Fluorescence imaging articles within Nature Communications

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  • Article
    | Open Access

    The authors demonstrate efficient excitation of nanodiamonds by a focused beam of helium ions, resulting in ionoluminescence. They use this for quantification and correlative localization of single particles within a whole cell at sub-30 nm resolution, and investigate nanodiamond radiosensitisation effects.

    • Zhaohong Mi
    • , Ce-Belle Chen
    •  & Andrew A. Bettiol

  • Article
    | Open Access

    Differentiation of hPSCs to cardiomyocytes suffers from high variability. Here the authors report a label-free live cell imaging platform based on autofluorescence imaging to enable the prediction of cardiomyocyte differentiation efficiency from hPSCs.

    • Tongcheng Qian
    • , Tiffany M. Heaster
    •  & Melissa C. Skala

  • Article
    | Open Access

    Limited understanding of the interactions between nanoparticle drug carriers and the blood-brain barrier underlies many translational failures in treatments of brain disorders. Here the authors use two-photon microscopy in mice to characterize the receptor-mediated transcytosis of nanoparticles at all steps of delivery from the blood to the brain in vivo.

    • Krzysztof Kucharz
    • , Kasper Kristensen
    •  & Martin Johannes Lauritzen

  • 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

    Voltage-sensitive dye imaging (VSDI) is a powerful technique for measuring membrane potential dynamics of neurons but the effective resolution is limited. Here, the authors developed an in silico model of VSDI to probe activity in a biologically detailed reconstruction of rodent neocortical microcircuits.

    • Taylor H. Newton
    • , Michael W. Reimann
    •  & Henry Markram

  • 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

    During bacterial cell division, the protein FtsZ is the main component of the contractile ring, though how precisely FtsZ treadmilling and its ability to deform membranes cooperate are unclear. Here, the authors show that dynamic FtsZ may deform lipid membranes via torsional stress that may provide sufficient force to constrict membranes in vivo and in vitro.

    • Diego A. Ramirez-Diaz
    • , Adrián Merino-Salomón
    •  & Petra Schwille

  • Article
    | Open Access

    It is challenging to develop DNA probes that allow staining of both organelle and nuclear DNA, are compatible with super resolution imaging and avoid UV-light photo-excitation. The authors overcome these issues with N-aryl pyrido cyanine derivatives showing high DNA specificity and membrane permeability.

    • Kakishi Uno
    • , Nagisa Sugimoto
    •  & Yoshikatsu Sato

  • Article
    | Open Access

    The FRET efficiency usually predominantly depends on the proximity of donor and acceptor. Here the authors report an anisotropy-based mode of FRET detection, FRET-induced Angular Displacement Evaluation via Dim donor (FADED), to allow quantification of the relative angle between donor and acceptor.

    • Danai Laskaratou
    • , Guillermo Solís Fernández
    •  & Hideaki Mizuno

  • Article
    | Open Access

    Relatively little is known about cell-matrix interactions and the intracellular transduction of an initial ligand-receptor binding event on the single-molecule level. Here authors combine ligand-decorated DNA tension sensors with DNA-PAINT super-resolution microscopy to study the mechanical engagement of single integrin receptors and the downstream influence on actin bundling.

    • Thomas Schlichthaerle
    • , Caroline Lindner
    •  & Ralf Jungmann

  • Article
    | Open Access

    J-aggregation has been proved to be an efficient strategy for the development of fluorescent imaging agents in the NIR-II spectral region but the design of appropriate J-aggregates is challenging. Here, the authors demonstrate J-aggregation of a BODIPY dye with NIR-II emission and demonstrate lymph node imaging for fluorescence guided surgery.

    • Kang Li
    • , Xingchen Duan
    •  & Zhipeng Liu

  • Article
    | Open Access

    Quantifying rapid and small cellular forces is a major challenge in mechanobiology. Here, the authors show a >2-fold spatially and >10-fold temporally force sampling improvement combining traction force microscopy with total internal reflection fluorescence super-resolution structured illumination microscopy.

    • Liliana Barbieri
    • , Huw Colin-York
    •  & Marco Fritzsche

  • Article
    | Open Access

    Quantifying rapidly progressing three-dimensional forces generated by cells remains a major challenge in mechanobiology. Here, the authors show that combining traction force microscopy with astigmatic imaging permits sensitive out-of-plane force estimation on the second timescale.

    • Di Li
    • , Huw Colin-York
    •  & Marco Fritzsche

  • Article
    | Open Access

    The mechanism by which parathyroid hormone mediates the switch from bone resorption to bone formation is unclear. Here, the authors show that SLPI regulates the communication between osteoblasts and osteoclasts to promote the anabolic effect of parathyroid hormone.

    • Akito Morimoto
    • , Junichi Kikuta
    •  & Masaru Ishii

  • Article
    | Open Access

    Performing multiple FRET measurements at once can be challenging. Here the authors report a method to discriminate between overlapping FRET pairs, even if the fluorophores display almost identical absorption and emission spectra, based on the photochromism of the donor fluorophores.

    • Thijs Roebroek
    • , Wim Vandenberg
    •  & Peter Dedecker

  • Article
    | Open Access

    Gluten is a crucial quality determinant of wheat-based food products, however, its structure remains unknown due to the lack of imaging techniques. Here, the authors report the 3D structure of gluten in millimeter scale and at submicron resolution by combining an optical clearing reagent with two-photon microscopy.

    • Takenobu Ogawa
    •  & Yasuki Matsumura

  • Article
    | Open Access

    It is challenging to map complex processes in brain tissue. Here the authors report a toolkit enabling large-scale multiplexed IHC and automated cell classification whereby they use a conventional epifluorescence microscope and deep neural networks to phenotype all major cell classes of the brain.

    • Dragan Maric
    • , Jahandar Jahanipour
    •  & Badrinath Roysam

  • 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

    Monitoring the activity of the processive motor protein kinesin-1 in live cells is currently difficult. Here the authors report the fluorogenic small molecule QPD-OTf, a kinesin-1 substrate that causes activity-dependent dye precipitation.

    • Simona Angerani
    • , Eric Lindberg
    •  & Nicolas Winssinger

  • 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

    The role of mTORC1 in AML has not yet been proven due to the mixed results of its inhibitors in clinical trials. Here the authors show the real-time dynamics of the mTORC1 pathway in association with AML growth and response to chemotherapy with fluorescent markers, providing guidance for timed intervention with pathway-specific inhibitors.

    • Toshihiko Oki
    • , Francois Mercier
    •  & David T. Scadden

  • Article
    | Open Access

    High resolution imaging of large biological volumes typically takes a long time from hours to days. Here the authors use a Bessel light-sheet approach combined with a content-aware compressed sensing computational pipeline to image whole mouse organs at subcellular resolution in a few minutes.

    • Chunyu Fang
    • , Tingting Yu
    •  & Peng Fei

  • Article
    | Open Access

    Accurate cell detection in dense bacterial biofilms is challenging. Here, the authors report an image analysis pipeline that is able to accurately segment and classify single bacterial cells in 3D fluorescence images: Bacterial Cell Morphometry 3D (BCM3D).

    • Mingxing Zhang
    • , Ji Zhang
    •  & Andreas Gahlmann

  • Article
    | Open Access

    Current media for neuronal cell and organoid cultures are suboptimal for functional imaging and optogenetics experiments, owing to phototoxicity and unphysiological performance. Here the authors formulate an optimised neuronal medium to support live cell imaging and electrophysiological activity.

    • Michael Zabolocki
    • , Kasandra McCormack
    •  & Cedric Bardy

  • Article
    | Open Access

    Determining molecular clustering in Photoactivated Localization Microscopy (PALM) experiments requires knowledge of the blinking properties of the fluorophore to prevent overcounting artefacts. Here the authors develop an experimental and analytical framework to determine the blinking parameters of fluorophores and incorporate this information into cluster analysis.

    • René Platzer
    • , Benedikt K. Rossboth
    •  & Mario Brameshuber

  • Article
    | Open Access

    The transcriptional regulator YAP shuttles rapidly between the cytoplasm and nucleus, but whether and how dynamics such as amplitude and frequency affect target gene transcription is unclear. Here, using live imaging of endogenous YAP and target-gene transcription, the authors show that YAP-dependent signalling is encoded through rapid and concerted changes in the nucleo-cytoplasmic distribution of YAP.

    • J. Matthew Franklin
    • , Rajarshi P. Ghosh
    •  & Jan T. Liphardt

  • Article
    | Open Access

    Conventional bioluminescence imaging usually operates in the visible region and its performance is limited by strong tissue absorption and scattering. Here, the authors present bioluminescence probes (BPs) with emission in the second near infrared (NIR-II) region, and show the NIR-II-BPs could sensitively recognize tumor metastasis with a high tumor-to-normal tissue ratio.

    • Lingfei Lu
    • , Benhao Li
    •  & Fan Zhang

  • Article
    | Open Access

    Detection of amyloid beta deposits is often performed with fluorescent compounds that bind plaques. Here the authors develop turn-on chemiluminescent probes that bind amyloid beta plaques in vivo, and amplify the signal via chemiluminescence resonance energy transfer to the plaque-binding fluorescent molecule CRANAD-3.

    • Jing Yang
    • , Wei Yin
    •  & Chongzhao Ran

  • Article
    | Open Access

    Existing fluorescent protein-based sensor measurements are limited to 4 or fewer simultaneously recorded modalities due to spectral overlap. Here the authors introduce Multiplexed Optical Sensors in Arrayed Islands of Cells (MOSAIC), which enables parallel recording of tens of physiological parameters using dense arrays of cell islands, each expressing a different fluorescent sensor.

    • Christopher A. Werley
    • , Stefano Boccardo
    •  & Adam E. Cohen

  • 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

    How chromosome replication and segregation is organised in E. coli is a matter of debate. Here the authors visualise the bacterial chromosome and the replisomes during DNA replication, providing support for a previously suggested train track model.

    • Aleksandre Japaridze
    • , Christos Gogou
    •  & Cees Dekker

  • 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

    Deep tissue imaging has been limited by the low brightness of probes emitting in the second near-infrared window. Here, the authors use femtosecond laser irradiation to grow a protective shell on Ag2S nanoparticles, achieving 80-fold quantum yield enhancement and imaging with low excitation intensities.

    • Harrisson D. A. Santos
    • , Irene Zabala Gutiérrez
    •  & Daniel Jaque

  • Article
    | Open Access

    The three-dimensional architecture of the genome affects genomic functions. Here, the authors developed Multiplexed Imaging of Nucleome Architectures to measure multiscale chromatin folding, RNA profiles, and associations of numerous genomic regions with nuclear lamina and nucleoli in the same, single cells in heterogeneous tissue.

    • Miao Liu
    • , Yanfang Lu
    •  & Siyuan Wang

  • Article
    | Open Access

    Extracellular vesicles (EVs) in plasma can affect pathogenesis of parasites, but details remain unclear. Here, Toda et al. characterize plasma-derived EVs from Plasmodium vivax patients and show that PvEVs are preferentially taken up by human spleen fibroblasts, facilitating parasite cytoadherence.

    • Haruka Toda
    • , Miriam Diaz-Varela
    •  & Hernando A. del Portillo

  • Article
    | Open Access

    Though DNA framework-based scaffolds for biomolecular assembly are attractive for bioimaging applications, realizing super-multiplex fluorescent amplifiers remains a challenge. Here, the authors report a topological engineering approach to designing fractal DNA frameworks for multiplexed amplifiers.

    • Jiang Li
    • , Jiangbing Dai
    •  & Chunhai Fan

  • Article
    | Open Access

    Glucagon is elevated Type-2 diabetes, which contributes to poor glucose control in patients with the disease. Here the authors report that secretion of the hormone is controlled by paracrine inhibition, and that resistance of α-cells to somatostatin can explain hyperglucagonemia in type-2 diabetes.

    • Muhmmad Omar-Hmeadi
    • , Per-Eric Lund
    •  & Sebastian Barg

  • Article
    | Open Access

    TagRFP is a bright red fluorescent protein, but undergoes photoconversion to a dark state, making it undesirable for conventional fluorescence microscopy. Here, the authors introduce stabilising mutations to create super-TagRFP (stagRFP) and demonstrate its application as both a FRET acceptor and FRET donor.

    • Gary C. H. Mo
    • , Clara Posner
    •  & Jin Zhang

  • Article
    | Open Access

    Super-resolution imaging of multiple target proteins in the same sample can provide important information of cellular nanostructure, but has not been routinely achieved. Here, the authors present a fully automated 3D STORM approach using a re-staining protocol to image 15 targets in single cells and 16 targets in neuronal tissue.

    • Maja Klevanski
    • , Frank Herrmannsdoerfer
    •  & Thomas Kuner

  • Article
    | Open Access

    The characterization of clusters in single-molecule microscopy data is vital to reconstruct emerging spatial patterns. Here, the authors present a fast and accurate machine-learning approach to clustering, to address the issues related to the size of the data and to sample heterogeneity.

    • David J. Williamson
    • , Garth L. Burn
    •  & Dylan M. Owen

  • Article
    | Open Access

    Near-infrared (NIR) fluorophores have attracted interest for bioimaging; yet availability, biocompatibility and application can be an issue. Here, the authors report on the development of Egyptian Blue nanosheets with high NIR fluorescence and photostability demonstrating bioimaging applications in vivo.

    • Gabriele Selvaggio
    • , Alexey Chizhik
    •  & Sebastian Kruss

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