Biological techniques articles within Nature Communications

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  • Article
    | Open Access

    Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) are a powerful tool for neuroscience, but the standard DREADD ligand, CNO, has significant drawbacks. Here the authors report two novel high-potency DREADD ligands and a novel DREADD radiotracer for imaging purposes.

    • Jordi Bonaventura
    • , Mark A. G. Eldridge
    •  & Michael Michaelides

  • Article
    | Open Access

    Vascular surfaces are rapidly remodeled during systemic inflammatory responses and sepsis. Here, the authors combine in vivo biotinylation and high-resolution mass spectrometry to characterize organ-level changes of the murine vascular cell surface proteome induced by MRSA sepsis.

    • Alejandro Gómez Toledo
    • , Gregory Golden
    •  & Jeffrey D. Esko

  • Article
    | Open Access

    Meiotic crossovers (COs) are essential for proper chromosome segregation and generating novel combinations of alleles. Here, the authors develop haplotype-specific oligos on maize chromosome 10 for fluorescence in situ hybridization and analyze CO patterns in an intermated recombinant population derived from B73 and Mo17.

    • Lívia do Vale Martins
    • , Fan Yu
    •  & Jiming Jiang

  • Article
    | Open Access

    How do diversity (entropy) and integration of activity across brain regions interact to support consciousness? Here the authors show that anaesthetised individuals and patients with disorders of consciousness exhibit overlapping reductions in both diversity and integration in the brain’s default mode network.

    • Andrea I. Luppi
    • , Michael M. Craig
    •  & Emmanuel A. Stamatakis

  • Article
    | Open Access

    The lymphatic vasculature is essential to maintain fluid homeostasis and immune surveillance, including in the brain where lymphatic vessels were only recently identified. Here, Jacob et al. provide an anatomical map of lymphatic vessels in the vertebral column, where they find these contribute to fluid drainage and immune responses.

    • Laurent Jacob
    • , Ligia Simoes Braga Boisserand
    •  & Jean-Leon Thomas

  • Article
    | Open Access

    Nanosecond imaging techniques, such as fluorescence lifetime imaging microscopy (FLIM), are limited by low efficiency of current detectors. Here, the authors implement an electro-optic approach using Pockels cells for wide-field image gating and demonstrate high throughput FLIM on standard camera sensors.

    • Adam J. Bowman
    • , Brannon B. Klopfer
    •  & Mark A. Kasevich

  • Article
    | Open Access

    High-throughput assays for TCR specificity are a bottleneck in understanding T cell immunity and harnessing it for medicine. Here the authors develop a functional screening method to identify T cell specificity in the natural context of peptide-MHC presentation, enabling detection of physiologically relevant T cell antigens from large libraries of peptide-coding sequences.

    • Govinda Sharma
    • , Craig M. Rive
    •  & Robert A. Holt

  • Article
    | Open Access

    Microdroplets are used as chemical and biological reactors; however, stability and inter-droplet transfer are major issues. Here, the authors report on the development of dendritic glycerol-based surfactants for the creation of stable microdroplets and demonstrate application for PCR, minimal emulsion, and cell encapsulation.

    • Mohammad Suman Chowdhury
    • , Wenshan Zheng
    •  & Rainer Haag

  • Article
    | Open Access

    Dystrophin-deficient mice are used to test corrective strategies for Duchenne muscular dystrophy, but evaluation of dystrophin expression requires collection of tissue samples from specific muscles and time points. Here, the authors generate mice in which dystrophin expression is coupled to luciferase, and show that bioluminescence allows non-invasive monitoring of dystrophin expression following genome editing.

    • Leonela Amoasii
    • , Hui Li
    •  & Eric N. Olson

  • Article
    | Open Access

    Light sheet microscopy holds potential for imaging dynamics in 3D biological specimens, but is limited by scan speed and camera acquisition rate. Here the authors address both issues by developing speed-optimized Objective Coupled Planar Illumination and parallelizing image acquisition across cameras to achieve 40 Hz imaging over thick samples.

    • Cody J. Greer
    •  & Timothy E. Holy

  • Article
    | Open Access

    Cellular systems have numerous mechanisms to control gene expression. Here the authors build a Tet-On system with conditional destablising elements to regulate gene expression and protein stability, allowing fine modulation of mESC signalling pathways.

    • Elisa Pedone
    • , Lorena Postiglione
    •  & Lucia Marucci

  • Article
    | Open Access

    Human centromeric nucleosomes contain the specific CENP-A histone variant, which replaces canonical histone H3 and epigenetically marks the centromeres. Here the authors show that CENP-A nucleosomes form large supramolecular clusters during the G1 phase of the cell cycle which are arranged as rosette-like structures.

    • Leonid Andronov
    • , Khalid Ouararhni
    •  & Ali Hamiche

  • 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

    One aspect of ageing on immunity is attributed to accelerated thymic atrophy, but the underlying mechanism is still lacking. Here the authors show, using conditional reporter mouse models, that both atrophy and regeneration of the thymus are regulated by rate-limiting morphological changes in epithelial stroma, independent of cell death or proliferation.

    • Thomas Venables
    • , Ann V. Griffith
    •  & Howard T. Petrie

  • Article
    | Open Access

    Multiplexed imaging of synaptic proteins can provide useful information on the heterogeneity of synaptic architecture and plasticity. Here the authors use high affinity locked nucleic acid probes and low affinity DNA imaging probes to achieve multiplexed confocal and super-resolution imaging of synaptic and cytoskeletal proteins.

    • Syuan-Ming Guo
    • , Remi Veneziano
    •  & Mark Bathe

  • Article
    | Open Access

    Protein phosphatases play an essential role in signal transduction, but are understudied due to the difficulties in detecting phosphate removal and the lack of good inhibitors. Here the authors develop a light-activated protein phosphatase using photocaged, unnatural amino acids and use it to study ERK nuclear translocation.

    • Taylor M. Courtney
    •  & Alexander Deiters

  • Article
    | Open Access

    Here, employing laser capture microdissection and omics, the authors determine the effects of fiber-deprived diet on the spatial structure of the murine colon microbiome, finding that the absence of dietary fiber and polysaccharides leads to local changes along the colon and deterioration of the mucus layer.

    • Alessandra Riva
    • , Orest Kuzyk
    •  & David Berry

  • Article
    | Open Access

    Synthetic RNA-based devices can dynamically control a wide range of processes. Here the authors develop a quantitative and high-throughput mammalian cell-based RNA-seq assay to efficiently engineer ribozyme switches.

    • Joy S. Xiang
    • , Matias Kaplan
    •  & Christina D. Smolke

  • Article
    | Open Access

    Meiotic crossovers (COs) generate genetic variation and ensure proper chromosome segregation. Here, the authors develop a method for identifying COs at kilobase resolution in pooled recombinants using linked-read sequencing data, and apply it to investigate genome-wide CO landscapes of Arabidopsis thaliana.

    • Hequan Sun
    • , Beth A. Rowan
    •  & Korbinian Schneeberger

  • Article
    | Open Access

    Sequential acquisition and image reconstruction in super-resolved structured illumination microscopy (SR-SIM) is time-consuming. Here the authors optimise both acquisition and reconstruction software to achieve multicolour SR-SIM at video frame-rates with reconstructed images displaying with only milliseconds delay during the experiment.

    • Andreas Markwirth
    • , Mario Lachetta
    •  & Marcel Müller

  • Article
    | Open Access

    Cardiomyocytes obtained from human induced pluripotent stem cells are increasingly used for drug testing, but they are not always predictive of the heart contractile responses. Here the authors develop a method to measure cytosolic calcium, action potentials and contraction simultaneously, to achieve higher sensitivity for drug screenings.

    • Berend J. van Meer
    • , Ana Krotenberg
    •  & Christine L. Mummery

  • Article
    | Open Access

    Light-up aptamers are widely used for fluorescence visualization of non-coding RNA in vivo. Here the authors employ single-molecule fluorescence-force spectroscopy to characterize the mechanical responses of the G-Quadruplex based light-up aptamers Spinach2, iMangoIII and MangoIV, which is of interest for the development of improved fluorogenic modules for imaging applications.

    • Jaba Mitra
    •  & Taekjip Ha

  • Article
    | Open Access

    Chronic cranial windows (CCW) enable long-term imaging of brain activity, but usually they only provide passive optical access to the tissue. Here the authors develop an active CCW integrated with an ultrasound detector which enables long-term photoacoustic imaging of the cortical vasculature in live mice with higher image quality.

    • Hao Li
    • , Biqin Dong
    •  & Cheng Sun

  • Article
    | Open Access

    Performance anxiety can impair motor skill, and even affect expert athletes and musicians. Here, the authors show that anxiety affects performance at the ‘junction’ between two well-learned action sequences, and that this affect is associated with activity in dorsal anterior cingulate cortex (dACC).

    • Gowrishankar Ganesh
    • , Takehiro Minamoto
    •  & Masahiko Haruno

  • Article
    | Open Access

    The role of CTCF-bound insulator elements in enhancer-gene interactions and transcriptional regulation remains poorly understood. Here, the authors investigate multiple epigenome editing strategies for perturbing individual CTCF-bound insulators, and evaluate their effects on genome topology and transcription.

    • Daniel R. Tarjan
    • , William A. Flavahan
    •  & Bradley E. Bernstein

  • 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

  • Comment
    | Open Access

    John Fenn’s electrospray mass spectrometry (ESMS) was awarded the chemistry Nobel Prize in 2002 and is now the basis of the entire field of MS-based proteomics. Technological progress continues unabated, enabling single cell sensitivity and clinical applications.

    • Matthias Mann

  • Comment
    | Open Access

    The establishment of the Orbitrap analyzer as a major player in mass spectrometry based proteomics is traced back to the first public presentation of this technology 20 years ago; when a proof-of-principle application led the way to further advancements and biological applications.

    • Alexander Makarov

  • Article
    | Open Access

    The actin-remodelling protein L-plastin promotes tumour migration and invasion. Here, the authors show that L-plastin is regulated spatially by ROS-induced thiol oxidation which inhibits its actin-bundling function and cell spreading and filopodial extension formation in tumor cells.

    • Emre Balta
    • , Robert Hardt
    •  & Yvonne Samstag

  • 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

    The nature of the signals that propagate through feedforward networks is not well understood. Here, the authors combine microfabrication, multilayer cortical cultures, and optogenetic stimulation to show that NMDA-mediated synaptic current generates a sustained phase of activity that propagates firing rate signals.

    • Jérémie Barral
    • , Xiao-Jing Wang
    •  & Alex D. Reyes

  • Article
    | Open Access

    Comprehensive mapping of binary protein-protein interactions requires to combine several complementary assays. Here, the authors show that complete coverage could be reached with a minimal number of assays as long as they explore various experimental conditions.

    • Soon Gang Choi
    • , Julien Olivet
    •  & Yves Jacob

  • Article
    | Open Access

    The use of antibodies to capture and profile exosomes limits the number of target proteins that can be detected. Here the authors develop a proximity-dependent barcoding assay that allows profiling of 38 surface proteins on individual exosomes from heterogeneous samples such as serum and seminal fluid.

    • Di Wu
    • , Junhong Yan
    •  & Masood Kamali-Moghaddam

  • Article
    | Open Access

    There is little known about the function or molecular identity of the electron-dense stereocilia coat, which is transiently present at the surface of stereocilia. In this study authors screened a database of hair-cell-enriched translated proteins to identify the expression of Polycystic Kidney and Hepatic Disease 1-Like 1 (PKHD1L1), a large, mostly extracellular protein, and show that it forms the coat at the tips of stereocilia and is required for normal hearing in mice

    • Xudong Wu
    • , Maryna V. Ivanchenko
    •  & David P. Corey

  • Article
    | Open Access

    Meiotic DSB formation, repair and recombination occur in a continuum of substages termed leptonema, zygonema, pachynema, and diplonema. Here, authors develop a method for isolating pure sub-populations of nuclei that allows for detailed study of meiotic substages.

    • Kwan-Wood Gabriel Lam
    • , Kevin Brick
    •  & R. Daniel Camerini-Otero

  • Article
    | Open Access

    Titers of monoterpenoids production in yeast are low due to the fact that the geranyl diphosphate (GPP)-based pathway can redirect metabolic fluxes to growth. Here, the authors build an orthogonal pathway by selecting the cis isomer of GPP as an alternative precursor and achieve high titer monoterpene production.

    • Codruta Ignea
    • , Morten H. Raadam
    •  & Sotirios C. Kampranis

  • Article
    | Open Access

    The benefit of combined CDK4/6 and anti-HER2 therapy in breast cancer is limited due to acquired resistance. Here, the authors perform single-cell analysis and show an immature myeloid cell population to infiltrate resistant tumors, and that combined cabozantinib and checkpoint therapy overcome this resistance with a sustained efficacy.

    • Qingfei Wang
    • , Ian H. Guldner
    •  & Siyuan Zhang

  • Article
    | Open Access

    Here, the authors show that reticulocytes derived from immortalized erythroblasts support invasion and development of Plasmodium falciparum and use CRISPR-mediated gene knockout and complementation of an invasion receptor to demonstrate utility of this model system for research in malaria invasion.

    • Timothy J. Satchwell
    • , Katherine E. Wright
    •  & Jake Baum

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