Zebrafish articles within Nature Communications

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  • Article
    | Open Access

    Maturation of innate immune cells is a graded stereotypic process which is often conserved across species. Here authors label distinct neutrophil leukocyte developmental stages via generating combinations of transgenic zebrafish reporter strains, followed by transcriptome analysis of different neutrophil maturation stages and comparison to the gene expression profile of developing neutrophils from humans and mice.

    • Stefanie Kirchberger
    • , Mohamed R. Shoeb
    •  & Martin Distel

  • Article
    | Open Access

    The mesothelium supports homeostasis and regeneration, yet its development origins remain unclear. Here, the authors uncovered the earliest mesothelium progenitor cells in zebrafish, linking Hand2 gene function to mesothelium formation and its re-activation to mesothelioma tumors.

    • Karin D. Prummel
    • , Helena L. Crowell
    •  & Christian Mosimann

  • Article
    | Open Access

    The role of the transcriptional effector SMAD4 in vertebrate embryo development remains unresolved. Here the authors show that in the absence of Smad4, dorsal/ventral embryo patterning is disrupted due to the loss of BMP signaling, while Nodal signaling is maintained, but insufficient for optimal endoderm specification.

    • Luca Guglielmi
    • , Claire Heliot
    •  & Caroline S. Hill

  • Article
    | Open Access

    The gene regulatory network controlling the bifurcation of common progenitors into the neural retina and retinal-pigmented epithelium programs remains poorly understood. Here the authors study transcriptome dynamics and chromatin accessibility during this process in zebrafish, revealing network redundancy, as well as context-dependent and sequential transcription factor activity.

    • Lorena Buono
    • , Jorge Corbacho
    •  & Juan-Ramón Martínez-Morales

  • Article
    | Open Access

    Early stages of embryogenesis are known to depend on subcellular localization and transport of maternal mRNA, but systematic analyses have been hindered by a lack of methods for tracking of RNA. Here the authors combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development, revealing insights into this process.

    • Karoline Holler
    • , Anika Neuschulz
    •  & Jan Philipp Junker

  • Article
    | Open Access

    Raman spectroscopic imaging (RSI) can provide information on the chemical composition of a sample, but application to living organisms has lacked sufficient spatial resolution and signal strength. Here the authors apply confocal RSI to whole-mount zebrafish embryos to distinguish different infectious bacteria and to living zebrafish embryos to monitor the wound healing process.

    • Håkon Høgset
    • , Conor C. Horgan
    •  & Molly M. Stevens

  • Article
    | Open Access

    Multi-view SPIM imaging can improve coverage of large samples such as whole embryos, but the procedure increases phototoxicity and involves manual steps that can introduce inconsistencies. Here the authors develop a smart rotation workflow that performs on-the-fly image analysis and identifies optimal set of views to maximize sample coverage.

    • Jiaye He
    •  & Jan Huisken

  • 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

    Calcium signalling downstream of VEGF is essential for VEGF-induced angiogenesis. Here Savage et al. show that Transmembrane Protein 33 (TMEM33) is required for angiogenesis and the endothelial calcium response to VEGF, revealing a function for TMEM33 in multicellular organisms.

    • Aaron M. Savage
    • , Sathishkumar Kurusamy
    •  & Robert N. Wilkinson

  • Article
    | Open Access

    During early embryogenesis, critical cardiac specification events occur. Here the authors isolate cardiac progenitor cells from early zebrafish embryos and characterize accessible chromatin regions specific to this cell population, finding that many of these regions overlap with conserved non-coding elements that are ortholgous to accessible chromatin regions in human.

    • Xuefei Yuan
    • , Mengyi Song
    •  & Michael D. Wilson

  • Article
    | Open Access

    Wnt signaling is known to regulate the formation of the blood-brain barrier. Here Hübner et al. dissect the underlying mechanisms using high resolution live imaging in zebrafish, and find that Wnt regulates anastomosis of angiogenic sprouts in the brain by counteracting sphingosine-1-phosphate receptor signaling.

    • Kathleen Hübner
    • , Pauline Cabochette
    •  & Wiebke Herzog

  • Article
    | Open Access

    Iridophores interact with other cells to give zebrafish their stripes, but what drives their form shifts is unknown. Here, modelling allows the authors to identify robust cues that may specify iridophore form and to find changes to these cues that likely account for altered patterns on related fish.

    • Alexandria Volkening
    •  & Björn Sandstede

  • Article
    | Open Access

    Lipoprotein lipase (LPL) hydrolyzes triglycerides to supply free fatty acids (FFAs) to muscle for energy and adipocytes for storage. Here, the authors demonstrate that Lpl and its product, the FFA docosahexaenoic acid (DHA) are required for haematopoietic stem progenitor cell expansion during zebrafish embryogenesis.

    • Chao Liu
    • , Tianxu Han
    •  & Yury I. Miller

  • Article
    | Open Access

    It is not clear if it is the embryonic origin or anatomical location of cardiomyocytes that restrict their contribution to zebrafish heart regeneration. Here, the authors show a plasticity of embryonic precursors following tbx5a fate mapping and that trabecular cardiomyocytes help to rebuild the cortical myocardium.

    • Héctor Sánchez-Iranzo
    • , María Galardi-Castilla
    •  & Nadia Mercader

  • Article
    | Open Access

    Chemical screens can identify small molecules that affect biological development, with potential therapeutic value. Here, the authors use a modular approach in a screen in zebrafish embryos, varying concentration, genotype and timing to target segmentation disorders, birth defects that affect the spinal column.

    • Sandra Richter
    • , Ulrike Schulze
    •  & Andrew C. Oates

  • Article
    | Open Access

    Βeta-cells have recently been shown to be heterogeneous with regard to morphology and function. Here, the authors show that β-cells in zebrafish switch from proliferative to functional states with increasing time since β-cell birth, leading to functional and proliferative heterogeneity.

    • Sumeet Pal Singh
    • , Sharan Janjuha
    •  & Nikolay Ninov

  • Article
    | Open Access

    Multicolour information is required to study the complex interplay of biological tissues. Here, Jahr et al.acquire spectral information at high resolution for each pixel in a hyperspectral light sheet microscope, while maintaining its perpendicular illumination and low phototoxicity.

    • Wiebke Jahr
    • , Benjamin Schmid
    •  & Jan Huisken

  • Article
    | Open Access

    The heart forms from combining the first with the second heart field, which in mammals creates left and right ventricle. Here transgenic zebrafish and physiology studies reveal that transcription factors controlling septation in mammals already in teleosts guide muscle coupling by controlling the relative contribution of the two fields to the heart.

    • Christian Mosimann
    • , Daniela Panáková
    •  & Leonard I. Zon

  • Article
    | Open Access

    Zebrafish is a model system for which for no reliable heritable gene silencing method is available. Here the authors provide a system for heritable miRNA-mediated knockdown and demonstrate tunable silencing of the smn1gene that recapitulate different forms of spinal muscular atrophy.

    • Jean Giacomotto
    • , Silke Rinkwitz
    •  & Thomas S. Becker

  • Article
    | Open Access

    Pigment pattern formation in zebrafish depends on the interactions between the pigment cells. Here the authors present a mathematical model based on mutual interaction of pigment cells in the absence of cell motion, revising the current model of the pattern formation that relies on reaction–diffusion Turing patterns.

    • D. Bullara
    •  & Y. De Decker

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