Cellular imaging articles within Nature Communications

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  • 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

  • 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 regulation of microtubule (MT) dynamics in cancer cells within the tumor microenvironment is less understood. Here, the authors develop an imaging platform to examine MT dynamics in live xenograft models and show that pro-tumor macrophages modulate MT coherence and alignment to promote cancer cell migration.

    • Gaurav Luthria
    • , Ran Li
    •  & Miles A. Miller

  • 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

    Therapeutic siRNA becomes trapped in endosomes, limiting its efficacy. Here the authors use fluorescently-tagged galectin-9 as a biosensor for membrane damage to monitor endosomal escape of cholesterol-conjugated siRNA following treatment of small molecule membrane-destabilising drugs.

    • Hampus Du Rietz
    • , Hampus Hedlund
    •  & Anders Wittrup

  • Article
    | Open Access

    Aldosterone-producing zona glomerulosa cells in the adrenal gland arrange into rosette structures known to be important for morphogenesis. Here the authors show that the cells in the rosettes produce coordinated calcium activity bursts in response to angiotensin II that correlate with aldosterone production level.

    • Nick A. Guagliardo
    • , Peter M. Klein
    •  & Mark P. Beenhakker

  • Article
    | Open Access

    Selective ERK5 inhibitors target ERK5 kinase activity, but they do not phenocopy the effects of ERK5 genetic depletion. Here, the authors demonstrate that the direct interaction of these inhibitors to ERK5 kinase domain induces conformational changes that promote ERK5 nuclear translocation and transcriptional activities.

    • Pamela A. Lochhead
    • , Julie A. Tucker
    •  & Simon J. Cook

  • Article
    | Open Access

    Although loss of BRCA1 leads to defects in DNA double-strand break repair by homologous recombination (HR) and renders cells hypersensitive to PARP inhibitors, resistance to the drugs can arise. Here the authors reveal that PALB2 chromatin recruitment restores HR in BRCA1-deficient cells depleted of 53BP1.

    • Rimma Belotserkovskaya
    • , Elisenda Raga Gil
    •  & Stephen P. Jackson

  • 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

    Traction force microscopy is an effective method for measuring cellular forces but it is limited by planar geometry. Here the authors develop a facile method to produce deformable hydrogel particles and a reference-free computational method to resolve surface traction forces from particle shape deformation.

    • Daan Vorselen
    • , Yifan Wang
    •  & Julie A. Theriot

  • Article
    | Open Access

    Here, using high spatiotemporal resolution light-sheet and fluorescence microscopy, the authors investigate the role of cytoskeletal components on the intracellular transport of Rab11A and influenza virus (IAV) vRNP), and show a preference for Rab11A movement along microtubules that is not essential for IAV vRNP transport.

    • Amar R. Bhagwat
    • , Valerie Le Sage
    •  & Seema S. Lakdawala

  • 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

    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

    Internalized receptors are recycled back to the cell surface, but their precise mechanisms are unclear. Here, the authors show that the flotillin membrane proteins may regulate the transfer of internalized T cell receptors into Rab5 and Rab11-positive endosomes to support its rapid recycling.

    • Gregory M. I. Redpath
    • , Manuela Ecker
    •  & Jérémie Rossy

  • 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

    Pancreatic islets are composed of alpha-, beta-, as well as delta-cells and appropriate regulation of glucose homeostasis relies on auto- and paracrine cellular communication. Here, the authors study the role of delta-cell filopodia in this context by employing optogenetic and calcium imaging approaches.

    • Rafael Arrojo e Drigo
    • , Stefan Jacob
    •  & Per-Olof Berggren

  • Article
    | Open Access

    Biomechanical studies of eukaryotic cells have been limited due to low sensitivity and axial resolution in interferometric imaging. Here, the authors present depth-resolved confocal reflectance interferometric microscopy with high sensitivity and temporal resolution, which enables quantification of nucleic envelope and plasma membrane fluctuations.

    • Vijay Raj Singh
    • , Yi An Yang
    •  & Peter T. C. So

  • 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

    In bacteria, DNA replication and segregation are commonly coupled. Here, by investigating the dynamics of these processes in the marine bacterium Hyphomonas neptunium, the authors unravel a two-step chromosomal segregation process reminiscent of eukaryotic mitosis, providing insights into the evolution of bacterial cell organization.

    • Alexandra Jung
    • , Anne Raßbach
    •  & Martin Thanbichler

  • 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

    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

    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

    Phenotypically identical mammalian cells often display considerable variability in transcript levels of individual genes. Here the authors document how different genes propagate their expression levels in cell lineages and suggest a potential role of transcriptional memory for generating spatial patterns of gene expression.

    • Nicholas E. Phillips
    • , Aleksandra Mandic
    •  & David M. Suter

  • Article
    | Open Access

    The process of alveologenesis is incompletely understood, partly due to the lack of applicable real-time imaging methods. Here the authors describe the process of alveologenesis and the behaviour of epithelial cells in real-time, using widefield microscopy and image deconvolution in precision-cut lung slices, revealing the dominant role of epithelial cell migration.

    • Khondoker M. Akram
    • , Laura L. Yates
    •  & Charlotte H. Dean

  • Article
    | Open Access

    Damaged epithelial tissues are known to compensate for cell death through compensatory cell divisions to maintain epithelial integrity. Here, the authors show in living epithelia that dying cells stimulate adjacent stem cells to divide through caspase-dependent production of Wnt8a-containing apoptotic bodies.

    • Courtney K. Brock
    • , Stephen T. Wallin
    •  & George T. Eisenhoffer

  • Article
    | Open Access

    Quantitative study of endoplasmic reticulum (ER) structure and dynamics has been a challenge. Here, the authors introduce software to automatically extract ER network elements from multi-dimensional fluorescence images of plant ER and to quantify structure, topology, protein localization and dynamics.

    • Charlotte Pain
    • , Verena Kriechbaumer
    •  & Mark Fricker

  • 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

    Automated analysis of RNA localisation in smFISH data has been elusive. Here, the authors simulate and use a large dataset of images to design and validate a framework for highly accurate classification of sub-cellular RNA localisation patterns from smFISH experiments.

    • Aubin Samacoits
    • , Racha Chouaib
    •  & Florian Mueller

  • Article
    | Open Access

    Endoplasmic reticulum (ER) functioning requires a constant supply of ATP, but the exchanger required for ATP uptake into the ER is unknown. Here, the authors report that SLC35B1, here named AXER, or ATP/ADP exchanger into the ER, can transport ATP into the ER.

    • Marie-Christine Klein
    • , Katharina Zimmermann
    •  & Ilka Haferkamp

  • Article
    | Open Access

    The actin-based motor Myosin1d is needed to establish left–right asymmetry in Drosophila. Here the authors show that myosin 1d has a role in lumen formation, vacuole trafficking and left-right asymmetry establishment during zebrafish development.

    • Manush Saydmohammed
    • , Hisato Yagi
    •  & Michael Tsang

  • Article
    | Open Access

    Current approaches to conditionally deplete target proteins require site-specific genetic engineering or have poor temporal control. Here the authors overcome these limitations by combining the AID system with nanobodies to reversibly degrade GFP-tagged proteins in living cells and zebrafish.

    • Katrin Daniel
    • , Jaroslav Icha
    •  & Jörg Mansfeld

  • Article
    | Open Access

    AND-1, the vertebrate orthologue of Ctf4, is a critical player during DNA replication and for maintenance of genome integrity. Here the authors use a conditional AND-1 depletion system in avian DT40 cells to reveal the consequences of the lack of AND-1 on cell proliferation and DNA replication.

    • Takuya Abe
    • , Ryotaro Kawasumi
    •  & Dana Branzei

  • Article
    | Open Access

    Intraluminal vesicles are formed by the endosomal sorting complex required for transport (ESCRT) machinery. Here, the authors unravel the timing of vesicle budding, and that endosomal clathrin regulates concerted recruitment of ESCRT subcomplexes, required for efficient membrane remodeling.

    • Eva Maria Wenzel
    • , Sebastian Wolfgang Schultz
    •  & Camilla Raiborg

  • Article
    | Open Access

    Methods to study anti-cancer drugs cytotoxicity are often low throughput and rely on population average. Here the authors present an automated image-based cytometry method to quantify multiple cytotoxicity parameters in single cells, and use it to study the effect of PARP inhibitors in cancer cells.

    • Jone Michelena
    • , Aleksandra Lezaja
    •  & Matthias Altmeyer

  • Article
    | Open Access

    Single molecule tracking of fluorescent proteins in live cells is temporally limited by fluorophore photobleaching. Here the authors show using fluorophore pairs that FRET competes with photobleaching to improve photostability and allow longer-term tracking of both single proteins and complexes.

    • Srinjan Basu
    • , Lisa-Maria Needham
    •  & Ernest D. Laue

  • Article
    | Open Access

    Natriuretic peptides (NPs) are important hormones that regulate cardiovascular physiology by increasing cGMP levels in cardiomyocytes. Here the authors use scanning ion conductance microscopy and a cGMP FRET sensor to identify a differential localisation pattern for the natriuretic peptide receptors within the heart.

    • Hariharan Subramanian
    • , Alexander Froese
    •  & Viacheslav O. Nikolaev

  • Article
    | Open Access

    Many cell capture systems exist but the characterisation and controlled release of single cells is a challenge. Here, the authors report on the development of a duel trigger release system using a combination of photo and electro triggers to allow for light based analysis without unwanted release.

    • Stephen G. Parker
    • , Ying Yang
    •  & J. Justin Gooding

  • Article
    | Open Access

    During sperm capacitation physiological changes occur that are required for fertilization. Here, the authors describe four sperm zinc signatures during invitro capacitation that are indicative of sperm quality and capacity to fertilize.

    • Karl Kerns
    • , Michal Zigo
    •  & Peter Sutovsky

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