Experimental organisms

  • Article
    | Open Access

    Actin-based structures in cells and tissues are built and maintained through a poorly understood balance between assembly and disassembly. Here, our findings provide insights into how factors known to promote these opposing effects dynamically integrate to shape cells and tissue systems.

    • Elena E. Grintsevich
    • , Giasuddin Ahmed
    •  & Jonathan R. Terman
  • Article
    | Open Access

    Intricate color patterns are a defining aspect of morphological diversity in the Felidae. Here the authors apply morphological and single-cell gene expression analysis to fetal skin of domestic cats to identify when, where, and how, during fetal development, felid color patterns are established.

    • Christopher B. Kaelin
    • , Kelly A. McGowan
    •  & Gregory S. Barsh
  • Article
    | Open Access

    The only known animal polyketide-nonribosomal peptides, the nemamides, are biosynthesized by two megasynthetases in the canal-associated neurons (CANs) of C. elegans. Here, the authors map the biosynthetic roles of individual megasynthetase domains and identify additional enzymes in the CANs required for nemamide biosynthesis.

    • Likui Feng
    • , Matthew T. Gordon
    •  & Rebecca A. Butcher
  • Article
    | Open Access

    It remains unclear how spatial information controls endothelial cell identity and behavior in the developing heart. Here the authors perform single cell RNA sequencing at key developmental timepoints in mice to interrogate cellular contributions to coronary vessel patterning and maturation in the epicardium.

    • Pearl Quijada
    • , Michael A. Trembley
    •  & Eric M. Small
  • 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

    The E3 ligase Hakai can interact with the m6A methylation machinery but its function is still unclear. Here, the authors show that Hakai is a conserved component of the m6A methyltransferase complex and provide functional and molecular insights into its role in regulating m6A levels in Drosophila.

    • Praveen Bawankar
    • , Tina Lence
    •  & Jean-Yves Roignant
  • 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

    Pupariation in Drosophila is triggered by the steroid-hormone ecdysone and requires coordination between associated behavioral and body-reshaping motor subprograms. The authors show that coordination requires ecdysone-dependent Dilp8-Lgr3 signaling between the cuticle epidermis and interneurons.

    • Fabiana Heredia
    • , Yanel Volonté
    •  & Alisson M. Gontijo
  • 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

    The development of a widely adopted cryopreservation method remains a major challenge in Drosophila melanogaster research. Here the authors report a robust cryopreservation protocol of Drosophila embryos and showcase its implementation in 25 distinct strains from different sources.

    • Li Zhan
    • , Min-gang Li
    •  & John Bischof
  • Article
    | Open Access

    C. elegans miRNAs associate with AGO proteins ALG-1 and ALG-2. Here the authors provide a map of miRNAs loaded into ALG-1 and ALG-2 from intestine, body wall muscles and nervous system in C. elegans providing insights into spatial and temporal AGO loading flexibility.

    • Christopher A. Brosnan
    • , Alexander J. Palmer
    •  & Steven Zuryn
  • Article
    | Open Access

    Prokaryotic cell transcriptomics has been limited to mixed or sub-population dynamics and individual cells within heterogeneous populations. Here the authors develop a ‘TRANSITomic’ approach to profile transcriptomes of single Burkholderia pseudomallei cells as they transit through host cell infection.

    • Yun Heacock-Kang
    • , Ian A. McMillan
    •  & Tung T. Hoang
  • Article
    | Open Access

    Sensory perception and metabolic homeostasis are known to deteriorate with ageing, while mechanisms underlying their deterioration remain poorly understood. Here, the authors demonstrate that decrease of intraflagellar transport in the cilia of sensory neurons impairs sensory perception and metabolism in ageing C. elegans.

    • Yincong Zhang
    • , Xiaona Zhang
    •  & Yidong Shen
  • Article
    | Open Access

    Sex chromosome gene content and expression is unusual. Here the authors use single cell RNA-Seq on Drosophila larvae to demonstrate that the single X and pair of 4th chromosomes are specifically inactivated in primary spermatocytes, while genes on the single Y chromosome become maximally active in primary spermatocytes.

    • Sharvani Mahadevaraju
    • , Justin M. Fear
    •  & Brian Oliver
  • 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

    Bacterial and fungal pathogens that cross the blood-brain-barrier (BBB) can cause severe disease. Here, Benmimoun et al. develop a model to study BBB crossing in the developing Drosophila brain and discover Group B Streptococcus factors important for BBB crossing and virulence, one of which, a lipoprotein, they confirm in mice.

    • Billel Benmimoun
    • , Florentia Papastefanaki
    •  & Pauline Spéder
  • Article
    | Open Access

    Skeletal muscle plays a key role in regulating systemic glucose and metabolic homeostasis. Here, the authors show that the catalytic activity of Vav2, an activator of Rho GTPases, modulates those processes by favoring the responsiveness of this tissue to insulin and related factors.

    • Sonia Rodríguez-Fdez
    • , L. Francisco Lorenzo-Martín
    •  & Xosé R. Bustelo
  • Article
    | Open Access

    Yeast exhibit oscillations that share features with circadian rhythms. The authors show that bioenergetic constraints promote oscillatory behaviour: resources are stored until supplies can support translational bursting, this is licensed by ion transport and release from membrane-less compartments.

    • John S. O’ Neill
    • , Nathaniel P. Hoyle
    •  & Helen C. Causton
  • Article
    | Open Access

    In the fly Drosophila melanogaster commensal bacteria and dietary essential amino acids control food choice behavior. Here, by using chemically defined diets and metabolomics, the authors show that Acetobacter pomorum (Ap) and Lactobacilli plantarum (Lp) engage in a mutualistic metabolic relationship to overcome detrimental diets, and identify Ap as the bacterium altering the host’s feeding decisions.

    • Sílvia F. Henriques
    • , Darshan B. Dhakan
    •  & Carlos Ribeiro
  • Article
    | Open Access

    Pseudogenes are key markers of genome remodelling processes. Here the authors present genome-wide annotation of the pseudogenes in the mouse reference genome and 18 inbred mouse strains, update human pseudogene annotations, and characterise the transcription and evolution of mouse pseudogenes.

    • Cristina Sisu
    • , Paul Muir
    •  & Mark Gerstein
  • Article
    | Open Access

    Calorimetry is widely used for metabolic studies, but measurements of single cells and small organisms are limited by the sensitivity of current techniques. Here the authors develop a sensitive platform for performing time-resolved metabolic measurements of single C. elegans worms from larval to adult stages.

    • Sunghoon Hur
    • , Rohith Mittapally
    •  & Edgar Meyhofer
  • Article
    | Open Access

    Ribosome engineering is an emerging powerful approach for synthetic protein synthesis. Here the authors invert the Ribo-T system, using the engineered ribosome to translate the proteome while the native ribosome translates specific mRNA.

    • Nikolay A. Aleksashin
    • , Teresa Szal
    •  & Alexander S. Mankin
  • Article
    | Open Access

    Data-independent acquisition-mass spectrometry (MS) typically requires many preparatory MS runs to produce experiment-specific spectral libraries. Here, the authors show that empirical correction of in silico predicted spectral libraries enables efficient generation of high-quality experiment-specific libraries.

    • Brian C. Searle
    • , Kristian E. Swearingen
    •  & Mathias Wilhelm
  • Article
    | Open Access

    The roots of psychopathology take shape during adverse parent-infant interactions, shown through infant attachment quality. Using rodents, the authors show that blunted infant cortical processing of the mother determines attachment quality through a stress hormone-dependent mechanism.

    • Maya Opendak
    • , Emma Theisen
    •  & Regina M. Sullivan
  • Article
    | Open Access

    Aneuploidy (abnormal chromosome number) can enable rapid adaptation to stress conditions, but it also entails fitness costs from gene imbalance. Here, the authors experimentally evolve yeast while forcing maintenance of aneuploidy to identify the mechanisms that promote tolerance of aneuploidy.

    • Alaattin Kaya
    • , Marco Mariotti
    •  & Vadim N. Gladyshev
  • 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

    The 302-neuron connectome of the nematode C. elegans has been completely mapped, yet the design principles that explain how the connectome structure determines its function are unknown. Here, the authors show that physical principles of symmetry and mathematical tools of symmetry groups can be used to understand C. elegans neural locomotion circuits.

    • Flaviano Morone
    •  & Hernán A. Makse
  • Article
    | Open Access

    The entire mRNA interactome capture has been established but identification of specific mRNA-binding proteins has been challenging. Here, the authors developed an in vivo RNA–protein crosslinking and RNA pulldown approach and characterized novel interactors of the C. elegans gld-1 mRNA, including DAZ-1 and miR-84.

    • Kathrin Theil
    • , Koshi Imami
    •  & Nikolaus Rajewsky
  • Article
    | Open Access

    The relationship between metabolomic and behavioral changes is not well understood. Here, the authors analyze metabolome changes in D. melanogaster heads and bodies during hunger and satiety, and develop the Flyscape tool to visualize the resulting metabolic networks and integrate them with other omics data.

    • Daniel Wilinski
    • , Jasmine Winzeler
    •  & Monica Dus
  • Article
    | Open Access

    High frequency semen exposure has been associated with activation of anti-HIV mechanisms in HIV negative sex workers. Here, Abdulhaqq et al. show that repeated vaginal exposure to semen reduces vaginal infection by SIV in non-human primates, and is associated with lower CCR5 expression in CD4 T-cells and a local type-I interferon response.

    • Shaheed A. Abdulhaqq
    • , Melween Martinez
    •  & Luis J. Montaner
  • Article
    | Open Access

    Present understanding of Plasmodium vivax biology is hampered by its inability to grow in vitro. Here, the authors developed an in vitro culture of its simian counterpart, P. cynomolgi, which shares morphological and phenotypic similarities with P. vivax, initiating a new phase in vivax research.

    • Adeline C. Y. Chua
    • , Jessica Jie Ying Ong
    •  & Pablo Bifani
  • Article
    | Open Access

    In humans, copy-number variants of the CYFIP1 gene have been associated with autism spectrum disorders and schizophrenia. Here, the authors characterize Cyfip1-heterozygous mice, revealing that they display deficits in brain white matter structure and functional connectivity along with abnormal behaviours.

    • Nuria Domínguez-Iturza
    • , Adrian C. Lo
    •  & Claudia Bagni
  • Article
    | Open Access

    People with a genetic deletion of the 15q11.2 locus are at increased risk for psychiatric disorders and white matter disturbances, but the gene(s) responsible are unclear. Here, the authors show that low dosage of CYFIP1, present in the human 15q11.2 region, alters white matter structure and cognition in rats.

    • Ana I. Silva
    • , Josephine E. Haddon
    •  & Lawrence S. Wilkinson