Biological techniques articles within Nature Communications

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  • Article |

    Ferromagnetic nanoantennas support plasmons and exhibit magneto-optical activity under external magnetic fields. Maccaferri et al. show how designed phase compensation in the electric response of these nanostructures enables them to act as ultrasensitive label-free molecular sensors with high figures of merit.

    • Nicolò Maccaferri
    • , Keith E. Gregorczyk
    •  & Paolo Vavassori

  • Article
    | Open Access

    Herpes simplex virus type-1 (HSV-1) is a widespread human pathogen, the structure of which is not yet fully characterized. Here, the authors apply dSTORM super-resolution microscopy in combination with advanced data analysis tools to locate the position of four key protein layers in HSV-1 with unprecedented precision.

    • Romain F. Laine
    • , Anna Albecka
    •  & Clemens F. Kaminski

  • Article |

    Strand-specific RNA-seq (ssRNA-seq) data often lack information on 5′ and 3′ ends of transcripts. Here the authors present a novel method for ssRNA-seq that enables the simultaneous profiling of gene expression, TSSs and polyadenylation sites at near-base resolution with a single library.

    • Saurabh Agarwal
    • , Todd S. Macfarlan
    •  & Shigeki Iwase

  • Article |

    Perfluorinated organic molecules have shown many uses, including as imaging agents. Here, the authors report that fluorinated gold nanoparticles offer an effective means of mass spectrometry tissue imaging, in addition to facilitating X-ray analysis providing complementary information to mass spectral images.

    • Michael E. Kurczy
    • , Zheng-Jiang Zhu
    •  & Gary Siuzdak

  • Article |

    Carbon dioxide influences plant–water relations and gas exchange by regulating stomatal aperture. Here, Tian et al. characterize RHC1, a MATE family transporter that under elevated carbon dioxide concentrations promotes stomatal closure via activation of the SLAC1 anion channel.

    • Wang Tian
    • , Congcong Hou
    •  & Sheng Luan

  • Article
    | Open Access

    Jasmonate regulates multiple aspects of plant growth, development and stress responses. Here, Larrieu et al. develop a fluorescent biosensor that allows jasmonate perception to be monitored at previously unobtainable levels of spatiotemporal resolution in Arabidopsis.

    • Antoine Larrieu
    • , Antony Champion
    •  & Laurent Laplaze

  • Article
    | Open Access

    Common variants account for only a small amount of the heritable risk for developing asthma. Using a meta-analysis approach, Igartua et al. identify one low-frequency missense mutation and two genes with functional variants that are associated with asthma, but only in specific ethnic groups.

    • Catherine Igartua
    • , Rachel A. Myers
    •  & Carole Ober

  • Article |

    Particle tracking with ultra-high resolution in optical and magnetic tweezers has so far relied on laser detection through photodiodes. Here, Huhle et al. demonstrate three-dimensional particle tracking with Ångström accuracy and real-time GPU-accelerated data processing at kHz rates using camera-based imaging.

    • Alexander Huhle
    • , Daniel Klaue
    •  & Ralf Seidel

  • Article |

    As hypoxia is a hallmark of tumour microenvironment, hypoxia-sensing probes are used for tumour imaging. Here, the authors report a hypoxia probe with increased sensitivity, water solubility and functional pH range, allowing in vivodetection of early metastases as small as a few thousand cells.

    • Xianchuang Zheng
    • , Xin Wang
    •  & Xiqun Jiang

  • Article
    | Open Access

    Models for protein diffusion in cells assume a large macromolecular crowding effect. Here Di Rienzo et al.visualize GFP diffusion at the millisecond timescale to observe unobstructed Brownian motion in mammalian cells for distances up to 100 nm, revealing minimal influence of macromolecular crowding.

    • Carmine Di Rienzo
    • , Vincenzo Piazza
    •  & Francesco Cardarelli

  • Article
    | Open Access

    Super-resolution optical fluctuation imaging provides 3D images of biological specimens via blinking fluorophores. Geissbuehler et al. present a multiplexed version of this method that captures images at multiple focal planes simultaneously, reducing the acquisition time compared with standard approaches.

    • Stefan Geissbuehler
    • , Azat Sharipov
    •  & Marcel Leutenegger

  • Article |

    Efforts to improve the performance of optogenetic tools for neuroscience research have mostly been focused on mutating the opsin backbones or mining-related algal genomes. Here the authors show that analogues of the chromophore, retinal, can be used for colour tuning of rhodopsins and altering their photocycle kinetics in several model organisms.

    • N. AzimiHashemi
    • , K. Erbguth
    •  & J. F. Liewald

  • Article
    | Open Access

    Activating mutations of the tyrosine kinase Kit are commonly found in mast cell neoplasms and gastrointestinal stromal tumours. Here the authors show that mutant Kit, through the activation of PI3K and STAT3 pathways, elicits proliferative and survival signals from endolysosomes and from the endoplasmic reticulum.

    • Yuuki Obata
    • , Shota Toyoshima
    •  & Ryo Abe

  • Article |

    Mutations in the enzyme superoxide dismutase 1 (SOD1) underlie a form of neurodegenerative disease called amyotrophic lateral sclerosis. Here the authors employ in-cell NMR to show that SOD1 mutants adopt unstructured conformations that are unable to bind zinc and may form toxic SOD1 aggregates.

    • Enrico Luchinat
    • , Letizia Barbieri
    •  & Lucia Banci

  • Article
    | Open Access

    The microbial RNA-guided CRISPR/Cas9 system has robust genome-editing activities, but the off-target effects of the Cas9 nuclease have only recently begun to be analysed. Here the authors provide evidence for high specificity of the Cas9 nuclease on targeting of the Tafazzin gene in human-induced pluripotent stem cells and demonstrate the impact of single-nucleotide variations of the human genome on Cas9 specificity.

    • Luhan Yang
    • , Dennis Grishin
    •  & George Church

  • Article |

    Genome editing has yet to be performed in non-bilaterian phyla. Here, Ikmi et al. develop techniques to use both TALEN and CRISPR/Cas9 in the sea anemone, Nematostella vectensis, and further leverage a locus expressing an endogenous fluorescent protein as a landing site for homologous recombination-mediated transgenesis.

    • Aissam Ikmi
    • , Sean A. McKinney
    •  & Matthew C. Gibson

  • Article
    | Open Access

    One challenge facing the use of programmable nucleases in genome engineering is the requirement for homologous recombination. Here, Nakade et al.harness microhomology-mediated end-joining as a means of inserting exogenous coding sequences into the genome using both TALEN and CRISPR/Cas9 technologies.

    • Shota Nakade
    • , Takuya Tsubota
    •  & Ken-ichi T. Suzuki

  • Article
    | Open Access

    Single-molecule localization microscopy depends on the use of photo-modulatable fluorescent probes; however, many cannot be used in live-cell studies due to poor cell permeability. Pan et al.present a strategy for constructing cell-permeable probes and use it to image actin filament dynamics and lysosomes.

    • Deng Pan
    • , Zhe Hu
    •  & Yu-Hui Zhang

  • Article
    | Open Access

    The 18-kDa translocator protein (TSPO) has been implicated in steroid biogenesis and neuroinflammation. Here, the authors create viable and fertile global TSPO knockout mice, challenging the assumption that TSPO is essential for mouse development but suggesting that it may have a role under certain disease conditions.

    • Richard B. Banati
    • , Ryan J. Middleton
    •  & Guo-Jun Liu

  • Article |

    Multimodal and stimuli-responsive imaging agents can yield more biological information than more typical single-mode or inert imaging probes. Here, the authors have made a dual-modal MRI-fluorescence probe and demonstrate its ability to image redox status in vivo.

    • Molly A. Sowers
    • , Jessica R. McCombs
    •  & Jeremiah A. Johnson

  • Article |

    Protein SUMOylation plays an important role in regulation of many cellular processes. Lamoliatte et al.use a monoclonal antibody specific for SUMO3 tryptic peptides to enhance proteomic identification of SUMOylated proteins, and dramatically expand the number of sites known to be modified by SUMO3.

    • Frédéric Lamoliatte
    • , Danielle Caron
    •  & Pierre Thibault

  • Article
    | Open Access

    Brain–machine interfaces offer the possibility of controlling prosthetic devices using changes in brain activity. Folcher et al.couple such a system wirelessly to an optogenetic implant in mice to control expression of a transgene, demonstrating its potential for mind-controlled drug delivery.

    • Marc Folcher
    • , Sabine Oesterle
    •  & Martin Fussenegger

  • Article |

    AUF1 is an RNA-binding protein believed to function mostly by regulating the decay of its target transcripts. Here, Yoon et al.systematically identify the targets of AUF1 and provide insights into how AUF1 functions to regulate various cellular processes by enhancing the decay, stability or translation of specific RNAs.

    • Je-Hyun Yoon
    • , Supriyo De
    •  & Myriam Gorospe

  • Article |

    Current calcium-sensitive probes based on red fluorescent proteins are unsuitable for two-photon excitation at the near-infrared wavelengths commonly used for green fluorescent probes. Wu et al. use a structure-guided approach to engineer a red fluorescent probe with optimal two-photon excitation at these wavelengths.

    • Jiahui Wu
    • , Ahmed S. Abdelfattah
    •  & Robert E. Campbell

  • Article |

    The fission yeast, Schizosaccharomyces pombe, is a valuable model organism, but the lack of a portable RNA Pol III promoter has prevented the implementation of the CRISPR/Cas9 system. Here the authors develop a CRISPR/Cas9 system that achieves selection-free specific mutagenesis with very high efficiencies in S. pombe.

    • Jake Z. Jacobs
    • , Keith M. Ciccaglione
    •  & Mikel Zaratiegui

  • Article |

    Current genetically encoded sensors for hydrogen peroxide, such as HyPer, emit in the green region giving potential for overlap with other probes. Here, the authors report HyPerRed, a red fluorescent redox probe capable of monitoring intracellular hydrogen peroxide.

    • Yulia G. Ermakova
    • , Dmitry S. Bilan
    •  & Vsevolod V. Belousov

  • Article
    | Open Access

    Monitoring neuronal activity in the rodent in vivobrain is commonly done using micro-electrode arrays but these devices are not normally compatible with optical technologies. Here the authors design a transparent and flexible electrode array based on graphene that allows them to combine electrophysiological recordings with optogenetic and imaging experiments.

    • Dong-Wook Park
    • , Amelia A. Schendel
    •  & Justin C. Williams

  • Article |

    Monitoring neuronal activity of large populations of neurons at high-temporal and spatial resolution is important to understand neurophysiology but requires improved tools and methods. Here the authors develop a transparent and flexible electrode based on graphene that allows them to combine electrophysiological recordings with calcium imaging.

    • Duygu Kuzum
    • , Hajime Takano
    •  & Brian Litt

  • Article |

    Magneto-fluorescent nanoparticles hold promise for bioimaging applications, but synthesizing uniform particles with tunable sizes remains challenging. Chen et al. propose an approach for co-assembling magnetic particles with fluorescent quantum dots, leading to well-defined core-shell structures.

    • Ou Chen
    • , Lars Riedemann
    •  & Moungi G. Bawendi

  • Article
    | Open Access

    Next-generation sequencing technology has made the generation of huge amounts of genetic data possible, but phenotype characterization remains slow and difficult. Here the authors develop a high-throughput phenotyping facility for rice that is able to accurately identify and characterize traits related to morphology, biomass and yield.

    • Wanneng Yang
    • , Zilong Guo
    •  & Lizhong Xiong

  • Article |

    Respiratory syncytial virus (RSV) causes severe respiratory disease in young children. Here, Rameix-Welti et al. create fluorescent and bioluminescent RSV strains that allow real-time analysis of viral replication and screening of antiviral compounds in cultured cells and in live animals.

    • Marie-Anne Rameix-Welti
    • , Ronan Le Goffic
    •  & Jean-François Eléouët

  • Article |

    The essential nature of replicative polymerases has hampered the study of polymerase-δ mutations found in colorectal cancer cells. Here, using polymerase-δ mutations as a proof of principle, the authors present an inducible single vector system that replaces any endogenous gene with an RNAi-resistant mutant version.

    • Medini Manohar Ghodgaonkar
    • , Patrick Kehl
    •  & Josef Jiricny

  • Article |

    Protein–protein interactions are fundamental to nearly all molecular and cellular processes. Here Taslimi et al.describe a versatile new optogenetic module that can be used to visualize protein–protein interactions, as well as reversibly control them with light with spatiotemporal resolution.

    • Amir Taslimi
    • , Justin D. Vrana
    •  & Chandra L. Tucker

  • Article
    | Open Access

    Single molecule fluorescence microscopy is a powerful technique to study protein dynamics in cells, but it has not been applied to adult animals. The authors use complementation-activated light microscopy in C. elegansto discover that dystrophin regulates the diffusion properties of voltage-dependent calcium ion channels at the surface of body-wall muscle cells.

    • Hong Zhan
    • , Ramunas Stanciauskas
    •  & Fabien Pinaud

  • Article |

    1H magnetic resonance can detect endogenous metabolites at physiological concentrations but its application in animal models is challenged by low sensitivity. Here the authors focus ultrahigh magnetic fields on metabolites whose spectral signatures are selectively excited, and achieve microarchitectural insight of rat brains after a stroke.

    • Noam Shemesh
    • , Jens T. Rosenberg
    •  & Lucio Frydman

  • Article |

    The non-invasive detection and imaging of bacterial infection in living organisms is increasingly important. Here, the authors demonstrate the use of labelled carbon nanotubes as bacterial probes in living hosts, and are able to image deep tissue infections with higher signal amplification than dye imaging.

    • Neelkanth M. Bardhan
    • , Debadyuti Ghosh
    •  & Angela M. Belcher

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