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.

scholarly journals Correlative SMLM and electron tomography reveals endosome nanoscale domains

2019 ◽  
Author(s):  
Christian Franke ◽  
Urska Repnik ◽  
Sandra Segeletz ◽  
Nicolas Brouilly ◽  
Yannis Kalaidzidis ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Light Microscopy ◽  
Single Molecule ◽  
Electron Tomography ◽  
Small Gtpase ◽  
Molecular Organization ◽  
Functional Domains ◽  
Localization Microscopy ◽  
Early Endosomes ◽  
Single Molecule Localization Microscopy

AbstractMany cellular organelles, including endosomes, show compartmentalization into distinct functional domains, which however cannot be resolved by diffraction-limited light microscopy. Single molecule localization microscopy (SMLM) offers nanoscale resolution but data interpretation is often inconclusive when the ultrastructural context is missing. Correlative light electron microscopy (CLEM) combining SMLM with electron microscopy (EM) enables correlation of functional sub-domains of organelles in relation to their underlying ultrastructure at nanometer resolution. However, the specific demands for EM sample preparation and the requirements for fluorescent single-molecule photo-switching are opposed. Here, we developed a novel superCLEM workflow that combines triple-colour SMLM (dSTORM & PALM) and electron tomography using semi-thin Tokuyasu thawed cryosections. We applied the superCLEM approach to directly visualize nanoscale compartmentalization of endosomes in HeLa cells. Internalized, fluorescently labelled Transferrin and EGF were resolved into morphologically distinct domains within the same endosome. We found that the small GTPase Rab5 is organized in nano-domains on the globular part of early endosomes. The simultaneous visualization of several proteins in functionally distinct endosomal sub-compartments demonstrates the potential of superCLEM to link the ultrastructure of organelles with their molecular organization at nanoscale resolution.SynopsisSuborganelle compartmentalization cannot be resolved by diffraction limited light microscopy and not interpreted without knowledge of the underlying ultrastructure. This work shows a novel superCLEM workflow that combines multi-colour single-molecule localization-microscopy with electron tomography to map several functional domains on early endosomes. superCLEM reveals that the small GTPase Rab5 is organized in nano-domains largely devoid from cargo molecules Transferrin and EGF and opens new possibilities to perform structure-function analysis of organelles at the nanoscale.

scholarly journals Cost-efficient nanoscopy reveals nanoscale architecture of liver cells and platelets

Nanophotonics ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 1299-1313 ◽  
Author(s):  
Hong Mao ◽  
Robin Diekmann ◽  
Hai Po H. Liang ◽  
Victoria C. Cogger ◽  
David G. Le Couteur ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Endothelial Cells ◽  
Single Molecule ◽  
Nanometer Scale ◽  
Color Channel ◽  
Liver Sinusoidal Endothelial Cells ◽  
Localization Microscopy ◽  
Cost Efficient ◽  
Core Facilities ◽  
Single Molecule Localization Microscopy

AbstractSingle-molecule localization microscopy (SMLM) provides a powerful toolkit to specifically resolve intracellular structures on the nanometer scale, even approaching resolution classically reserved for electron microscopy (EM). Although instruments for SMLM are technically simple to implement, researchers tend to stick to commercial microscopes for SMLM implementations. Here we report the construction and use of a “custom-built” multi-color channel SMLM system to study liver sinusoidal endothelial cells (LSECs) and platelets, which costs significantly less than a commercial system. This microscope allows the introduction of highly affordable and low-maintenance SMLM hardware and methods to laboratories that, for example, lack access to core facilities housing high-end commercial microscopes for SMLM and EM. Using our custom-built microscope and freely available software from image acquisition to analysis, we image LSECs and platelets with lateral resolution down to about 50 nm. Furthermore, we use this microscope to examine the effect of drugs and toxins on cellular morphology.

scholarly journals Molecular resolution imaging by post-labeling expansion single-molecule localization microscopy (Ex-SMLM)

2020 ◽  
Author(s):  
Fabian U. Zwettler ◽  
Sebastian Reinhard ◽  
Davide Gambarotto ◽  
Toby D. M. Bell ◽  
Virginie Hamel ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Single Molecule ◽  
Super Resolution ◽  
Reference Structure ◽  
Positional Error ◽  
Localization Microscopy ◽  
Resolution Imaging ◽  
Endogenous Proteins ◽  
Super Resolution Microscopy ◽  
Single Molecule Localization Microscopy

AbstractExpansion microscopy (ExM) enables super-resolution fluorescence imaging of physically expanded biological samples with conventional microscopes. By combining expansion microscopy (ExM) with single-molecule localization microscopy (SMLM) it is potentially possible to approach the resolution of electron microscopy. However, current attempts to combine both methods remained challenging because of protein and fluorophore loss during digestion or denaturation, gelation, and the incompatibility of expanded polyelectrolyte hydrogels with photoswitching buffers. Here we show that re-embedding of expanded hydrogels enables dSTORM imaging of expanded samples and demonstrate that post-labeling ExM resolves the current limitations of super-resolution microscopy. Using microtubules as a reference structure and centrioles, we demonstrate that post-labeling Ex-SMLM preserves ultrastructural details, improves the labeling efficiency and reduces the positional error arising from linking fluorophores into the gel thus paving the way for super-resolution imaging of immunolabeled endogenous proteins with true molecular resolution.

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.

scholarly journals CorRelator: An interactive and flexible toolkit for high-precision cryo-correlative light and electron microscopy

2020 ◽  
Author(s):  
Jie E. Yang ◽  
Matthew R. Larson ◽  
Bryan S. Sibert ◽  
Samantha Shrum ◽  
Elizabeth R. Wright
Keyword(s):  
Electron Microscopy ◽  
Light And Electron Microscopy ◽  
Cryo Electron Microscopy ◽  
Cellular Environment ◽  
Transmission Electron ◽  
Desktop Application ◽  
Fluorescence Light Microscopy ◽  
Cross Platform ◽  
Fluorescence Light ◽  
Correlation Process

AbstractCryo-correlative light and electron microscopy (CLEM) is a technique that uses the spatiotemporal cues from fluorescence light microscopy (FLM) to investigate the high-resolution ultrastructure of biological samples by cryo-electron microscopy (cryo-EM). Cryo-CLEM provides advantages for identifying and distinguishing fluorescently labeled proteins, macromolecular complexes, and organelles from the cellular environment. Challenges remain on how correlation workflows and software tools are implemented on different microscope platforms to support microscopy-driven structural studies. Here, we present an open-source desktop application tool, CorRelator, to bridge between cryo-FLM and cryo-EM/ET data collection instruments. CorRelator was designed to be flexible for both on-the-fly and post-acquisition correlation schemes. The CorRelator workflow is easily adapted to any fluorescence and transmission electron microscope (TEM) system configuration. CorRelator was benchmarked under cryogenic and ambient temperature conditions using several FLM and TEM instruments, demonstrating that CorRelator is a rapid and efficient application for image and position registration in CLEM studies. CorRelator is a cross-platform software featuring an intuitive Graphical User Interface (GUI) that guides the user through the correlation process. CorRelator source code is available at: https://github.com/wright-cemrc-projects/corr.

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.

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