1
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Broch F, El Hajji L, Pietrancosta N, Gautier A. Engineering of Tunable Allosteric-like Fluorogenic Protein Sensors. ACS Sens 2023; 8:3933-3942. [PMID: 37830919 DOI: 10.1021/acssensors.3c01536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Optical protein sensors that enable detection of relevant biomolecules of interest play central roles in biological research. Coupling fluorescent reporters with protein sensing units has enabled the development of a wide range of biosensors that recognize analytes with high selectivity. In these sensors, analyte recognition induces a conformational change in the protein sensing unit that can modulate the optical signal of the fluorescent reporter. Here, we explore various designs for the creation of tunable allosteric-like fluorogenic protein sensors through incorporation of sensing protein units within the chemogenetic fluorescence-activating and absorption-shifting tag (FAST) that selectively binds and stabilizes the fluorescent state of 4-hydroxybenzylidene rhodanine (HBR) analogs. Conformational coupling allowed us to design analyte-responsive optical protein sensors through allosteric-like modulation of fluorogen binding.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Lina El Hajji
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Nicolas Pietrancosta
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Neuroscience Paris Seine-Institut de Biologie Paris Seine (NPS-IBPS) INSERM, CNRS, Sorbonne Université, 75005 Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Institut Universitaire de France, 75231 Paris, France
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2
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Kamino K, Kadakia N, Avgidis F, Liu ZX, Aoki K, Shimizu T, Emonet T. Optimal inference of molecular interaction dynamics in FRET microscopy. Proc Natl Acad Sci U S A 2023; 120:e2211807120. [PMID: 37014867 PMCID: PMC10104582 DOI: 10.1073/pnas.2211807120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 02/10/2023] [Indexed: 04/05/2023] Open
Abstract
Intensity-based time-lapse fluorescence resonance energy transfer (FRET) microscopy has been a major tool for investigating cellular processes, converting otherwise unobservable molecular interactions into fluorescence time series. However, inferring the molecular interaction dynamics from the observables remains a challenging inverse problem, particularly when measurement noise and photobleaching are nonnegligible-a common situation in single-cell analysis. The conventional approach is to process the time-series data algebraically, but such methods inevitably accumulate the measurement noise and reduce the signal-to-noise ratio (SNR), limiting the scope of FRET microscopy. Here, we introduce an alternative probabilistic approach, B-FRET, generally applicable to standard 3-cube FRET-imaging data. Based on Bayesian filtering theory, B-FRET implements a statistically optimal way to infer molecular interactions and thus drastically improves the SNR. We validate B-FRET using simulated data and then apply it to real data, including the notoriously noisy in vivo FRET time series from individual bacterial cells to reveal signaling dynamics otherwise hidden in the noise.
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Affiliation(s)
- Keita Kamino
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Institute of Molecular Biology, Academia Sinica, Taipei115, Taiwan
- PRESTO, Japan Science and Technology Agency, Kawaguchi-shi, Saitama332-0012, Japan
| | - Nirag Kadakia
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Swartz Foundation for Theoretical Neuroscience, Yale University, New Haven, CT06511
| | | | - Zhe-Xuan Liu
- Institute of Physics, National Yang Ming Chiao Tung University, Hsinchu30010, Taiwan
| | - Kazuhiro Aoki
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi240-0193, Japan
| | | | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Department of Physics, Yale University, New Haven, CT06511
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3
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Day-Cooney J, Dalangin R, Zhong H, Mao T. Genetically encoded fluorescent sensors for imaging neuronal dynamics in vivo. J Neurochem 2023; 164:284-308. [PMID: 35285522 DOI: 10.1111/jnc.15608] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/29/2022]
Abstract
The brain relies on many forms of dynamic activities in individual neurons, from synaptic transmission to electrical activity and intracellular signaling events. Monitoring these neuronal activities with high spatiotemporal resolution in the context of animal behavior is a necessary step to achieve a mechanistic understanding of brain function. With the rapid development and dissemination of highly optimized genetically encoded fluorescent sensors, a growing number of brain activities can now be visualized in vivo. To date, cellular calcium imaging, which has been largely used as a proxy for electrical activity, has become a mainstay in systems neuroscience. While challenges remain, voltage imaging of neural populations is now possible. In addition, it is becoming increasingly practical to image over half a dozen neurotransmitters, as well as certain intracellular signaling and metabolic activities. These new capabilities enable neuroscientists to test previously unattainable hypotheses and questions. This review summarizes recent progress in the development and delivery of genetically encoded fluorescent sensors, and highlights example applications in the context of in vivo imaging.
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Affiliation(s)
- Julian Day-Cooney
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Rochelin Dalangin
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA
| | - Haining Zhong
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Tianyi Mao
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
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4
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Hao Y, Plested AJ. Seeing glutamate at central synapses. J Neurosci Methods 2022; 375:109531. [DOI: 10.1016/j.jneumeth.2022.109531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/15/2022]
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5
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Chandris P, Giannouli CC, Panayotou G. Imaging Approaches for the Study of Metabolism in Real Time Using Genetically Encoded Reporters. Front Cell Dev Biol 2022; 9:725114. [PMID: 35118062 PMCID: PMC8804523 DOI: 10.3389/fcell.2021.725114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Metabolism comprises of two axes in order to serve homeostasis: anabolism and catabolism. Both axes are interbranched with the so-called bioenergetics aspect of metabolism. There is a plethora of analytical biochemical methods to monitor metabolites and reactions in lysates, yet there is a rising need to monitor, quantify and elucidate in real time the spatiotemporal orchestration of complex biochemical reactions in living systems and furthermore to analyze the metabolic effect of chemical compounds that are destined for the clinic. The ongoing technological burst in the field of imaging creates opportunities to establish new tools that will allow investigators to monitor dynamics of biochemical reactions and kinetics of metabolites at a resolution that ranges from subcellular organelle to whole system for some key metabolites. This article provides a mini review of available toolkits to achieve this goal but also presents a perspective on the open space that can be exploited to develop novel methodologies that will merge classic biochemistry of metabolism with advanced imaging. In other words, a perspective of "watching metabolism in real time."
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Affiliation(s)
- Panagiotis Chandris
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Vari, Greece
| | | | - George Panayotou
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, Vari, Greece
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6
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Hong S, Pawel GT, Pei R, Lu Y. Recent progress in developing fluorescent probes for imaging cell metabolites. Biomed Mater 2021; 16. [PMID: 33915523 DOI: 10.1088/1748-605x/abfd11] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/29/2021] [Indexed: 01/12/2023]
Abstract
Cellular metabolites play a crucial role in promoting and regulating cellular activities, but it has been difficult to monitor these cellular metabolites in living cells and in real time. Over the past decades, iterative development and improvements of fluorescent probes have been made, resulting in the effective monitoring of metabolites. In this review, we highlight recent progress in the use of fluorescent probes for tracking some key metabolites, such as adenosine triphosphate, cyclic adenosine monophosphate, cyclic guanosine 5'-monophosphate, Nicotinamide adenine dinucleotide (NADH), reactive oxygen species, sugar, carbon monoxide, and nitric oxide for both whole cell and subcellular imaging.
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Affiliation(s)
- Shanni Hong
- Department of Medical Imaging Technology, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, People's Republic of China.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America.,CAS Key Laboratory of Nano-Bio Interfaces, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, People's Republic of China
| | - Gregory T Pawel
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interfaces, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, People's Republic of China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
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7
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Bi X, Beck C, Gong Y. Genetically Encoded Fluorescent Indicators for Imaging Brain Chemistry. BIOSENSORS 2021; 11:116. [PMID: 33920418 PMCID: PMC8069469 DOI: 10.3390/bios11040116] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Genetically encoded fluorescent indicators, combined with optical imaging, enable the detection of physiologically or behaviorally relevant neural activity with high spatiotemporal resolution. Recent developments in protein engineering and screening strategies have improved the dynamic range, kinetics, and spectral properties of genetically encoded fluorescence indicators of brain chemistry. Such indicators have detected neurotransmitter and calcium dynamics with high signal-to-noise ratio at multiple temporal and spatial scales in vitro and in vivo. This review summarizes the current trends in these genetically encoded fluorescent indicators of neurotransmitters and calcium, focusing on their key metrics and in vivo applications.
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Affiliation(s)
| | | | - Yiyang Gong
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; (X.B.); (C.B.)
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8
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Jacobs AH, Schelhaas S, Viel T, Waerzeggers Y, Winkeler A, Zinnhardt B, Gelovani J. Imaging of Gene and Cell-Based Therapies: Basis and Clinical Trials. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00060-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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9
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Kaur A, Kaur P, Ahuja S. Förster resonance energy transfer (FRET) and applications thereof. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:5532-5550. [PMID: 33210685 DOI: 10.1039/d0ay01961e] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
FRET is a nonradiative process of energy transfer that is based on the dipole-dipole interactions between molecules that are fluorescent. Transfer of energy takes place rapidly from a donor molecule to an acceptor molecule in juxtaposition such as 0 to 10 nm without photonic radiation. FRET has occupied a center stage in biotechnology and biological studies. It is used to gain information on conformation changes in single molecules. The pharmaceutical industry has also developed large fluorescence detection systems with very small sample sizes, at the level of single molecules, using fluorescence correlation spectroscopy.
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Affiliation(s)
- Amrita Kaur
- Computer Science and Engineering Department, Thapar Institute of Engineering and Technology, Patiala, 147001, India
| | - Pardeep Kaur
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab 140407, India.
| | - Sahil Ahuja
- Computer Science and Engineering Department, Thapar Institute of Engineering and Technology, Patiala, 147001, India
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10
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Aissa HB, Gautier A. Engineering Glowing Chemogenetic Hybrids for Spying on Cells. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hela Ben Aissa
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
| | - Arnaud Gautier
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
- Institut Universitaire de France Paris France
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11
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Broch F, Gautier A. Illuminating Cellular Biochemistry: Fluorogenic Chemogenetic Biosensors for Biological Imaging. Chempluschem 2020; 85:1487-1497. [PMID: 32644262 DOI: 10.1002/cplu.202000413] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/18/2020] [Indexed: 12/19/2022]
Abstract
Cellular activity is defined by the precise spatiotemporal regulation of various components, such as ions, small molecules, or proteins. Studying cell physiology consequently requires the optical recording of these processes, notably by using fluorescent biosensors. The recent development of various fluorogenic systems greatly expanded the palette of reporters to be included in these sensors design. Fluorogenic reporters consist of a protein or RNA tag that can complex either an endogenous or a synthetic fluorogenic dye (so-called fluorogen). The intrinsic nature of these tags, along with the high tunability of their cognate chromophore provide interesting features such as far-red to near-infrared emission, oxygen independence, or unprecedented color versatility. These engineered photoreceptors, self-labelling proteins, or noncovalent aptamers and protein tags were rapidly identified as promising reporters to observe biological events. This Minireview focuses on the new perspectives they offer to design unique and innovative biosensors, thus pushing the boundaries of cellular imaging.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France.,Institut Universitaire de France, France
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12
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13
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Zhang Z, Cheng X, Zhao Y, Yang Y. Lighting Up Live-Cell and In Vivo Central Carbon Metabolism with Genetically Encoded Fluorescent Sensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:293-314. [PMID: 32119572 DOI: 10.1146/annurev-anchem-091619-091306] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
As the core component of cell metabolism, central carbon metabolism, consisting of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle converts nutrients into metabolic precursors for biomass and energy to sustain the life of virtually all extant species. The metabolite levels or distributions in central carbon metabolism often change dynamically with cell fates, development, and disease progression. However, traditional biochemical methods require cell lysis, making it challenging to obtain spatiotemporal information about metabolites in living cells and in vivo. Genetically encoded fluorescent sensors allow the rapid, sensitive, specific, and real-time readout of metabolite dynamics in living organisms, thereby offering the potential to fill the gap in current techniques. In this review, we introduce recent progress made in the development of genetically encoded fluorescent sensors for central carbon metabolism and discuss their advantages, disadvantages, and applications. Moreover, several future directions of metabolite sensors are also proposed.
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Affiliation(s)
- Zhuo Zhang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Research Unit of Chinese Academy of Medical Sciences, East China University of Science and Technology, Shanghai 200237, China; ,
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiawei Cheng
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Research Unit of Chinese Academy of Medical Sciences, East China University of Science and Technology, Shanghai 200237, China; ,
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yuzheng Zhao
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Research Unit of Chinese Academy of Medical Sciences, East China University of Science and Technology, Shanghai 200237, China; ,
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yi Yang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Research Unit of Chinese Academy of Medical Sciences, East China University of Science and Technology, Shanghai 200237, China; ,
- CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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14
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Live cell imaging of signaling and metabolic activities. Pharmacol Ther 2019; 202:98-119. [DOI: 10.1016/j.pharmthera.2019.06.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/31/2019] [Indexed: 12/15/2022]
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15
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Franke JM, Raliski BK, Boggess SC, Natesan DV, Koretsky ET, Zhang P, Kulkarni RU, Deal PE, Miller EW. BODIPY Fluorophores for Membrane Potential Imaging. J Am Chem Soc 2019; 141:12824-12831. [PMID: 31339313 PMCID: PMC7285656 DOI: 10.1021/jacs.9b05912] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorophores based on the BODIPY scaffold are prized for their tunable excitation and emission profiles, mild syntheses, and biological compatibility. Improving the water-solubility of BODIPY dyes remains an outstanding challenge. The development of water-soluble BODIPY dyes usually involves direct modification of the BODIPY fluorophore core with ionizable groups or substitution at the boron center. While these strategies are effective for the generation of water-soluble fluorophores, they are challenging to implement when developing BODIPY-based indicators: direct modification of BODIPY core can disrupt the electronics of the dye, complicating the design of functional indicators; and substitution at the boron center often renders the resultant BODIPY incompatible with the chemical transformations required to generate fluorescent sensors. In this study, we show that BODIPYs bearing a sulfonated aromatic group at the meso position provide a general solution for water-soluble BODIPYs. We outline the route to a suite of 5 new sulfonated BODIPYs with 2,6-disubstitution patterns spanning a range of electron-donating and -withdrawing propensities. To highlight the utility of these new, sulfonated BODIPYs, we further functionalize them to access 13 new, BODIPY-based, voltage-sensitive fluorophores (VF). The most sensitive of these BODIPY VF dyes displays a 48% ΔF/F per 100 mV in mammalian cells. Two additional BODIPY VFs show good voltage sensitivity (≥24% ΔF/F) and excellent brightness in cells. These compounds can report on action potential dynamics in both mammalian neurons and human stem cell-derived cardiomyocytes. Accessing a range of substituents in the context of a water-soluble BODIPY fluorophore provides opportunities to tune the electronic properties of water-soluble BODIPY dyes for functional indicators.
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Affiliation(s)
- Jenna M. Franke
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Benjamin K. Raliski
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Steven C. Boggess
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Divya V. Natesan
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Evan T. Koretsky
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Patrick Zhang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Rishikesh U. Kulkarni
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Parker E. Deal
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Evan W. Miller
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, United States
- Department of Helen Wills Neuroscience Institute. University of California, Berkeley, California 94720, United States
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16
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Abstract
Creative engineering of fluorescent proteins has yielded a variety of tools for visualization of biochemical events in vivo. In this issue of Cell Chemical Biology, To et al. (2016) describe a fluorogenic green fluorescent protein that is activated by caspase-3 activity and enables imaging of apoptosis in developing zebrafish embryos (To et al., 2016).
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Affiliation(s)
- Matthew D Wiens
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Xiaocen Lu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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17
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Inoue M, Takeuchi A, Manita S, Horigane SI, Sakamoto M, Kawakami R, Yamaguchi K, Otomo K, Yokoyama H, Kim R, Yokoyama T, Takemoto-Kimura S, Abe M, Okamura M, Kondo Y, Quirin S, Ramakrishnan C, Imamura T, Sakimura K, Nemoto T, Kano M, Fujii H, Deisseroth K, Kitamura K, Bito H. Rational Engineering of XCaMPs, a Multicolor GECI Suite for In Vivo Imaging of Complex Brain Circuit Dynamics. Cell 2019; 177:1346-1360.e24. [PMID: 31080068 DOI: 10.1016/j.cell.2019.04.007] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/28/2019] [Accepted: 04/02/2019] [Indexed: 12/15/2022]
Abstract
To decipher dynamic brain information processing, current genetically encoded calcium indicators (GECIs) are limited in single action potential (AP) detection speed, combinatorial spectral compatibility, and two-photon imaging depth. To address this, here, we rationally engineered a next-generation quadricolor GECI suite, XCaMPs. Single AP detection was achieved within 3-10 ms of spike onset, enabling measurements of fast-spike trains in parvalbumin (PV)-positive interneurons in the barrel cortex in vivo and recording three distinct (two inhibitory and one excitatory) ensembles during pre-motion activity in freely moving mice. In vivo paired recording of pre- and postsynaptic firing revealed spatiotemporal constraints of dendritic inhibition in layer 1 in vivo, between axons of somatostatin (SST)-positive interneurons and apical tufts dendrites of excitatory pyramidal neurons. Finally, non-invasive, subcortical imaging using red XCaMP-R uncovered somatosensation-evoked persistent activity in hippocampal CA1 neurons. Thus, the XCaMPs offer a critical enhancement of solution space in studies of complex neuronal circuit dynamics. VIDEO ABSTRACT.
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Affiliation(s)
- Masatoshi Inoue
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Atsuya Takeuchi
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satoshi Manita
- Department of Neurophysiology, Faculty of Medicine, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Shin-Ichiro Horigane
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Neuroscience I, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi 464-8601, Japan; Department of Molecular/Cellular Neuroscience, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Masayuki Sakamoto
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryosuke Kawakami
- Laboratory of Molecular and Cellular Biophysics, Research Institute for Electronic Science, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan; Department of Molecular Medicine for Pathogenesis, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Kazushi Yamaguchi
- Laboratory of Molecular and Cellular Biophysics, Research Institute for Electronic Science, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Kouhei Otomo
- Laboratory of Molecular and Cellular Biophysics, Research Institute for Electronic Science, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Hiroyuki Yokoyama
- New Industry Creation Hatchery Center (NICHe), Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Ryang Kim
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tatsushi Yokoyama
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sayaka Takemoto-Kimura
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Neuroscience I, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi 464-8601, Japan; Department of Molecular/Cellular Neuroscience, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Saitama, Japan
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Niigata 951-8585, Japan
| | - Michiko Okamura
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yayoi Kondo
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sean Quirin
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Takeshi Imamura
- Department of Molecular Medicine for Pathogenesis, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Niigata 951-8585, Japan
| | - Tomomi Nemoto
- Laboratory of Molecular and Cellular Biophysics, Research Institute for Electronic Science, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan
| | - Hajime Fujii
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kazuo Kitamura
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Neurophysiology, Faculty of Medicine, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Haruhiko Bito
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan.
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18
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Dürst CD, Wiegert JS, Helassa N, Kerruth S, Coates C, Schulze C, Geeves MA, Török K, Oertner TG. High-speed imaging of glutamate release with genetically encoded sensors. Nat Protoc 2019; 14:1401-1424. [PMID: 30988508 PMCID: PMC6751072 DOI: 10.1038/s41596-019-0143-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/22/2019] [Indexed: 11/08/2022]
Abstract
The strength of an excitatory synapse depends on its ability to release glutamate and on the density of postsynaptic receptors. Genetically encoded glutamate indicators (GEGIs) allow eavesdropping on synaptic transmission at the level of cleft glutamate to investigate properties of the release machinery in detail. Based on the sensor iGluSnFR, we recently developed accelerated versions of GEGIs that allow investigation of synaptic release during 100-Hz trains. Here, we describe the detailed procedures for design and characterization of fast iGluSnFR variants in vitro, transfection of pyramidal cells in organotypic hippocampal cultures, and imaging of evoked glutamate transients with two-photon laser-scanning microscopy. As the released glutamate spreads from a point source-the fusing vesicle-it is possible to localize the vesicle fusion site with a precision exceeding the optical resolution of the microscope. By using a spiral scan path, the temporal resolution can be increased to 1 kHz to capture the peak amplitude of fast iGluSnFR transients. The typical time frame for these experiments is 30 min per synapse.
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Affiliation(s)
- Céline D Dürst
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, Hamburg, Germany
| | - J Simon Wiegert
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, Hamburg, Germany
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, Hamburg, Germany
| | - Nordine Helassa
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London, UK
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Silke Kerruth
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London, UK
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry, Prague, Czech Republic
| | - Catherine Coates
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London, UK
| | - Christian Schulze
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, Hamburg, Germany
| | | | - Katalin Török
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London, UK
| | - Thomas G Oertner
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, Hamburg, Germany.
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19
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Boggess SC, Gandhi SS, Siemons BA, Huebsch N, Healy KE, Miller EW. New Molecular Scaffolds for Fluorescent Voltage Indicators. ACS Chem Biol 2019; 14:390-396. [PMID: 30735344 PMCID: PMC6499379 DOI: 10.1021/acschembio.8b00978] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The ability to non-invasively monitor membrane potential dynamics in excitable cells like neurons and cardiomyocytes promises to revolutionize our understanding of the physiology and pathology of the brain and heart. Here, we report the design, synthesis, and application of a new class of fluorescent voltage indicators that make use of a fluorene-based molecular wire as a voltage-sensing domain to provide fast and sensitive measurements of membrane potential in both mammalian neurons and human-derived cardiomyocytes. We show that the best of the new probes, fluorene VoltageFluor 2 (fVF 2), readily reports on action potentials in mammalian neurons, detects perturbations to the cardiac action potential waveform in human induced pluripotent stem cell-derived cardiomyocytes, shows a substantial decrease in phototoxicity compared to existing molecular wire-based indicators, and can monitor cardiac action potentials for extended periods of time. Together, our results demonstrate the generalizability of a molecular wire approach to voltage sensing and highlight the utility of fVF 2 for interrogating membrane potential dynamics.
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Affiliation(s)
- Steven C. Boggess
- Departments of Chemistry, University of California, Berkeley, California 94720, United States
| | - Shivaani S. Gandhi
- Departments of Chemistry, University of California, Berkeley, California 94720, United States
| | - Brian A. Siemons
- Departments of Bioengineering, University of California, Berkeley, California 94720, United States
- Departments of Materials Science & Engineering, University of California, Berkeley, California 94720, United States
| | - Nathaniel Huebsch
- Departments of Bioengineering, University of California, Berkeley, California 94720, United States
- Departments of Materials Science & Engineering, University of California, Berkeley, California 94720, United States
| | - Kevin E. Healy
- Departments of Bioengineering, University of California, Berkeley, California 94720, United States
- Departments of Materials Science & Engineering, University of California, Berkeley, California 94720, United States
| | - Evan W. Miller
- Departments of Chemistry, University of California, Berkeley, California 94720, United States
- Departments of Molecular & Cell Biology, University of California, Berkeley, California 94720, United States
- Departments of Helen Wills Neuroscience Institute. University of California, Berkeley, California 94720, United States
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20
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van der Velden J, Stienen GJM. Cardiac Disorders and Pathophysiology of Sarcomeric Proteins. Physiol Rev 2019; 99:381-426. [PMID: 30379622 DOI: 10.1152/physrev.00040.2017] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The sarcomeric proteins represent the structural building blocks of heart muscle, which are essential for contraction and relaxation. During recent years, it has become evident that posttranslational modifications of sarcomeric proteins, in particular phosphorylation, tune cardiac pump function at rest and during exercise. This delicate, orchestrated interaction is also influenced by mutations, predominantly in sarcomeric proteins, which cause hypertrophic or dilated cardiomyopathy. In this review, we follow a bottom-up approach starting from a description of the basic components of cardiac muscle at the molecular level up to the various forms of cardiac disorders at the organ level. An overview is given of sarcomere changes in acquired and inherited forms of cardiac disease and the underlying disease mechanisms with particular reference to human tissue. A distinction will be made between the primary defect and maladaptive/adaptive secondary changes. Techniques used to unravel functional consequences of disease-induced protein changes are described, and an overview of current and future treatments targeted at sarcomeric proteins is given. The current evidence presented suggests that sarcomeres not only form the basis of cardiac muscle function but also represent a therapeutic target to combat cardiac disease.
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Affiliation(s)
- Jolanda van der Velden
- Amsterdam UMC, Vrije Universiteit Amsterdam, Physiology, Amsterdam Cardiovascular Sciences, Amsterdam , The Netherlands ; and Department of Physiology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Ger J M Stienen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Physiology, Amsterdam Cardiovascular Sciences, Amsterdam , The Netherlands ; and Department of Physiology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
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21
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22
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 301] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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23
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Luo F, Wei Y, Wang Z, Luo M, Hu J. Genetically Encoded Neural Activity Indicators. BRAIN SCIENCE ADVANCES 2018. [DOI: 10.26599/bsa.2018.9050007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Recent years have witnessed the fascinating development of imaging approaches to studying neural activities; this progress has been based on an influx of ideas and methods from molecular biology and optical engineering. Here we review the design and application of genetically encoded indicators for calcium ions, membrane potential and neurotransmitters. We also summarize common strategies for the design and optimization of genetically encoded neural activity indicators.
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Affiliation(s)
- Fang Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yin Wei
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ziyue Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Minmin Luo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Ji Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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24
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Nguyen NH, Kim JR, Park S. Application of Transcription Factor-based 3-Hydroxypropionic Acid Biosensor. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0390-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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25
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Wang H, Jing M, Li Y. Lighting up the brain: genetically encoded fluorescent sensors for imaging neurotransmitters and neuromodulators. Curr Opin Neurobiol 2018; 50:171-178. [PMID: 29627516 PMCID: PMC5984720 DOI: 10.1016/j.conb.2018.03.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 02/07/2023]
Abstract
Measuring the precise dynamics of specific neurotransmitters and neuromodulators in the brain is essential for understanding how information is transmitted and processed. Thanks to the development and optimization of various genetically encoded sensors, we are approaching the stage in which a few key neurotransmitters/neuromodulators can be imaged with high cell specificity and good signal-to-noise ratio. Here, we summarize recent progress regarding these sensors, focusing on their design principles, properties, potential applications, and current limitations. We also highlight the G protein-coupled receptor (GPCR) scaffold as a promising platform that may enable the scalable development of the next generation of sensors, enabling the rapid, sensitive, and specific detection of a large repertoire of neurotransmitters/neuromodulators in vivo at cellular or even subcellular resolution.
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Affiliation(s)
- Huan Wang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
| | - Miao Jing
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Beijing 100871, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Beijing 100871, China.
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26
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Helassa N, Dürst CD, Coates C, Kerruth S, Arif U, Schulze C, Wiegert JS, Geeves M, Oertner TG, Török K. Ultrafast glutamate sensors resolve high-frequency release at Schaffer collateral synapses. Proc Natl Acad Sci U S A 2018; 115:5594-5599. [PMID: 29735711 PMCID: PMC6003469 DOI: 10.1073/pnas.1720648115] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Glutamatergic synapses display a rich repertoire of plasticity mechanisms on many different time scales, involving dynamic changes in the efficacy of transmitter release as well as changes in the number and function of postsynaptic glutamate receptors. The genetically encoded glutamate sensor iGluSnFR enables visualization of glutamate release from presynaptic terminals at frequencies up to ∼10 Hz. However, to resolve glutamate dynamics during high-frequency bursts, faster indicators are required. Here, we report the development of fast (iGlu f ) and ultrafast (iGlu u ) variants with comparable brightness but increased Kd for glutamate (137 μM and 600 μM, respectively). Compared with iGluSnFR, iGlu u has a sixfold faster dissociation rate in vitro and fivefold faster kinetics in synapses. Fitting a three-state model to kinetic data, we identify the large conformational change after glutamate binding as the rate-limiting step. In rat hippocampal slice culture stimulated at 100 Hz, we find that iGlu u is sufficiently fast to resolve individual glutamate release events, revealing that glutamate is rapidly cleared from the synaptic cleft. Depression of iGlu u responses during 100-Hz trains correlates with depression of postsynaptic EPSPs, indicating that depression during high-frequency stimulation is purely presynaptic in origin. At individual boutons, the recovery from depression could be predicted from the amount of glutamate released on the second pulse (paired pulse facilitation/depression), demonstrating differential frequency-dependent filtering of spike trains at Schaffer collateral boutons.
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Affiliation(s)
- Nordine Helassa
- Molecular and Clinical Sciences Research Institute, St George's, University of London, SW17 0RE London, United Kingdom
| | - Céline D Dürst
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, 20251 Hamburg, Germany
| | - Catherine Coates
- Molecular and Clinical Sciences Research Institute, St George's, University of London, SW17 0RE London, United Kingdom
| | - Silke Kerruth
- Molecular and Clinical Sciences Research Institute, St George's, University of London, SW17 0RE London, United Kingdom
| | - Urwa Arif
- Molecular and Clinical Sciences Research Institute, St George's, University of London, SW17 0RE London, United Kingdom
| | - Christian Schulze
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, 20251 Hamburg, Germany
| | - J Simon Wiegert
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, 20251 Hamburg, Germany
| | - Michael Geeves
- School of Biosciences, University of Kent, CT2 7NZ Canterbury, United Kingdom
| | - Thomas G Oertner
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, 20251 Hamburg, Germany
| | - Katalin Török
- Molecular and Clinical Sciences Research Institute, St George's, University of London, SW17 0RE London, United Kingdom;
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27
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Kim H, Beack S, Han S, Shin M, Lee T, Park Y, Kim KS, Yetisen AK, Yun SH, Kwon W, Hahn SK. Multifunctional Photonic Nanomaterials for Diagnostic, Therapeutic, and Theranostic Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30. [PMID: 29363198 DOI: 10.1002/adma.201701460] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 10/20/2017] [Indexed: 05/08/2023]
Abstract
The last decade has seen dramatic progress in the principle, design, and fabrication of photonic nanomaterials with various optical properties and functionalities. Light-emitting and light-responsive nanomaterials, such as semiconductor quantum dots, plasmonic metal nanoparticles, organic carbon, and polymeric nanomaterials, offer promising approaches to low-cost and effective diagnostic, therapeutic, and theranostic applications. Reasonable endeavors have begun to translate some of the promising photonic nanomaterials to the clinic. Here, current research on the state-of-the-art and emerging photonic nanomaterials for diverse biomedical applications is reviewed, and the remaining challenges and future perspectives are discussed.
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Affiliation(s)
- Hyemin Kim
- PHI BIOMED Co., #613, 12 Gangnam-daero 65-gil, Seocho-gu, Seoul, 06612, South Korea
| | - Songeun Beack
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Seulgi Han
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Myeonghwan Shin
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Taehyung Lee
- Department of Chemical Engineering, POSTECH, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Yoonsang Park
- Department of Chemical Engineering, POSTECH, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Ki Su Kim
- Wellman Center for Photomedicine, Massachusetts General Hospital, 65 Landsdowne St., UP-5, Cambridge, MA, 02139, USA
| | - Ali K Yetisen
- Wellman Center for Photomedicine, Massachusetts General Hospital, 65 Landsdowne St., UP-5, Cambridge, MA, 02139, USA
| | - Seok Hyun Yun
- Wellman Center for Photomedicine, Massachusetts General Hospital, 65 Landsdowne St., UP-5, Cambridge, MA, 02139, USA
| | - Woosung Kwon
- Department of Chemical and Biological Engineering, Sookmyung Women's University, 100 Cheongpa-ro 47-gil, Seoul, 04310, South Korea
| | - Sei Kwang Hahn
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea
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28
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McNamara G, Difilippantonio M, Ried T, Bieber FR. Microscopy and Image Analysis. ACTA ACUST UNITED AC 2018; 94:4.4.1-4.4.89. [DOI: 10.1002/cphg.42] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Michael Difilippantonio
- Division of Cancer Treatment and Diagnosis National Cancer Institute, National Institutes of Health Bethesda Maryland
| | - Thomas Ried
- Section of Cancer Genomics Genetics Branch Center for Cancer Research National Cancer Institute, National Institutes of Health Bethesda Maryland
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29
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Rose CR, Felix L, Zeug A, Dietrich D, Reiner A, Henneberger C. Astroglial Glutamate Signaling and Uptake in the Hippocampus. Front Mol Neurosci 2018; 10:451. [PMID: 29386994 PMCID: PMC5776105 DOI: 10.3389/fnmol.2017.00451] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 12/22/2017] [Indexed: 12/22/2022] Open
Abstract
Astrocytes have long been regarded as essentially unexcitable cells that do not contribute to active signaling and information processing in the brain. Contrary to this classical view, it is now firmly established that astrocytes can specifically respond to glutamate released from neurons. Astrocyte glutamate signaling is initiated upon binding of glutamate to ionotropic and/or metabotropic receptors, which can result in calcium signaling, a major form of glial excitability. Release of so-called gliotransmitters like glutamate, ATP and D-serine from astrocytes in response to activation of glutamate receptors has been demonstrated to modulate various aspects of neuronal function in the hippocampus. In addition to receptors, glutamate binds to high-affinity, sodium-dependent transporters, which results in rapid buffering of synaptically-released glutamate, followed by its removal from the synaptic cleft through uptake into astrocytes. The degree to which astrocytes modulate and control extracellular glutamate levels through glutamate transporters depends on their expression levels and on the ionic driving forces that decrease with ongoing activity. Another major determinant of astrocytic control of glutamate levels could be the precise morphological arrangement of fine perisynaptic processes close to synapses, defining the diffusional distance for glutamate, and the spatial proximity of transporters in relation to the synaptic cleft. In this review, we will present an overview of the mechanisms and physiological role of glutamate-induced ion signaling in astrocytes in the hippocampus as mediated by receptors and transporters. Moreover, we will discuss the relevance of astroglial glutamate uptake for extracellular glutamate homeostasis, focusing on how activity-induced dynamic changes of perisynaptic processes could shape synaptic transmission at glutamatergic synapses.
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Affiliation(s)
- Christine R Rose
- Institute of Neurobiology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Lisa Felix
- Institute of Neurobiology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Andre Zeug
- Cellular Neurophysiology, Hannover Medical School, Hannover, Germany
| | - Dirk Dietrich
- Department of Neurosurgery, University of Bonn Medical School, Bonn, Germany
| | - Andreas Reiner
- Cellular Neurobiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Christian Henneberger
- Institute of Cellular Neurosciences, University of Bonn Medical School, Bonn, Germany.,German Center for Degenerative Diseases (DZNE), Bonn, Germany.,Institute of Neurology, University College London, London, United Kingdom
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30
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Image Restoration for Fluorescence Planar Imaging with Diffusion Model. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2010512. [PMID: 29279843 PMCID: PMC5723955 DOI: 10.1155/2017/2010512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/05/2017] [Indexed: 11/17/2022]
Abstract
Fluorescence planar imaging (FPI) is failure to capture high resolution images of deep fluorochromes due to photon diffusion. This paper presents an image restoration method to deal with this kind of blurring. The scheme of this method is conceived based on a reconstruction method in fluorescence molecular tomography (FMT) with diffusion model. A new unknown parameter is defined through introducing the first mean value theorem for definite integrals. System matrix converting this unknown parameter to the blurry image is constructed with the elements of depth conversion matrices related to a chosen plane named focal plane. Results of phantom and mouse experiments show that the proposed method is capable of reducing the blurring of FPI image caused by photon diffusion when the depth of focal plane is chosen within a proper interval around the true depth of fluorochrome. This method will be helpful to the estimation of the size of deep fluorochrome.
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31
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Hung YP, Teragawa C, Kosaisawe N, Gillies TE, Pargett M, Minguet M, Distor K, Rocha-Gregg BL, Coloff JL, Keibler MA, Stephanopoulos G, Yellen G, Brugge JS, Albeck JG. Akt regulation of glycolysis mediates bioenergetic stability in epithelial cells. eLife 2017; 6:27293. [PMID: 29239720 PMCID: PMC5730373 DOI: 10.7554/elife.27293] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 12/05/2017] [Indexed: 12/26/2022] Open
Abstract
Cells use multiple feedback controls to regulate metabolism in response to nutrient and signaling inputs. However, feedback creates the potential for unstable network responses. We examined how concentrations of key metabolites and signaling pathways interact to maintain homeostasis in proliferating human cells, using fluorescent reporters for AMPK activity, Akt activity, and cytosolic NADH/NAD+ redox. Across various conditions, including glycolytic or mitochondrial inhibition or cell proliferation, we observed distinct patterns of AMPK activity, including both stable adaptation and highly dynamic behaviors such as periodic oscillations and irregular fluctuations that indicate a failure to reach a steady state. Fluctuations in AMPK activity, Akt activity, and cytosolic NADH/NAD+ redox state were temporally linked in individual cells adapting to metabolic perturbations. By monitoring single-cell dynamics in each of these contexts, we identified PI3K/Akt regulation of glycolysis as a multifaceted modulator of single-cell metabolic dynamics that is required to maintain metabolic stability in proliferating cells.
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Affiliation(s)
- Yin P Hung
- Department of Cell Biology, Harvard Medical School, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States.,Department of Pathology, Brigham and Women's Hospital, Boston, United States
| | - Carolyn Teragawa
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Nont Kosaisawe
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Taryn E Gillies
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Marta Minguet
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Kevin Distor
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Briana L Rocha-Gregg
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Jonathan L Coloff
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Mark A Keibler
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Gary Yellen
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, United States
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32
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Abstract
Fluorescent protein-based biosensors are indispensable molecular tools for life science research. The invention and development of high-fidelity biosensors for a particular molecule or molecular event often catalyze important scientific breakthroughs. Understanding the structural and functional organization of brain activities remain a subject for which optical sensors are in desperate need and of growing interest. Here, we review genetically encoded fluorescent sensors for imaging neuronal activities with a focus on the design principles and optimizations of various sensors. New bioluminescent sensors useful for deep-tissue imaging are also discussed. By highlighting the protein engineering efforts and experimental applications of these sensors, we can consequently analyze factors influencing their performance. Finally, we remark on how future developments can fill technological gaps and lead to new discoveries.
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Affiliation(s)
- Zhijie Chen
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA 94720, USA
| | - Tan M. Truong
- Center for Membrane and Cell Physiology, and Biomedical Sciences (BIMS) Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui-wang Ai
- Center for Membrane and Cell Physiology, and Biomedical Sciences (BIMS) Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence:
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Tsai CF, Lin HY, Hsu WL, Tsai CH. The novel mitochondria localization of influenza A virus NS1 visualized by FlAsH labeling. FEBS Open Bio 2017; 7:1960-1971. [PMID: 29226082 PMCID: PMC5715299 DOI: 10.1002/2211-5463.12336] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 12/11/2022] Open
Abstract
The nonstructural protein 1 (NS1) of the influenza A virus (IAV) is a multifunctional protein that counteracts host cell antiviral responses and inhibits host cell pre‐mRNA processing. NS1 contains two nuclear localization signals that facilitate NS1 shuttling between cytoplasm and nucleus. In this study, we initially observed the novel mitochondria localization of NS1 in a subset of transfected cells. We then further monitored the localization dynamics of the NS1 protein in live cells infected with IAV expressing NS1 with insertion of a tetracysteine‐tag. The resulting mutant virus showed similar levels of infectivity and expression pattern of NS1 to those of wild‐type IAV. Pulse labeling using a biarsenical compound (fluorescein arsenical hairpin binder) allowed us to visualize the dynamic subcellular distribution of NS1 real time. We detected NS1 in mitochondria at a very early infection time point [1.5 h postinfection (hpi)] and observed the formation of a granular structure pattern in the nucleus at 4 hpi. This is the first identification of the novel mitochondria localization of NS1. The possible role of NS1 at an early infection time point is discussed.
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Affiliation(s)
- Chuan-Fu Tsai
- Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan
| | - Hsin-Yi Lin
- Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan
| | - Wei-Li Hsu
- Graduate Institute of Microbiology and Public Health National Chung Hsing University Taichung Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology National Chung Hsing University Taichung Taiwan
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Liu J, Li F, Chen L, Guan Y, Tian L, Xiong Y, Liu G, Tian Y. Quantitative imaging of Candida utilis and its organelles by soft X-ray Nano-CT. J Microsc 2017; 270:64-70. [PMID: 28960304 DOI: 10.1111/jmi.12650] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/28/2017] [Accepted: 09/07/2017] [Indexed: 01/06/2023]
Abstract
Soft X-ray microscopy has excellent characteristics for imaging cells and subcellular structures. In this paper, the yeast strain, Candida utilis, was imaged by soft X-ray microscopy and three-dimensional volumes were reconstructed with the SART-TV method. We performed segmentation on the reconstruction in three dimensions and identified several types of subcellular architecture within the specimen cells based on their linear absorption coefficient (LAC) values. Organelles can be identified by the correlation between the soft X-ray LAC values and the subcellular architectures. Quantitative analyses of the volume ratio of organelles to whole cell in different phases were also carried out according to the three-dimensional datasets. With such excellent features, soft X-ray imaging has a great influence in the field of biological cellular and subcellular research.
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Affiliation(s)
- J Liu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - F Li
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - L Chen
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Y Guan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - L Tian
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Y Xiong
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - G Liu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Y Tian
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, P. R. China
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Zhang X, Cao X, Zhu S. Reconstruction of fluorescence molecular tomography with a cosinoidal level set method. Biomed Eng Online 2017; 16:86. [PMID: 28655316 PMCID: PMC5488366 DOI: 10.1186/s12938-017-0377-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/20/2017] [Indexed: 11/29/2022] Open
Abstract
Background Implicit shape-based reconstruction method in fluorescence molecular tomography (FMT) is capable of achieving higher image clarity than image-based reconstruction method. However, the implicit shape method suffers from a low convergence speed and performs unstably due to the utilization of gradient-based optimization methods. Moreover, the implicit shape method requires priori information about the number of targets. Methods A shape-based reconstruction scheme of FMT with a cosinoidal level set method is proposed in this paper. The Heaviside function in the classical implicit shape method is replaced with a cosine function, and then the reconstruction can be accomplished with the Levenberg–Marquardt method rather than gradient-based methods. As a result, the priori information about the number of targets is not required anymore and the choice of step length is avoided. Results Numerical simulations and phantom experiments were carried out to validate the proposed method. Results of the proposed method show higher contrast to noise ratios and Pearson correlations than the implicit shape method and image-based reconstruction method. Moreover, the number of iterations required in the proposed method is much less than the implicit shape method. Conclusions The proposed method performs more stably, provides a faster convergence speed than the implicit shape method, and achieves higher image clarity than the image-based reconstruction method.
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Affiliation(s)
- Xuanxuan Zhang
- Engineering Research Center of Molecular and Neuro Imaging of the Ministry of Education & School of Life Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China.
| | - Xu Cao
- Engineering Research Center of Molecular and Neuro Imaging of the Ministry of Education & School of Life Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China
| | - Shouping Zhu
- Engineering Research Center of Molecular and Neuro Imaging of the Ministry of Education & School of Life Science and Technology, Xidian University, Xi'an, 710071, Shaanxi, China
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Gujrati V, Mishra A, Ntziachristos V. Molecular imaging probes for multi-spectral optoacoustic tomography. Chem Commun (Camb) 2017; 53:4653-4672. [DOI: 10.1039/c6cc09421j] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In this review, we discuss recent progress in emerging optoacoustic probes, their mechanisms, applications and challenges for biological imaging using MSOT.
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Affiliation(s)
- Vipul Gujrati
- Institute for Biological and Medical Imaging
- Helmholtz Zentrum München
- Neuherberg 85764
- Germany
- Chair for Biological Imaging
| | - Anurag Mishra
- Institute for Biological and Medical Imaging
- Helmholtz Zentrum München
- Neuherberg 85764
- Germany
| | - Vasilis Ntziachristos
- Institute for Biological and Medical Imaging
- Helmholtz Zentrum München
- Neuherberg 85764
- Germany
- Chair for Biological Imaging
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Ekman AA, Chen JH, Guo J, McDermott G, Le Gros MA, Larabell CA. Mesoscale imaging with cryo-light and X-rays: Larger than molecular machines, smaller than a cell. Biol Cell 2017; 109:24-38. [PMID: 27690365 PMCID: PMC5261833 DOI: 10.1111/boc.201600044] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 12/11/2022]
Abstract
In the context of cell biology, the term mesoscale describes length scales ranging from that of an individual cell, down to the size of the molecular machines. In this spatial regime, small building blocks self-organise to form large, functional structures. A comprehensive set of rules governing mesoscale self-organisation has not been established, making the prediction of many cell behaviours difficult, if not impossible. Our knowledge of mesoscale biology comes from experimental data, in particular, imaging. Here, we explore the application of soft X-ray tomography (SXT) to imaging the mesoscale, and describe the structural insights this technology can generate. We also discuss how SXT imaging is complemented by the addition of correlative fluorescence data measured from the same cell. This combination of two discrete imaging modalities produces a 3D view of the cell that blends high-resolution structural information with precise molecular localisation data.
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Affiliation(s)
- Axel A. Ekman
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jian-Hua Chen
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jessica Guo
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Gerry McDermott
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mark A. Le Gros
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn A. Larabell
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Zhang P, Hu Y, Ma R, Li L, Lu J. Enhanced green fluorescence protein/layered double hydroxide composite ultrathin films: bio-hybrid assembly and potential application as a fluorescent biosensor. J Mater Chem B 2016; 5:160-166. [PMID: 32263444 DOI: 10.1039/c6tb02638a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein immobilization is of significant interest for applications in biosensing, drug delivery and bioconversion, and challenges still remain for the in vitro immobilization and application of proteins. Due to it being non-specific to species, easy to express in cells and able to exhibit fluorescence after expression without the need for cofactors or chaperones, green fluorescent protein (GFP), together with its differently colored mutants, has been widely studied and applied. This article reports the fabrication of enhanced green fluorescent protein (EGFP)/layered double hydroxide nanosheet (EGFP/LDH)n ultrathin films (UTFs) via a layer-by-layer assembly technique based on electrostatic and hydrogen-bond interactions, and this realized the immobilization of EGFP. The obtained UTFs show a long-range-ordered periodic layered stacking structure and strong fluorescence originating from EGFP, which also retains its predominant β-barrel structure well in the LDH laminates. The inorganic LDH laminates play an important role in protecting and improving the structure and properties of the EGFP in the UTFs. Furthermore, the UTFs exhibit a reversible fluorescence response between different pH environments or different wet or dry environments, and also could detect some small biological medicine molecules such as protoporphyrin, and thus they have the potential to be a novel type of biological fluorescence sensor.
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Affiliation(s)
- Ping Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, P. Box 98, Beisanhuan East Road 15, Beijing, 100029, P. R. China.
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Hyperspectral Imaging Using Intracellular Spies: Quantitative Real-Time Measurement of Intracellular Parameters In Vivo during Interaction of the Pathogenic Fungus Aspergillus fumigatus with Human Monocytes. PLoS One 2016; 11:e0163505. [PMID: 27727286 PMCID: PMC5058474 DOI: 10.1371/journal.pone.0163505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022] Open
Abstract
Hyperspectral imaging (HSI) is a technique based on the combination of classical spectroscopy and conventional digital image processing. It is also well suited for the biological assays and quantitative real-time analysis since it provides spectral and spatial data of samples. The method grants detailed information about a sample by recording the entire spectrum in each pixel of the whole image. We applied HSI to quantify the constituent pH variation in a single infected apoptotic monocyte as a model system. Previously, we showed that the human-pathogenic fungus Aspergillus fumigatus conidia interfere with the acidification of phagolysosomes. Here, we extended this finding to monocytes and gained a more detailed analysis of this process. Our data indicate that melanised A. fumigatus conidia have the ability to interfere with apoptosis in human monocytes as they enable the apoptotic cell to recover from mitochondrial acidification and to continue with the cell cycle. We also showed that this ability of A. fumigatus is dependent on the presence of melanin, since a non-pigmented mutant did not stop the progression of apoptosis and consequently, the cell did not recover from the acidic pH. By conducting the current research based on the HSI, we could measure the intracellular pH in an apoptotic infected human monocyte and show the pattern of pH variation during 35 h of measurements. As a conclusion, we showed the importance of melanin for determining the fate of intracellular pH in a single apoptotic cell.
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Wang F, Bélanger E, Paquet ME, Côté DC, De Koninck Y. Probing pain pathways with light. Neuroscience 2016; 338:248-271. [PMID: 27702648 DOI: 10.1016/j.neuroscience.2016.09.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 02/06/2023]
Abstract
We have witnessed an accelerated growth of photonics technologies in recent years to enable not only monitoring the activity of specific neurons, while animals are performing certain types of behavior, but also testing whether specific cells, circuits, and regions are sufficient or necessary for initiating, maintaining, or altering this or that behavior. Compared to other sensory systems, however, such as the visual or olfactory system, photonics applications in pain research are only beginning to emerge. One reason pain studies have lagged behind is that many of the techniques originally developed cannot be directly implemented to study key relay sites within pain pathways, such as the skin, dorsal root ganglia, spinal cord, and brainstem. This is due, in part, to difficulties in accessing these structures with light. Here we review a number of recent advances in design and delivery of light-sensitive molecular probes (sensors and actuators) into pain relay circuits to help decipher their structural and functional organization. We then discuss several challenges that have hampered hardware access to specific structures including light scattering, tissue movement and geometries. We review a number of strategies to circumvent these challenges, by delivering light into, and collecting it from the different key sites to unravel how nociceptive signals are encoded at each level of the neuraxis. We conclude with an outlook on novel imaging modalities for label-free chemical detection and opportunities for multimodal interrogation in vivo. While many challenges remain, these advances offer unprecedented opportunities to bridge cellular approaches with context-relevant behavioral testing, an essential step toward improving translation of basic research findings into clinical applications.
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Affiliation(s)
- Feng Wang
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada
| | - Erik Bélanger
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada; Centre d'optique, photonique et laser, Université Laval, Québec, QC, Canada
| | - Marie-Eve Paquet
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada; Département de biochimie, microbiologie et bioinformatique, Université Laval, Québec, QC, Canada
| | - Daniel C Côté
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada; Centre d'optique, photonique et laser, Université Laval, Québec, QC, Canada; Département de physique, de génie physique et d'optique, Université Laval, Québec, QC, Canada
| | - Yves De Koninck
- Institut universitaire en santé mentale de Québec, Université Laval, Québec, QC, Canada; Centre d'optique, photonique et laser, Université Laval, Québec, QC, Canada; Département de psychiatrie et neurosciences, Université Laval, Québec, QC, Canada.
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Mehrotra P. Biosensors and their applications - A review. J Oral Biol Craniofac Res 2016; 6:153-9. [PMID: 27195214 PMCID: PMC4862100 DOI: 10.1016/j.jobcr.2015.12.002] [Citation(s) in RCA: 503] [Impact Index Per Article: 62.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/05/2015] [Indexed: 10/22/2022] Open
Abstract
The various types of biosensors such as enzyme-based, tissue-based, immunosensors, DNA biosensors, thermal and piezoelectric biosensors have been deliberated here to highlight their indispensable applications in multitudinous fields. Some of the popular fields implementing the use of biosensors are food industry to keep a check on its quality and safety, to help distinguish between the natural and artificial; in the fermentation industry and in the saccharification process to detect precise glucose concentrations; in metabolic engineering to enable in vivo monitoring of cellular metabolism. Biosensors and their role in medical science including early stage detection of human interleukin-10 causing heart diseases, rapid detection of human papilloma virus, etc. are important aspects. Fluorescent biosensors play a vital role in drug discovery and in cancer. Biosensor applications are prevalent in the plant biology sector to find out the missing links required in metabolic processes. Other applications are involved in defence, clinical sector, and for marine applications.
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Jackson SR, Wong AC, Travis AR, Catrina IE, Bratu DP, Wright DW, Jayagopal A. Applications of Hairpin DNA-Functionalized Gold Nanoparticles for Imaging mRNA in Living Cells. Methods Enzymol 2016; 572:87-103. [PMID: 27241751 DOI: 10.1016/bs.mie.2016.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Molecular imaging agents are useful for imaging molecular processes in living systems in order to elucidate the function of molecular mediators in health and disease. Here, we demonstrate a technique for the synthesis, characterization, and application of hairpin DNA-functionalized gold nanoparticles (hAuNPs) as fluorescent hybridization probes for imaging mRNA expression and spatiotemporal dynamics in living cells. These imaging probes feature gold colloids linked to fluorophores via engineered oligonucleotides to resemble a molecular beacon in which the gold colloid serves as the fluorescence quencher in a fluorescence resonance energy transfer system. Target-specific hybridization of the hairpin oligonucleotide enables fluorescence de-quenching and subsequent emission with high signal to noise ratios. hAuNPs exhibit high specificity without adverse toxicity or the need for transfection reagents. Furthermore, tunability of hAuNP emission profiles by selection of spectrally distinct fluorophores enables multiplexed mRNA imaging applications. Therefore, hAuNPs are promising tools for imaging gene expression in living cells. As a representative application of this technology, we discuss the design and applications of hAuNP targeted against distinct matrix metalloproteinase enzymes for the multiplexed detection of mRNA expression in live breast cancer cells using flow cytometry and fluorescence microscopy.
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Affiliation(s)
- S R Jackson
- Vanderbilt University, Nashville, TN, United States
| | - A C Wong
- Vanderbilt University, Nashville, TN, United States
| | - A R Travis
- Vanderbilt University, Nashville, TN, United States
| | - I E Catrina
- Hunter College, City University of New York, New York, NY, United States
| | - D P Bratu
- Hunter College, City University of New York, New York, NY, United States; Program in Molecular, Cellular, and Developmental Biology, and Program in Biochemistry, The Graduate Center, City University of New York, New York, NY, United States
| | - D W Wright
- Vanderbilt University, Nashville, TN, United States
| | - A Jayagopal
- Pharma Research and Early Development (pRED), F. Hoffman-La Roche Ltd., Basel, Switzerland.
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Bradbury MS, Pauliah M, Zanzonico P, Wiesner U, Patel S. Intraoperative mapping of sentinel lymph node metastases using a clinically translated ultrasmall silica nanoparticle. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2015; 8:535-53. [PMID: 26663853 DOI: 10.1002/wnan.1380] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 09/29/2015] [Accepted: 10/12/2015] [Indexed: 12/22/2022]
Abstract
The management of regional lymph nodes in patients with melanoma has undergone a significant paradigm shift over the past several decades, transitioning from the use of more aggressive surgical approaches, such as lymph node basin dissection, to the application of minimally invasive sentinel lymph node (SLN) biopsy methods to detect the presence of nodal micrometastases. SLN biopsy has enabled reliable, highly accurate, and low-morbidity staging of regional lymph nodes in early stage melanoma as a means of guiding treatment decisions and improving patient outcomes. The accurate identification and staging of lymph nodes is an important prognostic factor, identifying those patients for whom the expected benefits of nodal resection outweigh attendant surgical risks. However, currently used standard-of-care technologies for SLN detection are associated with significant limitations. This has fueled the development of clinically promising platforms that can serve as intraoperative visualization tools to aid accurate and specific determination of tumor-bearing lymph nodes, map cancer-promoting biological properties at the cellular/molecular levels, and delineate nodes from adjacent critical structures. Among a number of promising cancer-imaging probes that might facilitate achievement of these ends is a first-in-kind ultrasmall tumor-targeting inorganic (silica) nanoparticle, designed to overcome translational challenges. The rationale driving these considerations and the application of this platform as an intraoperative treatment tool for guiding resection of cancerous lymph nodes is discussed and presented within the context of alternative imaging technologies. WIREs Nanomed Nanobiotechnol 2016, 8:535-553. doi: 10.1002/wnan.1380 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Michelle S Bradbury
- Department of Radiology, Sloan Kettering Institute for Cancer Research, New York, NY, USA.,Department of Molecular Pharmacology and Chemistry Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Mohan Pauliah
- Department of Radiology, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Pat Zanzonico
- Department of Medical Physics, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Ulrich Wiesner
- Department of Material Science & Engineering, Cornell University, Ithaca, NY, USA
| | - Snehal Patel
- Department of Surgery, Sloan Kettering Institute for Cancer Research, New York, NY, USA
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Storace D, Rad MS, Han Z, Jin L, Cohen LB, Hughes T, Baker BJ, Sung U. Genetically Encoded Protein Sensors of Membrane Potential. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 859:493-509. [PMID: 26238066 DOI: 10.1007/978-3-319-17641-3_20] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Organic voltage-sensitive dyes offer very high spatial and temporal resolution for imaging neuronal function. However these dyes suffer from the drawbacks of non-specificity of cell staining and low accessibility of the dye to some cell types. Further progress in imaging activity is expected from the development of genetically encoded fluorescent sensors of membrane potential. Cell type specificity of expression of these fluorescent protein (FP) voltage sensors can be obtained via several different mechanisms. One is cell type specificity of infection by individual virus subtypes. A second mechanism is specificity of promoter expression in individual cell types. A third, depends on the offspring of transgenic animals with cell type specific expression of cre recombinase mated with an animal that has the DNA for the FP voltage sensor in all of its cells but its expression is dependent on the recombinase activity. Challenges remain. First, the response time constants of many of the new FP voltage sensors are slower (2-10 ms) than those of organic dyes. This results in a relatively small fractional fluorescence change, ΔF/F, for action potentials. Second, the largest signal presently available is only ~40% for a 100 mV depolarization and many of the new probes have signals that are substantially smaller. Large signals are especially important when attempting to detect fast events because the shorter measurement interval results in a relatively small number of detected photons and therefore a relatively large shot noise (see Chap. 1). Another kind of challenge has occurred when attempts were made to transition from one species to another or from one cell type to another or from cell culture to in vivo measurements.Several laboratories have recently described a number of novel FP voltage sensors. Here we attempt to critically review the current status of these developments in terms of signal size, time course, and in vivo function.
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Affiliation(s)
- Douglas Storace
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06520, USA
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González-Vera JA, Morris MC. Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases. Proteomes 2015; 3:369-410. [PMID: 28248276 PMCID: PMC5217393 DOI: 10.3390/proteomes3040369] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/30/2015] [Accepted: 10/23/2015] [Indexed: 12/20/2022] Open
Abstract
Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.
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Affiliation(s)
- Juan A González-Vera
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
| | - May C Morris
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
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Abstract
Nanomaterials possess unique features which make them particularly attractive for biosensing applications. In particular, carbon nanotubes (CNTs) can serve as scaffolds for immobilization of biomolecules at their surface, and combine several exceptional physical, chemical, electrical, and optical characteristics properties which make them one of the best suited materials for the transduction of signals associated with the recognition of analytes, metabolites, or disease biomarkers. Here we provide a comprehensive review on these carbon nanostructures, in which we describe their structural and physical properties, functionalization and cellular uptake, biocompatibility, and toxicity issues. We further review historical developments in the field of biosensors, and describe the different types of biosensors which have been developed over time, with specific focus on CNT-conjugates engineered for biosensing applications, and in particular detection of cancer biomarkers.
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Affiliation(s)
| | - May C. Morris
- Cell Cycle Biosensors and Inhibitors, Faculté de Pharmacie, Institut des Biomolécules Max Mousseron, Centre National de la Recherche Scientifique-UMR 5247Montpellier, France
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Mahajan A, Goh V, Basu S, Vaish R, Weeks AJ, Thakur MH, Cook GJ. Bench to bedside molecular functional imaging in translational cancer medicine: to image or to imagine? Clin Radiol 2015; 70:1060-82. [PMID: 26187890 DOI: 10.1016/j.crad.2015.06.082] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 06/03/2015] [Accepted: 06/08/2015] [Indexed: 02/05/2023]
Abstract
Ongoing research on malignant and normal cell biology has substantially enhanced the understanding of the biology of cancer and carcinogenesis. This has led to the development of methods to image the evolution of cancer, target specific biological molecules, and study the anti-tumour effects of novel therapeutic agents. At the same time, there has been a paradigm shift in the field of oncological imaging from purely structural or functional imaging to combined multimodal structure-function approaches that enable the assessment of malignancy from all aspects (including molecular and functional level) in a single examination. The evolving molecular functional imaging using specific molecular targets (especially with combined positron-emission tomography [PET] computed tomography [CT] using 2- [(18)F]-fluoro-2-deoxy-D-glucose [FDG] and other novel PET tracers) has great potential in translational research, giving specific quantitative information with regard to tumour activity, and has been of pivotal importance in diagnoses and therapy tailoring. Furthermore, molecular functional imaging has taken a key place in the present era of translational cancer research, producing an important tool to study and evolve newer receptor-targeted therapies, gene therapies, and in cancer stem cell research, which could form the basis to translate these agents into clinical practice, popularly termed "theranostics". Targeted molecular imaging needs to be developed in close association with biotechnology, information technology, and basic translational scientists for its best utility. This article reviews the current role of molecular functional imaging as one of the main pillars of translational research.
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Affiliation(s)
- A Mahajan
- Division of Imaging Sciences and Biomedical Engineering, King's College London, UK; Department of Radiodiagnosis, Tata Memorial Centre, Mumbai, 400012, India.
| | - V Goh
- Division of Imaging Sciences and Biomedical Engineering, King's College London, UK
| | - S Basu
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Tata Memorial Hospital Annexe, Mumbai, 400 012, India
| | - R Vaish
- Department of Head and Neck Surgical Oncology, Tata Memorial Centre, Mumbai, 400012, India
| | - A J Weeks
- Division of Imaging Sciences and Biomedical Engineering, King's College London, UK
| | - M H Thakur
- Department of Radiodiagnosis, Tata Memorial Centre, Mumbai, 400012, India
| | - G J Cook
- Division of Imaging Sciences and Biomedical Engineering, King's College London, UK; Department of Nuclear Medicine, Guy's and St Thomas NHS Foundation Trust Hospital, London, UK
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Do M, Isaacson SA, McDermott G, Le Gros MA, Larabell CA. Imaging and characterizing cells using tomography. Arch Biochem Biophys 2015; 581:111-21. [PMID: 25602704 PMCID: PMC4506273 DOI: 10.1016/j.abb.2015.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/29/2014] [Accepted: 01/11/2015] [Indexed: 12/11/2022]
Abstract
We can learn much about cell function by imaging and quantifying sub-cellular structures, especially if this is done non-destructively without altering said structures. Soft X-ray tomography (SXT) is a high-resolution imaging technique for visualizing cells and their interior structure in 3D. A tomogram of the cell, reconstructed from a series of 2D projection images, can be easily segmented and analyzed. SXT has a very high specimen throughput compared to other high-resolution structure imaging modalities; for example, tomographic data for reconstructing an entire eukaryotic cell is acquired in a matter of minutes. SXT visualizes cells without the need for chemical fixation, dehydration, or staining of the specimen. As a result, the SXT reconstructions are close representations of cells in their native state. SXT is applicable to most cell types. The deep penetration of soft X-rays allows cells, even mammalian cells, to be imaged without being sectioned. Image contrast in SXT is generated by the differential attenuation soft X-ray illumination as it passes through the specimen. Accordingly, each voxel in the tomographic reconstruction has a measured linear absorption coefficient (LAC) value. LAC values are quantitative and give rise to each sub-cellular component having a characteristic LAC profile, allowing organelles to be identified and segmented from the milieu of other cell contents. In this chapter, we describe the fundamentals of SXT imaging and how this technique can answer real world questions in the study of the nucleus. We also describe the development of correlative methods for the localization of specific molecules in a SXT reconstruction. The combination of fluorescence and SXT data acquired from the same specimen produces composite 3D images, rich with detailed information on the inner workings of cells.
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Affiliation(s)
- Myan Do
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Samuel A Isaacson
- Department of Mathematics and Statistics, Boston University, Boston, MA 02215, United States
| | - Gerry McDermott
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Mark A Le Gros
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Carolyn A Larabell
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
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