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Pramanik SK, Sreedharan S, Tiwari R, Dutta S, Kandoth N, Barman S, Aderinto SO, Chattopadhyay S, Das A, Thomas JA. Nanoparticles for super-resolution microscopy: intracellular delivery and molecular targeting. Chem Soc Rev 2022; 51:9882-9916. [PMID: 36420611 DOI: 10.1039/d1cs00605c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Following an overview of the approaches and techniques used to acheive super-resolution microscopy, this review presents the advantages supplied by nanoparticle based probes for these applications. The various clases of nanoparticles that have been developed toward these goals are then critically described and these discussions are illustrated with a variety of examples from the recent literature.
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Affiliation(s)
- Sumit Kumar Pramanik
- CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat 364002, India.
| | - Sreejesh Sreedharan
- Human Science Research Centre, University of Derby, Kedleston road, DE22 1GB, UK
| | - Rajeshwari Tiwari
- CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat 364002, India.
| | - Sourav Dutta
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, West Bengal, India.
| | - Noufal Kandoth
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, West Bengal, India.
| | - Surajit Barman
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, West Bengal, India.
| | - Stephen O Aderinto
- Department of Chemistry, University of Sheffield, Western Bank, Sheffield, S3 7HF, UK.
| | - Samit Chattopadhyay
- Department of Biological Sciences, BITS-Pilani, K K Birla Goa Campus, NH 17B, Zuarinagar, Goa 403726, India.
| | - Amitava Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, West Bengal, India.
| | - Jim A Thomas
- Department of Chemistry, University of Sheffield, Western Bank, Sheffield, S3 7HF, UK.
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2
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Computerized fluorescence microscopy of microbial cells. World J Microbiol Biotechnol 2021; 37:189. [PMID: 34617135 DOI: 10.1007/s11274-021-03159-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
The upgrading of fluorescence microscopy by the introduction of computer technologies has led to the creation of a new methodology, computerized fluorescence microscopy (CFM). CFM improves subjective visualization and combines it with objective quantitative analysis of the microscopic data. CFM has opened up two fundamentally new opportunities for studying microorganisms. The first is the quantitative measurement of the fluorescence parameters of the targeted fluorophores in association with certain structures of individual cells. The second is the expansion of the boundaries of visualization/resolution of intracellular components beyond the "diffraction limit" of light microscopy into the nanometer range. This enables to obtain unique information about the localization and dynamics of intracellular processes at the molecular level. The purpose of this review is to demonstrate the potential of CFM in the study of fundamental aspects of the structural and functional organization of microbial cells. The basics of computer processing and analysis of digital images are briefly described. The fluorescent molecules used in CFM with an emphasis on fluorescent proteins are characterized. The main methods of super-resolution microscopy (nanoscopy) are presented. The capabilities of various CFM methods for exploring microbial cells at the subcellular level are illustrated by the examples of various studies on yeast and bacteria.
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3
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Che Y, Siprashvili Z, Kovalski JR, Jiang T, Wozniak G, Elcavage L, Khavari PA. KRAS regulation by small non-coding RNAs and SNARE proteins. Nat Commun 2019; 10:5118. [PMID: 31712554 PMCID: PMC6848142 DOI: 10.1038/s41467-019-13106-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 10/13/2019] [Indexed: 12/30/2022] Open
Abstract
KRAS receives and relays signals at the plasma membrane (PM) where it transmits extracellular growth factor signals to downstream effectors. SNORD50A/B were recently found to bind KRAS and inhibit its tumorigenic action by unknown mechanisms. KRAS proximity protein labeling was therefore undertaken in SNORD50A/B wild-type and knockout cells, revealing that SNORD50A/B RNAs shape the composition of proteins proximal to KRAS, notably by inhibiting KRAS proximity to the SNARE vesicular transport proteins SNAP23, SNAP29, and VAMP3. To remain enriched on the PM, KRAS undergoes cycles of endocytosis, solubilization, and vesicular transport to the PM. Here we report that SNAREs are essential for the final step of this process, with KRAS localization to the PM facilitated by SNAREs but antagonized by SNORD50A/B. Antagonism between SNORD50A/B RNAs and specific SNARE proteins thus controls KRAS localization, signaling, and tumorigenesis, and disrupting SNARE-enabled KRAS function represents a potential therapeutic opportunity in KRAS-driven cancer.
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Affiliation(s)
- Yonglu Che
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, 94305, USA
| | - Zurab Siprashvili
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, 94305, USA
| | - Joanna R Kovalski
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, 94305, USA
| | - Tiffany Jiang
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
| | - Glenn Wozniak
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
| | - Lara Elcavage
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, 94305, USA.
- Program in Cancer Biology, Stanford University, Stanford, CA, 94305, USA.
- VA Palo Alto Healthcare System, Palo Alto, CA, 94304, USA.
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4
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Zhu X, Zhang J, Liu J, Zhang Y. Recent Progress of Rare-Earth Doped Upconversion Nanoparticles: Synthesis, Optimization, and Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1901358. [PMID: 31763145 PMCID: PMC6865011 DOI: 10.1002/advs.201901358] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/18/2019] [Indexed: 05/09/2023]
Abstract
Upconversion is a nonlinear optical phenomenon that involves the emission of high-energy photons by sequential absorption of two or more low-energy excitation photons. Due to their excellent physiochemical properties such as deep penetration depth, little damage to samples, and high chemical stability, upconversion nanoparticles (UCNPs) are extensively applied in bioimaging, biosensing, theranostic, and photochemical reactions. Here, recent achievements in the synthesis, optimization, and applications of UCNP-based nanomaterials are reviewed. The state-of-the-art approaches to synthesize UCNPs in the past few years are introduced first, followed by a summary of several strategies to optimize upconversion emissive properties and various applications of UCNPs. Lastly, the challenges and future perspectives of UCNPs are provided as a conclusion.
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Affiliation(s)
- Xiaohui Zhu
- School of Environmental and Chemical EngineeringShanghai University99 Shangda Road, Baoshan DistrictShanghai200444China
| | - Jing Zhang
- School of Environmental and Chemical EngineeringShanghai University99 Shangda Road, Baoshan DistrictShanghai200444China
| | - Jinliang Liu
- School of Environmental and Chemical EngineeringShanghai University99 Shangda Road, Baoshan DistrictShanghai200444China
| | - Yong Zhang
- School of Environmental and Chemical EngineeringShanghai University99 Shangda Road, Baoshan DistrictShanghai200444China
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeBlock E4 #04‐08, 4 Engineering Drive 3Singapore117583Singapore
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Krmpot AJ, Nikolić SN, Oasa S, Papadopoulos DK, Vitali M, Oura M, Mikuni S, Thyberg P, Tisa S, Kinjo M, Nilsson L, Terenius L, Rigler R, Vukojević V. Functional Fluorescence Microscopy Imaging: Quantitative Scanning-Free Confocal Fluorescence Microscopy for the Characterization of Fast Dynamic Processes in Live Cells. Anal Chem 2019; 91:11129-11137. [PMID: 31364842 DOI: 10.1021/acs.analchem.9b01813] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Functional fluorescence microscopy imaging (fFMI), a time-resolved (21 μs/frame) confocal fluorescence microscopy imaging technique without scanning, is developed for quantitative characterization of fast reaction-transport processes in solution and in live cells. The method is based on massively parallel fluorescence correlation spectroscopy (FCS). Simultaneous excitation of fluorescent molecules in multiple spots in the focal plane is achieved using a diffractive optical element (DOE). Fluorescence from the DOE-generated 1024 illuminated spots is detected in a confocal arrangement by a matching matrix detector comprising 32 × 32 single-photon avalanche photodiodes (SPADs). Software for data acquisition and fast auto- and cross-correlation analysis by parallel signal processing using a graphic processing unit (GPU) allows temporal autocorrelation across all pixels in the image frame in 4 s and cross-correlation between first- and second-order neighbor pixels in 45 s. We present here this quantitative, time-resolved imaging method with single-molecule sensitivity and demonstrate its usefulness for mapping in live cell location-specific differences in the concentration and translational diffusion of molecules in different subcellular compartments. In particular, we show that molecules without a specific biological function, e.g., the enhanced green fluorescent protein (eGFP), exhibit uniform diffusion. In contrast, molecules that perform specialized biological functions and bind specifically to their molecular targets show location-specific differences in their concentration and diffusion, exemplified here for two transcription factor molecules, the glucocorticoid receptor (GR) before and after nuclear translocation and the Sex combs reduced (Scr) transcription factor in the salivary gland of Drosophila ex vivo.
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Affiliation(s)
- Aleksandar J Krmpot
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden.,Institute of Physics Belgrade , University of Belgrade , Belgrade 11080 , Serbia
| | - Stanko N Nikolić
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden.,Institute of Physics Belgrade , University of Belgrade , Belgrade 11080 , Serbia
| | - Sho Oasa
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden
| | | | | | - Makoto Oura
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science , Hokkaido University , Sapporo , Hokkaido 001-0021 , Japan
| | - Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science , Hokkaido University , Sapporo , Hokkaido 001-0021 , Japan
| | - Per Thyberg
- Department of Applied Physics , AlbaNova University Center, Royal Institute of Technology , Stockholm 10691 , Sweden
| | - Simone Tisa
- Micro Photon Devices (MPD) , Bolzano 39100 , Italy
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science , Hokkaido University , Sapporo , Hokkaido 001-0021 , Japan
| | - Lennart Nilsson
- Department of Biosciences and Nutrition , Karolinska Institutet , Huddinge 14183 , Sweden
| | - Lars Terenius
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden
| | - Rudolf Rigler
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden.,Department of Medical Biochemistry and Biophysics (MBB) , Karolinska Institutet , Stockholm 17177 , Sweden
| | - Vladana Vukojević
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden
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Ultrastructure and dynamics of the actin-myosin II cytoskeleton during mitochondrial fission. Nat Cell Biol 2019; 21:603-613. [PMID: 30988424 PMCID: PMC6499663 DOI: 10.1038/s41556-019-0313-6] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/14/2019] [Indexed: 02/05/2023]
Abstract
Mitochondrial fission involves the preconstriction of an organelle followed by scission by dynamin-related protein Drp1. Preconstriction is facilitated by actin and non-muscle myosin II through a mechanism that remains unclear, largely due to the unknown cytoskeletal ultrastructure at mitochondrial constrictions. Here, using platinum replica electron microscopy, we show that mitochondria in cells are embedded in an interstitial cytoskeletal network that contains abundant unbranched actin filaments. Both spontaneous and induced mitochondrial constrictions typically associate with a criss-cross array of long actin filaments that comprise part of this interstitial network. Non-muscle myosin II is found adjacent to mitochondria but is not specifically enriched at the constriction sites. During ionomycin-induced mitochondrial fission, F-actin clouds colocalize with mitochondrial constriction sites, whereas dynamic myosin II clouds are present in the vicinity of constrictions. We propose that myosin II promotes mitochondrial constriction by inducing stochastic deformations of the interstitial actin network, which applies pressure on the mitochondrial surface and thus initiates curvature-sensing mechanisms that complete mitochondrial constriction.
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7
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Novak D, Mojovic M, Pavicevic A, Zatloukalova M, Hernychova L, Bartosik M, Vacek J. Electrochemistry and electron paramagnetic resonance spectroscopy of cytochrome c and its heme-disrupted analogs. Bioelectrochemistry 2018; 119:136-141. [DOI: 10.1016/j.bioelechem.2017.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 11/30/2022]
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8
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Abstract
Superresolution microscopy has become increasingly widespread over the past 5 years and allows users to image biological processes below the diffraction limit of traditional fluorescence microscopy where resolution is restricted to approximately 250 nm. Superresolution refers to a wide range of techniques which employ different approaches to circumvent the diffraction limit. Two of these approaches, structured illumination microscopy (SIM) and single-molecule localization microscopy (SMLM), which provide a doubling and tenfold increase in resolution respectively, are dominating the field. This is partly because of the insights into biology they offer and partly because of their commercialization by the main microscope manufacturers. This chapter provides background to the two techniques, practical considerations for their use, and protocols for their application to platelet biology.
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Klementieva NV, Bozhanova NG, Zagaynova EV, Lukyanov KA, Mishin AS. Fluorophores for single-molecule localization microscopy. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017030074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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10
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Cristino L, Imperatore R, Di Marzo V. Techniques for the Cellular and Subcellular Localization of Endocannabinoid Receptors and Enzymes in the Mammalian Brain. Methods Enzymol 2017; 593:61-98. [DOI: 10.1016/bs.mie.2017.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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11
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Leahy M, Thompson K, Zafar H, Alexandrov S, Foley M, O'Flatharta C, Dockery P. Functional imaging for regenerative medicine. Stem Cell Res Ther 2016; 7:57. [PMID: 27095443 PMCID: PMC4837501 DOI: 10.1186/s13287-016-0315-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In vivo imaging is a platform technology with the power to put function in its natural structural context. With the drive to translate stem cell therapies into pre-clinical and clinical trials, early selection of the right imaging techniques is paramount to success. There are many instances in regenerative medicine where the biological, biochemical, and biomechanical mechanisms behind the proposed function of stem cell therapies can be elucidated by appropriate imaging. Imaging techniques can be divided according to whether labels are used and as to whether the imaging can be done in vivo. In vivo human imaging places additional restrictions on the imaging tools that can be used. Microscopies and nanoscopies, especially those requiring fluorescent markers, have made an extraordinary impact on discovery at the molecular and cellular level, but due to their very limited ability to focus in the scattering tissues encountered for in vivo applications they are largely confined to superficial imaging applications in research laboratories. Nanoscopy, which has tremendous benefits in resolution, is limited to the near-field (e.g. near-field scanning optical microscope (NSNOM)) or to very high light intensity (e.g. stimulated emission depletion (STED)) or to slow stochastic events (photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM)). In all cases, nanoscopy is limited to very superficial applications. Imaging depth may be increased using multiphoton or coherence gating tricks. Scattering dominates the limitation on imaging depth in most tissues and this can be mitigated by the application of optical clearing techniques that can impose mild (e.g. topical application of glycerol) or severe (e.g. CLARITY) changes to the tissue to be imaged. Progression of therapies through to clinical trials requires some thought as to the imaging and sensing modalities that should be used. Smoother progression is facilitated by the use of comparable imaging modalities throughout the discovery and trial phases, giving label-free techniques an advantage wherever they can be used, although this is seldom considered in the early stages. In this paper, we will explore the techniques that have found success in aiding discovery in stem cell therapies and try to predict the likely technologies best suited to translation and future directions.
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Affiliation(s)
- Martin Leahy
- Tissue Optics & Microcirculation Imaging Group, School of Physics, National University of Ireland (NUI), Galway, Ireland. .,Chair of Applied Physics, National University of Ireland (NUI), Galway, Ireland.
| | - Kerry Thompson
- Centre for Microscopy and Imaging, Anatomy, School of Medicine, National University of Ireland (NUI), Galway, Ireland
| | - Haroon Zafar
- Tissue Optics & Microcirculation Imaging Group, School of Physics, National University of Ireland (NUI), Galway, Ireland
| | - Sergey Alexandrov
- Tissue Optics & Microcirculation Imaging Group, School of Physics, National University of Ireland (NUI), Galway, Ireland
| | - Mark Foley
- Medical Physics Research Cluster, School of Physics, National University of Ireland (NUI), Galway, Ireland
| | - Cathal O'Flatharta
- Regenerative Medicine Institute (REMEDI), National University of Ireland (NUI), Galway, Ireland
| | - Peter Dockery
- Centre for Microscopy and Imaging, Anatomy, School of Medicine, National University of Ireland (NUI), Galway, Ireland
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Abstract
PURPOSE OF REVIEW Throughout history, development of novel microscopy techniques has been of fundamental importance to advance the vascular biology field.This review offers a concise summary of the most recently developed imaging techniques and discusses how they can be applied to vascular biology. In addition, we reflect upon the most important fluorescent reporters for vascular research that are currently available. RECENT FINDINGS Recent advances in light sheet-based imaging techniques now offer the ability to live image the vascular system in whole organs or even in whole animals during development and in pathological conditions with a satisfactory spatial and temporal resolution. Conversely, super resolution microscopy now allows studying cellular processes at a near-molecular resolution. SUMMARY Major recent improvements in a number of imaging techniques now allow study of vascular biology in ways that could not be considered previously. Researchers now have well-developed tools to specifically examine the dynamic nature of vascular development during angiogenic sprouting, remodeling and regression as well as the vascular responses in disease situations in vivo. In addition, open questions in endothelial and lymphatic cell biology that require subcellular resolution such as actin dynamics, junctional complex formation and stability, vascular permeability and receptor trafficking can now be approached with high resolution.
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Affiliation(s)
- Bàrbara Laviña
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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13
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Abstract
Single-molecule localization microscopy (SMLM) is rapidly gaining popularity in the life sciences as an efficient approach to visualize molecular distribution with nanoscale precision. However, it has been challenging to obtain and analyze such data within a cellular context in tissue preparations. Here we describe a 5-d tissue processing and immunostaining procedure that is optimized for SMLM, and we provide example applications to fixed mouse brain, heart and kidney tissues. We then describe how to perform correlated confocal and 3D-superresolution imaging on these sections, which allows the visualization of nanoscale protein localization within labeled subcellular compartments of identified target cells in a few minutes. Finally, we describe the use of VividSTORM (http://katonalab.hu/index.php/vividstorm), an open-source software for correlated confocal and SMLM image analysis, which facilitates the measurement of molecular abundance, clustering, internalization, surface density and intermolecular distances in a cell-specific and subcellular compartment-restricted manner. The protocol requires only basic skills in tissue staining and microscopy.
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Griffié J, Boelen L, Burn G, Cope AP, Owen DM. Topographic prominence as a method for cluster identification in single-molecule localisation data. JOURNAL OF BIOPHOTONICS 2015; 8:925-934. [PMID: 25663080 DOI: 10.1002/jbio.201400127] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/03/2014] [Accepted: 12/19/2014] [Indexed: 06/04/2023]
Abstract
Single-molecule localisation based super-resolution fluorescence imaging produces maps of the coordinates of fluorescent molecules in a region of interest. Cluster analysis algorithms provide information concerning the clustering characteristics of these molecules, often through the generation of cluster heat maps based on local molecular density. The goal of this study was to generate a new cluster analysis method based on a topographic approach. In particular, a topographic map of the level of clustering across a region is generated based on Getis' variant of Ripley's K-function. By using the relative heights (topographic prominence, TP) of the peaks in the map, cluster characteristics can be identified more accurately than by using previously demonstrated height thresholds. Analogous to geological TP, the concepts of wet and dry TP and topographic isolation are introduced to generate binary maps. The algorithm is validated using simulated and experimental data and found to significantly outperform previous cluster identification methods. Illustration of the topographic prominence based cluster analysis algorithm.
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Affiliation(s)
- Juliette Griffié
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, United Kingdom
| | - Lies Boelen
- Section of Immunology, Division of Infectious Diseases, Faculty of Medicine, Imperial College London, Praed Street, St Mary's Campus, London, United Kingdom
| | - Garth Burn
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, United Kingdom
| | - Andrew P Cope
- Academic Department of Rheumatology, Division of Immunology, Infection and Inflammatory Disease, Faculty of Life Sciences and Medicine, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, United Kingdom
| | - Dylan M Owen
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, United Kingdom.
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15
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Wang C, Fukazawa A, Taki M, Sato Y, Higashiyama T, Yamaguchi S. A Phosphole Oxide Based Fluorescent Dye with Exceptional Resistance to Photobleaching: A Practical Tool for Continuous Imaging in STED Microscopy. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507939] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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16
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Wang C, Fukazawa A, Taki M, Sato Y, Higashiyama T, Yamaguchi S. A Phosphole Oxide Based Fluorescent Dye with Exceptional Resistance to Photobleaching: A Practical Tool for Continuous Imaging in STED Microscopy. Angew Chem Int Ed Engl 2015; 54:15213-7. [PMID: 26493944 DOI: 10.1002/anie.201507939] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 12/26/2022]
Abstract
The development of stimulated emission depletion (STED) microscopy represented a major breakthrough in cellular and molecular biology. However, the intense laser beams required for both excitation and STED usually provoke rapid photobleaching of fluorescent molecular probes, which significantly limits the performance and practical utility of STED microscopy. We herein developed a photoresistant fluorescent dye C-Naphox as a practical tool for STED imaging. With excitation using either a λ=405 or 488 nm laser in protic solvents, C-Naphox exhibited an intense red/orange fluorescence (quantum yield ΦF >0.7) with a large Stokes shift (circa 5900 cm(-1) ). Even after irradiation with a Xe lamp (300 W, λex =460 nm, full width at half maximum (FWHM)=11 nm) for 12 hours, 99.5 % of C-Naphox remained intact. The high photoresistance of C-Naphox allowed repeated STED imaging of HeLa cells. Even after recording 50 STED images, 83 % of the initial fluorescence intensity persisted.
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Affiliation(s)
- Chenguang Wang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan)
| | - Aiko Fukazawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan).
| | - Masayasu Taki
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan).
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan)
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan). .,Division of Biological Science, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan).
| | - Shigehiro Yamaguchi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan). .,Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602 (Japan).
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Nikolova LS, Metzstein MM. Intracellular lumen formation in Drosophila proceeds via a novel subcellular compartment. Development 2015; 142:3964-73. [PMID: 26428009 DOI: 10.1242/dev.127902] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/17/2015] [Indexed: 12/28/2022]
Abstract
Cellular tubes have diverse morphologies, including multicellular, unicellular and subcellular architectures. Subcellular tubes are found prominently within the vertebrate vasculature, the insect breathing system and the nematode excretory apparatus, but how such tubes form is poorly understood. To characterize the cellular mechanisms of subcellular tube formation, we have refined methods of high pressure freezing/freeze substitution to prepare Drosophila larvae for transmission electron microscopic (TEM) analysis. Using our methods, we have found that subcellular tube formation may proceed through a previously undescribed multimembrane intermediate composed of vesicles bound within a novel subcellular compartment. We have also developed correlative light/TEM procedures to identify labeled cells in TEM-fixed larval samples. Using this technique, we have found that Vacuolar ATPase (V-ATPase) and the V-ATPase regulator Rabconnectin-3 are required for subcellular tube formation, probably in a step resolving the intermediate compartment into a mature lumen. In general, our ultrastructural analysis methods could be useful for a wide range of cellular investigations in Drosophila larvae.
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Affiliation(s)
- Linda S Nikolova
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Mark M Metzstein
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
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18
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Kyrychenko A. Using fluorescence for studies of biological membranes: a review. Methods Appl Fluoresc 2015; 3:042003. [DOI: 10.1088/2050-6120/3/4/042003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Standard fluorescent proteins as dual-modality probes for correlative experiments in an integrated light and electron microscope. J Chem Biol 2015. [DOI: 10.1007/s12154-015-0143-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Moreau M, Cochard P. [Nobel Prize in Chemistry 2014 - from microscopy to nanoscopy: a revolution in resolution]. Med Sci (Paris) 2014; 30:1169-76. [PMID: 25537048 DOI: 10.1051/medsci/20143012021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marc Moreau
- Centre de Biologie du Développement,UMR 5547 CNRS-Université Paul Sabatier (Toulouse 3), 118, route de Narbonne, 31062 Toulouse Cedex 4, France
| | - Philippe Cochard
- Centre de Biologie du Développement,UMR 5547 CNRS-Université Paul Sabatier (Toulouse 3), 118, route de Narbonne, 31062 Toulouse Cedex 4, France
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Cui Y, Irudayaraj J. Inside single cells: quantitative analysis with advanced optics and nanomaterials. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:387-407. [PMID: 25430077 DOI: 10.1002/wnan.1321] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/17/2014] [Accepted: 10/29/2014] [Indexed: 01/08/2023]
Abstract
Single-cell explorations offer a unique window to inspect molecules and events relevant to mechanisms and heterogeneity constituting the central dogma of biology. A large number of nucleic acids, proteins, metabolites, and small molecules are involved in determining and fine-tuning the state and function of a single cell at a given time point. Advanced optical platforms and nanotools provide tremendous opportunities to probe intracellular components with single-molecule accuracy, as well as promising tools to adjust single-cell activity. To obtain quantitative information (e.g., molecular quantity, kinetics, and stoichiometry) within an intact cell, achieving the observation with comparable spatiotemporal resolution is a challenge. For single-cell studies, both the method of detection and the biocompatibility are critical factors as they determine the feasibility, especially when considering live-cell analysis. Although a considerable proportion of single-cell methodologies depend on specialized expertise and expensive instruments, it is our expectation that the information content and implication will outweigh the costs given the impact on life science enabled by single-cell analysis.
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Affiliation(s)
- Yi Cui
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA
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Abstract
Dissecting the subcellular distribution of a fatty-acylated protein is key to the understanding of the molecular mechanisms regulating protein movement and function in a cell. This protocol describes how to perform single-cell imaging of palmitoylation in a fatty-acylated protein of interest with high sensitivity using click chemistry, proximity ligation and fluorescence microscopy. The initial steps in this protocol involve optimization of conditions for (i) metabolic incorporation of an alkynyl analog of palmitic acid into cellular proteins coupled with click chemistry and (ii) detecting a specific protein of interest with primary antibodies using automated fluorescence microscopy, followed by (iii) imaging palmitoylation of the target fatty-acylated protein of interest, such as Wnt, Sonic Hedgehog or H-Ras. Furthermore, we outline strategies for imaging specific fatty-acylated proteins with subcellular organelles and/or total proteome palmitoylation, and we discuss special considerations that need to be given depending on the experimental design. The use of clickable fatty acids with proximity ligation may have promising applications to the investigation of fatty acylation cell biology. The entire protocol takes ∼3 weeks to complete.
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Abstract
In this review, we introduce the principles of spatial resolution improvement in super-resolution microscopies that were recently developed. These super-resolution techniques utilize the interaction of light and fluorescent probes in order to break the diffraction barrier that limits spatial resolution. The imaging property of each super-resolution technique is also compared with the corresponding conventional one. Typical applications of the super-resolution techniques in biological research are also introduced.
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Affiliation(s)
- Masahito Yamanaka
- Department of Applied Physics Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Nicholas I Smith
- Department of Applied Physics Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Katsumasa Fujita
- Department of Applied Physics Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
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Ellinger D, Voigt CA. The use of nanoscale fluorescence microscopic to decipher cell wall modifications during fungal penetration. FRONTIERS IN PLANT SCIENCE 2014; 5:270. [PMID: 24995012 PMCID: PMC4061529 DOI: 10.3389/fpls.2014.00270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 05/25/2014] [Indexed: 05/08/2023]
Abstract
Plant diseases are one of the most studied subjects in the field of plant science due to their impact on crop yield and food security. Our increased understanding of plant-pathogen interactions was mainly driven by the development of new techniques that facilitated analyses on a subcellular and molecular level. The development of labeling technologies, which allowed the visualization and localization of cellular structures and proteins in live cell imaging, promoted the use of fluorescence and laser-scanning microscopy in the field of plant-pathogen interactions. Recent advances in new microscopic technologies opened their application in plant science and in the investigation of plant diseases. In this regard, in planta Förster/Fluorescence resonance energy transfer has demonstrated to facilitate the measurement of protein-protein interactions within the living tissue, supporting the analysis of regulatory pathways involved in plant immunity and putative host-pathogen interactions on a nanoscale level. Localization microscopy, an emerging, non-invasive microscopic technology, will allow investigations with a nanoscale resolution leading to new possibilities in the understanding of molecular processes.
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Affiliation(s)
| | - Christian A. Voigt
- *Correspondence: Christian A. Voigt, Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany e-mail:
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Correlative Light Microscopy and Electron Tomography to Study Von Willebrand Factor Exocytosis from Vascular Endothelial Cells. Methods Cell Biol 2014; 124:71-92. [DOI: 10.1016/b978-0-12-801075-4.00004-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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