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Aldebert D, Suarez B, Bettega F, Boucher E, Garnaud C, Cornet M. Easy-to-use imaging-cytometry assay to analyze chitin patterns in yeasts. J Mycol Med 2024; 34:101493. [PMID: 38945044 DOI: 10.1016/j.mycmed.2024.101493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 05/30/2024] [Accepted: 06/07/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND & AIM Pathogenic fungi are a major threat to public health, and fungal infections are becoming increasingly common and treatment resistant. Chitin, a component of the fungal cell wall, modifies host immunity and contributes to antifungal resistance. Moreover, chitin content is regulated by chitin synthases and chitinases. However, the specific roles and mechanisms remain unclear. In this study, we developed a cytometric imaging assay to quantify chitin content and identify the distribution of chitin in the yeast cell wall. METHODS The Candida albicans SC5314 and Nakaseomyces glabratus (ex. C. glabrata) ATCC2001 reference strains, as well as 106 clinical isolates, were used. Chitin content, distribution, and morphological parameters were analysed in 12 yeast species. Moreover, machine learning statistical software was used to evaluate the ability of the cytometric imaging assay to predict yeast species using the values obtained for these parameters. RESULTS Our imaging-cytometry assay was repeatable, reproducible, and sensitive to variations in chitin content in C. albicans mutants or after antifungal stimulation. The evaluated parameters classified the yeast species into the correct clade with an accuracy of 85 %. CONCLUSION Our findings demonstrate that this easy-to-use assay is an effective tool for the exploration of chitin content in yeast species.
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Affiliation(s)
- Delphine Aldebert
- Univ. Grenoble Alpes, CNRS, UMR 5525, CHU Grenoble Alpes, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France.
| | - Bastien Suarez
- Univ. Grenoble Alpes, CNRS, UMR 5525, CHU Grenoble Alpes, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - François Bettega
- Univ. Grenoble Alpes, Inserm, CHU Grenoble Alpes, HP2, 38000 Grenoble, France
| | - Emilie Boucher
- Univ. Grenoble Alpes, CNRS, UMR 5525, CHU Grenoble Alpes, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Cecile Garnaud
- Univ. Grenoble Alpes, CNRS, UMR 5525, CHU Grenoble Alpes, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Muriel Cornet
- Univ. Grenoble Alpes, CNRS, UMR 5525, CHU Grenoble Alpes, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
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2
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Bell TN, Kusi-Appiah AE, Tocci V, Lyu P, Zhu L, Zhu F, Van Winkle D, Cao H, Singh MS, Lenhert S. Scalable lipid droplet microarray fabrication, validation, and screening. PLoS One 2024; 19:e0304736. [PMID: 38968248 PMCID: PMC11226032 DOI: 10.1371/journal.pone.0304736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 05/16/2024] [Indexed: 07/07/2024] Open
Abstract
High throughput screening of small molecules and natural products is costly, requiring significant amounts of time, reagents, and operating space. Although microarrays have proven effective in the miniaturization of screening for certain biochemical assays, such as nucleic acid hybridization or antibody binding, they are not widely used for drug discovery in cell culture due to the need for cells to internalize lipophilic drug candidates. Lipid droplet microarrays are a promising solution to this problem as they are capable of delivering lipophilic drugs to cells at dosages comparable to solution delivery. However, the scalablility of the array fabrication, assay validation, and screening steps has limited the utility of this approach. Here we take several new steps to scale up the process for lipid droplet array fabrication, assay validation in cell culture, and drug screening. A nanointaglio printing process has been adapted for use with a printing press. The arrays are stabilized for immersion into aqueous solution using a vapor coating process. In addition to delivery of lipophilic compounds, we found that we are also able to encapsulate and deliver a water-soluble compound in this way. The arrays can be functionalized by extracellular matrix proteins such as collagen prior to cell culture as the mechanism for uptake is based on direct contact with the lipid delivery vehicles rather than diffusion of the drug out of the microarray spots. We demonstrate this method for delivery to 3 different cell types and the screening of 92 natural product extracts on a microarray covering an area of less than 0.1 cm2. The arrays are suitable for miniaturized screening, for instance in high biosafety level facilities where space is limited and for applications where cell numbers are limited, such as in functional precision medicine.
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Affiliation(s)
- Tracey N. Bell
- Department of Biological Science and Integrative NanoScience Institute, Florida State University, Tallahassee, Florida, United States of America
| | - Aubrey E. Kusi-Appiah
- Department of Biological Science and Integrative NanoScience Institute, Florida State University, Tallahassee, Florida, United States of America
| | - Vincent Tocci
- Department of Biological Science and Integrative NanoScience Institute, Florida State University, Tallahassee, Florida, United States of America
| | - Pengfei Lyu
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
| | - Lei Zhu
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, United States of America
| | - Fanxiu Zhu
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - David Van Winkle
- Department of Physics, Florida State University, Tallahassee, Florida, United States of America
| | - Hongyuan Cao
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
| | - Mandip S. Singh
- College of Pharmacy and Pharmaceutical Science, Florida A&M University, Tallahassee, Florida, United States of America
| | - Steven Lenhert
- Department of Biological Science and Integrative NanoScience Institute, Florida State University, Tallahassee, Florida, United States of America
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3
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Nikolic N, Anagnostidis V, Tiwari A, Chait R, Gielen F. Droplet-based methodology for investigating bacterial population dynamics in response to phage exposure. Front Microbiol 2023; 14:1260196. [PMID: 38075890 PMCID: PMC10703435 DOI: 10.3389/fmicb.2023.1260196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/23/2023] [Indexed: 02/12/2024] Open
Abstract
An alarming rise in antimicrobial resistance worldwide has spurred efforts into the search for alternatives to antibiotic treatments. The use of bacteriophages, bacterial viruses harmless to humans, represents a promising approach with potential to treat bacterial infections (phage therapy). Recent advances in microscopy-based single-cell techniques have allowed researchers to develop new quantitative methodologies for assessing the interactions between bacteria and phages, especially the ability of phages to eradicate bacterial pathogen populations and to modulate growth of both commensal and pathogen populations. Here we combine droplet microfluidics with fluorescence time-lapse microscopy to characterize the growth and lysis dynamics of the bacterium Escherichia coli confined in droplets when challenged with phage. We investigated phages that promote lysis of infected E. coli cells, specifically, a phage species with DNA genome, T7 (Escherichia virus T7) and two phage species with RNA genomes, MS2 (Emesvirus zinderi) and Qβ (Qubevirus durum). Our microfluidic trapping device generated and immobilized picoliter-sized droplets, enabling stable imaging of bacterial growth and lysis in a temperature-controlled setup. Temporal information on bacterial population size was recorded for up to 25 h, allowing us to determine growth rates of bacterial populations and helping us uncover the extent and speed of phage infection. In the long-term, the development of novel microfluidic single-cell and population-level approaches will expedite research towards fundamental understanding of the genetic and molecular basis of rapid phage-induced lysis and eco-evolutionary aspects of bacteria-phage dynamics, and ultimately help identify key factors influencing the success of phage therapy.
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Affiliation(s)
- Nela Nikolic
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
- Translational Research Exchange @ Exeter, University of Exeter, Exeter, United Kingdom
| | - Vasileios Anagnostidis
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Anuj Tiwari
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Remy Chait
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Fabrice Gielen
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
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4
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Çelebi İ, Aslan M, Ünlü MS. A spatially uniform illumination source for widefield multi-spectral optical microscopy. PLoS One 2023; 18:e0286988. [PMID: 37851606 PMCID: PMC10584126 DOI: 10.1371/journal.pone.0286988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/30/2023] [Indexed: 10/20/2023] Open
Abstract
Illumination uniformity is a critical parameter for excitation and data extraction quality in widefield biological imaging applications. However, typical imaging systems suffer from spatial and spectral non-uniformity due to non-ideal optical elements, thus require complex solutions for illumination corrections. We present Effective Uniform Color-Light Integration Device (EUCLID), a simple and cost-effective illumination source for uniformity corrections. EUCLID employs a diffuse-reflective, adjustable hollow cavity that allows for uniform mixing of light from discrete light sources and modifies the source field distribution to compensate for spatial non-uniformity introduced by optical components in the imaging system. In this study, we characterize the light coupling efficiency of the proposed design and compare the uniformity performance with the conventional method. EUCLID demonstrates a remarkable illumination improvement for multi-spectral imaging in both Nelsonian and Koehler alignment with a maximum spatial deviation of ≈ 1% across a wide field-of-view.
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Affiliation(s)
- İris Çelebi
- Department of Electrical and Computer Engineering Boston University, Boston, MA, United States of America
| | - Mete Aslan
- Department of Electrical and Computer Engineering Boston University, Boston, MA, United States of America
| | - M. Selim Ünlü
- Department of Electrical and Computer Engineering Boston University, Boston, MA, United States of America
- Department of Biomedical Engineering, Boston University, Boston, MA, United States of America
- iRiS Kinetics Inc, Boston, MA, United States of America
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5
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Besse L, Rumiac T, Reynaud-Angelin A, Messaoudi C, Soler MN, Lambert SAE, Pennaneach V. Protocol for automated multivariate quantitative-image-based cytometry analysis by fluorescence microscopy of asynchronous adherent cells. STAR Protoc 2023; 4:102446. [PMID: 37453067 PMCID: PMC10365954 DOI: 10.1016/j.xpro.2023.102446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/31/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Here, we present a protocol for multivariate quantitative-image-based cytometry (QIBC) analysis by fluorescence microscopy of asynchronous adherent cells. We describe steps for the preparation, treatment, and fixation of cells, sample staining, and imaging for QIBC. We then detail image analysis with our open source Fiji script developed for QIBC and present multiparametric data visualization. Our QIBC Fiji script integrates modern artificial-intelligence-based tools, applying deep learning, for robust automated nuclei segmentation with minimal user adjustments, a major asset for efficient QIBC analysis. For complete details on the use and execution of this protocol, please refer to Besse et al. (2023).1.
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Affiliation(s)
- Laetitia Besse
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France
| | - Typhaine Rumiac
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France; Université Paris-Saclay, CNRS UMR3348, Orsay, France; Equipe Labélisée Ligue Nationale Contre Le Cancer, 91400 Orsay, France; Inovarion, 75005 Paris, France
| | - Anne Reynaud-Angelin
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France; Université Paris-Saclay, CNRS UMR3348, Orsay, France; Equipe Labélisée Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Cédric Messaoudi
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France
| | - Marie-Noëlle Soler
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France
| | - Sarah A E Lambert
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France; Université Paris-Saclay, CNRS UMR3348, Orsay, France; Equipe Labélisée Ligue Nationale Contre Le Cancer, 91400 Orsay, France.
| | - Vincent Pennaneach
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France; Université Paris-Saclay, CNRS UMR3348, Orsay, France; Equipe Labélisée Ligue Nationale Contre Le Cancer, 91400 Orsay, France.
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6
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Watkin SAJ, Hashemi A, Thomson DR, Nock VM, Dobson RCJ, Pearce FG. Laminar flow-based microfluidic systems for molecular interaction analysis-Part 2: Data extraction, processing and analysis. Methods Enzymol 2023; 682:429-464. [PMID: 36948710 DOI: 10.1016/bs.mie.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The rate at which fluorescently-labeled biomolecules, that are flowing at a constant speed in a microfluidic channel, diffuse into an adjacent buffer stream can be used to calculate the diffusion coefficient of the molecule, which then gives a measure of its size. Experimentally, determining the rate of diffusion involves capturing concentration gradients in fluorescence microscopy images at different distances along the length of the microfluidic channel, where distance corresponds to residence time, based on the flow velocity. The preceding chapter in this journal covered the development of the experimental setup, including information about the microscope camera detection systems used to acquire fluorescence microscopy data. In order to calculate diffusion coefficients from fluorescence microscopy images, intensity data are extracted from the images and then appropriate methods of processing and analyzing the data, including the mathematical models used for fitting, are applied to the extracted data. This chapter begins with a brief overview of digital imaging and analysis principles, before introducing custom software for extracting the intensity data from the fluorescence microscopy images. Subsequently, methods and explanations for performing the necessary corrections and appropriate scaling of the data are provided. Finally, the mathematics of one-dimensional molecular diffusion is described, and analytical approaches to obtaining the diffusion coefficient from the fluorescence intensity profiles are discussed and compared.
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Affiliation(s)
- Serena A J Watkin
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Azadeh Hashemi
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Department of Electrical & Computer Engineering, University of Canterbury, Christchurch, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| | - Dion R Thomson
- Protein Science & Engineering Team, Callaghan Innovation, Christchurch, New Zealand
| | - Volker M Nock
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Department of Electrical & Computer Engineering, University of Canterbury, Christchurch, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.
| | - F Grant Pearce
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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7
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Schöler U, Merten AL, Schürmann S, Friedrich O. Quantitative Live-Cell Ca 2+ Imaging During Isotropic Cell Stretch. Methods Mol Biol 2023; 2644:155-176. [PMID: 37142921 DOI: 10.1007/978-1-0716-3052-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Cell viability of many cell types strongly relies on their ability to adjust to mechanical conditions and alterations. Cellular mechanisms for sensing and responding to mechanical forces and pathophysiological variations in these processes have become an emerging research field in recent years. An important signaling molecule involved in mechanotransduction as in many cellular processes is Ca2+. New experimental methods to probe cellular Ca2+ signaling live under conditions of mechanical stimulation facilitate new insights into previously overlooked aspects of mechanical regulation of cells.Here, we describe a protocol for using Ca2+ imaging in combination with a cell stretching device, the IsoStretcher. Cells grown on elastic membranes can be isotopically stretched in-plane, and their intracellular Ca2+ level can be accessed online on the single cell level using fluorescent calcium indicator dyes. We show a protocol for functional screening of mechanosensitive ion channels and related drug screenings using BJ cells, a foreskin fibroblast cell line that strongly reacts to acute mechanical stimulation.
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Affiliation(s)
- Ulrike Schöler
- Institute of Medical Biotechnology, Department of Chemical and Biological Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Anna-Lena Merten
- Institute of Medical Biotechnology, Department of Chemical and Biological Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sebastian Schürmann
- Institute of Medical Biotechnology, Department of Chemical and Biological Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Oliver Friedrich
- Institute of Medical Biotechnology, Department of Chemical and Biological Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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8
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Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules. Proc Natl Acad Sci U S A 2022; 119:e2117467119. [PMID: 36215467 PMCID: PMC9586272 DOI: 10.1073/pnas.2117467119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein-carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM-substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose-CBM bond rupture forces exceeding 15 pN.
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9
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Donker L, Houtekamer R, Vliem M, Sipieter F, Canever H, Gómez-González M, Bosch-Padrós M, Pannekoek WJ, Trepat X, Borghi N, Gloerich M. A mechanical G2 checkpoint controls epithelial cell division through E-cadherin-mediated regulation of Wee1-Cdk1. Cell Rep 2022; 41:111475. [DOI: 10.1016/j.celrep.2022.111475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
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10
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Davidović A, Chait R, Batt G, Ruess J. Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. PLoS Comput Biol 2022; 18:e1009950. [PMID: 35303737 PMCID: PMC8967023 DOI: 10.1371/journal.pcbi.1009950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/30/2022] [Accepted: 02/21/2022] [Indexed: 01/30/2023] Open
Abstract
Understanding and characterising biochemical processes inside single cells requires experimental platforms that allow one to perturb and observe the dynamics of such processes as well as computational methods to build and parameterise models from the collected data. Recent progress with experimental platforms and optogenetics has made it possible to expose each cell in an experiment to an individualised input and automatically record cellular responses over days with fine time resolution. However, methods to infer parameters of stochastic kinetic models from single-cell longitudinal data have generally been developed under the assumption that experimental data is sparse and that responses of cells to at most a few different input perturbations can be observed. Here, we investigate and compare different approaches for calculating parameter likelihoods of single-cell longitudinal data based on approximations of the chemical master equation (CME) with a particular focus on coupling the linear noise approximation (LNA) or moment closure methods to a Kalman filter. We show that, as long as cells are measured sufficiently frequently, coupling the LNA to a Kalman filter allows one to accurately approximate likelihoods and to infer model parameters from data even in cases where the LNA provides poor approximations of the CME. Furthermore, the computational cost of filtering-based iterative likelihood evaluation scales advantageously in the number of measurement times and different input perturbations and is thus ideally suited for data obtained from modern experimental platforms. To demonstrate the practical usefulness of these results, we perform an experiment in which single cells, equipped with an optogenetic gene expression system, are exposed to various different light-input sequences and measured at several hundred time points and use parameter inference based on iterative likelihood evaluation to parameterise a stochastic model of the system.
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Affiliation(s)
- Anđela Davidović
- Department of Computational Biology, Institut Pasteur, Paris, France
| | - Remy Chait
- Biosciences, Living Systems Institute, University of Exeter, Exeter, The United Kingdom
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Gregory Batt
- Department of Computational Biology, Institut Pasteur, Paris, France
- Inria Paris, Paris, France
| | - Jakob Ruess
- Department of Computational Biology, Institut Pasteur, Paris, France
- Inria Paris, Paris, France
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11
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Halpern AR, Lee MY, Howard MD, Woodworth MA, Nicovich PR, Vaughan JC. Versatile, do-it-yourself, low-cost spinning disk confocal microscope. BIOMEDICAL OPTICS EXPRESS 2022; 13:1102-1120. [PMID: 35284165 PMCID: PMC8884209 DOI: 10.1364/boe.442087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/20/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Confocal microscopy is an invaluable tool for 3D imaging of biological specimens, however, accessibility is often limited to core facilities due to the high cost of the hardware. We describe an inexpensive do-it-yourself (DIY) spinning disk confocal microscope (SDCM) module based on a commercially fabricated chromium photomask that can be added on to a laser-illuminated epifluorescence microscope. The SDCM achieves strong performance across a wide wavelength range (∼400-800 nm) as demonstrated through a series of biological imaging applications that include conventional microscopy (immunofluorescence, small-molecule stains, and fluorescence in situ hybridization) and super-resolution microscopy (single-molecule localization microscopy and expansion microscopy). This low-cost and simple DIY SDCM is well-documented and should help increase accessibility to confocal microscopy for researchers.
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Affiliation(s)
- Aaron R Halpern
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | - Min Yen Lee
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | - Marco D Howard
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | - Marcus A Woodworth
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | | | - Joshua C Vaughan
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
- University of Washington, Department of Physiology and Biophysics, Seattle, WA 98195, USA
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12
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Levine A, Liktor-Busa E, Lipinski AA, Couture S, Balasubramanian S, Aicher SA, Langlais PR, Vanderah TW, Largent-Milnes TM. Sex differences in the expression of the endocannabinoid system within V1M cortex and PAG of Sprague Dawley rats. Biol Sex Differ 2021; 12:60. [PMID: 34749819 PMCID: PMC8577021 DOI: 10.1186/s13293-021-00402-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/25/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Several chronic pain disorders, such as migraine and fibromyalgia, have an increased prevalence in the female population. The underlying mechanisms of this sex-biased prevalence have yet to be thoroughly documented, but could be related to endogenous differences in neuromodulators in pain networks, including the endocannabinoid system. The cellular endocannabinoid system comprises the endogenous lipid signals 2-AG (2-arachidonoylglycerol) and AEA (anandamide); the enzymes that synthesize and degrade them; and the cannabinoid receptors. The relative prevalence of different components of the endocannabinoid system in specific brain regions may alter responses to endogenous and exogenous ligands. METHODS Brain tissue from naïve male and estrous staged female Sprague Dawley rats was harvested from V1M cortex, periaqueductal gray, trigeminal nerve, and trigeminal nucleus caudalis. Tissue was analyzed for relative levels of endocannabinoid enzymes, ligands, and receptors via mass spectrometry, unlabeled quantitative proteomic analysis, and immunohistochemistry. RESULTS Mass spectrometry revealed significant differences in 2-AG and AEA concentrations between males and females, as well as between female estrous cycle stages. Specifically, 2-AG concentration was lower within female PAG as compared to male PAG (*p = 0.0077); female 2-AG concentration within the PAG did not demonstrate estrous stage dependence. Immunohistochemistry followed by proteomics confirmed the prevalence of 2-AG-endocannabinoid system enzymes in the female PAG. CONCLUSIONS Our results suggest that sex differences exist in the endocannabinoid system in two CNS regions relevant to cortical spreading depression (V1M cortex) and descending modulatory networks in pain/anxiety (PAG). These basal differences in endogenous endocannabinoid mechanisms may facilitate the development of chronic pain conditions and may also underlie sex differences in response to therapeutic intervention.
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Affiliation(s)
- Aidan Levine
- Department of Pharmacology, University of Arizona, 1501 N. Campbell Ave., Life Sciences North Rm 621, Tucson, AZ, 85724, USA
| | - Erika Liktor-Busa
- Department of Pharmacology, University of Arizona, 1501 N. Campbell Ave., Life Sciences North Rm 621, Tucson, AZ, 85724, USA
| | - Austin A Lipinski
- Endocrinology Division, Department of Medicine, University of Arizona, Tucson, AZ, 85724, USA
| | - Sarah Couture
- Department of Pharmacology, University of Arizona, 1501 N. Campbell Ave., Life Sciences North Rm 621, Tucson, AZ, 85724, USA
| | - Shreya Balasubramanian
- Department of Pharmacology, University of Arizona, 1501 N. Campbell Ave., Life Sciences North Rm 621, Tucson, AZ, 85724, USA
| | - Sue A Aicher
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Paul R Langlais
- Endocrinology Division, Department of Medicine, University of Arizona, Tucson, AZ, 85724, USA
| | - Todd W Vanderah
- Department of Pharmacology, University of Arizona, 1501 N. Campbell Ave., Life Sciences North Rm 621, Tucson, AZ, 85724, USA
| | - Tally M Largent-Milnes
- Department of Pharmacology, University of Arizona, 1501 N. Campbell Ave., Life Sciences North Rm 621, Tucson, AZ, 85724, USA.
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13
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Regression Based Iterative Illumination Compensation Method for Multi-Focal Whole Slide Imaging System. SENSORS 2021; 21:s21217085. [PMID: 34770394 PMCID: PMC8587722 DOI: 10.3390/s21217085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 12/04/2022]
Abstract
Image quality, resolution and scanning time are critical in digital pathology. In order to create a high-resolution digital image, the scanner systems execute stitching algorithms to the digitized images. Due to the heterogeneity of the tissue sample, complex optical path, non-acceptable sample quality or rapid stage movement, the intensities on pictures can be uneven. The evincible and visible intensity distortions can have negative effect on diagnosis and quantitative analysis. Utilizing the common areas of the neighboring field-of-views, we can estimate compensations to eliminate the inhomogeneities. We implemented and validated five different approaches for compensating output images created with an area scanner system. The proposed methods are based on traditional methods such as adaptive histogram matching, regression-based corrections and state-of-the art methods like the background and shading correction (BaSiC) method. The proposed compensation methods are suitable for both brightfield and fluorescent images, and robust enough against dust, bubbles, and optical aberrations. The proposed methods are able to correct not only the fixed-pattern artefacts but the stochastic uneven illumination along the neighboring or above field-of-views utilizing iterative approaches and multi-focal compensations.
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14
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Hobson CM, Aaron JS, Heddleston JM, Chew TL. Visualizing the Invisible: Advanced Optical Microscopy as a Tool to Measure Biomechanical Forces. Front Cell Dev Biol 2021; 9:706126. [PMID: 34552926 PMCID: PMC8450411 DOI: 10.3389/fcell.2021.706126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/09/2021] [Indexed: 01/28/2023] Open
Abstract
The importance of mechanical force in biology is evident across diverse length scales, ranging from tissue morphogenesis during embryo development to mechanotransduction across single adhesion proteins at the cell surface. Consequently, many force measurement techniques rely on optical microscopy to measure forces being applied by cells on their environment, to visualize specimen deformations due to external forces, or even to directly apply a physical perturbation to the sample via photoablation or optogenetic tools. Recent developments in advanced microscopy offer improved approaches to enhance spatiotemporal resolution, imaging depth, and sample viability. These advances can be coupled with already existing force measurement methods to improve sensitivity, duration and speed, amongst other parameters. However, gaining access to advanced microscopy instrumentation and the expertise necessary to extract meaningful insights from these techniques is an unavoidable hurdle. In this Live Cell Imaging special issue Review, we survey common microscopy-based force measurement techniques and examine how they can be bolstered by emerging microscopy methods. We further explore challenges related to the accompanying data analysis in biomechanical studies and discuss the various resources available to tackle the global issue of technology dissemination, an important avenue for biologists to gain access to pre-commercial instruments that can be leveraged for biomechanical studies.
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Affiliation(s)
- Chad M. Hobson
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States
| | - Jesse S. Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States
| | - John M. Heddleston
- Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, FL, United States
| | - Teng-Leong Chew
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States
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15
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Berry K, Taormina M, Maltzer Z, Turner K, Gorham M, Nguyen T, Serafin R, Nicovich PR. Characterization of a fiber-coupled EvenField illumination system for fluorescence microscopy. OPTICS EXPRESS 2021; 29:24349-24362. [PMID: 34614682 DOI: 10.1364/oe.430440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
Fluorescence microscopy benefits from spatially and temporally homogeneous illumination with the illumination area matched to the shape and size of the camera sensor. Fiber-coupled illumination schemes have the added benefit of straightforward and robust alignment and ease of installation compared to free-space coupled illumination. Commercial and open-source fiber-coupled, homogenized illumination schemes have recently become available to the public; however, there have been no published comparisons of speckle reduction schemes to date. We characterize three different multimode fibers in combination with two laser speckle reduction devices and compare spatial and temporal profiles to a commercial unit. This work yields a new design, the EvenField Illuminator, which is freely available for researchers to integrate into their own imaging systems.
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16
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Olevsko I, Szederkenyi K, Corridon J, Au A, Delhomme B, Bastien T, Fernandes J, Yip C, Oheim M, Salomon A. A simple, inexpensive and multi-scale 3-D fluorescent test sample for optical sectioning microscopies. Microsc Res Tech 2021; 84:2625-2635. [PMID: 34008289 DOI: 10.1002/jemt.23813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/05/2021] [Accepted: 04/27/2021] [Indexed: 11/11/2022]
Abstract
Fluorescence standards allow for quality control and for the comparison of data sets across instruments and laboratories in applications of quantitative fluorescence. For example, users of microscopy core facilities can expect a homogenous and time-invariant illumination and an uniform detection sensitivity, which are prerequisites for imaging analysis, tracking or fluorimetric pH or Ca2+ -concentration measurements. Similarly, confirming the three-dimensional (3-D) resolution of optical sectioning microscopes calls for a regular calibration with a standardized point source. The test samples required for such measurements are typically different ones, they are often expensive and they depend much on the very microscope technique used. Similarly, the ever-increasing choice among microscope techniques and geometries increases the demand for comparison across instruments. Here, we advocate and demonstrate the multiple uses of a surprisingly versatile and simple 3-D test sample that can complement existing and much more expensive calibration samples: commercial tissue paper labeled with a fluorescent highlighter pen. We provide relevant sample characteristics and show examples ranging from the sub-μm to cm scale, acquired on epifluorescence, confocal, image scanning, two-photon (2P) and light-sheet microscopes.
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Affiliation(s)
- Ilya Olevsko
- Department of Chemistry, Bar-Ilan University, Institute of Nanotechnology and Advanced Materials (BINA), Ramat-Gan, Israel
| | - Kaitlin Szederkenyi
- Université de Paris, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, Paris, France.,University of Toronto, Donnelly Centre for Cellular & Biomolecular Research, Toronto, Ontario, Canada
| | - Jennifer Corridon
- Université de Paris, CNRS UMS 2009, INSERM US 36, BioMedTech Facilities, Paris, France.,Université de Paris, Service Commun de Microscopie (SCM), Paris, France
| | - Aaron Au
- University of Toronto, Donnelly Centre for Cellular & Biomolecular Research, Toronto, Ontario, Canada
| | - Brigitte Delhomme
- Université de Paris, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, Paris, France
| | - Thierry Bastien
- Université de Paris, CNRS UMS 2009, INSERM US 36, BioMedTech Facilities, Paris, France.,Université de Paris, Plateforme de Prototypage, Paris, France
| | - Julien Fernandes
- UTechS Photonic BioImaging, C2RT, Institut Pasteur, Paris, France
| | - Christopher Yip
- University of Toronto, Donnelly Centre for Cellular & Biomolecular Research, Toronto, Ontario, Canada
| | - Martin Oheim
- Université de Paris, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, Paris, France.,Université de Paris, CNRS UMS 2009, INSERM US 36, BioMedTech Facilities, Paris, France.,Université de Paris, Service Commun de Microscopie (SCM), Paris, France
| | - Adi Salomon
- Department of Chemistry, Bar-Ilan University, Institute of Nanotechnology and Advanced Materials (BINA), Ramat-Gan, Israel.,Université de Paris, CNRS, SPPIN - Saints-Pères Paris Institute for the Neurosciences, Paris, France
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17
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Brookshire C, Uchic M, Kramb V, Lesthaeghe T, Hirakawa K. L's approach: illumination pattern estimation technique for optical microscopy. J Microsc 2020; 281:243-254. [PMID: 33040347 DOI: 10.1111/jmi.12968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/11/2020] [Accepted: 10/07/2020] [Indexed: 11/29/2022]
Abstract
We propose a novel solution to the correction of illumination nonuniformity without removing the imaging sample. Calibration of the spatial illumination pattern in reflectance microscopy is challenging due to the fact that the illumination source is colocated with the objective lens and therefore cannot be observed directly. Our proposed methodology overcomes this by collecting three spatially translated images in a strategic way. We prove that 'log-illumination pattern' recovery can be reformulated as a deconvolution of log-ratio of captured images, and develop an efficient, noise-robust implementation. Experiments with simulated and reflectance microscopy data verify the effectiveness of our proposed approach. LAY DESCRIPTION: The proposed technique overcomes a common problem of nonuniform illumination in microscopy. For the case of reflectance microscopy, we show that a few images with large amounts of overlap can be used to recover the illumination pattern. In conjunction with an image formation model, the recovered illumination pattern may be used to correct the images captured under similar illumination conditions.
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Affiliation(s)
| | - Michael Uchic
- Air Force Research Laboratory, Materials and Manufacturing Directorate, Wright-Patterson AFB, Ohio, U.S.A
| | - Victoria Kramb
- University of Dayton Research Institute, 300 College Park Dayton, Ohio, U.S.A
| | - Tyler Lesthaeghe
- University of Dayton Research Institute, 300 College Park Dayton, Ohio, U.S.A
| | - Keigo Hirakawa
- University of Dayton, 300 College Park Dayton, Ohio, U.S.A.,University of Dayton Research Institute, 300 College Park Dayton, Ohio, U.S.A
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18
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Smith M, Querido E, Chartrand P, Sfeir A. Quantitative Imaging of MS2-Tagged hTR in Cajal Bodies: Photobleaching and Photoactivation. STAR Protoc 2020; 1:100112. [PMID: 33377008 PMCID: PMC7756913 DOI: 10.1016/j.xpro.2020.100112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Advances in imaging technologies, gene editing, and fluorescent molecule development have made real-time imaging of nucleic acids practical. Here, we detail methods for imaging the human telomerase RNA template, hTR via the use of three inserted MS2 stem loops and cognate MS2 coat protein (MCP) tagged with superfolder GFP or photoactivatable GFP. These technologies enable tracking of the dynamics of RNA species through Cajal bodies and offer insight into their residence time in Cajal bodies through photobleaching and photoactivation experiments. For complete details on the use and execution of this protocol, please refer to Laprade et al. (2020).
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Affiliation(s)
- Michael Smith
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Emmanuelle Querido
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Canada
| | - Pascal Chartrand
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Canada
| | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
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19
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Single-Molecule Imaging of Telomerase RNA Reveals a Recruitment-Retention Model for Telomere Elongation. Mol Cell 2020; 79:115-126.e6. [DOI: 10.1016/j.molcel.2020.05.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/13/2020] [Accepted: 05/03/2020] [Indexed: 11/23/2022]
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20
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Model M. Comparison of cell volume measurements by fluorescence and absorption exclusion microscopy. J Microsc 2020; 280:12-18. [PMID: 32472565 DOI: 10.1111/jmi.12929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 01/06/2023]
Abstract
There are two light microscopic methods for cell volume measurement based on volume exclusion. One method, sometimes referred to as FLEX, utilises negative staining by an external fluorescent dye, and cell volume is found from attenuation of fluorescence under a wide-field microscope. The other method (TTD) is based on exclusion of an external absorbing dye, resulting in an increased intensity of transmission image. In this work, we compared these two methods. TTD measurements were consistent, reproducible and identical to those obtained by confocal scanning. In our hands, FLEX based on either sodium fluorescein of fluorescent dextran, usually resulted in underestimation of cell volume, which were insignificant in shallow chambers but became more severe with increased chamber depth. We have not been able to exactly pinpoint the source of the problem; it may have been undetected accumulation of dye in the cells or, more likely, some unappreciated aspects of image formation under epi-illumination. We also discuss applicability of both methods to in-flow volume measurements. LAY DESCRIPTION: Cell volume is a parameter important for many cell biological and physiological applications, and many different methods have been proposed for its measurement. Two light microscopic methods based on volume exclusion deserve special attention due to their speed and simplicity. In one of them (transmission-through-dye, or TTD), cells are placed in a shallow chamber, and a strongly absorbing external dye is added to the cell-containing medium. The sample is imaged in transmission at a wavelength of maximum dye absorption. Because cells with intact membranes exclude the dye, they appear brighter on a transmission image, and their contrast quantitatively reflects cell thickness. By summation of thickness values over the cell area, cell volume can be obtained. The other method sometimes referred to as FLEX utilises exclusion of a fluorescent dye. Cells appear darker than the background under wide-field fluorescence observation in accordance with their thicknesses, and cell volume is computed by thickness summation over the area, like in TTD. In this work, we compared the accuracy of TTD and FLEX for volume measurements. TTD and confocal scanning produced virtually identical results, which suggests that TTD data are accurate. On the other hand, cell volumes measured by FLEX were consistently smaller than by TTD. The discrepancy always increased with the depth of the chamber, although the exact relationship varied between experiments. By contrast, TTD results were insensitive to chamber depth. Thus, it appears that FLEX underestimates cell volume. The reason for that is not entirely clear. Accumulation of the fluorescent dye inside the cell could be a possibility, although we found no evidence for that. Most likely, the reason lies with some unappreciated aspects of wide-field fluorescence image formation, which has not been well-characterised for the type of negative staining used in FLEX. In our opinion, TTD is the method of choice, at least for stationary cells. On the other hand, due to linear dependence of intensity on volume, FLEX might offer advantages for high-throughput flow volume imaging, although realisation of such an experiment has yet to be worked out.
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Affiliation(s)
- M Model
- Department of Biological Sciences, Kent State University, Kent, Ohio, U.S.A
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21
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Liu RX, Ma J, Wang B, Tian T, Guo N, Liu SJ. No DCX-positive neurogenesis in the cerebral cortex of the adult primate. Neural Regen Res 2020; 15:1290-1299. [PMID: 31960815 PMCID: PMC7047795 DOI: 10.4103/1673-5374.272610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Whether endogenous neurogenesis occurs in the adult cortex remains controversial. An increasing number of reports suggest that doublecortin (DCX)-positive neurogenesis persists in the adult primate cortex, attracting enormous attention worldwide. In this study, different DCX antibodies were used together with NeuN antibodies in immunohistochemistry and western blot assays using adjacent cortical sections from adult monkeys. Antibody adsorption, antigen binding, primary antibody omission and antibody-free experiments were used to assess specificity of the signals. We found either strong fluorescent signals, medium-weak intensity signals in some cells, weak signals in a few perikarya or near complete lack of labeling in adjacent cortical sections incubated with the various DCX antibodies. The putative DCX-positive cells in the cortex were also positive for NeuN, a specific marker of mature neurons. However, further experiments showed that most of these signals were either the result of antibody cross reactivity, the non-specificity of secondary antibodies or tissue autofluorescence. No confirmed DCX-positive cells were detected in the adult macaque cortex by immunofluorescence. Our findings show that DCX-positive neurogenesis does not occur in the cerebral cortex of adult primates, and that false-positive signals (artefacts) are caused by antibody cross reactivity and autofluorescence. The experimental protocols were approved by the Institutional Animal Care and Use Committee of the Institute of Neuroscience, Beijing, China (approval No. IACUC-AMMS-2014-501).
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Affiliation(s)
- Ruo-Xu Liu
- Institute of Military Cognition and Brain Sciences, Beijing, China
| | - Jie Ma
- Institute of Military Cognition and Brain Sciences, Beijing, China
| | - Bin Wang
- Institute of Military Cognition and Brain Sciences, Beijing, China
| | - Tian Tian
- Department of Pharmacy, Medical College, Huanghe S&T University, Zhengzhou, Henan Province, China
| | - Ning Guo
- Institute of Military Cognition and Brain Sciences, Beijing, China
| | - Shao-Jun Liu
- Institute of Military Cognition and Brain Sciences, Beijing, China
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22
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Kesten C, Gámez‐Arjona FM, Menna A, Scholl S, Dora S, Huerta AI, Huang H, Tintor N, Kinoshita T, Rep M, Krebs M, Schumacher K, Sánchez‐Rodríguez C. Pathogen-induced pH changes regulate the growth-defense balance in plants. EMBO J 2019; 38:e101822. [PMID: 31736111 PMCID: PMC6912046 DOI: 10.15252/embj.2019101822] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 10/11/2019] [Accepted: 10/17/2019] [Indexed: 01/06/2023] Open
Abstract
Environmental adaptation of organisms relies on fast perception and response to external signals, which lead to developmental changes. Plant cell growth is strongly dependent on cell wall remodeling. However, little is known about cell wall-related sensing of biotic stimuli and the downstream mechanisms that coordinate growth and defense responses. We generated genetically encoded pH sensors to determine absolute pH changes across the plasma membrane in response to biotic stress. A rapid apoplastic acidification by phosphorylation-based proton pump activation in response to the fungus Fusarium oxysporum immediately reduced cellulose synthesis and cell growth and, furthermore, had a direct influence on the pathogenicity of the fungus. In addition, pH seems to influence cellulose structure. All these effects were dependent on the COMPANION OF CELLULOSE SYNTHASE proteins that are thus at the nexus of plant growth and defense. Hence, our discoveries show a remarkable connection between plant biomass production, immunity, and pH control, and advance our ability to investigate the plant growth-defense balance.
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Affiliation(s)
| | | | | | - Stefan Scholl
- Centre for Organismal Studies, Cell BiologyHeidelberg UniversityHeidelbergGermany
| | - Susanne Dora
- Department of BiologyETH ZurichZurichSwitzerland
| | | | | | - Nico Tintor
- Department of PhytopathologyUniversity of AmsterdamAmsterdamThe Netherlands
| | - Toshinori Kinoshita
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusa, NagoyaJapan
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityChikusa, NagoyaJapan
| | - Martijn Rep
- Department of PhytopathologyUniversity of AmsterdamAmsterdamThe Netherlands
| | - Melanie Krebs
- Centre for Organismal Studies, Cell BiologyHeidelberg UniversityHeidelbergGermany
| | - Karin Schumacher
- Centre for Organismal Studies, Cell BiologyHeidelberg UniversityHeidelbergGermany
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23
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Adam N, Degelman E, Briggs S, Wazen RM, Colarusso P, Riabowol K, Beattie T. Telomere analysis using 3D fluorescence microscopy suggests mammalian telomere clustering in hTERT-immortalized Hs68 fibroblasts. Commun Biol 2019; 2:451. [PMID: 31815205 PMCID: PMC6893014 DOI: 10.1038/s42003-019-0692-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/04/2019] [Indexed: 12/16/2022] Open
Abstract
Telomere length and dynamics are central to understanding cell aging, genomic instability and cancer. Currently, there are limited guidelines for analyzing telomeric features in 3D using different cellular models. Image processing for telomere analysis is of increasing interest in many fields, however a lack of standardization can make comparisons and reproducibility an issue. Here we provide a user's guide for quantitative immunofluorescence microscopy of telomeres in interphase cells that covers image acquisition, processing and analysis. Strategies for determining telomere size and number are identified using normal human diploid Hs68 fibroblasts. We demonstrate how to accurately determine telomere number, length, volume, and degree of clustering using quantitative immunofluorescence. Using this workflow, we make the unexpected observation that hTERT-immortalized Hs68 cells with longer telomeres have fewer resolvable telomeres in interphase. Rigorous quantification indicates that this is due to telomeric clustering, leading to systematic underestimation of telomere number and overestimation of telomere size.
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Affiliation(s)
- Nancy Adam
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB Canada
| | - Erin Degelman
- Cumming School of Medicine, University of Calgary, Calgary, AB Canada
| | - Sophie Briggs
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB Canada
| | - Rima-Marie Wazen
- Live Cell Imaging Laboratory, Cumming School of Medicine, University of Calgary, Calgary, AB Canada
| | - Pina Colarusso
- Live Cell Imaging Laboratory, Cumming School of Medicine, University of Calgary, Calgary, AB Canada
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB Canada
| | - Karl Riabowol
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB Canada
- Department of Oncology, University of Calgary, Calgary, AB Canada
| | - Tara Beattie
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB Canada
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24
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Drawbond R, Spendier K. TIRF Microscope Image Sequences of Fluorescent IgE-FcεRI Receptor Complexes inside a FcεRI-Centric Synapse in RBL-2H3 Cells. DATA 2019; 4:111. [PMID: 32704503 PMCID: PMC7377353 DOI: 10.3390/data4030111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Total internal reflection fluorescence (TIRF) microscope image sequences are commonly used to study receptors in live cells. The dataset presented herein facilitates the study of the IgE-FcεRI receptor signaling complex (IgE-RC) in rat basophilic leukemia (RBL-2H3) cells coming into contact with a supported lipid bilayer with 25 mol% N-dinitrophenyl-aminocaproyl phosphatidylethanolamine, modeling an immunological synapse. TIRF microscopy was used to image IgE-RCs within this FcεRI-centric synapse by loading RBL-2H3 cells with fluorescent anti-dinitrophenyl (anti-DNP) immunoglobulin E (IgE) in suspension for 24 h. Fluorescent anti-DNP IgE (IgE488) concentrations of this suspension increased from 10% to 100% and corresponding non-fluorescent anti-DNP IgE concentrations decreased from 90% to 0%. After the removal of unbound anti-DNP IgE, multiple image sequences were taken for each of these ten conditions. Prior to imaging, anti-DNP IgE-primed RBL-2H3 cells were either kept for a few minutes, for about 30 min, or for about one hour in Hanks buffer. The dataset contains 482 RBL-2H3 model synapse image stacks, dark images to correct for background intensity, and TIRF illumination profile images to correct for non-uniform TIRF illumination. After background subtraction, non-uniform illumination correction, and conversion of pixel units from analog-to-digital units to photo electrons, the average pixel intensity was calculated. The average pixel intensity within FcεRI-centric synapses for all three Hanks buffer conditions increased linearly at a rate of 0.42 ± 0.02 photo electrons per pixel per % IgE488 in suspension. RBL-2H3 cell degranulation was tested by detecting β-hexosaminidase activity. Prolonged RBL-2H3 cell exposure to Hanks buffer inhibited exocytosis in RBL-2H3 cells.
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Affiliation(s)
- Rachel Drawbond
- UCCS Center of the Biofrontiers Institute, University of Colorado at Colorado Springs, Colorado Springs, CO 80918, USA
- Department of Mathematics, University of Colorado at Colorado Springs, Colorado Springs, CO 80918, USA
| | - Kathrin Spendier
- Department of Mathematics, University of Colorado at Colorado Springs, Colorado Springs, CO 80918, USA
- Department of Physics and Energy Science, University of Colorado at Colorado Springs, Colorado Springs, CO 80918, USA
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25
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Jost APT, Waters JC. Designing a rigorous microscopy experiment: Validating methods and avoiding bias. J Cell Biol 2019; 218:1452-1466. [PMID: 30894402 PMCID: PMC6504886 DOI: 10.1083/jcb.201812109] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 01/06/2023] Open
Abstract
Images generated by a microscope are never a perfect representation of the biological specimen. Microscopes and specimen preparation methods are prone to error and can impart images with unintended attributes that might be misconstrued as belonging to the biological specimen. In addition, our brains are wired to quickly interpret what we see, and with an unconscious bias toward that which makes the most sense to us based on our current understanding. Unaddressed errors in microscopy images combined with the bias we bring to visual interpretation of images can lead to false conclusions and irreproducible imaging data. Here we review important aspects of designing a rigorous light microscopy experiment: validation of methods used to prepare samples and of imaging system performance, identification and correction of errors, and strategies for avoiding bias in the acquisition and analysis of images.
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26
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Depth measurement of molecular permeation using inclined confocal microscopy. PLoS One 2019; 14:e0214504. [PMID: 30917189 PMCID: PMC6436738 DOI: 10.1371/journal.pone.0214504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 03/15/2019] [Indexed: 12/31/2022] Open
Abstract
We report a new technique for the high time-resolved depth measurement of molecular concentration distribution in a permeable hydrogel film with micro-depth precision. We developed an inclined observation technique in a laser-induced fluorescence (LIF) system, based on confocal microscopy, which measures the concentration distribution in the depth direction at less than micrometre intervals. The focal plane of confocal microscopy was tilted to enable simultaneous depth scanning in the microscopic field of view inside the permeable substrate. Our system achieved real-time and non-contact depth measurement of concentration distribution in the permeable hydrogel film. Simultaneous depth concentration measurement was realised with < 1 μm/pixel resolution over a maximum depth range of 570 μm, depending on the tilt angle of the stage and optical conditions. Our system measured the concentration of fluorescence materials based on the fluorescence intensities at several depth positions with a minimum concentration resolution of 1.3 nmol/L. Applying the proposed system to real-time concentration imaging, we successfully visualised unsteady concentration transport phenomena, and estimated the mass transport coefficient through the liquid-hydrogel interface. Our findings are useful for investigating the mass transport of physical, biological, and medical phenomena in permeable substrates.
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27
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Harink B, Nguyen H, Thorn K, Fordyce P. An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs). PLoS One 2019; 14:e0203725. [PMID: 30901328 PMCID: PMC6430362 DOI: 10.1371/journal.pone.0203725] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/20/2019] [Indexed: 12/26/2022] Open
Abstract
Multiplexed bioassays, in which multiple analytes of interest are probed in parallel within a single small volume, have greatly accelerated the pace of biological discovery. Bead-based multiplexed bioassays have many technical advantages, including near solution-phase kinetics, small sample volume requirements, many within-assay replicates to reduce measurement error, and, for some bead materials, the ability to synthesize analytes directly on beads via solid-phase synthesis. To allow bead-based multiplexing, analytes can be synthesized on spectrally encoded beads with a 1:1 linkage between analyte identity and embedded codes. Bead-bound analyte libraries can then be pooled and incubated with a fluorescently-labeled macromolecule of interest, allowing downstream quantification of interactions between the macromolecule and all analytes simultaneously via imaging alone. Extracting quantitative binding data from these images poses several computational image processing challenges, requiring the ability to identify all beads in each image, quantify bound fluorescent material associated with each bead, and determine their embedded spectral code to reveal analyte identities. Here, we present a novel open-source Python software package (the mrbles analysis package) that provides the necessary tools to: (1) find encoded beads in a bright-field microscopy image; (2) quantify bound fluorescent material associated with bead perimeters; (3) identify embedded ratiometric spectral codes within beads; and (4) return data aggregated by embedded code and for each individual bead. We demonstrate the utility of this package by applying it towards analyzing data generated via multiplexed measurement of calcineurin protein binding to MRBLEs (Microspheres with Ratiometric Barcode Lanthanide Encoding) containing known and mutant binding peptide motifs. We anticipate that this flexible package should be applicable to a wide variety of assays, including simple bead or droplet finding analysis, quantification of binding to non-encoded beads, and analysis of multiplexed assays that use ratiometric, spectrally encoded beads.
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Affiliation(s)
- Björn Harink
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Huy Nguyen
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Kurt Thorn
- Department of Biochemistry & Biophysics, University of California, San Francisco, United States of America
| | - Polly Fordyce
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- ChEM-H Institute, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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28
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Kelley JB, Paschal BM. Fluorescence-based quantification of nucleocytoplasmic transport. Methods 2018; 157:106-114. [PMID: 30419335 DOI: 10.1016/j.ymeth.2018.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/26/2018] [Accepted: 11/06/2018] [Indexed: 02/02/2023] Open
Abstract
The sequestration of DNA within the membrane-bound nucleus is a defining characteristic of eukaryotic cells. Replication and transcription are therefore restricted to the nucleus, however, the regulation of these events relies on cytoplasmic processes including protein synthesis and signal transduction pathways. Because a variety of cellular activities depend on nuclear transport, researchers from diverse fields have found it useful to examine the nuclear localization of proteins of interest. Here we present some important technical considerations for studying nuclear and cytoplasmic localization, and provide guidance for quantifying protein levels using fluorescence microscopy and ImageJ software. We include discussion of the use of regions of interest and image segmentation for quantification of protein localization. Nucleocytoplasmic transport is fundamentally important for controlling protein levels and activity in the nucleus or cytoplasm, and quantitative analysis can provide insight into how biological output is achieved.
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Affiliation(s)
- Joshua B Kelley
- Department of Molecular and Biomedical Sciences, University of Maine, United States.
| | - Bryce M Paschal
- Center for Cell Signaling, Department of Biochemistry and Molecular Genetics, University of Virginia, United States
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29
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Zarski P, Ryder AG. Super Stable Fluorescein Isothiocyanate Isomer I Monolayer for Total Internal Reflection Fluorescence Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:10913-10923. [PMID: 30145901 DOI: 10.1021/acs.langmuir.8b02509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Total internal reflection fluorescence microscopy (TIRFM) is an important method in surface science and for the analysis of surface-bound macromolecules. Here, we developed and explored the use of a novel fluorescein isothiocyanate isomer I (FITC)-adsorbed monolayer for alignment and validation of TIRFM measurements and configurations. Aqueous solutions of FITC exist as several different protolytic forms (dianionic, anionic, neutral, and cationic) with each form having different emission characteristics. However, the emission behavior of FITC adsorbed on hydrophilic, hydrophobic, and unmodified glass surfaces at different pH was unknown. TIRFM imaging and spectroscopy were used to study FITC and FITC-labeled bovine serum albumin (BSA-FITC) monolayers generated on three different glass surfaces. Monolayer emission intensity, spectra, and the photobleaching profiles were all dependent on pH and the surface properties of the glass. Very strangely, however, at pH 5.0 on hydrophobic surfaces, the FITC monolayers produced were both bright and apparently unbleachable over ∼20 min of imaging (60 s total exposure). During monolayer formation at pH 5.0, we saw clear evidence for concentration-based quenching, indicating high surface coverage. When the monolayer had been rinsed with buffer to remove unbound FITC, we observed an increase in emission intensity during illumination indicative of some form of photoactivated species being present. Eventually, the fluorescence emission stabilized and remained constant for extended periods of time with no evidence of photobleaching. We hypothesize that during the adsorption process (a hydrophobic-hydrophobic interaction) there was conversion to the fluorescent quinoid form of FITC. In contrast, at pH 7.4 and 9.6 on hydrophobic surfaces, FITC monolayers had well-defined, fast photobleaching kinetics (decay to ∼50% intensity in 5-10 s). The equivalent BSA-FITC monolayers were slightly brighter, with similar photobleaching kinetics. While the precise mechanism for this unusual behavior is still unknown, all these low-cost monolayers were easily prepared, were reproducible, and can serve as convenient test samples for TIRFM alignment, calibration, and validation prior to undertaking measurements with more sensitive biogenic or biological specimens.
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Affiliation(s)
- Przemyslaw Zarski
- Nanoscale Biophotonics Laboratory, School of Chemistry , National University of Ireland , University Road , Galway H91 CF50 , Ireland
| | - Alan G Ryder
- Nanoscale Biophotonics Laboratory, School of Chemistry , National University of Ireland , University Road , Galway H91 CF50 , Ireland
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30
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Pauza AG, Rysevaite-Kyguoliene K, Malinauskas M, Lukosiene JI, Alaburda P, Stankevicius E, Kupcinskas J, Saladzinskas Z, Tamelis A, Pauziene N. Alterations in enteric calcitonin gene-related peptide in patients with colonic diverticular disease: CGRP in diverticular disease. Auton Neurosci 2018; 216:63-71. [PMID: 30274796 DOI: 10.1016/j.autneu.2018.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/04/2018] [Accepted: 09/16/2018] [Indexed: 02/06/2023]
Abstract
Diverticular disease (DD) is one of the most prevalent diseases of the large bowel. Lately, imbalance of neuro-muscular transmission has been recognized as a major etiological factor for DD. Neuronal calcitonin gene-related peptide (CGRP) is a potent gastrointestinal smooth muscle relaxant shown to have a widespread effect within the alimentary tract. Nevertheless, CGRPergic innervation of the enteric ganglia has never been considered in the context of motility impairment observed in DD patients. Changes in CGRP and calcitonin receptor-like receptor (CRLR) abundance within enteric ganglia were investigated in sigmoid samples from symptomatic and asymptomatic DD patients using quantitative fluorescence microscopy. CGRP effect on gastrointestinal smooth muscle was investigated using organ bath technique. We found CGRP levels within the enteric ganglia to be declined by up to 52% in symptomatic DD patients. Conversely, CRLR within the enteric ganglia was upregulated by 41% in symptomatic DD. Longitudinal smooth muscle displayed an elevated (+10.5%) relaxant effect to the exogenous application of CGRP in colonic strips from symptomatic DD patients. Samples from asymptomatic DD patients consistently showed intermediate values across different experiments. In conclusion, the present study demonstrates that CGRPergic signaling is subject to alteration in DD. Our results suggest that a hypersensitization mechanism to gradually decreasing levels of CGRP-IR nerve fibers takes place during DD progression. Alterations to CGRPergic signaling in DD disease may have implications for physiological abnormalities associated with colonic DD.
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Affiliation(s)
- A G Pauza
- Institute of Anatomy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | | | - M Malinauskas
- Institute of Physiology and Pharmacology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - J I Lukosiene
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - P Alaburda
- Institute of Anatomy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - E Stankevicius
- Institute of Physiology and Pharmacology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - J Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania; Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Z Saladzinskas
- Department of Surgery, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - A Tamelis
- Department of Surgery, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - N Pauziene
- Institute of Anatomy, Lithuanian University of Health Sciences, Kaunas, Lithuania.
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31
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Lee JY, Kitaoka M. A beginner's guide to rigor and reproducibility in fluorescence imaging experiments. Mol Biol Cell 2018; 29:1519-1525. [PMID: 29953344 PMCID: PMC6080651 DOI: 10.1091/mbc.e17-05-0276] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 04/25/2018] [Accepted: 04/27/2018] [Indexed: 02/01/2023] Open
Abstract
Fluorescence light microscopy is an indispensable approach for the investigation of cell biological mechanisms. With the development of cutting-edge tools such as genetically encoded fluorescent proteins and superresolution methods, light microscopy is more powerful than ever at providing insight into a broad range of phenomena, from bacterial fission to cancer metastasis. However, as with all experimental approaches, care must be taken to ensure reliable and reproducible data collection, analysis, and reporting. Each step of every imaging experiment, from design to execution to communication to data management, should be critically assessed for bias, rigor, and reproducibility. This Perspective provides a basic "best practices" guide for designing and executing fluorescence imaging experiments, with the goal of introducing researchers to concepts that will help empower them to acquire images with rigor.
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Affiliation(s)
- Jen-Yi Lee
- Molecular Imaging Center, Cancer Research Laboratory, University of California, Berkeley, Berkeley, CA 94720
| | - Maiko Kitaoka
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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32
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Lu Y, Ho CS, McIntyre RS, Wang W, Ho RC. Effects of vortioxetine and fluoxetine on the level of Brain Derived Neurotrophic Factors (BDNF) in the hippocampus of chronic unpredictable mild stress-induced depressive rats. Brain Res Bull 2018; 142:1-7. [PMID: 29933036 DOI: 10.1016/j.brainresbull.2018.06.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 06/01/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022]
Abstract
Vortioxetine is a novel antidepressant capable of improving depressive and cognitive symptoms associated with major depressive disorder (MDD). This study established whether treatment with vortioxetine, fluoxetine or vehicle alters the modulation of brain-derived neurotrophic factor (BDNF) under the 21-day chronic unpredictable mild stress (CUMS) condition in 54 Sprague-Dawley rats. Vortioxetine mitigated the reduction in rearing behavior by CUMS in the OFT on day 7 and 21, as well as sucrose preference on day 21. Histological examination by H&E staining showed that most hippocampal neurons in the CUMS + FLU and CUMS + VOR groups were intact, although some of them demonstrated karyopyknosis. The mean optical density value of hippocampal BDNF was significantly higher in the CUMS + VOR group than the CUMS and CUMS + FLU groups. There was a trend towards a higher number of hippocampal BDNF-positive cells in the CUMS + VOR group, although it did not reach statistical significance. In conclusion, vortioxetine, but not fluoxetine, increased hippocampal BDNF levels in rats subject to CUMS.
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Affiliation(s)
- Yanxia Lu
- Department of Clinical Psychology and Psychiatry, School of Public Health, Zhejiang University College of Medicine, Hangzhou, China.
| | - Cyrus S Ho
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Psychological Medicine, National University Health System, Singapore
| | - Roger S McIntyre
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada; Mood Disorders Psychopharmacology Unit, University Health Network, Toronto, ON, Canada; Department of Psychiatry, University of Toronto, Toronto, ON, Canada; Department of Toxicology and Pharmacology, University of Toronto, Toronto, ON, Canada
| | - Wei Wang
- Department of Clinical Psychology and Psychiatry, School of Public Health, Zhejiang University College of Medicine, Hangzhou, China.
| | - Roger C Ho
- Department of Psychological Medicine, National University Health System, Singapore; Biomedical Institute for Global Health Research and Technology (BIGHEART), National University of Singapore
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33
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Blasse C, Saalfeld S, Etournay R, Sagner A, Eaton S, Myers EW. PreMosa: extracting 2D surfaces from 3D microscopy mosaics. Bioinformatics 2018; 33:2563-2569. [PMID: 28383656 DOI: 10.1093/bioinformatics/btx195] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 04/04/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation A significant focus of biological research is to understand the development, organization and function of tissues. A particularly productive area of study is on single layer epithelial tissues in which the adherence junctions of cells form a 2D manifold that is fluorescently labeled. Given the size of the tissue, a microscope must collect a mosaic of overlapping 3D stacks encompassing the stained surface. Downstream interpretation is greatly simplified by preprocessing such a dataset as follows: (i) extracting and mapping the stained manifold in each stack into a single 2D projection plane, (ii) correcting uneven illumination artifacts, (iii) stitching the mosaic planes into a single, large 2D image and (iv) adjusting the contrast. Results We have developed PreMosa, an efficient, fully automatic pipeline to perform the four preprocessing tasks above resulting in a single 2D image of the stained manifold across which contrast is optimized and illumination is even. Notable features are as follows. First, the 2D projection step employs a specially developed algorithm that actually finds the manifold in the stack based on maximizing contrast, intensity and smoothness. Second, the projection step comes first, implying all subsequent tasks are more rapidly solved in 2D. And last, the mosaic melding employs an algorithm that globally adjusts contrasts amongst the 2D tiles so as to produce a seamless, high-contrast image. We conclude with an evaluation using ground-truth datasets and present results on datasets from Drosophila melanogaster wings and Schmidtae mediterranea ciliary components. Availability and Implementation PreMosa is available under https://cblasse.github.io/premosa. Contact blasse@mpi-cbg.de or myers@mpi-cbg.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Corinna Blasse
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Stephan Saalfeld
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Raphaël Etournay
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.,Department of Neuroscience, Institut Pasteur, Paris 75015, France
| | - Andreas Sagner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.,The Francis Crick Institute, London NW1 1AT, UK
| | - Suzanne Eaton
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.,Center for Systems Biology Dresden, Germany
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34
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Chait R, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer-interfaced control of individual cells. Nat Commun 2017; 8:1535. [PMID: 29142298 PMCID: PMC5688142 DOI: 10.1038/s41467-017-01683-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/09/2017] [Indexed: 12/03/2022] Open
Abstract
Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell–cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior. Individual bacteria interact with each other and their environment to produce population-level patterns of gene expression. Here the authors use an automated platform combined with optogenetic feedback to manipulate population behaviors through dynamic control of individual cells.
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Affiliation(s)
- Remy Chait
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
| | - Jakob Ruess
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Inria Saclay, Ile-de-France, Palaiseau, 91120, France.,Institut Pasteur, 75724, Paris Cedex 15, France
| | - Tobias Bergmiller
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
| | - Gašper Tkačik
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
| | - Călin C Guet
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.
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35
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Larson KM, Zhang L, Badger GJ, Jay GD. Early genetic restoration of lubricin expression in transgenic mice mitigates chondrocyte peroxynitrite release and caspase-3 activation. Osteoarthritis Cartilage 2017; 25:1488-1495. [PMID: 28579418 PMCID: PMC5565702 DOI: 10.1016/j.joca.2017.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 05/10/2017] [Accepted: 05/25/2017] [Indexed: 02/02/2023]
Abstract
OBJECTIVE This study investigated the ability of endogenous lubricin secretion to restore joint health following a brief <21 day, postnatal lubricin-null state, in a C57BL/6J Prg4 gene trap (GT) mouse under the control of cre-recombinase. Previously we showed that re-expression of lubricin at 21 days was partly restorative of joint lubrication. DESIGN The tibio-femoral joints of adult C57BL/6J mice containing lubricin, lacking lubricin, and postnatally lacking lubricin until restoration of lubricin expression at 7 days or 14 days of age were evaluated ex vivo. At 8-weeks of age, whole joint coefficient of friction (COF), and caspase-3 activation were measured and the tibial-femoral joints histologically analyzed for degenerative changes, following progressive cyclic loading. The peroxynitrite content of femoral head cartilage from these mice prior to cyclic loading was measured. RESULTS Mice that underwent gene recombination at 7 and 14 days of age did not reestablish low COF as joint cycling time increased and were histopathologically indistinguishable from the joints of lubricin-null littermates. However, cartilage from tibio-femoral joints that underwent recombination at 7 and 14 days of age had significantly fewer caspase-3 positive cells and significantly reduced peroxynitrite content compared to lubricin-null littermates. CONCLUSIONS The biological effects of lubricin, which include limiting inflammation via peroxynitrite production and caspase-3 activation, may be achieved without completely restituting low COF. However, fully recapitulating low COF may require undamaged cartilage surfaces or absence of biofouling, which may interfere with the activity of lubricin.
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Affiliation(s)
- Katherine M. Larson
- Center for Biomedical Engineering and School of Engineering, Brown University, Providence, RI, USA
| | - Ling Zhang
- Emergency Medicine Research Laboratory, Department of Emergency Medicine, Rhode Island Hospital, Providence, RI, USA
| | - Gary J. Badger
- Department of Medical Biostatistics, University of Vermont, Burlington, VT, USA
| | - Gregory D. Jay
- Center for Biomedical Engineering and School of Engineering, Brown University, Providence, RI, USA,Emergency Medicine Research Laboratory, Department of Emergency Medicine, Rhode Island Hospital, Providence, RI, USA,Department of Emergency Medicine, Warren Alpert Medical School of Brown University, Providence, RI, USA
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36
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Mudrak NJ, Rana PS, Model MA. Calibrated brightfield-based imaging for measuring intracellular protein concentration. Cytometry A 2017; 93:297-304. [PMID: 28561905 DOI: 10.1002/cyto.a.23145] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/09/2016] [Accepted: 12/28/2016] [Indexed: 01/05/2023]
Abstract
Intracellular protein concentration is an essential cell characteristic, which manifests itself through the refractive index. The latter can be measured from two or more mutually defocused brightfield images analyzed using the TIE (transport-of-intensity equation). In practice, however, TIE does not always achieve quantitatively accurate results on biological cells. Therefore, we have developed a calibration procedure that involves successive imaging of cells in solutions containing different amounts of added protein. This allows one to directly relate the output of TIE (T) to intracellular protein concentration C (g/L). The resultant relationship has a simple form: C ≈ 1.0(T/V), where V is the cell volume (μm3 ) and 1.0 is an empirical coefficient. We used calibrated TIE imaging to characterize the regulatory volume increase (RVI) in adherent HeLa cells placed in a hyperosmotic solution. We found that while no RVI occurs over the first 30-60 min, the protein concentration fully recovers after 20 h. Because interpretation of such long experiments may depend on whether protein concentration varies significantly throughout the cell cycle, we measured this parameter in three cell lines: HeLa, MDCK and DU145. Our data indicate that protein concentration remains relatively stable in these cells. © 2017 International Society for Advancement of Cytometry.
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Affiliation(s)
- Nathan J Mudrak
- Department of Biological Sciences, Kent State University, Kent, Ohio, 44242
| | - Priyanka S Rana
- Department of Biological Sciences, Kent State University, Kent, Ohio, 44242
| | - Michael A Model
- Department of Biological Sciences, Kent State University, Kent, Ohio, 44242
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37
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Teeple E, Karamchedu NP, Larson KM, Zhang L, Badger GJ, Fleming BC, Jay GD. Arthroscopic irrigation of the bovine stifle joint increases cartilage surface friction and decreases superficial zone lubricin. J Biomech 2016; 49:3106-3110. [PMID: 27511596 PMCID: PMC5056145 DOI: 10.1016/j.jbiomech.2016.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 11/21/2022]
Abstract
The purpose of this study was to determine the effects of arthroscopic irrigation on cartilage superficial zone lubricin and surface friction. Arthroscopic partial meniscectomy is one of the most commonly performed orthopedic surgeries in the United States, but rates of osteoarthritis progression following this procedure are high. The effect of arthroscopic irrigation on articular surface lubrication has not been previously considered as a contributing factor in outcomes after arthroscopy. Fourteen bovine stifle joints were randomized to receive arthroscopic irrigation (n=7) or no treatment (n=7). Full-thickness osteochondral explants from these joints underwent friction testing to measure static and dynamic coefficients of friction. Following mechanical testing, samples were fixed and stained for lubricin. Percent integrated density, a measure of the amount of lubricin in the superficial zone (0-100µm depth), was determined. Static and dynamic coefficients of friction were found to be significantly greater in arthroscopy specimens compared to controls (p=0.02 and p<0.001, respectively). Percent integrated density of lubricin in the superficial zone was significantly lower in arthroscopy specimens compared to controls (p<0.001).
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Affiliation(s)
- Erin Teeple
- Department of Occupational and Environmental Medicine, Harvard School of Public Health, Boston, MA, USA; Department of Orthopedic Surgery, Brigham and Women׳s Hospital, Boston, MA, USA
| | - Naga Padmini Karamchedu
- Bioengineering Laboratory, Department of Orthopaedics, Warren Alpert Medical School, Brown University/Rhode Island Hospital, Providence, RI, USA
| | | | - Ling Zhang
- Department of Emergency Medicine, Brown University/Rhode Island Hospital, Providence, RI, USA
| | - Gary J Badger
- Department of Medical Biostatistics, University of Vermont, Burlington, VT, USA
| | - Braden C Fleming
- School of Engineering, Brown University, Providence, RI, USA; Bioengineering Laboratory, Department of Orthopaedics, Warren Alpert Medical School, Brown University/Rhode Island Hospital, Providence, RI, USA
| | - Gregory D Jay
- School of Engineering, Brown University, Providence, RI, USA; Department of Emergency Medicine, Brown University/Rhode Island Hospital, Providence, RI, USA.
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38
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Bhadriraju K, Halter M, Amelot J, Bajcsy P, Chalfoun J, Vandecreme A, Mallon BS, Park KY, Sista S, Elliott JT, Plant AL. Large-scale time-lapse microscopy of Oct4 expression in human embryonic stem cell colonies. Stem Cell Res 2016; 17:122-9. [PMID: 27286574 PMCID: PMC5012928 DOI: 10.1016/j.scr.2016.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/15/2016] [Accepted: 05/20/2016] [Indexed: 01/06/2023] Open
Abstract
Identification and quantification of the characteristics of stem cell preparations is critical for understanding stem cell biology and for the development and manufacturing of stem cell based therapies. We have developed image analysis and visualization software that allows effective use of time-lapse microscopy to provide spatial and dynamic information from large numbers of human embryonic stem cell colonies. To achieve statistically relevant sampling, we examined >680 colonies from 3 different preparations of cells over 5 days each, generating a total experimental dataset of 0.9 terabyte (TB). The 0.5 Giga-pixel images at each time point were represented by multi-resolution pyramids and visualized using the Deep Zoom Javascript library extended to support viewing Giga-pixel images over time and extracting data on individual colonies. We present a methodology that enables quantification of variations in nominally-identical preparations and between colonies, correlation of colony characteristics with Oct4 expression, and identification of rare events.
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Affiliation(s)
- Kiran Bhadriraju
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Michael Halter
- Biosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Julien Amelot
- Software Systems Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Peter Bajcsy
- Software Systems Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Joe Chalfoun
- Software Systems Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Antoine Vandecreme
- Software Systems Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Barbara S Mallon
- The NIH Stem Cell Unit, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, NIH, U.S. Department of Health and Human Services, Bethesda, MD, USA
| | - Kye-Yoon Park
- The NIH Stem Cell Unit, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, NIH, U.S. Department of Health and Human Services, Bethesda, MD, USA
| | - Subhash Sista
- Biosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - John T Elliott
- Biosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Anne L Plant
- Biosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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Abstract
Probes and biosensors that incorporate luminescent Tb(III) or Eu(III) complexes are promising for cellular imaging because time-gated microscopes can detect their long-lifetime (approximately milliseconds) emission without interference from short-lifetime (approximately nanoseconds) fluorescence background. Moreover, the discrete, narrow emission bands of Tb(III) complexes make them uniquely suited for multiplexed imaging applications because they can serve as Förster resonance energy transfer (FRET) donors to two or more differently colored acceptors. However, lanthanide complexes have low photon emission rates that can limit the image signal/noise ratio, which has a square-root dependence on photon counts. This work describes the performance of a wide-field, time-gated microscope with respect to its ability to image Tb(III) luminescence and Tb(III)-mediated FRET in cultured mammalian cells. The system employed a UV-emitting LED for low-power, pulsed excitation and an intensified CCD camera for gated detection. Exposure times of ∼1 s were needed to collect 5-25 photons per pixel from cells that contained micromolar concentrations of a Tb(III) complex. The observed photon counts matched those predicted by a theoretical model that incorporated the photophysical properties of the Tb(III) probe and the instrument's light-collection characteristics. Despite low photon counts, images of Tb(III)/green fluorescent protein FRET with a signal/noise ratio ≥ 7 were acquired, and a 90% change in the ratiometric FRET signal was measured. This study shows that the sensitivity and precision of lanthanide-based cellular microscopy can approach that of conventional FRET microscopy with fluorescent proteins. The results should encourage further development of lanthanide biosensors that can measure analyte concentration, enzyme activation, and protein-protein interactions in live cells.
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KASK PEET, PALO KAUPO, HINNAH CHRIS, POMMERENCKE THORA. Flat field correction for high‐throughput imaging of fluorescent samples. J Microsc 2016; 263:328-40. [DOI: 10.1111/jmi.12404] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 01/12/2016] [Accepted: 02/16/2016] [Indexed: 11/26/2022]
Affiliation(s)
- PEET KASK
- PerkinElmer Cellular Technologies Germany GmbH Hamburg Germany
| | - KAUPO PALO
- PerkinElmer Cellular Technologies Germany GmbH Hamburg Germany
| | - CHRIS HINNAH
- PerkinElmer Cellular Technologies Germany GmbH Hamburg Germany
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41
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Beal J, Haddock-Angelli T, Gershater M, de Mora K, Lizarazo M, Hollenhorst J, Rettberg R. Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli. PLoS One 2016; 11:e0150182. [PMID: 26937966 PMCID: PMC4777433 DOI: 10.1371/journal.pone.0150182] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/10/2016] [Indexed: 11/18/2022] Open
Abstract
We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1.54-fold standard deviation for the ratio between strong promoters to 5.75-fold for the ratio between the strongest and weakest promoter, and while host strain did not affect expression ratios, choice of instrument did. This result shows that high quantitative precision and reproducibility of results is possible, while at the same time indicating areas needing improved laboratory practices.
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Affiliation(s)
- Jacob Beal
- Raytheon BBN Technologies, Cambridge, MA, United States of America
- * E-mail:
| | | | | | - Kim de Mora
- iGEM Foundation, Cambridge, MA, United States of America
| | | | | | - Randy Rettberg
- iGEM Foundation, Cambridge, MA, United States of America
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42
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Wang L, Bell P, Somanathan S, Wang Q, He Z, Yu H, McMenamin D, Goode T, Calcedo R, Wilson JM. Comparative Study of Liver Gene Transfer With AAV Vectors Based on Natural and Engineered AAV Capsids. Mol Ther 2015; 23:1877-87. [PMID: 26412589 PMCID: PMC4700115 DOI: 10.1038/mt.2015.179] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/17/2015] [Indexed: 12/13/2022] Open
Abstract
Vectors based on the clade E family member adeno-associated virus (AAV) serotype 8 have shown promise in patients with hemophilia B and have emerged as best in class for human liver gene therapies. We conducted a thorough evaluation of liver-directed gene therapy using vectors based on several natural and engineered capsids including the clade E AAVrh10 and the largely uncharacterized and phylogenically distinct AAV3B. Included in this study was a putatively superior hepatotropic capsid, AAVLK03, which is very similar to AAV3B. Vectors based on these capsids were benchmarked against AAV8 and AAV2 in a number of in vitro and in vivo model systems including C57BL/6 mice, immune-deficient mice that are partially repopulated with human hepatocytes, and nonhuman primates. Our studies in nonhuman primates and human hepatocytes demonstrated high level transduction of the clade E-derived vectors and equally high transduction with vectors based on AAV3B. In contrast to previous reports, AAVLK03 vectors are not superior to either AAV3B or AAV8. Vectors based on AAV3B should be considered for liver-directed gene therapy when administered following, or before, treatment with the serologically distinct clade E vectors.
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Affiliation(s)
- Lili Wang
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Peter Bell
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Suryanarayan Somanathan
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Qiang Wang
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Zhenning He
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hongwei Yu
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Deirdre McMenamin
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Tamara Goode
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Roberto Calcedo
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - James M Wilson
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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43
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Bajcsy P, Cardone A, Chalfoun J, Halter M, Juba D, Kociolek M, Majurski M, Peskin A, Simon C, Simon M, Vandecreme A, Brady M. Survey statistics of automated segmentations applied to optical imaging of mammalian cells. BMC Bioinformatics 2015; 16:330. [PMID: 26472075 PMCID: PMC4608288 DOI: 10.1186/s12859-015-0762-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 10/07/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The goal of this survey paper is to overview cellular measurements using optical microscopy imaging followed by automated image segmentation. The cellular measurements of primary interest are taken from mammalian cells and their components. They are denoted as two- or three-dimensional (2D or 3D) image objects of biological interest. In our applications, such cellular measurements are important for understanding cell phenomena, such as cell counts, cell-scaffold interactions, cell colony growth rates, or cell pluripotency stability, as well as for establishing quality metrics for stem cell therapies. In this context, this survey paper is focused on automated segmentation as a software-based measurement leading to quantitative cellular measurements. METHODS We define the scope of this survey and a classification schema first. Next, all found and manually filteredpublications are classified according to the main categories: (1) objects of interests (or objects to be segmented), (2) imaging modalities, (3) digital data axes, (4) segmentation algorithms, (5) segmentation evaluations, (6) computational hardware platforms used for segmentation acceleration, and (7) object (cellular) measurements. Finally, all classified papers are converted programmatically into a set of hyperlinked web pages with occurrence and co-occurrence statistics of assigned categories. RESULTS The survey paper presents to a reader: (a) the state-of-the-art overview of published papers about automated segmentation applied to optical microscopy imaging of mammalian cells, (b) a classification of segmentation aspects in the context of cell optical imaging, (c) histogram and co-occurrence summary statistics about cellular measurements, segmentations, segmented objects, segmentation evaluations, and the use of computational platforms for accelerating segmentation execution, and (d) open research problems to pursue. CONCLUSIONS The novel contributions of this survey paper are: (1) a new type of classification of cellular measurements and automated segmentation, (2) statistics about the published literature, and (3) a web hyperlinked interface to classification statistics of the surveyed papers at https://isg.nist.gov/deepzoomweb/resources/survey/index.html.
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Affiliation(s)
- Peter Bajcsy
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Antonio Cardone
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Joe Chalfoun
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Michael Halter
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Derek Juba
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | | | - Michael Majurski
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Adele Peskin
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Carl Simon
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Mylene Simon
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Antoine Vandecreme
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Mary Brady
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
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44
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Chalfoun J, Majurski M, Bhadriraju K, Lund S, Bajcsy P, Brady M. Background intensity correction for terabyte-sized time-lapse images. J Microsc 2014; 257:226-37. [PMID: 25623496 DOI: 10.1111/jmi.12205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 11/14/2014] [Indexed: 12/26/2022]
Abstract
Several computational challenges associated with large-scale background image correction of terabyte-sized fluorescent images are discussed and analysed in this paper. Dark current, flat-field and background correction models are applied over a mosaic of hundreds of spatially overlapping fields of view (FOVs) taken over the course of several days, during which the background diminishes as cell colonies grow. The motivation of our work comes from the need to quantify the dynamics of OCT-4 gene expression via a fluorescent reporter in human stem cell colonies. Our approach to background correction is formulated as an optimization problem over two image partitioning schemes and four analytical correction models. The optimization objective function is evaluated in terms of (1) the minimum root mean square (RMS) error remaining after image correction, (2) the maximum signal-to-noise ratio (SNR) reached after downsampling and (3) the minimum execution time. Based on the analyses with measured dark current noise and flat-field images, the most optimal GFP background correction is obtained by using a data partition based on forming a set of submosaic images with a polynomial surface background model. The resulting image after correction is characterized by an RMS of about 8, and an SNR value of a 4 × 4 downsampling above 5 by Rose criterion. The new technique generates an image with half RMS value and double SNR value when compared to an approach that assumes constant background throughout the mosaic. We show that the background noise in terabyte-sized fluorescent image mosaics can be corrected computationally with the optimized triplet (data partition, model, SNR driven downsampling) such that the total RMS value from background noise does not exceed the magnitude of the measured dark current noise. In this case, the dark current noise serves as a benchmark for the lowest noise level that an imaging system can achieve. In comparison to previous work, the past fluorescent image background correction methods have been designed for single FOV and have not been applied to terabyte-sized images with large mosaic FOVs, low SNR and diminishing access to background information over time as cell colonies span entirely multiple FOVs. The code is available as open-source from the following link https://isg.nist.gov/.
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Affiliation(s)
- J Chalfoun
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, U.S.A
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45
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Piccinini F, Pierini M, Lucarelli E, Bevilacqua A. Semi-quantitative monitoring of confluence of adherent mesenchymal stromal cells on calcium-phosphate granules by using widefield microscopy images. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2014; 25:2395-2410. [PMID: 24863020 DOI: 10.1007/s10856-014-5242-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 05/13/2014] [Indexed: 06/03/2023]
Abstract
The analysis of cell confluence and proliferation is essential to design biomaterials and scaffolds to use as bone substitutes in clinical applications. Accordingly, several approaches have been proposed in the literature to estimate the area of the scaffold covered by cells. Nevertheless, most of the approaches rely on sophisticated equipment not employed for routine analyses, while the rest of them usually do not provide significant statistics about the cell distribution. This research aims at studying confluence and proliferation of mesenchymal stromal cells (MSC) adherent on OSPROLIFE(®), a commercial biomaterial in the form of granules. In particular, we propose a Computer Vision approach that can routinely be employed to monitor the surface of the single granules covered by cells because only a standard widefield fluorescent microscope is required. In order to acquire significant statistics data, we analyse wide-area images built by using MicroMos v2.0, an updated version of a previously published software specific for stitching brightfield and phase-contrast images manually acquired via a widefield microscope. In particular, MicroMos v2.0 permits to build accurate "mosaics" of fluorescent images, after correcting vignetting and photo-bleaching effects, providing a consistent representation of a sample region containing numerous granules. Then, our method allows to make automatically a statistically significant estimate of the percentage of the area of the single granules covered by cells. Finally, by analysing hundreds of granules at different time intervals we also obtained reliable data regarding cell proliferation, confirming that not only MSC adhere onto the OSPROLIFE(®) granules, but even proliferate over time.
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Affiliation(s)
- Filippo Piccinini
- Advanced Research Center on Electronic Systems for Information and Communication Technologies "E. De Castro" (ARCES), University of Bologna, Via Toffano 2/2, I-40125, Bologna, Italy,
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46
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Singh S, Bray MA, Jones TR, Carpenter AE. Pipeline for illumination correction of images for high-throughput microscopy. J Microsc 2014; 256:231-6. [PMID: 25228240 PMCID: PMC4359755 DOI: 10.1111/jmi.12178] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/12/2014] [Indexed: 12/24/2022]
Abstract
The presence of systematic noise in images in high-throughput microscopy experiments can significantly impact the accuracy of downstream results. Among the most common sources of systematic noise is non-homogeneous illumination across the image field. This often adds an unacceptable level of noise, obscures true quantitative differences and precludes biological experiments that rely on accurate fluorescence intensity measurements. In this paper, we seek to quantify the improvement in the quality of high-content screen readouts due to software-based illumination correction. We present a straightforward illumination correction pipeline that has been used by our group across many experiments. We test the pipeline on real-world high-throughput image sets and evaluate the performance of the pipeline at two levels: (a) Z′-factor to evaluate the effect of the image correction on a univariate readout, representative of a typical high-content screen, and (b) classification accuracy on phenotypic signatures derived from the images, representative of an experiment involving more complex data mining. We find that applying the proposed post-hoc correction method improves performance in both experiments, even when illumination correction has already been applied using software associated with the instrument. To facilitate the ready application and future development of illumination correction methods, we have made our complete test data sets as well as open-source image analysis pipelines publicly available. This software-based solution has the potential to improve outcomes for a wide-variety of image-based HTS experiments.
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Affiliation(s)
- S Singh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, U.S.A
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47
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Halter M, Bier E, DeRose PC, Cooksey GA, Choquette SJ, Plant AL, Elliott JT. An automated protocol for performance benchmarking a widefield fluorescence microscope. Cytometry A 2014; 85:978-85. [DOI: 10.1002/cyto.a.22519] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 07/11/2014] [Accepted: 07/22/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Michael Halter
- Biosystems and Biomaterials Division, Materials Measurement Laboratory; National Institute of Standards and Technology; Gaithersburg Maryland 20899
| | - Elianna Bier
- Department of Physics; Augsburg College; Minneapolis Minnesota 55454
| | - Paul C. DeRose
- Biosystems and Biomaterials Division, Materials Measurement Laboratory; National Institute of Standards and Technology; Gaithersburg Maryland 20899
| | - Gregory A. Cooksey
- Biosystems and Biomaterials Division, Materials Measurement Laboratory; National Institute of Standards and Technology; Gaithersburg Maryland 20899
| | - Steven J. Choquette
- Biosystems and Biomaterials Division, Materials Measurement Laboratory; National Institute of Standards and Technology; Gaithersburg Maryland 20899
| | - Anne L. Plant
- Biosystems and Biomaterials Division, Materials Measurement Laboratory; National Institute of Standards and Technology; Gaithersburg Maryland 20899
| | - John T. Elliott
- Biosystems and Biomaterials Division, Materials Measurement Laboratory; National Institute of Standards and Technology; Gaithersburg Maryland 20899
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48
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Diaz-de-Quijano D, Palacios P, Horňák K, Felip M. 3D restoration microscopy improves quantification of enzyme-labeled fluorescence-based single-cell phosphatase activity in plankton. Cytometry A 2014; 85:841-53. [PMID: 24845646 DOI: 10.1002/cyto.a.22486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 01/22/2014] [Accepted: 04/30/2014] [Indexed: 11/10/2022]
Abstract
The ELF or fluorescence-labeled enzyme activity (FLEA) technique is a culture-independent single-cell tool for assessing plankton enzyme activity in close-to-in situ conditions. We demonstrate that single-cell FLEA quantifications based on two-dimensional (2D) image analysis were biased by up to one order of magnitude relative to deconvolved 3D. This was basically attributed to out-of-focus light, and partially to object size. Nevertheless, if sufficient cells were measured (25-40 cells), biases in individual 2D cell measurements were partially compensated, providing useful and comparable results to deconvolved 3D. We also discuss how much caution should be used when comparing the single-cell enzyme activities of different sized bacterio- and/or phytoplankton populations measured on 2D images. Finally, a novel method based on deconvolved 3D images (wide field restoration microscopy; WFR) was devised to improve the discrimination of similar single-cell enzyme activities, the comparison of enzyme activities between different size cells, the measurement of low fluorescence intensities, the quantification of less numerous species, and the combination of the FLEA technique with other single-cell methods. These improvements in cell enzyme activity measurements will provide a more precise picture of individual species' behavior in nature, which is essential to understand their functional role and evolutionary history.
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Affiliation(s)
- Daniel Diaz-de-Quijano
- Unitat de Limnologia, Departament d'Ecologia i Centre de Recerca d'Alta Muntanya, CEAB-CSIC-Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
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49
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Model M. Intensity calibration and flat-field correction for fluorescence microscopes. CURRENT PROTOCOLS IN CYTOMETRY 2014; 68:10.14.1-10.14.10. [PMID: 24692055 DOI: 10.1002/0471142956.cy1014s68] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Standardization in fluorescence microscopy involves calibration of intensity in reproducible units and correction for spatial nonuniformity of illumination (flat-field or shading correction). Both goals can be achieved using concentrated solutions of fluorescent dyes. When a drop of a highly concentrated fluorescent dye is placed between a slide and a coverslip it produces a spatially uniform field, resistant to photobleaching and with reproducible quantum yield; it can be used as a brightness standard for wide-field and confocal microscopes. For wide-field microscopes, calibration can be further extended to absolute molecular units. This can be done by imaging a solution of known concentration and known depth; the latter can be prepared by placing a small spherical lens in a diluted solution of the same fluorophore that is used in the biological specimen.
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Affiliation(s)
- Michael Model
- Department of Biological Sciences, Kent State University, Kent, Ohio
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50
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Oslizlo A, Stefanic P, Dogsa I, Mandic-Mulec I. Private link between signal and response in Bacillus subtilis quorum sensing. Proc Natl Acad Sci U S A 2014; 111:1586-91. [PMID: 24425772 PMCID: PMC3910598 DOI: 10.1073/pnas.1316283111] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria coordinate their behavior using quorum sensing (QS), whereby cells secrete diffusible signals that generate phenotypic responses associated with group living. The canonical model of QS is one of extracellular signaling, where signal molecules bind to cognate receptors and cause a coordinated response across many cells. Here we study the link between QS input (signaling) and QS output (response) in the ComQXPA QS system of Bacillus subtilis by characterizing the phenotype and fitness of comQ null mutants. These lack the enzyme to produce the ComX signal and do not activate the ComQXPA QS system in other cells. In addition to the activation effect of the signal, however, we find evidence of a second, repressive effect of signal production on the QS system. Unlike activation, which can affect other cells, repression acts privately: the de-repression of QS in comQ cells is intracellular and only affects mutant cells lacking ComQ. As a result, the QS signal mutants have an overly responsive QS system and overproduce the secondary metabolite surfactin in the presence of the signal. This surfactin overproduction is associated with a strong fitness cost, as resources are diverted away from primary metabolism. Therefore, by acting as a private QS repressor, ComQ may be protected against evolutionary competition from loss-of-function mutations. Additionally, we find that surfactin participates in a social selection mechanism that targets signal null mutants in coculture with signal producers. Our study shows that by pleiotropically combining intracellular and extracellular signaling, bacteria may generate evolutionarily stable QS systems.
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Affiliation(s)
- Anna Oslizlo
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Polonca Stefanic
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Iztok Dogsa
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Ines Mandic-Mulec
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
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