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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] [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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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] [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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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] [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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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] [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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Biddlestone J, Druker J, Shmakova A, Ferguson G, Swedlow JR, Rocha S. Analysis of global RNA synthesis at the single cell level following hypoxia. J Vis Exp 2014. [PMID: 24895009 PMCID: PMC4184815 DOI: 10.3791/51420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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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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: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [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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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] [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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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] [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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Porter IM, Schleicher K, Porter M, Swedlow JR. Bod1 regulates protein phosphatase 2A at mitotic kinetochores. Nat Commun 2013; 4:2677. [PMID: 24157919 PMCID: PMC3826647 DOI: 10.1038/ncomms3677] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/26/2013] [Indexed: 12/25/2022] Open
Abstract
Mitotic entry and progression require the activation of several mitotic kinases and the proper regulation and localization of several phosphatases. The activity and localization of each of these enzymes is tightly controlled through a series of specific activators, inhibitors and regulatory subunits. Two proteins, Ensa and Arpp-19, were recently identified as specific inhibitors of PP2A-B55 and are critical for allowing full activity of Cdk1/cyclin B and entry into mitosis. Here we show that Bod1, a protein required for proper chromosome alignment at mitosis, shares sequence similarity with Ensa and Arpp-19 and specifically inhibits the kinetochore-associated PP2A-B56 holoenzyme. PP2A-B56 regulates the stability of kinetochore-microtubule attachments by dephosphorylating several kinetochore proteins. Loss of Bod1 changes the balance of phosphorylation at kinetochores, causing defects in kinetochore function. Bod1, Ensa and Arpp-19 define a family of specific PP2A inhibitors that regulate specific PP2A holoenzymes at distinct locations and points in the cell cycle.
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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 2012; 19:1203-7. [PMID: 23211764 PMCID: PMC4048199 DOI: 10.1038/nsmb.2426] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/24/2012] [Indexed: 11/09/2022]
Abstract
This report describes the outcomes of the Data Management Challenges in 3D Electron Microscopy workshop. Key topics discussed include data models, validation and raw-data archiving. The meeting participants agreed that the EMDataBank should take the lead in addressing these issues, and concrete action points were agreed upon that will have a substantial impact on the accessibility of three-dimensional EM data in biology and medicine.
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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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] [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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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] [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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Das RM, Wilcock AC, Swedlow JR, Storey KG. High-resolution live imaging of cell behavior in the developing neuroepithelium. J Vis Exp 2012:3920. [PMID: 22525126 PMCID: PMC3466664 DOI: 10.3791/3920] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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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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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Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, MacDonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR. OMERO: flexible, model-driven data management for experimental biology. Nat Methods 2012; 9:245-53. [PMID: 22373911 PMCID: PMC3437820 DOI: 10.1038/nmeth.1896] [Citation(s) in RCA: 342] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Data-intensive research depends on tools that manage multidimensional, heterogeneous datasets. We built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available at http://openmicroscopy.org/.
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Stuurman N, Swedlow JR. Software tools, data structures, and interfaces for microscope imaging. Cold Spring Harb Protoc 2012; 2012:50-61. [PMID: 22194261 DOI: 10.1101/pdb.top067504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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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43
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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] [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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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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Posch M, Khoudoli GA, Swift S, King EM, DeLuca JG, Swedlow JR. Sds22 regulates aurora B activity and microtubule-kinetochore interactions at mitosis. J Cell Biol 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] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 09/08/2010] [Indexed: 11/22/2022] Open
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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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: 639] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [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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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] [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] [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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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] [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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