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Li W, Li X, Zhang C, Wang H, Zhu Y, Wang Y, Yan W, Liu L, Qu J. Research of Pulmonary Fibrosis Lesions Based on FLIM and SHG Imaging Microscopy. Anal Chem 2024. [PMID: 39012837 DOI: 10.1021/acs.analchem.4c01303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Two-photon fluorescence lifetime microscopy (TP-FLIM) is a powerful quantitative imaging technique that characterizes and analyzes the structure and function of biological samples through a combination of intensity and lifetime imaging. Because TP-FLIM is independent of the fluorescence signal intensity and the fluorophore concentration, it is widely used in high-throughput, high-content drug screening and clinical diagnostics. Second harmonic generation (SHG) imaging technology has the advantages of high spatial resolution and imaging depth inherent to nonlinear optical imaging. Second harmonics often appear in noncentrosymmetric structures. Collagen tissue in biological organisms is a good example of these structures, showing strong harmonic effects. Therefore, SHG has been widely used for imaging of specific tissue structure imaging. TP-FLIM technology is highly sensitive for quantitatively detecting changes in microenvironments. The objective of this study is to examine pathological pulmonary fibrosis slices using a combined approach of TP-FLIM and SHG technology. The fluorescence lifetime data of pulmonary collagen fibers are analyzed by using phasor plot analysis methods, and normal collagen fibers and fibrotic collagen fibers are distinguished by calculating the aspect ratio from the SHG images formed by the collagen fibers. Our study provides a new method for a deeper understanding of the pathological mechanisms and clinical diagnosis of pulmonary fibrosis and other collagen fiber-related disorders.
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Affiliation(s)
- Wei Li
- College of Physics and Optoelectronic Engineering, Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xiaoyu Li
- College of Physics and Optoelectronic Engineering, Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Chenshuang Zhang
- College of Physics and Optoelectronic Engineering, Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - He Wang
- College of Physics and Optoelectronic Engineering, Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yinru Zhu
- College of Physics and Optoelectronic Engineering, Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yunyun Wang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Chongxin Judicial Expertise Center, Wuhan, Hubei 430415, China
| | - Wei Yan
- College of Physics and Optoelectronic Engineering, Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Liwei Liu
- College of Physics and Optoelectronic Engineering, Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Junle Qu
- College of Physics and Optoelectronic Engineering, Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen, Guangdong 518060, China
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2
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Biswas B, Shah D, Cox-Vázquez SJ, Vázquez RJ. Sensing cholesterol-induced rigidity in model membranes with time-resolved fluorescence spectroscopy and microscopy. J Mater Chem B 2024; 12:6570-6576. [PMID: 38899544 DOI: 10.1039/d4tb00872c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Here, we report the characterization of cholesterol levels on membrane fluidity with a twisted intramolecular charge transfer (TICT) membrane dye, namely DI-8-ANEPPS, using fluorescence lifetime techniques such as time-correlated single photon counting (TCSPC) and fluorescence lifetime imaging microscopy (FLIM). The characterized liposomes comprised a 3 : 1 ratio of POPC and POPG, respectively, 1% DI-8-ANEPPS, and increasing cholesterol levels from 0% to 50%. Fluorescence lifetime characterization revealed that increasing the cholesterol levels from 0% to 50% increases the fluorescence lifetime of DI-8-ANEPPS from 2.36 ns to 3.65 ns, a 55% increment. Such lengthening in the fluorescence lifetime is concomitant with reduced Stokes shifts and higher quantum yield, revealing that localized excitation (LE) dominates over TICT states with increased cholesterol levels. Fluorescence anisotropy measurements revealed a less isotropic environment in the membrane upon increasing cholesterol levels, suggesting a shift from liquid-disorder (Lα) to liquid-order (LO) upon adding cholesterol. Local electrostatic and dipole characterization experiments revealed that changes in the zeta-potential (ζ-potential) and transmembrane dipole potential (Ψd) induced by changes in cholesterol levels or the POPC : POPG ratio play a minimal role in the fluorescence lifetime outcome of DI-8-ANEPPS. Instead, these results indicate that the cholesterol's effect in restricting the degree of movement of DI-8-ANEPPS dominates its photophysics over the cholesterol effect on the local dipole strength. We envision that time-resolved spectroscopy and microscopy, coupled with TICT dyes, could be a convenient tool in exploring the complex interplay between membrane lipids, sterols, and proteins and provide novel insights into membrane fluidity, organization, and function.
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Affiliation(s)
- Bidisha Biswas
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
| | - Dhari Shah
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
| | - Sarah J Cox-Vázquez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
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3
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Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D. De novo design of proteins housing excitonically coupled chlorophyll special pairs. Nat Chem Biol 2024; 20:906-915. [PMID: 38831036 PMCID: PMC11213709 DOI: 10.1038/s41589-024-01626-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.
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Affiliation(s)
- Nathan M Ennist
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Shunzhi Wang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Madison A Kennedy
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mariano Curti
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | | | | | - Rachel L Redler
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Valentin Maffeis
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - Saeed Shareef
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Anthony V Sica
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ash Sueh Hua
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Arundhati P Deshmukh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adam P Moyer
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Derrick R Hicks
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Avi Z Swartz
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ralph A Cacho
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Novy
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Amala Phadkule
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Damian Ekiert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Gira Bhabha
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin R Caram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elisabet Romero
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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4
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Trujillo J, Khan AS, Adhikari DP, Stoneman MR, Chacko JV, Eliceiri KW, Raicu V. Implementation of FRET Spectrometry Using Temporally Resolved Fluorescence: A Feasibility Study. Int J Mol Sci 2024; 25:4706. [PMID: 38731924 PMCID: PMC11083457 DOI: 10.3390/ijms25094706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Förster resonance energy transfer (FRET) spectrometry is a method for determining the quaternary structure of protein oligomers from distributions of FRET efficiencies that are drawn from pixels of fluorescence images of cells expressing the proteins of interest. FRET spectrometry protocols currently rely on obtaining spectrally resolved fluorescence data from intensity-based experiments. Another imaging method, fluorescence lifetime imaging microscopy (FLIM), is a widely used alternative to compute FRET efficiencies for each pixel in an image from the reduction of the fluorescence lifetime of the donors caused by FRET. In FLIM studies of oligomers with different proportions of donors and acceptors, the donor lifetimes may be obtained by fitting the temporally resolved fluorescence decay data with a predetermined number of exponential decay curves. However, this requires knowledge of the number and the relative arrangement of the fluorescent proteins in the sample, which is precisely the goal of FRET spectrometry, thus creating a conundrum that has prevented users of FLIM instruments from performing FRET spectrometry. Here, we describe an attempt to implement FRET spectrometry on temporally resolved fluorescence microscopes by using an integration-based method of computing the FRET efficiency from fluorescence decay curves. This method, which we dubbed time-integrated FRET (or tiFRET), was tested on oligomeric fluorescent protein constructs expressed in the cytoplasm of living cells. The present results show that tiFRET is a promising way of implementing FRET spectrometry and suggest potential instrument adjustments for increasing accuracy and resolution in this kind of study.
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Affiliation(s)
- Justin Trujillo
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
| | - Aliyah S. Khan
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
| | - Dhruba P. Adhikari
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
| | - Michael R. Stoneman
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
| | - Jenu V. Chacko
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53705, USA; (J.V.C.); (K.W.E.)
| | - Kevin W. Eliceiri
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53705, USA; (J.V.C.); (K.W.E.)
- Departments of Biomedical Engineering and Medical Physics, University of Wisconsin-Madison, Madison, WI 53705, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Valerica Raicu
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
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5
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Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 DOI: 10.1111/jmi.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
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Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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6
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Yang JZ, Zhang AN, Wu QY, Li J, Meng Z, Zhao Q. 64 picosecond time resolved time-correlated single photon counting imaging. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024; 95:023701. [PMID: 38299997 DOI: 10.1063/5.0174067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 01/03/2024] [Indexed: 02/02/2024]
Abstract
High-speed imaging of dynamic scenes is a challenging and important task in many applications. However, conventional imaging methods based on charge coupled devices or complementary metal oxide semiconductors have limitations in temporal resolution and photon sensitivity. To address this problem, we propose a novel high-speed imaging scheme that combines single-pixel imaging with single photon detection and time-correlated single photon counting. Our scheme can achieve high-speed imaging with 64 ps resolution by repeating the motion scenes and using binary outputs from single photon detectors. We demonstrate our scheme by reconstructing the switching process of a digital micro-mirror device and a liquid crystal spatial light modulator. Our scheme can be further improved to 1 ps resolution by using a more accurate time-correlated single photon counting system. Moreover, our scheme can adapt to different speed scenes by adjusting the temporal resolution and reducing the sampling time. Our high temporal resolution imaging scheme further expands the application areas of single-pixel imaging and provides solutions for scenes requiring single photon detection and higher temporal resolution, such as reproducible chemical reaction processes imaging, cellular or sub-cellular bio imaging, single-molecule imaging of rotary motors, high-speed equipment inspection, and other periodic high-speed scenes imaging.
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Affiliation(s)
- Jia-Zhi Yang
- Center for Quantum Technology Research and Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - An-Ning Zhang
- Center for Quantum Technology Research and Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Qing-Yuan Wu
- Center for Quantum Technology Research and Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Jian Li
- Center for Quantum Technology Research and Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Zhe Meng
- Center for Quantum Technology Research and Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Qing Zhao
- Center for Quantum Technology Research and Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
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7
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Patel V, Aggarwal P, Sarvaiya J, Maity P, Ravichandiran V, Kaity S. Exploring novel and fast stability or sameness evaluation tool for different categories of injectable formulations. Eur J Pharm Sci 2023; 190:106551. [PMID: 37562551 DOI: 10.1016/j.ejps.2023.106551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/19/2023] [Accepted: 07/30/2023] [Indexed: 08/12/2023]
Abstract
The establishment of drug product stability and sameness is the heart of generic formulation development. For regulatory filing, various instrumental methods are used on a case basis to establish the generic and innovator product sameness in multiple aspects. Here in the present study, we explored the applicability of the Time-correlated single photon counting (TCS-PC) technique as a fast, reliable, and nondestructive method for establishing the sameness of three different categories of injectable formulations, namely, Amphotericin B liposome for injection, enoxaparin injection, and iron sucrose injection. All three category formulations were evaluated in their native and artificially induced post degradation state to identify the discrimination power of the used instrumental techniques. The degradation of materials were confirmed by high performance liquid chromatography (HPLC). Based on the product category, pre and post-degradation samples were evaluated by selective instrumental methods like differential scanning calorimetry (DSC), nuclear magnetic resonance (NMR), fluorescence spectroscopy, particle size analysis by dynamic light scattering (DLS), small angle X-ray scattering (SAXS), Raman spectroscopy, inductively coupled plasma optical-emission spectrometry (ICP-OES) and circular dichroism study. All pre and post-degradation samples were further analyzed by TCS-PC. We observed that, TCS-PC can identify the differences between the initial and post degradation samples in very less time with promising discrimination power across the different injectable formulation types. Thus TCS-PC can be used as a fast and promising stability or sameness evaluation tool for different injectable drug products.
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Affiliation(s)
- Vaibhavi Patel
- School of Engineering and Technology, National Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Punita Aggarwal
- School of Engineering and Technology, National Forensic Sciences University, Gandhinagar, Gujarat, India; National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, West Bengal, India
| | - Jayrajsinh Sarvaiya
- Center of Excellence FTF, National Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Prasenjit Maity
- School of Engineering and Technology, National Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Velayutham Ravichandiran
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, West Bengal, India
| | - Santanu Kaity
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, West Bengal, India.
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Gest AMM, Lazzari-Dean JR, Ortiz G, Yaeger-Weiss SK, Boggess SC, Miller EW. A red-emitting carborhodamine for monitoring and measuring membrane potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561080. [PMID: 37873283 PMCID: PMC10592620 DOI: 10.1101/2023.10.06.561080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Biological membrane potentials, or voltages, are a central facet of cellular life. Optical methods to visualize cellular membrane voltages with fluorescent indicators are an attractive complement to traditional electrode-based approaches, since imaging methods can be high throughput, less invasive, and provide more spatial resolution than electrodes. Recently developed fluorescent indicators for voltage largely report changes in membrane voltage by monitoring voltage-dependent fluctuations in fluorescence intensity. However, it would be useful to be able to not only monitor changes, but also measure values of membrane potentials. This study discloses a new fluorescent indicator which can address both. We describe the synthesis of a new sulfonated tetramethyl carborhodamine fluorophore. When this carborhodamine is conjugated with an electron-rich, methoxy (-OMe) containing phenylenevinylene molecular wire, the resulting molecule, CRhOMe, is a voltage-sensitive fluorophore with red/far-red fluorescence. Using CRhOMe, changes in cellular membrane potential can be read out using fluorescence intensity or lifetime. In fluorescence intensity mode, CRhOMe tracks fast-spiking neuronal action potentials with greater signal-to-noise than state-of-the-art BeRST (another voltage-sensitive fluorophore). CRhOMe can also measure values of membrane potential. The fluorescence lifetime of CRhOMe follows a single exponential decay, substantially improving the quantification of membrane potential values using fluorescence lifetime imaging microscopy (FLIM). The combination of red-shifted excitation and emission, mono-exponential decay, and high voltage sensitivity enable fast FLIM recording of action potentials in cardiomyocytes. The ability to both monitor and measure membrane potentials with red light using CRhOMe makes it an important approach for studying biological voltages.
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Affiliation(s)
| | | | - Gloria Ortiz
- Department of Chemistry, University of California, Berkeley
| | | | | | - Evan W Miller
- Department of Chemistry, University of California, Berkeley
- Department of Molecular & Cell Biology, University of California, Berkeley
- Helen Wills Neuroscience Institute, University of California, Berkeley
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9
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Lin HH, Kuo MW, Fan TC, Yu AL, Yu J. YULINK regulates vascular formation in zebrafish and HUVECs. Biol Res 2023; 56:7. [PMID: 36843032 PMCID: PMC9969694 DOI: 10.1186/s40659-023-00415-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/18/2023] [Indexed: 02/28/2023] Open
Abstract
BACKGROUND The distinct arterial and venous cell fates are dictated by a combination of various genetic factors which form diverse types of blood vessels such as arteries, veins, and capillaries. We report here that YULINK protein is involved in vasculogenesis, especially venous formation. METHODS In this manuscript, we employed gene knockdown, yeast two-hybrid, FLIM-FRET, immunoprecipitation, and various imaging technologies to investigate the role of YULINK gene in zebrafish and human umbilical vein endothelial cells (HUVECs). RESULTS Knockdown of YULINK during the arterial-venous developmental stage of zebrafish embryos led to the defective venous formation and abnormal vascular plexus formation. Knockdown of YULINK in HUVECs impaired their ability to undergo cell migration and differentiation into a capillary-like tube formation. In addition, the phosphorylated EPHB4 was decreased in YULINK knockdown HUVECs. Yeast two-hybrid, FLIM-FRET, immunoprecipitation, as well as imaging technologies showed that YULINK colocalized with endosome related proteins (EPS15, RAB33B or TICAM2) and markers (Clathrin and RHOB). VEGF-induced VEGFR2 internalization was also compromised in YULINK knockdown HUVECs, demonstrating to the involvement of YULINK. CONCLUSION This study suggests that YULINK regulates vasculogenesis, possibly through endocytosis in zebrafish and HUVECs.
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Affiliation(s)
- Hsin-Hung Lin
- grid.28665.3f0000 0001 2287 1366Chemical Biology and Molecular Biophysics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan ,grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan
| | - Ming-Wei Kuo
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan
| | - Tan-Chi Fan
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan
| | - Alice L. Yu
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California, San Diego, CA USA
| | - John Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333, Taoyuan, Taiwan. .,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
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10
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Zhao Y, Kim HS, Zou X, Huang L, Liang X, Li Z, Kim JS, Lin W. Harnessing Dual-Fluorescence Lifetime Probes to Validate Regulatory Mechanisms of Organelle Interactions. J Am Chem Soc 2022; 144:20854-20865. [DOI: 10.1021/jacs.2c08966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yuping Zhao
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China
| | - Hyeong Seok Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Xiang Zou
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China
| | - Ling Huang
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China
| | - Xing Liang
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China
| | - Zihong Li
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Weiying Lin
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China
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11
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Vasilev C, Swainsbury DJK, Cartron ML, Martin EC, Kumar S, Hobbs JK, Johnson MP, Hitchcock A, Hunter CN. FRET measurement of cytochrome bc 1 and reaction centre complex proximity in live Rhodobacter sphaeroides cells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148508. [PMID: 34793767 DOI: 10.1016/j.bbabio.2021.148508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/27/2021] [Accepted: 11/09/2021] [Indexed: 11/30/2022]
Abstract
In the model purple phototrophic bacterium Rhodobacter (Rba.) sphaeroides, solar energy is converted via coupled electron and proton transfer reactions within the intracytoplasmic membranes (ICMs), infoldings of the cytoplasmic membrane that form spherical 'chromatophore' vesicles. These bacterial 'organelles' are ideal model systems for studying how the organisation of the photosynthetic complexes therein shape membrane architecture. In Rba. sphaeroides, light-harvesting 2 (LH2) complexes transfer absorbed excitation energy to dimeric reaction centre (RC)-LH1-PufX complexes. The PufX polypeptide creates a channel that allows the lipid soluble electron carrier quinol, produced by RC photochemistry, to diffuse to the cytochrome bc1 complex, where quinols are oxidised to quinones, with the liberated protons used to generate a transmembrane proton gradient and the electrons returned to the RC via cytochrome c2. Proximity between cytochrome bc1 and RC-LH1-PufX minimises quinone/quinol/cytochrome c2 diffusion distances within this protein-crowded membrane, however this distance has not yet been measured. Here, we tag the RC and cytochrome bc1 with yellow or cyan fluorescent proteins (YFP/CFP) and record the lifetimes of YFP/CFP Förster resonance energy transfer (FRET) pairs in whole cells. FRET analysis shows that that these complexes lie on average within 6 nm of each other. Complementary high-resolution atomic force microscopy (AFM) of intact, purified chromatophores verifies the close association of cytochrome bc1 complexes with RC-LH1-PufX dimers. Our results provide a structural basis for the close kinetic coupling between RC-LH1-PufX and cytochrome bc1 observed by spectroscopy, and explain how quinols/quinones and cytochrome c2 shuttle on a millisecond timescale between these complexes, sustaining efficient photosynthetic electron flow.
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Affiliation(s)
- Cvetelin Vasilev
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.
| | - David J K Swainsbury
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Michael L Cartron
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Elizabeth C Martin
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Sandip Kumar
- Department of Physics and Astronomy, University of Sheffield, Sheffield, S3 7HR, United Kingdom; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Jamie K Hobbs
- Department of Physics and Astronomy, University of Sheffield, Sheffield, S3 7HR, United Kingdom
| | - Matthew P Johnson
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Andrew Hitchcock
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
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12
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Saikia N, Yanez-Orozco IS, Qiu R, Hao P, Milikisiyants S, Ou E, Hamilton GL, Weninger KR, Smirnova TI, Sanabria H, Ding F. Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100616. [PMID: 34888535 PMCID: PMC8654206 DOI: 10.1016/j.xcrp.2021.100616] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
SNAP-25 (synaptosomal-associated protein of 25 kDa) is a prototypical intrinsically disordered protein (IDP) that is unstructured by itself but forms coiled-coil helices in the SNARE complex. With high conformational heterogeneity, detailed structural dynamics of unbound SNAP-25 remain elusive. Here, we report an integrative method to probe the structural dynamics of SNAP-25 by combining replica-exchange discrete molecular dynamics (rxDMD) simulations and label-based experiments at ensemble and single-molecule levels. The rxDMD simulations systematically characterize the coil-to-molten globular transition and reconstruct structural ensemble consistent with prior ensemble experiments. Label-based experiments using Förster resonance energy transfer and double electron-electron resonance further probe the conformational dynamics of SNAP-25. Agreements between simulations and experiments under both ensemble and single-molecule conditions allow us to assign specific helix-coil transitions in SNAP-25 that occur in submillisecond timescales and potentially play a vital role in forming the SNARE complex. We expect that this integrative approach may help further our understanding of IDPs.
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Affiliation(s)
- Nabanita Saikia
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Department of Chemistry, Navajo Technical University, Chinle, AZ 86503, USA
| | | | - Ruoyi Qiu
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Pengyu Hao
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Sergey Milikisiyants
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Erkang Ou
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - George L. Hamilton
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Keith R. Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Tatyana I. Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Lead contact
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13
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Hwang W, Kim D, Moon S, Kim DY. Achieving a high photon count rate in digital time-correlated single photon counting using a hybrid photodetector. OPTICS EXPRESS 2021; 29:9797-9804. [PMID: 33820132 DOI: 10.1364/oe.419896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
We report an enhanced photon count rate in a digitally implemented time-correlated single-photon counting (TCSPC) system by utilizing a hybrid photodetector (HPD). In our digital TCSPC scheme, the photoelectronic responses from a single photon-sensitive photodetector are digitally analyzed through a high-speed analog-to-digital convertor (ADC). By virtue of the HPD which provides nearly a constant signal gain, the single-photon pulses can be effectively distinguished from pulses of simultaneously detected multiple photons by the pulse heights. Consequently, our digital TCSPC system can selectively collect single-photon signals even in the presence of intense multi-photon detections with its temporal accuracy not to be compromised. In our experiment of fluorescence lifetime measurement, the maximum count rate of single photons nearly reached the theoretical limit given by the Poisson statistics. This demonstrated that the digital TCSPC combined with the HPD provides an ultimate solution for the TCSPC implementation for high photon count rates.
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14
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Tavakoli M, Jazani S, Sgouralis I, Heo W, Ishii K, Tahara T, Pressé S. Direct Photon-by-Photon Analysis of Time-Resolved Pulsed Excitation Data using Bayesian Nonparametrics. CELL REPORTS. PHYSICAL SCIENCE 2020; 1:100234. [PMID: 34414380 PMCID: PMC8373049 DOI: 10.1016/j.xcrp.2020.100234] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Lifetimes of chemical species are typically estimated by either fitting time-correlated single-photon counting (TCSPC) histograms or phasor analysis from time-resolved photon arrivals. While both methods yield lifetimes in a computationally efficient manner, their performance is limited by choices made on the number of distinct chemical species contributing photons. However, the number of species is encoded in the photon arrival times collected for each illuminated spot and need not be set by hand a priori. Here, we propose a direct photon-by-photon analysis of data drawn from pulsed excitation experiments to infer, simultaneously and self-consistently, the number of species and their associated lifetimes from a few thousand photons. We do so by leveraging new mathematical tools within the Bayesian nonparametric. We benchmark our method for both simulated and experimental data for 1-4 species.
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Affiliation(s)
- Meysam Tavakoli
- Department of Physics, Indiana University-Purdue University, Indianapolis, IN 46202, USA
| | - Sina Jazani
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Ioannis Sgouralis
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wooseok Heo
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Steve Pressé
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Lead Contact
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15
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Roy K, Ghosh D, Sarkar K, Devi P, Kumar P. Chlorophyll( a)/Carbon Quantum Dot Bio-Nanocomposite Activated Nano-Structured Silicon as an Efficient Photocathode for Photoelectrochemical Water Splitting. ACS APPLIED MATERIALS & INTERFACES 2020; 12:37218-37226. [PMID: 32814382 DOI: 10.1021/acsami.0c10279] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Solar-driven water splitting is considered as a futuristic sustainable way to generate hydrogen and chemical storage of solar energy. Further, considering the technological competence, silicon is one of the potential materials for developing large-scale and cost-effective photocathodes (PCs), but it lacks efficacy and stability. Here, we show that chlorophyll(a)/carbon quantum dots (Chl/CQDs) bio-nanocomposite (b-NC)-decorated Si-nanowires (SiNWs) as PC can surpass the reported efficiency for photoelectrochemical (PEC) hydrogen generation along with stability. The optimized heterojunction (Chl/CQDs_SiNW) significantly enhances broad-band solar absorption and protects Si surface from corrosion. Further, the appropriate band alignment enforces efficient photogenerated charge separation and possesses directional exciton transport property via the Förster resonance energy transfer (FRET) mechanism. This synergic effect demonstrates an ∼18 times increase in photocurrent density (26.36 mA/cm2) compared to pristine SiNW PC at 1.07 V vs reversible hydrogen electrode (RHE). The efficiency reaches ∼7.86%, which is comparably the highest reported for hybrid Si-based photocathodes. Hydrogen evaluation rate was measured to be ∼113 μmol/h at 0.8 V vs RHE under 1 sun illumination. With Si-process line compatibility, this new finding opens a new direction toward the development of Si-based efficient and stable PCs at a large scale for commercial applications.
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Affiliation(s)
- Krishnendu Roy
- School of Materials Science, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Dibyendu Ghosh
- School of Materials Science, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - K Sarkar
- School of Materials Science, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Pooja Devi
- Central Scientific Instruments Organization, Sector-30C, Chandigarh 160030, India
| | - Praveen Kumar
- School of Materials Science, Indian Association for the Cultivation of Science, Kolkata 700032, India
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16
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Barkauskas DS, Medley G, Liang X, Mohammed YH, Thorling CA, Wang H, Roberts MS. Using in vivo multiphoton fluorescence lifetime imaging to unravel disease-specific changes in the liver redox state. Methods Appl Fluoresc 2020; 8:034003. [PMID: 32422610 DOI: 10.1088/2050-6120/ab93de] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multiphoton fluorescence lifetime microscopy has revolutionized studies of pathophysiological and xenobiotic dynamics, enabling the spatial and temporal quantification of these processes in intact organs in vivo. We have previously used multiphoton fluorescence lifetime microscopy to characterise the morphology and amplitude weighted mean fluorescence lifetime of the endogenous fluorescent metabolic cofactor nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) of mouse livers in vivo following induction of various disease states. Here, we extend the characterisation of liver disease models by using nonlinear regression to estimate the unbound, bound fluorescence lifetimes for NAD(P)H, flavin adenine dinucleotide (FAD), along with metabolic ratios and examine the impact of using multiple segmentation methods. We found that NAD(P)H amplitude ratio, and fluorescence lifetime redox ratio can be used as discriminators of diseased liver from normal liver. The redox ratio provided a sensitive measure of the changes in hepatic fibrosis and biliary fibrosis. Hepatocellular carcinoma was associated with an increase in spatial heterogeneity and redox ratio coupled with a decrease in mean fluorescence lifetime. We conclude that multiphoton fluorescence lifetime microscopy parameters and metabolic ratios provided insights into the in vivo redox state of diseased compared to normal liver that were not apparent from a global, mean fluorescence lifetime measurement alone.
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Affiliation(s)
- Deborah S Barkauskas
- Therapeutics Research Group, University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
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17
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Skalsky S, Zhang Y, Alanis JA, Fonseka HA, Sanchez AM, Liu H, Parkinson P. Heterostructure and Q-factor engineering for low-threshold and persistent nanowire lasing. LIGHT, SCIENCE & APPLICATIONS 2020; 9:43. [PMID: 32194957 PMCID: PMC7078256 DOI: 10.1038/s41377-020-0279-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 02/10/2020] [Accepted: 03/02/2020] [Indexed: 05/28/2023]
Abstract
Continuous room temperature nanowire lasing from silicon-integrated optoelectronic elements requires careful optimisation of both the lasing cavity Q-factor and population inversion conditions. We apply time-gated optical interferometry to the lasing emission from high-quality GaAsP/GaAs quantum well nanowire laser structures, revealing high Q-factors of 1250 ± 90 corresponding to end-facet reflectivities of R = 0.73 ± 0.02. By using optimised direct-indirect band alignment in the active region, we demonstrate a well-refilling mechanism providing a quasi-four-level system leading to multi-nanosecond lasing and record low room temperature lasing thresholds (~6 μJ cm-2 pulse-1) for III-V nanowire lasers. Our findings demonstrate a highly promising new route towards continuously operating silicon-integrated nanolaser elements.
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Affiliation(s)
- Stefan Skalsky
- Department of Physics and Astronomy and The Photon Science Institute, The University of Manchester, Manchester, M13 9PL UK
| | - Yunyan Zhang
- Department of Electronic and Electrical Engineering, University College London, London, WC1E 7JE UK
| | - Juan Arturo Alanis
- Department of Physics and Astronomy and The Photon Science Institute, The University of Manchester, Manchester, M13 9PL UK
| | - H. Aruni Fonseka
- Department of Physics, University of Warwick, Coventry, CV4 7AL UK
| | - Ana M. Sanchez
- Department of Physics, University of Warwick, Coventry, CV4 7AL UK
| | - Huiyun Liu
- Department of Electronic and Electrical Engineering, University College London, London, WC1E 7JE UK
| | - Patrick Parkinson
- Department of Physics and Astronomy and The Photon Science Institute, The University of Manchester, Manchester, M13 9PL UK
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18
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Schalk IJ, Rigouin C, Godet J. An overview of siderophore biosynthesis among fluorescent Pseudomonads and new insights into their complex cellular organization. Environ Microbiol 2020; 22:1447-1466. [PMID: 32011068 DOI: 10.1111/1462-2920.14937] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/25/2020] [Accepted: 01/28/2020] [Indexed: 01/02/2023]
Abstract
Siderophores are iron-chelating molecules produced by bacteria to access iron, a key nutrient. These compounds have highly diverse chemical structures, with various chelating groups. They are released by bacteria into their environment to scavenge iron and bring it back into the cells. The biosynthesis of siderophores requires complex enzymatic processes and expression of the enzymes involved is very finely regulated by iron availability and diverse transcriptional regulators. Recent data have also highlighted the organization of the enzymes involved in siderophore biosynthesis into siderosomes, multi-enzymatic complexes involved in siderophore synthesis. An understanding of siderophore biosynthesis is of great importance, as these compounds have many potential biotechnological applications because of their metal-chelating properties and their key role in bacterial growth and virulence. This review focuses on the biosynthesis of siderophores produced by fluorescent Pseudomonads, bacteria capable of colonizing a large variety of ecological niches. They are characterized by the production of chromopeptide siderophores, called pyoverdines, which give the typical green colour characteristic of fluorescent pseudomonad cultures. Secondary siderophores are also produced by these strains and can have highly diverse structures (such as pyochelins, pseudomonine, yersiniabactin, corrugatin, achromobactin and quinolobactin).
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Affiliation(s)
- Isabelle J Schalk
- CNRS, UMR7242, ESBS, Illkirch, Strasbourg, France.,Université de Strasbourg, UMR7242, ESBS, Illkirch, Strasbourg, France
| | - Coraline Rigouin
- CNRS, UMR7242, ESBS, Illkirch, Strasbourg, France.,Université de Strasbourg, UMR7242, ESBS, Illkirch, Strasbourg, France
| | - Julien Godet
- Université de Strasbourg, Laboratoire de BioImagerie et Pathologies, UMR CNRS, 7021, Illkirch, France
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19
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Godet J, Mély Y. Exploring protein-protein interactions with large differences in protein expression levels using FLIM-FRET. Methods Appl Fluoresc 2019; 8:014007. [PMID: 31791032 DOI: 10.1088/2050-6120/ab5dd2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Many molecular processes within a cell are carried out by molecular machines built from a large number of proteins organized by their protein-protein interactions (PPIs). Exploring PPIs in their cellular context is critical to better understand the proteins functions. Förster resonance energy transfer measured by fluorescence lifetime imaging (FLIM-FRET) enables to monitor PPIs and to map their spatial organization in a living cell with high spatial and temporal specificity. But both the accurate measurement and the interpretation of multi-exponential FLIM-FRET data associated to mixtures of interacting and non-interacting proteins are difficult. Here we show that a simple diagram plot can find interesting visualization properties by clustering pixels with similar decay signatures. FLIM diagram plot can be used to provide valuable information about stoichiometry and binding mode in PPIs, even in the presence of large differences in protein expression levels of the different interacting partners. The proposed FLIM diagram plot is a useful visual approach for a more straightforward interpretation of complex lifetime data. This approach was applied for revealing critical features of PPIs in live Pseudomonas aeruginosa.
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Affiliation(s)
- Julien Godet
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, Illkirch, France. Groupe Méthode Recherche Clinique, Pôle de Santé Publique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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20
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Schneckenburger H. Förster resonance energy transfer-what can we learn and how can we use it? Methods Appl Fluoresc 2019; 8:013001. [PMID: 31715588 DOI: 10.1088/2050-6120/ab56e1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The present manuscript gives a short overview on Förster Resonance Energy Transfer (FRET) of molecular interactions in the nanometre range. First, its principle is described and a short historical overview is given. Subsequently some principal methods and applications of FRET sensing and imaging are described (with some emphasis on fluorescence lifetime imaging, FLIM), and finally two innovative FRET techniques are presented in more detail. Applications are focused on measurements of living cells.
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21
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Yu W, Guo B, Zhang H, Zhou J, Yu X, Zhu L, Xue D, Liu W, Sun X, Qian J. NIR-II fluorescence in vivo confocal microscopy with aggregation-induced emission dots. Sci Bull (Beijing) 2019; 64:410-416. [PMID: 36659732 DOI: 10.1016/j.scib.2019.02.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 01/21/2023]
Abstract
Significantly reduced tissue scattering of fluorescence signals in the second near-infrared (NIR-II, 1,000-1,700 nm) spectral region offers opportunities for large-depth in vivo bioimaging. Nowadays, most reported works concerning NIR-II fluorescence in vivo bioimaging are realized by wide-field illumination and 2D-arrayed detection (e.g., via InGaAs camera), which has high temporal resolution but limited spatial resolution due to out-of-focus signals. Combining NIR-II fluorescence imaging with confocal microscopy is a good approach to achieve high-spatial resolution visualization of biosamples even at deep tissues. In this presented work, a NIR-II fluorescence confocal microscopic system was setup. By using a kind of aggregation-induced emission (AIE) dots as NIR-II fluorescent probes, 800 μm-deep 3D in vivo cerebrovascular imaging of a mouse was obtained, and the spatial resolution at 700 μm depth could reach 8.78 μm. Moreover, the time-correlated single photon counting (TCSPC) technique and femtosecond laser excitation were introduced into NIR-II fluorescence confocal microscopy, and in vivo confocal NIR-II fluorescence lifetime microscopic imaging (FLIM) of mouse cerebral vasculature was successfully realized.
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Affiliation(s)
- Wenbin Yu
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Bing Guo
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Hequn Zhang
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Jing Zhou
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Xiaoming Yu
- Department of Urology, Sir Run-Run Shaw Hospital College of Medicine, Innovation Center for Minimally Invasive Technique and Device, Zhejiang University, Hangzhou 310016, China
| | - Liang Zhu
- Interdisciplinary Institute of Neuroscience and Technology (ZIINT), Zhejiang University, Hangzhou 310058, China
| | - Dingwei Xue
- Department of Urology, Sir Run-Run Shaw Hospital College of Medicine, Innovation Center for Minimally Invasive Technique and Device, Zhejiang University, Hangzhou 310016, China
| | - Wen Liu
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Xianhe Sun
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Jun Qian
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China; Joint Research Laboratory of Optics of Zhejiang, Normal University and Zhejiang University, Zhejiang Normal University, Jinhua 321000, China.
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22
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Koren K, Moßhammer M, Scholz VV, Borisov SM, Holst G, Kühl M. Luminescence Lifetime Imaging of Chemical Sensors-A Comparison between Time-Domain and Frequency-Domain Based Camera Systems. Anal Chem 2019; 91:3233-3238. [PMID: 30758940 DOI: 10.1021/acs.analchem.8b05869] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Luminescence lifetime based imaging is still the most reliable method for generating chemical images using chemical sensor technology. However, only few commercial systems are available that enable imaging lifetimes within the relevant nanosecond to microsecond range. In this technical note we compare the performance of an older time-domain (TD) based camera system with a frequency-domain (FD) based camera system regarding their measuring characteristics and applicability for O2 and pH imaging in environmental samples and with different indicator dye systems emitting in the visible and near-infrared part of the spectrum. We conclude that the newly introduced FD imaging system delivers comparable if not better results than its predecessor, now enabling robust and simple chemical imaging based on FD luminescence lifetime measurements.
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Affiliation(s)
- Klaus Koren
- Aarhus University Centre for Water Technology, Section for Microbiology, Department of Bioscience , Aarhus University , Ny Munkegade , DK-8000 Aarhus C , Denmark
| | - Maria Moßhammer
- Marine Biological Section, Department of Biology , University of Copenhagen , Strandpromenaden 5 , DK-3000 Helsingør , Denmark
| | - Vincent V Scholz
- Center for Electromicrobiology , Aarhus University , DK-8000 Aarhus , Denmark
| | - Sergey M Borisov
- Institute of Analytical Chemistry and Food Chemistry , Graz University of Technology , Stremayrgasse 9 , AT-8010 Graz , Austria
| | | | - Michael Kühl
- Marine Biological Section, Department of Biology , University of Copenhagen , Strandpromenaden 5 , DK-3000 Helsingør , Denmark.,Climate Change Cluster , University of Technology Sydney , Ultimo , NSW 2007 , Australia
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23
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Schwarz J, J Leopold H, Leighton R, Miller RC, Aplin CP, Boersma AJ, Heikal AA, Sheets ED. Macromolecular crowding effects on energy transfer efficiency and donor-acceptor distance of hetero-FRET sensors using time-resolved fluorescence. Methods Appl Fluoresc 2019; 7:025002. [PMID: 30690439 DOI: 10.1088/2050-6120/ab0242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Living cells are crowded with macromolecules and organelles, which affect a myriad of biochemical processes. As a result, there is a need for sensitive molecular sensors for quantitative, site-specific assessment of macromolecular crowding. Here, we investigated the excited-state dynamics of recently developed hetero-FRET sensors (mCerulean3-linker-mCitrine) in homogeneous and heterogeneous environments using time-resolved fluorescence measurements, which are compatible with fluorescence lifetime imaging microscopy (FLIM). The linker in these FRET constructs, which tether the mCerulean3 (the donor) and mCitrine (the acceptor), vary in both length and flexibility. Glycerol and Ficoll-70 solutions were used for homogeneous and heterogeneous environments, respectively, at variable concentrations. The wavelength-dependent studies suggest that the 425-nm excitation and the 475-nm emission of the donor are best suited for quantitative assessment of the energy transfer efficiency and the donor-acceptor distance of these FRET probes. Under the same experimental conditions, the enzymatically cleaved counterpart of these probes was used as a control as well as a means to account for the changes in the environmental refractive indices. Our results indicate that the energy transfer efficiency of these FRET probes increases as the linker becomes shorter and more flexible in pure buffer at room temperature. In addition, the FRET probes favor a compact structure with enhanced energy transfer efficiency and a shorter donor-acceptor distance in the heterogeneous, polymer-crowded environment due to steric hindrance. In contrast, the stretched conformation of these FRET probes is more favorable in the viscous, homogeneous environment with a reduced energy transfer efficiency and relatively larger donor-acceptor distance as compared with those in pure buffer, which was attributed to a reduced structural fluctuation of the mCerulean3-mCitrine FRET pair in the viscous, more restrictive glycerol-enriched buffer. Our findings will help to advance the potential of these hetero-FRET probes using FLIM for spatio-temporal assessment of the compartmentalized crowding in living cells.
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Affiliation(s)
- Jacob Schwarz
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, MN, United States of America
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Leopold HJ, Leighton R, Schwarz J, Boersma AJ, Sheets ED, Heikal AA. Crowding Effects on Energy-Transfer Efficiencies of Hetero-FRET Probes As Measured Using Time-Resolved Fluorescence Anisotropy. J Phys Chem B 2019; 123:379-393. [PMID: 30571116 DOI: 10.1021/acs.jpcb.8b09829] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Macromolecular crowding is prevalent in all living cells due to the presence of large biomolecules and organelles. Cellular crowding is heterogeneous and is known to influence biomolecular transport, biochemical reactions, and protein folding. Emerging evidence suggests that some cell pathologies may be correlated with compartmentalized crowding. As a result, there is a need for robust biosensors that are sensitive to crowding as well as quantitative, noninvasive fluorescence methods that are compatible with living cells studies. Here, we have developed a model that describes the rotational dynamics of hetero-Förster resonance energy transfer (FRET) biosensors as a means to determine the energy-transfer efficiency and donor-acceptor distance. The model was tested on wavelength-dependent time-resolved fluorescence anisotropy of hetero-FRET probes (mCerulean3-linker-mCitrine) with variable linkers in both crowded (Ficoll-70) and viscous (glycerol) solutions at room temperature. Our results indicate that the energy-transfer efficiencies of these FRET probes increase as the linker becomes shorter and more flexible in pure buffer at room temperature. In addition, the FRET probes favor compact structures with enhanced energy-transfer efficiencies and a shorter donor-acceptor distance in the heterogeneous, polymer-crowded environment due to steric hindrance. In contrast, the extended conformation of these FRET probes is more favorable in viscous, homogeneous environments with a reduced energy-transfer efficiency compared to those in pure buffer, which we attribute to reduced structural fluctuations of the mCerulean3-mCitrine FRET pair in the glycerol-enriched buffer. Our results represent an important step toward the application of quantitative and noninvasive time-resolved fluorescence anisotropy of hetero-FRET probes to investigate compartmentalized macromolecular crowding and protein-protein interactions in living cells as well as in controlled environments.
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Affiliation(s)
- Hannah J Leopold
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Ryan Leighton
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Jacob Schwarz
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Arnold J Boersma
- DW1-Leibniz Institute for Interactive Materials , Forckenbeckstr. 50 , 52056 Aachen , Germany
| | - Erin D Sheets
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Ahmed A Heikal
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
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25
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Sharma A, Kumar R, Aier I, Semwal R, Tyagi P, Varadwaj P. Sense of Smell: Structural, Functional, Mechanistic Advancements and Challenges in Human Olfactory Research. Curr Neuropharmacol 2019; 17:891-911. [PMID: 30520376 PMCID: PMC7052838 DOI: 10.2174/1570159x17666181206095626] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/08/2018] [Accepted: 11/28/2018] [Indexed: 02/07/2023] Open
Abstract
Olfaction, the sense of smell detects and discriminate odors as well as social cues which influence our innate responses. The olfactory system in human beings is found to be weak as compared to other animals; however, it seems to be very precise. It can detect and discriminate millions of chemical moieties (odorants) even in minuscule quantities. The process initiates with the binding of odorants to specialized olfactory receptors, encoded by a large family of Olfactory Receptor (OR) genes belonging to the G-protein-coupled receptor superfamily. Stimulation of ORs converts the chemical information encoded in the odorants, into respective neuronal action-potentials which causes depolarization of olfactory sensory neurons. The olfactory bulb relays this signal to different parts of the brain for processing. Odors are encrypted using a combinatorial approach to detect a variety of chemicals and encode their unique identity. The discovery of functional OR genes and proteins provided an important information to decipher the genomic, structural and functional basis of olfaction. ORs constitute 17 gene families, out of which 4 families were reported to contain more than hundred members each. The olfactory machinery is not limited to GPCRs; a number of non- GPCRs is also employed to detect chemosensory stimuli. The article provides detailed information about such olfaction machinery, structures, transduction mechanism, theories of odor perception, and challenges in the olfaction research. It covers the structural, functional and computational studies carried out in the olfaction research in the recent past.
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Affiliation(s)
| | | | | | | | | | - Pritish Varadwaj
- Address correspondence to this author at the Department of Applied Science, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India; E-mail:
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26
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Wang L, Chen B, Yan W, Yang Z, Peng X, Lin D, Weng X, Ye T, Qu J. Resolution improvement in STED super-resolution microscopy at low power using a phasor plot approach. NANOSCALE 2018; 10:16252-16260. [PMID: 30124714 DOI: 10.1039/c8nr03584a] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Stimulated emission depletion (STED) microscopy is a powerful super-resolution microscopy technique that has achieved significant results in breaking the resolution limit and relevant applications. In principle, STED super resolution is obtained by stimulated emission partially inhibiting the spontaneous emission in the periphery of a diffraction-limited area. However, very high depletion laser power is generally necessary for the enhancement of imaging resolution, which is harmful to live biological specimens due to its high phototoxicity and photo-bleaching effects. Therefore, further improving the STED resolution at a lower depletion power level has recently attracted increasing interest from researchers in various fields. In this work, a phasor plot approach combined with fluorescence lifetime imaging microscopy (FLIM) is used to resolve the abovementioned problem based on a long- and short-lifetime criterion. Firstly, the time-resolved data obtained by STED-FLIM is converted to the frequency domain via a phasor approach. Next, partial data is extracted according to the information on the phase and amplitude for resolution improvement. Then, fluorescent microspheres (100 nm in diameter) are observed under different depletion powers, resulting in a series of improved resolution through phasor plots. Finally, this method is applied to image human Nup153 in fixed HeLa cells, providing a 86 nm higher resolution than that in traditional STED imaging at a depletion power of 20 mW.
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Affiliation(s)
- Luwei Wang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
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27
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Boyer PD, Ganesh S, Qin Z, Holt BD, Buehler MJ, Islam MF, Dahl KN. Delivering Single-Walled Carbon Nanotubes to the Nucleus Using Engineered Nuclear Protein Domains. ACS APPLIED MATERIALS & INTERFACES 2016; 8:3524-34. [PMID: 26783632 DOI: 10.1021/acsami.5b12602] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) have great potential for cell-based therapies due to their unique intrinsic optical and physical characteristics. Consequently, broad classes of dispersants have been identified that individually suspend SWCNTs in water and cell media in addition to reducing nanotube toxicity to cells. Unambiguous control and verification of the localization and distribution of SWCNTs within cells, particularly to the nucleus, is needed to advance subcellular technologies utilizing nanotubes. Here we report delivery of SWCNTs to the nucleus by noncovalently attaching the tail domain of the nuclear protein lamin B1 (LB1), which we engineer from the full-length LMNB1 cDNA. More than half of this low molecular weight globular protein is intrinsically disordered but has an immunoglobulin-fold composed of a central hydrophobic core, which is highly suitable for associating with SWCNTs, stably suspending SWCNTs in water and cell media. In addition, LB1 has an exposed nuclear localization sequence to promote active nuclear import of SWCNTs. These SWCNTs-LB1 dispersions in water and cell media display near-infrared (NIR) absorption spectra with sharp van Hove peaks and an NIR fluorescence spectra, suggesting that LB1 individually disperses nanotubes. The dispersing capability of SWCNTs by LB1 is similar to that by albumin proteins. The SWCNTs-LB1 dispersions with concentrations ≥150 μg/mL (≥30 μg/mL) in water (cell media) remain stable for ≥75 days (≥3 days) at 4 °C (37 °C). Further, molecular dynamics modeling of association of LB1 with SWCNTs reveal that the exposure of the nuclear localization sequence is independent of LB1 binding conformation. Measurements from confocal Raman spectroscopy and microscopy, NIR fluorescence imaging of SWCNTs, and fluorescence lifetime imaging microscopy show that millions of these SWCNTs-LB1 complexes enter HeLa cells, localize to the nucleus of cells, and interact with DNA. We postulate that the modification of native cellular proteins as noncovalent dispersing agents to provide specific transport will open new possibilities to utilize both SWCNT and protein properties for multifunctional subcellular targeting applications. Specifically, nuclear targeting could allow delivery of anticancer therapies, genetic treatments, or DNA to the nucleus.
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Affiliation(s)
| | | | - Zhao Qin
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | | | - Markus J Buehler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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Mothersole DJ, Jackson PJ, Vasilev C, Tucker JD, Brindley AA, Dickman MJ, Hunter CN. PucC and LhaA direct efficient assembly of the light-harvesting complexes in Rhodobacter sphaeroides. Mol Microbiol 2015; 99:307-27. [PMID: 26419219 PMCID: PMC4949548 DOI: 10.1111/mmi.13235] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2015] [Indexed: 01/21/2023]
Abstract
The mature architecture of the photosynthetic membrane of the purple phototroph Rhodobacter sphaeroides has been characterised to a level where an atomic-level membrane model is available, but the roles of the putative assembly proteins LhaA and PucC in establishing this architecture are unknown. Here we investigate the assembly of light-harvesting LH2 and reaction centre-light-harvesting1-PufX (RC-LH1-PufX) photosystem complexes using spectroscopy, pull-downs, native gel electrophoresis, quantitative mass spectrometry and fluorescence lifetime microscopy to characterise a series of lhaA and pucC mutants. LhaA and PucC are important for specific assembly of LH1 or LH2 complexes, respectively, but they are not essential; the few LH1 subunits found in ΔlhaA mutants assemble to form normal RC-LH1-PufX core complexes showing that, once initiated, LH1 assembly round the RC is cooperative and proceeds to completion. LhaA and PucC form oligomers at sites of initiation of membrane invagination; LhaA associates with RCs, bacteriochlorophyll synthase (BchG), the protein translocase subunit YajC and the YidC membrane protein insertase. These associations within membrane nanodomains likely maximise interactions between pigments newly arriving from BchG and nascent proteins within the SecYEG-SecDF-YajC-YidC assembly machinery, thereby co-ordinating pigment delivery, the co-translational insertion of LH polypeptides and their folding and assembly to form photosynthetic complexes.
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Affiliation(s)
- David J Mothersole
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Philip J Jackson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.,ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Cvetelin Vasilev
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Jaimey D Tucker
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
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29
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Wang W, Liu Q, Zhan C, Barhoumi A, Yang T, Wylie RG, Armstrong PA, Kohane DS. Efficient Triplet-Triplet Annihilation-Based Upconversion for Nanoparticle Phototargeting. NANO LETTERS 2015; 15:6332-8. [PMID: 26158690 DOI: 10.1021/acs.nanolett.5b01325] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
High-efficiency upconverted light would be a desirable stimulus for triggered drug delivery. Here we present a general strategy to achieve photoreactions based on triplet-triplet annihilation upconversion (TTA-UC) and Förster resonance energy transfer (FRET). We designed PLA-PEG micellar nanoparticles containing in their cores hydrophobic photosensitizer and annihilator molecules which, when stimulated with green light, would undergo TTA-UC. The upconverted energy was then transferred by FRET to a hydrophobic photocleavable group (DEACM), also in the core. The DEACM was bonded to (and thus inactivated) the cell-binding peptide cyclo-(RGDfK), which was bound to the PLA-PEG chain. Cleavage of DEACM by FRET reactivated the PLA-PEG-bound peptide and allowed it to move from the particle core to the surface. TTA-UC followed by FRET allowed photocontrolled binding of cell adhesion with green light LED irradiation at low irradiance for short periods. These are attractive properties in phototriggered systems.
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Affiliation(s)
- Weiping Wang
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School , 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Qian Liu
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School , 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Changyou Zhan
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School , 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Aoune Barhoumi
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School , 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Tianshe Yang
- Institute of Advanced Materials, School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications , 9 Wenyuan Road, Nanjing 210023, People's Republic of China
| | - Ryan G Wylie
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School , 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Patrick A Armstrong
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School , 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Daniel S Kohane
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School , 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Holt BD, Law JJ, Boyer PD, Wilson LJ, Dahl KN, Islam MF. Subcellular Partitioning and Analysis of Gd3+-Loaded Ultrashort Single-Walled Carbon Nanotubes. ACS APPLIED MATERIALS & INTERFACES 2015; 7:14593-602. [PMID: 26098461 DOI: 10.1021/acsami.5b04851] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Magnetic resonance imaging (MRI) is of vast clinical utility, with tens of millions of scans performed annually. Chemical contrast agents (CAs) can greatly enhance the diagnostic potential of MRI, and ∼50% of MRI scans use CAs. However, CAs have significant limitations such as low contrast enhancement, lack of specificity, and potential toxicity. Recently developed, Gd3+-loaded ultrashort single-walled carbon nanotubes, also referred to as gadonanotubes or GNTs, exhibit ∼40 times the relaxivities of clinical CAs, representing a potential major advance in clinically relevant MRI CA materials. Although initial cytotoxicity and MRI studies have suggested great promise for GNTs, relatively little is known regarding their subcellular interactions, which are crucial for further, safe development of GNTs as CAs. In this work, we administered GNTs to a well-established human cell line (HeLa) and to murine macrophage-like cells (J774A.1). GNTs were not acutely cytotoxic and did not reduce proliferation, except for the highest exposure concentration of 27 μg/mL for J774A.1 macrophages, yet bulk uptake of GNTs occurred in minutes at picogram quantities, or millions of GNTs per cell. J774A.1 macrophages internalized substantially more GNTs than HeLa cells in a dose-dependent manner, and Raman imaging of the subcellular distribution of GNTs revealed perinuclear localization. Fluorescence intensity and lifetime imaging demonstrated that GNTs did not grossly alter subcellular compartments, including filamentous-actin structures. Together, these results provide subcellular evidence necessary to establish GNTs as a new MRI CA material.
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Affiliation(s)
| | - Justin J Law
- ‡Department of Chemistry and Smalley Center for Nanoscale Science and Technology, Rice University, Houston, Texas 77251, United States
| | | | - Lon J Wilson
- ‡Department of Chemistry and Smalley Center for Nanoscale Science and Technology, Rice University, Houston, Texas 77251, United States
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31
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Sewell D, Kim H, Ha T, Ma P. A parameter estimation method for fluorescence lifetime data. BMC Res Notes 2015; 8:230. [PMID: 26054354 PMCID: PMC4467687 DOI: 10.1186/s13104-015-1176-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 05/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND When modeling single-molecule fluorescence lifetime experimental data, the analysis often involves fitting a biexponential distribution to binned data. When dealing with small sample sizes, there is the potential for convergence failure in numerical optimization, for convergence to local optima resulting in physically unreasonable parameter estimates, and also for overfitting the data. RESULTS To avoid the problems that arise in small sample sizes, we have developed a gamma conversion method to estimate the lifetime components. The key idea is to use a gamma distribution for initial numerical optimization and then convert the gamma parameters to biexponential ones via moment matching. A simulation study is undertaken with 30 unique configurations of parameter values. We also performed the same analysis on data obtained from a fluorescence lifetime experiment using the fluorophore Cy3. In both the simulation study and the real data analysis, fitting the biexponential directly led to a large number of data sets whose estimates were physically unreasonable, while using the gamma conversion yielded estimates consistently close to the true values. CONCLUSIONS Our analysis shows that using numerical optimization methods to fit the biexponential distribution directly can lead to failure to converge, convergence to physically unreasonable parameter estimates, and overfitting the data. The proposed gamma conversion method avoids these numerical difficulties, yielding better results.
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Affiliation(s)
- Daniel Sewell
- Department of Statistics, University of Illinois Urbana-Champaign, 725 S. Wright St., Champaign, IL, 61820, USA.
| | - Hajin Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea. .,Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Republic of Korea.
| | - Taekjip Ha
- Department of Physics, University of Illinois Urbana-Champaign, 1110 W. Green St., 61801, Urbana, IL, USA.
| | - Ping Ma
- Department of Statistics, University of Georgia, 101 Cedar Street, Athens, GA, 30602, USA.
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32
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Becker W. Fluorescence lifetime imaging by multi-dimensional time correlated single photon counting. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.medpho.2015.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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34
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Nedbal J, Visitkul V, Ortiz-Zapater E, Weitsman G, Chana P, Matthews DR, Ng T, Ameer-Beg SM. Time-domain microfluidic fluorescence lifetime flow cytometry for high-throughput Förster resonance energy transfer screening. Cytometry A 2015; 87:104-18. [PMID: 25523156 PMCID: PMC4440390 DOI: 10.1002/cyto.a.22616] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 11/12/2014] [Accepted: 12/03/2014] [Indexed: 01/22/2023]
Abstract
Sensing ion or ligand concentrations, physico-chemical conditions, and molecular dimerization or conformation change is possible by assays involving fluorescent lifetime imaging. The inherent low throughput of imaging impedes rigorous statistical data analysis on large cell numbers. We address this limitation by developing a fluorescence lifetime-measuring flow cytometer for fast fluorescence lifetime quantification in living or fixed cell populations. The instrument combines a time-correlated single photon counting epifluorescent microscope with microfluidics cell-handling system. The associated computer software performs burst integrated fluorescence lifetime analysis to assign fluorescence lifetime, intensity, and burst duration to each passing cell. The maximum safe throughput of the instrument reaches 3,000 particles per minute. Living cells expressing spectroscopic rulers of varying peptide lengths were distinguishable by Förster resonant energy transfer measured by donor fluorescence lifetime. An epidermal growth factor (EGF)-stimulation assay demonstrated the technique's capacity to selectively quantify EGF receptor phosphorylation in cells, which was impossible by measuring sensitized emission on a standard flow cytometer. Dual-color fluorescence lifetime detection and cell-specific chemical environment sensing were exemplified using di-4-ANEPPDHQ, a lipophilic environmentally sensitive dye that exhibits changes in its fluorescence lifetime as a function of membrane lipid order. To our knowledge, this instrument opens new applications in flow cytometry which were unavailable due to technological limitations of previously reported fluorescent lifetime flow cytometers. The presented technique is sensitive to lifetimes of most popular fluorophores in the 0.5-5 ns range including fluorescent proteins and is capable of detecting multi-exponential fluorescence lifetime decays. This instrument vastly enhances the throughput of experiments involving fluorescence lifetime measurements, thereby providing statistically significant quantitative data for analysis of large cell populations. © 2014 International Society for Advancement of Cytometry.
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Affiliation(s)
- Jakub Nedbal
- Division of Cancer Studies, King's College LondonUnited Kingdom
- Randall Division of Cell and Molecular Biophysics, King's College LondonUnited Kingdom
| | - Viput Visitkul
- Randall Division of Cell and Molecular Biophysics, King's College LondonUnited Kingdom
| | - Elena Ortiz-Zapater
- Division of Asthma, Allergy & Lung Biology, King's College LondonUnited Kingdom
| | | | - Prabhjoat Chana
- Immune Monitoring Laboratory, NIHR Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College LondonUnited Kingdom
| | - Daniel R Matthews
- Queensland Brain Institute, The University of QueenslandSt Lucia, Australia
| | - Tony Ng
- Division of Cancer Studies, King's College LondonUnited Kingdom
- Randall Division of Cell and Molecular Biophysics, King's College LondonUnited Kingdom
- UCL Cancer Institute, University College LondonUnited Kingdom
| | - Simon M Ameer-Beg
- Division of Cancer Studies, King's College LondonUnited Kingdom
- Randall Division of Cell and Molecular Biophysics, King's College LondonUnited Kingdom
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35
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Chosrowjan H, Taniguchi S, Tanaka F. Ultrafast fluorescence upconversion technique and its applications to proteins. FEBS J 2015; 282:3003-15. [DOI: 10.1111/febs.13180] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Haik Chosrowjan
- Division of Laser Biochemistry; Institute for Laser Technology; Utsubo-Honmachi; Nishiku Osaka Japan
| | - Seiji Taniguchi
- Division of Laser Biochemistry; Institute for Laser Technology; Utsubo-Honmachi; Nishiku Osaka Japan
| | - Fumio Tanaka
- Division of Laser Biochemistry; Institute for Laser Technology; Utsubo-Honmachi; Nishiku Osaka Japan
- Department of Chemistry; Faculty of Science; Chulalongkorn University; Bangkok Thailand
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36
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Affiliation(s)
- Lydia Kisley
- Department of Chemistry and Department of Electrical and Computer
Engineering,
Rice Quantum Institute, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Christy F. Landes
- Department of Chemistry and Department of Electrical and Computer
Engineering,
Rice Quantum Institute, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
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37
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Holt BD, Dahl KN, Islam MF. Differential sub-cellular processing of single-wall carbon nanotubes via interfacial modifications. J Mater Chem B 2015; 3:6274-6284. [DOI: 10.1039/c5tb00705d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Real-space and fluorescence lifetime imaging reveal that non-covalently attached dispersing agents influence sub-cellular trafficking and localization of carbon nanotubes.
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Affiliation(s)
- Brian D. Holt
- Department of Materials Science and Engineering
- Carnegie Mellon University
- Pittsburgh
- USA
| | - Kris Noel Dahl
- Department of Biomedical Engineering
- Carnegie Mellon University
- Pittsburgh
- USA
- Department of Chemical Engineering
| | - Mohammad F. Islam
- Department of Materials Science and Engineering
- Carnegie Mellon University
- Pittsburgh
- USA
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Kavanagh DM, Smyth AM, Martin KJ, Dun A, Brown ER, Gordon S, Smillie KJ, Chamberlain LH, Wilson RS, Yang L, Lu W, Cousin MA, Rickman C, Duncan RR. A molecular toggle after exocytosis sequesters the presynaptic syntaxin1a molecules involved in prior vesicle fusion. Nat Commun 2014; 5:5774. [PMID: 25517944 PMCID: PMC4284649 DOI: 10.1038/ncomms6774] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/06/2014] [Indexed: 01/05/2023] Open
Abstract
Neuronal synapses are among the most scrutinized of cellular systems, serving as a model for all membrane trafficking studies. Despite this, synaptic biology has proven difficult to interrogate directly in situ due to the small size and dynamic nature of central synapses and the molecules within them. Here we determine the spatial and temporal interaction status of presynaptic proteins, imaging large cohorts of single molecules inside active synapses. Measuring rapid interaction dynamics during synaptic depolarization identified the small number of syntaxin1a and munc18-1 protein molecules required to support synaptic vesicle exocytosis. After vesicle fusion and subsequent SNARE complex disassembly, a prompt switch in syntaxin1a and munc18-1-binding mode, regulated by charge alteration on the syntaxin1a N-terminal, sequesters monomeric syntaxin1a from other disassembled fusion complex components, preventing ectopic SNARE complex formation, readying the synapse for subsequent rounds of neurotransmission.
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Affiliation(s)
- Deirdre M. Kavanagh
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, Edinburgh EH14 4AS, UK
- Edinburgh Super-Resolution Imaging Consortium, www.esric.org
| | - Annya M. Smyth
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, Edinburgh EH14 4AS, UK
- Edinburgh Super-Resolution Imaging Consortium, www.esric.org
- Centre for Integrative Physiology, University of Edinburgh, George Square, Edinburgh EH8 9XD, UK
| | - Kirsty J. Martin
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, Edinburgh EH14 4AS, UK
- Edinburgh Super-Resolution Imaging Consortium, www.esric.org
| | - Alison Dun
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, Edinburgh EH14 4AS, UK
- Edinburgh Super-Resolution Imaging Consortium, www.esric.org
| | - Euan R. Brown
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, Edinburgh EH14 4AS, UK
- Edinburgh Super-Resolution Imaging Consortium, www.esric.org
| | - Sarah Gordon
- Centre for Integrative Physiology, University of Edinburgh, George Square, Edinburgh EH8 9XD, UK
| | - Karen J. Smillie
- Centre for Integrative Physiology, University of Edinburgh, George Square, Edinburgh EH8 9XD, UK
| | - Luke H. Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Rhodri S. Wilson
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, Edinburgh EH14 4AS, UK
- Edinburgh Super-Resolution Imaging Consortium, www.esric.org
| | - Lei Yang
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, Edinburgh EH14 4AS, UK
- Edinburgh Super-Resolution Imaging Consortium, www.esric.org
| | - Weiping Lu
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, Edinburgh EH14 4AS, UK
- Edinburgh Super-Resolution Imaging Consortium, www.esric.org
| | - Michael A. Cousin
- Centre for Integrative Physiology, University of Edinburgh, George Square, Edinburgh EH8 9XD, UK
| | - Colin Rickman
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, Edinburgh EH14 4AS, UK
- Edinburgh Super-Resolution Imaging Consortium, www.esric.org
| | - Rory R. Duncan
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot Watt University, Edinburgh EH14 4AS, UK
- Edinburgh Super-Resolution Imaging Consortium, www.esric.org
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39
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Maximum entropy analysis of data simulations and practical aspects of time-resolved fluorescence measurements in the study of molecular interactions. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2013.12.079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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40
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Chan JCK, Diebold ED, Buckley BW, Mao S, Akbari N, Jalali B. Digitally synthesized beat frequency-multiplexed fluorescence lifetime spectroscopy. BIOMEDICAL OPTICS EXPRESS 2014; 5:4428-36. [PMID: 25574449 PMCID: PMC4285616 DOI: 10.1364/boe.5.004428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 09/24/2014] [Accepted: 10/25/2014] [Indexed: 05/02/2023]
Abstract
Frequency domain fluorescence lifetime imaging is a powerful technique that enables the observation of subtle changes in the molecular environment of a fluorescent probe. This technique works by measuring the phase delay between the optical emission and excitation of fluorophores as a function of modulation frequency. However, high-resolution measurements are time consuming, as the excitation modulation frequency must be swept, and faster low-resolution measurements at a single frequency are prone to large errors. Here, we present a low cost optical system for applications in real-time confocal lifetime imaging, which measures the phase vs. frequency spectrum without sweeping. Deemed Lifetime Imaging using Frequency-multiplexed Excitation (LIFE), this technique uses a digitally-synthesized radio frequency comb to drive an acousto-optic deflector, operated in a cat's-eye configuration, to produce a single laser excitation beam modulated at multiple beat frequencies. We demonstrate simultaneous fluorescence lifetime measurements at 10 frequencies over a bandwidth of 48 MHz, enabling high speed frequency domain lifetime analysis of single- and multi-component sample mixtures.
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Affiliation(s)
- Jacky C. K. Chan
- Departments of Electrical Engineering, University of California, Los Angeles, CA 90095,
USA
| | - Eric D. Diebold
- Departments of Electrical Engineering, University of California, Los Angeles, CA 90095,
USA
- Department of Bioengineering, University of California, Los Angeles, CA 90095,
USA
| | - Brandon W. Buckley
- Departments of Electrical Engineering, University of California, Los Angeles, CA 90095,
USA
| | - Sien Mao
- Departments of Electrical Engineering, University of California, Los Angeles, CA 90095,
USA
| | - Najva Akbari
- Departments of Electrical Engineering, University of California, Los Angeles, CA 90095,
USA
| | - Bahram Jalali
- Departments of Electrical Engineering, University of California, Los Angeles, CA 90095,
USA
- Department of Bioengineering, University of California, Los Angeles, CA 90095,
USA
- Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095,
USA
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41
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Raicu V, Singh DR. FRET spectrometry: a new tool for the determination of protein quaternary structure in living cells. Biophys J 2014; 105:1937-45. [PMID: 24209838 DOI: 10.1016/j.bpj.2013.09.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 09/11/2013] [Accepted: 09/12/2013] [Indexed: 11/30/2022] Open
Abstract
Förster resonance energy transfer (FRET) is an exquisitely sensitive method for detection of molecular interactions and conformational changes in living cells. The recent advent of fluorescence imaging technology with single-molecule (or molecular-complex) sensitivity, together with refinements in the kinetic theory of FRET, provide the necessary tool kits for determining the stoichiometry and relative disposition of the protomers within protein complexes (i.e., quaternary structure) of membrane receptors and transporters in living cells. In contrast to standard average-based methods, this method relies on the analysis of distributions of apparent FRET efficiencies, E(app), across the image pixels of individual cells expressing proteins of interest. The most probable quaternary structure of the complex is identified from the number of peaks in the E(app) distribution and their dependence on a single parameter, termed pairwise FRET efficiency. Such peaks collectively create a unique FRET spectrum corresponding to each oligomeric configuration of the protein. Therefore, FRET could quite literally become a spectrometric method--akin to that of mass spectrometry--for sorting protein complexes according to their size and shape.
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Affiliation(s)
- Valerică Raicu
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin; Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin.
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42
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Hiersemenzel K, Brown ER, Duncan RR. Imaging large cohorts of single ion channels and their activity. Front Endocrinol (Lausanne) 2013; 4:114. [PMID: 24027557 PMCID: PMC3762133 DOI: 10.3389/fendo.2013.00114] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/16/2013] [Indexed: 01/16/2023] Open
Abstract
As calcium is the most important signaling molecule in neurons and secretory cells, amongst many other cell types, it follows that an understanding of calcium channels and their regulation of exocytosis is of vital importance. Calcium imaging using calcium dyes such as Fluo3, or FRET-based dyes that have been used widely has provided invaluable information, which combined with modeling has estimated the subtypes of channels responsible for triggering the exocytotic machinery as well as inferences about the relative distances away from vesicle fusion sites these molecules adopt. Importantly, new super-resolution microscopy techniques, combined with novel Ca(2+) indicators and imaginative imaging approaches can now define directly the nano-scale locations of very large cohorts of single channel molecules in relation to single vesicles. With combinations of these techniques the activity of individual channels can be visualized and quantified using novel Ca(2+) indicators. Fluorescently labeled specific channel toxins can also be used to localize endogenous assembled channel tetramers. Fluorescence lifetime imaging microscopy and other single-photon-resolution spectroscopic approaches offer the possibility to quantify protein-protein interactions between populations of channels and the SNARE protein machinery for the first time. Together with simultaneous electrophysiology, this battery of quantitative imaging techniques has the potential to provide unprecedented detail describing the locations, dynamic behaviors, interactions, and conductance activities of many thousands of channel molecules and vesicles in living cells.
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Affiliation(s)
- Katia Hiersemenzel
- Edinburgh Super-Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, UK
| | - Euan R. Brown
- Edinburgh Super-Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, UK
| | - Rory R. Duncan
- Edinburgh Super-Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, UK
- *Correspondence: Rory R. Duncan, Edinburgh Super-Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK e-mail:
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Polyglutamine domain flexibility mediates the proximity between flanking sequences in huntingtin. Proc Natl Acad Sci U S A 2013; 110:14610-5. [PMID: 23898200 DOI: 10.1073/pnas.1301342110] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Huntington disease (HD) is a neurodegenerative disorder caused by a CAG expansion within the huntingtin gene that encodes a polymorphic glutamine tract at the amino terminus of the huntingtin protein. HD is one of nine polyglutamine expansion diseases. The clinical threshold of polyglutamine expansion for HD is near 37 repeats, but the mechanism of this pathogenic length is poorly understood. Using Förster resonance energy transfer, we describe an intramolecular proximity between the N17 domain and the downstream polyproline region that flanks the polyglutamine tract of huntingtin. Our data support the hypothesis that the polyglutamine tract can act as a flexible domain, allowing the flanking domains to come into close spatial proximity. This flexibility is impaired with expanded polyglutamine tracts, and we can detect changes in huntingtin conformation at the pathogenic threshold for HD. Altering the structure of N17, either via phosphomimicry or with small molecules, also affects the proximity between the flanking domains. The structural capacity of N17 to fold back toward distal regions within huntingtin requires an interacting protein, protein kinase C and casein kinase 2 substrate in neurons 1 (PACSIN1). This protein has the ability to bind both N17 and the polyproline region, stabilizing the interaction between these two domains. We also developed an antibody-based FRET assay that can detect conformational changes within endogenous huntingtin in wild-type versus HD fibroblasts. Therefore, we hypothesize that wild-type length polyglutamine tracts within huntingtin can form a flexible domain that is essential for proper functional intramolecular proximity, conformations, and dynamics.
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Bharde AA, Palankar R, Fritsch C, Klaver A, Kanger JS, Jovin TM, Arndt-Jovin DJ. Magnetic nanoparticles as mediators of ligand-free activation of EGFR signaling. PLoS One 2013; 8:e68879. [PMID: 23894364 PMCID: PMC3720882 DOI: 10.1371/journal.pone.0068879] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 06/03/2013] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Magnetic nanoparticles (NPs) are of particular interest in biomedical research, and have been exploited for molecular separation, gene/drug delivery, magnetic resonance imaging, and hyperthermic cancer therapy. In the case of cultured cells, magnetic manipulation of NPs provides the means for studying processes induced by mechanotransduction or by local clustering of targeted macromolecules, e.g. cell surface receptors. The latter are normally activated by binding of their natural ligands mediating key signaling pathways such as those associated with the epidermal growth factor (EGFR). However, it has been reported that EGFR may be dimerized and activated even in the absence of ligands. The present study assessed whether receptor clustering induced by physical means alone suffices for activating EGFR in quiescent cells. METHODOLOGY/PRINCIPAL FINDINGS The EGFR on A431 cells was specifically targeted by superparamagnetic iron oxide NPs (SPIONs) carrying either a ligand-blocking monoclonal anti-EGFR antibody or a streptavidin molecule for targeting a chimeric EGFR incorporating a biotinylated amino-terminal acyl carrier peptide moiety. Application of a magnetic field led to SPION magnetization and clustering, resulting in activation of the EGFR, a process manifested by auto and transphosphorylation and downstream signaling. The magnetically-induced early signaling events were similar to those inherent to the ligand dependent EGFR pathways. Magnetization studies indicated that the NPs exerted magnetic dipolar forces in the sub-piconewton range with clustering dependent on Brownian motion of the receptor-SPION complex and magnetic field strength. CONCLUSIONS/SIGNIFICANCE We demonstrate that EGFR on the cell surface that have their ligand binding-pocket blocked by an antibody are still capable of transphosphorylation and initiation of signaling cascades if they are clustered by SPIONs either attached locally or targeted to another site of the receptor ectodomain. The results suggest that activation of growth factor receptors may be triggered by ligand-independent molecular crowding resulting from overexpression and/or sequestration in membrane microdomains.
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Affiliation(s)
- Atul A. Bharde
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Raghavendra Palankar
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Cornelia Fritsch
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Arjen Klaver
- Nanobiophysics, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Johannes S. Kanger
- Nanobiophysics, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Thomas M. Jovin
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Donna J. Arndt-Jovin
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail:
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Ziomkiewicz I, Loman A, Klement R, Fritsch C, Klymchenko AS, Bunt G, Jovin TM, Arndt-Jovin DJ. Dynamic conformational transitions of the EGF receptor in living mammalian cells determined by FRET and fluorescence lifetime imaging microscopy. Cytometry A 2013; 83:794-805. [DOI: 10.1002/cyto.a.22311] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Iwona Ziomkiewicz
- Laboratory of Cellular Dynamics; Max Planck Institute for Biophysical Chemistry; 37077; Göttingen; Germany
| | - Anastasia Loman
- Department of Neuro- and Sensory Physiology; University Medicine Göttingen; 37075; Göttingen; Germany
| | | | - Cornelia Fritsch
- Laboratory of Cellular Dynamics; Max Planck Institute for Biophysical Chemistry; 37077; Göttingen; Germany
| | - Andrey S. Klymchenko
- Laboratoire de Biophotonique et Pharmacologie; UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg; 67401; France
| | | | - Thomas M. Jovin
- Laboratory of Cellular Dynamics; Max Planck Institute for Biophysical Chemistry; 37077; Göttingen; Germany
| | - Donna J. Arndt-Jovin
- Laboratory of Cellular Dynamics; Max Planck Institute for Biophysical Chemistry; 37077; Göttingen; Germany
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Adair BD, Xiong JP, Alonso JL, Hyman BT, Arnaout MA. EM structure of the ectodomain of integrin CD11b/CD18 and localization of its ligand-binding site relative to the plasma membrane. PLoS One 2013; 8:e57951. [PMID: 23469114 PMCID: PMC3585415 DOI: 10.1371/journal.pone.0057951] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 01/27/2013] [Indexed: 11/19/2022] Open
Abstract
One-half of the integrin α-subunit Propeller domains contain and extra vWFA domain (αA domain), which mediates integrin binding to extracellular physiologic ligands via its metal-ion-dependent adhesion site (MIDAS). We used electron microscopy to determine the 3D structure of the αA-containing ectodomain of the leukocyte integrin CD11b/CD18 (αMβ2) in its inactive state. A well defined density for αA was observed within a bent ectodomain conformation, while the structure of the ectodomain in complex with the Fab fragment of mAb107, which binds at the MIDAS face of CD11b and stabilizes the inactive state, further revealed that αA is restricted to a relatively small range of orientations relative to the Propeller domain. Using Fab 107 as probe in fluorescent lifetime imaging microscopy (FLIM) revealed that αA is positioned relatively far from the membrane surface in the inactive state, and a systematic orientation search revealed that the MIDAS face would be accessible to extracellular ligand in the inactive state of the full-length cellular integrin. These studies are the first to define the 3D EM structure of an αA-containing integrin ectodomain and to position the ligand-binding face of αA domain in relation to the plasma membrane, providing new insights into current models of integrin activation.
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Affiliation(s)
- Brian D. Adair
- Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Jian-Ping Xiong
- Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - José Luis Alonso
- Leukocyte Biology and Inflammation Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Bradley T. Hyman
- Division of Nephrology, and Institute for Neurodegenerative Disease, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - M. Amin Arnaout
- Structural Biology Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
- Leukocyte Biology and Inflammation Program, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
- * E-mail:
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Abstract
BACKGROUND One of the major hurdles in studying diabetes pathophysiology is the lack of adequate methodology that allows for direct and real-time determination of glucose transport and metabolism in cells and tissues. In this article, we present a new methodology that adopts frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM) to visualize and quantify the dynamics of intracellular glucose within living cells using a biosensor protein based on fluorescence resonance energy transfer (FRET). METHOD The biosensor protein was developed by fusing a FRET pair, an AcGFP1 donor and a mCherry acceptor to N- and C- termini of a mutant glucose-binding protein (GBP), respectively. The probe was expressed and biosynthesized inside the cells, offering continuous monitoring of glucose dynamics in real time through fluorescence lifetime imaging microscopy (FLIM) measurement. RESULTS We transfected the deoxyribonucleic acid of the AcGFP1-GBP-mCherry sensor into murine myoblast cells, C2C12, and continuously monitored the changes in intracellular glucose concentrations in response to the variation in extracellular glucose, from which we determined glucose uptake and clearance rates. The distribution of intracellular glucose concentration was also characterized. We detected a high glucose concentration in a region close to the cell membrane and a low glucose concentration in a region close to the nucleus. The monoexponential decay of AcGFP1 was distinguished using FD-FLIM. CONCLUSIONS This work enables continuous glucose monitoring (CGM) within living cells using FD-FLIM and a biosensor protein. The sensor protein developed offers a new means for quantitatively analyzing glucose homeostasis at the cellular level. Data accumulated from these studies will help increase our understanding of the pathology of diabetes.
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Affiliation(s)
| | - Sha Jin
- Department of Biomedical Engineering, College of Engineering, University of Arkansas, Fayetteville, Arkansas
| | - Kaiming Ye
- Department of Biomedical Engineering, College of Engineering, University of Arkansas, Fayetteville, Arkansas
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Saeger J, Hytönen VP, Klotzsch E, Vogel V. GFP's mechanical intermediate states. PLoS One 2012; 7:e46962. [PMID: 23118864 PMCID: PMC3485268 DOI: 10.1371/journal.pone.0046962] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 09/07/2012] [Indexed: 11/19/2022] Open
Abstract
Green fluorescent protein (GFP) mutants have become the most widely used fluorescence markers in the life sciences, and although they are becoming increasingly popular as mechanical force or strain probes, there is little direct information on how their fluorescence changes when mechanically stretched. Here we derive high-resolution structural models of the mechanical intermediate states of stretched GFP using steered molecular dynamics (SMD) simulations. These structures were used to produce mutants of EGFP and EYFP that mimic GFP's different mechanical intermediates. A spectroscopic analysis revealed that a population of EGFP molecules with a missing N-terminal α-helix was significantly dimmed, while the fluorescence lifetime characteristic of the anionic chromophore state remained unaffected. This suggests a mechanism how N-terminal deletions can switch the protonation state of the chromophore, and how the fluorescence of GFP molecules in response to mechanical disturbance might be turned off.
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Affiliation(s)
- John Saeger
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Vesa P. Hytönen
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- Institute of Biomedical Technology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Enrico Klotzsch
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Viola Vogel
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- * E-mail:
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Using FLIM-FRET to measure conformational changes of transglutaminase type 2 in live cells. PLoS One 2012; 7:e44159. [PMID: 22952912 PMCID: PMC3432096 DOI: 10.1371/journal.pone.0044159] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/30/2012] [Indexed: 12/24/2022] Open
Abstract
Transglutaminase type 2 (TG2) is a ubiquitously expressed member of the transglutaminase family, capable of mediating a transamidation reaction between a variety of protein substrates. TG2 also has a unique role as a G-protein with GTPase activity. In response to GDP/GTP binding and increases in intracellular calcium levels, TG2 can undergo a large conformational change that reciprocally modulates the enzymatic activities of TG2. We have generated a TG2 biosensor that allows for quantitative assessment of TG2 conformational changes in live cells using Förster resonance energy transfer (FRET), as measured by fluorescence lifetime imaging microscopy (FLIM). Quantifying FRET efficiency with this biosensor provides a robust assay to quickly measure the effects of cell stress, changes in calcium levels, point mutations and chemical inhibitors on the conformation and localization of TG2 in living cells. The TG2 FRET biosensor was validated using established TG2 conformational point mutants, as well as cell stress events known to elevate intracellular calcium levels. We demonstrate in live cells that inhibitors of TG2 transamidation activity can differentially influence the conformation of the enzyme. The irreversible inhibitor of TG2, NC9, forces the enzyme into an open conformation, whereas the reversible inhibitor CP4d traps TG2 in the closed conformation. Thus, this biosensor provides new mechanistic insights into the action of two TG2 inhibitors and defines two new classes based on ability to alter TG2 conformation in addition to inhibiting transamidation activity. Future applications of this biosensor could be to discover small molecules that specifically alter TG2 conformation to affect GDP/GTP or calcium binding.
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