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Molenaar C, Weeks KL. Nucleocytoplasmic shuttling: The ins and outs of quantitative imaging. Clin Exp Pharmacol Physiol 2018; 45:1087-1094. [DOI: 10.1111/1440-1681.12969] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 04/15/2018] [Accepted: 05/03/2018] [Indexed: 11/27/2022]
Affiliation(s)
| | - Kate L Weeks
- Baker Heart and Diabetes Institute; Melbourne Victoria Australia
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2
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Day KJ, La Rivière PJ, Chandler T, Bindokas VP, Ferrier NJ, Glick BS. Improved deconvolution of very weak confocal signals. F1000Res 2017; 6:787. [PMID: 28868135 PMCID: PMC5553083 DOI: 10.12688/f1000research.11773.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/04/2017] [Indexed: 12/21/2023] Open
Abstract
Deconvolution is typically used to sharpen fluorescence images, but when the signal-to-noise ratio is low, the primary benefit is reduced noise and a smoother appearance of the fluorescent structures. 3D time-lapse (4D) confocal image sets can be improved by deconvolution. However, when the confocal signals are very weak, the popular Huygens deconvolution software erases fluorescent structures that are clearly visible in the raw data. We find that this problem can be avoided by prefiltering the optical sections with a Gaussian blur. Analysis of real and simulated data indicates that the Gaussian blur prefilter preserves meaningful signals while enabling removal of background noise. This approach is very simple, and it allows Huygens to be used with 4D imaging conditions that minimize photodamage.
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Affiliation(s)
- Kasey J. Day
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, 60637, USA
| | | | - Talon Chandler
- Department of Radiology, University of Chicago, Chicago, IL, 5841, USA
| | - Vytas P. Bindokas
- Integrated Light Microscopy Core Facility, University of Chicago, Chicago, IL, 60637, USA
| | - Nicola J. Ferrier
- Computation Institute, University of Chicago Mathematics and Computer Science, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Benjamin S. Glick
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, 60637, USA
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Day KJ, La Rivière PJ, Chandler T, Bindokas VP, Ferrier NJ, Glick BS. Improved deconvolution of very weak confocal signals. F1000Res 2017; 6:787. [PMID: 28868135 PMCID: PMC5553083 DOI: 10.12688/f1000research.11773.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/04/2017] [Indexed: 11/20/2022] Open
Abstract
Deconvolution is typically used to sharpen fluorescence images, but when the signal-to-noise ratio is low, the primary benefit is reduced noise and a smoother appearance of the fluorescent structures. 3D time-lapse (4D) confocal image sets can be improved by deconvolution. However, when the confocal signals are very weak, the popular Huygens deconvolution software erases fluorescent structures that are clearly visible in the raw data. We find that this problem can be avoided by prefiltering the optical sections with a Gaussian blur. Analysis of real and simulated data indicates that the Gaussian blur prefilter preserves meaningful signals while enabling removal of background noise. This approach is very simple, and it allows Huygens to be used with 4D imaging conditions that minimize photodamage.
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Affiliation(s)
- Kasey J Day
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, 60637, USA
| | | | - Talon Chandler
- Department of Radiology, University of Chicago, Chicago, IL, 5841, USA
| | - Vytas P Bindokas
- Integrated Light Microscopy Core Facility, University of Chicago, Chicago, IL, 60637, USA
| | - Nicola J Ferrier
- Computation Institute, University of Chicago Mathematics and Computer Science, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Benjamin S Glick
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, 60637, USA
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4
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Grossi M, Morgunova M, Cheung S, Scholz D, Conroy E, Terrile M, Panarella A, Simpson JC, Gallagher WM, O'Shea DF. Lysosome triggered near-infrared fluorescence imaging of cellular trafficking processes in real time. Nat Commun 2016; 7:10855. [PMID: 26927507 PMCID: PMC4773516 DOI: 10.1038/ncomms10855] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 01/21/2016] [Indexed: 12/22/2022] Open
Abstract
Bioresponsive NIR-fluorophores offer the possibility for continual visualization of dynamic cellular processes with added potential for direct translation to in vivo imaging. Here we show the design, synthesis and lysosome-responsive emission properties of a new NIR fluorophore. The NIR fluorescent probe design differs from typical amine functionalized lysosomotropic stains with off/on fluorescence switching controlled by a reversible phenol/phenolate interconversion. Emission from the probe is shown to be highly selective for the lysosomes in co-imaging experiments using a HeLa cell line expressing the lysosomal-associated membrane protein 1 fused to green fluorescent protein. The responsive probe is capable of real-time continuous imaging of fundamental cellular processes such as endocytosis, lysosomal trafficking and efflux in 3D and 4D. The advantage of the NIR emission allows for direct translation to in vivo tumour imaging, which is successfully demonstrated using an MDA-MB-231 subcutaneous tumour model. This bioresponsive NIR fluorophore offers significant potential for use in live cellular and in vivo imaging, for which currently there is a deficit of suitable molecular fluorescent tools.
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Affiliation(s)
- Marco Grossi
- Department of Pharmaceutical and Medicinal Chemistry, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Ireland
| | - Marina Morgunova
- Department of Pharmaceutical and Medicinal Chemistry, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Ireland
| | - Shane Cheung
- Department of Pharmaceutical and Medicinal Chemistry, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Ireland
- School of Chemistry and Chemical Biology, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dimitri Scholz
- School of Biomolecular and Biomedical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Emer Conroy
- School of Biomolecular and Biomedical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Marta Terrile
- School of Biomolecular and Biomedical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Angela Panarella
- School of Biology and Environmental Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jeremy C. Simpson
- School of Biology and Environmental Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - William M. Gallagher
- School of Biomolecular and Biomedical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Donal F. O'Shea
- Department of Pharmaceutical and Medicinal Chemistry, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Ireland
- School of Chemistry and Chemical Biology, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Michel G, Matthes HWD, Hachet-Haas M, El Baghdadi K, de Mey J, Pepperkok R, Simpson JC, Galzi JL, Lecat S. Plasma membrane translocation of REDD1 governed by GPCRs contributes to mTORC1 activation. J Cell Sci 2013; 127:773-87. [PMID: 24338366 DOI: 10.1242/jcs.136432] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The mTORC1 kinase promotes cell growth in response to growth factors by activation of receptor tyrosine kinase. It is regulated by the cellular energy level and the availability of nutrients. mTORC1 activity is also inhibited by cellular stresses through overexpression of REDD1 (regulated in development and DNA damage responses). We report the identification of REDD1 in a fluorescent live-imaging screen aimed at discovering new proteins implicated in G-protein-coupled receptor signaling, based on translocation criteria. Using a sensitive and quantitative plasma membrane localization assay based on bioluminescent resonance energy transfer, we further show that a panel of endogenously expressed GPCRs, through a Ca(2+)/calmodulin pathway, triggers plasma membrane translocation of REDD1 but not of its homolog REDD2. REDD1 and REDD2 share a conserved mTORC1-inhibitory motif characterized at the functional and structural level and differ most in their N-termini. We show that the N-terminus of REDD1 and its mTORC1-inhibitory motif participate in the GPCR-evoked dynamic interaction of REDD1 with the plasma membrane. We further identify REDD1 as a novel effector in GPCR signaling. We show that fast activation of mTORC1 by GPCRs correlates with fast and maximal translocation of REDD1 to the plasma membrane. Overexpression of functional REDD1 leads to a reduction of mTORC1 activation by GPCRs. By contrast, depletion of endogenous REDD1 protein unleashes mTORC1 activity. Thus, translocation to the plasma membrane appears to be an inactivation mechanism of REDD1 by GPCRs, which probably act by sequestering its functional mTORC1-inhibitory motif that is necessary for plasma membrane targeting.
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Affiliation(s)
- Grégory Michel
- GPCRs, Pain and Inflammation Team, UMR7242, CNRS-University of Strasbourg, LabEx Medalis, 67412 Illkirch, France
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van Teeffelen S, Shaevitz JW, Gitai Z. Image analysis in fluorescence microscopy: bacterial dynamics as a case study. Bioessays 2012; 34:427-36. [PMID: 22415868 DOI: 10.1002/bies.201100148] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Fluorescence microscopy is the primary tool for studying complex processes inside individual living cells. Technical advances in both molecular biology and microscopy have made it possible to image cells from many genetic and environmental backgrounds. These images contain a vast amount of information, which is often hidden behind various sources of noise, convoluted with other information and stochastic in nature. Accessing the desired biological information therefore requires new tools of computational image analysis and modeling. Here, we review some of the recent advances in computational analysis of images obtained from fluorescence microscopy, focusing on bacterial systems. We emphasize techniques that are readily available to molecular and cell biologists but also point out examples where problem-specific image analyses are necessary. Thus, image analysis is not only a toolkit to be applied to new images but also an integral part of the design and implementation of a microscopy experiment.
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Affiliation(s)
- Sven van Teeffelen
- Princeton University, Department of Molecular Biology, Princeton, NJ, USA
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Adanja I, Megalizzi V, Debeir O, Decaestecker C. A new method to address unmet needs for extracting individual cell migration features from a large number of cells embedded in 3D volumes. PLoS One 2011; 6:e22263. [PMID: 21789244 PMCID: PMC3137636 DOI: 10.1371/journal.pone.0022263] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 06/22/2011] [Indexed: 01/02/2023] Open
Abstract
Background In vitro cell observation has been widely used by biologists and pharmacologists for screening molecule-induced effects on cancer cells. Computer-assisted time-lapse microscopy enables automated live cell imaging in vitro, enabling cell behavior characterization through image analysis, in particular regarding cell migration. In this context, 3D cell assays in transparent matrix gels have been developed to provide more realistic in vitro 3D environments for monitoring cell migration (fundamentally different from cell motility behavior observed in 2D), which is related to the spread of cancer and metastases. Methodology/Principal Findings In this paper we propose an improved automated tracking method that is designed to robustly and individually follow a large number of unlabeled cells observed under phase-contrast microscopy in 3D gels. The method automatically detects and tracks individual cells across a sequence of acquired volumes, using a template matching filtering method that in turn allows for robust detection and mean-shift tracking. The robustness of the method results from detecting and managing the cases where two cell (mean-shift) trackers converge to the same point. The resulting trajectories quantify cell migration through statistical analysis of 3D trajectory descriptors. We manually validated the method and observed efficient cell detection and a low tracking error rate (6%). We also applied the method in a real biological experiment where the pro-migratory effects of hyaluronic acid (HA) were analyzed on brain cancer cells. Using collagen gels with increased HA proportions, we were able to evidence a dose-response effect on cell migration abilities. Conclusions/Significance The developed method enables biomedical researchers to automatically and robustly quantify the pro- or anti-migratory effects of different experimental conditions on unlabeled cell cultures in a 3D environment.
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Affiliation(s)
- Ivan Adanja
- Laboratory of Image Synthesis and Analysis (LISA), Faculty of Applied Science, Université Libre de Bruxelles (U.L.B.), Brussels, Belgium
| | - Véronique Megalizzi
- Laboratory of Toxicology, Faculty of Pharmacy, Université Libre de Bruxelles (U.L.B.), Brussels, Belgium
| | - Olivier Debeir
- Laboratory of Image Synthesis and Analysis (LISA), Faculty of Applied Science, Université Libre de Bruxelles (U.L.B.), Brussels, Belgium
| | - Christine Decaestecker
- Laboratory of Image Synthesis and Analysis (LISA), Faculty of Applied Science, Université Libre de Bruxelles (U.L.B.), Brussels, Belgium
- Laboratory of Toxicology, Faculty of Pharmacy, Université Libre de Bruxelles (U.L.B.), Brussels, Belgium
- * E-mail:
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Abstract
Movements are implicit in the chromosome behaviors of bouquet formation, pairing and synapsis during meiotic prophase. In S. cerevisiae, the positions of chromosomes, specific structures, and individual chromosomal loci marked by fluorescent fusion proteins are easily visualized in living cells. Time-lapse analyses have revealed rapid and varied chromosome movements throughout meiotic prophase. To facilitate the analysis of these movements, we have developed a simple, inexpensive, and efficient method to prepare sporulating cells for fluorescence microscopy. This method produces a monolayer of cells that progress from meiosis through spore formation, allows visualization of hundreds of cells in a single high-resolution frame and is suitable for most methods of fluorescence microscopy.
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Abstract
The light microscope has long been used to document the localization of fluorescent molecules in cell biology research. With advances in digital cameras and the discovery and development of genetically encoded fluorophores, there has been a huge increase in the use of fluorescence microscopy to quantify spatial and temporal measurements of fluorescent molecules in biological specimens. Whether simply comparing the relative intensities of two fluorescent specimens, or using advanced techniques like Förster resonance energy transfer (FRET) or fluorescence recovery after photobleaching (FRAP), quantitation of fluorescence requires a thorough understanding of the limitations of and proper use of the different components of the imaging system. Here, I focus on the parameters of digital image acquisition that affect the accuracy and precision of quantitative fluorescence microscopy measurements.
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Affiliation(s)
- Jennifer C Waters
- Harvard Medical School, Department of Cell Biology, Boston, MA 02115, USA.
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Mitochondrial complex I deficiency in GDAP1-related autosomal dominant Charcot-Marie-Tooth disease (CMT2K). Neurogenetics 2008; 10:145-50. [DOI: 10.1007/s10048-008-0166-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 11/25/2008] [Indexed: 12/13/2022]
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