Zhu X, Zhang Y, Wang Y, Tian D, Belmont AS, Swedlow JR, Ma J. Nucleome Browser: an integrative and multimodal data navigation platform for 4D Nucleome. Nat Methods 2022; 19:911-913. [PMID: 35864167 PMCID: PMC9357120 DOI: 10.1038/s41592-022-01559-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Xiaopeng Zhu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yuchuan Wang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Dechao Tian
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Andrew S Belmont
- Department of Cell and Development Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Jason R Swedlow
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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6
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Ropelewski AJ, Rizzo MA, Swedlow JR, Huisken J, Osten P, Khanjani N, Weiss K, Bakalov V, Engle M, Gridley L, Krzyzanowski M, Madden T, Maiese D, Mandal M, Waterfield J, Williams D, Hamilton CM, Huggins W. Standard metadata for 3D microscopy. Sci Data 2022; 9:449. [PMID: 35896564 PMCID: PMC9329339 DOI: 10.1038/s41597-022-01562-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/13/2022] [Indexed: 01/04/2023] Open
Abstract
Recent advances in fluorescence microscopy techniques and tissue clearing, labeling, and staining provide unprecedented opportunities to investigate brain structure and function. These experiments' images make it possible to catalog brain cell types and define their location, morphology, and connectivity in a native context, leading to a better understanding of normal development and disease etiology. Consistent annotation of metadata is needed to provide the context necessary to understand, reuse, and integrate these data. This report describes an effort to establish metadata standards for three-dimensional (3D) microscopy datasets for use by the Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative and the neuroscience research community. These standards were built on existing efforts and developed with input from the brain microscopy community to promote adoption. The resulting 3D Microscopy Metadata Standards (3D-MMS) includes 91 fields organized into seven categories: Contributors, Funders, Publication, Instrument, Dataset, Specimen, and Image. Adoption of these metadata standards will ensure that investigators receive credit for their work, promote data reuse, facilitate downstream analysis of shared data, and encourage collaboration.
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Affiliation(s)
- Alexander J Ropelewski
- Biomedical Applications Group, Pittsburgh Supercomputing Center, 300 S Craig Street, Pittsburgh, PA, 15213, USA
| | - Megan A Rizzo
- Department of Physiology, University of Maryland School of Medicine, 660 West Redwood Street, Baltimore, MD, 21201, USA
| | - Jason R Swedlow
- Centre for Gene Regulation & Expression, Division of Computational Biology, University of Dundee, Nethergate, Dundee, Scotland, DD1 4HN, United Kingdom
| | - Jan Huisken
- Morgridge Institute for Research, 330 N Orchard Street, Madison, WI, 53715, USA
| | - Pavel Osten
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Neda Khanjani
- Mark and Mary Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine of University of Southern California, 1975 Zonal Avenue, Los Angeles, CA, 90033, USA
| | - Kurt Weiss
- Morgridge Institute for Research, 330 N Orchard Street, Madison, WI, 53715, USA
| | - Vesselina Bakalov
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Michelle Engle
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Lauren Gridley
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Michelle Krzyzanowski
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Tom Madden
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Deborah Maiese
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Meisha Mandal
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Justin Waterfield
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - David Williams
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Carol M Hamilton
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Wayne Huggins
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA.
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7
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Hartley M, Kleywegt GJ, Patwardhan A, Sarkans U, Swedlow JR, Brazma A. The BioImage Archive - Building a Home for Life-Sciences Microscopy Data. J Mol Biol 2022; 434:167505. [PMID: 35189131 DOI: 10.1016/j.jmb.2022.167505] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 01/15/2023]
Abstract
Despite the huge impact of data resources in genomics and structural biology, until now there has been no central archive for biological data for all imaging modalities. The BioImage Archive is a new data resource at the European Bioinformatics Institute (EMBL-EBI) designed to fill this gap. In its initial development BioImage Archive accepts bioimaging data associated with publications, in any format, from any imaging modality from the molecular to the organism scale, excluding medical imaging. The BioImage Archive will ensure reproducibility of published studies that derive results from image data and reduce duplication of effort. Most importantly, the BioImage Archive will help scientists to generate new insights through reuse of existing data to answer new biological questions, and provision of training, testing and benchmarking data for development of tools for image analysis. The archive is available at https://www.ebi.ac.uk/bioimage-archive/.
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Affiliation(s)
- Matthew Hartley
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Gerard J Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jason R Swedlow
- Division of Computational Biology, Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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8
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Gruber FS, Johnston ZC, Norcross NR, Georgiou I, Wilson C, Read KD, Gilbert IH, Swedlow JR, Martins da Silva S, Barratt CLR. Compounds enhancing human sperm motility identified using a high-throughput phenotypic screening platform. Hum Reprod 2022; 37:466-475. [PMID: 35048946 PMCID: PMC8888995 DOI: 10.1093/humrep/deac007] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/04/2021] [Indexed: 12/14/2022] Open
Abstract
STUDY QUESTION Can a high-throughput screening (HTS) platform facilitate male fertility drug discovery? SUMMARY ANSWER An HTS platform identified a large number of compounds that enhanced sperm motility. WHAT IS KNOWN ALREADY Several efforts to find small molecules modulating sperm function have been performed but none have used high-throughput technology. STUDY DESIGN, SIZE, DURATION Healthy donor semen samples were used and samples were pooled (3-5 donors per pool). Primary screening was performed singly; dose-response screening was performed in duplicate (using independent donor pools). PARTICIPANTS/MATERIALS, SETTING, METHODS Spermatozoa isolated from healthy donors were prepared by density gradient centrifugation and incubated in 384-well plates with compounds (6.25 μM) to identify those compounds with enhancing effects on motility. Approximately 17 000 compounds from the libraries, ReFRAME, Prestwick, Tocris, LOPAC, CLOUD and MMV Pathogen Box, were screened. Dose-response experiments of screening hits were performed to confirm the enhancing effect on sperm motility. Experiments were performed in a university setting. MAIN RESULTS AND THE ROLE OF CHANCE From our primary single concentration screening, 105 compounds elicited an enhancing effect on sperm motility compared to dimethylsulphoxide-treated wells. Confirmed enhancing compounds were grouped based on their annotated targets/target classes. A major target class, phosphodiesterase inhibitors, were identified, in particular PDE10A inhibitors as well as number of compounds not previously known to enhance human sperm motility, such as those related to GABA signalling. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION Although this approach provides data about the activity of the compound, it is only a starting point. For example, further substantive experiments are necessary to provide a more comprehensive picture of each compound's activity, the effect on the kinetics of the cell populations and subpopulations, and their potential mechanisms of action. Compounds have been tested with prepared donor spermatozoa, incubated under non-capacitating conditions, and only incubated with compounds for a relatively short period of time. Therefore, the effect of compounds under different conditions, for example in whole semen, for longer incubation times, or using samples from patient groups, may be different and require further study. All experiments were performed in vitro. WIDER IMPLICATIONS OF THE FINDINGS This phenotypic screening assay identified a large number of compounds that increased sperm motility. In addition to furthering our understanding of human sperm function, for example identifying new avenues for discovery, we highlight potential compounds as promising start-point for a medicinal chemistry programme for potential enhancement of male fertility. Moreover, with disclosure of the results of screening, we present a substantial resource to inform further work in the field. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by the Bill and Melinda Gates Foundation, Scottish Funding Council and Scottish Universities Life Science Alliance. C.L.R.B. is Editor for RBMO. C.L.R.B. receives funding from Chief Scientists Office (Scotland), ESHRE and Genus PLC, consulting fees from Exscientia and lecture fees from Cooper Surgical and Ferring. S.M.d.S. is an Associate Editor of Human Reproduction, and an Associate Editor of Reproduction and Fertility. S.M.d.S. receives funding from Cooper Surgical and British Dietetic Society. No other authors declared a COI.
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Affiliation(s)
- Franz S Gruber
- National Phenotypic Screening Centre, School of Life Sciences, University of Dundee, Dundee, UK
| | - Zoe C Johnston
- Reproductive Medicine Research Group, Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Neil R Norcross
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discover, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Irene Georgiou
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discover, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Caroline Wilson
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discover, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Kevin D Read
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discover, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Ian H Gilbert
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discover, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Jason R Swedlow
- National Phenotypic Screening Centre, School of Life Sciences, University of Dundee, Dundee, UK
- Division of Computational Biology and Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Sarah Martins da Silva
- Reproductive Medicine Research Group, Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Christopher L R Barratt
- Reproductive Medicine Research Group, Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
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9
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Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. MITI minimum information guidelines for highly multiplexed tissue images. Nat Methods 2022; 19:262-267. [PMID: 35277708 PMCID: PMC9009186 DOI: 10.1038/s41592-022-01415-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition, curation and release. We describe a Minimum Information about highly multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology.
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Affiliation(s)
- Denis Schapiro
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
| | - Artem Sokolov
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Yu-An Chen
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, OR, USA
| | - Yubin Xie
- Program in Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeremy Muhlich
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Raquel Arias-Camison
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Sarah Arena
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | | | | | - Madison Tyler
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Erik A Burlingame
- Oregon Health and Science University, Portland, OR, USA
- Indica Labs, Albuquerque, NM, USA
| | - Young H Chang
- Oregon Health and Science University, Portland, OR, USA
| | - Samouil L Farhi
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Julia L Drewes
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dana Pe'er
- Program in Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Markus D Herrmann
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter Bankhead
- Edinburgh Pathology, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Joseph T Roland
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - John M Herndon
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Michael Angelo
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Garry Nolan
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Jason R Swedlow
- Division of Computational Biology and Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Nikolaus Schultz
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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10
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Boehm U, Nelson G, Brown CM, Bagley S, Bajcsy P, Bischof J, 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, Nitschke R. Author Correction: QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy. Nat Methods 2022; 19:256. [PMID: 34980905 DOI: 10.1038/s41592-021-01387-x] [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: 11/09/2022]
Affiliation(s)
- Ulrike Boehm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Glyn Nelson
- Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Claire M Brown
- Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada
| | - Steve Bagley
- Visualisation, Irradiation & Analysis, Cancer Research UK Manchester Institute, Alderley Park, Macclesfield, UK
| | - Peter Bajcsy
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Aurelien Dauphin
- Unite 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, UK
| | - John E Eriksson
- Turku Bioscience Centre, Euro-Bioimaging ERIC, Turku, Finland
| | - Orestis Faklaris
- BCM, University of Montpellier, CNRS, INSERM, Montpellier, France
| | | | - 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, Leuven, Flanders, Belgium.,VIB-KU Leuven Center for Brain and Disease, Leuven, Flanders, Belgium.,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 (BAM), Berlin, Germany
| | - Lucas C Schuetz
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
| | - Arne Seitz
- Faculty of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | | | - Jason R Swedlow
- Divisions of Computational Biology and Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Roland Nitschke
- Life Imaging Center and Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs University, Freiburg, Germany.
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11
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Moore J, Allan C, Besson S, Burel JM, Diel E, Gault D, Kozlowski K, Lindner D, Linkert M, Manz T, Moore W, Pape C, Tischer C, Swedlow JR. OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies. Nat Methods 2021; 18:1496-1498. [PMID: 34845388 PMCID: PMC8648559 DOI: 10.1038/s41592-021-01326-w] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/19/2021] [Indexed: 02/04/2023]
Abstract
The rapid pace of innovation in biological imaging and the diversity of its applications have prevented the establishment of a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging. Critically, a common metadata format used in all these vessels can deliver truly findable, accessible, interoperable and reusable bioimaging data.
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Affiliation(s)
| | | | | | | | - Erin Diel
- Glencoe Software, Inc., Seattle, WA, USA
| | | | | | | | | | | | | | - Constantin Pape
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Jason R Swedlow
- University of Dundee, Dundee, UK.
- Glencoe Software, Inc., Seattle, WA, USA.
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12
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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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13
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Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A. REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. Nat Methods 2021; 18:1418-1422. [PMID: 34021280 DOI: 10.1038/s41592-021-01166-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford and SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | | | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jean-Karim Hériché
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andrii Iudin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | - Terry Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.,Kymab Ltd., Babraham Research Campus, Cambridge, UK
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | - Helen R Saibil
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
| | | | - Jason R Swedlow
- Division of Computational Biology and Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Christian Tischer
- Centre for Bioimage Analysis, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Virginie Uhlmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Mary Barlow
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Cesare Catavitello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.,Ebury UK, London, UK
| | - Christopher Cawthorne
- Nuclear Medicine and Molecular Imaging, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | | | - Elizabeth Duke
- Diamond Light Source, Harwell Science and Innovation Campus, Harwell, UK.,European Molecular Biology Laboratory, Hamburg, Germany
| | - Perrine Paul-Gilloteaux
- Université de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France.,Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, Nantes, France
| | - Emmanuel Gustin
- Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science and Innovation Campus, Harwell, UK
| | - Pasi Kankaanpää
- Turku BioImaging, University of Turku and Åbo Akademi University, Turku, Finland.,Euro-BioImaging ERIC, Turku, Finland
| | | | - Jo McEntyre
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Josh Moore
- Division of Computational Biology and Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | | | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | | | | | - Jim Swoger
- European Molecular Biology Laboratory, Barcelona, Spain
| | - Nadine Utz
- German BioImaging e.V., University of Konstanz, Konstanz, Germany
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frances Wong
- Division of Computational Biology and Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Peijun Zhang
- Diamond Light Source, Harwell Science and Innovation Campus, Harwell, UK.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gerard J Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
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14
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Swedlow JR, Kankaanpää P, Sarkans U, Goscinski W, Galloway G, Malacrida L, Sullivan RP, Härtel S, Brown CM, Wood C, Keppler A, Paina F, Loos B, Zullino S, Longo DL, Aime S, Onami S. A global view of standards for open image data formats and repositories. Nat Methods 2021; 18:1440-1446. [PMID: 33948027 DOI: 10.1038/s41592-021-01113-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jason R Swedlow
- Divisions of Computational Biology and Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Pasi Kankaanpää
- Turku BioImaging, Åbo Akademi University and University of Turku, Turku, Finland.,Euro-BioImaging ERIC, Turku, Finland
| | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Wojtek Goscinski
- Monash eResearch Centre, Monash University, Melbourne, Victoria, Australia
| | - Graham Galloway
- National Imaging Facility, The University of Queensland, Brisbane, Queensland, Australia
| | - Leonel Malacrida
- Advanced Bioimaging Unit, Institut Pasteur Montevideo and Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Ryan P Sullivan
- Microscopy Australia, The University of Sydney, Sydney, Australia
| | - Steffen Härtel
- National Center for Health Information Systems (CENS), Center for Medical Informatics and Telemedicine (CIMT), and Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago, Chile
| | - Claire M Brown
- Advanced BioImaging Facility (ABIF), McGill University and Canada BioImaging, Montreal, Quebec, Canada
| | - Christopher Wood
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Antje Keppler
- Euro-BioImaging Bio-Hub, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Federica Paina
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Ben Loos
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Sara Zullino
- Molecular Imaging Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Euro-BioImaging ERIC, Torino, Italy
| | - Dario Livio Longo
- Institute of Biostructures and Bioimaging (IBB), National Research Council of Italy (CNR), Torino, Italy
| | - Silvio Aime
- Molecular Imaging Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Euro-BioImaging ERIC, Torino, Italy
| | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
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15
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Gonzalez-Beltran AN, Masuzzo P, Ampe C, Bakker GJ, Besson S, Eibl RH, Friedl P, Gunzer M, Kittisopikul M, Dévédec SEL, Leo S, Moore J, Paran Y, Prilusky J, Rocca-Serra P, Roudot P, Schuster M, Sergeant G, Strömblad S, Swedlow JR, van Erp M, Van Troys M, Zaritsky A, Sansone SA, Martens L. Community standards for open cell migration data. Gigascience 2020; 9:giaa041. [PMID: 32396199 PMCID: PMC7317087 DOI: 10.1093/gigascience/giaa041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/08/2023] Open
Abstract
Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited owing to the diversity of experimental protocols and non-standardized output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardized data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardization efforts by the Cell Migration Standardisation Organisation (CMSO), an open community-driven organization to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration.
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Affiliation(s)
- Alejandra N Gonzalez-Beltran
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford OX1 3QG, Oxford, UK
| | - Paola Masuzzo
- VIB-UGent Center for Medical Biotechnology, VIB, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
- Institute for Globally Distributed Open Research and Education (IGDORE), Kabupaten Gianyar, Bali 80571, Indonesia
| | - Christophe Ampe
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Gert-Jan Bakker
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands
| | - Sébastien Besson
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK
| | - Robert H Eibl
- German Cancer Research Center, DKFZ Alumni Association, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Peter Friedl
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands
- David H. Koch Center for Applied Genitourinary Medicine, UT MD Anderson Cancer Center, 6767 Bertner Ave, Mitchell Basic Science Research Building, 77030 Houston, TX, USA
- Cancer Genomics Center, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
- Leibniz Institute for Analytical Sciences, ISAS, Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany
| | - Mark Kittisopikul
- Department of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390, USA
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, PO box 9502 2300 RA Leiden, The Netherlands
| | - Simone Leo
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK
- Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Loc. Piscina Manna, Edificio 1, 09050 Pula (CA) , Italy
| | - Josh Moore
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK
| | - Yael Paran
- IDEA Bio-Medical Ltd, 2 Prof. Bergman St., Rehovot 76705, Israel
| | - Jaime Prilusky
- Life Science Core Facilities, Weizmann Institute of Science, P.O. Box 26 Rehovot 76100, Israel
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford OX1 3QG, Oxford, UK
| | - Philippe Roudot
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390, USA
| | - Marc Schuster
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
| | - Gwendolien Sergeant
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Staffan Strömblad
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, SE-141 83 Huddinge, Sweden
| | - Jason R Swedlow
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK
| | - Merijn van Erp
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands
| | - Marleen Van Troys
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Assaf Zaritsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, P.O.B. 653, 8410501 Beer-Sheva, Israel
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford OX1 3QG, Oxford, UK
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
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16
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Zdańkowski P, Trusiak M, McGloin D, Swedlow JR. Numerically Enhanced Stimulated Emission Depletion Microscopy with Adaptive Optics for Deep-Tissue Super-Resolved Imaging. ACS Nano 2020; 14:394-405. [PMID: 31841303 DOI: 10.1021/acsnano.9b05891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In stimulated emission depletion (STED) nanoscopy, the major origin of decreased signal-to-noise ratio within images can be attributed to sample photobleaching and strong optical aberrations. This is due to STED utilizing a high-power depletion laser (increasing the risk of photodamage), while the depletion beam is very sensitive to sample-induced aberrations. Here, we demonstrate a custom-built STED microscope with automated aberration correction that is capable of 3D super-resolution imaging through thick, highly aberrating tissue. We introduce and investigate a state of the art image denoising method by block-matching and collaborative 3D filtering (BM3D) to numerically enhance fine object details otherwise mixed with noise and further enhance the image quality. Numerical denoising provides an increase in the final effective resolution of the STED imaging of 31% using the well established Fourier ring correlation metric. Results achieved through the combination of aberration correction and tailored image processing are experimentally validated through super-resolved 3D imaging of axons in differentiated induced pluripotent stem cells growing under an 80 μm thick layer of tissue with lateral and axial resolution of 204 and 310 nm, respectively.
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Affiliation(s)
- Piotr Zdańkowski
- Centre for Gene Regulation and Expression, School of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
- SUPA, School of Science and Engineering , University of Dundee , Dundee DD1 4HN , United Kingdom
- Institute of Micromechanics and Photonics , Warsaw University of Technology , 8 A. Boboli Street , Warsaw 02-525 , Poland
| | - Maciej Trusiak
- Institute of Micromechanics and Photonics , Warsaw University of Technology , 8 A. Boboli Street , Warsaw 02-525 , Poland
| | - David McGloin
- SUPA, School of Science and Engineering , University of Dundee , Dundee DD1 4HN , United Kingdom
- School of Electrical and Data Engineering , University of Technology Sydney , Ultimo , New South Wales 2007 , Australia
| | - Jason R Swedlow
- Centre for Gene Regulation and Expression, School of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
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17
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Besson S, Leigh R, Linkert M, Allan C, Burel JM, Carroll M, Gault D, Gozim R, Li S, Lindner D, Moore J, Moore W, Walczysko P, Wong F, Swedlow JR. Bringing Open Data to Whole Slide Imaging. Digit Pathol (2019) 2019; 2019:3-10. [PMID: 31579322 DOI: 10.1007/978-3-030-23937-4_1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Faced with the need to support a growing number of whole slide imaging (WSI) file formats, our team has extended a long-standing community file format (OME-TIFF) for use in digital pathology. The format makes use of the core TIFF specification to store multi-resolution (or "pyramidal") representations of a single slide in a flexible, performant manner. Here we describe the structure of this format, its performance characteristics, as well as an open-source library support for reading and writing pyramidal OME-TIFFs.
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Affiliation(s)
- Sébastien Besson
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Roger Leigh
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Melissa Linkert
- Glencoe Software, Inc, 800 5th Ave, #101-259, Seattle, WA 98104, USA
| | - Chris Allan
- Glencoe Software, Inc, 800 5th Ave, #101-259, Seattle, WA 98104, USA
| | - Jean-Marie Burel
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Mark Carroll
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - David Gault
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Riad Gozim
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Simon Li
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Dominik Lindner
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Josh Moore
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Will Moore
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Petr Walczysko
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Frances Wong
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Jason R Swedlow
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom.,Glencoe Software, Inc, 800 5th Ave, #101-259, Seattle, WA 98104, USA
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18
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Zdankowski P, McGloin D, Swedlow JR. Full volume super-resolution imaging of thick mitotic spindle using 3D AO STED microscope. Biomed Opt Express 2019; 10:1999-2009. [PMID: 31086714 PMCID: PMC6484978 DOI: 10.1364/boe.10.001999] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/09/2019] [Accepted: 02/11/2019] [Indexed: 05/08/2023]
Abstract
Stimulated emission depletion (STED) nanoscopy is one of a suite of modern optical microscopy techniques capable of bypassing the conventional diffraction limit in fluorescent imaging. STED makes use of a spiral phase mask to enable 2D super-resolution imaging whereas to achieve full volumetric 3D super-resolution an additional bottle-beam phase mask must be applied. The resolution achieved in biological samples 10 µm or thicker is limited by aberrations induced mainly by scattering due to refractive index heterogeneity in the sample. These aberrations impact the fidelity of both types of phase mask, and have limited the application of STED to thicker biological systems. Here we apply an automated adaptive optics solution to correct the performance of both STED masks, enhancing robustness and expanding the capabilities of this nanoscopic technique. Corroboration in terms of successful high-quality imaging of the full volume of a 15µm mitotic spindle with resolution of 50nm x 50nm x 150nm achieved in all three dimensions is presented.
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Affiliation(s)
- Piotr Zdankowski
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
- SUPA, School of Science and Engineering, University of Dundee, Dundee, DD1 4HN UK
- Warsaw University of Technology, Institute of Micromechanics and Photonics, 8 A. Boboli St., 02-525 Warsaw, Poland
| | - David McGloin
- SUPA, School of Science and Engineering, University of Dundee, Dundee, DD1 4HN UK
- School of Electrical and Data Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Jason R. Swedlow
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
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19
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O'Donoghue SI, Baldi BF, Clark SJ, Darling AE, Hogan JM, Kaur S, Maier-Hein L, McCarthy DJ, Moore WJ, Stenau E, Swedlow JR, Vuong J, Procter JB. Visualization of Biomedical Data. Annu Rev Biomed Data Sci 2018. [DOI: 10.1146/annurev-biodatasci-080917-013424] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The rapid increase in volume and complexity of biomedical data requires changes in research, communication, and clinical practices. This includes learning how to effectively integrate automated analysis with high–data density visualizations that clearly express complex phenomena. In this review, we summarize key principles and resources from data visualization research that help address this difficult challenge. We then survey how visualization is being used in a selection of emerging biomedical research areas, including three-dimensional genomics, single-cell RNA sequencing (RNA-seq), the protein structure universe, phosphoproteomics, augmented reality–assisted surgery, and metagenomics. While specific research areas need highly tailored visualizations, there are common challenges that can be addressed with general methods and strategies. Also common, however, are poor visualization practices. We outline ongoing initiatives aimed at improving visualization practices in biomedical research via better tools, peer-to-peer learning, and interdisciplinary collaboration with computer scientists, science communicators, and graphic designers. These changes are revolutionizing how we see and think about our data.
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Affiliation(s)
- Seán I. O'Donoghue
- Data61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Eveleigh NSW 2015, Australia
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW), Kensington NSW 2033, Australia
| | - Benedetta Frida Baldi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
| | - Susan J. Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
| | - Aaron E. Darling
- The ithree Institute, University of Technology Sydney, Ultimo NSW 2007, Australia
| | - James M. Hogan
- School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane QLD, 4000, Australia
| | - Sandeep Kaur
- School of Computer Science and Engineering, University of New South Wales (UNSW), Kensington NSW 2033, Australia
| | - Lena Maier-Hein
- Division of Computer Assisted Medical Interventions (CAMI), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Davis J. McCarthy
- European Bioinformatics Institute (EBI), European Molecular Biology Laboratory (EMBL), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- St. Vincent's Institute of Medical Research, Fitzroy VIC 3065, Australia
| | - William J. Moore
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Esther Stenau
- Division of Computer Assisted Medical Interventions (CAMI), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jason R. Swedlow
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Jenny Vuong
- Data61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Eveleigh NSW 2015, Australia
| | - James B. Procter
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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20
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Ostrowski A, Cianfanelli FR, Porter M, Mariano G, Peltier J, Wong JJ, Swedlow JR, Trost M, Coulthurst SJ. Killing with proficiency: Integrated post-translational regulation of an offensive Type VI secretion system. PLoS Pathog 2018; 14:e1007230. [PMID: 30052683 PMCID: PMC6082577 DOI: 10.1371/journal.ppat.1007230] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/08/2018] [Accepted: 07/17/2018] [Indexed: 11/20/2022] Open
Abstract
The Type VI secretion system (T6SS) is widely used by bacterial pathogens as an effective weapon against bacterial competitors and is also deployed against host eukaryotic cells in some cases. It is a contractile nanomachine which delivers toxic effector proteins directly into target cells by dynamic cycles of assembly and firing. Bacterial cells adopt distinct post-translational regulatory strategies for deployment of the T6SS. 'Defensive' T6SSs assemble and fire in response to incoming attacks from aggressive neighbouring cells, and can utilise the Threonine Protein Phosphorylation (TPP) regulatory pathway to achieve this control. However, many T6SSs are 'offensive', firing at all-comers without the need for incoming attack or other cell contact-dependent signal. Post-translational control of the offensive mode has been less well defined but can utilise components of the same TPP pathway. Here, we used the anti-bacterial T6SS of Serratia marcescens to elucidate post-translational regulation of offensive T6SS deployment, using single-cell microscopy and genetic analyses. We show that the integration of the TPP pathway with the negative regulator TagF to control core T6SS machine assembly is conserved between offensive and defensive T6SSs. Signal-dependent PpkA-mediated phosphorylation of Fha is required to overcome inhibition of membrane complex assembly by TagF, whilst PppA-mediated dephosphorylation promotes spatial reorientation and efficient killing. In contrast, the upstream input of the TPP pathway defines regulatory strategy, with a new periplasmic regulator, RtkS, shown to interact with the PpkA kinase in S. marcescens. We propose a model whereby the opposing actions of the TPP pathway and TagF impose a delay on T6SS re-assembly after firing, providing an opportunity for spatial re-orientation of the T6SS in order to maximise the efficiency of competitor cell targeting. Our findings provide a better understanding of how bacterial cells deploy competitive weapons effectively, with implications for the structure and dynamics of varied polymicrobial communities.
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Affiliation(s)
- Adam Ostrowski
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Francesca R. Cianfanelli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michael Porter
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Giuseppina Mariano
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Julien Peltier
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jun Jie Wong
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jason R. Swedlow
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Matthias Trost
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, United Kingdom
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sarah J. Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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21
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Schleicher K, Porter M, Ten Have S, Sundaramoorthy R, Porter IM, Swedlow JR. The Ndc80 complex targets Bod1 to human mitotic kinetochores. Open Biol 2018; 7:rsob.170099. [PMID: 29142109 PMCID: PMC5717335 DOI: 10.1098/rsob.170099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 04/25/2017] [Accepted: 10/16/2017] [Indexed: 12/26/2022] Open
Abstract
Regulation of protein phosphatase activity by endogenous protein inhibitors is an important mechanism to control protein phosphorylation in cells. We recently identified Biorientation defective 1 (Bod1) as a small protein inhibitor of protein phosphatase 2A containing the B56 regulatory subunit (PP2A-B56). This phosphatase controls the amount of phosphorylation of several kinetochore proteins and thus the establishment of load-bearing chromosome-spindle attachments in time for accurate separation of sister chromatids in mitosis. Like PP2A-B56, Bod1 directly localizes to mitotic kinetochores and is required for correct segregation of mitotic chromosomes. In this report, we have probed the spatio-temporal regulation of Bod1 during mitotic progression. Kinetochore localization of Bod1 increases from nuclear envelope breakdown until metaphase. Phosphorylation of Bod1 at threonine 95 (T95), which increases Bod1's binding to and inhibition of PP2A-B56, peaks in prometaphase when PP2A-B56 localization to kinetochores is highest. We demonstrate here that kinetochore targeting of Bod1 depends on the outer kinetochore protein Ndc80 and not PP2A-B56. Crucially, Bod1 depletion functionally affects Ndc80 phosphorylation at the N-terminal serine 55 (S55), as well as a number of other phosphorylation sites within the outer kinetochore, including Knl1 at serine 24 and 60 (S24, S60), and threonine T943 and T1155 (T943, T1155). Therefore, Ndc80 recruits a phosphatase inhibitor to kinetochores which directly feeds forward to regulate Ndc80, and Knl1 phosphorylation, including sites that mediate the attachment of microtubules to kinetochores.
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Affiliation(s)
- Katharina Schleicher
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael Porter
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Sara Ten Have
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Iain M Porter
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Jason R Swedlow
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
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22
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Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ. Building bridges between cellular and molecular structural biology. eLife 2017; 6:e25835. [PMID: 28682240 PMCID: PMC5524535 DOI: 10.7554/elife.25835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/30/2017] [Indexed: 11/13/2022] Open
Abstract
The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.
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Affiliation(s)
- Ardan Patwardhan
- Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Sarah J Butcher
- Institute of Biotechnology and the Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, London, United Kingdom
| | - David Gault
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Corey Hecksel
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Andrii Iudin
- Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Martin L Jones
- Electron Microscopy Science Technology Platform, Francis Crick Institute, London, United Kingdom
| | - Paul K Korir
- Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Abraham J Koster
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ingvar Lagerstedt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Catherine L Lawson
- Center for Integrative Proteomics Research and the Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Piscataway, United States
| | - David Mastronarde
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, United States
| | | | - Helen Parkinson
- Molecular Archival Resources, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses, Francis Crick Institute, London, United Kingdom
| | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Helen R Saibil
- Institute of Structural and Molecular Biology, Department of Crystallography, Birkbeck College, London, United Kingdom
| | - Sirarat Sarntivijai
- Molecular Archival Resources, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Irene Solanes Valero
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Sriram Subramaniam
- Laboratory for Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Jason R Swedlow
- Centre for Gene Regulation and Expression and the Division of Computational Biology, University of Dundee, Dundee, United Kingdom
| | - Ilinca Tudose
- Molecular Archival Resources, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Martyn Winn
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot, United Kingdom
| | - Gerard J Kleywegt
- Molecular and Cellular Structure Cluster, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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23
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Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR. The Image Data Resource: A Bioimage Data Integration and Publication Platform. Nat Methods 2017; 14:775-781. [PMID: 28775673 PMCID: PMC5536224 DOI: 10.1038/nmeth.4326] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This Resource describes the Image Data Resource (IDR), a prototype online system for biological image data that links experimental and analytic data across multiple data sets and promotes image data sharing and reanalysis. Access to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR). IDR links data from several imaging modalities, including high-content screening, multi-dimensional microscopy and digital pathology, with public genetic or chemical databases and cell and tissue phenotypes expressed using controlled ontologies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable reanalysis, we also established a computational resource based on Jupyter notebooks that allows remote access to the entire IDR. IDR is also an open-source platform for publishing imaging data. Thus IDR provides an online resource and a software infrastructure that promotes and extends publication and reanalysis of scientific image data.
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Affiliation(s)
- Eleanor Williams
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Josh Moore
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Simon W Li
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Gabriella Rustici
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Aleksandra Tarkowska
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Anatole Chessel
- Pharmacology & Genetics Departments and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, Palaiseau, France
| | - Simone Leo
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK.,Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Pula(CA), Italy
| | - Bálint Antal
- Pharmacology & Genetics Departments and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Richard K Ferguson
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
| | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Rafael E Carazo Salas
- Pharmacology & Genetics Departments and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,School of Cell and Molecular Medicine, University of Bristol, Bristol, UK
| | - Jason R Swedlow
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK
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24
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Esmaeeli-Nieh S, Fenckova M, Porter IM, Motazacker MM, Nijhof B, Castells-Nobau A, Asztalos Z, Weißmann R, Behjati F, Tzschach A, Felbor U, Scherthan H, Sayfati SM, Ropers HH, Kahrizi K, Najmabadi H, Swedlow JR, Schenck A, Kuss AW. BOD1 Is Required for Cognitive Function in Humans and Drosophila. PLoS Genet 2016; 12:e1006022. [PMID: 27166630 PMCID: PMC4864283 DOI: 10.1371/journal.pgen.1006022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 04/08/2016] [Indexed: 11/19/2022] Open
Abstract
Here we report a stop-mutation in the BOD1 (Biorientation Defective 1) gene, which co-segregates with intellectual disability in a large consanguineous family, where individuals that are homozygous for the mutation have no detectable BOD1 mRNA or protein. The BOD1 protein is required for proper chromosome segregation, regulating phosphorylation of PLK1 substrates by modulating Protein Phosphatase 2A (PP2A) activity during mitosis. We report that fibroblast cell lines derived from homozygous BOD1 mutation carriers show aberrant localisation of the cell cycle kinase PLK1 and its phosphatase PP2A at mitotic kinetochores. However, in contrast to the mitotic arrest observed in BOD1-siRNA treated HeLa cells, patient-derived cells progressed through mitosis with no apparent segregation defects but at an accelerated rate compared to controls. The relatively normal cell cycle progression observed in cultured cells is in line with the absence of gross structural brain abnormalities in the affected individuals. Moreover, we found that in normal adult brain tissues BOD1 expression is maintained at considerable levels, in contrast to PLK1 expression, and provide evidence for synaptic localization of Bod1 in murine neurons. These observations suggest that BOD1 plays a cell cycle-independent role in the nervous system. To address this possibility, we established two Drosophila models, where neuron-specific knockdown of BOD1 caused pronounced learning deficits and significant abnormalities in synapse morphology. Together our results reveal novel postmitotic functions of BOD1 as well as pathogenic mechanisms that strongly support a causative role of BOD1 deficiency in the aetiology of intellectual disability. Moreover, by demonstrating its requirement for cognitive function in humans and Drosophila we provide evidence for a conserved role of BOD1 in the development and maintenance of cognitive features.
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Affiliation(s)
- Sahar Esmaeeli-Nieh
- Department for Human Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michaela Fenckova
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, Netherlands
| | - Iain M. Porter
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - M. Mahdi Motazacker
- Department for Human Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bonnie Nijhof
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, Netherlands
| | - Anna Castells-Nobau
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, Netherlands
| | - Zoltan Asztalos
- Department Genetics, Aktogen Limited, University of Cambridge, Cambridge, United Kingdom
- Aktogen Hungary Ltd., Bay Zoltán Nonprofit Ltd., Institute for Biotechnology, Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Robert Weißmann
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Farkhondeh Behjati
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Andreas Tzschach
- Department for Human Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ute Felbor
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Harry Scherthan
- Department for Human Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institut für Radiobiologie der Bundeswehr in Verbindung mit der Universität Ulm, München, Germany
| | - Seyed Morteza Sayfati
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H. Hilger. Ropers
- Department for Human Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Jason R. Swedlow
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, Netherlands
| | - Andreas W. Kuss
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
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25
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Li S, Besson S, Blackburn C, Carroll M, Ferguson RK, Flynn H, Gillen K, Leigh R, Lindner D, Linkert M, Moore WJ, Ramalingam B, Rozbicki E, Rustici G, Tarkowska A, Walczysko P, Williams E, Allan C, Burel JM, Moore J, Swedlow JR. Metadata management for high content screening in OMERO. Methods 2016; 96:27-32. [PMID: 26476368 PMCID: PMC4773399 DOI: 10.1016/j.ymeth.2015.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/13/2015] [Indexed: 01/18/2023] Open
Abstract
High content screening (HCS) experiments create a classic data management challenge-multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of "final" results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org.
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Affiliation(s)
- Simon Li
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Sébastien Besson
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Colin Blackburn
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Mark Carroll
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Richard K Ferguson
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Helen Flynn
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Kenneth Gillen
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Roger Leigh
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Dominik Lindner
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | | | - William J Moore
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Balaji Ramalingam
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | | | - Gabriella Rustici
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Aleksandra Tarkowska
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Petr Walczysko
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Eleanor Williams
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | | | - Jean-Marie Burel
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Josh Moore
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK; Glencoe Software, Inc., Seattle, WA, USA
| | - Jason R Swedlow
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK; Glencoe Software, Inc., Seattle, WA, USA.
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26
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Ortmann B, Bensaddek D, Carvalhal S, Moser SC, Mudie S, Griffis ER, Swedlow JR, Lamond AI, Rocha S. CDK-dependent phosphorylation of PHD1 on serine 130 alters its substrate preference in cells. J Cell Sci 2015; 129:191-205. [PMID: 26644182 PMCID: PMC4732302 DOI: 10.1242/jcs.179911] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/18/2015] [Indexed: 12/28/2022] Open
Abstract
PHD1 (also known as EGLN2) belongs to a family of prolyl hydroxylases (PHDs) that are involved in the control of the cellular response to hypoxia. PHD1 is also able to regulate mitotic progression through the regulation of the crucial centrosomal protein Cep192, establishing a link between the oxygen-sensing and the cell cycle machinery. Here, we demonstrate that PHD1 is phosphorylated by CDK2, CDK4 and CDK6 at S130. This phosphorylation fluctuates with the cell cycle and can be induced through oncogenic activation. Functionally, PHD1 phosphorylation leads to increased induction of hypoxia-inducible factor (HIF) protein levels and activity during hypoxia. PHD1 phosphorylation does not alter its intrinsic enzymatic activity, but instead decreases the interaction between PHD1 and HIF1α. Interestingly, although phosphorylation of PHD1 at S130 lowers its activity towards HIF1α, this modification increases the activity of PHD1 towards Cep192. These results establish a mechanism by which cell cycle mediators, such as CDKs, temporally control the activity of PHD1, directly altering the regulation of HIF1α and Cep192. Summary: CDK-mediated phosphorylation of PHD1 at serine 130 controls target specificity and confers cell cycle regulation of PHD1.
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Affiliation(s)
- Brian Ortmann
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Dalila Bensaddek
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sara Carvalhal
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sandra C Moser
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sharon Mudie
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Eric R Griffis
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jason R Swedlow
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sonia Rocha
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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27
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Burel JM, Besson S, Blackburn C, Carroll M, Ferguson RK, Flynn H, Gillen K, Leigh R, Li S, Lindner D, Linkert M, Moore WJ, Ramalingam B, Rozbicki E, Tarkowska A, Walczysko P, Allan C, Moore J, Swedlow JR. Publishing and sharing multi-dimensional image data with OMERO. Mamm Genome 2015. [PMID: 26223880 PMCID: PMC4602067 DOI: 10.1007/s00335-015-9587-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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] [Indexed: 12/28/2022]
Abstract
Imaging data are used in the life and biomedical sciences to measure the molecular and structural composition and dynamics of cells, tissues, and organisms. Datasets range in size from megabytes to terabytes and usually contain a combination of binary pixel data and metadata that describe the acquisition process and any derived results. The OMERO image data management platform allows users to securely share image datasets according to specific permissions levels: data can be held privately, shared with a set of colleagues, or made available via a public URL. Users control access by assigning data to specific Groups with defined membership and access rights. OMERO’s Permission system supports simple data sharing in a lab, collaborative data analysis, and even teaching environments. OMERO software is open source and released by the OME Consortium at www.openmicroscopy.org.
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Affiliation(s)
- Jean-Marie Burel
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Sébastien Besson
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Colin Blackburn
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Mark Carroll
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Richard K Ferguson
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Helen Flynn
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Kenneth Gillen
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Roger Leigh
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Simon Li
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Dominik Lindner
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | | | - William J Moore
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Balaji Ramalingam
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | | | - Aleksandra Tarkowska
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Petr Walczysko
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | | | - Josh Moore
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.,Glencoe Software, Inc., Seattle, WA, USA
| | - Jason R Swedlow
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK. .,Glencoe Software, Inc., Seattle, WA, USA.
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28
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Patwardhan A, Ashton A, Brandt R, Butcher S, Carzaniga R, Chiu W, Collinson L, Doux P, Duke E, Ellisman MH, Franken E, Grünewald K, Heriche JK, Koster A, Kühlbrandt W, Lagerstedt I, Larabell C, Lawson CL, Saibil HR, Sanz-García E, Subramaniam S, Verkade P, Swedlow JR, Kleywegt GJ. A 3D cellular context for the macromolecular world. Nat Struct Mol Biol 2014; 21:841-5. [PMID: 25289590 PMCID: PMC4346196 DOI: 10.1038/nsmb.2897] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community.
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Affiliation(s)
- Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | | | - Sarah Butcher
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Raffaella Carzaniga
- Electron Microscopy Unit, Cancer Research UK London Research Institute, London, UK
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Lucy Collinson
- Electron Microscopy Unit, Cancer Research UK London Research Institute, London, UK
| | - Pascal Doux
- FEI Visualization Sciences Group, Mérignac, France
| | | | - Mark H Ellisman
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego, San Diego, California, USA
| | - Erik Franken
- FEI Electron Optics B.V., Eindhoven, the Netherlands
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Jean-Karim Heriche
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Abraham Koster
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Ingvar Lagerstedt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, California, USA
| | - Catherine L Lawson
- Research Collaboratory for Structural Bioinformatics, Rutgers University, Piscataway, New Jersey, USA
| | - Helen R Saibil
- Institute of Structural and Molecular Biology, Department of Crystallography, Birkbeck College, London, UK
| | - Eduardo Sanz-García
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Sriram Subramaniam
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Paul Verkade
- Wolfson Bioimaging Facility, School of Biochemistry, University of Bristol, Bristol, UK
| | - Jason R Swedlow
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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29
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Abstract
Hypoxia or lowering of the oxygen availability is involved in many physiological and pathological processes. At the molecular level, cells initiate a particular transcriptional program in order to mount an appropriate and coordinated cellular response. The cell possesses several oxygen sensor enzymes that require molecular oxygen as cofactor for their activity. These range from prolyl-hydroxylases to histone demethylases. The majority of studies analyzing cellular responses to hypoxia are based on cellular populations and average studies, and as such single cell analysis of hypoxic cells are seldom performed. Here we describe a method of analysis of global RNA synthesis at the single cell level in hypoxia by using Click-iT RNA imaging kits in an oxygen controlled workstation, followed by microscopy analysis and quantification. Using cancer cells exposed to hypoxia for different lengths of time, RNA is labeled and measured in each cell. This analysis allows the visualization of temporal and cell-to-cell changes in global RNA synthesis following hypoxic stress.
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Affiliation(s)
- John Biddlestone
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, UK
| | - Jimena Druker
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, UK
| | - Alena Shmakova
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, UK
| | - Gus Ferguson
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, UK
| | - Jason R Swedlow
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, UK
| | - Sonia Rocha
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, UK;
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30
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Lagerstedt I, Moore WJ, Patwardhan A, Sanz-García E, Best C, Swedlow JR, Kleywegt GJ. Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB. J Struct Biol 2013; 184:173-81. [PMID: 24113529 PMCID: PMC3898923 DOI: 10.1016/j.jsb.2013.09.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 11/25/2022]
Abstract
The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed.
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Affiliation(s)
- Ingvar Lagerstedt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - William J. Moore
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Eduardo Sanz-García
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Christoph Best
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Jason R. Swedlow
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Gerard J. Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, United Kingdom
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31
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Moser SC, Bensaddek D, Ortmann B, Maure JF, Mudie S, Blow JJ, Lamond AI, Swedlow JR, Rocha S. PHD1 links cell-cycle progression to oxygen sensing through hydroxylation of the centrosomal protein Cep192. Dev Cell 2013; 26:381-92. [PMID: 23932902 PMCID: PMC3757158 DOI: 10.1016/j.devcel.2013.06.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [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: 10/10/2012] [Revised: 05/13/2013] [Accepted: 06/13/2013] [Indexed: 01/08/2023]
Abstract
PHD1 belongs to the family of prolyl-4-hydroxylases (PHDs) that is responsible for posttranslational modification of prolines on specific target proteins. Because PHD activity is sensitive to oxygen levels and certain byproducts of the tricarboxylic acid cycle, PHDs act as sensors of the cell’s metabolic state. Here, we identify PHD1 as a critical molecular link between oxygen sensing and cell-cycle control. We show that PHD1 function is required for centrosome duplication and maturation through modification of the critical centrosome component Cep192. Importantly, PHD1 is also required for primary cilia formation. Cep192 is hydroxylated by PHD1 on proline residue 1717. This hydroxylation is required for binding of the E3 ubiquitin ligase SCFSkp2, which ubiquitinates Cep192, targeting it for proteasomal degradation. By modulating Cep192 levels, PHD1 thereby affects the processes of centriole duplication and centrosome maturation and contributes to the regulation of cell-cycle progression. The prolyl-4-hydroxylase PHD1 is required for mitotic progression PHD1 hydroxylates centrosomal protein Cep192 in vitro and in vivo Hydroxylation of Cep192 at Pro1717 modulates Cep192 stability and function Hydroxylation of Cep192 is required for E3 ligase SCFSkp2 binding to Cep192
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Affiliation(s)
- Sandra C Moser
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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32
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Beck J, Maerki S, Posch M, Metzger T, Persaud A, Scheel H, Hofmann K, Rotin D, Pedrioli P, Swedlow JR, Peter M, Sumara I. Ubiquitylation-dependent localization of PLK1 in mitosis. Nat Cell Biol 2013; 15:430-9. [PMID: 23455478 PMCID: PMC7116173 DOI: 10.1038/ncb2695] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 01/18/2013] [Indexed: 11/09/2022]
Abstract
Polo-like kinase 1 (PLK1) critically regulates mitosis through its dynamic localization to kinetochores, centrosomes and the midzone. The polo-box domain (PBD) and activity of PLK1 mediate its recruitment to mitotic structures, but the mechanisms regulating PLK1 dynamics remain poorly understood. Here, we identify PLK1 as a target of the cullin 3 (CUL3)-based E3 ubiquitin ligase, containing the BTB adaptor KLHL22, which regulates chromosome alignment and PLK1 kinetochore localization but not PLK1 stability. In the absence of KLHL22, PLK1 accumulates on kinetochores, resulting in activation of the spindle assembly checkpoint (SAC). CUL3-KLHL22 ubiquitylates Lys 492, located within the PBD, leading to PLK1 dissociation from kinetochore phosphoreceptors. Expression of a non-ubiquitylatable PLK1-K492R mutant phenocopies inactivation of CUL3-KLHL22. KLHL22 associates with the mitotic spindle and its interaction with PLK1 increases on chromosome bi-orientation. Our data suggest that CUL3-KLHL22-mediated ubiquitylation signals degradation-independent removal of PLK1 from kinetochores and SAC satisfaction, which are required for faithful mitosis.
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MESH Headings
- Adaptor Proteins, Signal Transducing/antagonists & inhibitors
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Sequence
- Blotting, Western
- Cell Cycle Proteins/antagonists & inhibitors
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Centrosome/metabolism
- Chromosomes, Human/genetics
- Cullin Proteins/antagonists & inhibitors
- Cullin Proteins/genetics
- Cullin Proteins/metabolism
- HeLa Cells
- Humans
- Immunoprecipitation
- Kinetochores/metabolism
- Microscopy, Fluorescence
- Microtubules/metabolism
- Mitosis/physiology
- Molecular Sequence Data
- Phosphorylation
- Protein Array Analysis
- Protein Serine-Threonine Kinases/antagonists & inhibitors
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/antagonists & inhibitors
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA, Messenger/genetics
- RNA, Small Interfering/genetics
- Sequence Homology, Amino Acid
- Signal Transduction
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Spindle Apparatus/metabolism
- Ubiquitin/metabolism
- Ubiquitination
- Polo-Like Kinase 1
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Affiliation(s)
- Jochen Beck
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Sarah Maerki
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Markus Posch
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland
| | - Thibaud Metzger
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
| | | | | | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | | | | | - Jason R. Swedlow
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland
| | - Matthias Peter
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Izabela Sumara
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
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33
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Patwardhan A, Carazo JM, Carragher B, Henderson R, Heymann JB, Hill E, Jensen GJ, Lagerstedt I, Lawson CL, Ludtke SJ, Mastronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano COS, Sanz-García E, Scheres SHW, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Kleywegt GJ. Data management challenges in three-dimensional EM. Nat Struct Mol Biol 2013; 19:1203-7. [PMID: 23211764 DOI: 10.1038/nsmb.2426] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/24/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
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34
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Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE. Erratum: Corrigendum: Biological imaging software tools. Nat Methods 2012. [DOI: 10.1038/nmeth1012-1031b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath B, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurman N, Swedlow JR, Tomancak P, Carpenter AE. Biological imaging software tools. Nat Methods 2012; 9:697-710. [PMID: 22743775 PMCID: PMC3659807 DOI: 10.1038/nmeth.2084] [Citation(s) in RCA: 337] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the inherent challenges and the overall status of available software for bioimage informatics, focusing on open-source options.
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Affiliation(s)
| | - Michael R. Berthold
- Department of Computer and Information Science, Universität Konstanz, Konstanz, Germany
| | | | | | - B.S. Manjunath
- Center for Bio-image Informatics, Department of Electrical and Computer Engineering, University of California, Santa Barbara, California, USA
| | - Maryann E. Martone
- National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, California USA
| | - Robert F. Murphy
- Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Hanchuan Peng
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia USA
| | - Anne L. Plant
- Biochemical Science Division, NIST, Gaithersburg, Maryland, USA
| | - Badrinath Roysam
- Department of Electrical and Computer Engineering, University of Houston, Houston, Texas USA
| | - Nico Stuurman
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
| | - Jason R. Swedlow
- Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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36
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Dikovskaya D, Khoudoli G, Newton IP, Chadha GS, Klotz D, Visvanathan A, Lamond A, Swedlow JR, Näthke IS. The adenomatous polyposis coli protein contributes to normal compaction of mitotic chromatin. PLoS One 2012; 7:e38102. [PMID: 22719865 PMCID: PMC3374815 DOI: 10.1371/journal.pone.0038102] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 05/03/2012] [Indexed: 11/23/2022] Open
Abstract
The tumour suppressor Adenomatous Polyposis Coli (APC) is required for proper mitosis; however, the exact role of APC in mitosis is not understood. Using demembranated sperm chromatin exposed to meiotic Xenopus egg extract and HeLa cells expressing fluorescently labelled histones, we established that APC contributes to chromatin compaction. Sperm chromatin in APC-depleted Xenopus egg extract frequently formed tight round or elongated structures. Such abnormally compacted chromatin predominantly formed spindles with low microtubule content. Furthermore, in mitotic HeLa cells expressing GFP- and mCherry-labelled H2B histones, depletion of APC caused a decrease in the donor fluorescence lifetime of neighbouring fluorophores, indicative of excessive chromatin compaction. Profiling the chromatin-associated proteome of sperm chromatin incubated with Xenopus egg extracts revealed temporal APC-dependent changes in the abundance of histones, closely mirrored by chromatin-associated Topoisomerase IIa, condensin I complex and Kif4. In the absence of APC these factors initially accumulated on chromatin, but then decreased faster than in controls. We also found and validated significant APC-dependent changes in chromatin modifiers Set-a and Rbbp7. Both were decreased on chromatin in APC-depleted extract; in addition, the kinetics of association of Set-a with chromatin was altered in the absence of APC.
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Affiliation(s)
- Dina Dikovskaya
- Cell and Developmental Biology, University of Dundee, Dundee, Scotland, United Kingdom
| | - Guennadi Khoudoli
- Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Ian P. Newton
- Cell and Developmental Biology, University of Dundee, Dundee, Scotland, United Kingdom
| | - Gaganmeet S. Chadha
- Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Daniel Klotz
- Cell and Developmental Biology, University of Dundee, Dundee, Scotland, United Kingdom
| | - Ashwat Visvanathan
- Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Angus Lamond
- Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Jason R. Swedlow
- Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Inke S. Näthke
- Cell and Developmental Biology, University of Dundee, Dundee, Scotland, United Kingdom
- * E-mail:
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37
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Abstract
The embryonic spinal cord consists of cycling neural progenitor cells that give rise to a large percentage of the neuronal and glial cells of the central nervous system (CNS). Although much is known about the molecular mechanisms that pattern the spinal cord and elicit neuronal differentiation, we lack a deep understanding of these early events at the level of cell behavior. It is thus critical to study the behavior of neural progenitors in real time as they undergo neurogenesis. In the past, real-time imaging of early embryonic tissue has been limited by cell/tissue viability in culture as well as the phototoxic effects of fluorescent imaging. Here we present a novel assay for imaging such tissue for long periods of time, utilizing a novel ex vivo slice culture protocol and wide-field fluorescence microscopy (Fig. 1). This approach achieves long-term time-lapse monitoring of chick embryonic spinal cord progenitor cells with high spatial and temporal resolution. This assay may be modified to image a range of embryonic tissues. In addition to the observation of cellular and sub-cellular behaviors, the development of novel and highly sensitive reporters for gene activity (for example, Notch signaling) makes this assay a powerful tool with which to understand how signaling regulates cell behavior during embryonic development.
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Affiliation(s)
- Raman M Das
- Neural Development Group, Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee, UK
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38
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Abstract
The current revolution in biological microscopy stems from the realisation that advances in optics and computational tools and automation make the modern microscope an instrument that can access all scales relevant to modern biology – from individual molecules all the way to whole tissues and organisms and from single snapshots to time-lapse recordings sampling from milliseconds to days. As these and more new technologies appear, the challenges of delivering them to the community grows as well. I discuss some of these challenges, and the examples where openly shared technology have made an impact on the field.
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Affiliation(s)
- Jason R Swedlow
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland, UK.
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39
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Abstract
The arrival of electronic photodetectors in biological microscopy has led to a revolution in the application of imaging in cell and developmental biology. The extreme photosensitivity of electronic photodetectors has enabled the routine use of multidimensional data acquisition spanning space and time and spectral range in live cell and tissue imaging. These techniques have provided key insights into the molecular and structural dynamics of living biology. However, digital photodetectors offer another advantage-they provide a linear mapping between the photon flux coming from the sample and the electronic sample they produce. Thus, an image presented as a visual representation of the sample is also a quantitative measurement of photon flux. These quantitative measurements are the basis of subsequent processing and analysis to improve signal contrast, to compare changes in the concentration of signal, and to reveal changes in cell structure and dynamics. For this reason, many laboratories and companies have committed their resources to software development, resulting in the availability of a large number of image-processing and analysis packages. In this article, we review the software tools for image data analysis that are now available and give some examples of their use in imaging experiments to reveal new insights into biological mechanisms. In our final section, we highlight some of the new directions for image analysis that are significant unmet challenges and present our own ideas for future directions.
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40
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Vilas-Boas F, Fior R, Swedlow JR, Storey KG, Henrique D. A novel reporter of notch signalling indicates regulated and random Notch activation during vertebrate neurogenesis. BMC Biol 2011; 9:58. [PMID: 21880129 PMCID: PMC3201213 DOI: 10.1186/1741-7007-9-58] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [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: 07/26/2011] [Accepted: 08/31/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Building the complex vertebrate nervous system involves the regulated production of neurons and glia while maintaining a progenitor cell population. Neurogenesis starts asynchronously in different regions of the embryo and occurs over a long period of time, allowing progenitor cells to be exposed to multiple extrinsic signals that regulate the production of different cell types. Notch-mediated cell-cell signalling is one of the mechanisms that maintain the progenitor pool, however, little is known about how the timing of Notch activation is related to the cell cycle and the distinct modes of cell division that generate neurons. An essential tool with which to investigate the role of Notch signalling on cell by cell basis is the development a faithful reporter of Notch activity. RESULTS Here we present a novel reporter for Notch activity based on the promoter of the well characterised Notch target chick Hes5-1, coupled with multiple elements that confer instability, including a destabilized nuclear Venus fluorescent protein and the 3' untranslated region (UTR) of Hes5-1. We demonstrate that this reporter faithfully recapitulates the endogenous expression of Hes5-1 and that it robustly responds to Notch activation in the chick neural tube. Analysis of the patterns of Notch activity revealed by this reporter indicates that although Notch is most frequently activated prior to mitosis it can be activated at any time within the cell cycle. Notch active progenitors undergoing mitosis generate two daughters that both continue to experience Notch signalling. However, cells lacking Notch activity before and during mitosis generate daughters with dissimilar Notch activity profiles. CONCLUSIONS A novel Notch reporter with multiple destabilisation elements provides a faithful read-out of endogenous Notch activity on a cell-by-cell basis, as neural progenitors progress through the cell cycle in the chick neural tube. Notch activity patterns in this cell population provide evidence for distinct Notch signalling dynamics underlying different cell division modes and for the involvement of random initiation of Notch signalling within the neuroepithelium. These findings highlight the importance of single-cell analysis in the study of the complexity of Notch activity and provide new insights into the mechanisms underlying cell fate decisions in neural progenitors.
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Affiliation(s)
- Filipe Vilas-Boas
- Instituto de Medicina Molecular and Instituto de Histologia e Biologia do Desenvolvimento, Faculdade de Medicina da Universidade de Lisboa, Av Prof, Egas Moniz, 1649-028 Lisboa, Portugal
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41
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Affiliation(s)
- Jason R Swedlow
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland, UK.
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42
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Abstract
Proper mitotic chromosome structure is essential for faithful chromosome segregation. Mounting evidence suggests that mitotic chromosome assembly is a progressive, dynamic process that requires topoisomerase II, condensins and cohesin and the activity of several signalling molecules. Current results suggest how these different activities might interact to achieve the familiar form of the mitotic chromosome.
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Affiliation(s)
- Sandra C Moser
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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Posch M, Khoudoli GA, Swift S, King EM, Deluca JG, Swedlow JR. Sds22 regulates aurora B activity and microtubule-kinetochore interactions at mitosis. ACTA ACUST UNITED AC 2010; 191:61-74. [PMID: 20921135 PMCID: PMC2953433 DOI: 10.1083/jcb.200912046] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [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] [Indexed: 11/22/2022]
Abstract
We have studied Sds22, a conserved regulator of protein phosphatase 1 (PP1) activity, and determined its role in modulating the activity of aurora B kinase and kinetochore-microtubule interactions. Sds22 is required for proper progression through mitosis and localization of PP1 to mitotic kinetochores. Depletion of Sds22 increases aurora B T-loop phosphorylation and the rate of recovery from monastrol arrest. Phospho-aurora B accumulates at kinetochores in Sds22-depleted cells juxtaposed to critical kinetochore substrates. Sds22 modulates sister kinetochore distance and the interaction between Hec1 and the microtubule lattice and, thus, the activation of the spindle assembly checkpoint. These results demonstrate that Sds22 specifically defines PP1 function and localization in mitosis. Sds22 regulates PP1 targeting to the kinetochore, accumulation of phospho-aurora B, and force generation at the kinetochore-microtubule interface.
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Affiliation(s)
- Markus Posch
- Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, UK
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Linkert M, Rueden CT, Allan C, Burel JM, Moore W, Patterson A, Loranger B, Moore J, Neves C, Macdonald D, Tarkowska A, Sticco C, Hill E, Rossner M, Eliceiri KW, Swedlow JR. Metadata matters: access to image data in the real world. J Cell Biol 2010; 189:777-82. [PMID: 20513764 PMCID: PMC2878938 DOI: 10.1083/jcb.201004104] [Citation(s) in RCA: 624] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 05/05/2010] [Indexed: 11/22/2022] Open
Abstract
Data sharing is important in the biological sciences to prevent duplication of effort, to promote scientific integrity, and to facilitate and disseminate scientific discovery. Sharing requires centralized repositories, and submission to and utility of these resources require common data formats. This is particularly challenging for multidimensional microscopy image data, which are acquired from a variety of platforms with a myriad of proprietary file formats (PFFs). In this paper, we describe an open standard format that we have developed for microscopy image data. We call on the community to use open image data standards and to insist that all imaging platforms support these file formats. This will build the foundation for an open image data repository.
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Affiliation(s)
- Melissa Linkert
- Laboratory for Optical and Computational Instrumentation, Department of Molecular Biology, Graduate School, University of Wisconsin at Madison, Madison, WI 53711, USA
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Jaqaman K, King EM, Amaro AC, Winter JR, Dorn JF, Elliott HL, McHedlishvili N, McClelland SE, Porter IM, Posch M, Toso A, Danuser G, McAinsh AD, Meraldi P, Swedlow JR. Kinetochore alignment within the metaphase plate is regulated by centromere stiffness and microtubule depolymerases. ACTA ACUST UNITED AC 2010; 188:665-79. [PMID: 20212316 PMCID: PMC2835940 DOI: 10.1083/jcb.200909005] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [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] [Indexed: 01/11/2023]
Abstract
An automated, quantitative 4D image analysis method is used to track kinetochore dynamics in metaphase cells. During mitosis in most eukaryotic cells, chromosomes align and form a metaphase plate halfway between the spindle poles, about which they exhibit oscillatory movement. These movements are accompanied by changes in the distance between sister kinetochores, commonly referred to as breathing. We developed a live cell imaging assay combined with computational image analysis to quantify the properties and dynamics of sister kinetochores in three dimensions. We show that baseline oscillation and breathing speeds in late prometaphase and metaphase are set by microtubule depolymerases, whereas oscillation and breathing periods depend on the stiffness of the mechanical linkage between sisters. Metaphase plates become thinner as cells progress toward anaphase as a result of reduced oscillation speed at a relatively constant oscillation period. The progressive slowdown of oscillation speed and its coupling to plate thickness depend nonlinearly on the stiffness of the mechanical linkage between sisters. We propose that metaphase plate formation and thinning require tight control of the state of the mechanical linkage between sisters mediated by centromeric chromatin and cohesion.
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Platani M, Santarella-Mellwig R, Posch M, Walczak R, Swedlow JR, Mattaj IW. The Nup107-160 nucleoporin complex promotes mitotic events via control of the localization state of the chromosome passenger complex. Mol Biol Cell 2010; 20:5260-75. [PMID: 19864462 DOI: 10.1091/mbc.e09-05-0377] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human Nup107-160 nucleoporin complex plays a major role in formation of the nuclear pore complex and is localized to kinetochores in mitosis. Here we report that Seh1, a component of the Nup107-160 complex, functions in chromosome alignment and segregation by regulating the centromeric localization of Aurora B and other chromosome passenger complex proteins. Localization of CENP-E is not affected by Seh1 depletion and analysis by electron microscopy showed that microtubule kinetochore attachments are intact. Seh1-depleted cells show impaired Aurora B localization, which results in severe defects in biorientation and organization of the spindle midzone and midbody. Our results indicate that a major function of the Nup107 complex in mitosis is to ensure the proper localization of the CPC at the centromere.
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Affiliation(s)
- Melpomeni Platani
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH93JR, United Kingdom.
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Swedlow JR, Eliceiri KW. Open source bioimage informatics for cell biology. Trends Cell Biol 2009; 19:656-60. [PMID: 19833518 PMCID: PMC2789254 DOI: 10.1016/j.tcb.2009.08.007] [Citation(s) in RCA: 40] [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] [Received: 07/13/2009] [Revised: 08/23/2009] [Accepted: 08/25/2009] [Indexed: 01/02/2023]
Abstract
Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery.
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Affiliation(s)
- Jason R Swedlow
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, Scotland DD1 5EH, UK.
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Swedlow JR, Andrews PD, Platani M. In vivo imaging of mammalian cells: cell engineering and viability. Cold Spring Harb Protoc 2009; 2009:pdb.ip69. [PMID: 20147260 DOI: 10.1101/pdb.ip69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
INTRODUCTIONThere are a number of instances in which the use of live cell imaging has provided critical insight into cellular and tissue function. It has therefore become a requisite analytical tool for use in cell biology, neurobiology, and developmental biology, as well as a routine method practiced in many biomedical research laboratories. The technical requirements for performing live cell imaging include a capacity to engineer appropriate cells for the imaging experiment and access to a digital image acquisition system. The availability of fluorescent protein (FP) technology allows the molecular specificity of fluorescent markers to be used in a genetically encoded manner. In this article, we describe techniques for the generation and maintenance of fluorescently labeled cells and their use in live cell imaging experiments.
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Abstract
INTRODUCTIONLive cell imaging provides a powerful technique for the analysis of molecular dynamics within cells. Advances in imaging technology and probe design have established this approach as an important tool in modern biology. It is now possible to obtain commercial turnkey systems for digital imaging using a number of different imaging modalities. Nevertheless, it still requires considerable technical care and expertise to conduct a successful experiment. To perform a successful imaging experiment, it is important to maximize the signal-to-noise ratio (S:N) while minimizing damage to the cells. In this article, we focus on the use of fluorescence microscopy in live cell imaging, although most of the points discussed are relevant to any type of imaging. We describe many of the methods and considerations that are required for performing a successful imaging experiment in living cells. However, we do not provide a single recipe for success: The approach is much too empirical and depends on careful observation of the particular cells under investigation.
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