Biological techniques articles within Nature Communications

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  • Article
    | Open Access

    Large population testing is a key step to controlling the COVID-19 pandemic. Here, the authors develop a targeted mass spectrometry system for peptide-based SARS-CoV-2 detection, allowing analysis of over 500 swab samples per day and enabling virus detection even after prolonged sample storage at room temperature.

    • Karina Helena Morais Cardozo
    • , Adriana Lebkuchen
    •  & Valdemir Melechco Carvalho

  • 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

    Genome-wide maps of evolutionary constraint and large-scale compendia of epigenomic and transcription factor data provide complementary information for genome annotation. Here, the authors develop the Constrained Non-Exonic Predictor (CNEP) that enables better understanding of their relationship.

    • Olivera Grujic
    • , Tanya N. Phung
    •  & Jason Ernst

  • Article
    | Open Access

    Genomic aberrations disrupting chromosome spatial domains can lead to disease. Here, the authors investigate the impact of DNA damage response and repair on 3D genome folding, comparing wild type cells and ataxia telangiectasia mutated patient cells, and characterise both cell type-specific and shared changes to genome organization during the response to damage.

    • Jacob T. Sanders
    • , Trevor F. Freeman
    •  & Rachel Patton McCord

  • Article
    | Open Access

    Designing efficient, rapid and low-cost diagnostic technologies targeting nucleic acids remains a challenge. Here the authors present a disposable silicon-based integrated Point-of-Need transducer produced in a standard wet lab and able to chemically-amplify and detect pathogen-specific sequences of nucleic acids quantitatively in real-time.

    • Estefania Nunez-Bajo
    • , Alexander Silva Pinto Collins
    •  & Firat Güder

  • Article
    | Open Access

    Reliable plasmonic biosensors with high throughput and ease of use are highly sought after. Here, the authors report a plasmon-enhanced fluorescence antibody-aptamer biosensor based on a gold nanoparticle array, and demonstrate its use for effective specific detection of a malaria marker, at femtomolar level, in whole blood.

    • Antonio Minopoli
    • , Bartolomeo Della Ventura
    •  & Raffaele Velotta

  • Article
    | Open Access

    Accurate cell detection in dense bacterial biofilms is challenging. Here, the authors report an image analysis pipeline that is able to accurately segment and classify single bacterial cells in 3D fluorescence images: Bacterial Cell Morphometry 3D (BCM3D).

    • Mingxing Zhang
    • , Ji Zhang
    •  & Andreas Gahlmann

  • Article
    | Open Access

    Light scattering represents the main limitation to image at depth in biological microscopy. The authors present a strategy to characterize light propagation in and out of a scattering medium based on linear fluorescence feedback and from the same measurements exploit memory effect correlations to image and reconstruct extended objects.

    • Antoine Boniface
    • , Jonathan Dong
    •  & Sylvain Gigan

  • Article
    | Open Access

    Immune cells express immunoproteasomes (i20S), which bind to specialized regulators, contain different catalytic subunits and generate immunogenic peptides. HDX-MS—based assessment of the differences between the conformational dynamics of standard and i20s reveals specific, allosteric changes in i20S and upon regulator binding.

    • Jean Lesne
    • , Marie Locard-Paulet
    •  & Julien Marcoux

  • Article
    | Open Access

    The role of cohesin in organizing a functional nuclear architecture remains poorly understood. Here the authors show that cohesin depleted cells pass through endomitosis forming a multilobulated nucleus able to proceed through S-phase with typical features of active and inactive nuclear compartments and spatio-temporal patterns of replication domains.

    • Marion Cremer
    • , Katharina Brandstetter
    •  & Thomas Cremer

  • Article
    | Open Access

    Existing neural interfaces are limited in accessing one, small brain region. Here, the authors introduce a scaffold with helix hollow channels, which direct multisite multifunctional fibre probes into the brain at different angles, allowing for simultaneous recording and stimulation across distant regions.

    • Shan Jiang
    • , Dipan C. Patel
    •  & Xiaoting Jia

  • Article
    | Open Access

    Existing tools to study hearing are limited. Here the authors report Bio-OptoAcoustic (BOA) stimulation wherein they use optical forces to generate localised sound and activate the auditory system of zebrafish larvae.

    • Itia A. Favre-Bulle
    • , Michael A. Taylor
    •  & Ethan K. Scott

  • Article
    | Open Access

    Ex vivo engineering of antigen-specific T cells has shown therapeutic efficacy but can be costly and scarce. Here the authors show that in vitro-transcribed antigen receptor mRNA packaged in nanocarriers can directly induce, in vivo, transient their expression in circulating T cells to provide therapeutic effects in mouse models of cancer or viral infection.

    • N. N. Parayath
    • , S. B. Stephan
    •  & M. T. Stephan

  • Article
    | Open Access

    Sorghum is a source of lignocellulosic biomass for the production of renewable fuels. Here the authors characterise the sorghum secondary cell wall using multi-dimensional magic angle spinning solid-state NMR and present a model dominated by interactions between three-fold screw xylan and amorphous cellulose.

    • Yu Gao
    • , Andrew S. Lipton
    •  & Jenny C. Mortimer

  • Article
    | Open Access

    Gdx-Clo is a bacterial transporter from the small multidrug resistance (SMR) family. Here, the authors use solid supported membrane electrophysiology to characterize Gdx-Clo functionally and report crystal structures of Gdx-Clo which confirm the dual topology architecture and offer insight into substrate binding and transport mechanism.

    • Ali A. Kermani
    • , Christian B. Macdonald
    •  & Randy B. Stockbridge

  • Article
    | Open Access

    Senescence is a state of stable proliferative arrest. Here, the authors perform Hi-C analysis on oncogenic RAS-induced senescence in human fibroblasts and characterize the changes in the 3D genome folding associated with the senescence-specific gene expression profile, which are mediated in part through cohesin redistribution on chromatin.

    • Ioana Olan
    • , Aled J. Parry
    •  & Masashi Narita

  • Article
    | Open Access

    Myo-Inositol phosphates (InsPs) and pyrophosphates (PP-InsPs) are important second messengers but their analysis remains challenging. Here, the authors develop a capillary electrophoresis-mass spectrometry method for the identification and quantitation of InsP and PP-InsP isomers in cells and tissues.

    • Danye Qiu
    • , Miranda S. Wilson
    •  & Henning J. Jessen

  • Article
    | Open Access

    The success of protein evolution is dependent on the sequence context mutations are introduced into. Here the authors present UMIC-seq that allows consensus generation for closely related genes by using unique molecular identifiers linked to gene variants.

    • Paul Jannis Zurek
    • , Philipp Knyphausen
    •  & Florian Hollfelder

  • Article
    | Open Access

    Monitoring hemodynamics in the brain is important in understanding medical imaging data and mechanisms of disease. Here the authors use high-throughput two-photon microscopy with an axially-extended Bessel focus to measure vessel size and blood flow down to capillary scale in the awake mouse brain.

    • Jiang Lan Fan
    • , Jose A. Rivera
    •  & Na Ji

  • Article
    | Open Access

    The assembly of actin filaments into distinct cytoskeletal structures plays a critical role in cell physiology. Here, the authors use a combination of live cell imaging and in vitro single molecule binding measurements to show that tandem calponin homology domains (CH1–CH2) are sensitive to actin filament conformation, biasing their subcellular localization.

    • Andrew R. Harris
    • , Pamela Jreij
    •  & Daniel A. Fletcher

  • Article
    | Open Access

    The vesicles that transport proteins between intracellular organelles are small, short-lived, and elusive. Here, the authors show that capture of these vesicles through relocalizing tethers to mitochondria allows their contents to be characterised by organelle proteomics.

    • John J. H. Shin
    • , Oliver M. Crook
    •  & Sean Munro

  • Article
    | Open Access

    PTSD has been associated with DNA methylation of specific loci in the genome, but studies have been limited by small sample sizes. Here, the authors perform a meta-analysis of DNA methylation data from 10 different cohorts and identify CpGs in AHRR that are associated with PTSD.

    • Alicia K. Smith
    • , Andrew Ratanatharathorn
    •  & Caroline M. Nievergelt

  • Article
    | Open Access

    Current state-of-the-art diagnostics for infectious diseases are sensitive but require extensive equipment. Here the authors develop an enhanced recombinase polymerase amplification reaction for SARS-CoV-2 that allows for inexpensive and rapid testing with minimal equipment.

    • Jason Qian
    • , Sarah A. Boswell
    •  & Michael Springer

  • Article
    | Open Access

    Protein O-GlcNAcylation is involved in regulating gene expression and maintaining cellular homeostasis. Here, the authors develop a chemical reporter-based strategy for the proteomic profiling and genome-wide mapping of genotoxic stress-induced O-GlcNAcylated chromatin-associated proteins.

    • Yubo Liu
    • , Qiushi Chen
    •  & Jianing Zhang

  • Article
    | Open Access

    The liver possesses the ability to regenerate following sudden injury. Here, the authors use single-cell RNA-sequencing and in situ transcriptional analyses to identify a new phase of liver regeneration in mice aimed at maintaining essential functions throughout the regenerative process.

    • Chad M. Walesky
    • , Kellie E. Kolb
    •  & Wolfram Goessling

  • Article
    | Open Access

    The ability to measure strain in cells and tissues in vitro with minimal perturbation and at high spatial resolution has proven challenging. Here the authors develop a fluorescently-labelled fibronectin square lattice mesh that can be applied to the surface of cells and tissues to enable direct quantification and mapping of strain over time.

    • Daniel J. Shiwarski
    • , Joshua W. Tashman
    •  & Adam W. Feinberg

  • Article
    | Open Access

    Here the authors visualize SARS-CoV-2 infected cells by in situ cryo-electron tomography, delineating the structural organization and conformational changes that occur during virus replication and budding; and provide insight into vRNP architecture and RNA networks in double membrane vesicles.

    • Steffen Klein
    • , Mirko Cortese
    •  & Petr Chlanda

  • Article
    | Open Access

    Label-free protein characterization at surfaces requires digestion or matrix application prior to mass spectrometry. Here, the authors report the assignment of undigested proteins at surfaces by de novo sequencing and apply the methodology to a protein monolayer biochip and for in situ depth profiling of proteins through human skin.

    • Anna M. Kotowska
    • , Gustavo F. Trindade
    •  & David J. Scurr

  • Article
    | Open Access

    Traces from single-molecule fluorescence microscopy (SMFM) experiments exhibit photophysical artifacts that typically make analysis time-consuming. Here, the authors have developed an easily accessible software, AutoSiM, for two distinct applications of deep learning to the efficient processing of SMFM time traces.

    • Jieming Li
    • , Leyou Zhang
    •  & Nils G. Walter

  • Article
    | Open Access

    How COVID-19 pathology differs from other drivers of pneumonia is unclear. Here the authors analyze urine from patients with COVID-19 and identify an immunosuppressive protein expression pattern that is distinct from the pattern in healthy individuals or patients with non-COVID-19 pneumonia.

    • Wenmin Tian
    • , Nan Zhang
    •  & Catherine C. L. Wong

  • Article
    | Open Access

    The putative causal agent of citrus greening Candidatus Liberibacter asiaticus (CLas) cannot be cultured, which hampers finding new therapies to control this devastating disease. Here, the authors show that hairy roots support CLas propagation and enable high throughput antimicrobial screening.

    • Sonia Irigoyen
    • , Manikandan Ramasamy
    •  & Kranthi K. Mandadi

  • 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

    Chromatin loops bridging distant loci within chromosomes can be detected by a variety of techniques such as Hi-C. Here the authors present Chromosight, an algorithm applied on mammalian, bacterial, viral and yeast genomes, able to detect various types of pattern in chromosome contact maps, including chromosomal loops.

    • Cyril Matthey-Doret
    • , Lyam Baudry
    •  & Axel Cournac

  • Article
    | Open Access

    Here, the authors tailor an acetylated galactoglucomannan (AcGGM) fibre from spruce wood to specifically enrich Roseburia and Faecalibacterium - beneficial species which have the enzymatic machinery to breakdown the fibre and generate butyrate. They subsequently perform a piglet feeding trial, metagenomics and metaproteomics, together showing that AcGGM-fed pigs exhibit not only increased Roseburia and Faecalibacterium populations with AcGGM-specific mannan-specific esterases, but also secondary metabolic pathways.

    • Leszek Michalak
    • , John Christian Gaby
    •  & Bjørge Westereng

  • Article
    | Open Access

    The HIV-1 RNA-binding protein rev facilitates nuclear export of viral RNA. Here, the authors use native mass spectrometry to study the interactions between rev-derived peptides and rev response elements of HIV-1 RNA, providing mechanistic insights into rev recognition and recruitment.

    • Eva-Maria Schneeberger
    • , Matthias Halper
    •  & Kathrin Breuker

  • Article
    | Open Access

    Current cell segmentation methods for Saccharomyces cerevisiae face challenges under a variety of standard experimental and imaging conditions. Here the authors develop a convolutional neural network for accurate, label-free cell segmentation.

    • Nicola Dietler
    • , Matthias Minder
    •  & Sahand Jamal Rahi

  • Article
    | Open Access

    Identifying chemical-genetic interactions in mammalian cells is limited to low-throughput or computational methods. Here, the authors present QMAP-Seq, a broadly accessible and scalable approach that uses NGS for pooled high-throughput chemical-genetic profiling in mammalian cells.

    • Sonia Brockway
    • , Geng Wang
    •  & Marc L. Mendillo

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