Sensors and probes articles within Nature Communications

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  • Article
    | Open Access

    Fiber optic implantation in deep areas of the rodent’s brain for MRI combined with optogenetics is challenging. Here the authors use an MRI-guided robotic arm as the navigation method for accurate fiber optic placement and precise microinjection during multi-modal fMRI, optogenetics and calcium recordings.

    • Yi Chen
    • , Patricia Pais-Roldan
    •  & Xin Yu

  • Article
    | Open Access

    The identification of single point mutations is an important step toward personalizing detection and treatment. Here the authors design a gold-bridged nanoparticle for sensing MutS affinities to point mutations, and compile an atlas of the affinity data for detecting BRCA1 mutations in cell lines.

    • Xingyi Ma
    • , Sojin Song
    •  & Sang Jun Sim

  • Article
    | Open Access

    FRET sensors hardly achieve visualization of spatiotemporal dynamics of protein activity in vivo. Here the authors present intensiometric small GTPase biosensors based on dimerization-dependent fluorescent proteins that enable monitoring of activity of small GTPases in the brains of behaving mice at a single spine resolution.

    • Jihoon Kim
    • , Sangkyu Lee
    •  & Won Do Heo

  • Article
    | Open Access

    Tagging and tracking cells with multiplexed labels can help study complex cellular behaviors in living systems. Here, Jo et al. propose and demonstrate the use of Fabry-Perot-like resonances in dielectric microspheres as such a label and call these reflectophores.

    • Yongjae Jo
    • , Junhwan Kwon
    •  & Myunghwan Choi

  • Article
    | Open Access

    Bacterially encoded environmental sensor proteins are potentially a rich source of transcriptional control but only a few have been harnessed for biotechnological applications. Here the authors develop a general strategy for designing custom-made monogenic synthetic sensors and validate the approach by designing two sense-and-respond regulators for benzoate.

    • Javier F. Juárez
    • , Begoña Lecube-Azpeitia
    •  & George M. Church

  • Article
    | Open Access

    The mechanism of protein dislocation into the cytosol during antigen cross-presentation is poorly understood. Here the authors engineer a dislocation reporter fusing a glycosylated luciferase variant to the Fc region of IgG1, and find that dislocation is the rate limiting step in cross-presentation.

    • Qiao Lu
    • , Jeff E. Grotzke
    •  & Peter Cresswell

  • Article
    | Open Access

    Surface enhanced Raman scattering is a bio-analytical tool and the development and optimisation of probes is an active area of investigation. Here, the authors report on the development and testing of biocompatible semiconductor zinc oxide quantum probes on a platform for cell adhesion and analysis.

    • Rupa Haldavnekar
    • , Krishnan Venkatakrishnan
    •  & Bo Tan

  • Article
    | Open Access

    Bacterial phytochrome-based probes improved sensitivity in photoacoustic computed tomography. Here the authors engineer a small near-infrared switchable photochromic probe that allows multi-contrast imaging at depths and can be adapted to study protein–protein interactions in deep-seated tumors.

    • Lei Li
    • , Anton A. Shemetov
    •  & Vladislav V. Verkhusha

  • Article
    | Open Access

    Poly ADP-ribosylation (PARylation) is a highly dynamic post-translation protein modification, but most methods only detect stable PARylation events. Here the authors develop a split-GFP-based sensor for PARylation detection in live cells and use it to identify a new centrosomal PARylation target.

    • Dragomir B. Krastev
    • , Stephen J. Pettitt
    •  & Christopher J. Lord

  • Article
    | Open Access

    Methylated RNA bases influence many life processes, but current detection methods lack the ability to detect individual methylations in single cells. Here, the authors use fluorescence hybridization probes sensitive to methylation to detect specific epitranscriptomic modifications at the single-cell level.

    • Rohan T. Ranasinghe
    • , Martin R. Challand
    •  & David Klenerman

  • Article
    | Open Access

    Traditional methods for the assembly of plasmonic nanoparticles into photo-responsive probes suffer from multiple problems. Here the authors use split fluorescent protein fragments as molecular glue to form stable nanoclusters for surface enhanced Raman scattering and photoacoustic imaging in live cells.

    • Tuğba Köker
    • , Nathalie Tang
    •  & Fabien Pinaud

  • Article
    | Open Access

    Ubiquitylation is a dynamic post-translational modification involved in the regulation of numerous cellular processes. Here the authors describe Ub-ProT: a method to measure the length of substrate-attached ubiquitin chains in biological samples, and demonstrate a critical role for chain length in directing substrates to specific cellular pathways.

    • Hikaru Tsuchiya
    • , Daocharad Burana
    •  & Yasushi Saeki

  • Article
    | Open Access

    A pool of quality control proteins (QC) maintains the protein-folding homeostasis in the cell, but its quantitative analysis is challenging. Here the authors develop a FRET sensor based on the protein barnase, able to quantify QC holdase activity and its ability to suppress protein aggregation.

    • Rebecca J. Wood
    • , Angelique R. Ormsby
    •  & Danny M. Hatters

  • Article
    | Open Access

    Red-shifted bioluminescence emission is needed to improve deep tissue imaging resolution. Here, the authors develop a click beetle red luciferase mutant and two naphthyl-luciferin substrates, and show the ability of the new luciferin/luciferase pairing for deep tissue multispectral tomography in mice.

    • Mary P. Hall
    • , Carolyn C. Woodroofe
    •  & Laura Mezzanotte

  • Article
    | Open Access

    The extracellular matrix is under variable strain, but we lack the tools to detect differences in strain. Here the authors develop a probe based on a bacterial fibronectin-binding peptide that binds to relaxed fibronectin fibrils and detects relaxed matrix in cell culture, tissue slices and in vivo.

    • Simon Arnoldini
    • , Alessandra Moscaroli
    •  & Viola Vogel

  • Article
    | Open Access

    The interrogation of enzyme activity involves the ensemble averaging of many cells, loss of spatial relationships and is often biased to abundant proteins. Here the authors develop activity-dependent proximity ligation to quantify enzyme activity at the cellular and sub-cellular level in relevant biological contexts.

    • Gang Li
    • , Jeffrey E. Montgomery
    •  & Raymond E. Moellering

  • Article
    | Open Access

    Existing pH-sensitive red fluorescent protein probes don’t perform well in monitoring exocytosis and endocytosis. Here, the authors combine organic dyes with self-labeling tags or antibodies to develop semisynthetic protein conjugates that can image synaptic vesicle fusion events in living cells.

    • Magalie Martineau
    • , Agila Somasundaram
    •  & David Perrais

  • Article
    | Open Access

    Studying interactions between lysosomes and mitochondria in living cells is difficult due to the limitations of existing probes. Here, the authors develop new cell-permeable fluorescent probes to image the dynamics of lysosomes and their physical interactions with mitochondria using super-resolution microscopy.

    • Yubing Han
    • , Meihua Li
    •  & Yu-Hui Zhang

  • Article
    | Open Access

    Visualization of synaptic activity in the living brain is challenging. This study devises a simple and efficient scheme that reports synaptic vesicle recycling in vivo using SynaptoZip, a genetically encoded sensor of past synaptic activities.

    • Mattia Ferro
    • , Jacopo Lamanna
    •  & Antonio Malgaroli

  • Article
    | Open Access

    Generally, fluorescence imaging needs to be done in a dark environment using molecules with spectrally separated emissions. Here, Quérard et al. develop a protocol for high-speed imaging and remote sensing of spectrally overlapping reversible photoswitchable fluorophores in ambient light.

    • Jérôme Quérard
    • , Ruikang Zhang
    •  & Ludovic Jullien

  • Article
    | Open Access

    Fluorescence imaging in the near-infrared window between 1500–1700 nm (NIR-IIb window) offers superior spatial resolution and tissue penetration depth, but few NIR-IIb probes exist. Here, the authors synthesize rare earth down-converting nanocrystals as promising fluorescent probes for in vivo imaging in this spectral region.

    • Yeteng Zhong
    • , Zhuoran Ma
    •  & Hongjie Dai

  • Article
    | Open Access

    Single fluorescent protein biosensors are susceptible to expression and instrumental artifacts. Here Ast et al. describe a dual fluorescent protein design whereby a reference fluorescent protein is nested within a reporter fluorescent protein to control for such artifacts while preserving sensitivity and dynamic range.

    • Cindy Ast
    • , Jessica Foret
    •  & Wolf B. Frommer

  • Article
    | Open Access

    Split fluorescent proteins (FPs) have been widely used to visualise proteins in cells. Here the authors develop a screen for engineering new split FPs, and report a yellow-green split-mNeonGreen2 with reduced background, a red split-sfCherry2 for multicolour labeling, and its photoactivatable variant for super-resolution use.

    • Siyu Feng
    • , Sayaka Sekine
    •  & Bo Huang

  • Article
    | Open Access

    Fluorescent sensors for small biomolecules are needed to shed insight into real-time cellular processes. Here the authors develop RealThiol, a sensor that can quantitatively monitor glutathione dynamics in living cells, and measure increased antioxidant capability of activated neurons and glutathione changes during ferroptosis.

    • Xiqian Jiang
    • , Jianwei Chen
    •  & Jin Wang

  • Article
    | Open Access

    Cellular signalling is often facilitated by membrane protein clustering, but detection of protein clustering at high spatiotemporal resolution is challenging. Here the authors develop a single-chain FRET sensor they name CliF to look at intermolecular associations and dynamics of TCR-CD3 clusters on the T cell surface.

    • Yuanqing Ma
    • , Elvis Pandzic
    •  & Katharina Gaus

  • Article
    | Open Access

    Analysis of virus replication on a single-cell level is often hampered by a lack of specific or sensitive enough reagents. Here, Douamet al. use RNA-flow technique to track (+) and (−) strand RNA of yellow fever virus in hematopoietic cells in mouse models and identify virus-host interactions that affect disease outcome.

    • Florian Douam
    • , Gabriela Hrebikova
    •  & Alexander Ploss

  • Article
    | Open Access

    The role of force in activating integrin cell adhesion receptors is not known. Here the authors develop fluorescent tension sensors for αL and β2 integrins and show that in migrating T cells force is transduced across the β2 integrin, and that this correlates with an active conformational state.

    • Pontus Nordenfelt
    • , Hunter L. Elliott
    •  & Timothy A. Springer

  • Article
    | Open Access

    In the construction of single fluorescent protein biosensors, selection of the insertion point of a fluorescent protein into a ligand-binding domain is a rate-limiting step. Here, the authors develop an unbiased, high-throughput approach, called domain insertion profiling with DNA sequencing (DIP-seq), to generate a novel trehalose biosensor.

    • Dana C. Nadler
    • , Stacy-Anne Morgan
    •  & David F. Savage

  • Article
    | Open Access

    Measurement of low-affinity protein–protein interactions is challenging; surface plasmon resonance requires high concentrations of reagents. Here the authors combine magneto-nanosensors with microfluidic chips and protein-conjugated magnetic nanoparticles to discover a low-affinity interaction between T-cell inhibitory receptors PD-L1 and PD-L2.

    • Jung-Rok Lee
    • , Daniel J. B. Bechstein
    •  & Shan X. Wang

  • Article
    | Open Access

    The enteric nervous system (ENS) plays a key role in regulating gut motility and homeostasis yet it remains a challenging system to record from. Here, the authors develop a novel abdominal window permitting simultaneous optical and electrical recording of mouse ENS system activity over prolonged time periods.

    • Nikolai Rakhilin
    • , Bradley Barth
    •  & Xiling Shen

  • Article
    | Open Access

    Current dyes for second harmonic generation (SHG) imaging strongly fluoresce, limiting their application. Here the authors develop a SHG-specific dye, Ap3, that partitions into cell membranes, displays sensitivity to membrane potential and has virtually no fluorescence emission at SHG imaging wavelengths.

    • Mutsuo Nuriya
    • , Shun Fukushima
    •  & Tatsuo Arai

  • Article
    | Open Access

    Tagging proteins with fluorescent proteins is a powerful method for both imaging and non-imaging applications. Here the authors use the eleventh β-strand of sfGFP and sfCherry as epitope tags for multicolour imaging and amplified signals by tandem arrangement; shortness of the tag enabled introduction into genomic loci using CRISPR/Cas9.

    • Daichi Kamiyama
    • , Sayaka Sekine
    •  & Bo Huang

  • Article
    | Open Access

    Nitric oxide is a volatile free radical second messenger with a large number of biological effects. Here Eroglu et al. develop genetically encoded fluorescent biosensors for nitric oxide and use them to visualise subcellular nitric oxide dynamics in single cells.

    • Emrah Eroglu
    • , Benjamin Gottschalk
    •  & Roland Malli

  • Article
    | Open Access

    Synthetic oligonucleotides are the main cost factor for studies in DNA nanotechnology. Here, the authors present a selective oligonucleotide amplification method, based on three rounds of rolling-circle amplification, that produces nanomole amounts of single-stranded oligonucleotides per millilitre reaction.

    • Thorsten L. Schmidt
    • , Brian J. Beliveau
    •  & William M. Shih

  • Article
    | Open Access

    Existing DNA stains for live cell microscopy are either toxic, require illumination with blue light, or are not compatible with super-resolution microscopy. Here the authors develop SiRHoechst, a non-toxic far-red DNA stain that is compatible with super-resolution microscopy.

    • Gražvydas Lukinavičius
    • , Claudia Blaukopf
    •  & Kai Johnsson

  • Article |

    Quantitative live cell imaging of protein trafficking suffers from misfolding and inappropriate disulphide bond formation of fluorescent proteins in the secretory pathway. Here, the authors present an optimized collection of fluorescent proteins suitable for use in oxidizing subcellular compartments.

    • Lindsey M. Costantini
    • , Mikhail Baloban
    •  & Erik L. Snapp

  • Article
    | Open Access

    DNA intercalators, a type of fluorescent probes widely used to visualize DNA, can perturb DNA structure and stability. Here, the authors show how DNA-binding affinity can be tuned using DNA tension, ionic strength and dye species, and how this can be used to minimize DNA structural perturbations.

    • Andreas S. Biebricher
    • , Iddo Heller
    •  & Gijs J. L. Wuite

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