Cellular imaging articles within Nature Communications

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  • Article
    | Open Access

    Live imaging of organoid growth remains a challenge: it requires long-term imaging of several samples simultaneously and dedicated analysis pipelines. Here the authors report an experimental and image processing framework to turn long-term light-sheet imaging of intestinal organoids into digital organoids.

    • Gustavo de Medeiros
    • , Raphael Ortiz
    •  & Prisca Liberali

  • Article
    | Open Access

    It is estimated that about 80% of endocytosed material is recycled back to the plasma membrane. Here, the authors show that kiss-and-run of Rab5 early endocytic and Rab11 recycling vesicles on sorting endosomes allow cargo flow, providing more robustness and fidelity to the sorting process.

    • Jachen A. Solinger
    • , Harun-Or Rashid
    •  & Anne Spang

  • Article
    | Open Access

    The DEAD box protein DDX1 is known to form large aggregates in the cytoplasm of early mouse embryos. Here the authors identify DDX1-containing vesicles and show that loss of Ddx1 affects their integrity, compromising mitochondria function and causing embryonic lethality.

    • Yixiong Wang
    • , Lubna Yasmin
    •  & Roseline Godbout

  • 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

    The Ca2+ modulated pulsatile glucagon and insulin secretions by pancreatic α and β cells are critical in glucose homeostasis. Here the authors show that the Ca2+ oscillations of α and β cells are phase-locked, and that the oscillation pattern is tuned by paracrine interactions between α and β cells.

    • Huixia Ren
    • , Yanjun Li
    •  & Chao Tang

  • Article
    | Open Access

    Bacteria have evolved proteinaceous microcompartments (BMCs) to control the passage of metabolites and facilitate catabolism in a micro-environment. Here, Yang et al. apply fluorescence microscopy to characterize the protein-protein interaction and assembly involved in the de novo biogenesis of propanediol-utilization (Pdu) metabolosomes and show that Pdu BMCs undergo a combination of ‘Shell first’ and ‘Cargo first’ assembly.

    • Mengru Yang
    • , Nicolas Wenner
    •  & Lu-Ning Liu

  • Article
    | Open Access

    Cell segmentation of single-cell spatial proteomics data remains a challenge and often relies on the selection of a membrane marker, which is not always known. Here, the authors introduce RAMCES, a method that selects the optimal membrane markers to use for more accurate cell segmentation.

    • Monica T. Dayao
    • , Maigan Brusko
    •  & Ziv Bar-Joseph

  • 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

    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

  • Article
    | Open Access

    During pyroptosis, gasdermin D (GSDMD) forms plasma membrane pores that initiate cell lysis. Here, the authors develop optogenetically activatable human GSDMD to assess GSDMD pore behavior and show that they are dynamic and can close, which can be a pyroptosis regulatory mechanism.

    • Ana Beatriz Santa Cruz Garcia
    • , Kevin P. Schnur
    •  & Gary C. H. Mo

  • Article
    | Open Access

    Upon intestinal injury, bone marrow derived monocytes are recruited to the damaged site through the bloodstream. Authors here show that peritoneal cavity macrophages directly migrate to the damaged intestine in an ATP and hyaluronan dependent manner, and participate in the restoration of tissue integrity.

    • Masaki Honda
    • , Masashi Kadohisa
    •  & Taizo Hibi

  • Article
    | Open Access

    Currently, genetically encoded calcium indicators are not suitable for direct quantification. Here the authors engineer a fluorescence lifetime imaging calcium biosensor, Turquoise Calcium Fluorescence LIfeTime Sensor (Tq-Ca-FLITS), and measure intracellular calcium concentrations in human-derived organoids.

    • Franka H. van der Linden
    • , Eike K. Mahlandt
    •  & Joachim Goedhart

  • 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

    The visualisation of the bone metastasis process in a spatial temporal manner is lacking. Here, the authors use three-dimensional quantitative imaging and show that mouse mammary tumour cells preferentially home to endothelial subtype type H vessels within the bone marrow and remodel this vasculature by producing granulocyte-colony stimulating factor.

    • Raymond K. H. Yip
    • , Joel S. Rimes
    •  & Jane E. Visvader

  • 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

    Neutrophils migrate with remarkably stable front-rear polarization. Using optogenetic receptor control to induce reversal of polarization in restrictive microfluidic channels, the authors find that myosin II promotes this stability by suppressing transmission of receptor inputs at the cell rear.

    • Amalia Hadjitheodorou
    • , George R. R. Bell
    •  & Julie A. Theriot

  • 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

    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

    Extracellular vesicles (EVs) play a role in intercellular communication, however the precise biogenesis of different populations of EVs are not clear. Here, the authors follow the intracellular trafficking of two proteins before their secretion in EVs and report the biogenesis and protein markers of EV subtypes: ectosomes budding from the plasma membrane as well as exosomes from late endosomes.

    • Mathilde Mathieu
    • , Nathalie Névo
    •  & Clotilde Théry

  • 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

    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

    Studying dynamic processes in mechanobiology has been challenging due to lack of appropriate tools. Here, the authors present an interference-based method, illuminated via two rapidly alternating wavelengths, which enables real-time mapping of nanoscale forces with sub-second mechanical fluctuations.

    • Andrew T. Meek
    • , Nils M. Kronenberg
    •  & Malte C. Gather

  • 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

    During transcription, RNA polymerase II (RNAP2) is recruited to promoters and phosphorylated stepwise; so far, these steps have not been visualized in a single-copy gene in live cells. Here the authors use single-molecule microscopy to visualize endogenous phosphorylated RNAP2 and nascent mRNA synthesis at a single locus in living cells.

    • Linda S. Forero-Quintero
    • , William Raymond
    •  & Timothy J. Stasevich

  • 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

    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

    Deep learning methods show great promise for the analysis of microscopy images but there is currently an accessibility barrier to many users. Here the authors report a convenient entry-level deep learning platform that can be used at no cost: ZeroCostDL4Mic.

    • Lucas von Chamier
    • , Romain F. Laine
    •  & Ricardo Henriques

  • Article
    | Open Access

    While recent studies suggest that transcriptional activators form condensates at active loci, less is known about the distribution of repressor proteins. Here, the authors develop an expression assay in living Ciona embryos and visualize puncta of Hes repressors, with the Groucho/TLE corepressor, observing that the Hes.a/Gro puncta have the properties of viscous liquid droplets that undergo limited fusion events due to association with DNA.

    • Nicholas Treen
    • , Shunsuke F. Shimobayashi
    •  & Michael Levine

  • Article
    | Open Access

    Phytoplankton account for a large proportion of global primary production and comprise a number of phylogenetically distinct lineages. Here, Uwizeye et al. use FIB-SEM to study ultrastructural plasticity of 7 distinct taxa and describe how subcellular organisation is linked to energy metabolism.

    • Clarisse Uwizeye
    • , Johan Decelle
    •  & Giovanni Finazzi

  • 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

    Mitochondrial oxidation-induced cell death is an important physiological process activated by cancer therapeutics, but its investigation is challenging. Here, the authors report a multifunctional iridium(III) photosensitiser, Ir-OA, able to induce mitochondrial oxidative stress and monitor the corresponding changes in mitochondrial properties.

    • Chaiheon Lee
    • , Jung Seung Nam
    •  & Tae-Hyuk Kwon

  • 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

    53BP1 is a crucial factor involved in double strand break repair which blocks DNA end resection affecting DNA repair pathway choice. Here the authors reveal by live cell nuclear architecture analysis the spatiotemporal dynamics of 53BP1 oligomerization during a DSB DNA damage response.

    • Jieqiong Lou
    • , David G. Priest
    •  & Elizabeth Hinde

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