Super-resolution microscopy articles within Nature Communications

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  • Article
    | Open Access

    Application of correlative light and electron microscopy (CLEM) in plants remains challenging. Here, the authors use Click-iT chemistry as a tool for CLEM, due to its unique properties in resin permeability and super-resolution microscopy. They use this approach to study cellular physiology in Arabidopsis.

    • Michal Franek
    • , Lenka Koptašíková
    •  & Jíří Fajkus

  • Article
    | Open Access

    Current approaches for volumetric super-resolution microscopy can yield large and complex PSF spatial footprints. Here, the authors show a super-resolution microscopy approach using a hexagonal microlens array, which offers speed improvements in volumetric imaging compared to other single-molecule methods.

    • Sam Daly
    • , João Ferreira Fernandes
    •  & Steven F. Lee

  • Article
    | Open Access

    There is a lack of universal tools to analyse protein assemblies and quantify underlying structures in single-molecule localization microscopy. Here, the authors present SEMORE, a semi-automatic machine learning framework for system- and input-dependent analysis of super-resolution data.

    • Steen W. B. Bender
    • , Marcus W. Dreisler
    •  & Nikos S. Hatzakis

  • Article
    | Open Access

    Researchers developed an open-hardware structured illumination microscopy add-on. This affordable upgrade provides super-resolution capabilities for normal optical microscopes. Detailed instructions enable easy reproduction to help democratize advanced microscopy.

    • Mélanie T. M. Hannebelle
    • , Esther Raeth
    •  & Georg E. Fantner

  • Article
    | Open Access

    Stimulator of interferon genes (STING) is known to translocate from ER to Golgi while orchestrating type I interferon responses to DNA. Here, the authors show single-molecule resolution images of STING clustering at the trans-Golgi network, where it acts as a scaffold to trigger downstream signaling.

    • Haruka Kemmoku
    • , Kanoko Takahashi
    •  & Tomohiko Taguchi

  • Article
    | Open Access

    The wide variety of cellular processes involving biomolecular condensation makes their quantification a challenging task. Here, the authors present an integrated platform based on single-photon microscopy to study complex biomolecular processes.

    • Eleonora Perego
    • , Sabrina Zappone
    •  & Giuseppe Vicidomini

  • Article
    | Open Access

    The detailed 3D organization of human centromere components is unknown. Here, the authors use super-resolution microscopy to present a working model for a common core centromere structure.

    • Ayantika Sen Gupta
    • , Chris Seidel
    •  & Jennifer L. Gerton

  • Article
    | Open Access

    The authors present phase intensity nanoscope (PINE), which uses an integrated phase-intensity multilayer thin film to localize randomly distributed nanoprobes and resolve sub-10 nm cellular architectures. They demonstrate dynamic imaging of nanoscopic reorganization over 250 h and find that nanoscale rearrangements emerging into macroscale rearrangements are synchronized.

    • Guangjie Cui
    • , Yunbo Liu
    •  & Somin Eunice Lee

  • Article
    | Open Access

    The optical field inside a nanophotonic particle accelerator is revealed. To this end, the authors developed a field imaging technique for spatial and spectral resolution on the nanometer scale.

    • Tal Fishman
    • , Urs Haeusler
    •  & Ido Kaminer

  • Article
    | Open Access

    Current liquid-based optical clearing protocols can suffer from solvent evaporation and photobleaching. Here, the authors develop a solid high-refractive-index polymer to embed mouse and human tissues for clearing and antifade high-resolution 3D imaging.

    • Fu-Ting Hsiao
    • , Hung-Jen Chien
    •  & Shiue-Cheng Tang

  • Article
    | Open Access

    Existing single-molecule localization microscopy analyses overlook important temporal information in living cells. Here, the authors report nanoscale spatiotemporal indexing clustering (NASTIC), which leverages a video game algorithm to fast-track the investigation of the complex temporal dynamics of protein clustering.

    • Tristan P. Wallis
    • , Anmin Jiang
    •  & Frédéric A. Meunier

  • Article
    | Open Access

    Multi-frame super-resolution microscopy is hampered by long acquisition times and phototoxicity, which hinder its use for live-cell imaging. Here, authors propose a deep-learning-based single-frame super-resolution approach to image cellular dynamics with high spatiotemporal resolution.

    • Rong Chen
    • , Xiao Tang
    •  & Shuhuai Yao

  • Article
    | Open Access

    Single-molecule 3D tracking is critical to understand macromolecular dynamics but achieving this at a sub-millisecond resolution remains challenging. Here the authors present a 3D tracking method based on cross-entropy minimization and the true excitation point spread function.

    • Elias Amselem
    • , Bo Broadwater
    •  & Johan Elf

  • Article
    | Open Access

    The antigen-B-cell-receptor interaction is the driving force of terminal B cell development that spans from B cell activation to antibody secreting plasma cells. Here authors determine, using DNA-PAINT super-resolution microscopy, how antigen affinity and valency define antigen binding to BCR in an in vitro system allowing precision control of these parameters.

    • Alexey Ferapontov
    • , Marjan Omer
    •  & Søren Egedal Degn

  • Article
    | Open Access

    Visualizing endogenous GPCRs is challenging. Here the authors generate mice with an enzyme self-label genome-edited into the endogenous glucagon-like peptide-1 receptor locus, design fluorescent dyes for specific labelling in complex tissue, and reveal tissue-level organisation and dynamics of an endogenous class B GPCR.

    • Julia Ast
    • , Daniela Nasteska
    •  & David J. Hodson

  • Article
    | Open Access

    Structured Illumination Microscopy allows for the visualization of biological structures at resolutions below the diffraction limit, but this imaging modality is still hampered by high experimental complexity. Here, the authors present a combination of interferometry and machine learning to construct a structured illumination microscope for super resolution imaging of dynamic sub-cellular biological structures in multiple colors.

    • Edward N. Ward
    • , Lisa Hecker
    •  & Clemens F. Kaminski

  • Article
    | Open Access

    Super-resolution microscopy techniques can be challenging for live cells and thick samples. Here, the authors propose a method to reduce beam intensity and remove out-of-focus fluorescence background in image-scanning microscopy (ISM) and its combination with stimulated emission depletion (STED).

    • Giorgio Tortarolo
    • , Alessandro Zunino
    •  & Giuseppe Vicidomini

  • Article
    | Open Access

    The presented Mean-Shift Super Resolution (MSSR) algorithm can extend spatial resolution within a single microscopy image. Its applicability extends across a wide range of experimental and instrumental configurations and it is compatible with other super-resolution microscopy approaches.

    • Esley Torres-García
    • , Raúl Pinto-Cámara
    •  & Adán Guerrero

  • Article
    | Open Access

    Spatially resolved proteomics is an emerging approach for mapping proteome heterogeneity. Here, the authors report a method based on the combination of hydrogel-based tissue transformation with mass spectrometry-based proteomics, that enables proteome profiling with a lateral resolution of 160 µm.

    • Lu Li
    • , Cuiji Sun
    •  & Kiryl D. Piatkevich

  • Article
    | Open Access

    Single-molecule localization microscopy relies on stochastic blinking events, treated as independent events without assignment to a particular emitter. Here, BaGoL takes low precision localizations generated from multiple emitter blinkings during DNAPAINT and dSTORM and finds the underlying emitter positions with high precision.

    • Mohamadreza Fazel
    • , Michael J. Wester
    •  & Keith A. Lidke

  • Article
    | Open Access

    The authors demonstrate a label-free superresolution imaging method by using a hyperbolic material as a substrate for tailored light-matter interactions. The hyperbolic material enhanced scattering, combined with dark-field detection, result in 5.5-fold resolution improvement beyond the diffraction limit.

    • Yeon Ui Lee
    • , Shilong Li
    •  & Zhaowei Liu

  • Article
    | Open Access

    The authors report high-efficiency emission depletion through a surface migration emission depletion mechanism, which takes advantage of the effects of surface quenching and energy migration in nanocrystals. They demonstrate super-resolution microscopy with very low depletion saturation intensities.

    • Rui Pu
    • , Qiuqiang Zhan
    •  & Xiaogang Liu

  • Article
    | Open Access

    Trypanosomes can sense signal molecules and coordinate their movement in response to such signals, a phenomenon termed social motility (SoMo). Here, Bachmaier et al show that cyclic AMP response protein 3 (CARP3) localization to the flagellar tip and its interaction with a number of different adenylate cyclases is essential for migration to tsetse fly salivary glands and for SoMo, therewith linking SoMo and cAMP signaling to trypanosome transmission.

    • Sabine Bachmaier
    • , Giacomo Giacomelli
    •  & Michael Boshart

  • Article
    | Open Access

    DNA-PAINT image acquisition is limited by speed. Here the authors use the neural network DeepSTORM to predict fluorophore positions from high emitter density DNA-PAINT data in order to achieve image acquisition in one minute; they demonstrate multi-colour and large-area imaging of semi-thin neuronal tissue.

    • Kaarjel K. Narayanasamy
    • , Johanna V. Rahm
    •  & Mike Heilemann

  • Article
    | Open Access

    Meshworks of claudin polymers control the paracellular transport and barrier properties of epithelial tight junctions. Here, the authors show different claudin nanoscale organization principles, finding that claudin segregation enables barrier formation and paracellular ion flux across tight junctions.

    • Hannes Gonschior
    • , Christopher Schmied
    •  & Martin Lehmann

  • Article
    | Open Access

    Podosomes are actin structures important in multiple cell functions. Here, the authors use iPALM microscopy to reveal an “hourglass” shape of the podosome actin core, a protruding “knob” at the bottom of the core, and two actin networks extending from it.

    • J. Cody Herron
    • , Shiqiong Hu
    •  & Klaus M. Hahn

  • Article
    | Open Access

    Here, the authors develop a UV-compatible photonic integrated circuit for structured illumination microscopy on a conventional wide-field microscope. Operating at a wavelength of 360 nm, they generate switchable far-field fringe patterns, and demonstrate autofluorescence imaging of yeast cells.

    • Chupao Lin
    • , Juan Santo Domingo Peñaranda
    •  & Nicolas Le Thomas

  • Article
    | Open Access

    Stress granules are non-membranous organelles connected to stress responses and age-related disease. Here, the authors identify a conserved yeast protein, Lsm7, that facilitates stress granule formation through dynamic liquid-liquid phase separation condensates upon 2-deoxy-D-glucose-induced stress.

    • Michelle Lindström
    • , Lihua Chen
    •  & Beidong Liu

  • Article
    | Open Access

    A subset of uropathogenic Escherichia coli are able to halt division and grow into highly filamentous cells during infection of bladder epithelial cells. Here, authors aim to determine the mechanism, and understand the dynamics of cell division machinery during infection-related filamentation.

    • Bill Söderström
    • , Matthew J. Pittorino
    •  & Iain G. Duggin

  • Article
    | Open Access

    Here, the authors generated an artificial RNA molecule, or aptamer, specific for the Amyotrophic Lateral Sclerosis protein TDP-43. By interacting avidly with its target, the aptamer can be exploited to track TDP-43 phase transition in vitro and in cells.

    • Elsa Zacco
    • , Owen Kantelberg
    •  & Gian Gaetano Tartaglia

  • Article
    | Open Access

    Multi-channel SMLM imaging is powerful. Here the authors report globLoc, a GPU-based global fitting algorithm, to extract maximum information from multichannel single molecule data; this gives improved localisation precision for biplane and 4Pi-SMLM and colour assignment in multi-colour astigmatic SMLM.

    • Yiming Li
    • , Wei Shi
    •  & Jonas Ries

  • Article
    | Open Access

    The authors introduce stimulated-emission induced excitation depletion (STExD) nanoscopy using a single pair of low-power, near-infrared, continue-wave lasers. Emission of multichromatic probes is inhibited by cascade amplified depletion in lanthanide upconversion systems induced by manipulating their common sensitizer.

    • Xin Guo
    • , Rui Pu
    •  & Qiuqiang Zhan

  • Article
    | Open Access

    The actin-based molecular motors, myosins, have also been linked to transcription, but their precise role has remained elusive. Here the authors show RNA polymerase II (RNAPII) is lost from chromatin upon myosin perturbation and that myosin acts as a molecular anchor to maintain RNAPII spatial organisation.

    • Yukti Hari-Gupta
    • , Natalia Fili
    •  & Christopher P. Toseland

  • Article
    | Open Access

    Focus-locking improves localization precision in single-molecule microscopy, but fiducials are often deposited at random and provide limited 3D compensation. Here, the authors fabricate 3D optical fiducials with nanometer accuracy by two-photon direct laser writing, and demonstrate isotropic 3D focus locking.

    • Simao Coelho
    • , Jongho Baek
    •  & Katharina Gaus

  • Article
    | Open Access

    Site-specific labelling of proteins can be performed with unnatural amino acids combined with bioorthogonal click chemistry. Here the authors establish this in living neurons, using neurofilament light chain; they show combination with CRISPR/Cas9 engineering to tag the endogenous protein.

    • Aleksandra Arsić
    • , Cathleen Hagemann
    •  & Ivana Nikić-Spiegel

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