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Super-resolution microscopy

Popularization of super-resolution imaging techniques has allowed cell biologists to probe cell structure and function in previously unattainable detail. These methodologies continue to evolve, with new improvements that allow tailoring the available techniques to a particular need and application. This collection showcases primary research articles, reviews and protocols and highlights these recent developments by exemplifying the new, interesting applications of super-resolution microscopy as well as related tool development. We hope that this compilation of works will inspire future research with the aim to resolve outstanding challenges and further expand the utility of super-resolution imaging across biological and medical disciplines. 


  • Nature Methods | Perspective

    This Perspective reviews nanoscopy via stimulated emission depletion (STED), focusing on challenges for biologists and how technical advances are helping to meet these challenges.

    • Giuseppe Vicidomini
    • , Paolo Bianchini
    •  &  Alberto Diaspro
  • Nature Reviews Neuroscience | Review Article

    An axon's function is dictated by its morphology and, thus, by the properties and organization of the axonal cytoskeleton. Leterrier et al. describe how advances in super-resolution and live-cell imaging are transforming our understanding of the molecular architecture of the axonal shaft.

    • Christophe Leterrier
    • , Pankaj Dubey
    •  &  Subhojit Roy
  • Nature Reviews Molecular Cell Biology | Review Article

    Fluorescence nanoscopy enables the optical imaging of cellular components with resolutions at the nanometre scale. With the growing availability of super-resolution microscopes, nanoscopy methods are being increasingly applied. Quantitative, multicolour, live-cell nanoscopy and the corresponding labelling strategies are under continuous development.

    • Steffen J. Sahl
    • , Stefan W. Hell
    •  &  Stefan Jakobs
  • Nature Reviews Chemistry | Review Article

    Synaptic vesicles participate in neuronal communication by storing and releasing neurotransmitter molecules. The neurotransmitters can be detected using electrochemistry and mass spectrometry, and vesicle structural elements can be detected by super-resolution microscopy. This Review describes these analytical techniques and how they unravel the mechanisms of cell communication.

    • Nhu T. N. Phan
    • , Xianchan Li
    •  &  Andrew G. Ewing
  • Nature Reviews Microbiology | Review Article

    In this Review, De Niz et al. discuss the contribution of key imaging tools to advances in our understanding of Plasmodium spp. biology and host–pathogen interactions over the past decade. These advances, pertaining to parasite structure and motility, as well as the liver and blood stages, have led to paradigm shifts in our knowledge of malaria.

    • Mariana De Niz
    • , Paul-Christian Burda
    • , Gesine Kaiser
    • , Hernando A. del Portillo
    • , Tobias Spielmann
    • , Freddy Frischknecht
    •  &  Volker T. Heussler

Applications in biology

  • Nature Neuroscience | Article

    The authors show that Munc13-1 molecules form multiple supramolecular self-assemblies that serve as vesicular release sites. Having multiple Munc13-1 assemblies affords a stable synaptic weight, which confers robustness of synaptic computation.

    • Hirokazu Sakamoto
    • , Tetsuroh Ariyoshi
    • , Naoya Kimpara
    • , Kohtaroh Sugao
    • , Isamu Taiko
    • , Kenji Takikawa
    • , Daisuke Asanuma
    • , Shigeyuki Namiki
    •  &  Kenzo Hirose
  • Nature | Letter

    In budding yeast, glucose withdrawal, via the Rag GTPases, leads to TORC1 inhibition through its re-organization into a giant, vacuole-associated helix named a TOROID (TORC1 organized in inhibited domain).

    • Manoël Prouteau
    • , Ambroise Desfosses
    • , Christian Sieben
    • , Clélia Bourgoint
    • , Nour Lydia Mozaffari
    • , Davide Demurtas
    • , Alok K. Mitra
    • , Paul Guichard
    • , Suliana Manley
    •  &  Robbie Loewith
  • Nature Cell Biology | Article

    Shi et al. map the ciliary transition zone by STORM imaging, characterizing protein arrangements in nested rings and finding that mutations in RPGRIP1L that are associated with the ciliopathy Joubert syndrome disrupt SMO ciliary localization.

    • Xiaoyu Shi
    • , Galo Garcia III
    • , Julie C. Van De Weghe
    • , Ryan McGorty
    • , Gregory J. Pazour
    • , Dan Doherty
    • , Bo Huang
    •  &  Jeremy F. Reiter
  • Nature Microbiology | Article

    Deubiquitinase OTULIN targets linear (M1-linked) ubiquitin chain patches on cytosolic Salmonella Typhimurium to modulate NEMO, IKKα/IKKβ and NF-ĸB signalling and regulate secretion of pro-inflammatory cytokines and bacterial proliferation.

    • Sjoerd J. L. van Wijk
    • , Franziska Fricke
    • , Lina Herhaus
    • , Jalaj Gupta
    • , Katharina Hötte
    • , Francesco Pampaloni
    • , Paolo Grumati
    • , Manuel Kaulich
    • , Yu-shin Sou
    • , Masaaki Komatsu
    • , Florian R. Greten
    • , Simone Fulda
    • , Mike Heilemann
    •  &  Ivan Dikic

Methods & Protocols

  • Nature Photonics | Letter

    A spatial resolution of 30 nm (=λ/31) exceeding the diffraction limit is achieved by super-resolution fluorescence microscopy. The nanoscopic imaging scheme can be applied to coherent quantum-mechanical systems such as quantum dots, as well as colour centres.

    • Timo Kaldewey
    • , Andreas V. Kuhlmann
    • , Sascha R. Valentin
    • , Arne Ludwig
    • , Andreas D. Wieck
    •  &  Richard J. Warburton
  • Nature Communications | Article | open

    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
    • , Zuzana Kvíčalová
    • , Florian Levet
    • , Aleš Benda
    • , Sebastian Letschert
    • , Markus Sauer
    • , Tomáš Brdička
    • , Theo Lasser
    •  &  Marek Cebecauer
  • Nature Communications | Article | open

    Studying interactions between lysosomes and mitochondria in living cells is difficult due to the limitations of existing probes. Here, the authors develop new cell-permeable fluorescent probes to image the dynamics of lysosomes and their physical interactions with mitochondria using super-resolution microscopy.

    • Yubing Han
    • , Meihua Li
    • , Fengwu Qiu
    • , Meng Zhang
    •  &  Yu-Hui Zhang
  • Nature Methods | Article

    An automated system for data acquisition and analysis enables high-content screening localization microscopy and increases the throughput and information content of super-resolution microscopy methods such as dSTORM, DNA-PAINT and (spt)PALM.

    • Anne Beghin
    • , Adel Kechkar
    • , Corey Butler
    • , Florian Levet
    • , Marine Cabillic
    • , Olivier Rossier
    • , Gregory Giannone
    • , Rémi Galland
    • , Daniel Choquet
    •  &  Jean-Baptiste Sibarita
  • Nature Communications | Article | open

    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
    • , Baoju Wang
    • , Qiusheng Wu
    • , Rui Pu
    • , Chao Zhou
    • , Bingru Huang
    • , Xingyun Peng
    • , Hans Ågren
    •  &  Sailing He
  • Nature Communications | Article | open

    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
    • , Franziska R. Winter
    • , Nicolai T. Urban
    • , Steffen J. Sahl
    • , Katrin I. Willig
    •  &  Stefan W. Hell

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