Super-resolution microscopy articles within Nature Communications

Featured

  • Article
    | Open Access

    Super-resolution microscopy using wavelengths in the near infrared (NIR) optical window is particularly appealing for live cell and tissue imaging, yet largely unexplored. Here the authors present NIR-STED nanoscopy of living mammalian cells using the new bacteriophytochrome-based fluorescent protein SNIFP.

    • Maria Kamper
    • , Haisen Ta
    •  & Stefan Jakobs

  • Article
    | Open Access

    Self-interacting chromatin domains encompass genes and their cis-regulatory elements. Here the authors use high-resolution chromosome conformation capture and super-resolution imaging to study a 70 kb domain that includes the mouse α-globin regulatory locus and find that a tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions.

    • Jill M. Brown
    • , Nigel A. Roberts
    •  & Veronica J. Buckle

  • Article
    | Open Access

    Processive chitinase is a linear molecular motor which moves on the surface of crystalline chitin. Here authors use single-molecule imaging, X-ray crystallography and simulations on chitinase A (SmChiA) and show that Brownian motion along the single chitin chain is rectified forward by substrate-assisted catalysis.

    • Akihiko Nakamura
    • , Kei-ichi Okazaki
    •  & Ryota Iino

  • Article
    | Open Access

    A known limitation of super-resolution STED microscopy is the need of high laser power which can cause photobleaching and phototoxicity. Here the authors further optimize this method and show that modulating STED intensity during acquisition results in an enhanced resolution and reduced background.

    • Maria J. Sarmento
    • , Michele Oneto
    •  & Luca Lanzanò

  • Article
    | Open Access

    The actin-based motor Myosin1d is needed to establish left–right asymmetry in Drosophila. Here the authors show that myosin 1d has a role in lumen formation, vacuole trafficking and left-right asymmetry establishment during zebrafish development.

    • Manush Saydmohammed
    • , Hisato Yagi
    •  & Michael Tsang

  • Article
    | Open Access

    Super-resolution microscopy often suffers from low contrast and slow recording times. Here the authors present an optical implementation which makes the fluorescent proteins’ ON–OFF switching cycles more efficient, enhancing contrast and spatio-temporal resolution in 3D cell and tissue imaging.

    • Luciano A. Masullo
    • , Andreas Bodén
    •  & Ilaria Testa

  • Article
    | Open Access

    Many RNA viruses that replicate in the cytoplasm express proteins that localize to nucleoli, but the nucleolar functions remain largely unknown. Here, the authors show that the Henipavirus matrix protein mimics an endogenous Treacle partner of the DNA-damage response, resulting in suppression of rRNA biogenesis.

    • Stephen M. Rawlinson
    • , Tianyue Zhao
    •  & Gregory W. Moseley

  • Article
    | Open Access

    Single molecule tracking of fluorescent proteins in live cells is temporally limited by fluorophore photobleaching. Here the authors show using fluorophore pairs that FRET competes with photobleaching to improve photostability and allow longer-term tracking of both single proteins and complexes.

    • Srinjan Basu
    • , Lisa-Maria Needham
    •  & Ernest D. Laue

  • Article
    | Open Access

    3D single-molecule localization is limited in depth and often requires using a wide range of point spread functions (PSFs). Here the authors present an optical solution featuring a deformable mirror to generate different PSFs and easy-to-use software for super-resolution imaging up to 5 µm deep.

    • Andrey Aristov
    • , Benoit Lelandais
    •  & Christophe Zimmer

  • Article
    | Open Access

    HIV particles contain a relatively low amount of viral envelope (Env), but underlying packaging mechanisms are poorly understood. Here, the authors use superresolution microscopy and show that Env distribution is biased toward the necks of cell-associated particles during assembly.

    • Carmen A. Buttler
    • , Nairi Pezeshkian
    •  & Schuyler B. van Engelenburg

  • Article
    | Open Access

    Self-assembled DNA nanostructures hold potential as nanomachines or platforms for organized chemical synthesis, but methods for assembly quality control are lacking. Here the authors use DNA-PAINT to quantify the incorporation and accessibility of individual strands in a DNA origami platform with molecular resolution.

    • Maximilian T. Strauss
    • , Florian Schueder
    •  & Ralf Jungmann

  • Article
    | Open Access

    Characterization of adsorbed molecular layers on surfaces is the key to wide-ranging applications, but elucidating the structure and composition of such adlayers remains challenging. Here the authors develop an approach to unveil the nanoscale structure and composition of adlayers through spectrally resolved super-resolution microscopy.

    • Limin Xiang
    • , Michal Wojcik
    •  & Ke Xu

  • Article
    | Open Access

    Nanobodies (Nbs) coupled to organic dyes are increasingly used for super-resolution cell imaging, but producing gene-specific Nbs is time-consuming. Here the authors present a peptide-tag/Nb combination for dSTORM imaging which can be easily adapted to different targets in fixed and live cells.

    • David Virant
    • , Bjoern Traenkle
    •  & Ulrich Rothbauer

  • Article
    | Open Access

    Elucidating molecular organisation requires precise localisation and analysis. Here the authors develop SODA software for automatic and quantitative mapping of statistically coupled molecules, and use it to unravel spatial organisation of thousands of synaptic proteins in SIM and 3DSTORM microscopy.

    • Thibault Lagache
    • , Alexandre Grassart
    •  & Jean-Christophe Olivo-Marin

  • Article
    | Open Access

    Quantitatively studying components of the presynapse requires high resolution optical methods. Here the authors use confocal microscopy as well as 2D- and 3D-STED nanoscopy to quantify the number and activity of active zone Ca2+ channels in inner hair cells.

    • Jakob Neef
    • , Nicolai T. Urban
    •  & Tobias Moser

  • Article
    | Open Access

    Light-sheet single-molecule 3D super-resolution microscopes can’t image close to a coverslip or may require complex apparatus. Here the authors overcome such limitations using a tilted light sheet strategy with long axial range point spread functions on a standard inverted microscope.

    • Anna-Karin Gustavsson
    • , Petar N. Petrov
    •  & W. E. Moerner

  • Article
    | Open Access

    Existing methods for nanoscale visualization of biological targets in thick samples require complex hardware. Here, the authors combine the standard spinning disk confocal (SDC) microscopy with DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) to image proteins, DNA and RNA deep in cells.

    • Florian Schueder
    • , Juanita Lara-Gutiérrez
    •  & Ralf Jungmann

  • Article
    | Open Access

    Eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that exist at the kilo-megabase scale. Here Cattoni et al. combine super-resolution microscopy with DNA-labeling methods to quantify absolute frequencies of interactions within TADs.

    • Diego I. Cattoni
    • , Andrés M. Cardozo Gizzi
    •  & Marcelo Nollmann

  • Article
    | Open Access

    The ability to quantify the organization of cell membrane molecules is limited by the density of labeling and experimental conditions. Here, the authors use super-resolution optical fluctuation (SOFI) for molecular density and clustering analyses, and investigate nanoscale distribution of CD4 glycoprotein.

    • Tomáš Lukeš
    • , Daniela Glatzová
    •  & Marek Cebecauer

  • Article
    | Open Access

    Upconversion nanoparticles, which do not suffer from the photophysical artifacts that limit fluorescent molecules, offer an exciting opportunity for biological super-resolution imaging. Here, Zhan et al. develop an efficient STED mechanism using optimized lanthanide upconversion nanoparticles, enabling cytoskeleton nanoscopic imaging.

    • Qiuqiang Zhan
    • , Haichun Liu
    •  & Sailing He

  • Article
    | Open Access

    The dopamine transporter (DAT) has a crucial role in the regulation of neurotransmission. Here, the authors use super-resolution imaging to show that DAT clusters into cholesterol-dependent membrane regions that are reversibly regulated by ionotropic glutamate receptors activation.

    • Troels Rahbek-Clemmensen
    • , Matthew D. Lycas
    •  & Ulrik Gether

  • Article
    | Open Access

    Ratiometric fluorescent pH probes are useful tools to monitor acidification of vesicles during endocytosis, but the size of vesicles is below the diffraction limit. Here the authors develop a family of ratiometric pH sensors for use in STED super-resolution microscopy, and optimize their delivery to endosomes.

    • Douglas S. Richardson
    • , Carola Gregor
    •  & Stefan W. Hell

  • Article
    | Open Access

    Respiratory syncytial virus (RSV) induces formation of inclusion bodies (IBs) sheltering viral RNA synthesis. Here, Rincheval et al. identify highly dynamic IB-associated granules (IBAGs) that accumulate newly synthetized viral mRNA and the viral M2-1 protein but exclude viral genomic RNA and RNA polymerase complexes.

    • Vincent Rincheval
    • , Mickael Lelek
    •  & Marie-Anne Rameix-Welti

  • Article
    | Open Access

    To become infectious, HIV-1 particles undergo a maturation process involving the clustering of envelope glycoprotein Env. Here, Chojnacki et al. employ super-resolution STED-FCS microscopy to study dynamics of Env molecules on HIV-1 particles and show that Env undergoes a maturation-induced increase in mobility.

    • Jakub Chojnacki
    • , Dominic Waithe
    •  & Christian Eggeling

  • Article
    | Open Access

    The contribution of ligands for cytokine receptor dimerization is still not fully understood. Here, the authors show the efficient ligand-induced dimerization of type II interleukin-4 receptor at the plasma membrane and the kinetic trapping of signalling complexes by actin-dependent membrane microdomains.

    • David Richter
    • , Ignacio Moraga
    •  & Jacob Piehler

  • Article
    | Open Access

    The measurement of molecular diffusion at sub-diffraction scales has been achieved in 2D space using STED-FCS, but an implementation for 3D diffusion is lacking. Here the authors present an analytical approach to probe diffusion in 3D space using STED-FCS and measure the diffusion of EGFP at different spatial scales.

    • Luca Lanzanò
    • , Lorenzo Scipioni
    •  & Giuseppe Vicidomini

  • Article
    | Open Access

    Phosphorylated histone H2AX is an early signalling event of DNA double-strand breaks. Here the authors use super-resolution microscopy and ChIP-seq and identify ‘nano-domains’ – chromatin loops decorated by γH2AX and flanked by CTCF.

    • Francesco Natale
    • , Alexander Rapp
    •  & M. Cristina Cardoso

  • Article
    | Open Access

    Cardiac trabeculae (which are sponge-like muscular structures) form mostly as a result of cardiomyocyte (CM) delamination in zebrafish. Here, the authors identify Nrg2a in zebrafish as a key regulator of trabeculation, and atrial and non-contractile CMs also respond to Nrg2a despite not forming trabeculae.

    • S. Javad Rasouli
    •  & Didier Y. R. Stainier

  • Article
    | Open Access

    Super-resolution localization microscopy produces biophysical information in the form of estimated positions of single molecules. Here, Lindénet al. estimate the uncertainty of single localizations, and show that this additional information can improve data analysis and localization precision.

    • Martin Lindén
    • , Vladimir Ćurić
    •  & Johan Elf

  • Article
    | Open Access

    N-acetyl-muramic acid (NAM) is a core component of the bacterial peptidoglycan (PG) cell wall, and is recognised by the innate immune system. Here the authors engineer Gram-negative and Gram-positive bacteria to incorporate a modified NAM into the backbone of PG, which can be labelled with click chemistry for imaging and tracking.

    • Hai Liang
    • , Kristen E. DeMeester
    •  & Catherine L. Grimes

  • Article
    | Open Access

    In vitro models of actin organization show the formation of vortices, asters and stars. Here Fritzsche et al. show that such actin structures form in living cells in a manner dependent on the Arp2/3 complex but not myosin, and such structures influence membrane architecture but not cortex elasticity.

    • M. Fritzsche
    • , D. Li
    •  & C. Eggeling

  • Article
    | Open Access

    Localisation microscopy enables nanometre-scale imaging of biological samples, but the method is too slow to use on dynamic systems. Here, the authors develop a mathematical model that optimises the number of frames required and estimates the maximum speed for super-resolution imaging.

    • Patrick Fox-Roberts
    • , Richard Marsh
    •  & Susan Cox

  • Article
    | Open Access

    The near-field interaction of single emitters and plasmonic structures can alter the perceived physical location of the emitter. Here, Raabet al. use DNA origami and far-field super-resolution microscopy to quantitatively evaluate this localization offset for gold nanoparticles.

    • Mario Raab
    • , Carolin Vietz
    •  & Philip Tinnefeld

  • Article
    | Open Access

    Light-matter interactions with single quantum emitters are generally difficult to measure with both high-resolution and a large field of view. Here, Johlin et al. develop far-field super-resolution fluorescence methods to map near-field emitter-nanostructure interactions over several microns.

    • Eric Johlin
    • , Jacopo Solari
    •  & Erik C. Garnett

  • Article
    | Open Access

    Live cell super-resolution imaging requires a high temporal resolution, which remains a challenge. Here the authors combine photo-activated localization microscopy (PALM) with super-resolution optical fluctuation imaging (SOFI) to achieve high spatiotemporal resolution and quantitative imaging of focal adhesion dynamics.

    • Hendrik Deschout
    • , Tomas Lukes
    •  & Aleksandra Radenovic

  • Article
    | Open Access

    Nanoscopy of non-adherent cells is currently not possible, due to their movement in solution. Here the authors immobilize and manipulate fixedE. coli by multiple optical traps; their holographic optical tweezers enable dSTORM imaging of orthogonal planes via 3D realignment of the sample.

    • Robin Diekmann
    • , Deanna L. Wolfson
    •  & Thomas Huser

  • Article
    | Open Access

    Single-molecule localization microscopy offers super-resolution imaging, but needs a long acquisition time and a toxic photochemical environment. Here, the authors demonstrate a multiple signal classification algorithm that achieves a resolution of 50 nm with as few as 50 frames in a biologically conducive environment.

    • Krishna Agarwal
    •  & Radek Macháň

  • Article
    | Open Access

    MICU1 is a regulatory subunit of mitochondrial Ca2+ channels that shields mitochondria from Ca2+ overload. Here the authors show that MICU1 methylation by PRMT1 reduces Ca2+ sensitivity, which is normalized by UCP2/3, re-establishing mitochondrial Ca2+uptake activity.

    • Corina T. Madreiter-Sokolowski
    • , Christiane Klec
    •  & Wolfgang F. Graier

  • Article
    | Open Access

    Near-infrared fluorescent proteins are non-invasive probes for deep tissue imaging, but because of the dimeric state they perform poorly in protein labelling. Here, the authors engineered three spectrally resolvable monomeric near-infrared probes with improved brightness for multiscale imaging.

    • Daria M. Shcherbakova
    • , Mikhail Baloban
    •  & Vladislav V. Verkhusha

  • Article
    | Open Access

    Super-resolution fluorescent imaging typically makes use of intense phototoxic illumination. Here the authors achieve live-cell super-resolution imaging using low-illumination standard microscopes with the aid of a new analytical approach called Super-Resolution Radial Fluctuations (SRRF), provided as an ImageJ plugin.

    • Nils Gustafsson
    • , Siân Culley
    •  & Ricardo Henriques

  • Article
    | Open Access

    The ULK1 complex is required during autophagosome nucleation, but where autophagic membranes initiate is unknown. Here the authors use super-resolution microscopy to propose that autophagosomes originate from tubulovesicular structures in the ER that align with ATG9 vesicles and recruit ULK1.

    • Eleftherios Karanasios
    • , Simon A. Walker
    •  & Nicholas T. Ktistakis

  • Article
    | Open Access

    Photon localization microscopy uses stochastic emission events from fluorescent molecules to enable super-resolution imaging, but spectroscopic information is lost. Here, the authors improve the spatial resolution of this technique with a method that also detects each blink’s fluorescence spectrum.

    • Biqin Dong
    • , Luay Almassalha
    •  & Hao F. Zhang

  • Article
    | Open Access

    There is a need to characterize devices during operation in real-time and at nanoscopic length scales. Here, King et al. perform electroluminescence-STED imaging with a polymer based light-emitting diode, revealing nanoscopic defects that would be unresolvable with traditional optical microscopy.

    • John T. King
    •  & Steve Granick

  • Article
    | Open Access

    Existing DNA stains for live cell microscopy are either toxic, require illumination with blue light, or are not compatible with super-resolution microscopy. Here the authors develop SiRHoechst, a non-toxic far-red DNA stain that is compatible with super-resolution microscopy.

    • Gražvydas Lukinavičius
    • , Claudia Blaukopf
    •  & Kai Johnsson

  • Article
    | Open Access

    Tracking and stabilizing sample drifts is crucial towards realizing nanometer resolution in superresolution microscopy; metal nanoparticles can provide drift information but diffraction remains a challenge. Here, Bonet al. combine intensity and phase information to reach three-dimensional subnanometre accuracies.

    • Pierre Bon
    • , Nicolas Bourg
    •  & Sandrine Lévêque-Fort

Browse broader subjects

Browse Super-resolution microscopy across other nature.com journals