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Lai JZ, Lin CY, Chen SJ, Cheng YM, Abe M, Lin TC, Chien FC. Temporal-Focusing Multiphoton Excitation Single-Molecule Localization Microscopy Using Spontaneously Blinking Fluorophores. Angew Chem Int Ed Engl 2024; 63:e202404942. [PMID: 38641901 DOI: 10.1002/anie.202404942] [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: 03/12/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Single-molecule localization microscopy (SMLM) based on temporal-focusing multiphoton excitation (TFMPE) and single-wavelength excitation is used to visualize the three-dimensional (3D) distribution of spontaneously blinking fluorophore-labeled subcellular structures in a thick specimen with a nanoscale-level spatial resolution. To eliminate the photobleaching effect of unlocalized molecules in out-of-focus regions for improving the utilization rate of the photon budget in 3D SMLM imaging, SMLM with single-wavelength TFMPE achieves wide-field and axially confined two-photon excitation (TPE) of spontaneously blinking fluorophores. TPE spectral measurement of blinking fluorophores is then conducted through TFMPE imaging at a tunable excitation wavelength, yielding the optimal TPE wavelength for increasing the number of detected photons from a single blinking event during SMLM. Subsequently, the TPE fluorescence of blinking fluorophores is recorded to obtain a two-dimensional TFMPE-SMLM image of the microtubules in cancer cells with a localization precision of 18±6 nm and an overall imaging resolution of approximately 51 nm, which is estimated based on the contribution of Nyquist resolution and localization precision. Combined with astigmatic imaging, the system is capable of 3D TFMPE-SMLM imaging of brain tissue section of a 5XFAD transgenic mouse with the pathological features of Alzheimer's disease, revealing the distribution of neurotoxic amyloid-beta peptide deposits.
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Affiliation(s)
- Jian-Zong Lai
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Chun-Yu Lin
- College of Photonics, National Yang Ming Chiao Tung University, No.301, Sec.2, Gaofa 3rd Rd., Guiren Dist., Tainan City, 71150, Taiwan
| | - Shean-Jen Chen
- College of Photonics, National Yang Ming Chiao Tung University, No.301, Sec.2, Gaofa 3rd Rd., Guiren Dist., Tainan City, 71150, Taiwan
| | - Yu-Min Cheng
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Manabu Abe
- Department of Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8526, Japan
| | - Tzu-Chau Lin
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Fan-Ching Chien
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
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2
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Petersen EN, Pavel MA, Hansen SS, Gudheti M, Wang H, Yuan Z, Murphy KR, Ja W, Ferris HA, Jorgensen E, Hansen SB. Mechanical activation of TWIK-related potassium channel by nanoscopic movement and rapid second messenger signaling. eLife 2024; 12:RP89465. [PMID: 38407149 PMCID: PMC10942622 DOI: 10.7554/elife.89465] [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] [Indexed: 02/27/2024] Open
Abstract
Rapid conversion of force into a biological signal enables living cells to respond to mechanical forces in their environment. The force is believed to initially affect the plasma membrane and then alter the behavior of membrane proteins. Phospholipase D2 (PLD2) is a mechanosensitive enzyme that is regulated by a structured membrane-lipid site comprised of cholesterol and saturated ganglioside (GM1). Here we show stretch activation of TWIK-related K+ channel (TREK-1) is mechanically evoked by PLD2 and spatial patterning involving ordered GM1 and 4,5-bisphosphate (PIP2) clusters in mammalian cells. First, mechanical force deforms the ordered lipids, which disrupts the interaction of PLD2 with the GM1 lipids and allows a complex of TREK-1 and PLD2 to associate with PIP2 clusters. The association with PIP2 activates the enzyme, which produces the second messenger phosphatidic acid (PA) that gates the channel. Co-expression of catalytically inactive PLD2 inhibits TREK-1 stretch currents in a biological membrane. Cellular uptake of cholesterol inhibits TREK-1 currents in culture and depletion of cholesterol from astrocytes releases TREK-1 from GM1 lipids in mouse brain. Depletion of the PLD2 ortholog in flies results in hypersensitivity to mechanical force. We conclude PLD2 mechanosensitivity combines with TREK-1 ion permeability to elicit a mechanically evoked response.
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Affiliation(s)
- E Nicholas Petersen
- Departments of Molecular Medicine, The Scripps Research Institute, ScrippsJupiterUnited States
- Scripps Research Skaggs Graduate School of Chemical and Biological Science, The Scripps Research Institute, Scripps,JupiterUnited States
| | - Mahmud Arif Pavel
- Departments of Molecular Medicine, The Scripps Research Institute, ScrippsJupiterUnited States
| | - Samuel S Hansen
- Departments of Molecular Medicine, The Scripps Research Institute, ScrippsJupiterUnited States
| | - Manasa Gudheti
- Division of Endocrinology and Metabolism, Center for Brain Immunology and Glia, Department of Neuroscience, University of VirginiaCharlottesvilleUnited States
| | - Hao Wang
- Departments of Molecular Medicine, The Scripps Research Institute, ScrippsJupiterUnited States
- Scripps Research Skaggs Graduate School of Chemical and Biological Science, The Scripps Research Institute, Scripps,JupiterUnited States
| | - Zixuan Yuan
- Departments of Molecular Medicine, The Scripps Research Institute, ScrippsJupiterUnited States
- Scripps Research Skaggs Graduate School of Chemical and Biological Science, The Scripps Research Institute, Scripps,JupiterUnited States
| | - Keith R Murphy
- Department of Neuroscience, The Scripps Research Institute, ScrippsJupiterUnited States
- Center on Aging,The Scripps Research Institute, ScrippsJupiterUnited States
| | - William Ja
- Department of Neuroscience, The Scripps Research Institute, ScrippsJupiterUnited States
- Center on Aging,The Scripps Research Institute, ScrippsJupiterUnited States
| | - Heather A Ferris
- Division of Endocrinology and Metabolism, Center for Brain Immunology and Glia, Department of Neuroscience, University of VirginiaCharlottesvilleUnited States
| | - Erik Jorgensen
- Department of Biology, Howard Hughes Medical Institute, University of UtahSalt Lake CityUnited States
| | - Scott B Hansen
- Departments of Molecular Medicine, The Scripps Research Institute, ScrippsJupiterUnited States
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3
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Zhai F, Hao L, Chen X, Jiang T, Guo Q, Xie L, Ma Y, Du X, Zheng Z, Chen K, Fan J. Single-molecule tracking of PprI in D. radiodurans without interference of autoblinking. Front Microbiol 2023; 14:1256711. [PMID: 38029090 PMCID: PMC10652783 DOI: 10.3389/fmicb.2023.1256711] [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: 07/11/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Autoblinking is a widespread phenomenon and exhibits high level of intensity in some bacteria. In Deinococcus radiodurans (D. radiodurans), strong autoblinking was found to be indistinguishable from PAmCherry and greatly prevented single-molecule tracking of proteins of interest. Here we employed the bright photoswitchable fluorescent protein mMaple3 to label PprI, one essential DNA repair factor, and characterized systematically the fluorescence intensity and bleaching kinetics of both autoblinking and PprI-mMaple3 molecules within cells grown under three different conditions. Under minimal media, we can largely separate autoblinking from mMaple3 molecules and perform reliably single-molecule tracking of PprI in D. radiodurans, by means of applying signal-to-noise ratio and constraining the minimal length for linking the trajectories. We observed three states of PprI molecules, which bear different subcellular localizations and distinct functionalities. Our strategy provides a useful means to study the dynamics and distributions of proteins of interest in bacterial cells with high level of autoblinking.
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Affiliation(s)
- Fanfan Zhai
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, Sichuan, China
| | - Li Hao
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xiaomin Chen
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ting Jiang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Qianhong Guo
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Liping Xie
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ying Ma
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, Sichuan, China
| | - Xiaobo Du
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, Sichuan, China
| | - Zhiqin Zheng
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- NHC Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang, Sichuan, China
- School of Biological Engineering and Wuliangye Liquor, Sichuan University of Science and Engineering, Yibin, Sichuan, China
| | - Kun Chen
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou, Zhejiang, China
| | - Jun Fan
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou, Zhejiang, China
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4
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Wimmenauer C, Heinzel T. Identification of nanoparticles as vesicular cargo via Airy scanning fluorescence microscopy and spatial statistics. NANOSCALE ADVANCES 2023; 5:3512-3520. [PMID: 37383069 PMCID: PMC10295176 DOI: 10.1039/d3na00188a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/08/2023] [Indexed: 06/30/2023]
Abstract
Many biomedical applications of nanoparticles on the cellular level require a characterisation of their subcellular distribution. Depending on the nanoparticle and its preferred intracellular compartment, this may be a nontrivial task, and consequently, the available methodologies are constantly increasing. Here, we show that super-resolution microscopy in combination with spatial statistics (SMSS), comprising the pair correlation and the nearest neighbour function, is a powerful tool to identify spatial correlations between nanoparticles and moving vesicles. Furthermore, various types of motion like for example diffusive, active or Lévy flight transport can be distinguished within this concept via suitable statistical functions, which also contain information about the factors limiting the motion, as well as regarding characteristic length scales. The SMSS concept fills a methodological gap related to mobile intracellular nanoparticle hosts and its extension to further scenarios is straightforward. It is exemplified on MCF-7 cells after exposure to carbon nanodots, demonstrating that these particles are stored predominantly in the lysosomes.
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Affiliation(s)
- Christian Wimmenauer
- Institute of Experimental Condensed Matter Physics, Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Germany
| | - Thomas Heinzel
- Institute of Experimental Condensed Matter Physics, Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Germany
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5
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Zhang Y, Wang G, Huang P, Sun E, Kweon J, Li Q, Zhe J, Ying LL, Zhang HF. Minimizing Molecular Misidentification in Imaging Low-Abundance Protein Interactions Using Spectroscopic Single-Molecule Localization Microscopy. Anal Chem 2022; 94:13834-13841. [PMID: 36165784 PMCID: PMC9859736 DOI: 10.1021/acs.analchem.2c02417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Super-resolution microscopy can capture spatiotemporal organizations of protein interactions with resolution down to 10 nm; however, the analyses of more than two proteins involving low-abundance protein are challenging because spectral crosstalk and heterogeneities of individual fluorescent labels result in molecular misidentification. Here we developed a deep learning-based imaging analysis method for spectroscopic single-molecule localization microscopy to minimize molecular misidentification in three-color super-resolution imaging. We characterized the 3-fold reduction of molecular misidentification in the new imaging method using pure samples of different photoswitchable fluorophores and visualized three distinct subcellular proteins in U2-OS cell lines. We further validated the protein counts and interactions of TOMM20, DRP1, and SUMO1 in a well-studied biological process, Staurosporine-induced apoptosis, by comparing the imaging results with Western-blot analyses of different subcellular portions.
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Affiliation(s)
- Yang Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
| | - Gaoxiang Wang
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
- Department of Hematology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan Hubei, 430030, China
| | - Peizhou Huang
- Department of Biomedical Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Edison Sun
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
| | - Junghun Kweon
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
| | - Qianru Li
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
- Department of Pharmacology, Northwestern University, Chicago IL, 60611, USA
| | - Ji Zhe
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
- Department of Pharmacology, Northwestern University, Chicago IL, 60611, USA
| | - Leslie L. Ying
- Department of Biomedical Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
- Department of Electrical Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Hao F. Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
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6
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Ejdrup AL, Lycas MD, Lorenzen N, Konomi A, Herborg F, Madsen KL, Gether U. A density-based enrichment measure for assessing colocalization in single-molecule localization microscopy data. Nat Commun 2022; 13:4388. [PMID: 35902578 PMCID: PMC9334352 DOI: 10.1038/s41467-022-32064-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/15/2022] [Indexed: 11/20/2022] Open
Abstract
Dual-color single-molecule localization microscopy (SMLM) provides unprecedented possibilities for detailed studies of colocalization of different molecular species in a cell. However, the informational richness of the data is not fully exploited by current analysis tools that often reduce colocalization to a single value. Here, we describe a tool specifically designed for determination of co-localization in both 2D and 3D from SMLM data. The approach uses a function that describes the relative enrichment of one molecular species on the density distribution of a reference species. The function reframes the question of colocalization by providing a density-context relevant to multiple biological questions. Moreover, the function visualize enrichment (i.e. colocalization) directly in the images for easy interpretation. We demonstrate the approach’s functionality on both simulated data and cultured neurons, and compare it to current alternative measures. The method is available in a Python function for easy and parameter-free implementation. Full information gained from single-molecule localisation microscopy (SMLM) isn't exploited by current analysis tools. Here the authors report relative enrichment which uses a density-based colocalisation measure for both 2D and 3D SMLM data; they apply it to both simulated data and cultured neurons.
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Affiliation(s)
- Aske L Ejdrup
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Matthew D Lycas
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Lorenzen
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ainoa Konomi
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Freja Herborg
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth L Madsen
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulrik Gether
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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7
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Liu X, Guy CS, Boada-Romero E, Green DR, Flanagan ME, Cheng C, Zhang H. Unbiased and robust analysis of co-localization in super-resolution images. Stat Methods Med Res 2022; 31:1484-1499. [PMID: 35450486 PMCID: PMC9648350 DOI: 10.1177/09622802221094133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Spatial data from high-resolution images abound in many scientific disciplines. For example, single-molecule localization microscopy, such as stochastic optical reconstruction microscopy, provides super-resolution images to help scientists investigate co-localization of proteins and hence their interactions inside cells, which are key events in living cells. However, there are few accurate methods for analyzing co-localization in super-resolution images. The current methods and software are prone to produce false-positive errors and are restricted to only 2-dimensional images. In this paper, we develop a novel statistical method to effectively address the problems of unbiased and robust quantification and comparison of protein co-localization for multiple 2- and 3-dimensional image datasets. This method significantly improves the analysis of protein co-localization using super-resolution image data, as shown by its excellent performance in simulation studies and an analysis of co-localization of protein light chain 3 and lysosomal-associated membrane protein 1 in cell autophagy. Moreover, this method is directly applicable to co-localization analyses in other disciplines, such as diagnostic imaging, epidemiology, environmental science, and ecology.
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Affiliation(s)
- Xueyan Liu
- Department of Mathematics, 5784University of New Orleans, New Orleans, LA, USA
| | - Clifford S Guy
- Department of Immunology, 5417St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Emilio Boada-Romero
- Department of Immunology, 5417St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Douglas R Green
- Department of Immunology, 5417St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Margaret E Flanagan
- Department of Pathology, 12244Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hui Zhang
- Division of Biostatistics, Department of Preventive Medicine, 12244Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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8
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Lee WTC, Gupta D, Rothenberg E. Single-molecule imaging of replication fork conflicts at genomic DNA G4 structures in human cells. Methods Enzymol 2021; 661:77-94. [PMID: 34776224 DOI: 10.1016/bs.mie.2021.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA G-quadruplexes (G4s) are stable, non-canonical DNA secondary structures formed within guanine(G)-rich sequences. While extensively studied in vitro, evidence of the occurrence of G4s in vivo has only recently emerged. The formation of G4 structures may pose an obstacle for diverse DNA transactions including replication, which is linked to mutagenesis and genomic instability. A fundamental question in the field has been whether and how the formation of G4s is coupled to the progression of replication forks. This process has remained undefined largely due to the lack of experimental approaches capable of monitoring the presence of G4s and their association with the replication machinery in cells. Here, we describe a detailed multicolor single-molecule localization microscopy (SMLM) protocol for detecting nanoscale spatial-association of DNA G4s with the cellular replisome complex. This method offers a unique platform for visualizing the mechanisms of G4 formation at the molecular level, as well as addressing key biological questions as to the functional roles of these structures in the maintenance of genome integrity.
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Affiliation(s)
- Wei Ting C Lee
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States.
| | - Dipika Gupta
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States.
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States.
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9
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Swinkels M, Atiq F, Bürgisser PE, Slotman JA, Houtsmuller AB, de Heus C, Klumperman J, Leebeek FWG, Voorberg J, Jansen AJG, Bierings R. Quantitative 3D microscopy highlights altered von Willebrand factor α-granule storage in patients with von Willebrand disease with distinct pathogenic mechanisms. Res Pract Thromb Haemost 2021; 5:e12595. [PMID: 34532631 PMCID: PMC8440947 DOI: 10.1002/rth2.12595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Platelets play a key role in hemostasis through plug formation and secretion of their granule contents at sites of endothelial injury. Defects in von Willebrand factor (VWF), a platelet α-granule protein, are implicated in von Willebrand disease (VWD), and may lead to defective platelet adhesion and/or aggregation. Studying VWF quantity and subcellular localization may help us better understand the pathophysiology of VWD. OBJECTIVE Quantitative analysis of the platelet α-granule compartment and VWF storage in healthy individuals and VWD patients. PATIENTS/METHODS Structured illumination microscopy (SIM) was used to study VWF content and organization in platelets of healthy individuals and patients with VWD in combination with established techniques. RESULTS SIM capably quantified clear morphological and granular changes in platelets stimulated with proteinase-activated receptor 1 (PAR-1) activating peptide and revealed a large intra- and interdonor variability in VWF-positive object numbers within healthy resting platelets, similar to variation in secreted protein acidic and rich in cysteine (SPARC). We subsequently characterized VWD platelets to identify changes in the α-granule compartment of patients with different VWF defects, and were able to stratify two patients with type 3 VWD rising from different pathological mechanisms. We further analyzed VWF storage in α-granules of a patient with homozygous p.C1190R using electron microscopy and found discrepant VWF levels and different degrees of multimerization in platelets of patients with heterozygous p.C1190 in comparison to VWF in plasma. CONCLUSIONS Our findings highlight the utility of quantitative imaging approaches in assessing platelet granule content, which may help to better understand VWF storage in α-granules and to gain new insights in the etiology of VWD.
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Affiliation(s)
- Maurice Swinkels
- Department of HematologyErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Ferdows Atiq
- Department of HematologyErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Petra E. Bürgisser
- Department of HematologyErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Johan A. Slotman
- Department of PathologyOptical Imaging CenterErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Adriaan B. Houtsmuller
- Department of PathologyOptical Imaging CenterErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Cilia de Heus
- Department of Cell BiologyUniversity Medical CenterUtrechtThe Netherlands
| | - Judith Klumperman
- Department of Cell BiologyUniversity Medical CenterUtrechtThe Netherlands
| | - Frank W. G. Leebeek
- Department of HematologyErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Jan Voorberg
- Molecular and Cellular HemostasisSanquin Research and Landsteiner LaboratoryAmsterdam University Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
- Experimental Vascular MedicineAmsterdam University Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Arend Jan Gerard Jansen
- Department of HematologyErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
| | - Ruben Bierings
- Department of HematologyErasmus MCUniversity Medical Center RotterdamRotterdamThe Netherlands
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10
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Bohrer CH, Yang X, Thakur S, Weng X, Tenner B, McQuillen R, Ross B, Wooten M, Chen X, Zhang J, Roberts E, Lakadamyali M, Xiao J. A pairwise distance distribution correction (DDC) algorithm to eliminate blinking-caused artifacts in SMLM. Nat Methods 2021; 18:669-677. [PMID: 34059826 PMCID: PMC9040192 DOI: 10.1038/s41592-021-01154-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 04/12/2021] [Indexed: 02/04/2023]
Abstract
Single-molecule localization microscopy (SMLM) relies on the blinking behavior of a fluorophore, which is the stochastic switching between fluorescent and dark states. Blinking creates multiple localizations belonging to the same fluorophore, confounding quantitative analyses and interpretations. Here we present a method, termed distance distribution correction (DDC), to eliminate blinking-caused repeat localizations without any additional calibrations. The approach relies on obtaining the true pairwise distance distribution of different fluorophores naturally from the imaging sequence by using distances between localizations separated by a time much longer than the average fluorescence survival time. We show that, using the true pairwise distribution, we can define and maximize the likelihood, obtaining a set of localizations void of blinking artifacts. DDC results in drastic improvements in obtaining the closest estimate of the true spatial organization and number of fluorescent emitters in a wide range of applications, enabling accurate reconstruction and quantification of SMLM images.
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Affiliation(s)
- Christopher H. Bohrer
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Shreyasi Thakur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaoli Weng
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Brian Tenner
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Ryan McQuillen
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Brian Ross
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Matthew Wooten
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xin Chen
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Elijah Roberts
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Melike Lakadamyali
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
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11
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Marin Z, Graff M, Barentine AES, Soeller C, Chung KKH, Fuentes LA, Baddeley D. PYMEVisualize: an open-source tool for exploring 3D super-resolution data. Nat Methods 2021; 18:582-584. [PMID: 34002092 DOI: 10.1038/s41592-021-01165-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Zach Marin
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Michael Graff
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew E S Barentine
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Christian Soeller
- Living Systems Institute and Biomedical Physics, University of Exeter, Exeter, UK
| | - Kenny Kwok Hin Chung
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Lukas A Fuentes
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - David Baddeley
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand. .,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
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12
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Bohrer CH, Yang X, Thakur S, Weng X, Tenner B, McQuillen R, Ross B, Wooten M, Chen X, Zhang J, Roberts E, Lakadamyali M, Xiao J. A pairwise distance distribution correction (DDC) algorithm to eliminate blinking-caused artifacts in SMLM. Nat Methods 2021. [PMID: 34059826 DOI: 10.1101/768051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Single-molecule localization microscopy (SMLM) relies on the blinking behavior of a fluorophore, which is the stochastic switching between fluorescent and dark states. Blinking creates multiple localizations belonging to the same fluorophore, confounding quantitative analyses and interpretations. Here we present a method, termed distance distribution correction (DDC), to eliminate blinking-caused repeat localizations without any additional calibrations. The approach relies on obtaining the true pairwise distance distribution of different fluorophores naturally from the imaging sequence by using distances between localizations separated by a time much longer than the average fluorescence survival time. We show that, using the true pairwise distribution, we can define and maximize the likelihood, obtaining a set of localizations void of blinking artifacts. DDC results in drastic improvements in obtaining the closest estimate of the true spatial organization and number of fluorescent emitters in a wide range of applications, enabling accurate reconstruction and quantification of SMLM images.
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Affiliation(s)
- Christopher H Bohrer
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Shreyasi Thakur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaoli Weng
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Brian Tenner
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Ryan McQuillen
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Brian Ross
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Matthew Wooten
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xin Chen
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Elijah Roberts
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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13
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Tameling C, Stoldt S, Stephan T, Naas J, Jakobs S, Munk A. Colocalization for super-resolution microscopy via optimal transport. NATURE COMPUTATIONAL SCIENCE 2021; 1:199-211. [PMID: 35874932 PMCID: PMC7613136 DOI: 10.1038/s43588-021-00050-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Super-resolution fluorescence microscopy is a widely used technique in cell biology. Stimulated emission depletion (STED) microscopy enables the recording of multiple-color images with subdiffraction resolution. The enhanced resolution leads to new challenges regarding colocalization analysis of macromolecule distributions. We demonstrate that well-established methods for the analysis of colocalization in diffraction-limited datasets and for coordinate-stochastic nanoscopy are not equally well suited for the analysis of high-resolution STED images. We propose optimal transport colocalization, which measures the minimal transporting cost below a given spatial scale to match two protein intensity distributions. Its validity on simulated data as well as on dual-color STED recordings of yeast and mammalian cells is demonstrated. We also extend the optimal transport colocalization methodology to coordinate-stochastic nanoscopy.
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Affiliation(s)
- Carla Tameling
- Institute for Mathematical Stochastics, University of Göttingen, Göttingen, Germany
| | - Stefan Stoldt
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Till Stephan
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Julia Naas
- Institute for Mathematical Stochastics, University of Göttingen, Göttingen, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Axel Munk
- Institute for Mathematical Stochastics, University of Göttingen, Göttingen, Germany
- Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen, Göttingen, Germany
- Max Planck Fellow Group Statistical Inverse Problems in Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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14
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Pálinkás HL, Békési A, Róna G, Pongor L, Papp G, Tihanyi G, Holub E, Póti Á, Gemma C, Ali S, Morten MJ, Rothenberg E, Pagano M, Szűts D, Győrffy B, Vértessy BG. Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments. eLife 2020; 9:e60498. [PMID: 32956035 PMCID: PMC7505663 DOI: 10.7554/elife.60498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/23/2020] [Indexed: 12/17/2022] Open
Abstract
Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug treatments in human cancer cell line models derived from HCT116. We developed a straightforward U-DNA sequencing method (U-DNA-Seq) that was combined with in situ super-resolution imaging. Using a novel robust analysis pipeline, we found broad regions with elevated probability of uracil occurrence both in treated and non-treated cells. Correlation with chromatin markers and other genomic features shows that non-treated cells possess uracil in the late replicating constitutive heterochromatic regions, while drug treatment induced a shift of incorporated uracil towards segments that are normally more active/functional. Data were corroborated by colocalization studies via dSTORM microscopy. This approach can be applied to study the dynamic spatio-temporal nature of genomic uracil.
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Affiliation(s)
- Hajnalka L Pálinkás
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
- Doctoral School of Multidisciplinary Medical Science, University of SzegedSzegedHungary
| | - Angéla Békési
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Gergely Róna
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Howard Hughes Medical Institute, New York University School of MedicineNew YorkUnited States
| | - Lőrinc Pongor
- Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis UniversityBudapestHungary
| | - Gábor Papp
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Gergely Tihanyi
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Eszter Holub
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Ádám Póti
- Genome Stability Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Carolina Gemma
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital CampusLondonUnited Kingdom
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital CampusLondonUnited Kingdom
| | - Michael J Morten
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Howard Hughes Medical Institute, New York University School of MedicineNew YorkUnited States
| | - Dávid Szűts
- Genome Stability Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Balázs Győrffy
- Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis UniversityBudapestHungary
| | - Beáta G Vértessy
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
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15
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Wu YL, Tschanz A, Krupnik L, Ries J. Quantitative Data Analysis in Single-Molecule Localization Microscopy. Trends Cell Biol 2020; 30:837-851. [PMID: 32830013 DOI: 10.1016/j.tcb.2020.07.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022]
Abstract
Super-resolution microscopy, and specifically single-molecule localization microscopy (SMLM), is becoming a transformative technology for cell biology, as it allows the study of cellular structures with nanometer resolution. Here, we review a wide range of data analyses approaches for SMLM that extract quantitative information about the distribution, size, shape, spatial organization, and stoichiometry of macromolecular complexes to guide biological interpretation. We present a case study using the nuclear pore complex as an example that highlights the power of combining complementary approaches by identifying its symmetry, ringlike structure, and protein copy number. In face of recent technical and computational advances, this review serves as a guideline for selecting appropriate analysis tools and controls to exploit the potential of SMLM for a wide range of biological questions.
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Affiliation(s)
- Yu-Le Wu
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Aline Tschanz
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Leonard Krupnik
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany; Faculty of Chemistry and Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Jonas Ries
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany.
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16
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Abstract
The FtsZ protein is a highly conserved bacterial tubulin homolog. In vivo, the functional form of FtsZ is the polymeric, ring-like structure (Z-ring) assembled at the future division site during cell division. While it is clear that the Z-ring plays an essential role in orchestrating cytokinesis, precisely what its functions are and how these functions are achieved remain elusive. In this article, we review what we have learned during the past decade about the Z-ring's structure, function, and dynamics, with a particular focus on insights generated by recent high-resolution imaging and single-molecule analyses. We suggest that the major function of the Z-ring is to govern nascent cell pole morphogenesis by directing the spatiotemporal distribution of septal cell wall remodeling enzymes through the Z-ring's GTP hydrolysis-dependent treadmilling dynamics. In this role, FtsZ functions in cell division as the counterpart of the cell shape-determining actin homolog MreB in cell elongation.
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Affiliation(s)
- Ryan McQuillen
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; ,
| | - Jie Xiao
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; ,
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17
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Hériché JK, Alexander S, Ellenberg J. Integrating Imaging and Omics: Computational Methods and Challenges. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-080917-013328] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescence microscopy imaging has long been complementary to DNA sequencing- and mass spectrometry–based omics in biomedical research, but these approaches are now converging. On the one hand, omics methods are moving from in vitro methods that average across large cell populations to in situ molecular characterization tools with single-cell sensitivity. On the other hand, fluorescence microscopy imaging has moved from a morphological description of tissues and cells to quantitative molecular profiling with single-molecule resolution. Recent technological developments underpinned by computational methods have started to blur the lines between imaging and omics and have made their direct correlation and seamless integration an exciting possibility. As this trend continues rapidly, it will allow us to create comprehensive molecular profiles of living systems with spatial and temporal context and subcellular resolution. Key to achieving this ambitious goal will be novel computational methods and successfully dealing with the challenges of data integration and sharing as well as cloud-enabled big data analysis.
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Affiliation(s)
- Jean-Karim Hériché
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Stephanie Alexander
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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18
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Taraska JW. A primer on resolving the nanoscale structure of the plasma membrane with light and electron microscopy. J Gen Physiol 2019; 151:974-985. [PMID: 31253697 PMCID: PMC6683668 DOI: 10.1085/jgp.201812227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Taraska reviews the imaging methods that are being used to understand the structure of the plasma membrane at the molecular level. The plasma membrane separates a cell from its external environment. All materials and signals that enter or leave the cell must cross this hydrophobic barrier. Understanding the architecture and dynamics of the plasma membrane has been a central focus of general cellular physiology. Both light and electron microscopy have been fundamental in this endeavor and have been used to reveal the dense, complex, and dynamic nanoscale landscape of the plasma membrane. Here, I review classic and recent developments in the methods used to image and study the structure of the plasma membrane, particularly light, electron, and correlative microscopies. I will discuss their history and use for mapping the plasma membrane and focus on how these tools have provided a structural framework for understanding the membrane at the scale of molecules. Finally, I will describe how these studies provide a roadmap for determining the nanoscale architecture of other organelles and entire cells in order to bridge the gap between cellular form and function.
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Affiliation(s)
- Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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19
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A tessellation-based colocalization analysis approach for single-molecule localization microscopy. Nat Commun 2019; 10:2379. [PMID: 31147535 PMCID: PMC6542817 DOI: 10.1038/s41467-019-10007-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 04/12/2019] [Indexed: 11/24/2022] Open
Abstract
Multicolor single-molecule localization microscopy (λSMLM) is a powerful technique to reveal the relative nanoscale organization and potential colocalization between different molecular species. While several standard analysis methods exist for pixel-based images, λSMLM still lacks such a standard. Moreover, existing methods only work on 2D data and are usually sensitive to the relative molecular organization, a very important parameter to consider in quantitative SMLM. Here, we present an efficient, parameter-free colocalization analysis method for 2D and 3D λSMLM using tessellation analysis. We demonstrate that our method allows for the efficient computation of several popular colocalization estimators directly from molecular coordinates and illustrate its capability to analyze multicolor SMLM data in a robust and efficient manner. Multicolour single-molecule localization microscopy lacks a standard analysis method. Here Levet et al. introduce Coloc-Tesseler, a parameter-free colocalisation analysis method based on tessellation analysis for the efficient analysis of multicolour SMLM data.
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20
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Liu H, Ye Z, Wang X, Wei L, Xiao L. Molecular and living cell dynamic assays with optical microscopy imaging techniques. Analyst 2019; 144:859-871. [PMID: 30444498 DOI: 10.1039/c8an01420e] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Generally, the message elucidated by the conventional analytical methods overlooks the heterogeneity of single objects, where the behavior of individual molecules is shielded. With the advent of optical microscopy imaging techniques, it is possible to identify, visualize and track individual molecules or nanoparticles under a biological environment with high temporal and spatial resolution. In this work, we summarize the commonly adopted optical microscopy techniques for bio-analytical assays in living cells, including total internal reflection fluorescence microscopy (TIRFM), super-resolution optical microscopy (SRM), and dark-field optical microscopy (DFM). The basic principles of these methods and some recent interesting applications in molecular detection and single-particle tracking are introduced. Moreover, the development in high-dimensional optical microscopy to achieve three-dimensional (3-D) as well as sub-diffraction localization and tracking of biomolecules is also highlighted.
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Affiliation(s)
- Hua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China.
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21
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Jimenez A, Friedl K, Leterrier C. About samples, giving examples: Optimized Single Molecule Localization Microscopy. Methods 2019; 174:100-114. [PMID: 31078795 DOI: 10.1016/j.ymeth.2019.05.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/28/2022] Open
Abstract
Super-resolution microscopy has profoundly transformed how we study the architecture of cells, revealing unknown structures and refining our view of cellular assemblies. Among the various techniques, the resolution of Single Molecule Localization Microscopy (SMLM) can reach the size of macromolecular complexes and offer key insights on their nanoscale arrangement in situ. SMLM is thus a demanding technique and taking advantage of its full potential requires specifically optimized procedures. Here we describe how we perform the successive steps of an SMLM workflow, focusing on single-color Stochastic Optical Reconstruction Microscopy (STORM) as well as multicolor DNA Points Accumulation for imaging in Nanoscale Topography (DNA-PAINT) of fixed samples. We provide detailed procedures for careful sample fixation and immunostaining of typical cellular structures: cytoskeleton, clathrin-coated pits, and organelles. We then offer guidelines for optimal imaging and processing of SMLM data in order to optimize reconstruction quality and avoid the generation of artifacts. We hope that the tips and tricks we discovered over the years and detail here will be useful for researchers looking to make the best possible SMLM images, a pre-requisite for meaningful biological discovery.
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Affiliation(s)
- Angélique Jimenez
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | - Karoline Friedl
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France; Abbelight, Paris, France
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22
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Feiner-Gracia N, Olea RA, Fitzner R, El Boujnouni N, van Asbeck AH, Brock R, Albertazzi L. Super-resolution Imaging of Structure, Molecular Composition, and Stability of Single Oligonucleotide Polyplexes. NANO LETTERS 2019; 19:2784-2792. [PMID: 31001985 PMCID: PMC6509642 DOI: 10.1021/acs.nanolett.8b04407] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 04/11/2019] [Indexed: 05/20/2023]
Abstract
The successful application of gene therapy relies on the development of safe and efficient delivery vectors. Cationic polymers such as cell-penetrating peptides (CPPs) can condense genetic material into nanoscale particles, called polyplexes, and induce cellular uptake. With respect to this point, several aspects of the nanoscale structure of polyplexes have remained elusive because of the difficulty in visualizing the molecular arrangement of the two components with nanometer resolution. This limitation has hampered the rational design of polyplexes based on direct structural information. Here, we used super-resolution imaging to study the structure and molecular composition of individual CPP-mRNA polyplexes with nanometer accuracy. We use two-color direct stochastic optical reconstruction microscopy (dSTORM) to unveil the impact of peptide stoichiometry on polyplex structure and composition and to assess their destabilization in blood serum. Our method provides information about the size and composition of individual polyplexes, allowing the study of such properties on a single polyplex basis. Furthermore, the differences in stoichiometry readily explain the differences in cellular uptake behavior. Thus, quantitative dSTORM of polyplexes is complementary to the currently used characterization techniques for understanding the determinants of polyplex activity in vitro and inside cells.
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Affiliation(s)
- Natalia Feiner-Gracia
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering of Catalonia
(IBEC), The Barcelona Institute of Science
and Technology (BIST), Carrer Baldiri
Reixac 15-21, 08024 Barcelona, Spain
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - R. Alis Olea
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering of Catalonia
(IBEC), The Barcelona Institute of Science
and Technology (BIST), Carrer Baldiri
Reixac 15-21, 08024 Barcelona, Spain
- Department
of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert Fitzner
- Department
of Mathematics and Computer Science, Eindhoven
University of Technology, Post Office
Box 513, 5600 MD Eindhoven, The Netherlands
| | - Najoua El Boujnouni
- Department
of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander H. van Asbeck
- Department
of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Roland Brock
- Department
of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lorenzo Albertazzi
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering of Catalonia
(IBEC), The Barcelona Institute of Science
and Technology (BIST), Carrer Baldiri
Reixac 15-21, 08024 Barcelona, Spain
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
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23
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Wasim L, Buhari FHM, Yoganathan M, Sicard T, Ereño-Orbea J, Julien JP, Treanor B. N-Linked Glycosylation Regulates CD22 Organization and Function. Front Immunol 2019; 10:699. [PMID: 31019513 PMCID: PMC6458307 DOI: 10.3389/fimmu.2019.00699] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 03/14/2019] [Indexed: 11/29/2022] Open
Abstract
The organization and clustering of cell surface proteins plays a critical role in controlling receptor signaling; however, the biophysical mechanisms regulating these parameters are not well understood. Elucidating these mechanisms is highly significant to our understanding of immune function in health and disease, given the importance of B cell receptor (BCR) signaling in directing B cells to produce antibodies for the clearance of pathogens, and the potential deleterious effects of dysregulated BCR signaling, such as in B cell malignancies or autoimmune disease. One of main inhibitory co-receptors on B cells is CD22, a sialic-acid binding protein, which interacts homotypically with other sialylated CD22 molecules, as well as heterotypically with IgM and CD45. Although the importance of CD22 in attenuating BCR signaling is well established, we still do not fully understand what mediates CD22 organization and association to BCRs. CD22 is highly glycosylated, containing 12 N-linked glycosylation sites on its extracellular domain, the function of which remain to be resolved. We were interested in how these glycosylation sites mediate homotypic vs. heterotypic interactions. To this end, we mutated five out of the six N-linked glycosylation residues on CD22 localized closest to the sialic acid binding site. Glycan site N101 was not mutated as this resulted in lack of CD22 expression. We used dual-color super-resolution imaging to investigate the impact of altered glycosylation of CD22 on the nanoscale organization of CD22 and its association with BCR. We show that mutation of these five glycosylation sites increased the clustering tendency of CD22 and resulted in higher density CD22 nanoclusters. Consistent with these findings of altered CD22 organization, we found that mutation of N-glycan sites attenuated CD22 phosphorylation upon BCR stimulation, and consequently, increased BCR signaling. Importantly, we identified that these sites may be ligands for the soluble secreted lectin, galectin-9, and are necessary for galectin-9 mediated inhibition of BCR signaling. Taken together, these findings implicate N-linked glycosylation in the organization and function of CD22, likely through regulating heterotypic interactions between CD22 and its binding partners.
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Affiliation(s)
- Laabiah Wasim
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | | | - Myuran Yoganathan
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Taylor Sicard
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - June Ereño-Orbea
- The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Jean-Philippe Julien
- Department of Immunology, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Bebhinn Treanor
- Department of Immunology, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
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24
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Padmanabhan P, Bademosi AT, Kasula R, Lauwers E, Verstreken P, Meunier FA. Need for speed: Super-resolving the dynamic nanoclustering of syntaxin-1 at exocytic fusion sites. Neuropharmacology 2019; 169:107554. [PMID: 30826343 DOI: 10.1016/j.neuropharm.2019.02.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 01/08/2023]
Abstract
Communication between cells relies on regulated exocytosis, a multi-step process that involves the docking, priming and fusion of vesicles with the plasma membrane, culminating in the release of neurotransmitters and hormones. Key proteins and lipids involved in exocytosis are subjected to Brownian movement and constantly switch between distinct motion states which are governed by short-lived molecular interactions. Critical biochemical reactions between exocytic proteins that occur in the confinement of nanodomains underpin the precise sequence of priming steps which leads to the fusion of vesicles. The advent of super-resolution microscopy techniques has provided the means to visualize individual molecules on the plasma membrane with high spatiotemporal resolution in live cells. These techniques are revealing a highly dynamic nature of the nanoscale organization of the exocytic machinery. In this review, we focus on soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) syntaxin-1, which mediates vesicular fusion. Syntaxin-1 is highly mobile at the plasma membrane, and its inherent speed allows fast assembly and disassembly of syntaxin-1 nanoclusters which are associated with exocytosis. We reflect on recent studies which have revealed the mechanisms regulating syntaxin-1 nanoclustering on the plasma membrane and draw inferences on the effect of synaptic activity, phosphoinositides, N-ethylmaleimide-sensitive factor (NSF), α-soluble NSF attachment protein (α-SNAP) and SNARE complex assembly on the dynamic nanoscale organization of syntaxin-1. This article is part of the special issue entitled 'Mobility and trafficking of neuronal membrane proteins'.
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Affiliation(s)
- Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Adekunle T Bademosi
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Ravikiran Kasula
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Elsa Lauwers
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia.
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Baumgart F, Arnold AM, Rossboth BK, Brameshuber M, Schütz GJ. What we talk about when we talk about nanoclusters. Methods Appl Fluoresc 2018; 7:013001. [PMID: 30412469 DOI: 10.1088/2050-6120/aaed0f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Superresolution microscopy results have sparked the idea that many membrane proteins are not randomly distributed across the plasma membrane but are instead arranged in nanoclusters. Frequently, these new results seemed to confirm older data based on biochemical and electron microscopy experiments. Recently, however, it was recognized that multiple countings of the very same fluorescently labeled protein molecule can be easily confused with true protein clusters. Various strategies have been developed, which are intended to solve the problem of discriminating true protein clusters from imaging artifacts. We believe that there is currently no perfect algorithm for this problem; instead, different approaches have different strengths and weaknesses. In this review, we discuss single molecule localization microscopy in view of its ability to detect nanoclusters of membrane proteins. To capture the different views on nanoclustering, we chose an unconventional style for this article: we placed its scientific content in the setting of a fictive conference, where five researchers from different fields discuss the problem of detecting and quantifying nanoclusters. Using this style, we feel that the different approaches common for different research areas can be well illustrated. Similarities to a short story by Raymond Carver are not unintentional.
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Chien FC, Lin CY, Abrigo G. Enhancing the blinking fluorescence of single-molecule localization imaging by using a surface-plasmon-polariton-enhanced substrate. Phys Chem Chem Phys 2018; 20:27245-27255. [PMID: 30182107 DOI: 10.1039/c8cp02942c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Super-resolution imaging based on single-molecule localization microscopy combined with the surface plasmon polariton (SPP)-enhanced fluorescence of spontaneously blinking fluorophores was demonstrated to visualize the nanoscale-level positioning information of cell-adhesion-associated proteins. Glass substrates with a deposited silver layer were utilized to induce a SPP-enhanced field on the silver surface and significantly strengthen the fluorescence signals of the fluorophores by more than 300%. The illumination power density for localization imaging at a spatial resolution of 25 ± 11 nm was 31.6 W cm-2. This low illumination power density will facilitate the reduction of phototoxicity of the biospecimens for single-molecule localization imaging. The proposed strategy provides a uniform distribution of the SPP-enhanced field on the silver surface, enabling visualization of the spatial distribution of labeled proteins without interference caused by the enhanced field distribution.
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Affiliation(s)
- Fan-Ching Chien
- Department of Optics and Photonics, National Central University, Taoyuan 32001, Taiwan.
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He H, Li S, Shi X, Wang X, Liu X, Wang Q, Guo A, Ge B, Khan NU, Huang F. Quantitative Nanoscopy of Small Blinking Graphene Nanocarriers in Drug Delivery. Bioconjug Chem 2018; 29:3658-3666. [DOI: 10.1021/acs.bioconjchem.8b00589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hua He
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Shan Li
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xinjian Shi
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xu Liu
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Qian Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Aijun Guo
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Naseer Ullah Khan
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
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Abstract
The galectin family of secreted lectins have emerged as important regulators of immune cell function; however, their role in B-cell responses is poorly understood. Here we identify IgM-BCR as a ligand for galectin-9. Furthermore, we show enhanced BCR microcluster formation and signaling in galectin-9-deficient B cells. Notably, treatment with exogenous recombinant galectin-9 nearly completely abolishes BCR signaling. We investigated the molecular mechanism for galectin-9-mediated inhibition of BCR signaling using super-resolution imaging and single-particle tracking. We show that galectin-9 merges pre-existing nanoclusters of IgM-BCR, immobilizes IgM-BCR, and relocalizes IgM-BCR together with the inhibitory molecules CD45 and CD22. In resting naive cells, we use dual-color super-resolution imaging to demonstrate that galectin-9 mediates the close association of IgM and CD22, and propose that the loss of this association provides a mechanism for enhanced activation of galectin-9-deficient B cells. The galectin family of secreted lectins are important regulators of immune cell function; however, their role in B cell responses is poorly understood. Here, the authors identify IgM-BCR as a ligand for galectin-9. In resting naive cells, they show that galectin-9 mediates a close association between IgM and CD22.
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Rona G, Roberti D, Yin Y, Pagan JK, Homer H, Sassani E, Zeke A, Busino L, Rothenberg E, Pagano M. PARP1-dependent recruitment of the FBXL10-RNF68-RNF2 ubiquitin ligase to sites of DNA damage controls H2A.Z loading. eLife 2018; 7:e38771. [PMID: 29985131 PMCID: PMC6037479 DOI: 10.7554/elife.38771] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/21/2018] [Indexed: 12/05/2022] Open
Abstract
The mammalian FBXL10-RNF68-RNF2 ubiquitin ligase complex (FRRUC) mono-ubiquitylates H2A at Lys119 to repress transcription in unstressed cells. We found that the FRRUC is rapidly and transiently recruited to sites of DNA damage in a PARP1- and TIMELESS-dependent manner to promote mono-ubiquitylation of H2A at Lys119, a local decrease of H2A levels, and an increase of H2A.Z incorporation. Both the FRRUC and H2A.Z promote transcriptional repression, double strand break signaling, and homologous recombination repair (HRR). All these events require both the presence and activity of the FRRUC. Moreover, the FRRUC and its activity are required for the proper recruitment of BMI1-RNF2 and MEL18-RNF2, two other ubiquitin ligases that mono-ubiquitylate Lys119 in H2A upon genotoxic stress. Notably, whereas H2A.Z is not required for H2A mono-ubiquitylation, impairment of the latter results in the inhibition of H2A.Z incorporation. We propose that the recruitment of the FRRUC represents an early and critical regulatory step in HRR.
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Affiliation(s)
- Gergely Rona
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Domenico Roberti
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Yandong Yin
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Julia K Pagan
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Harrison Homer
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Elizabeth Sassani
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Andras Zeke
- Institute of Enzymology, Research Center for Natural SciencesHungarian Academy of SciencesBudapestHungary
| | - Luca Busino
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Eli Rothenberg
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
| | - Michele Pagano
- Department of Biochemistry and Molecular PharmacologyNew York University School of MedicineNew YorkUnited States
- Perlmutter Cancer CenterNew York University School of MedicineNew YorkUnited States
- Howard Hughes Medical Institute, New York University School of MedicineNew YorkUnited States
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30
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Banerjee S, Maurya S, Roy R. Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018; 43:519-540. [PMID: 30002270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule fluorescence methods remain a challenging yet information-rich set of techniques that allow one to probe the dynamics, stoichiometry and conformation of biomolecules one molecule at a time. Viruses are small (nanometers) in size, can achieve cellular infections with a small number of virions and their lifecycle is inherently heterogeneous with a large number of structural and functional intermediates. Single-molecule measurements that reveal the complete distribution of properties rather than the average can hence reveal new insights into virus infections and biology that are inaccessible otherwise. This article highlights some of the methods and recent applications of single-molecule fluorescence in the field of virology. Here, we have focused on new findings in virus-cell interaction, virus cell entry and transport, viral membrane fusion, genome release, replication, translation, assembly, genome packaging, egress and interaction with host immune proteins that underline the advantage of single-molecule approach to the question at hand. Finally, we discuss the challenges, outlook and potential areas for improvement and future use of single-molecule fluorescence that could further aid our understanding of viruses.
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Affiliation(s)
- Sunaina Banerjee
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
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31
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Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018. [DOI: 10.1007/s12038-018-9769-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Baddeley D, Bewersdorf J. Biological Insight from Super-Resolution Microscopy: What We Can Learn from Localization-Based Images. Annu Rev Biochem 2018; 87:965-989. [PMID: 29272143 DOI: 10.1146/annurev-biochem-060815-014801] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Super-resolution optical imaging based on the switching and localization of individual fluorescent molecules [photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), etc.] has evolved remarkably over the last decade. Originally driven by pushing technological limits, it has become a tool of biological discovery. The initial demand for impressive pictures showing well-studied biological structures has been replaced by a need for quantitative, reliable data providing dependable evidence for specific unresolved biological hypotheses. In this review, we highlight applications that showcase this development, identify the features that led to their success, and discuss remaining challenges and difficulties. In this context, we consider the complex topic of defining resolution for this imaging modality and address some of the more common analytical methods used with this data.
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Affiliation(s)
- David Baddeley
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA; , .,Auckland Bioengineering Institute, University of Auckland, Auckland 1010, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA; , .,Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA
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33
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Aaron JS, Taylor AB, Chew TL. Image co-localization – co-occurrence versus correlation. J Cell Sci 2018; 131:131/3/jcs211847. [DOI: 10.1242/jcs.211847] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
ABSTRACT
Fluorescence image co-localization analysis is widely utilized to suggest biomolecular interaction. However, there exists some confusion as to its correct implementation and interpretation. In reality, co-localization analysis consists of at least two distinct sets of methods, termed co-occurrence and correlation. Each approach has inherent and often contrasting strengths and weaknesses. Yet, neither one can be considered to always be preferable for any given application. Rather, each method is most appropriate for answering different types of biological question. This Review discusses the main factors affecting multicolor image co-occurrence and correlation analysis, while giving insight into the types of biological behavior that are better suited to one approach or the other. Further, the limits of pixel-based co-localization analysis are discussed in the context of increasingly popular super-resolution imaging techniques.
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Affiliation(s)
- Jesse S. Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr., Ashburn, VA USA
| | - Aaron B. Taylor
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr., Ashburn, VA USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr., Ashburn, VA USA
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34
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Moser B, Hochreiter B, Herbst R, Schmid JA. Fluorescence colocalization microscopy analysis can be improved by combining object-recognition with pixel-intensity-correlation. Biotechnol J 2017; 12:1600332. [PMID: 27420480 PMCID: PMC5244660 DOI: 10.1002/biot.201600332] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/15/2016] [Accepted: 07/05/2016] [Indexed: 12/15/2022]
Abstract
The question whether two proteins interact with each other or whether a protein localizes to a certain region of the cell is often addressed with fluorescence microscopy and analysis of a potential colocalization of fluorescence markers. Since a mere visual estimation does not allow quantification of the degree of colocalization, different statistical methods of pixel-intensity correlation are commonly used to score it. We observed that these correlation coefficients are prone to false positive results and tend to show high values even for molecules that reside in different organelles. Our aim was to improve this type of analysis and we developed a novel method combining object-recognition based colocalization analysis with pixel-intensity correlation to calculate an object-corrected Pearson coefficient. We designed a macro for the Fiji-version of the software ImageJ and tested the performance systematically with various organelle markers revealing an improved robustness of our approach over classical methods. In order to prove that colocalization does not necessarily mean a physical interaction, we performed FRET (fluorescence resonance energy transfer) microscopy. This confirmed that non-interacting molecules can exhibit a nearly complete colocalization, but that they do not show any significant FRET signal in contrast to proteins that are bound to each other.
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Affiliation(s)
- Bernhard Moser
- Dept. of Vascular Biology and Thrombosis Research, Center for Physiology and PharmacologyMedical University of ViennaViennaAustria
| | - Bernhard Hochreiter
- Dept. of Vascular Biology and Thrombosis Research, Center for Physiology and PharmacologyMedical University of ViennaViennaAustria
| | - Ruth Herbst
- Inst. of Immunology, Center for Pathophysiology, Infectiology and ImmunologyMedical University of ViennaViennaAustria
| | - Johannes A. Schmid
- Dept. of Vascular Biology and Thrombosis Research, Center for Physiology and PharmacologyMedical University of ViennaViennaAustria
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Kinetic disruption of lipid rafts is a mechanosensor for phospholipase D. Nat Commun 2016; 7:13873. [PMID: 27976674 PMCID: PMC5171650 DOI: 10.1038/ncomms13873] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/04/2016] [Indexed: 12/24/2022] Open
Abstract
The sensing of physical force, mechanosensation, underlies two of five human senses—touch and hearing. How transduction of force in a membrane occurs remains unclear. We asked if a biological membrane could employ kinetic energy to transduce a signal absent tension. Here we show that lipid rafts are dynamic compartments that inactivate the signalling enzyme phospholipase D2 (PLD2) by sequestering the enzyme from its substrate. Mechanical disruption of the lipid rafts activates PLD2 by mixing the enzyme with its substrate to produce the signalling lipid phosphatidic acid (PA). We calculate a latency time of <650 μs for PLD activation by mixing. Our results establish a fast, non-tension mechanism for mechanotransduction where disruption of ordered lipids initiates a mechanosensitive signal for cell growth through mechanical mixing.
Mechanosensation by biological membranes can be relayed by mechanical tension to ion channels. Here the authors show that phospholipase D (PLD) is activated by mechanical disruption of lipid rafts which allows PLD to mix with its substrate in the lipid membrane, and propose a kinetic model of force transduction.
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36
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Xiao J, Dufrêne YF. Optical and force nanoscopy in microbiology. Nat Microbiol 2016; 1:16186. [PMID: 27782138 PMCID: PMC5839876 DOI: 10.1038/nmicrobiol.2016.186] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/01/2016] [Indexed: 12/31/2022]
Abstract
Microbial cells have developed sophisticated multicomponent structures and machineries to govern basic cellular processes, such as chromosome segregation, gene expression, cell division, mechanosensing, cell adhesion and biofilm formation. Because of the small cell sizes, subcellular structures have long been difficult to visualize using diffraction-limited light microscopy. During the last three decades, optical and force nanoscopy techniques have been developed to probe intracellular and extracellular structures with unprecedented resolutions, enabling researchers to study their organization, dynamics and interactions in individual cells, at the single-molecule level, from the inside out, and all the way up to cell-cell interactions in microbial communities. In this Review, we discuss the principles, advantages and limitations of the main optical and force nanoscopy techniques available in microbiology, and we highlight some outstanding questions that these new tools may help to answer.
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Affiliation(s)
- Jie Xiao
- Department of Biophysics &Biophysical Chemistry, The Johns Hopkins School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21212, USA
| | - Yves F Dufrêne
- Institute of Life Sciences, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium
- Walloon Excellence in Life sciences and Biotechnology (WELBIO), Belgium
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37
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Lyu Z, Coltharp C, Yang X, Xiao J. Influence of FtsZ GTPase activity and concentration on nanoscale Z-ring structure in vivo revealed by three-dimensional Superresolution imaging. Biopolymers 2016; 105:725-34. [PMID: 27310678 PMCID: PMC4958570 DOI: 10.1002/bip.22895] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/10/2016] [Accepted: 06/13/2016] [Indexed: 12/18/2022]
Abstract
FtsZ is an essential bacterial cytoskeletal protein that assembles into a ring-like structure (Z-ring) at midcell to carry out cytokinesis. In vitro, FtsZ exhibits polymorphism in polymerizing into different forms of filaments based on its GTPase activity, concentration, and buffer condition. In vivo, the Z-ring appeared to be punctate and heterogeneously organized, although continuous, homogenous Z-ring structures have also been observed. Understanding how the Z-ring is organized in vivo is important because it provides a structural basis for the functional role of the Z-ring in cytokinesis. Here, we assess the effects of both GTPase activity and FtsZ concentration on the organization of the Z-ring in vivo using three-dimensional (3D) superresolution microscopy. We found that the Z-ring became more homogenous when assembled in the presence of a GTPase-deficient mutant, and upon overexpression of either wt or mutant FtsZ. These results suggest that the in vivo organization of the Z-ring is largely dependent on the intrinsic polymerization properties of FtsZ, which are significantly influenced by the GTPase activity and concentration of FtsZ. Our work provides a unifying theme to reconcile previous observations of different Z-ring structures, and supports a model in which the wt Z-ring comprises loosely associated, heterogeneously distributed FtsZ clusters. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 725-734, 2016.
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Affiliation(s)
- Zhixin Lyu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Carla Coltharp
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
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38
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Mateos-Gil P, Letschert S, Doose S, Sauer M. Super-Resolution Imaging of Plasma Membrane Proteins with Click Chemistry. Front Cell Dev Biol 2016; 4:98. [PMID: 27668214 PMCID: PMC5016519 DOI: 10.3389/fcell.2016.00098] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/24/2016] [Indexed: 12/30/2022] Open
Abstract
Besides its function as a passive cell wall, the plasma membrane (PM) serves as a platform for different physiological processes such as signal transduction and cell adhesion, determining the ability of cells to communicate with the exterior, and form tissues. Therefore, the spatial distribution of PM components, and the molecular mechanisms underlying it, have important implications in various biological fields including cell development, neurobiology, and immunology. The existence of confined compartments in the plasma membrane that vary on many length scales from protein multimers to micrometer-size domains with different protein and lipid composition is today beyond all questions. As much as the physiology of cells is controlled by the spatial organization of PM components, the study of distribution, size, and composition remains challenging. Visualization of the molecular distribution of PM components has been impeded mainly due to two problems: the specific labeling of lipids and proteins without perturbing their native distribution and the diffraction-limit of fluorescence microscopy restricting the resolution to about half the wavelength of light. Here, we present a bioorthogonal chemical reporter strategy based on click chemistry and metabolic labeling for efficient and specific visualization of PM proteins and glycans with organic fluorophores in combination with super-resolution fluorescence imaging by direct stochastic optical reconstruction microscopy (dSTORM) with single-molecule sensitivity.
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Affiliation(s)
- Pablo Mateos-Gil
- Department of Biotechnology and Biophysics, Julius Maximilian University of Würzburg Würzburg, Germany
| | - Sebastian Letschert
- Department of Biotechnology and Biophysics, Julius Maximilian University of Würzburg Würzburg, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, Julius Maximilian University of Würzburg Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Julius Maximilian University of Würzburg Würzburg, Germany
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39
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Yin Y, Rothenberg E. Probing the Spatial Organization of Molecular Complexes Using Triple-Pair-Correlation. Sci Rep 2016; 6:30819. [PMID: 27545293 PMCID: PMC4992864 DOI: 10.1038/srep30819] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 07/08/2016] [Indexed: 11/25/2022] Open
Abstract
Super-resolution microscopy coupled with multiplexing techniques can resolve specific spatial arrangements of different components within molecular complexes. However, reliable quantification and analysis of such specific organization is extremely problematic because it is frequently obstructed by random co-localization incidents between crowded molecular species and the intrinsic heterogeneity of molecular complexes. To address this, we present a Triple-Pair-Correlation (TPC) analysis approach for unbiased interpretation of the spatial organization of molecular assemblies in crowded three-color super-resolution (SR) images. We validate this approach using simulated data, as well as SR images of DNA replication foci in human cells. This demonstrates the applicability of TPC in deciphering the specific spatial organization of molecular complexes hidden in dense multi-color super-resolution images.
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Affiliation(s)
- Yandong Yin
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 1st Avenue, New York, NY 10016, USA
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 1st Avenue, New York, NY 10016, USA
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40
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Chen J, Gao J, Zhang M, Cai M, Xu H, Jiang J, Tian Z, Wang H. Systemic localization of seven major types of carbohydrates on cell membranes by dSTORM imaging. Sci Rep 2016; 6:30247. [PMID: 27453176 PMCID: PMC4958959 DOI: 10.1038/srep30247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/01/2016] [Indexed: 12/13/2022] Open
Abstract
Carbohydrates on the cell surface control intercellular interactions and play a vital role in various physiological processes. However, their systemic distribution patterns are poorly understood. Through the direct stochastic optical reconstruction microscopy (dSTORM) strategy, we systematically revealed that several types of representative carbohydrates are found in clustered states. Interestingly, the results from dual-color dSTORM imaging indicate that these carbohydrate clusters are prone to connect with one another and eventually form conjoined platforms where different functional glycoproteins aggregate (e.g., epidermal growth factor receptor, (EGFR) and band 3 protein). A thorough understanding of the ensemble distribution of carbohydrates on the cell surface paves the way for elucidating the structure-function relationship of cell membranes and the critical roles of carbohydrates in various physiological and pathological cell processes.
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Affiliation(s)
- Junling Chen
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jing Gao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Min Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Mingjun Cai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Haijiao Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Junguang Jiang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Zhiyuan Tian
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
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Chen J, Gao J, Cai M, Xu H, Jiang J, Tian Z, Wang H. Mechanistic insights into the distribution of carbohydrate clusters on cell membranes revealed by dSTORM imaging. NANOSCALE 2016; 8:13611-13619. [PMID: 27362510 DOI: 10.1039/c6nr02513g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cell surface carbohydrates play significant roles in many physiological processes and act as primary markers to indicate various cellular physiological states. The functions of carbohydrates are always associated with their expression and distribution on cell membranes. Based on our previous work, we found that carbohydrates tend to form clusters; however, the underlying mechanism of these clusters remains unknown. Through the direct stochastic optical reconstruction microscopy (dSTORM) strategy, we found that with the contributions of lipid raft as a stable factor and actin cytoskeleton as a restrictive factor, carbohydrate clusters can stably exist with restricted size. Additionally, we revealed that the formation of most carbohydrate clusters (Gal and GlcANc clusters) depended on the carbohydrate-binding proteins (i.e., galectins) cross-linking their specific carbohydrate ligands. Our results clarify the organizational mechanism of carbohydrates on cell surfaces from their formation, stable existence and size-restriction, which promotes a better understanding of the relationship between the function and distribution of carbohydrates, as well as the structure of cell membranes.
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Affiliation(s)
- Junling Chen
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China. and University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jing Gao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China.
| | - Mingjun Cai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China.
| | - Haijiao Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China.
| | - Junguang Jiang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China.
| | - Zhiyuan Tian
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China.
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Laine RF, Kaminski Schierle GS, van de Linde S, Kaminski CF. From single-molecule spectroscopy to super-resolution imaging of the neuron: a review. Methods Appl Fluoresc 2016; 4:022004. [PMID: 28809165 PMCID: PMC5390958 DOI: 10.1088/2050-6120/4/2/022004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/09/2016] [Accepted: 05/19/2016] [Indexed: 12/03/2022]
Abstract
For more than 20 years, single-molecule spectroscopy has been providing invaluable insights into nature at the molecular level. The field has received a powerful boost with the development of the technique into super-resolution imaging methods, ca. 10 years ago, which overcome the limitations imposed by optical diffraction. Today, single molecule super-resolution imaging is routinely used in the study of macromolecular function and structure in the cell. Concomitantly, computational methods have been developed that provide information on numbers and positions of molecules at the nanometer-scale. In this overview, we outline the technical developments that have led to the emergence of localization microscopy techniques from single-molecule spectroscopy. We then provide a comprehensive review on the application of the technique in the field of neuroscience research.
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Affiliation(s)
- Romain F Laine
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Gabriele S Kaminski Schierle
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Sebastian van de Linde
- Department of Biotechnology and Biophysics, Julius-Maximilians-University, Am Hubland, D-97074 Würzburg, Germany
| | - Clemens F Kaminski
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
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Abstract
Bacterial cytokinesis is accomplished by the essential 'divisome' machinery. The most widely conserved divisome component, FtsZ, is a tubulin homolog that polymerizes into the 'FtsZ-ring' ('Z-ring'). Previous in vitro studies suggest that Z-ring contraction serves as a major constrictive force generator to limit the progression of cytokinesis. Here, we applied quantitative superresolution imaging to examine whether and how Z-ring contraction limits the rate of septum closure during cytokinesis in Escherichia coli cells. Surprisingly, septum closure rate was robust to substantial changes in all Z-ring properties proposed to be coupled to force generation: FtsZ's GTPase activity, Z-ring density, and the timing of Z-ring assembly and disassembly. Instead, the rate was limited by the activity of an essential cell wall synthesis enzyme and further modulated by a physical divisome-chromosome coupling. These results challenge a Z-ring-centric view of bacterial cytokinesis and identify cell wall synthesis and chromosome segregation as limiting processes of cytokinesis.
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Siraj N, El-Zahab B, Hamdan S, Karam TE, Haber LH, Li M, Fakayode SO, Das S, Valle B, Strongin RM, Patonay G, Sintim HO, Baker GA, Powe A, Lowry M, Karolin JO, Geddes CD, Warner IM. Fluorescence, Phosphorescence, and Chemiluminescence. Anal Chem 2015; 88:170-202. [PMID: 26575092 DOI: 10.1021/acs.analchem.5b04109] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Noureen Siraj
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Bilal El-Zahab
- Department of Mechanical and Materials Engineering, Florida International University , Miami, Florida 33174, United States
| | - Suzana Hamdan
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Tony E Karam
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Louis H Haber
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Min Li
- Process Development Center, Albemarle Corporation , Baton Rouge, Louisiana 70805, United States
| | - Sayo O Fakayode
- Department of Chemistry, Winston-Salem State University , Winston-Salem, North Carolina 27110, United States
| | - Susmita Das
- Department of Civil Engineering, Adamas Institute of Technology , Barasat, Kolkata 700126, West Bengal India
| | - Bertha Valle
- Department of Chemistry, Texas Southern University , Houston, Texas 77004, United States
| | - Robert M Strongin
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Gabor Patonay
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-4098, United States
| | - Herman O Sintim
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Gary A Baker
- Department of Chemistry, University of Missouri Columbia , Columbia, Missouri 65211-7600, United States
| | - Aleeta Powe
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40208, United States
| | - Mark Lowry
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Jan O Karolin
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Chris D Geddes
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Isiah M Warner
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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Barden AO, Goler AS, Humphreys SC, Tabatabaei S, Lochner M, Ruepp MD, Jack T, Simonin J, Thompson AJ, Jones JP, Brozik JA. Tracking individual membrane proteins and their biochemistry: The power of direct observation. Neuropharmacology 2015; 98:22-30. [PMID: 25998277 DOI: 10.1016/j.neuropharm.2015.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 04/13/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
Abstract
The advent of single molecule fluorescence microscopy has allowed experimental molecular biophysics and biochemistry to transcend traditional ensemble measurements, where the behavior of individual proteins could not be precisely sampled. The recent explosion in popularity of new super-resolution and super-localization techniques coupled with technical advances in optical designs and fast highly sensitive cameras with single photon sensitivity and millisecond time resolution have made it possible to track key motions, reactions, and interactions of individual proteins with high temporal resolution and spatial resolution well beyond the diffraction limit. Within the purview of membrane proteins and ligand gated ion channels (LGICs), these outstanding advances in single molecule microscopy allow for the direct observation of discrete biochemical states and their fluctuation dynamics. Such observations are fundamentally important for understanding molecular-level mechanisms governing these systems. Examples reviewed here include the effects of allostery on the stoichiometry of ligand binding in the presence of fluorescent ligands; the observation of subdomain partitioning of membrane proteins due to microenvironment effects; and the use of single particle tracking experiments to elucidate characteristics of membrane protein diffusion and the direct measurement of thermodynamic properties, which govern the free energy landscape of protein dimerization. The review of such characteristic topics represents a snapshot of efforts to push the boundaries of fluorescence microscopy of membrane proteins to the absolute limit. This article is part of the Special Issue entitled 'Fluorescent Tools in Neuropharmacology'.
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Affiliation(s)
- Adam O Barden
- Department of Chemistry, Washington State University, PO Box 644630, Pullman, WA, 99164-4630, United States
| | - Adam S Goler
- Department of Chemistry, Washington State University, PO Box 644630, Pullman, WA, 99164-4630, United States
| | - Sara C Humphreys
- Department of Chemistry, Washington State University, PO Box 644630, Pullman, WA, 99164-4630, United States
| | - Samaneh Tabatabaei
- Department of Chemistry, Washington State University, PO Box 644630, Pullman, WA, 99164-4630, United States
| | - Martin Lochner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Thomas Jack
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Jonathan Simonin
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Andrew J Thompson
- Pharmacology Department, Cambridge University, Tennis Court Road, Cambridge, CB2 1PD, United Kingdom
| | - Jeffrey P Jones
- Department of Chemistry, Washington State University, PO Box 644630, Pullman, WA, 99164-4630, United States
| | - James A Brozik
- Department of Chemistry, Washington State University, PO Box 644630, Pullman, WA, 99164-4630, United States.
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A multi-layered protein network stabilizes the Escherichia coli FtsZ-ring and modulates constriction dynamics. PLoS Genet 2015; 11:e1005128. [PMID: 25848771 PMCID: PMC4388696 DOI: 10.1371/journal.pgen.1005128] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/04/2015] [Indexed: 11/19/2022] Open
Abstract
The prokaryotic tubulin homolog, FtsZ, forms a ring-like structure (FtsZ-ring) at midcell. The FtsZ-ring establishes the division plane and enables the assembly of the macromolecular division machinery (divisome). Although many molecular components of the divisome have been identified and their interactions extensively characterized, the spatial organization of these proteins within the divisome is unclear. Consequently, the physical mechanisms that drive divisome assembly, maintenance, and constriction remain elusive. Here we applied single-molecule based superresolution imaging, combined with genetic and biophysical investigations, to reveal the spatial organization of cellular structures formed by four important divisome proteins in E. coli: FtsZ, ZapA, ZapB and MatP. We show that these interacting proteins are arranged into a multi-layered protein network extending from the cell membrane to the chromosome, each with unique structural and dynamic properties. Further, we find that this protein network stabilizes the FtsZ-ring, and unexpectedly, slows down cell constriction, suggesting a new, unrecognized role for this network in bacterial cell division. Our results provide new insight into the structure and function of the divisome, and highlight the importance of coordinated cell constriction and chromosome segregation. Bacterial cell division is a highly regulated process that must be coordinated with other cellular processes (i.e. DNA replication and chromosome segregation) to promote faithful reproduction. In Escherichia coli, this regulation is most often mediated through the polymerization of the prokaryotic tubulin homolog, FtsZ, which forms a ring-like structure (FtsZ-ring) at midcell. The establishment of the FtsZ-ring marks the site of division and enables the assembly of the macromolecular division machinery (divisome). Here we applied single-molecule based superresolution imaging to reveal the three-dimensional structure of FtsZ in the context of its regulatory proteins: ZapA, ZapB and MatP. We found that these four proteins exist in a multi-layered network that extends from the cell membrane to the chromosome. This layered organization not only helps to stabilize the FtsZ-ring, but also serves to coordinate division with DNA status by influencing constriction rate. Our results not only provide a comprehensive view of the divisome, but also allow new insight to be garnered regarding the structure and function of the divisome.
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Chen YH, Jones MJK, Yin Y, Crist SB, Colnaghi L, Sims RJ, Rothenberg E, Jallepalli PV, Huang TT. ATR-mediated phosphorylation of FANCI regulates dormant origin firing in response to replication stress. Mol Cell 2015; 58:323-38. [PMID: 25843623 DOI: 10.1016/j.molcel.2015.02.031] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 01/13/2015] [Accepted: 02/25/2015] [Indexed: 12/24/2022]
Abstract
Excess dormant origins bound by the minichromosome maintenance (MCM) replicative helicase complex play a critical role in preventing replication stress, chromosome instability, and tumorigenesis. In response to DNA damage, replicating cells must coordinate DNA repair and dormant origin firing to ensure complete and timely replication of the genome; how cells regulate this process remains elusive. Herein, we identify a member of the Fanconi anemia (FA) DNA repair pathway, FANCI, as a key effector of dormant origin firing in response to replication stress. Cells lacking FANCI have reduced number of origins, increased inter-origin distances, and slowed proliferation rates. Intriguingly, ATR-mediated FANCI phosphorylation inhibits dormant origin firing while promoting replication fork restart/DNA repair. Using super-resolution microscopy, we show that FANCI co-localizes with MCM-bound chromatin in response to replication stress. These data reveal a unique role for FANCI as a modulator of dormant origin firing and link timely genome replication to DNA repair.
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Affiliation(s)
- Yu-Hung Chen
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Mathew J K Jones
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA; Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yandong Yin
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Sarah B Crist
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Luca Colnaghi
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Robert J Sims
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Eli Rothenberg
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Prasad V Jallepalli
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA.
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Greenfeld M, van de Meent JW, Pavlichin DS, Mabuchi H, Wiggins CH, Gonzalez RL, Herschlag D. Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data. BMC Bioinformatics 2015; 16:3. [PMID: 25591752 PMCID: PMC4384321 DOI: 10.1186/s12859-014-0429-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 12/11/2014] [Indexed: 12/15/2022] Open
Abstract
Background Single-molecule techniques have emerged as incisive approaches for addressing a wide range of questions arising in contemporary biological research [Trends Biochem Sci 38:30–37, 2013; Nat Rev Genet 14:9–22, 2013; Curr Opin Struct Biol 2014, 28C:112–121; Annu Rev Biophys 43:19–39, 2014]. The analysis and interpretation of raw single-molecule data benefits greatly from the ongoing development of sophisticated statistical analysis tools that enable accurate inference at the low signal-to-noise ratios frequently associated with these measurements. While a number of groups have released analysis toolkits as open source software [J Phys Chem B 114:5386–5403, 2010; Biophys J 79:1915–1927, 2000; Biophys J 91:1941–1951, 2006; Biophys J 79:1928–1944, 2000; Biophys J 86:4015–4029, 2004; Biophys J 97:3196–3205, 2009; PLoS One 7:e30024, 2012; BMC Bioinformatics 288 11(8):S2, 2010; Biophys J 106:1327–1337, 2014; Proc Int Conf Mach Learn 28:361–369, 2013], it remains difficult to compare analysis for experiments performed in different labs due to a lack of standardization. Results Here we propose a standardized single-molecule dataset (SMD) file format. SMD is designed to accommodate a wide variety of computer programming languages, single-molecule techniques, and analysis strategies. To facilitate adoption of this format we have made two existing data analysis packages that are used for single-molecule analysis compatible with this format. Conclusion Adoption of a common, standard data file format for sharing raw single-molecule data and analysis outcomes is a critical step for the emerging and powerful single-molecule field, which will benefit both sophisticated users and non-specialists by allowing standardized, transparent, and reproducible analysis practices. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0429-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Max Greenfeld
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA. .,Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
| | | | | | - Hideo Mabuchi
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.
| | - Chris H Wiggins
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA.
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
| | - Daniel Herschlag
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA. .,Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA. .,Department of Biochemistry, B400, Stanford University, Stanford, CA, 94305, USA.
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