Super-resolution microscopy articles within Nature Communications

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  • Article
    | Open Access

    Single-molecule localisation microscopy does not give orientation information. Here the authors combine Stochastic Optical Reconstruction Microscopy (STORM) with single molecule orientation and wobbling measurements using four-polarisation image splitting, 4polar-STORM.

    • Caio Vaz Rimoli
    • , Cesar Augusto Valades-Cruz
    •  & Sophie Brasselet

  • Article
    | Open Access

    Super-resolution quantal imaging relates transmission at excitatory synapses to presynaptic molecular composition. The authors find that evoked transmission varies greatly between synapses and is uncorrelated and physically separate from spontaneous transmission, and identify responsible presynaptic proteins.

    • Zachary L. Newman
    • , Dariya Bakshinskaya
    •  & Ehud Y. Isacoff

  • Article
    | Open Access

    Cilia are microtubule-based organelles containing proteins transported from the cell body. Here, the authors show that the multicilia of mouse ependymal cells contain ribosomal components, tubulin mRNA,18 S rRNA and nascent tubulin peptides, suggesting local translation in the ciliary compartment.

    • Kai Hao
    • , Yawen Chen
    •  & Xueliang Zhu

  • Article
    | Open Access

    ATG9A is transmembrane autophagic machinery protein that delivers phospholipids to expanding autophagosomes. Mailler et al. show that ATG9A is required to mobilize lipids from lipid droplets for autophagosome expansion as well as mitochondrial fatty acid import and β-oxidation.

    • Elodie Mailler
    • , Carlos M. Guardia
    •  & Juan S. Bonifacino

  • Article
    | Open Access

    Visualisation of TARP localisation is hindered by existing imaging tools. Here the authors report a labelling and imaging platform using genetic code expansion and non-canonical amino acids; they use this to fluorescently label live neurons and localise TARP proteins using super resolution microscopy.

    • Diogo Bessa-Neto
    • , Gerti Beliu
    •  & Daniel Choquet

  • Article
    | Open Access

    Cellular deformations are largely driven by contractile forces generated by myosin motors in the submembraneous actin cortex. Here we show that these forces are controlled not simply by cortical myosin levels, but rather by myosins spatial arrangement, specifically the extent of their overlap with cortical actin.

    • Binh An Truong Quang
    • , Ruby Peters
    •  & Ewa K. Paluch

  • Article
    | Open Access

    Molecular orientation is often ignored during single-molecule localisation microscopy. Here, the authors use a Vortex point spread function in order to simultaneously estimate the 3D position, dipole orientation and degree of rotational constraint, within 30% of the Cramér-Rao bound limit.

    • Christiaan N. Hulleman
    • , Rasmus Ø. Thorsen
    •  & Bernd Rieger

  • Article
    | Open Access

    Determining the quality of localisation microscopy images is currently challenging. Here the authors report use of the Haar wavelet kernel analysis (HAWK) Method for the Assessment of Nanoscopy, termed HAWKMAN, to assess the reliability of localisation information.

    • Richard J. Marsh
    • , Ishan Costello
    •  & Susan Cox

  • Article
    | Open Access

    The authors have recently developed molecular force microscopy (MFM) which uses fluorescence polarisation to measure cell-surface receptor force orientation. Here they show that structured illumination microscopes, which inherently use fluorescence polarisation, can be used for MFM in a turn-key manner.

    • Aaron Blanchard
    • , J. Dale Combs
    •  & Khalid Salaita

  • Article
    | Open Access

    Calcium signals initiated by IP3 receptors in ER membranes regulate most cellular activities. Here, the authors show that KRas-induced actininteracting protein (KRAP) tethers a small subset of IP3 receptors to actin and licenses them to evoke cytosolic calcium signals.

    • Nagendra Babu Thillaiappan
    • , Holly A. Smith
    •  & Colin W. Taylor

  • Article
    | Open Access

    The authors demonstrate accurate localization in three dimensions by comprehensive calibration of an ordinary microscope, exploiting the latent information of intrinsic aberrations. Rigid transformation of the emitter positions tests the method and enables measurements in six degrees of freedom.

    • Craig R. Copeland
    • , Craig D. McGray
    •  & Samuel M. Stavis

  • Article
    | Open Access

    CD45 limits T cell activation, so its exclusion from the T cell immunological synapse is thought to occur as a means to enable TCR signalling. Here the authors use a variety of cellular imaging methods to show that CD45 is indeed excluded from the tips of the T cell microvilli and that this occurs prior to contact with antigen, indicating this exclusion is one of the initiating factors for antigen presentation and T cell activation.

    • Yunmin Jung
    • , Lai Wen
    •  & Klaus Ley

  • Article
    | Open Access

    Particle fusion can improve signal-to-noise ratio in single molecule localization microscopy, but is limited by structural heterogeneity. Here, the authors demonstrate an unsupervised classification method that differentiates structurally different DNA origami structures without prior knowledge.

    • Teun A.P.M. Huijben
    • , Hamidreza Heydarian
    •  & Bernd Rieger

  • Article
    | Open Access

    Gangliosides such as GM1 present in the outer leaflet of the plasma membrane of eukaryotic cells are essential for many cellular functions and pathogenic interactions. Here the authors show that the acyl chain structure of GM1 determines the establishment of nanodomains when actively clustered by actin, which depended on membrane cholesterol and phosphatidylserine or superimposed by the GM1-binding bacterial cholera toxin.

    • Senthil Arumugam
    • , Stefanie Schmieder
    •  & Ludger Johannes

  • Article
    | Open Access

    Super-resolution microscopy is often limited by photobleaching or uneven distribution of fluorophores. The authors present a label-free superresolution method termed VISTA, combining sample-expansion and vibrational imaging, with resolution down to 78 nm in protein-rich biological structures in cells and tissues.

    • Chenxi Qian
    • , Kun Miao
    •  & Lu Wei

  • Article
    | Open Access

    Recent advances in super-resolution microscopy have made it possible to measure chromatin 3D structure and transcription in thousands of single cells. Here, authors present a deep learning-based approach to characterise how chromatin structure relates to transcriptional state of individual cells and determine which structural features of chromatin regulation are important for gene expression state.

    • Aparna R. Rajpurkar
    • , Leslie J. Mateo
    •  & Alistair N. Boettiger

  • Article
    | Open Access

    It is difficult to apply SMLM to complex biological tissues. Here the authors report REALM, Robust and Effective Adaptive Optics in Localisation Microscopy, to improve SMLM in tissue and use this to resolve the organisation of spectrin in the axon initial segment in brain tissue.

    • Marijn E. Siemons
    • , Naomi A. K. Hanemaaijer
    •  & Lukas C. Kapitein

  • Article
    | Open Access

    Optical aberrations in Structured Illumination Microscopy (SIM) can lead to loss of resolution and artifacts making it unsuitable for thick samples. Here the authors combine Adaptive Optics and SIM (AO-3DSIM) to improve the 3D resolution and reduce artifacts, performing 3D-SIM in C.elegans.

    • Ruizhe Lin
    • , Edward T. Kipreos
    •  & Peter Kner

  • Article
    | Open Access

    The authors introduce stochastic optical scattering localization imaging (SOSLI) for non-invasive super-resolution imaging through scattering media. They capture multiple speckle patterns of photo-switchable point sources and use the speckle correlation to retrieve images with 100 nm resolution.

    • Dong Wang
    • , Sujit K. Sahoo
    •  & Cuong Dang

  • Article
    | Open Access

    Diffractive optical elements are broadly used due to their ability to reshape the wavefront efficiently and conveniently. By using liquid immersion, the authors here enable microscale 3D-printed optics to behave like nanoscopic structures while maintaining high performance.

    • Reut Orange-Kedem
    • , Elias Nehme
    •  & Yoav Shechtman

  • Article
    | Open Access

    Uniform illumination is a prerequisite for quantitative analyses in both classical fluorescence microscopy and single molecule localisation microscopy. Here, the authors introduce ASTER, an illumination technique that generates uniform illumination over large and adaptable fields of view, compatible with epifluorescence, HiLo and TIRF illumination schemes.

    • Adrien Mau
    • , Karoline Friedl
    •  & Sandrine Lévêque-Fort

  • Article
    | Open Access

    Adaptation of current algorithms to 3D SMLM data is currently problematic. Here the authors report a method that increases the signal-to-noise ratio and resolution of 3D single particle analysis in localization microscopy and enables determination of the symmetry groups of macromolecular complexes.

    • Hamidreza Heydarian
    • , Maarten Joosten
    •  & Bernd Rieger

  • Article
    | Open Access

    In the genome, repetitive guanine-rich sequences have the potential to spontaneously fold into non-canonical DNA secondary structures known as G-quadruplex (G4). Using novel single-molecule imaging approaches, the authors reveal that G4 formation within active replication forks locally perturb replisome dynamics and damage response signaling, which require RPA and FANCJ for regulation.

    • Wei Ting C. Lee
    • , Yandong Yin
    •  & Eli Rothenberg

  • Article
    | Open Access

    Encoding data in DNA is a promising approach to high density data storage. Here the authors present a prototype sequencing-free method that uses the spatial orientation of DNA strands with super-resolution microscopy readout.

    • George D. Dickinson
    • , Golam Md Mortuza
    •  & William L. Hughes

  • Article
    | Open Access

    Super-resolution microscopy and single molecule fluorescence spectroscopy require optimisation of the temporal or spatial resolution, which are usually mutually exclusive. Here the authors report a GPU-supported, camera-based strategy to achieve high spatial and temporal resolution from the same dataset.

    • Jagadish Sankaran
    • , Harikrushnan Balasubramanian
    •  & Thorsten Wohland

  • Article
    | Open Access

    Structured illumination microscopy is usually limited to 2 times spatial resolution improvement over the diffraction limit. Here, the authors introduce a metamaterial structure to generate speckle-like sub-diffraction limit illumination patterns in the near field, and achieve a 7-fold resolution improvement down to 40 nm.

    • Yeon Ui Lee
    • , Junxiang Zhao
    •  & Zhaowei Liu

  • Article
    | Open Access

    Supercritical angle localisation microscopy (SALM) allows the z-positions of single fluorophores to be extracted from the intensity of supercritical angle fluorescence. Here the authors improve the z-resolution of SALM, and report nanometre isotropic localisation precision on DNA origami structures.

    • Anindita Dasgupta
    • , Joran Deschamps
    •  & Jonas Ries

  • Article
    | Open Access

    Single-molecule localisation microscopy is limited by low labeling and detection efficiencies of the molecular probes. Here the authors report a framework to obtain absolute molecular quantities on a true molecular scale; the data reveal a ternary adhesion complex underlying cell-matrix adhesion.

    • Lisa S. Fischer
    • , Christoph Klingner
    •  & Carsten Grashoff

  • Article
    | Open Access

    How PRC1 recognises and interacts with its target genes remains poorly understood. Here, the authors use genome engineering and single particle tracking to dissect how PRC1 binds to chromatin in live mouse embryonic stem cells, revealing that this repressor is highly dynamic, with only a small fraction stably interacting with chromatin.

    • Miles K. Huseyin
    •  & Robert J. Klose

  • Article
    | Open Access

    Achieving high axial resolution is challenging in single-molecule localization microscopy. Here, the authors present a photometric method to decode the axial position of single molecules in a total internal reflection fluorescence microscope without hardware modification, and show nearly isotropic nanometric resolution.

    • Alan M. Szalai
    • , Bruno Siarry
    •  & Fernando D. Stefani

  • Article
    | Open Access

    DNA-PAINT is a super-resolution imaging technique which suffers from high background signals and non-specific binding. Here the authors report Repeat DNA-PAINT which is capable of supressing background noise and preventing photoinduced site loss, as well as decreasing the time taken for the sampling process.

    • Alexander H. Clowsley
    • , William T. Kaufhold
    •  & Christian Soeller

  • Article
    | Open Access

    Standard benchmarking of single-molecule localization microscopy cannot quantify nanoscale accuracy of arbitrary datasets. Here, the authors present Wasserstein-induced flux, a method using a chosen perturbation and knowledge of the imaging system to measure confidence of individual localizations.

    • Hesam Mazidi
    • , Tianben Ding
    •  & Matthew D. Lew

  • Article
    | Open Access

    The role of cohesin in organizing a functional nuclear architecture remains poorly understood. Here the authors show that cohesin depleted cells pass through endomitosis forming a multilobulated nucleus able to proceed through S-phase with typical features of active and inactive nuclear compartments and spatio-temporal patterns of replication domains.

    • Marion Cremer
    • , Katharina Brandstetter
    •  & Thomas Cremer

  • Article
    | Open Access

    The assembly of actin filaments into distinct cytoskeletal structures plays a critical role in cell physiology. Here, the authors use a combination of live cell imaging and in vitro single molecule binding measurements to show that tandem calponin homology domains (CH1–CH2) are sensitive to actin filament conformation, biasing their subcellular localization.

    • Andrew R. Harris
    • , Pamela Jreij
    •  & Daniel A. Fletcher

  • Article
    | Open Access

    Open standard microscopy is urgently needed to give low-cost solutions to researchers and to overcome the reproducibility crisis in science. Here the authors present a 3D-printed, open-source modular microscopy toolbox UC2 (You. See. Too.) for a few hundred Euros.

    • Benedict Diederich
    • , René Lachmann
    •  & Rainer Heintzmann

  • Article
    | Open Access

    Determining the orientation of single molecules in super resolution imaging is challenging. Here, by adding polarization control to phase control in the Fourier plane of the imaging path, parameters such as 3D spatial position, 3D orientation and wobbling or dithering angle can be determined from single molecules.

    • Valentina Curcio
    • , Luis A. Alemán-Castañeda
    •  & Miguel A. Alonso

  • Perspective
    | Open Access

    Despite their widespread use, many fundamental questions about the internal structure of microgels are still open. Here the authors describe several pathways toward a complete understanding of microgel colloids based on recent experimental advances in nanoscale characterization.

    • Frank Scheffold

  • Article
    | Open Access

    DNA-PAINT is a powerful super-resolution imaging method but is limited in speed due to slow exchange kinetics of the imaging strand. Here the authors present a method involving the addition of ethylene carbonate to the imaging buffer and modifications to the docking strand to improve the quality and speed of DNA-PAINT.

    • Fehmi Civitci
    • , Julia Shangguan
    •  & Xiaolin Nan

  • Article
    | Open Access

    High density environmentally sensitive (HIDE) probes allow for long time-lapse super-resolution imaging of live cells. Here the authors develop a second HIDE probe with a bio-orthogonal labelling strategy to enable two-color nanoscopy of two organelles over extended periods.

    • Ling Chu
    • , Jonathan Tyson
    •  & Derek K. Toomre

  • Article
    | Open Access

    p53 mutants can promote tumorigenesis by affecting fundamental cellular pathways and functions. In this study, the authors demonstrate a novel mutant-p53/HIF1α/miR-30d axis that impacts Golgi structure, trafficking, and secretion of proteins essential for tumor growth and metastasis.

    • Valeria Capaci
    • , Lorenzo Bascetta
    •  & Giannino Del Sal

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