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Tavakoli M, Jazani S, Sgouralis I, Shafraz OM, Sivasankar S, Donaphon B, Levitus M, Pressé S. Pitching single-focus confocal data analysis one photon at a time with Bayesian nonparametrics. PHYSICAL REVIEW. X 2020; 10:011021. [PMID: 34540355 PMCID: PMC8445401 DOI: 10.1103/physrevx.10.011021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Fluorescence time traces are used to report on dynamical properties of molecules. The basic unit of information in these traces is the arrival time of individual photons, which carry instantaneous information from the molecule, from which they are emitted, to the detector on timescales as fast as microseconds. Thus, it is theoretically possible to monitor molecular dynamics at such timescales from traces containing only a sufficient number of photon arrivals. In practice, however, traces are stochastic and in order to deduce dynamical information through traditional means-such as fluorescence correlation spectroscopy (FCS) and related techniques-they are collected and temporally autocorrelated over several minutes. So far, it has been impossible to analyze dynamical properties of molecules on timescales approaching data acquisition without collecting long traces under the strong assumption of stationarity of the process under observation or assumptions required for the analytic derivation of a correlation function. To avoid these assumptions, we would otherwise need to estimate the instantaneous number of molecules emitting photons and their positions within the confocal volume. As the number of molecules in a typical experiment is unknown, this problem demands that we abandon the conventional analysis paradigm. Here, we exploit Bayesian nonparametrics that allow us to obtain, in a principled fashion, estimates of the same quantities as FCS but from the direct analysis of traces of photon arrivals that are significantly smaller in size, or total duration, than those required by FCS.
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Affiliation(s)
- Meysam Tavakoli
- Department of Physics, Indiana University-Purdue University Indianapolis, IN 46202
| | - Sina Jazani
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287
| | - Ioannis Sgouralis
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287
| | - Omer M. Shafraz
- Department of Biomedical Engineering, University of California, Davis, CA 95616
| | - Sanjeevi Sivasankar
- Department of Biomedical Engineering, University of California, Davis, CA 95616
| | - Bryan Donaphon
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Marcia Levitus
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287
- Biodesign Institute, Arizona State University, Tempe, AZ 85287 and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Steve Pressé
- Corresponding author. ; Website: http://statphysbio.physics.asu.edu
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An alternative framework for fluorescence correlation spectroscopy. Nat Commun 2019; 10:3662. [PMID: 31413259 PMCID: PMC6694112 DOI: 10.1038/s41467-019-11574-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
Fluorescence correlation spectroscopy (FCS), is a widely used tool routinely exploited for in vivo and in vitro applications. While FCS provides estimates of dynamical quantities, such as diffusion coefficients, it demands high signal to noise ratios and long time traces, typically in the minute range. In principle, the same information can be extracted from microseconds to seconds long time traces; however, an appropriate analysis method is missing. To overcome these limitations, we adapt novel tools inspired by Bayesian non-parametrics, which starts from the direct analysis of the observed photon counts. With this approach, we are able to analyze time traces, which are too short to be analyzed by existing methods, including FCS. Our new analysis extends the capability of single molecule fluorescence confocal microscopy approaches to probe processes several orders of magnitude faster and permits a reduction of photo-toxic effects on living samples induced by long periods of light exposure. Fluorescence correlation spectroscopy is widely used for in vivo and in vitro applications, yet extracting information from experiments still requires long acquisition times. Here, the authors exploit Bayesian non-parametrics to directly analyze the output of confocal fluorescence experiments thereby probing physical processes on much faster timescales.
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Nagy M, Rácz D, Nagy ZL, Fehér PP, Kovács SL, Bankó C, Bacsó Z, Kiss A, Zsuga M, Kéki S. Amino-isocyanoacridines: Novel, Tunable Solvatochromic Fluorophores as Physiological pH Probes. Sci Rep 2019; 9:8250. [PMID: 31160696 PMCID: PMC6547668 DOI: 10.1038/s41598-019-44760-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/23/2019] [Indexed: 11/09/2022] Open
Abstract
Amino-isocyanoacridines (ICAAcs), as first members of their class, turned out to be a novel, multifunctional acridine orange (AO) type dye family with a number of additional favorable properties. They have enhanced solvatochromic emission range, low quantum yields (ΦF = 2.9-0.4%) in water, reduced basicity (pKa = 7.05-7.58), and their optical behavior could be fine-tuned by complexation with Ag(I) ions, too. Based on both their vibronic absorption and the charge transfer bands, ICAAcs can be applied as stable pH-probes with great precision (2-3% error) in the physiological pH range of 6-8 using UV-vis and fluorescence detection. The dyes are also able to sense pH change in different microenvironments, such as the Stern layer, as it was demonstrated on sodium lauryl sulfate micelles. The optical behavior of the ICAAc derivatives is discussed based on high-level quantum chemical calculations. All three dyes are well-applicable with conventional epifluorescence imaging. Furthermore, at the blue excitation, diMICAAc is optimally suited as a whole-cell probe for both the conventional microscopic and the laser-illumination studies, like flow- and imaging cytometric, or confocal laser-scanning microscopic examinations.
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Affiliation(s)
- Miklós Nagy
- Department of Applied Chemistry, University of Debrecen, 4010, Debrecen, Hungary
| | - Dávid Rácz
- Department of Applied Chemistry, University of Debrecen, 4010, Debrecen, Hungary
| | - Zsolt László Nagy
- Department of Applied Chemistry, University of Debrecen, 4010, Debrecen, Hungary
| | - Péter Pál Fehér
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Magyar tudósok körútja 2, Budapest, Hungary
| | - Sándor Lajos Kovács
- Department of Applied Chemistry, University of Debrecen, 4010, Debrecen, Hungary
| | - Csaba Bankó
- University of Debrecen, Medical and Health Science Center, Faculty of Medicine, Department of Biophysics and Cell Biology, 4010, Debrecen, Hungary
| | - Zsolt Bacsó
- University of Debrecen, Medical and Health Science Center, Faculty of Medicine, Department of Biophysics and Cell Biology, 4010, Debrecen, Hungary
| | - Alexandra Kiss
- Department of Biotechnology and Microbiology, Faculty of Science, University of Debrecen, Debrecen, 4010, Hungary
| | - Miklós Zsuga
- Department of Applied Chemistry, University of Debrecen, 4010, Debrecen, Hungary
| | - Sándor Kéki
- Department of Applied Chemistry, University of Debrecen, 4010, Debrecen, Hungary.
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Golda-VanEeckhoutte RL, Roof LT, Needoba JA, Peterson TD. Determination of intracellular pH in phytoplankton using the fluorescent probe, SNARF, with detection by fluorescence spectroscopy. J Microbiol Methods 2018; 152:109-118. [DOI: 10.1016/j.mimet.2018.07.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 02/04/2023]
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5
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Lee-Montiel FT, George SM, Gough AH, Sharma AD, Wu J, DeBiasio R, Vernetti LA, Taylor DL. Control of oxygen tension recapitulates zone-specific functions in human liver microphysiology systems. Exp Biol Med (Maywood) 2017; 242:1617-1632. [PMID: 28409533 PMCID: PMC5661766 DOI: 10.1177/1535370217703978] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/07/2017] [Indexed: 12/20/2022] Open
Abstract
This article describes our next generation human Liver Acinus MicroPhysiology System (LAMPS). The key demonstration of this study was that Zone 1 and Zone 3 microenvironments can be established by controlling the oxygen tension in individual devices over the range of ca. 3 to 13%. The oxygen tension was computationally modeled using input on the microfluidic device dimensions, numbers of cells, oxygen consumption rates of hepatocytes, the diffusion coefficients of oxygen in different materials and the flow rate of media in the MicroPhysiology System (MPS). In addition, the oxygen tension was measured using a ratiometric imaging method with the oxygen sensitive dye, Tris(2,2'-bipyridyl) dichlororuthenium(II) hexahydrate (RTDP) and the oxygen insensitive dye, Alexa 488. The Zone 1 biased functions of oxidative phosphorylation, albumin and urea secretion and Zone 3 biased functions of glycolysis, α1AT secretion, Cyp2E1 expression and acetaminophen toxicity were demonstrated in the respective Zone 1 and Zone 3 MicroPhysiology System. Further improvements in the Liver Acinus MicroPhysiology System included improved performance of selected nonparenchymal cells, the inclusion of a porcine liver extracellular matrix to model the Space of Disse, as well as an improved media to support both hepatocytes and non-parenchymal cells. In its current form, the Liver Acinus MicroPhysiology System is most amenable to low to medium throughput, acute through chronic studies, including liver disease models, prioritizing compounds for preclinical studies, optimizing chemistry in structure activity relationship (SAR) projects, as well as in rising dose studies for initial dose ranging. Impact statement Oxygen zonation is a critical aspect of liver functions. A human microphysiology system is needed to investigate the impact of zonation on a wide range of liver functions that can be experimentally manipulated. Because oxygen zonation has such diverse physiological effects in the liver, we developed and present a method for computationally modeling and measuring oxygen that can easily be implemented in all MPS models. We have applied this method in a liver MPS in which we are then able to control oxygenation in separate devices and demonstrate that zonation-dependent hepatocyte functions in the MPS recapitulate what is known about in vivo liver physiology. We believe that this advance allows a deep experimental investigation on the role of zonation in liver metabolism and disease. In addition, modeling and measuring oxygen tension will be required as investigators migrate from PDMS to plastic and glass devices.
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Affiliation(s)
| | - Subin M George
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260,USA
| | - Albert H Gough
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260,USA
| | - Anup D Sharma
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260,USA
| | - Juanfang Wu
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Richard DeBiasio
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Lawrence A Vernetti
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260,USA
| | - D Lansing Taylor
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260,USA
- Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
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6
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Clark AJ, Petty HR. Protocol for Biomarker Ratio Imaging Microscopy with Specific Application to Ductal Carcinoma In situ of the Breast. Front Cell Dev Biol 2016; 4:120. [PMID: 27857940 PMCID: PMC5093143 DOI: 10.3389/fcell.2016.00120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/14/2016] [Indexed: 01/01/2023] Open
Abstract
This protocol describes the methods and steps involved in performing biomarker ratio imaging microscopy (BRIM) using formalin fixed paraffin-embedded (FFPE) samples of human breast tissue. The technique is based on the acquisition of two fluorescence images of the same microscopic field using two biomarkers and immunohistochemical tools. The biomarkers are selected such that one biomarker correlates with breast cancer aggressiveness while the second biomarker anti-correlates with aggressiveness. When the former image is divided by the latter image, a computed ratio image is formed that reflects the aggressiveness of tumor cells while increasing contrast and eliminating path-length and other artifacts from the image. For example, the aggressiveness of epithelial cells may be assessed by computing ratio images of N-cadherin and E-cadherin images or CD44 and CD24 images, which specifically reflect the mesenchymal or stem cell nature of the constituent cells, respectively. This methodology is illustrated for tissue samples of ductal carcinoma in situ (DCIS) and invasive breast cancer. This tool should be useful in tissue studies of experimental cancer as well as the management of cancer patients.
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Affiliation(s)
- Andrea J Clark
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School Ann Arbor, MI, USA
| | - Howard R Petty
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School Ann Arbor, MI, USA
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7
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Di W, Czarny RS, Fletcher NA, Krebs MD, Clark HA. Comparative Study of Poly (ε-Caprolactone) and Poly(Lactic-co-Glycolic Acid) -Based Nanofiber Scaffolds for pH-Sensing. Pharm Res 2016; 33:2433-44. [PMID: 27380188 PMCID: PMC5007178 DOI: 10.1007/s11095-016-1987-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/27/2016] [Indexed: 01/12/2023]
Abstract
PURPOSE This study aims to develop biodegradable and biocompatible polymer-based nanofibers that continuously monitor pH within microenvironments of cultured cells in real-time. In the future, these fibers will provide a scaffold for tissue growth while simultaneously monitoring the extracellular environment. METHODS Sensors to monitor pH were created by directly electrospinning the sensor components within a polymeric matrix. Specifically, the entire fiber structure is composed of the optical equivalent of an electrode, a pH-sensitive fluorophore, an ionic additive, a plasticizer, and a polymer to impart mechanical stability. The resulting poly(ε-caprolactone) (PCL) and poly(lactic-co-glycolic acid) (PLGA) based sensors were characterized by morphology, dynamic range, reversibility and stability. Since PCL-based nanofibers delivered the most desirable analytical response, this matrix was used for cellular studies. RESULTS Electrospun nanofiber scaffolds (NFSs) were created directly out of optode material. The resulting NFS sensors respond to pH changes with a dynamic range centered at 7.8 ± 0.1 and 9.6 ± 0.2, for PCL and PLGA respectively. NFSs exhibited multiple cycles of reversibility with a lifetime of at least 15 days with preservation of response characteristics. By comparing the two NFSs, we found PCL-NFSs are more suitable for pH sensing due to their dynamic range and superior reversibility. CONCLUSION The proposed sensing platform successfully exhibits a response to pH and compatibility with cultured cells. NSFs will be a useful tool for creating 3D cellular scaffolds that can monitor the cellular environment with applications in fields such as drug discovery and tissue engineering.
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Affiliation(s)
- Wenjun Di
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, 02115, USA
| | - Ryan S Czarny
- Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado, 80401, USA
| | - Nathan A Fletcher
- Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado, 80401, USA
| | - Melissa D Krebs
- Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado, 80401, USA
| | - Heather A Clark
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, 02115, USA.
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8
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Clark AJ, Petty HR. Identification of lesion subtypes in biopsies of ductal carcinoma in situ of the breast using biomarker ratio imaging microscopy. Sci Rep 2016; 6:27039. [PMID: 27247112 PMCID: PMC4887986 DOI: 10.1038/srep27039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 05/12/2016] [Indexed: 12/19/2022] Open
Abstract
Although epidemiological studies propose aggressive and non-aggressive forms of ductal carcinoma in situ (DCIS), they cannot be identified with conventional histopathology. We now report a retrospective study of human biopsy samples using biomarker ratio imaging microscopy (BRIM). Using BRIM, micrographs of biomarkers whose expression correlates with breast cancer aggressiveness are divided by micrographs of biomarkers whose expression negatively correlates with aggressiveness to create computed micrographs reflecting aggressiveness. The biomarker pairs CD44/CD24, N-cadherin/E-cadherin, and CD74/CD59 stratified DCIS samples. BRIM identified subpopulations of DCIS lesions with ratiometric properties resembling either benign fibroadenoma or invasive carcinoma samples. Our work confirms the existence of distinct subpopulations of DCIS lesions, which will likely have utility in breast cancer research and clinical practice.
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Affiliation(s)
- Andrea J Clark
- Department of Ophthalmology and Visual Sciences, 1000 Wall Street, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Howard R Petty
- Department of Ophthalmology and Visual Sciences, 1000 Wall Street, University of Michigan Medical School, Ann Arbor, MI, USA
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9
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Deak AT, Jean-Quartier C, Bondarenko AI, Groschner LN, Malli R, Graier WF, Waldeck-Weiermair M. Assessment of mitochondrial Ca²⁺ uptake. Methods Mol Biol 2015; 1264:421-39. [PMID: 25631032 DOI: 10.1007/978-1-4939-2257-4_35] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mitochondrial Ca(2+) uptake regulates mitochondrial function and contributes to cell signaling. Accordingly, quantifying mitochondrial Ca(2+) signals and elaborating the mechanisms that accomplish mitochondrial Ca(2+) uptake are essential to gain our understanding of cell biology. Here, we describe the benefits and drawbacks of various established old and new techniques to assess dynamic changes of mitochondrial Ca(2+) concentration ([Ca(2+)]mito) in a wide range of applications.
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Affiliation(s)
- András T Deak
- Institute of Molecular Biology and Biochemistry, Center of Molecular Medicine, Medical University of Graz, Harrachgasse 21/III, 8010, Graz, Austria
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Oheim M, van 't Hoff M, Feltz A, Zamaleeva A, Mallet JM, Collot M. New red-fluorescent calcium indicators for optogenetics, photoactivation and multi-color imaging. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:2284-306. [PMID: 24681159 DOI: 10.1016/j.bbamcr.2014.03.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 03/09/2014] [Indexed: 01/15/2023]
Abstract
Most chemical and, with only a few exceptions, all genetically encoded fluorimetric calcium (Ca(2+)) indicators (GECIs) emit green fluorescence. Many of these probes are compatible with red-emitting cell- or organelle markers. But the bulk of available fluorescent-protein constructs and transgenic animals incorporate green or yellow fluorescent protein (GFP and YFP respectively). This is, in part, not only heritage from the tendency to aggregate of early-generation red-emitting FPs, and due to their complicated photochemistry, but also resulting from the compatibility of green-fluorescent probes with standard instrumentation readily available in most laboratories and core imaging facilities. Photochemical constraints like limited water solubility and low quantum yield have contributed to the relative paucity of red-emitting Ca(2+) probes compared to their green counterparts, too. The increasing use of GFP and GFP-based functional reporters, together with recent developments in optogenetics, photostimulation and super-resolution microscopies, has intensified the quest for red-emitting Ca(2+) probes. In response to this demand more red-emitting chemical and FP-based Ca(2+)-sensitive indicators have been developed since 2009 than in the thirty years before. In this topical review, we survey the physicochemical properties of these red-emitting Ca(2+) probes and discuss their utility for biological Ca(2+) imaging. Using the spectral separability index Xijk (Oheim M., 2010. Methods in Molecular Biology 591: 3-16) we evaluate their performance for multi-color excitation/emission experiments, involving the identification of morphological landmarks with GFP/YFP and detecting Ca(2+)-dependent fluorescence in the red spectral band. We also establish a catalog of criteria for evaluating Ca(2+) indicators that ideally should be made available for each probe. This article is part of a Special Issue entitled: Calcium signaling in health and disease. Guest Editors: Geert Bultynck, Jacques Haiech, Claus W. Heizmann, Joachim Krebs, and Marc Moreau.
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Affiliation(s)
- Martin Oheim
- CNRS, UMR 8154, Paris F-75006, France; INSERM, U603, Paris F-75006, France; University Paris Descartes, PRES Sorbonne Paris Cité, Laboratory of Neurophysiology and New Microscopies, 45 rue des Saints Pères, Paris F-75006, France.
| | - Marcel van 't Hoff
- CNRS, UMR 8154, Paris F-75006, France; INSERM, U603, Paris F-75006, France; University Paris Descartes, PRES Sorbonne Paris Cité, Laboratory of Neurophysiology and New Microscopies, 45 rue des Saints Pères, Paris F-75006, France; University of Florence, LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
| | - Anne Feltz
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Paris F-75005, France; INSERM U1024, Paris F-75005, France; CNRS UMR 8197, Paris F-75005, France
| | - Alsu Zamaleeva
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Paris F-75005, France; INSERM U1024, Paris F-75005, France; CNRS UMR 8197, Paris F-75005, France
| | - Jean-Maurice Mallet
- UPMC Université́ Paris 06, Ecole Normale Supérieure (ENS), 24 rue Lhomond, Paris F-75005, France; CNRS UMR 7203, Paris F-75005, France
| | - Mayeul Collot
- UPMC Université́ Paris 06, Ecole Normale Supérieure (ENS), 24 rue Lhomond, Paris F-75005, France; CNRS UMR 7203, Paris F-75005, France
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Lee MH, Park N, Yi C, Han JH, Hong JH, Kim KP, Kang DH, Sessler JL, Kang C, Kim JS. Mitochondria-immobilized pH-sensitive off-on fluorescent probe. J Am Chem Soc 2014; 136:14136-42. [PMID: 25158001 PMCID: PMC4195376 DOI: 10.1021/ja506301n] [Citation(s) in RCA: 321] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
We
report here a mitochondria-targetable pH-sensitive probe that
allows for a quantitative measurement of mitochondrial pH changes,
as well as the real-time monitoring of pH-related physiological effects
in live cells. This system consists of a piperazine-linked naphthalimide
as a fluorescence off–on signaling unit, a cationic triphenylphosphonium
group for mitochondrial targeting, and a reactive benzyl chloride
subunit for mitochondrial fixation. It operates well in a mitochondrial
environment within whole cells and displays a desirable off–on
fluorescence response to mitochondrial acidification. Moreover, this
probe allows for the monitoring of impaired mitochondria undergoing
mitophagic elimination as the result of nutrient starvation. It thus
allows for the monitoring of the organelle-specific dynamics associated
with the conversion between physiological and pathological states.
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Affiliation(s)
- Min Hee Lee
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712-1224, United States
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12
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Wüstner D, Christensen T, Solanko LM, Sage D. Photobleaching kinetics and time-integrated emission of fluorescent probes in cellular membranes. Molecules 2014; 19:11096-130. [PMID: 25076144 PMCID: PMC6271172 DOI: 10.3390/molecules190811096] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/04/2014] [Accepted: 07/10/2014] [Indexed: 12/02/2022] Open
Abstract
Since the pioneering work of Hirschfeld, it is known that time-integrated emission (TiEm) of a fluorophore is independent of fluorescence quantum yield and illumination intensity. Practical implementation of this important result for determining exact probe distribution in living cells is often hampered by the presence of autofluorescence. Using kinetic modelling of photobleaching combined with pixel-wise bleach rate fitting of decay models with an updated plugin to the ImageJ program, it is shown that the TiEm of a fluorophore in living cells can be determined exactly from the product of bleaching amplitude and time constant. This applies to mono-exponential bleaching from the first excited singlet and/or triplet state and to multi-exponential combinations of such processes. The TiEm can be used to correct for illumination shading and background autofluorescence without the need for fluorescent test layers or separate imaging of non-stained cells. We apply the method to simulated images and to images of cells, whose membranes were labelled with fluorescent sterols and sphingolipids. Our bleaching model can be extended to include a probability density function (PDF) of intrinsic bleach rate constants with a memory kernel. This approach results in a time-dependent bleach rate coefficient and is exemplified for fluorescent sterols in restricted intracellular environments, like lipid droplets. We show that for small deviations from the classical exponential bleaching, the TiEm of decay functions with rate coefficients remains largely independent of fluorescence lifetime and illumination, and thereby represents a faithful measure of probe distribution.
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Affiliation(s)
- Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark.
| | - Tanja Christensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark.
| | - Lukasz M Solanko
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark.
| | - Daniel Sage
- Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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13
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Kummer L, Hsu CW, Dagliyan O, MacNevin C, Kaufholz M, Zimmermann B, Dokholyan NV, Hahn KM, Plückthun A. Knowledge-based design of a biosensor to quantify localized ERK activation in living cells. ACTA ACUST UNITED AC 2014; 20:847-56. [PMID: 23790495 DOI: 10.1016/j.chembiol.2013.04.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 04/11/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
Abstract
Investigation of protein activation in living cells is fundamental to understanding how proteins are influenced by the full complement of upstream regulators they experience. Here, we describe the generation of a biosensor based on the DARPin binding scaffold suited for intracellular applications. Combining library selection and knowledge-based design, we created an ERK activity biosensor by derivatizing a DARPin specific for phosphorylated ERK with a solvatochromatic merocyanine dye, whose fluorescence increases upon pERK binding. The biosensor specifically responded to pERK2, recognized by its conformation, but not to ERK2 or other closely related mitogen-activated kinases tested. Activated endogenous ERK was visualized in mouse embryo fibroblasts, revealing greater activation in the nucleus, perinuclear regions, and especially the nucleoli. The DARPin-based biosensor will serve as a useful tool for studying biological functions of ERK in vitro and in vivo.
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Affiliation(s)
- Lutz Kummer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Chou HS, Hsiao MH, Hung WY, Yen TY, Lin HY, Liu DM. A pH-responsive amphiphilic chitosan–pyranine core–shell nanoparticle for controlled drug delivery, imaging and intracellular pH measurement. J Mater Chem B 2014; 2:6580-6589. [DOI: 10.1039/c4tb01080a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new type of CHC–PY core–shell nanoparticle provides multiple functionality, where a synergistic performance of nanotherapeutics, imaging and even diagnosis at a cellular resolution can be achieved simultaneously.
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Affiliation(s)
- Hao-Syun Chou
- Department of Materials Science and Engineering
- National Chiao Tung University
- Hsinchu, Taiwan
| | - Meng-Hsuan Hsiao
- Department of Materials Science and Engineering
- National Chiao Tung University
- Hsinchu, Taiwan
| | - Wei-Yang Hung
- Department of Materials Science and Engineering
- National Chiao Tung University
- Hsinchu, Taiwan
| | - Tin-Yo Yen
- Joint Honours of Biotechnology
- Department of Microbiology and Immunology
- University of British Columbia/British Columbia Institute of Technology
- Vancouver, Canada
| | - Hui-Yi Lin
- School of Pharmacy
- China Medical University
- TaiChung, Taiwan
| | - Dean-Mo Liu
- Department of Materials Science and Engineering
- National Chiao Tung University
- Hsinchu, Taiwan
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15
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Visualization of synaptic inhibition with an optogenetic sensor developed by cell-free protein engineering automation. J Neurosci 2013; 33:16297-309. [PMID: 24107961 DOI: 10.1523/jneurosci.4616-11.2013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We describe an engineered fluorescent optogenetic sensor, SuperClomeleon, that robustly detects inhibitory synaptic activity in single, cultured mouse neurons by reporting intracellular chloride changes produced by exogenous GABA or inhibitory synaptic activity. Using a cell-free protein engineering automation methodology that bypasses gene cloning, we iteratively constructed, produced, and assayed hundreds of mutations in binding-site residues to identify improvements in Clomeleon, a first-generation, suboptimal sensor. Structural analysis revealed that these improvements involve halide contacts and distant side chain rearrangements. The development of optogenetic sensors that respond to neural activity enables cellular tracking of neural activity using optical, rather than electrophysiological, signals. Construction of such sensors using in vitro protein engineering establishes a powerful approach for developing new probes for brain imaging.
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16
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Filter switching device for dual-wavelength videoimaging. J Fluoresc 2013; 6:103-6. [PMID: 24227084 DOI: 10.1007/bf00732049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/1995] [Accepted: 04/21/1996] [Indexed: 10/26/2022]
Abstract
An inexpensive, dual-wavelength, videoimaging system that can be used for parallel observation of two fluorescent dyes is described. All four filters, two for excitation and two for emission, are placed on the same oscillating holder. Filters are coupled with a single dichroic mirror having two spectral windows. A coil driven by an electronic circuit connected to photosensors, which determine the position of the holder, moves the magnet that shifts the position of the filters. Since the filter holder is placed between two springs, it oscillates with the frequency of mechanical resonance. As a result the filter switching did not require much power and did not produce significant vibrations of the base. Switching frequencies up to 4.5 s(-1) were reached with the first experimental device. System performance was tested using phospholipid vesicles loaded with water-soluble and membrane dyes. It has been demonstrated that the device can be used successfully in experiments on membrane fusion with rhodamine- and calcein-labeled liposomes.
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17
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Monteith A, Marszalec W, Chan P, Logan J, Yu W, Schwarz N, Wokosin D, Hockberger P. Imaging of mitochondrial and non-mitochondrial responses in cultured rat hippocampal neurons exposed to micromolar concentrations of TMRM. PLoS One 2013; 8:e58059. [PMID: 23483968 PMCID: PMC3587568 DOI: 10.1371/journal.pone.0058059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 01/31/2013] [Indexed: 11/24/2022] Open
Abstract
Tetramethylrhodamine methyl ester (TMRM) is a fluorescent dye used to study mitochondrial function in living cells. Previously, we reported that TMRM effectively labeled mitochondria of neurons deep within mouse brain slices. Use of micromolar concentration of dye, which was required to get sufficient staining for two-photon imaging, resulted in typical fluctuations of TMRM. With prolonged exposure, we recorded additional responses in some neurons that included slow oscillations and propagating waves of fluorescence. (Note: We use the terms “fluctuation” to refer to a change in the fluorescent state of an individual mitochondrion, “oscillation” to refer to a localized change in fluorescence in the cytosol, and “wave” to refer to a change in cytosolic fluorescence that propagated within a cell. Use of these terms does not imply any underlying periodicity.) In this report we describe similar results using cultured rat hippocampal neurons. Prolonged exposure of cultures to 2.5 µM TMRM produced a spontaneous increase in fluorescence in some neurons, but not glial cells, after 45–60 minutes that was followed by slow oscillations, waves, and eventually apoptosis. Spontaneous increases in fluorescence were insensitive to high concentrations of FCCP (100 µM) and thapsigargin (10 µM) indicating that they originated, at least in part, from regions outside of mitochondria. The oscillations did not correlate with changes in intracellular Ca2+, but did correlate with differences in fluorescence lifetime of the dye. Fluorescence lifetime and one-photon ratiometric imaging of TMRM suggested that the spontaneous increase and subsequent oscillations were due to movement of dye between quenched (hydrophobic) and unquenched (hydrophilic) compartments. We propose that these movements may be correlates of intracellular events involved in early stages of apoptosis.
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Affiliation(s)
- Andrew Monteith
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - William Marszalec
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Philip Chan
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Juliette Logan
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Weiming Yu
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Nicholas Schwarz
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - David Wokosin
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Philip Hockberger
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- * E-mail:
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18
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MacNevin CJ, Gremyachinskiy D, Hsu CW, Li L, Rougie M, Davis TT, Hahn KM. Environment-sensing merocyanine dyes for live cell imaging applications. Bioconjug Chem 2013; 24:215-23. [PMID: 23297747 DOI: 10.1021/bc3005073] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent biosensors based on environmentally sensitive dyes enable visualization and quantification of endogenous protein activation within living cells. Merocyanine dyes are especially useful for live cell imaging applications, as they are extraordinarily bright, have long wavelengths of excitation and emission, and can exhibit readily detectable fluorescence changes in response to environment. We sought to systematically examine the effects of structural features on key photophysical properties, including dye brightness, environmental responsiveness, and photostability, through the synthesis of a library of 25 merocyanine dyes, derived from combinatorial reaction of 5 donor and 5 acceptor heterocycles. Four of these dyes showed optimal properties for specific imaging applications and were subsequently prepared with reactive side chains and enhanced aqueous solubility using a one-pot synthetic method. The new dyes were then applied within a biosensor design for Cdc42 activation, where dye mero60 showed a remarkable 1470% increase in fluorescence intensity on binding activated Cdc42 in vitro. The dye-based biosensors were used to report activation of endogenous Cdc42 in living cells.
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19
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Wüstner D, Solanko LM, Lund FW, Sage D, Schroll HJ, Lomholt MA. Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation. BMC Bioinformatics 2012; 13:296. [PMID: 23148417 PMCID: PMC3557157 DOI: 10.1186/1471-2105-13-296] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 10/31/2012] [Indexed: 12/23/2022] Open
Abstract
Background Fluorescence loss in photobleaching (FLIP) is a widely used imaging technique, which provides information about protein dynamics in various cellular regions. In FLIP, a small cellular region is repeatedly illuminated by an intense laser pulse, while images are taken with reduced laser power with a time lag between the bleaches. Despite its popularity, tools are lacking for quantitative analysis of FLIP experiments. Typically, the user defines regions of interest (ROIs) for further analysis which is subjective and does not allow for comparing different cells and experimental settings. Results We present two complementary methods to detect and quantify protein transport and aggregation in living cells from FLIP image series. In the first approach, a stretched exponential (StrExp) function is fitted to fluorescence loss (FL) inside and outside the bleached region. We show by reaction–diffusion simulations, that the StrExp function can describe both, binding/barrier–limited and diffusion-limited FL kinetics. By pixel-wise regression of that function to FL kinetics of enhanced green fluorescent protein (eGFP), we determined in a user-unbiased manner from which cellular regions eGFP can be replenished in the bleached area. Spatial variation in the parameters calculated from the StrExp function allow for detecting diffusion barriers for eGFP in the nucleus and cytoplasm of living cells. Polyglutamine (polyQ) disease proteins like mutant huntingtin (mtHtt) can form large aggregates called inclusion bodies (IB’s). The second method combines single particle tracking with multi-compartment modelling of FL kinetics in moving IB’s to determine exchange rates of eGFP-tagged mtHtt protein (eGFP-mtHtt) between aggregates and the cytoplasm. This method is self-calibrating since it relates the FL inside and outside the bleached regions. It makes it therefore possible to compare release kinetics of eGFP-mtHtt between different cells and experiments. Conclusions We present two complementary methods for quantitative analysis of FLIP experiments in living cells. They provide spatial maps of exchange dynamics and absolute binding parameters of fluorescent molecules to moving intracellular entities, respectively. Our methods should be of great value for quantitative studies of intracellular transport.
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Affiliation(s)
- Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, DK-5230, Denmark.
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20
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Geilfus CM, Mühling KH. Transient alkalinization in the leaf apoplast of Vicia faba L. depends on NaCl stress intensity: an in situ ratio imaging study. PLANT, CELL & ENVIRONMENT 2012; 35:578-87. [PMID: 21954856 DOI: 10.1111/j.1365-3040.2011.02437.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The apoplast is suggested to be involved not only in the response, but also in the perception and transduction of various environmental signals. In this context, apoplastic alkalinization has previously been discussed as a general stress factor caused by abiotic and biotic stress events. In this study, an ion-sensitive fluorescence probe in combination with inverted fluorescence microscopy has been used for in planta monitoring of apoplastic shoot pH during challenging of Vicia faba L. plants by NaCl stress encountered at the roots. We demonstrate that transient increases in leaf apoplastic pH are dependent on the NaCl stress intensity. Moreover, we have visualized spatial pH gradients within the leaf apoplast. Our results indicate that these pH responses are propagated from root to leaf and that this occurs along the apoplast.
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Affiliation(s)
- Christoph-Martin Geilfus
- Institute of Plant Nutrition and Soil Science, Christian Albrechts University, Hermann-Rodewald-Strasse 2, Kiel, Germany
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21
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Trapani V, Schweigel-Röntgen M, Cittadini A, Wolf FI. Intracellular magnesium detection by fluorescent indicators. Methods Enzymol 2012; 505:421-44. [PMID: 22289466 DOI: 10.1016/b978-0-12-388448-0.00030-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Magnesium is essential for a wide variety of biochemical reactions and physiological functions, but its regulatory mechanisms (both at the cellular and at the systemic level) are still poorly characterized. Not least among the reasons for this gap are the technical difficulties in sensing minor changes occurring over a high background concentration. Specific fluorescent indicators are highly sensitive tools for dynamic evaluation of intracellular magnesium concentration. We herein discuss the main criteria to consider when choosing a magnesium-specific fluorescent indicator and provide examples among commercial as well as developmental sensors. We focus on spectrofluorimetric approaches to quantify Mg(2+) concentration in cell or mitochondria suspensions, and on imaging techniques to detect intracellular magnesium distribution and fluxes by live microscopy, reporting a detailed description of standard protocols for each method. The general guidelines we provide should be applicable to specific issues by any researcher in the field.
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Affiliation(s)
- Valentina Trapani
- Facoltà di Medicina e Chirurgia A. Gemelli, Istituto di Patologia Generale and Centro di Ricerche Oncologiche Giovanni XXIII, Università Cattolica del Sacro Cuore, Rome, Italy
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22
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Patil VS, Padalkar VS, Phatangare KR, Gupta VD, Umape PG, Sekar N. Synthesis of New ESIPT-Fluorescein: Photophysics of pH Sensitivity and Fluorescence. J Phys Chem A 2011; 116:536-45. [DOI: 10.1021/jp2073123] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vikas S. Patil
- Institute of Chemical Technology (Formerly UDCT), N. P. Marg, Matunga, Mumbai, 400 019 Maharashtra, India
| | - Vikas S. Padalkar
- Institute of Chemical Technology (Formerly UDCT), N. P. Marg, Matunga, Mumbai, 400 019 Maharashtra, India
| | - Kiran R. Phatangare
- Institute of Chemical Technology (Formerly UDCT), N. P. Marg, Matunga, Mumbai, 400 019 Maharashtra, India
| | - Vinod D. Gupta
- Institute of Chemical Technology (Formerly UDCT), N. P. Marg, Matunga, Mumbai, 400 019 Maharashtra, India
| | - Prashant G. Umape
- Institute of Chemical Technology (Formerly UDCT), N. P. Marg, Matunga, Mumbai, 400 019 Maharashtra, India
| | - Nagaiyan Sekar
- Institute of Chemical Technology (Formerly UDCT), N. P. Marg, Matunga, Mumbai, 400 019 Maharashtra, India
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23
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Sattelmacher B, Mühling KH, Pennewiß K. The apoplast - its significance for the nutrition of higher plants. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/jpln.1998.3581610502] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Jha RK, Wu YI, Zawistowski JS, MacNevin C, Hahn KM, Kuhlman B. Redesign of the PAK1 autoinhibitory domain for enhanced stability and affinity in biosensor applications. J Mol Biol 2011; 413:513-22. [PMID: 21888918 DOI: 10.1016/j.jmb.2011.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 08/10/2011] [Accepted: 08/11/2011] [Indexed: 11/16/2022]
Abstract
The inhibitory switch (IS) domain of p21-activated kinase 1 (PAK1) stabilizes full-length PAK1 in an inactive conformation by binding to the PAK1 kinase domain. Competitive binding of small guanosine triphosphatases to the IS domain disrupts the autoinhibitory interactions and exposes the IS domain binding site on the surface of the kinase domain. To build an affinity reagent that selectively binds the activated state of PAK1, we used molecular modeling to reengineer the isolated IS domain so that it was soluble and stable, did not bind to guanosine triphosphatases and bound more tightly to the PAK1 kinase domain. Three design strategies were tested: in the first and second cases, extension and redesign of the N-terminus were used to expand the hydrophobic core of the domain, and in the third case, the termini were redesigned to be adjacent in space so that the domain could be stabilized by insertion into a loop in a host cyan fluorescent protein (CFP). The best-performing design, called CFP-PAcKer, was based on the third strategy and bound the kinase domain of PAK1 with an affinity of 400 nM. CFP-PAcKer binds more tightly to a full-length variant of PAK1 that is stabilized in the "open" state (K(d)=3.3 μM) than to full-length PAK1 in the "closed" state (undetectable affinity), and binding can be monitored with fluorescence by placing an environmentally sensitive fluorescence dye on CFP-PAcKer adjacent to the binding site.
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Affiliation(s)
- Ramesh K Jha
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, USA
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25
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Read ND, Allan WTG, Knight H, Knight MR, Malhó R, Russell A, Shacklock PS, Trewavas AJ. Imaging and measurement of cytosolic free calcium in plant and fungal cells. J Microsc 2011. [DOI: 10.1111/j.1365-2818.1992.tb01507.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Aabo T, Banás AR, Glückstad J, Siegumfeldt H, Arneborg N. BioPhotonics workstation: a versatile setup for simultaneous optical manipulation, heat stress, and intracellular pH measurements of a live yeast cell. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:083707. [PMID: 21895251 DOI: 10.1063/1.3625274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this study we have modified the BioPhotonics workstation (BWS), which allows for using long working distance objective for optical trapping, to include traditional epi-fluorescence microscopy, using the trapping objectives. We have also added temperature regulation of sample stage, allowing for fast temperature variations while trapping. Using this modified BWS setup, we investigated the internal pH (pH(i)) response and membrane integrity of an optically trapped Saccharomyces cerevisiae cell at 5 mW subject to increasing temperatures. The pH(i) of the cell is obtained from the emission of 5-(and-6)-carboxyfluorescein diacetate, succinimidyl ester, at 435 and 485 nm wavelengths, while the permeability is indicated by the fluorescence of propidium iodide. We present images mapping the pH(i) and permeability of the cell at different temperatures and with enough spatial resolution to localize these attributes within the cell. The combined capability of optical trapping, fluorescence microscopy and temperature regulation offers a versatile tool for biological research.
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Affiliation(s)
- Thomas Aabo
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
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27
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Gulyani A, Vitriol E, Allen R, Wu J, Gremyachinskiy D, Lewis S, Dewar B, Graves LM, Kay BK, Kuhlman B, Elston T, Hahn KM. A biosensor generated via high-throughput screening quantifies cell edge Src dynamics. Nat Chem Biol 2011; 7:437-44. [PMID: 21666688 PMCID: PMC3135387 DOI: 10.1038/nchembio.585] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 04/19/2011] [Indexed: 01/24/2023]
Abstract
Fluorescent biosensors for living cells currently require laborious optimization and a unique design for each target. They are limited by the availability of naturally occurring ligands with appropriate target specificity. Here we describe a biosensor based on an engineered fibronectin monobody scaffold that can be tailored to bind different targets via high-throughput screening. We made this Src-family kinase (SFK) biosensor by derivatizing a monobody specific for activated SFKs with a bright dye whose fluorescence increases upon target binding. We identified sites for dye attachment and changes to eliminate vesiculation in living cells, providing a generalizable scaffold for biosensor production. This approach minimizes cell perturbation because it senses endogenous, unmodified target, and because sensitivity is enhanced by direct dye excitation. Automated correlation of cell velocities and SFK activity revealed that SFKs are activated specifically during protrusion. Activity correlates with velocity, and peaks 1-2 μm from the leading edge.
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Affiliation(s)
- Akash Gulyani
- Department of Pharmacology, University of North Carolina at Chapel Hill, 4009 Genetic Medicine, Campus Box 7365, Chapel Hill, NC 27599
| | - Eric Vitriol
- Department of Pharmacology, University of North Carolina at Chapel Hill, 4009 Genetic Medicine, Campus Box 7365, Chapel Hill, NC 27599
| | - Richard Allen
- Department of Pharmacology, University of North Carolina at Chapel Hill, 4009 Genetic Medicine, Campus Box 7365, Chapel Hill, NC 27599
| | - Jianrong Wu
- Department of Pharmacology, University of North Carolina at Chapel Hill, 4009 Genetic Medicine, Campus Box 7365, Chapel Hill, NC 27599
| | - Dmitriy Gremyachinskiy
- Department of Pharmacology, University of North Carolina at Chapel Hill, 4009 Genetic Medicine, Campus Box 7365, Chapel Hill, NC 27599
| | - Steven Lewis
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 3010 Genetic Medicine, Campus Box 7260, Chapel Hill, NC 27599
| | - Brian Dewar
- Department of Pharmacology, University of North Carolina at Chapel Hill, 4009 Genetic Medicine, Campus Box 7365, Chapel Hill, NC 27599
| | - Lee M. Graves
- Department of Pharmacology, University of North Carolina at Chapel Hill, 4009 Genetic Medicine, Campus Box 7365, Chapel Hill, NC 27599
| | - Brian K. Kay
- Department of Biological Sciences, University of Illinois at Chicago, 845 West Taylor Street (MC 066) Chicago, IL 60607
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 3010 Genetic Medicine, Campus Box 7260, Chapel Hill, NC 27599
| | - Tim Elston
- Department of Pharmacology, University of North Carolina at Chapel Hill, 4009 Genetic Medicine, Campus Box 7365, Chapel Hill, NC 27599
| | - Klaus M. Hahn
- Department of Pharmacology, University of North Carolina at Chapel Hill, 4009 Genetic Medicine, Campus Box 7365, Chapel Hill, NC 27599
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28
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Geilfus CM, Mühling KH. Real-Time Imaging of Leaf Apoplastic pH Dynamics in Response to NaCl Stress. FRONTIERS IN PLANT SCIENCE 2011; 2:13. [PMID: 22639578 PMCID: PMC3355670 DOI: 10.3389/fpls.2011.00013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 04/16/2011] [Indexed: 05/20/2023]
Abstract
Knowledge concerning apoplastic ion concentrations is important for the understanding of many processes in plant physiology. Ion-sensitive fluorescent probes in combination with quantitative imaging techniques offer opportunities to localize, visualize, and quantify apoplastic ion dynamics in situ. The application of this technique to the leaf apoplast is complicated because of problems associated with dye loading. We demonstrate a more sophisticated dye loading procedure that enables the mapping of spatial apoplastic ion gradients over a period of 3 h. The new technique has been used for the real-time monitoring of pH dynamics within the leaf apoplast in response to NaCl stress encountered by the roots.
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Affiliation(s)
| | - Karl H. Mühling
- Institute of Plant Nutrition and Soil Science, Christian Albrechts UniversityKiel, Germany
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29
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Bouchelouche PN. Dynamic, real time imaging of ion activities in single living cells using fluorescence video microscopy and image analysis. Scandinavian Journal of Clinical and Laboratory Investigation 2011. [DOI: 10.1080/00365519309090676] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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30
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Carroll CN, Naleway JJ, Haley MM, Johnson DW. Arylethynyl receptors for neutral molecules and anions: emerging applications in cellular imaging. Chem Soc Rev 2010; 39:3875-88. [PMID: 20820467 PMCID: PMC3062433 DOI: 10.1039/b926231h] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This critical review will focus on the application of shape-persistent receptors for anions that derive their rigidity and optoelectronic properties from the inclusion of arylethynyl linkages. It will highlight a few of the design strategies involved in engineering selective and sensitive fluorescent probes and how arylacetylenes can offer a design pathway to some of the more desirable properties of a selective sensor. Additionally, knowledge gained in the study of these receptors in organic media often leads to improved receptor design and the production of chromogenic and fluorogenic probes capable of detecting specific substrates among the multitude of ions present in biological systems. In this ocean of potential targets exists a large number of geometrically distinct anions, which present their own problems to the design of receptors with complementary binding for each preferred coordination geometry. Our interest in targeting charged substrates, specifically how previous work on receptors for cations or neutral guests can be adapted to anions, will be addressed. Additionally, we will focus on the design and development of supramolecular arylethynyl systems, their shape-persistence and fluorogenic or chromogenic optoelectronic responses to complexation. We will also examine briefly how the "chemistry in the cuvet" translates into biological media (125 references).
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Affiliation(s)
- Calden N. Carroll
- Department of Chemistry and the Materials Science Institute, 1253 University of Oregon, Eugene, Oregon 97403-1253 USA
- The Oregon Nanoscience and Microtechnologies Institute (ONAMI), P.O. Box 2041, Corvallis, OR 97339 USA url: http://onami.us/
| | - John J. Naleway
- The Oregon Nanoscience and Microtechnologies Institute (ONAMI), P.O. Box 2041, Corvallis, OR 97339 USA url: http://onami.us/
- Marker Gene Technologies, Inc., University of Oregon Riverfront Research Park, 1850 Millrace Drive, Eugene, OR 97403 USA
| | - Michael M. Haley
- Department of Chemistry and the Materials Science Institute, 1253 University of Oregon, Eugene, Oregon 97403-1253 USA
- The Oregon Nanoscience and Microtechnologies Institute (ONAMI), P.O. Box 2041, Corvallis, OR 97339 USA url: http://onami.us/
| | - Darren W. Johnson
- Department of Chemistry and the Materials Science Institute, 1253 University of Oregon, Eugene, Oregon 97403-1253 USA
- The Oregon Nanoscience and Microtechnologies Institute (ONAMI), P.O. Box 2041, Corvallis, OR 97339 USA url: http://onami.us/
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31
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Affiliation(s)
- Junyan Han
- Department of Chemistry, Texas A&M University, Box 30012, College Station, Texas 77841, USA
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32
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Tang B, Yu F, Li P, Tong L, Duan X, Xie T, Wang X. A near-infrared neutral pH fluorescent probe for monitoring minor pH changes: imaging in living HepG2 and HL-7702 cells. J Am Chem Soc 2010; 131:3016-23. [PMID: 19199620 DOI: 10.1021/ja809149g] [Citation(s) in RCA: 347] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A near-neutral pH near-infrared (NIR) fluorescent probe utilizing a fluorophore-spacer- receptor molecular framework that can modulate the fluorescence emission intensity through a fast photoinduced electron-transfer process was developed. Our strategy was to choose tricarbocyanine (Cy), a NIR fluorescent dye with high extinction coefficients, as a fluorophore, and 4'-(aminomethylphenyl)-2,2':6',2''-terpyridine (Tpy) as a receptor. The pH titration indicated that Tpy-Cy can monitor the minor physiological pH fluctuations with a pK(a) of approximately 7.10 near physiological pH, which is valuable for intracellular pH researches. The probe responds linearly and rapidly to minor pH fluctuations within the range of 6.70-7.90 and exhibits strong dependence on pH changes. As expected, the real-time imaging of cellular pH and the detection of pH in situ was achieved successfully in living HepG2 and HL-7702 cells by this probe. It is shown that the probe effectively avoids the influence of autofluorescence and native cellular species in biological systems and meanwhile exhibits high sensitivity, good photostability, and excellent cell membrane permeability.
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Affiliation(s)
- Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Engineering Research Center of Pesticide and Medicine Intermediate Clean Production, Ministry of Education, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China.
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Trapani V, Farruggia G, Marraccini C, Iotti S, Cittadini A, Wolf FI. Intracellular magnesium detection: imaging a brighter future. Analyst 2010; 135:1855-66. [DOI: 10.1039/c0an00087f] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
The activity of most cellular processes is sensitive to pH. Cells therefore tightly control cytosol pH within narrow bounds. Measurement of cytosolic pH is of interest in studying many processes, including pH regulatory transport proteins. Key approaches that have been used to determine intracellular pH include pH-sensitive microelectrodes, nuclear magnetic resonance, and pH-sensitive fluorescent proteins. Here we review these approaches while providing details on the use of pH-sensitive fluorescent dyes to measure cytosolic pH.
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The role of seawater endocytosis in the biomineralization process in calcareous foraminifera. Proc Natl Acad Sci U S A 2009; 106:21500-4. [PMID: 20007770 DOI: 10.1073/pnas.0906636106] [Citation(s) in RCA: 190] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Foraminifera are unicellular organisms that inhabit the oceans in various ecosystems. The majority of the foraminifera precipitate calcitic shells and are among the major CaCO(3) producers in the oceans. They comprise an important component of the global carbon cycle and also provide valuable paleoceanographic information based on the relative abundance of stable isotopes and trace elements (proxies) in their shells. Understanding the biomineralization processes in foraminifera is important for predicting their calcification response to ocean acidification and for reliable interpretation of the paleoceanographic proxies. Most models of biomineralization invoke the involvement of membrane ion transporters (channels and pumps) in the delivery of Ca(2+) and other ions to the calcification site. Here we show, in contrast, that in the benthic foraminiferan Amphistegina lobifera, (a shallow water species), transport of seawater via fluid phase endocytosis may account for most of the ions supplied to the calcification site. During their intracellular passage the seawater vacuoles undergo alkalization that elevates the CO(3)(2-) concentration and further enhances their calcifying potential. This mechanism of biomineralization may explain why many calcareous foraminifera can be good recorders of paleoceanographic conditions. It may also explain the sensitivity to ocean acidification that was observed in several planktonic and benthic species.
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Glykys J, Dzhala VI, Kuchibhotla KV, Feng G, Kuner T, Augustine G, Bacskai BJ, Staley KJ. Differences in cortical versus subcortical GABAergic signaling: a candidate mechanism of electroclinical uncoupling of neonatal seizures. Neuron 2009; 63:657-72. [PMID: 19755108 DOI: 10.1016/j.neuron.2009.08.022] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 08/19/2009] [Accepted: 08/19/2009] [Indexed: 01/24/2023]
Abstract
Electroclinical uncoupling of neonatal seizures refers to electrographic seizure activity that is not clinically manifest. Uncoupling increases after treatment with Phenobarbital, which enhances the GABA(A) receptor (GABA(A)R) conductance. The effects of GABA(A)R activation depend on the intracellular Cl(-) concentration ([Cl(-)](i)) that is determined by the inward Cl(-) transporter NKCC1 and the outward Cl(-) transporter KCC2. Differential maturation of Cl(-) transport observed in cortical versus subcortical regions should alter the efficacy of GABA-mediated inhibition. In perinatal rat pups, most thalamic neurons maintained low [Cl(-)](i) and were inhibited by GABA. Phenobarbital suppressed thalamic seizure activity. Most neocortical neurons maintained higher [Cl(-)](i), and were excited by GABA(A)R activation. Phenobarbital had insignificant anticonvulsant responses in the neocortex until NKCC1 was blocked. Regional differences in the ontogeny of Cl(-) transport may thus explain why seizure activity in the cortex is not suppressed by anticonvulsants that block the transmission of seizure activity through subcortical networks.
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Affiliation(s)
- Joseph Glykys
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02144, USA
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Direct pH measurements by using subcellular targeting of 5(and 6-) carboxyseminaphthorhodafluor in mammalian cells. Biotechniques 2009; 47:769-74. [DOI: 10.2144/000113220] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
As a means of reliably measuring intracellular pH, we have precisely targeted 5(and 6-) carboxyseminaphthorhodafluor to cellular subcompartments. This was accomplished by combining the well-established pH-sensitive dye with a protein-based reporter system. When expressed in cells, the reporter protein is designed to covalently bind ligands composed of a functional group and a reactive linker. In order to make a pH-sensitive ligand, we chemically coupled the pH sensor to a reactive linker. Several ligands of differing linker lengths were made and tested for their pH responsiveness in vitro. The most responsive of these ligands was then evaluated for its efficacy in live cell labeling and its use as an intracellular pH sensor for ratiometric confocal microscopy. Here we show that we could target this pH sensor within mammalian cells exclusively to either the nucleus or cytoplasm. Exhibiting the versatility of this reporter technology, we were also able to specifically limit pH sensor labeling to within the trafficking pathway of integrins and directly measure pH of this environment. Results correspond well with previously published reports. Both the simplicity and flexibility of the technology used in this study make possible the development of diverse targeted microenvironmental sensors or other moieties of interest.
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Povrozin YA, Markova LI, Tatarets AL, Sidorov VI, Terpetschnig EA, Patsenker LD. Near-infrared, dual-ratiometric fluorescent label for measurement of pH. Anal Biochem 2009; 390:136-40. [PMID: 19351524 DOI: 10.1016/j.ab.2009.03.047] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 03/24/2009] [Accepted: 03/30/2009] [Indexed: 11/29/2022]
Abstract
We describe the spectral properties of an amine-reactive, pH-sensitive, long-wavelength ratiometric fluorescent label having a pK(a) in the physiological pH range. The label exhibits its main absorption and emission in the near-infrared (NIR) region. On deprotonation, a blue shift of the excitation maximum is observed. Importantly, both the protonated and deprotonated forms of the label are fluorescent, with the deprotonated form having an extremely large Stokes shift of more than 100 nm. The spectral and photophysical properties of this pH label are compared with the properties of the protein-conjugated forms. Due to the observed pK(a) shift to the acidic pH range upon conjugation to proteins, such labels are ideal for studying phagocytic events and their regulation by drugs and/or environmental factors.
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Affiliation(s)
- Yevgen A Povrozin
- SSI Institute for Single Crystals of the National Academy of Sciences of Ukraine, 61001 Kharkov, Ukraine
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Garrett SC, Hodgson L, Rybin A, Toutchkine A, Hahn KM, Lawrence DS, Bresnick AR. A biosensor of S100A4 metastasis factor activation: inhibitor screening and cellular activation dynamics. Biochemistry 2007; 47:986-96. [PMID: 18154362 DOI: 10.1021/bi7021624] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
S100A4, a member of the S100 family of Ca2+-binding proteins, displays elevated expression in malignant human tumors compared with benign tumors, and increased expression correlates strongly with poor patient survival. S100A4 has a direct role in metastatic progression, likely due to the modulation of actomyosin cytoskeletal dynamics, which results in increased cellular motility. We developed a fluorescent biosensor (Mero-S100A4) that reports on the Ca2+-bound, activated form of S100A4. Direct attachment of a novel solvatochromatic reporter dye to S100A4 results in a sensor that, upon activation, undergoes a 3-fold enhancement in fluorescence, thus providing a sensitive assay for use in vitro and in vivo. In cells, localized activation of S100A4 at the cell periphery is observed during random migration and following stimulation with lysophosphatidic acid, a known activator of cell motility and proliferation. Additionally, a screen against a library of FDA-approved drugs with the biosensor identified an array of phenothiazines as inhibitors of myosin-II associated S100A4 function. These data demonstrate the utility of the new biosensor both for drug discovery and for probing the cellular dynamics controlled by the S100A4 metastasis factor.
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Affiliation(s)
- Sarah C Garrett
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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40
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Wang YL. Noise-induced systematic errors in ratio imaging: serious artefacts and correction with multi-resolution denoising. J Microsc 2007; 228:123-31. [PMID: 17970912 PMCID: PMC3029016 DOI: 10.1111/j.1365-2818.2007.01834.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ratio imaging is playing an increasingly important role in modern cell biology. Combined with ratiometric dyes or fluorescence resonance energy transfer (FRET) biosensors, the approach allows the detection of conformational changes and molecular interactions in living cells. However, the approach is conducted increasingly under limited signal-to-noise ratio (SNR), where noise from multiple images can easily accumulate and lead to substantial uncertainty in ratio values. This study demonstrates that a far more serious concern is systematic errors that generate artificially high ratio values at low SNR. Thus, uneven SNR alone may lead to significant variations in ratios among different regions of a cell. Although correct average ratios may be obtained by applying conventional noise reduction filters, such as a Gaussian filter before calculating the ratio, these filters have a limited performance at low SNR and are prone to artefacts such as generating discrete domains not found in the correct ratio image. Much more reliable restoration may be achieved with multi-resolution denoising filters that take into account the actual noise characteristics of the detector. These filters are also capable of restoring structural details and photometric accuracy, and may serve as a general tool for retrieving reliable information from low-light live cell images.
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Affiliation(s)
- Yu-Li Wang
- University of Massachusetts Medical School, 377 Plantation Street, Suite 327, Worcester, MA 01605, USA.
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41
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Rochon P, Jourdain M, Mangalaboyi J, Fourrier F, Soulié-Bégu S, Buys B, Dehlin G, Lesage JC, Chambrin MC, Mordon S. Evaluation of BCECF fluorescence ratio imaging to properly measure gastric intramucosal pH variations in vivo. JOURNAL OF BIOMEDICAL OPTICS 2007; 12:064014. [PMID: 18163830 DOI: 10.1117/1.2821698] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Our purpose is to evaluate intramucosal gastric pH video imaging by 2('),7(')-bis(carboxyethyl)-5,6-carboxyfluorescein (BCECF) fluorescence ratio techniques. We use a video endoscopic imaging system and BCECF as the pH fluorescent probe. Systemic in vivo pH variations are studied in 10 pigs: five in the control group and five with respiratory acidosis induced through rebreathing. The intramucosal pH of the gastric wall is measured every 5 s and the results demonstrate a good correlation (pearson correlation=0.832) between blood gases pH measurements and pH measured with the video endocopic imaging system. Our results confirm the feasibility of using BCECF fluorescence pH imaging to measure intramucosal pH in vivo.
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Affiliation(s)
- Philippe Rochon
- Lille University Hospital, Pavillon Vancostenobel, 59037 Lille Cedex, France
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Nakata E, Tsukiji S, Hamachi I. Development of New Methods to Introduce Unnatural Functional Molecules into Native Proteins for Protein Engineering. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.1268] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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44
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McNeil AK, Rescher U, Gerke V, McNeil PL. Requirement for annexin A1 in plasma membrane repair. J Biol Chem 2006; 281:35202-7. [PMID: 16984915 DOI: 10.1074/jbc.m606406200] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ca2+ entering a cell through a torn or disrupted plasma membrane rapidly triggers a combination of homotypic and exocytotic membrane fusion events. These events serve to erect a reparative membrane patch and then anneal it to the defect site. Annexin A1 is a cytosolic protein that, when activated by micromolar Ca2+, binds to membrane phospholipids, promoting membrane aggregation and fusion. We demonstrate here that an annexin A1 function-blocking antibody, a small peptide competitor, and a dominant-negative annexin A1 mutant protein incapable of Ca2+ binding all inhibit resealing. Moreover, we show that, coincident with a resealing event, annexin A1 becomes concentrated at disruption sites. We propose that Ca2+ entering through a disruption locally induces annexin A1 binding to membranes, initiating emergency fusion events whenever and wherever required.
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Affiliation(s)
- Anna K McNeil
- Department of Cellular Biology and Anatomy, Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, Georgia 30912, USA
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45
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Schulte A, Lorenzen I, Böttcher M, Plieth C. A novel fluorescent pH probe for expression in plants. PLANT METHODS 2006; 2:7. [PMID: 16600023 PMCID: PMC1475855 DOI: 10.1186/1746-4811-2-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 04/06/2006] [Indexed: 05/08/2023]
Abstract
BACKGROUND The pH is an important parameter controlling many metabolic and signalling pathways in living cells. Recombinant fluorescent pH indicators (pHluorins) have come into vogue for monitoring cellular pH. They are derived from the most popular Aequorea victoria GFP (Av-GFP). Here, we present a novel fluorescent pH reporter protein from the orange seapen Ptilosarcus gurneyi (Pt-GFP) and compare its properties with pHluorins for expression and use in plants. RESULTS pHluorins have a higher pH-sensitivity. However, Pt-GFP has a broader pH-responsiveness, an excellent dynamic ratio range and a better acid stability. We demonstrate how Pt-GFP expressing Arabidopsis thaliana report cytosolic pH-clamp and changes of cytosolic pH in the response to anoxia and salt-stress. CONCLUSION Pt-GFP appears to be the better choice when used for in vivo-recording of cellular pH in plants.
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Affiliation(s)
- Alexander Schulte
- Zentrum für Biochemie und Molekularbiologie, Universität Kiel, Am Botanischen Garten 9, 24118 Kiel, Germany
- Biochemisches Institut, Universität Kiel, Rudolf-Höber-Str. 1, 24098 Kiel, Germany
| | - Inken Lorenzen
- Biochemisches Institut, Universität Kiel, Rudolf-Höber-Str. 1, 24098 Kiel, Germany
| | - Markus Böttcher
- Botanisches Institut, Universität Kiel, Am Botanischen Garten 9, 24118 Kiel, Germany
- Institut für Physiologie, Universität zu Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Christoph Plieth
- Zentrum für Biochemie und Molekularbiologie, Universität Kiel, Am Botanischen Garten 9, 24118 Kiel, Germany
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M'Baye G, Shynkar VV, Klymchenko AS, Mély Y, Duportail G. Membrane dipole potential as measured by ratiometric 3-hydroxyflavone fluorescence probes: accounting for hydration effects. J Fluoresc 2006; 16:35-42. [PMID: 16400505 DOI: 10.1007/s10895-005-0022-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Accepted: 10/03/2005] [Indexed: 10/25/2022]
Abstract
We previously applied the electrochromic modulation of excited-state intramolecular proton-transfer (ESIPT) reaction for the design of novel 3-hydroxyflavone (3-HF) derivatives as fluorescent probes for measuring the dipole potential, Psi(D), in lipid bilayers (Klymchenko et al., Proc. Natl. Acad. Sci. USA, 2003, 100, 11219). In the present work, this method was revisited to take into account the influence of the bilayer hydration on the emission ratiometric response of 3-HF probes. For this reason, it was necessary to deconvolute the whole fluorescence spectra into three bands corresponding to the non H-bonded forms, normal N* and tautomer T* forms, both participating to the ESIPT reaction, and to the H-bonded H-N* form, excluded from this reaction. This allowed us to determine the pure N*/T* intensity ratio, without any contribution from the H-N* form emission depending essentially on the bilayer hydration. This new approach allowed us to confirm the correlation we obtained between the response of 3-HF probes on dipole potential modifications and the corresponding response of the reference fluorescent probe di-8-ANEPPS, thus further confirming the potency of 3-HF probes as excellent emission ratiometric probes to measure dipole potential in lipid membranes.
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Affiliation(s)
- Gora M'Baye
- Laboratoire de Pharmacologie et Physicochimie des Interactions Moléculaires et Cellulaires, Equipe Photophysique des Interactions Biomoléculaires, UMR 7034 du CNRS, Faculté de Pharmacie, Université Louis Pasteur, BP 60024, 67401, Illkirch, France
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Yushchenko DA, Shvadchak VV, Klymchenko AS, Duportail G, Mély Y, Pivovarenko VG. 2-Aryl-3-hydroxyquinolones, a new class of dyes with solvent dependent dual emission due to excited state intramolecular proton transfer. NEW J CHEM 2006. [DOI: 10.1039/b601400c] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Yushchenko DA, Shvadchak VV, Bilokin' MD, Klymchenko AS, Duportail G, Mély Y, Pivovarenko VG. Modulation of dual fluorescence in a 3-hydroxyquinolone dye by perturbation of its intramolecular proton transfer with solvent polarity and basicity. Photochem Photobiol Sci 2006; 5:1038-44. [PMID: 17077900 DOI: 10.1039/b610054f] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A representative of a new class of dyes with dual fluorescence due to an excited state intramolecular proton transfer (ESIPT) reaction, namely 1-methyl-2-(4-methoxy)phenyl-3-hydroxy-4(1H)-quinolone (QMOM), has been studied in a series of solvents covering a large range of polarity and basicity. A linear dependence of the logarithm of its two bands intensity ratio, log(I(N*)/I(T*)), upon the solvent polarity expressed as a function of the dielectric constant, (epsilon- 1)/(2epsilon + 1), is observed for a series of protic solvents. A linear dependence for log(I(N*)/I(T*)) is also found in aprotic solvents after taking into account the solvent basicity. In contrast, the positions of the absorption and the two emission bands of QMOM do not noticeably depend on the solvent polarity and basicity, indicating relatively small changes in the transition moment of QMOM upon excitation and emission. Time-resolved experiments in acetonitrile, ethyl acetate and dimethylformamide suggest an irreversible ESIPT reaction for this dye. According to the time-resolved data, an increase of solvent basicity results in a dramatic decrease of the ESIPT rate constant, probably due to the disruption of the intramolecular H-bond of the dye by the basic solvent. Due to this new sensor property, 3-hydroxyquinolones are promising candidates for the development of a new generation of environment-sensitive fluorescence dyes for probing interactions of biomolecules.
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Affiliation(s)
- Dmytro A Yushchenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, 01033, Kyiv, Ukraine
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Liu ZQ, Shi M, Li FY, Fang Q, Chen ZH, Yi T, Huang CH. Highly Selective Two-Photon Chemosensors for Fluoride Derived from Organic Boranes. Org Lett 2005; 7:5481-4. [PMID: 16288536 DOI: 10.1021/ol052323b] [Citation(s) in RCA: 239] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] Three organoboron compounds are shown to be two-photon fluorescent sensors for fluoride anion with high sensitivity and selectivity. The recognition mechanism is attributed to the unique steric structure of the bulky dimesitylboryl group and the Lewis acid-base interaction between trivalent boron atom and fluoride anion.
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Affiliation(s)
- Zhi-Qiang Liu
- Laboratory of Advanced Materials, Fudan University, 200433 Shanghai, PR China
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50
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Nakata E, Koshi Y, Koga E, Katayama Y, Hamachi I. Double-Modification of Lectin Using Two Distinct Chemistries for Fluorescent Ratiometric Sensing and Imaging Saccharides in Test Tube or in Cell. J Am Chem Soc 2005; 127:13253-61. [PMID: 16173755 DOI: 10.1021/ja052731a] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The site-selective incorporation of two different fluorophores into a naturally occurring protein (lectin, a sugar-binding protein) has been successfully carried out using two distinct orthogonal chemical methods. By post-photoaffinity labeling modification, Con A, a glucose- and mannose-selective lectin, was modified with fluorescein in the proximity of the sugar binding site (Tyr100 site), and the controlled acylation reaction provided the site-selective attachment of coumarin at Lys114. In this doubly modified Con A, the fluorescein emission changed upon the binding to the corresponding sugars, such as the glucose or mannose derivatives, whereas the coumarin emission was constant. Thus, the doubly modified Con A fluorescently sensed the glucose- and mannose-rich saccharides in a ratiometric manner while retaining the natural binding selectivity and affinity, regardless of the double modification. On the benefit of the ratiometric fluorescent analysis using two distinct probes, the sugar trimming process of a glycoprotein can be precisely monitored by the engineered Con A. Furthermore, the doubly modified Con A can be used not only for the convenient fluorescent imaging of saccharides localized on a cell surface, such as the MCF-7, a breast cancer cell having rich high-mannose branch, but also for the ratiometric fluorescent sensing of the glucose concentration inside HepG2 cells. These results demonstrated that the semisynthetic lectin modified doubly by two distinct chemistries is superior to the singly modified one in function, and thus, it may be potentially useful in cell, as well as in test tube.
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Affiliation(s)
- Eiji Nakata
- Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
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