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Lahlou A, Tehrani HS, Coghill I, Shpinov Y, Mandal M, Plamont MA, Aujard I, Niu Y, Nedbal L, Lazár D, Mahou P, Supatto W, Beaurepaire E, Eisenmann I, Desprat N, Croquette V, Jeanneret R, Le Saux T, Jullien L. Fluorescence to measure light intensity. Nat Methods 2023; 20:1930-1938. [PMID: 37996751 PMCID: PMC10703675 DOI: 10.1038/s41592-023-02063-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/02/2023] [Indexed: 11/25/2023]
Abstract
Despite the need for quantitative measurements of light intensity across many scientific disciplines, existing technologies for measuring light dose at the sample of a fluorescence microscope cannot simultaneously retrieve light intensity along with spatial distribution over a wide range of wavelengths and intensities. To address this limitation, we developed two rapid and straightforward protocols that use organic dyes and fluorescent proteins as actinometers. The first protocol relies on molecular systems whose fluorescence intensity decays and/or rises in a monoexponential fashion when constant light is applied. The second protocol relies on a broad-absorbing photochemically inert fluorophore to back-calculate the light intensity from one wavelength to another. As a demonstration of their use, the protocols are applied to quantitatively characterize the spatial distribution of light of various fluorescence imaging systems, and to calibrate illumination of commercially available instruments and light sources.
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Affiliation(s)
- Aliénor Lahlou
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France.
- Sony Computer Science Laboratories, Paris, France.
| | - Hessam Sepasi Tehrani
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Ian Coghill
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Yuriy Shpinov
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Mrinal Mandal
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Marie-Aude Plamont
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Isabelle Aujard
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Yuxi Niu
- Institute of Bio- and Geosciences/Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Ladislav Nedbal
- Institute of Bio- and Geosciences/Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Dusan Lazár
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, Palaiseau, France
| | - Willy Supatto
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, Palaiseau, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, Palaiseau, France
| | - Isabelle Eisenmann
- Laboratory of Physics of the École Normale Supérieure, University of PSL, CNRS, Sorbonne University, University of Paris City, Paris, France
- Institute of Biology of ENS (IBENS), École Normale Supérieure, CNRS, INSERM, University of PSL, Paris, France
| | - Nicolas Desprat
- Laboratory of Physics of the École Normale Supérieure, University of PSL, CNRS, Sorbonne University, University of Paris City, Paris, France
- Institute of Biology of ENS (IBENS), École Normale Supérieure, CNRS, INSERM, University of PSL, Paris, France
| | - Vincent Croquette
- Laboratory of Physics of the École Normale Supérieure, University of PSL, CNRS, Sorbonne University, University of Paris City, Paris, France
- Institute of Biology of ENS (IBENS), École Normale Supérieure, CNRS, INSERM, University of PSL, Paris, France
| | - Raphaël Jeanneret
- Laboratory of Physics of the École Normale Supérieure, University of PSL, CNRS, Sorbonne University, University of Paris City, Paris, France
- Institute of Biology of ENS (IBENS), École Normale Supérieure, CNRS, INSERM, University of PSL, Paris, France
| | - Thomas Le Saux
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France.
| | - Ludovic Jullien
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France.
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Abrams B, Pengo T, Wee TL, Deagle RC, Vuillemin N, Callahan LM, Smith MA, Kubow KE, Girard AM, Rappoport JZ, Bayles CJ, Cameron LA, Cole R, Brown CM. Tissue-Like 3D Standard and Protocols for Microscope Quality Management. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:616-634. [PMID: 37749742 PMCID: PMC10617369 DOI: 10.1093/micmic/ozad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/30/2022] [Accepted: 01/24/2023] [Indexed: 09/27/2023]
Abstract
This article outlines a global study conducted by the Association of Biomedical Resource Facilities (ABRF) Light Microscopy Research Group (LMRG). The results present a novel 3D tissue-like biologically relevant standard sample that is affordable and straightforward to prepare. Detailed sample preparation, instrument-specific image acquisition protocols and image analysis methods are presented and made available to the community. The standard consists of sub-resolution and large well characterized relative intensity fluorescence microspheres embedded in a 120 µm thick 3D gel with a refractive index of 1.365. The standard allows the evaluation of several properties as a function of depth. These include the following: 1) microscope resolution with automated analysis of the point-spread function (PSF), 2) automated signal-to-noise ratio analysis, 3) calibration and correction of fluorescence intensity loss, and 4) quantitative relative intensity. Results demonstrate expected refractive index mismatch dependent losses in intensity and resolution with depth, but the relative intensities of different objects at similar depths are maintained. This is a robust standard showing reproducible results across laboratories, microscope manufacturers and objective lens types (e.g., magnification, immersion medium). Thus, these tools will be valuable for the global community to benchmark fluorescence microscopes and will contribute to improved scientific rigor and reproducibility.
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Affiliation(s)
- Benjamin Abrams
- Life Sciences Microscopy Center, 150 Sinsheimer Labs, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA, RRID:SCR_021135
| | - Thomas Pengo
- Informatics Institute, University of Minnesota Twin Cities, Cancer and Cardiovascular Research Building, 2231 6th St SE, Minneapolis, MN 55449, USA
| | - Tse-Luen Wee
- Advanced BioImaging Facility (ABIF), McGill University, 3649 Prom, Sir William Osler, Bellini Building, Room 137, Montreal, QC H3G 0B1, Canada, RRID:SCR_017697
- Department of Physiology, McGill University, Montreal, QC
- Current affiliation: St. Giles Foundation Advanced Microscopy Center, Cold Spring Harbor Laboratory, One Bungtown Rd., Cold Spring Harbor, NY, 11724, USA, RRID:SCR_023023
| | - Rebecca C. Deagle
- Advanced BioImaging Facility (ABIF), McGill University, 3649 Prom, Sir William Osler, Bellini Building, Room 137, Montreal, QC H3G 0B1, Canada, RRID:SCR_017697
- Department of Physiology, McGill University, Montreal, QC
| | - Nelly Vuillemin
- Advanced BioImaging Facility (ABIF), McGill University, 3649 Prom, Sir William Osler, Bellini Building, Room 137, Montreal, QC H3G 0B1, Canada, RRID:SCR_017697
- Department of Physiology, McGill University, Montreal, QC
| | - Linda M. Callahan
- Department of Neuroscience, Del Monte Institute for Neuroscience, Univ. Rochester Medical Center, Rochester, NY 14642, USA
| | - Megan A. Smith
- Advanced BioImaging Facility (ABIF), McGill University, 3649 Prom, Sir William Osler, Bellini Building, Room 137, Montreal, QC H3G 0B1, Canada, RRID:SCR_017697
| | - Kristopher E. Kubow
- Biology Department, James Madison University, Bioscience Building, 951 Carrier Drive, Harrisonburg, VA 22807, USA, RRID:SCR_021904
| | - Anne-Marie Girard
- Center for Genome Research and Biocomputing, Oregon State University, 1500 SW Jefferson Way Corvallis, OR 97331, USA
| | - Joshua Z. Rappoport
- Center for Advanced Microscopy and Nikon Imaging Center, Feinberg School of Medicine, Northwestern Medicine, Northwestern University, Chicago, IL, USA
- Current affiliation: Boston College, 140 Commonwealth Avenue, Chestnut Hill, Massachusetts, USA
| | - Carol J. Bayles
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Lisa A. Cameron
- Light Microscopy Core Facility, Duke University, 4215 French Family Science Center, 124 Science Drive, Durham, NC 27708, USA
| | - Richard Cole
- New York State Dept of Health/Wadsworth Center, Advanced Light Microscopy & Image Analysis Core Facility, 150 New Scotland Ave, Albany, NY 12208, USA, RRID:SCR_021104
| | - Claire M. Brown
- Advanced BioImaging Facility (ABIF), McGill University, 3649 Prom, Sir William Osler, Bellini Building, Room 137, Montreal, QC H3G 0B1, Canada, RRID:SCR_017697
- Department of Physiology, McGill University, Montreal, QC
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3
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Cuny AP, Schlottmann FP, Ewald JC, Pelet S, Schmoller KM. Live cell microscopy: From image to insight. BIOPHYSICS REVIEWS 2022; 3:021302. [PMID: 38505412 PMCID: PMC10903399 DOI: 10.1063/5.0082799] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/18/2022] [Indexed: 03/21/2024]
Abstract
Live-cell microscopy is a powerful tool that can reveal cellular behavior as well as the underlying molecular processes. A key advantage of microscopy is that by visualizing biological processes, it can provide direct insights. Nevertheless, live-cell imaging can be technically challenging and prone to artifacts. For a successful experiment, many careful decisions are required at all steps from hardware selection to downstream image analysis. Facing these questions can be particularly intimidating due to the requirement for expertise in multiple disciplines, ranging from optics, biophysics, and programming to cell biology. In this review, we aim to summarize the key points that need to be considered when setting up and analyzing a live-cell imaging experiment. While we put a particular focus on yeast, many of the concepts discussed are applicable also to other organisms. In addition, we discuss reporting and data sharing strategies that we think are critical to improve reproducibility in the field.
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Affiliation(s)
| | - Fabian P. Schlottmann
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Jennifer C. Ewald
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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4
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Recent advances in the standardization of fluorescence microscopy for quantitative image analysis. Biophys Rev 2021; 14:33-39. [DOI: 10.1007/s12551-021-00871-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/22/2021] [Indexed: 12/19/2022] Open
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5
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Spectroscopic Approach to Correction and Visualisation of Bright-Field Light Transmission Microscopy Biological Data. PHOTONICS 2021. [DOI: 10.3390/photonics8080333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The most realistic information about a transparent sample such as a live cell can be obtained using bright-field light microscopy. Under high-intensity pulsing LED illumination, we captured a primary 12-bit-per-channel (bpc) response from an observed sample using a bright-field microscope equipped with a high-resolution (4872 × 3248) image sensor. In order to suppress data distortions originating from the light interactions with elements in the optical path, poor sensor reproduction (geometrical defects of the camera sensor and some peculiarities of sensor sensitivity), we propose a spectroscopic approach for the correction of these uncompressed 12 bpc data by simultaneous calibration of all parts of the experimental arrangement. Moreover, the final intensities of the corrected images are proportional to the photon fluxes detected by a camera sensor. It can be visualized in 8 bpc intensity depth after the Least Information Loss compression.
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6
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Schmidt GW, Cuny AP, Rudolf F. Preventing Photomorbidity in Long-Term Multi-color Fluorescence Imaging of Saccharomyces cerevisiae and S. pombe. G3 (BETHESDA, MD.) 2020; 10:4373-4385. [PMID: 33023973 PMCID: PMC7718758 DOI: 10.1534/g3.120.401465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022]
Abstract
Time-lapse imaging of live cells using multiple fluorescent reporters is an essential tool to study molecular processes in single cells. However, exposure to even moderate doses of visible excitation light can disturb cellular physiology and alter the quantitative behavior of the cells under study. Here, we set out to develop guidelines to avoid the confounding effects of excitation light in multi-color long-term imaging. We use widefield fluorescence microscopy to measure the effect of the administered excitation light on growth rate (here called photomorbidity) in yeast. We find that photomorbidity is determined by the cumulative light dose at each wavelength, but independent of the way excitation light is applied. Importantly, photomorbidity possesses a threshold light dose below which no effect is detectable (NOEL). We found, that the suitability of fluorescent proteins for live-cell imaging at the respective excitation light NOEL is equally determined by the cellular autofluorescence and the fluorescent protein brightness. Last, we show that photomorbidity of multiple wavelengths is additive and imaging conditions absent of photomorbidity can be predicted. Our findings enable researchers to find imaging conditions with minimal impact on physiology and can provide framework for how to approach photomorbidity in other organisms.
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Affiliation(s)
- Gregor W Schmidt
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland and
| | - Andreas P Cuny
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland and
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Fabian Rudolf
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland and
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
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7
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Nut and Bolt Microfluidics with Helical Minichannel for Counting CD4+ T-Cells. Bioengineering (Basel) 2019; 6:bioengineering6010024. [PMID: 30875995 PMCID: PMC6466421 DOI: 10.3390/bioengineering6010024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/07/2019] [Accepted: 03/12/2019] [Indexed: 01/01/2023] Open
Abstract
In this study, we developed the prototype of an optical imaging-based point-of-care (POC) device for monitoring human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) progression that can detect CD4+ T-lymphocytes in human blood. The proposed portable cell-counting system, Helios CD4 Analyzer (Helios), can acquire sample images and analyze the cells automatically using a simple fluorescence imaging module and sample cartridge with a three-dimensional (3D) helical minichannel. The helical minichannel formed on the cylindrical surface enables the sample cartridge to hold a cell suspension present in a fixed sample volume for absolute counting of the cells. With a given total channel length, the helical minichannel-based sample cartridge is smaller than the conventional sample cartridge with a planar microchannel. The implemented nut and bolt mechanism allows the scanning of a relatively large volume of the sample along the helical minichannel by just rotating the cylindrical chamber coupled with a single DC motor rather than using a two-axis motorized translation stage, which considerably simplifies the associated electromechanical parts. It has distinct advantages over the existing devices because of its small size and simple scanning mechanism. We optimized various imaging parameters to enhance the fluorescence detection efficiency of the prototype. Performance evaluations using human blood samples demonstrated good agreement for low CD4 count between the Helios and the PIMATM, one of the most widely used POC CD4+ analyzers.
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8
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Mahn M, Gibor L, Patil P, Cohen-Kashi Malina K, Oring S, Printz Y, Levy R, Lampl I, Yizhar O. High-efficiency optogenetic silencing with soma-targeted anion-conducting channelrhodopsins. Nat Commun 2018; 9:4125. [PMID: 30297821 PMCID: PMC6175909 DOI: 10.1038/s41467-018-06511-8] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/20/2018] [Indexed: 11/09/2022] Open
Abstract
Optogenetic silencing allows time-resolved functional interrogation of defined neuronal populations. However, the limitations of inhibitory optogenetic tools impose stringent constraints on experimental paradigms. The high light power requirement of light-driven ion pumps and their effects on intracellular ion homeostasis pose unique challenges, particularly in experiments that demand inhibition of a widespread neuronal population in vivo. Guillardia theta anion-conducting channelrhodopsins (GtACRs) are promising in this regard, due to their high single-channel conductance and favorable photon-ion stoichiometry. However, GtACRs show poor membrane targeting in mammalian cells, and the activity of such channels can cause transient excitation in the axon due to an excitatory chloride reversal potential in this compartment. Here, we address these problems by enhancing membrane targeting and subcellular compartmentalization of GtACRs. The resulting soma-targeted GtACRs show improved photocurrents, reduced axonal excitation and high light sensitivity, allowing highly efficient inhibition of neuronal activity in the mammalian brain. Current optogenetic inhibition methods like light-controlled ion pumps require high-intensity light and disrupt physiological ion gradients. Here, the authors somatically target the anion-conducting opsin GtACR to eliminate spiking in distal axons and improve photocurrents, thus enhancing its utility.
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Affiliation(s)
- Mathias Mahn
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Lihi Gibor
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Pritish Patil
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | | | - Shir Oring
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yoav Printz
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rivka Levy
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ilan Lampl
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ofer Yizhar
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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9
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de Leeuw R, Brazda P, Charl Moolman M, Kerssemakers JWJ, Solano B, Dekker NH. Measuring In Vivo Protein Dynamics Throughout the Cell Cycle Using Microfluidics. Methods Mol Biol 2017; 1624:237-252. [PMID: 28842888 DOI: 10.1007/978-1-4939-7098-8_18] [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: 12/29/2022]
Abstract
Studying the dynamics of intracellular processes and investigating the interaction of individual macromolecules in live cells is one of the main objectives of cell biology. These macromolecules move, assemble, disassemble, and reorganize themselves in distinct manners under specific physiological conditions throughout the cell cycle. Therefore, in vivo experimental methods that enable the study of individual molecules inside cells at controlled culturing conditions have proved to be powerful tools to obtain insights into the molecular roles of these macromolecules and how their individual behavior influence cell physiology. The importance of controlled experimental conditions is enhanced when the investigated phenomenon covers long time periods, or perhaps multiple cell cycles. An example is the detection and quantification of proteins during bacterial DNA replication. Wide-field microscopy combined with microfluidics is a suitable technique for this. During fluorescence experiments, microfluidics offer well-defined cellular orientation and immobilization, flow and medium interchangeability, and high-throughput long-term experimentation of cells. Here we present a protocol for the combined use of wide-field microscopy and microfluidics for the study of proteins of the Escherichia coli DNA replication process. We discuss the preparation and application of a microfluidic device, data acquisition steps, and image analysis procedures to determine the stoichiometry and dynamics of a replisome component throughout the cell cycle of live bacterial cells.
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Affiliation(s)
- Roy de Leeuw
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Delft, The Netherlands
| | - Peter Brazda
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Delft, The Netherlands
| | - M Charl Moolman
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Delft, The Netherlands
| | - J W J Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Delft, The Netherlands
| | - Belen Solano
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Delft, The Netherlands
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Delft, The Netherlands.
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10
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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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11
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Biophysical constraints of optogenetic inhibition at presynaptic terminals. Nat Neurosci 2016; 19:554-6. [PMID: 26950004 PMCID: PMC4926958 DOI: 10.1038/nn.4266] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/09/2016] [Indexed: 12/11/2022]
Abstract
We investigated the efficacy of optogenetic inhibition at presynaptic terminals using halorhodopsin, archaerhodopsin and chloride-conducting channelrhodopsins. Precisely timed activation of both archaerhodopsin and halorhodpsin at presynaptic terminals attenuated evoked release. However, sustained archaerhodopsin activation was paradoxically associated with increased spontaneous release. Activation of chloride-conducting channelrhodopsins triggered neurotransmitter release upon light onset. Our results indicate that the biophysical properties of presynaptic terminals dictate unique boundary conditions for optogenetic manipulation.
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12
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Gough A, Shun TY, Lansing Taylor D, Schurdak M. A metric and workflow for quality control in the analysis of heterogeneity in phenotypic profiles and screens. Methods 2015; 96:12-26. [PMID: 26476369 DOI: 10.1016/j.ymeth.2015.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/12/2015] [Accepted: 10/13/2015] [Indexed: 12/14/2022] Open
Abstract
Heterogeneity is well recognized as a common property of cellular systems that impacts biomedical research and the development of therapeutics and diagnostics. Several studies have shown that analysis of heterogeneity: gives insight into mechanisms of action of perturbagens; can be used to predict optimal combination therapies; and can be applied to tumors where heterogeneity is believed to be associated with adaptation and resistance. Cytometry methods including high content screening (HCS), high throughput microscopy, flow cytometry, mass spec imaging and digital pathology capture cell level data for populations of cells. However it is often assumed that the population response is normally distributed and therefore that the average adequately describes the results. A deeper understanding of the results of the measurements and more effective comparison of perturbagen effects requires analysis that takes into account the distribution of the measurements, i.e. the heterogeneity. However, the reproducibility of heterogeneous data collected on different days, and in different plates/slides has not previously been evaluated. Here we show that conventional assay quality metrics alone are not adequate for quality control of the heterogeneity in the data. To address this need, we demonstrate the use of the Kolmogorov-Smirnov statistic as a metric for monitoring the reproducibility of heterogeneity in an SAR screen, describe a workflow for quality control in heterogeneity analysis. One major challenge in high throughput biology is the evaluation and interpretation of heterogeneity in thousands of samples, such as compounds in a cell-based screen. In this study we also demonstrate that three heterogeneity indices previously reported, capture the shapes of the distributions and provide a means to filter and browse big data sets of cellular distributions in order to compare and identify distributions of interest. These metrics and methods are presented as a workflow for analysis of heterogeneity in large scale biology projects.
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Affiliation(s)
- Albert Gough
- University of Pittsburgh Drug Discovery Institute, 3501 Fifth Avenue, Pittsburgh, PA, USA; Dept. of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA, USA.
| | - Tong Ying Shun
- University of Pittsburgh Drug Discovery Institute, 3501 Fifth Avenue, Pittsburgh, PA, USA
| | - D Lansing Taylor
- University of Pittsburgh Drug Discovery Institute, 3501 Fifth Avenue, Pittsburgh, PA, USA; Dept. of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA, USA
| | - Mark Schurdak
- University of Pittsburgh Drug Discovery Institute, 3501 Fifth Avenue, Pittsburgh, PA, USA; Dept. of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA, USA
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13
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Slow unloading leads to DNA-bound β2-sliding clamp accumulation in live Escherichia coli cells. Nat Commun 2014; 5:5820. [PMID: 25520215 PMCID: PMC4284645 DOI: 10.1038/ncomms6820] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 11/11/2014] [Indexed: 11/26/2022] Open
Abstract
The ubiquitous sliding clamp facilitates processivity of the replicative polymerase and acts as a platform to recruit proteins involved in replication, recombination and repair. While the dynamics of the E. coli β2-sliding clamp have been characterized in vitro, its in vivo stoichiometry and dynamics remain unclear. To probe both β2-clamp dynamics and stoichiometry in live E. coli cells, we use custom-built microfluidics in combination with single-molecule fluorescence microscopy and photoactivated fluorescence microscopy. We quantify the recruitment, binding and turnover of β2-sliding clamps on DNA during replication. These quantitative in vivo results demonstrate that numerous β2-clamps in E. coli remain on the DNA behind the replication fork for a protracted period of time, allowing them to form a docking platform for other enzymes involved in DNA metabolism. DNA replication is accomplished by the replisome, a multi-protein complex that comprises the sliding clamp. Here, Moolman et al. present quantitative and dynamic measurements of the number of β2-sliding clamps at the single-cell level in live E. coli cells to shed light on key aspects of DNA replication.
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Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014; 114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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Jin D, Lu Y, Leif RC, Yang S, Rajendran M, Miller LW. How to build a time-gated luminescence microscope. ACTA ACUST UNITED AC 2014; 67:2.22.1-2.22.36. [PMID: 24510771 DOI: 10.1002/0471142956.cy0222s67] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The sensitivity of filter-based fluorescence microscopy techniques is limited by autofluorescence background. Time-gated detection is a practical way to suppress autofluorescence, enabling higher contrast and improved sensitivity. In the past few years, three groups of authors have demonstrated independent approaches to build robust versions of time-gated luminescence microscopes. Three detailed, step-by-step protocols are provided here for modifying standard fluorescent microscopes to permit imaging time-gated luminescence.
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Affiliation(s)
- Dayong Jin
- Advanced Cytometry Laboratories, MQ BioFocus Research Centre & Photonics Research Centre, Macquarie University, New South Wales, Australia
| | - Yiqing Lu
- Advanced Cytometry Laboratories, MQ BioFocus Research Centre & Photonics Research Centre, Macquarie University, New South Wales, Australia
| | | | - Sean Yang
- Newport Instruments, San Diego, California
| | - Megha Rajendran
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Lawrence W Miller
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
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17
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Challa AA, Stefanovic B. A novel role of vimentin filaments: binding and stabilization of collagen mRNAs. Mol Cell Biol 2011; 31:3773-89. [PMID: 21746880 PMCID: PMC3165730 DOI: 10.1128/mcb.05263-11] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 07/04/2011] [Indexed: 12/17/2022] Open
Abstract
The stem-loop in the 5' untranslated region (UTR) of collagen α1(I) and α2(I) mRNAs (5'SL) is the key element regulating their stability and translation. Stabilization of collagen mRNAs is the predominant mechanism for high collagen expression in fibrosis. LARP6 binds the 5'SL of α1(I) and α2(I) mRNAs with high affinity. Here, we report that vimentin filaments associate with collagen mRNAs in a 5'SL- and LARP6-dependent manner and stabilize collagen mRNAs. LARP6 interacts with vimentin filaments through its La domain and colocalizes with the filaments in vivo. Knockdown of LARP6 by small interfering RNA (siRNA) or mutation of the 5'SL abrogates the interaction of collagen mRNAs with vimentin filaments. Vimentin knockout fibroblasts produce reduced amounts of type I collagen due to decreased stability of collagen α1(I) and α2(I) mRNAs. Disruption of vimentin filaments using a drug or by expression of dominant-negative desmin reduces type I collagen expression, primarily due to decreased stability of collagen mRNAs. RNA fluorescence in situ hybridization (FISH) experiments show that collagen α1(I) and α2(I) mRNAs are associated with vimentin filaments in vivo. Thus, vimentin filaments may play a role in the development of tissue fibrosis by stabilizing collagen mRNAs. This finding will serve as a rationale for targeting vimentin in the development of novel antifibrotic therapies.
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Affiliation(s)
- Azariyas A. Challa
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, Florida 32306
| | - Branko Stefanovic
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, Florida 32306
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18
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Abstract
Cellular life can be described as a dynamic equilibrium of a highly complex network of interacting molecules. For this reason, it is no longer sufficient to “only” know the identity of the participants in a cellular process, but questions such as where, when, and for how long also have to be addressed to understand the mechanism being investigated. Additionally, ensemble measurements may not sufficiently describe individual steps of molecular mobility, spatial-temporal resolution, kinetic parameters, and geographical mapping. It is vital to investigate where individual steps exactly occur to enhance our understanding of the living cell. The nucleus, home too many highly complex multi-order processes, such as replication, transcription, splicing, etc., provides a complicated, heterogeneous landscape. Its dynamics were studied to a new level of detail by fluorescence correlation spectroscopy (FCS). Single-molecule tracking, while still in its infancy in cell biology, is becoming a more and more attractive method to deduce key elements of this organelle. Here we discuss the potential of tracking single RNAs and proteins in the nucleus. Their dynamics, localization, and interaction rates will be vital to our understanding of cellular life. To demonstrate this, we provide a review of the HIV life cycle, which is an extremely elegant balance of nuclear and cytoplasmic functions and provides an opportunity to study mechanisms deeply integrated within the structure of the nucleus. In summary, we aim to present a specific, dynamic view of nuclear cellular life based on single molecule and FCS data and provide a prospective for the future.
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19
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Gahlaut N, Miller LW. Time-resolved microscopy for imaging lanthanide luminescence in living cells. Cytometry A 2010; 77:1113-25. [PMID: 20824630 DOI: 10.1002/cyto.a.20964] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 07/29/2010] [Accepted: 08/02/2010] [Indexed: 11/12/2022]
Abstract
Time-resolved luminescence (TRL) microscopy can image signals from lanthanide coordination complexes or other probes with long emission lifetimes, thereby eliminating short-lifetime (<100 ns) autofluorescence background from biological specimens. However, lanthanide complexes emit far fewer photons per unit time than conventional fluorescent probes, making it difficult to rapidly acquire high quality images at probe concentrations that are relevant to live cell experiments. This article describes the development and characterization of a TRL microscope that employs a light-emitting diode (LED, λ(em) = 365 nm) for pulsed epi-illumination and an intensified charge-coupled device (ICCD) camera for gated, widefield detection. Europium chelate-impregnated microspheres were used to evaluate instrument performance in terms of short-lifetime fluorescence background rejection, photon collection efficiency, image contrast, and signal-to-noise ratio (SNR). About 200 nm microspheres were imaged within the time resolution limit of the ICCD (66.7 ms) with complete autofluorescence suppression. About 40 nm microspheres containing ~400 chelate molecules were detected within ~1-s acquisition times. A luminescent terbium complex, Lumi4-Tb®, was introduced into the cytoplasm of cultured cells at an estimated concentration of 300 nM by the method of osmotic lysis of pinocytic vesicles. Time-resolved images of the living, terbium complex-loaded cells were acquired within acquisition times as short as 333 ms, and the effects of increased exposure time and frame summing on image contrast and SNR were evaluated. The performance analyses show that TRL microscopy is sufficiently sensitive and precise to allow high-resolution, quantitative imaging of lanthanide luminescence in living cells under physiologically relevant experimental conditions.
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Affiliation(s)
- Nivriti Gahlaut
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
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20
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Powe AM, Das S, Lowry M, El-Zahab B, Fakayode SO, Geng ML, Baker GA, Wang L, McCarroll ME, Patonay G, Li M, Aljarrah M, Neal S, Warner IM. Molecular Fluorescence, Phosphorescence, and Chemiluminescence Spectrometry. Anal Chem 2010; 82:4865-94. [DOI: 10.1021/ac101131p] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Aleeta M. Powe
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Susmita Das
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Mark Lowry
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Bilal El-Zahab
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Sayo O. Fakayode
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Maxwell L. Geng
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Gary A. Baker
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Lin Wang
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Matthew E. McCarroll
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Gabor Patonay
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Min Li
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Mohannad Aljarrah
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Sharon Neal
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Isiah M. Warner
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
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