Super-resolution microscopy articles within Nature Communications

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  • Article
    | Open Access

    Imaging specific proteins in the ultrastructural context largely relies on correlative light/electron microscopy, but fluorophore incompatibility and registration issues limit its use. Here the authors develop an expansion microscopy method with pan-labeling of the proteome to obtain EM-equivalent light microscopy images.

    • Ons M’Saad
    •  & Joerg Bewersdorf

  • Article
    | Open Access

    The authors test expansion microscopy protocols for investigation of the molecular organisation of mammalian synaptonemal complexes (SCs) with structured illumination microscopy. They show that the molecular structure is preserved during expansion and ultrastructural details of SCs can be revealed.

    • Fabian U. Zwettler
    • , Marie-Christin Spindler
    •  & Markus Sauer

  • Article
    | Open Access

    Here, the authors generalize cumulant analysis by extending it into the spectral domain to allow multicolour super-resolution optical fluctuation imaging. The simultaneous acquisition of two spectral channels followed by spectral cross-cumulant analysis and unmixing allows denser spectral and spatial sampling of the super-resolved image.

    • K. S. Grußmayer
    • , S. Geissbuehler
    •  & T. Lasser

  • Article
    | Open Access

    Astrocytic Ca2+ signals can be fast and local, supporting the idea that astrocytes have the ability to regulate single synapses. Here, the authors report the organization of astrocytes at nanoscale level and identify nodes as a functional astrocytic component of tripartite synapses.

    • Misa Arizono
    • , V. V. G. Krishna Inavalli
    •  & U. Valentin Nägerl

  • Article
    | Open Access

    The organisation of plasma membrane receptors is important for their function. Here the authors combine lattice light-sheet microscopy with 3D single-molecule localisation microscopy (dSTORM) and single-particle tracking to study the distribution and motility of several surface receptors.

    • Felix Wäldchen
    • , Jan Schlegel
    •  & Markus Sauer

  • Article
    | Open Access

    Lipid droplets are organelles that regulate lipid metabolism but if organellar contacts play a role during lipolysis is unclear. Here, the authors show that peroxisomes and peroxisomal protein PEX5 play pivotal roles in the spatial and temporal regulation of fasting-induced lipolysis by translocating ATGL onto lipid droplets

    • Jinuk Kong
    • , Yul Ji
    •  & Jae Bum Kim

  • Article
    | Open Access

    Glucagon-like peptide-1 receptor is an important regulator of appetite and glucose homeostasis. Here the authors describe super-resolution microscopy and in vivo imaging compatible fluorescent probes, which reveal endogenous glucagon-like peptide-1 receptor distribution and dynamics in islets and brain.

    • Julia Ast
    • , Anastasia Arvaniti
    •  & David J. Hodson

  • Article
    | Open Access

    Monomeric near-infrared (NIR) fluorescent proteins (FPs) from bacterial phytochromes bring potential advantages, but their brightness in cells is lower than dimeric NIR FPs. Here the authors develop enhanced monomeric NIR FPs enabling imaging across different scales without the trade-off between brightness and monomeric state.

    • Mikhail E. Matlashov
    • , Daria M. Shcherbakova
    •  & Vladislav V. Verkhusha

  • Article
    | Open Access

    Here, the authors propose a new principle to achieve super-resolution for a wide class of targets. If an object is heated up by a beam, electromagnetic or acoustic, they show that the super-linearity of the induced thermal radiation leads to an arbitrarily high spatial compression factor relative to diffraction-limited beam profile.

    • Guillaume Graciani
    •  & François Amblard

  • Article
    | Open Access

    Thermal characterization of biological tissues can traditionally provide either large fields of view or high resolution. By the development of super-resolution infrared photo-thermal imaging, the authors reconstruct temperature-based maps of absorptive centers in millimeter-sized biological samples.

    • M. Bouzin
    • , M. Marini
    •  & M. Collini

  • Article
    | Open Access

    Podosomes are actin-based protrusions used by cells for invasion and local degradation but the structure underlying their protrusiveness and mechanosensitivity is unclear. Here, the authors report that podosomes have a modular actin nano-architecture whose organization differs on stiff or soft substrates.

    • Koen van den Dries
    • , Leila Nahidiazar
    •  & Alessandra Cambi

  • Article
    | Open Access

    The Bin/Amphiphysin/Rvs167 (BAR) domain superfamily, which includes FCH-BAR (F-BAR) domain proteins are membrane-sculpting proteins. Here the authors combine a range of techniques and show that the F-BAR domain of growth-arrest specific protein 7 (GAS7) forms two-dimensional sheets on flat membranes and that these oligomeric assemblies of GAS7 are required for the formation of phagocytic cups in macrophages.

    • Kyoko Hanawa-Suetsugu
    • , Yuzuru Itoh
    •  & Shiro Suetsugu

  • Article
    | Open Access

    Pluripotent stem cell colonies are encircled by large cornerstone focal adhesions (FAs). Here, using super-resolution imaging, the authors describe features in the nanoscale makeup of these stable FAs such as inverted vinculin, lateral talin segregation and distinct kank protein distributions.

    • Aki Stubb
    • , Camilo Guzmán
    •  & Johanna Ivaska

  • Article
    | Open Access

    Polarization microscopy has been combined with single-molecule localization, but it’s often limited in either speed or resolution. Here the authors present polarized Structured Illumination Microscopy (pSIM), a method that uses polarized laser excitation to measure dye orientation during fast super-resolution live cell imaging.

    • Karl Zhanghao
    • , Xingye Chen
    •  & Peng Xi

  • Article
    | Open Access

    Activatable fluorophores are of interest for a wide range of applications but the need for caging groups complicates their development and application. Here, the authors report on a photoactivatable silicon rhodamine derivative and its application in live cell imaging and single-particle tracking.

    • Michelle S. Frei
    • , Philipp Hoess
    •  & Kai Johnsson

  • Article
    | Open Access

    Epitope tags are widely used in various applications, but often lack versatility. Here, the authors introduce a small, alpha helical tag, which is recognized by a high affinity nanobody and can be used in a range of different applications, from protein purification to super-resolution imaging and in vivo detection of proteins.

    • Hansjörg Götzke
    • , Markus Kilisch
    •  & Steffen Frey

  • Article
    | Open Access

    Mitochondrial cristae organization and ER-mitochondria contact sites are critical structures for cellular function. Here, the authors use super-resolution microscopy to show that Miro GTPases form clusters required for normal ER-mitochondria contact sites formation and to link cristae organization to the mitochondrial transport machinery.

    • Souvik Modi
    • , Guillermo López-Doménech
    •  & Josef T. Kittler

  • Article
    | Open Access

    Replication of Toxoplasma gondii requires replication and distribution of essential organelles such as micronemes. Here, Periz et al. show that micronemes are recycled from the mother to the forming daughter cells using a highly dynamic F-actin network that supports multidirectional vesicle transport.

    • Javier Periz
    • , Mario Del Rosario
    •  & Markus Meissner

  • Article
    | Open Access

    Proper mitochondrial structure is critical for normal function. Here, the authors show with SIM that the mitochondrial Ca2+ uniporter complex and localization of component MICU1 is critical to maintaining cristae junction stability and overall mitochondrial membrane structure.

    • Benjamin Gottschalk
    • , Christiane Klec
    •  & Wolfgang F. Graier

  • Article
    | Open Access

    Super-resolution microscopy is a valuable tool in bioimaging, but often requires complex systems or post-processing. Here, the authors present super-linear excitation-emission (SEE) microscopy, which overcomes these limitations by taking advantage of markers with super-linear dependence between emission and excitation power.

    • Denitza Denkova
    • , Martin Ploschner
    •  & James A. Piper

  • Article
    | Open Access

    Single-molecule localization microscopy (SMLM) requires the use of fluorophores with specific sets of properties. Here the authors employ conventional BODIPY dyes as SMLM fluorophores by making use of rarely reported red-shifted ground state BODIPY dimers to image fatty acids, lipid droplets and lysosomes at single-molecule resolution.

    • Santosh Adhikari
    • , Joe Moscatelli
    •  & Elias M. Puchner

  • Article
    | Open Access

    Fourier ring correlation (FRC) analysis is commonly used in fluorescence microscopy to measure effective image resolution. Here, the authors demonstrate that FRC can also be leveraged in blind image restoration methods, such as image deconvolution.

    • Sami Koho
    • , Giorgio Tortarolo
    •  & Giuseppe Vicidomini

  • Article
    | Open Access

    Photoswitchable nanoparticles can be used for selective imaging in biological systems but usually have only one color. Here the authors develop a two-color fluorescent emissive system that allows full on-off switching of one component color of the system while the other color is unaffected, which has implications for super-resolution imaging.

    • Dojin Kim
    • , Keunsoo Jeong
    •  & Soo Young Park

  • Article
    | Open Access

    Modern high-resolution X-ray microscopy techniques suffer from limited field-of-view or longer acquisition times. Here the authors use structured illumination to enable fast, full-field super-resolution transmission microscopy, even for optically thick specimens and at hard X-ray energies.

    • Benedikt Günther
    • , Lorenz Hehn
    •  & Franz Pfeiffer

  • Article
    | Open Access

    Single-molecule methods often rely on point spread functions that are tailored to interpret specific information. Here the authors use a neural network to extract complex PSF information from experimental images, and demonstrate this by classifying color and axial positions of emitters.

    • Taehwan Kim
    • , Seonah Moon
    •  & Ke Xu

  • Article
    | Open Access

    3D single molecule localization microscopy suffers from several experimental biases that degrade the resolution or localization precision. Here the authors present a dual-view detection scheme combining supercritical angle fluorescence and astigmatic imaging to obtain precise and unbiased 3D super resolution images.

    • Clément Cabriel
    • , Nicolas Bourg
    •  & Sandrine Lévêque-Fort

  • Article
    | Open Access

    The use of TIRF microscopy for DNA-PAINT experiments is limited by inhomogeneous illumination. Here the authors show that quantitative analysis of single-molecule TIRF experiments can be improved by using a segment-wise analysis approach and overcome by using a beam-shaping device to give a flat-top illumination profile.

    • Florian Stehr
    • , Johannes Stein
    •  & Ralf Jungmann

  • Article
    | Open Access

    TIRF imaging is limited by the size and uniformity of the illumination. Here the authors present a waveguide solution to create a large area of uniform evanescent illumination suitable for single molecule imaging coupled with a customised sample holder containing a reservoir for DNA-PAINT solutions.

    • Anna Archetti
    • , Evgenii Glushkov
    •  & Suliana Manley

  • Article
    | Open Access

    We are currently short of methods that can extract objective parameters of dendritic spines useful for their categorization. Authors present in this study an automatic analytical pipeline for spine geometry using 3D-structured illumination microscopy, which can effectively extract many geometrical parameters of dendritic spines without bias and automatically categorize spine population based on their morphological features

    • Yutaro Kashiwagi
    • , Takahito Higashi
    •  & Shigeo Okabe

  • Article
    | Open Access

    Sample processing for biological imaging experiments involves elaborate protocols with low reproducibility and throughput. Here the authors develop an open-source system called NanoJ-Fluidics, composed of off-the-shelf Lego components and an ImageJ-based controller to achieve automated fixation, labelling and imaging of cells.

    • Pedro Almada
    • , Pedro M. Pereira
    •  & Ricardo Henriques

  • Article
    | Open Access

    Super-resolution microscopy with spontaneously blinking dyes is dependent on pH and polarity of the medium. Here the authors introduce a photoactivatable fluxional fluorophore for live cell imaging that allows control over the fraction of spontaneously blinking molecules independently of medium properties.

    • Elias A. Halabi
    • , Dorothea Pinotsi
    •  & Pablo Rivera-Fuentes

  • Article
    | Open Access

    Ciliogenesis is a complex process requiring hundreds of molecules, although few secreted proteins have been implicated. Here, the authors show that the secreted metalloproteases ADAMTS9 and ADAMTS20 intracellularly regulate ciliogenesis from unique periciliary vesicles with proteolytic activity.

    • Sumeda Nandadasa
    • , Caroline M. Kraft
    •  & Suneel S. Apte

  • Article
    | Open Access

    Signalling of the B cell receptor (BCR) is pivotal for survival and activation of naïve B cells. Here the authors show, using super-resolution microscopy techniques, that BCRs exist primarily as monomers and dimers in resting B cells, and oligomerize only on stimulation, thereby implicating a function of BCR clustering patterns on B cell biology.

    • Maria Angela Gomes de Castro
    • , Hanna Wildhagen
    •  & Felipe Opazo

  • Article
    | Open Access

    The resolution limitations when using the ubiquitous algorithms that process images obtained using modern techniques are not straightforward to define. Here, the authors examine the performance of localization algorithms and use spatial statistics to provide a metric for assessing the resolution limit of such algorithms.

    • Edward A. K. Cohen
    • , Anish V. Abraham
    •  & Raimund J. Ober

  • Article
    | Open Access

    Long acquisition time and high illumination intensities needed in super-resolution imaging often generate photobleaching and phototoxicity. Here the authors develop a non-deterministic scanning approach based on a real-time feedback system that enables faster acquisition with lower light doses for in vivo imaging.

    • Jes Dreier
    • , Marco Castello
    •  & Ilaria Testa

  • Article
    | Open Access

    The meiotic telomere complex (MAJIN, TERB1, TERB2) tethers telomere ends to the nuclear envelope. Here the authors present the crystal structure of human MAJIN-TERB2 and combine biophysical approaches and structured illumination microscopy analysis of mouse meiotic chromosomes to characterize the molecular architecture of the wider MAJIN-TERB2-TERB1 complex and its interactions with TRF1.

    • James M. Dunce
    • , Amy E. Milburn
    •  & Owen R. Davies

  • Article
    | Open Access

    Complex imaging systems like super-resolution microscopes currently require laborious parameter optimization before imaging. Here, the authors present an imaging optimization framework based on machine learning that performs simultaneous parameter optimization to simplify this procedure for a wide range of imaging tasks.

    • Audrey Durand
    • , Theresa Wiesner
    •  & Flavie Lavoie-Cardinal

  • Article
    | Open Access

    Polymer dynamics at entangled conditions has generally been simplified as motions governed by the two ends of each polymer chain. Abadi et al. characterize linear and cyclic dsDNA molecules with high resolution, revealing position-dependent chain motions which cannot be described by the reptation theory.

    • Maram Abadi
    • , Maged F. Serag
    •  & Satoshi Habuchi

  • 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

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