Neuroscience articles within Nature Methods

Featured

  • Brief Communication |

    The authors report Alexa Fluor 633 hydrazide to be artery-specific and use it to measure arteriole dilation dynamics in vivo in response to visual stimuli in mouse, rat and cat neocortex. They find that sensory stimulus–evoked arteriole dilation reduces the fluorescence recorded from underlying neurons.

    • Zhiming Shen
    • , Zhongyang Lu
    •  & Prakash Kara

  • Article |

    A device for generating precise spatial and temporal patterns of airborne odorants is reported. In combination with machine vision tracking software, the authors use the device to monitor navigation of freely moving Drosophila melanogaster larvae.

    • Marc Gershow
    • , Matthew Berck
    •  & Aravinthan D T Samuel

  • Article |

    Adenosine-to-inosine RNA editing modifies expressed sequences and enhances functional protein diversity. The authors report an in vivo fluorescent reporter that provides a readout of adenosine deaminase RNA-editing activity in Drosophila melanogaster neurons, showing evidence of inter-individual variability in editing activity.

    • James E C Jepson
    • , Yiannis A Savva
    •  & Robert A Reenan

  • Analysis |

    In this Analysis, the authors directly experimentally compare microbial opsins used for the control of neural activity. They extract essential principles and key parameters that can help end users with the design and interpretation of optogenetic experiments and guide tool developers in the characterization of future tools.

    • Joanna Mattis
    • , Kay M Tye
    •  & Karl Deisseroth

  • News & Views |

    Daisy-chaining light-sensitive ion channels, pumps and fluorescent proteins extends the possibilities for control of neuronal activity.

    • Thomas G Oertner

  • Article |

    The microbial rhodopsin protein, Archaerhodopsin 3, can function as a rapid and highly sensitive genetically encoded voltage indicator in mammalian cells that is capable of detecting single action potentials with a signal-to-noise ratio greater than 10. A mutant lacking proton pumping displays greater sensitivity but a slowed response.

    • Joel M Kralj
    • , Adam D Douglass
    •  & Adam E Cohen

  • Brief Communication |

    Presented is a study of gene regulation during development using a combination of chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq) and directed differentiation of mouse embryonic stem cells inducibly expressing epitope-tagged transcription factors.

    • Esteban O Mazzoni
    • , Shaun Mahony
    •  & Hynek Wichterle

  • Article |

    Molecular engineering allows stoichiometric and co-localized expression of two optogenetic actuators, spaced by a fluorescent protein and an additional transmembrane helix in a single protein fusion. The method provides modular optogenetic tools for bidirectional membrane potential control or synergistic effects on neuronal activity.

    • Sonja Kleinlogel
    • , Ulrich Terpitz
    •  & Ernst Bamberg

  • This Month |

    Pure oligodendrocyte populations can be made without cell sorting.

    • Monya Baker
    •  & Paul Tesar

  • Research Highlights |

    Two structure-driven studies of the culprits behind diseases associated with amyloid fibers give clues to stopping these agents in their tracks.

    • Irene Kaganman

  • Article |

    A framework and web interface for the large-scale and automated synthesis of human neuroimaging data extracted from the literature is presented. It is used to generate a large database of mappings between neural and cognitive states and to address long-standing inferential problems in the neuroimaging literature.

    • Tal Yarkoni
    • , Russell A Poldrack
    •  & Tor D Wager

  • Article |

    The Multi-Worm Tracker permits real-time, high-throughput, quantitative analysis of behavior in Caenorhabditis elegans. It should enable screens for genes implicated in complex worm behaviors. Also in this issue, Albrecht and Bargmann apply microfluidics to study worm chemosensory behavior with high spatial and temporal precision.

    • Nicholas A Swierczek
    • , Andrew C Giles
    •  & Rex A Kerr

  • Research Highlights |

    Two new reports describe variants of channelrhodopsin 2 with improved properties.

    • Erika Pastrana

  • Article |

    Software for the automated and accurate registration of multiple images of Drosophila melanogaster brain is reported. It is used to build a preliminary atlas of gene expression in the fly brain.

    • Hanchuan Peng
    • , Phuong Chung
    •  & Julie H Simpson

  • Research Highlights |

    Researchers have taken first steps toward functional connectomics. By combining large-scale serial electron microscopy and functional imaging data, the structure of neural networks can be related to their function.

    • Erika Pastrana

  • Research Highlights |

    A digital platform has been created to incorporate multiple brain data resources into a common global mouse atlas.

    • Erika Pastrana

  • Research Highlights |

    Analyzing brain signals from freely moving rodents in the wild is possible using a wireless neural recording system.

    • Erika Pastrana

  • Article |

    A genetic multicolor cell-labeling technique for Droshophila melanogaster, Flybow, is described and applied to the study of neural circuits. This method implements a variant of the mouse Brainbow strategy in combination with specific neuronal targeting using the Gal-4–upstream activating sequence system to select for membrane-tethered fluorescent proteins. Also in this issue, Hampel et al. report a similar strategy, Drosophila Brainbow, to select for epitope-tagged proteins detectable via immunofluorescence.

    • Dafni Hadjieconomou
    • , Shay Rotkopf
    •  & Iris Salecker

  • Article |

    A genetic multicolor cell-labeling technique for Droshophila melanogaster, Drosophila Brainbow, is described and applied to the study of neural circuits. This method implements a variant of the mouse Brainbow strategy in combination with specific neuronal targeting using the Gal-4–upstream activating sequence system to select for epitope-tagged proteins detectable with immunofluorescence. Also in this issue, Hadjieconomou et al. develop a similar strategy, Flybow, to select for membrane-tethered fluorescent proteins.

    • Stefanie Hampel
    • , Phuong Chung
    •  & Julie H Simpson

  • Resource |

    A genetic platform allows refinement of tissue-specific expression using the upstream activating sequence–GAL4 system in Drosophila melanogaster, facilitating the segmentation of complex expression patterns and allowing GAL4 expression patterns to be repurposed.

    • Daryl M Gohl
    • , Marion A Silies
    •  & Thomas R Clandinin

  • News & Views |

    Two systems allow precise optogenetic stimulation of specific neurons in freely behaving nematodes.

    • André E X Brown
    •  & William R Schafer

  • Article |

    An optogenetic illumination system based on the use of a digital micromirror device and video tracking software is reported, which allows real-time light delivery with high spatial resolution to specified targets in freely moving Caenorhabditis elegans. Also in this issue, Stirman et al. report a similar illumination system using a liquid crystal display projector. Both methods allow optogenetic perturbation of a variety of neural circuits in the behaving worm.

    • Andrew M Leifer
    • , Christopher Fang-Yen
    •  & Aravinthan D T Samuel

  • Article |

    An optogenetic illumination system based on the use of a liquid crystal display projector and video tracking software is reported, which allows real-time multispectral light delivery with high spatial resolution to specified targets in freely moving Caenorhabditis elegans. Also in this issue, Leifer et al. report a similar illumination system using a digital micromirror device. Both methods allow optogenetic perturbation of a variety of neural circuits in the behaving worm.

    • Jeffrey N Stirman
    • , Matthew M Crane
    •  & Hang Lu

  • Brief Communication |

    In vivo calcium imaging at multiple depths simultaneously is shown using multifocal two-photon microscopy and spatiotemporal multiplexing. This technique involves scanning the sample with multiple beams in parallel at different axial planes and is applied to monitor neuronal network activity in multiple cortical layers of an anesthetized mouse.

    • Adrian Cheng
    • , J Tiago Gonçalves
    •  & Carlos Portera-Cailliau

  • Research Highlights |

    Array tomography opens the door to the large-scale exploration of molecular diversity of individual brain synapses.

    • Erika Pastrana

  • Commentary |

    Optogenetics is routinely used to activate and inactivate genetically defined neuronal populations in vivo. A second optogenetic revolution will occur when spatially distributed and sparse neural assemblies can be precisely manipulated in behaving animals.

    • Simon Peron
    •  & Karel Svoboda

  • Commentary |

    Optogenetics is a technology that allows targeted, fast control of precisely defined events in biological systems as complex as freely moving mammals. By delivering optical control at the speed (millisecond-scale) and with the precision (cell type–specific) required for biological processing, optogenetic approaches have opened new landscapes for the study of biology, both in health and disease.

    • Karl Deisseroth

  • News Feature |

    Optogenetics grows from an idea into a discipline. Monya Baker reports.

    • Monya Baker

  • Research Highlights |

    Using a virtual reality setup and a deep window into the brain, researchers can image the activity of neurons as mice navigate virtual environments.

    • Erika Pastrana

  • Editorial |

    New tools are improving the prospects for transcranial light-based neuroscience, but better methods for using them are needed before they can reach their full potential.

  • Research Highlights |

    A nanoscale field-effect transistor with a three-dimensional probe-presentation design can record intracellular potentials from single cells.

    • Erika Pastrana

  • News & Views |

    Optogenetic stimulation by ultrashort laser pulses could allow neural circuits in the living brain to be probed with cellular resolution, despite pervasive light scattering. Now sophisticated new multiphoton stimulation systems that strike a better balance between lateral and axial resolution help realize this potential by matching the illumination volume to the soma's dimensions.

    • Shy Shoham

  • This Month |

    Linked fluorescent proteins are used to visualize voltage in living mouse brains.

    • Monya Baker

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