scholarly journals Parameter-free molecular super-structures quantification in single-molecule localization microscopy

2021 ◽  
Vol 220 (5) ◽  
Author(s):  
Mattia Marenda ◽  
Elena Lazarova ◽  
Sebastian van de Linde ◽  
Nick Gilbert ◽  
Davide Michieletto
Keyword(s):  
Single Molecule ◽  
Relevant Information ◽  
Localization Microscopy ◽  
Protein Clusters ◽  
Formal Framework ◽  
And Function ◽  
Nuclear Ribonucleoprotein ◽  
Molecular Components ◽  
Single Molecule Localization Microscopy

Understanding biological function requires the identification and characterization of complex patterns of molecules. Single-molecule localization microscopy (SMLM) can quantitatively measure molecular components and interactions at resolutions far beyond the diffraction limit, but this information is only useful if these patterns can be quantified and interpreted. We provide a new approach for the analysis of SMLM data that develops the concept of structures and super-structures formed by interconnected elements, such as smaller protein clusters. Using a formal framework and a parameter-free algorithm, (super-)structures formed from smaller components are found to be abundant in classes of nuclear proteins, such as heterogeneous nuclear ribonucleoprotein particles (hnRNPs), but are absent from ceramides located in the plasma membrane. We suggest that mesoscopic structures formed by interconnected protein clusters are common within the nucleus and have an important role in the organization and function of the genome. Our algorithm, SuperStructure, can be used to analyze and explore complex SMLM data and extract functionally relevant information.

scholarly journals In Situ Characterization of Bak Clusters Responsible for Cell Death Using Single Molecule Localization Microscopy

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Yusuke Nasu ◽  
Alexander Benke ◽  
Satoko Arakawa ◽  
Go J. Yoshida ◽  
Genki Kawamura ◽  
...  
Keyword(s):  
Cell Death ◽  
Single Molecule ◽  
In Situ Characterization ◽  
Localization Microscopy ◽  
Single Molecule Localization Microscopy

scholarly journals Nav1.5 single-molecule localization reveals different reorganization modes at cardiomyocyte domains

2019 ◽  
Author(s):  
Sarah H. Vermij ◽  
Jean-Sébastien Rougier ◽  
Esperanza Agulló-Pascual ◽  
Eli Rothenberg ◽  
Mario Delmar ◽  
...  
Keyword(s):  
Single Molecule ◽  
Interacting Proteins ◽  
Wild Type ◽  
Gene Encoding ◽  
Localization Microscopy ◽  
Lateral Membrane ◽  
T Tubules ◽  
And Function ◽  
Nanoscale Features ◽  
Single Molecule Localization Microscopy

ABSTRACTMutations in the gene encoding the sodium channel Nav1.5 cause various cardiac arrhythmias. This variety may arise from different determinants of Nav1.5 expression between cardiomyocyte domains. At the lateral membrane and T-tubules, Nav1.5 localization and function remain insufficiently characterized. We used novel single-molecule localization microscopy (SMLM) and modeling to define nanoscale features of Nav1.5 localization and distribution at the lateral membrane, groove, and T-tubules in wild-type, dystrophin-deficient (mdx) mice, and mice expressing C-terminally truncated Nav1.5 (ΔSIV). We show that Nav1.5 organizes as distinct clusters in the groove and T-tubules which density and distribution partially depend on SIV and dystrophin. We found that overall reduction in Nav1.5 expression in mdx and ΔSIV cells results in a non-uniform redistribution with Nav1.5 being specifically reduced at the groove of ΔSIV and increased in T-tubules of mdx cardiomyocytes. Nav1.5 mutations may therefore site-specifically affect Nav1.5 localization and distribution depending on site-specific interacting proteins.

Advances in Correlative Single-Molecule Localization Microscopy and Electron Microscopy

2015 ◽  
Vol 1 (1) ◽  
Author(s):  
Ulrike Endesfelder
Keyword(s):  
Electron Microscopy ◽  
Light Microscopy ◽  
Single Molecule ◽  
Light And Electron Microscopy ◽  
Fluorescence Labeling ◽  
Localization Microscopy ◽  
Fluorescence Light Microscopy ◽  
Fluorescence Light ◽  
And Function ◽  
Single Molecule Localization Microscopy

AbstractDuring the last few decades, correlative fluorescence light and electron microscopy (FLM-EM) has gained increased interest in the life sciences concomitant with the advent of fluorescence light microscopy. It has become, accompanied by numerous developments in both techniques, an important tool to study bio-cellular structure and function as it combines the specificity of fluorescence labeling with the high structural resolution and cellular context information given by the EM images. Having the recently introduced single-molecule localization microscopy techniques (SMLM) at hand, FLM-EM can now make use of improved fluorescence light microscopy resolution, single-molecule sensitivity and quantification strategies. Here, currently used methods for correlative SMLM and EM including the special requirements in sample preparation and imaging routines are summarized and an outlook on remaining challenges concerning methods and instrumentation is provided.

Single-Molecule Imaging of Active Mitochondrial Nitroreductases using a Photo-Crosslinking Fluorescent Sensor

2019 ◽  
Author(s):  
Zacharias Thiel ◽  
Pablo Rivera-Fuentes
Keyword(s):  
Subcellular Localization ◽  
Fluorescent Probe ◽  
Single Molecule ◽  
Mammalian Cells ◽  
Fluorescent Sensor ◽  
Biological Functions ◽  
Localization Microscopy ◽  
Drug Activation ◽  
Nitroreductase Activity ◽  
Single Molecule Localization Microscopy

Many biomacromolecules are known to cluster in microdomains with specific subcellular localization. In the case of enzymes, this clustering greatly defines their biological functions. Nitroreductases are enzymes capable of reducing nitro groups to amines and play a role in detoxification and pro-drug activation. Although nitroreductase activity has been detected in mammalian cells, the subcellular localization of this activity remains incompletely characterized. Here, we report a fluorescent probe that enables super-resolved imaging of pools of nitroreductase activity within mitochondria. This probe is activated sequentially by nitroreductases and light to give a photo-crosslinked adduct of active enzymes. In combination with a general photoactivatable marker of mitochondria, we performed two-color, threedimensional, single-molecule localization microscopy. These experiments allowed us to image the sub-mitochondrial organization of microdomains of nitroreductase activity.<br>

Single-Molecule Imaging of Active Mitochondrial Nitroreductases using a Photo-Crosslinking Fluorescent Sensor

2019 ◽  
Author(s):  
Zacharias Thiel ◽  
Pablo Rivera-Fuentes
Keyword(s):  
Subcellular Localization ◽  
Fluorescent Probe ◽  
Single Molecule ◽  
Mammalian Cells ◽  
Fluorescent Sensor ◽  
Biological Functions ◽  
Localization Microscopy ◽  
Drug Activation ◽  
Nitroreductase Activity ◽  
Single Molecule Localization Microscopy

Many biomacromolecules are known to cluster in microdomains with specific subcellular localization. In the case of enzymes, this clustering greatly defines their biological functions. Nitroreductases are enzymes capable of reducing nitro groups to amines and play a role in detoxification and pro-drug activation. Although nitroreductase activity has been detected in mammalian cells, the subcellular localization of this activity remains incompletely characterized. Here, we report a fluorescent probe that enables super-resolved imaging of pools of nitroreductase activity within mitochondria. This probe is activated sequentially by nitroreductases and light to give a photo-crosslinked adduct of active enzymes. In combination with a general photoactivatable marker of mitochondria, we performed two-color, threedimensional, single-molecule localization microscopy. These experiments allowed us to image the sub-mitochondrial organization of microdomains of nitroreductase activity.<br>

scholarly journals Single-molecule localization microscopy

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Mickaël Lelek ◽  
Melina T. Gyparaki ◽  
Gerti Beliu ◽  
Florian Schueder ◽  
Juliette Griffié ◽  
...  
Keyword(s):  
Single Molecule ◽  
Localization Microscopy ◽  
Single Molecule Localization Microscopy

scholarly journals Three-dimensional total-internal reflection fluorescence nanoscopy with nanometric axial resolution by photometric localization of single molecules

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alan M. Szalai ◽  
Bruno Siarry ◽  
Jerónimo Lukin ◽  
David J. Williamson ◽  
Nicolás Unsain ◽  
...  
Keyword(s):  
Single Molecule ◽  
Total Internal Reflection ◽  
Single Molecules ◽  
Fluorescence Microscope ◽  
Internal Reflection ◽  
Total Internal Reflection Fluorescence ◽  
Axial Position ◽  
Localization Microscopy ◽  
Localization Precision ◽  
Single Molecule Localization Microscopy

AbstractSingle-molecule localization microscopy enables far-field imaging with lateral resolution in the range of 10 to 20 nanometres, exploiting the fact that the centre position of a single-molecule’s image can be determined with much higher accuracy than the size of that image itself. However, attaining the same level of resolution in the axial (third) dimension remains challenging. Here, we present Supercritical Illumination Microscopy Photometric z-Localization with Enhanced Resolution (SIMPLER), a photometric method to decode the axial position of single molecules in a total internal reflection fluorescence microscope. SIMPLER requires no hardware modification whatsoever to a conventional total internal reflection fluorescence microscope and complements any 2D single-molecule localization microscopy method to deliver 3D images with nearly isotropic nanometric resolution. Performance examples include SIMPLER-direct stochastic optical reconstruction microscopy images of the nuclear pore complex with sub-20 nm axial localization precision and visualization of microtubule cross-sections through SIMPLER-DNA points accumulation for imaging in nanoscale topography with sub-10 nm axial localization precision.

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