Biological techniques articles within Nature Communications

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  • Article |

    Macromolecular complexes hold promise for future generations of drug delivery carriers, but probing their structures with high resolution is challenging. Here, the authors combine X-ray free-electron laser and synchrotron approaches to reveal the core-shell structure of RNA interference microsponges.

    • Marcus Gallagher-Jones
    • , Yoshitaka Bessho
    •  & Changyong Song

  • Article |

    Enzyme-linked immunosorbent assays are common biological analyses, but they can be hindered by non-specific binding and background interference. Here, the authors present an optofluidic laser-based ELISA technique with low detection limits and in the presence of significant non-specific binding.

    • Xiang Wu
    • , Maung Kyaw Khaing Oo
    •  & Xudong Fan

  • Article
    | Open Access

    Propagating waves of cortical neuronal activity are implicated in various cognitive processes and have been observed in anaesthetised animals. Here, the authors demonstrate the existence of propagating waves in awake monkeys during visual stimulation, and show that they are mediated by horizontal fibres in the cortex.

    • Lyle Muller
    • , Alexandre Reynaud
    •  & Alain Destexhe

  • Article |

    Genomic rearrangements have important functional consequences for cancer. Here, Choi and Meyerson use CRISPR/Cas technology to generate translocations and inversions that are known drivers of lung cancer, and demonstrate the utility of this technology for studying the role of genomic rearrangements in disease.

    • Peter S. Choi
    •  & Matthew Meyerson

  • Article |

    Aldehyde dehydrogenase (ALDH)-expressing stem cells can be stained and sorted using a green fluorescent substrate. Minn et al.synthesise a red-shifted fluorescent ALDH probe and demonstrate sorting and microscopic staining of cells in the presence of a green fluorescent marker.

    • Il Minn
    • , Haofan Wang
    •  & Martin G. Pomper

  • Article |

    Genetically encoded optical voltage sensors measure the electrical activity of various tissues with limited effectiveness, due to the sensors’ suboptimal performance metrics. Gong et al.create a sensor with increased brightness, fast kinetics and improved dynamic ranges when compared with previous sensors.

    • Yiyang Gong
    • , Mark J. Wagner
    •  & Mark J. Schnitzer

  • Article
    | Open Access

    Secondary ion mass spectrometry is effective for imaging cellular turnover, but it cannot identify subcellular structures such as organelles. Here the authors show a method for correlating this technique with high-resolution fluorescence microscopy, enabling the measurement of turnover in cellular compartments.

    • Sinem K. Saka
    • , Angela Vogts
    •  & Johannes T. Wessels

  • Article |

    The assessment of nanomaterial toxicity can be hampered by difficulties in determining cell dosage. Here, the authors present a simple method for determination of nanomaterial agglomerate density in liquid media, enabling accurate calculation of dose delivered to cells in an in vitrosystem.

    • Glen DeLoid
    • , Joel M. Cohen
    •  & Philip Demokritou

  • Article |

    Transcription activator-like effectors (TALEs) of pathogenic bacteria activate target genes in host plants to support infection. Here, the authors show that TALEs with single natural repeats of aberrant length tolerate one base pair deletions and may enable the bacteria to overcome natural plant resistance.

    • Annekatrin Richter
    • , Jana Streubel
    •  & Jens Boch

  • Article |

    Cellular heterogeneity is a feature of diverse disease processes, yet is masked in typical biochemical assays. Sarkar et al.develop a microfluidic device to access the contents of single cells in adherent culture, allowing biochemical measurements to be connected with phenotypic information.

    • Aniruddh Sarkar
    • , Sarah Kolitz
    •  & Jongyoon Han

  • Article |

    The direct detection of metabolites secreted by cells can indicate how cellular dynamics affects population development. Here, the authors present an integrated circuit-based method for electrochemical imaging of redox-active signalling molecules with spatial resolution within bacterial colonies.

    • Daniel L. Bellin
    • , Hassan Sakhtah
    •  & Kenneth L. Shepard

  • Article
    | Open Access

    Studies on Patient H.M. showed that bilateral resection of the hippocampus results in impaired consolidation of long-term memory. Annese et al.create a digital map of Henry Molaison’s brain and find that a significant portion of the posterior hippocampus is actually histologically intact.

    • Jacopo Annese
    • , Natalie M. Schenker-Ahmed
    •  & Suzanne Corkin

  • Article
    | Open Access

    Laminin-511 and its cell-binding domain support long-term self-renewal of human pluripotent stem cells in xeno-free culture conditions. Here the authors show that a xeno-free culture matrix consisting of a full-length laminin-521 and the cell–cell adhesion protein E-cadherin supports clonal expansion of human embryonic stem cells.

    • Sergey Rodin
    • , Liselotte Antonsson
    •  & Karl Tryggvason

  • Article |

    Colour changes in response to external stimuli are common in nature, from turkey skin to butterfly wings. Here, inspired by this behaviour, the authors have developed a sensor capable of providing an individual colour response to specific target chemicals using genetically engineered viruses.

    • Jin-Woo Oh
    • , Woo-Jae Chung
    •  & Seung-Wuk Lee

  • Article |

    Cas9 RNA-guided engineered nucleases (RGENs) induce site-specific DNA cleavages in cultured cells and organisms and are used widely as genome-editing tools. Here, the authors develop an RGEN-based technology to genotype both RGEN-induced mutations and cancer-associated mutations in human cell lines.

    • Jong Min Kim
    • , Daesik Kim
    •  & Jin-Soo Kim

  • Article
    | Open Access

    Lateral diffusion of transmembrane signalling molecules is implicated in neuronal communication but imaging in tissue is limited by poor temporal resolution. Here, the authors use quantum dots to label lipids and adhesion molecules, allowing them to track single-molecule motions in subcellular compartments.

    • B. Biermann
    • , S. Sokoll
    •  & M. Heine

  • Article |

    Genetically engineered mice are an important aspect of human disease research. Here, the authors use artificial transcription activator-like effector-nucleases to generate a mouse line with a conditionally targeted allele and suggest that this method can be easily adapted to any gene in the mouse genome.

    • Daniel Sommer
    • , Annika E. Peters
    •  & Marc Beyer

  • Article |

    RNA is central to many cellular functions, but in vivo structures of most RNAs are unknown. Here Kwok et al. present a universally applicable method, DMS/SHAPE-LMPCR, to identify structures of low-abundance transcripts in living cells, which reveals important features that are uniquely present in vivo.

    • Chun Kit Kwok
    • , Yiliang Ding
    •  & Philip C Bevilacqua

  • Article |

    Immunosequencing enables cost-effective sequencing of repertoires of immune cells, but it often suffers from amplification biases when attempting cell quantification. Here, the authors present a powerful multiplex PCR assay that allows for quantitative and unbiased analysis of frequency of different T cell receptors.

    • Christopher S. Carlson
    • , Ryan O. Emerson
    •  & Harlan Robins

  • Article
    | Open Access

    Screens for protein–protein interactions and for drugs that disrupt them typically use in vitro assays which fail to capture the complexity of the cell’s interior. By fixing proteins to distinct cellular locations, Herce et al.demonstrate a fluorescent-three-hybrid approach to probe such interactions in their cellular contexts.

    • Henry D. Herce
    • , Wen Deng
    •  & M. Cristina Cardoso

  • Article |

    Cells can adapt rapidly to survive and efficiently exploit constantly changing environments by varying their mutation rate. Here the authors construct an in silicosystem to modulate mutation rate, and demonstrate that this method can be used in the laboratory to create specific phenotypes.

    • Howard H. Chou
    •  & Jay D. Keasling

  • Article
    | Open Access

    Tumour biopsies contain contaminating normal cells and these can influence the analysis of tumour samples. In this study, Yoshihara et al.develop an algorithm based on gene expression profiles from The Cancer Genome Atlas to estimate the number of contaminating normal cells in tumour samples.

    • Kosuke Yoshihara
    • , Maria Shahmoradgoli
    •  & Roel G.W. Verhaak

  • Article |

    The ratio between ATP and ADP within the cell is a key indicator of metabolic status. Tantama et al. describe a ratiometric, genetically encoded fluorescent sensor for ATP:ADP that is now optimized for mammalian cells, and demonstrate that it can detect physiological changes in energy consumption and production.

    • Mathew Tantama
    • , Juan Ramón Martínez-François
    •  & Gary Yellen

  • Article |

    Current methods to image brown adipose tissue rely on radioactive tracers and specialized imaging equipment. Here Azhdarinia et al.report a peptide-based probe that selectively binds to the vascular endothelium of brown adipose tissue and allows the near-infrared imaging of brown fat in mice.

    • Ali Azhdarinia
    • , Alexes C. Daquinag
    •  & Mikhail G. Kolonin

  • Article |

    Magnetic stimulation is used therapeutically for neurological disorders, but its effectiveness is hindered by efficacy and safety limitations due to large device sizes. Here the authors show that sub-millimetre, micro-magnetic coils effectively stimulate hamster cochlear neurons, with minimal side effects.

    • Hyun-Joo Park
    • , Giorgio Bonmassar
    •  & John T. Gale

  • Article
    | Open Access

    Transport of DNA molecules across lipid membranes requires protein conduits such as the nuclear pore complex. Franceschiniet al.engineer an artificial sequence-selective DNA transporter by attaching gating oligonucleotides to a bacterial nanopore.

    • Lorenzo Franceschini
    • , Misha Soskine
    •  & Giovanni Maglia

  • Article
    | Open Access

    Mouse models of influenza infection that permit monitoring of infection in living animals are scarce. Here Pan et al. describe an engineered influenza virus expressing luciferase, which enables real-time in vivovisualization of viral infection and assessment of antiviral drugs.

    • Weiqi Pan
    • , Zhenyuan Dong
    •  & Ling Chen

  • Article |

    The metabolic reaction catalysed by the isocitrate dehydrogenase 1 (IDH1) enzyme is commonly perturbed in some glioma subtypes due to gain-of-function mutations in the IDH1 gene. Here, Chaumeil et al.present a method that detects mutant IDH1 activity by measuring the levels of different hyperpolarized metabolites produced by wild-type and mutant IDH1.

    • Myriam M. Chaumeil
    • , Peder E. Z. Larson
    •  & Sabrina M. Ronen

  • Article |

    Optogenetics can be used to induce an electrical response in cardiac cells and could become an alternative to electrical cardiac pacing. Here, Boyleet al.present a modelling framework for cardiac optogenetics and explore how optogenetic stimulation might be used to alter cardiac function.

    • Patrick M. Boyle
    • , John C. Williams
    •  & Natalia A. Trayanova

  • Article |

    Imaging cells within live animals is important in biomedical research, but this process is limited by the availability of probes. Ritsma et al.combine intravital microscopy with immunohistochemistry to increase the panel of available reagents and examine the role of T cells in the migration of breast cancer cells.

    • Laila Ritsma
    • , Nienke Vrisekoop
    •  & Jacco van Rheenen

  • Article
    | Open Access

    Systematic large-scale analysis of embryonic development requires the processing of large amounts of microscopy data. Here Schmid et al.solve this problem by developing a high-speed imaging system that projects zebrafish embryos onto a ‘world map’ in real time, revealing characteristic migration patterns in the early endoderm.

    • Benjamin Schmid
    • , Gopi Shah
    •  & Jan Huisken

  • Article |

    The short-wavelength infrared spectral region is of interest for bio-imaging applications as biological tissue is transparent to such light. Here Naczynski et al. fabricate rare-earth-based nanomaterials and demonstrate multispectral, real-time short-wavelength infrared in-vivoimaging.

    • D. J. Naczynski
    • , M. C. Tan
    •  & P. V. Moghe

  • Article |

    The complexity and dynamic range of mammalian proteomes has stymied comprehensive protein quantification for the past twenty years. Zhou et al. develop DEEP SEQ mass spectrometry and use it to quantify a murine stem cell proteome to a depth equivalent to RNA-seq-based ribosome profiling.

    • Feng Zhou
    • , Yu Lu
    •  & Jarrod A. Marto

  • Article |

    Genetically encoded calcium indicators are commonly used to study cellular activity, but their usefulness is limited by their response kinetics. Here the authors generate indicators with faster responses to calcium events in both Drosophila melanogasterand mammalian neurons.

    • Xiaonan R. Sun
    • , Aleksandra Badura
    •  & Samuel S. -H. Wang

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