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Mathur P, Fomitcheva Khartchenko A, Stavrakis S, Kaigala GV, deMello AJ. Quantifying Antibody Binding Kinetics on Fixed Cells and Tissues via Fluorescence Lifetime Imaging. Anal Chem 2022; 94:10967-10975. [PMID: 35895913 DOI: 10.1021/acs.analchem.2c01076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a method for monitoring spatially localized antigen-antibody binding events on physiologically relevant substrates (cell and tissue sections) using fluorescence lifetime imaging. Specifically, we use the difference between the fluorescence decay times of fluorescently tagged antibodies in free solution and in the bound state to track the bound fraction over time and hence deduce the binding kinetics. We make use of a microfluidic probe format to minimize the mass transport effects and localize the analysis to specific regions of interest on the biological substrates. This enables measurement of binding constants (kon) on surface-bound antigens and on cell blocks using model biomarkers. Finally, we directly measure p53 kinetics with differential biomarker expression in ovarian cancer tissue sections, observing that the degree of expression corresponds to the changes in kon, with values of 3.27-3.50 × 103 M-1 s-1 for high biomarker expression and 2.27-2.79 × 103 M-1 s-1 for low biomarker expression.
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Affiliation(s)
- Prerit Mathur
- Institute for Chemical and Bioengineering, Department of Chemistry & Applied Biosciences, Eidgenössische Technische Hochschule (ETH Zürich), Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.,IBM Research Europe─Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
| | - Anna Fomitcheva Khartchenko
- Institute for Chemical and Bioengineering, Department of Chemistry & Applied Biosciences, Eidgenössische Technische Hochschule (ETH Zürich), Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.,IBM Research Europe─Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, Department of Chemistry & Applied Biosciences, Eidgenössische Technische Hochschule (ETH Zürich), Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Govind V Kaigala
- IBM Research Europe─Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland.,School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Andrew J deMello
- Institute for Chemical and Bioengineering, Department of Chemistry & Applied Biosciences, Eidgenössische Technische Hochschule (ETH Zürich), Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
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Single-Molecule Imaging in Living Plant Cells: A Methodological Review. Int J Mol Sci 2021; 22:ijms22105071. [PMID: 34064786 PMCID: PMC8151321 DOI: 10.3390/ijms22105071] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 12/23/2022] Open
Abstract
Single-molecule imaging is emerging as a revolutionary approach to studying fundamental questions in plants. However, compared with its use in animals, the application of single-molecule imaging in plants is still underexplored. Here, we review the applications, advantages, and challenges of single-molecule fluorescence imaging in plant systems from the perspective of methodology. Firstly, we provide a general overview of single-molecule imaging methods and their principles. Next, we summarize the unprecedented quantitative details that can be obtained using single-molecule techniques compared to bulk assays. Finally, we discuss the main problems encountered at this stage and provide possible solutions.
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Ghosh A, Karedla N, Thiele JC, Gregor I, Enderlein J. Fluorescence lifetime correlation spectroscopy: Basics and applications. Methods 2018; 140-141:32-39. [DOI: 10.1016/j.ymeth.2018.02.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/09/2018] [Accepted: 02/10/2018] [Indexed: 10/18/2022] Open
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4
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Aggregation of cysteamine-capped gold nanoparticles in presence of ATP as an analytical tool for rapid detection of creatine kinase (CK-MM). Anal Chim Acta 2018; 1024:161-168. [PMID: 29776542 DOI: 10.1016/j.aca.2018.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/11/2018] [Accepted: 03/19/2018] [Indexed: 11/23/2022]
Abstract
Creatine kinase, a key biomarker associated with many debilitating physiological conditions has seldom been detected in biological fluids using functionalized gold nanoparticles (GNPs). We have developed a method based on the aggregation of cysteamine (Cys) functionalized GNPs in presence of ATP for effective detection of creatine kinase (CK-MM). Positively charged Cys-GNPs (brick red color) aggregate in presence of negatively charged ATP (blue color) but the process is prevented when CK-MM is added to the solution. The analytical response to the concentration of CK-MM is linear (R2 = 0.9850). The proposed method is selective in sensing the CK-MM for a range of 5.617 × 103 ng/ml, 0.5617 ng/ml. The limit of detection was found to be 0.569 ng/ml in solution and 0.553 ng/ml in human serum with high selectivity.
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Ghosh A, Isbaner S, Veiga-Gutiérrez M, Gregor I, Enderlein J, Karedla N. Quantifying Microsecond Transition Times Using Fluorescence Lifetime Correlation Spectroscopy. J Phys Chem Lett 2017; 8:6022-6028. [PMID: 29183125 DOI: 10.1021/acs.jpclett.7b02707] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Many complex luminescent emitters such as fluorescent proteins exhibit multiple emitting states that result in rapid fluctuations of their excited-state lifetime. Here, we apply fluorescence lifetime correlation spectroscopy (FLCS) to resolve the photophysical state dynamics of the prototypical fluorescence protein enhanced green fluorescent protein (EGFP). We quantify the microsecond transition rates between its two fluorescent states, which have otherwise highly overlapping emission spectra. We relate these transitions to a room-temperature angstrom-scale rotational isomerism of an amino acid next to its fluorescent center. With this study, we demonstrate the power of FLCS for studying the rapid transition dynamics of a broad range of light-emitting systems with complex multistate photophysics, which cannot be easily done by other methods.
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Affiliation(s)
- Arindam Ghosh
- III. Institute of Physics, Georg August University , 37077 Göttingen, Germany
| | - Sebastian Isbaner
- III. Institute of Physics, Georg August University , 37077 Göttingen, Germany
| | | | - Ingo Gregor
- III. Institute of Physics, Georg August University , 37077 Göttingen, Germany
| | - Jörg Enderlein
- III. Institute of Physics, Georg August University , 37077 Göttingen, Germany
| | - Narain Karedla
- III. Institute of Physics, Georg August University , 37077 Göttingen, Germany
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6
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Uslu VV, Grossmann G. The biosensor toolbox for plant developmental biology. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:138-47. [PMID: 26802805 DOI: 10.1016/j.pbi.2015.12.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 12/01/2015] [Accepted: 12/02/2015] [Indexed: 05/14/2023]
Abstract
Plant development is highly interconnected with the metabolic state of tissues and cells. Current research efforts focus on the identification of the links and mechanisms that govern the interplay between metabolic and gene-regulatory networks. Genetically encoded sensors that allow detection of small molecules in vivo and at high spatio-temporal resolution promise to be the tools of choice for quantifying and visualizing the dynamics of metabolite flux in plants. We provide an overview about current approaches to measure signaling molecules, such as hormones, calcium and sugars, as well as for monitoring the metabolic state via energy equivalents and pH. Biosensors show great potential to address questions of plant development but there are also limitations where alternative approaches are needed.
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Affiliation(s)
- Veli V Uslu
- Ruprecht-Karls-Universität Heidelberg, Department of Plant Molecular Biology, Centre for Organismal Studies, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Guido Grossmann
- Ruprecht-Karls-Universität Heidelberg, CellNetworks Excellence Cluster and Centre for Organismal Studies, Im Neuenheimer Feld 329, 69120 Heidelberg, Germany.
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Galler K, Bräutigam K, Große C, Popp J, Neugebauer U. Making a big thing of a small cell--recent advances in single cell analysis. Analyst 2015; 139:1237-73. [PMID: 24495980 DOI: 10.1039/c3an01939j] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single cell analysis is an emerging field requiring a high level interdisciplinary collaboration to provide detailed insights into the complex organisation, function and heterogeneity of life. This review is addressed to life science researchers as well as researchers developing novel technologies. It covers all aspects of the characterisation of single cells (with a special focus on mammalian cells) from morphology to genetics and different omics-techniques to physiological, mechanical and electrical methods. In recent years, tremendous advances have been achieved in all fields of single cell analysis: (1) improved spatial and temporal resolution of imaging techniques to enable the tracking of single molecule dynamics within single cells; (2) increased throughput to reveal unexpected heterogeneity between different individual cells raising the question what characterizes a cell type and what is just natural biological variation; and (3) emerging multimodal approaches trying to bring together information from complementary techniques paving the way for a deeper understanding of the complexity of biological processes. This review also covers the first successful translations of single cell analysis methods to diagnostic applications in the field of tumour research (especially circulating tumour cells), regenerative medicine, drug discovery and immunology.
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Affiliation(s)
- Kerstin Galler
- Integrated Research and Treatment Center "Center for Sepsis Control and Care", Jena University Hospital, Erlanger Allee 101, 07747 Jena, Germany
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Moussa R, Baierl A, Steffen V, Kubitzki T, Wiechert W, Pohl M. An evaluation of genetically encoded FRET-based biosensors for quantitative metabolite analyses in vivo. J Biotechnol 2014; 191:250-9. [PMID: 25107505 DOI: 10.1016/j.jbiotec.2014.07.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/25/2014] [Accepted: 07/07/2014] [Indexed: 10/24/2022]
Abstract
A broad range of genetically-encoded fluorescence biosensors has been developed, allowing the detection of signaling intermediates and metabolites in real time. Many of these biosensors are based on Foerster Resonance Energy Transfer (FRET). The two biosensors of the well-known "Venus-flytrap" type exemplarily studied in this work are composed of a central sugar binding protein flanked by two green fluorescent protein derivatives, namely ECFP as well as Citrine and EYFP, respectively. In order to evaluate FRET-based biosensors as an in vivo tool for quantitative metabolite analyses, we have thoroughly studied the effects of pH, buffer salts, ionic strength, temperature and several intracellular metabolites on the signal intensity of both biosensors and both fluorescence proteins. Almost all micro-environmental variations led to considerably different FRET signals, because either the fluorescent proteins or the metabolite binding domains were affected by the tested parameters. This resulted not only in altered FRET ratios between the apo state and the saturated state but also in significant shifts of the apparent binding constant. This underlines the necessity of careful controls in order to allow reliable quantitative measurements in vivo.
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Affiliation(s)
- Roland Moussa
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
| | - Anna Baierl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
| | - Victoria Steffen
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
| | - Tina Kubitzki
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
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9
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Schwarzer R, Levental I, Gramatica A, Scolari S, Buschmann V, Veit M, Herrmann A. The cholesterol-binding motif of the HIV-1 glycoprotein gp41 regulates lateral sorting and oligomerization. Cell Microbiol 2014; 16:1565-81. [PMID: 24844300 DOI: 10.1111/cmi.12314] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/24/2014] [Accepted: 05/13/2014] [Indexed: 12/12/2022]
Abstract
Enveloped viruses often use membrane lipid rafts to assemble and bud, augment infection and spread efficiently. However, the molecular bases and functional consequences of the partitioning of viral glycoproteins into microdomains remain intriguing questions in virus biology. Here, we measured Foerster resonance energy transfer by fluorescence lifetime imaging microscopy (FLIM-FRET) to study the role of distinct membrane proximal regions of the human immunodeficiency virus glycoprotein gp41 for lipid raft partitioning in living Chinese hamster ovary cells (CHO-K1). Gp41 was labelled with a fluorescent protein at the exoplasmic face of the membrane, preventing any interference of the fluorophore with the proposed role of the transmembrane and cytoplasmic domains in lateral organization of gp41. Raft localization was deduced from interaction with an established raft marker, a fluorescently tagged glycophosphatidylinositol anchor and the cholesterol recognition amino acid consensus (CRAC) was identified as the crucial lateral sorting determinant in CHO-K1 cells. Interestingly, the raft association of gp41 indicates a substantial cell-to-cell heterogeneity of the plasma membrane microdomains. In complementary fluorescence polarization microscopy, a distinct CRAC requirement was found for the oligomerization of the gp41 variants. Our data provide further insight into the molecular basis and biological implications of the cholesterol dependent lateral sorting of viral glycoproteins for virus assembly at cellular membranes.
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Affiliation(s)
- Roland Schwarzer
- Department of Biology, Molecular Biophysics, Humboldt University, 10115, Berlin, Germany
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Drepper T, Gensch T, Pohl M. Advanced in vivo applications of blue light photoreceptors as alternative fluorescent proteins. Photochem Photobiol Sci 2014; 12:1125-34. [PMID: 23660639 DOI: 10.1039/c3pp50040c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ultimate ambition in cell biology, microbiology and biomedicine is to unravel complex physiological and pathophysiological processes within living organisms. To conquer this challenge, fluorescent proteins (FPs) are used as versatile in vivo reporters and biosensors to study gene regulation as well as the synthesis, localization and function of proteins in living cells. The most widely used FPs are the green fluorescent protein (GFP) and its derivatives and relatives. Their use as in vivo reporter proteins, however, is sometimes restricted by different environmental and cellular factors. Consequently, a whole range of alternative, cofactor-dependent reporter proteins have been developed recently. In this perspective, we summarize the advantages and limitations of the novel class of cyan-green fluorescent flavoproteins in comparison to members of the GFP family and discuss some correlated consequences for the use of FPs as in vivo reporters.
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Affiliation(s)
- Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Jülich, 52425 Juelich, Germany.
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Mérola F, Fredj A, Betolngar DB, Ziegler C, Erard M, Pasquier H. Newly engineered cyan fluorescent proteins with enhanced performances for live cell FRET imaging. Biotechnol J 2013; 9:180-91. [DOI: 10.1002/biot.201300198] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/17/2013] [Accepted: 10/31/2013] [Indexed: 11/06/2022]
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12
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Stender AS, Marchuk K, Liu C, Sander S, Meyer MW, Smith EA, Neupane B, Wang G, Li J, Cheng JX, Huang B, Fang N. Single cell optical imaging and spectroscopy. Chem Rev 2013; 113:2469-527. [PMID: 23410134 PMCID: PMC3624028 DOI: 10.1021/cr300336e] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Anthony S. Stender
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Kyle Marchuk
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Chang Liu
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Suzanne Sander
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Matthew W. Meyer
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Emily A. Smith
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Bhanu Neupane
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Gufeng Wang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Junjie Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Ji-Xin Cheng
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Bo Huang
- Department of Pharmaceutical Chemistry and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Ning Fang
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
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Erard M, Fredj A, Pasquier H, Beltolngar DB, Bousmah Y, Derrien V, Vincent P, Merola F. Minimum set of mutations needed to optimize cyan fluorescent proteins for live cell imaging. ACTA ACUST UNITED AC 2013. [DOI: 10.1039/c2mb25303h] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Quantitative glucose and ATP sensing in mammalian cells. Pharm Res 2011; 28:2745-57. [PMID: 21691894 DOI: 10.1007/s11095-011-0492-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 05/24/2011] [Indexed: 01/08/2023]
Abstract
The functioning and survival of mammalian cells requires an active energy metabolism. Metabolic dysfunction plays an important role in many human diseases, including diabetes, cancer, inherited mitochondrial disorders, and metabolic syndrome. The monosaccharide glucose constitutes a key source of cellular energy. Following its import across the plasma membrane, glucose is converted into pyruvate by the glycolysis pathway. Pyruvate oxidation supplies substrates for the ATP-generating mitochondrial oxidative phosphorylation (OXPHOS) system. To gain cell-biochemical knowledge about the operation and regulation of the cellular energy metabolism in the healthy and diseased state, quantitative knowledge is required about (changes in) metabolite concentrations under (non) steady-state conditions. This information can, for instance, be used to construct more realistic in silico models of cell metabolism, which facilitates understanding the consequences of metabolic dysfunction as well as on- and off-target effects of mitochondrial drugs. Here we review the current state-of-the-art live-cell quantification of two key cellular metabolites, glucose and ATP, using protein-based sensors. The latter apply the principle of FRET (fluorescence resonance energy transfer) and allow measurements in different cell compartments by fluorescence microscopy. We further summarize the properties and applications of the FRET-based sensors, their calibration, pitfalls, and future perspectives.
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