Volume 16 Issue 10, October 2019

Volume 16 Issue 10

Special Feature: Nature Methods turns 15!

This month we celebrate the fifteen-year anniversary of Nature Methods. The cover artwork comprises images from previous covers of Nature Methods throughout the years.

Cover design: Erin Dewalt.

Editorial

  • Editorial |

    We celebrate the 15th anniversary issue of Nature Methods with a look back on the past decade and a half, and a look forward to the future of methods development.

This Month

  • This Month |

    Building nice, shiny instruments to solve unsolved problems, and the physics of sailing.

    • Vivien Marx

Correspondence

  • Correspondence |

    • Lloyd M. Smith
    • , Paul M. Thomas
    • , Michael R. Shortreed
    • , Leah V. Schaffer
    • , Ryan T. Fellers
    • , Richard D. LeDuc
    • , Trisha Tucholski
    • , Ying Ge
    • , Jeffrey N. Agar
    • , Lissa C. Anderson
    • , Julia Chamot-Rooke
    • , Joseph Gault
    • , Joseph A. Loo
    • , Ljiljana Paša-Tolić
    • , Carol V. Robinson
    • , Hartmut Schlüter
    • , Yury O. Tsybin
    • , Marta Vilaseca
    • , Juan Antonio Vizcaíno
    • , Paul O. Danis
    •  & Neil L. Kelleher

Comment

  • Comment |

    Single-particle techniques offer an unprecedented opportunity to understand the role of structural variability in biological function. They also call into question the meaning of ‘a structure’ and its relevance to function.

    • Abbas Ourmazd

Feature

  • Feature |

    To mark the 15th anniversary of Nature Methods, we asked scientists from across diverse fields of basic biology research for their views on the most exciting and essential methodological challenges that their communities are poised to tackle in the near future.

    • Polina Anikeeva
    • , Edward Boyden
    • , Clifford Brangwynne
    • , Ibrahim I. Cissé
    • , Oliver Fiehn
    • , Petra Fromme
    • , Anne-Claude Gingras
    • , Casey S. Greene
    • , Edith Heard
    • , Stefan W. Hell
    • , Elizabeth Hillman
    • , Grant Jay Jensen
    • , Rachel Karchin
    • , Laura L. Kiessling
    • , Benjamin P. Kleinstiver
    • , Rob Knight
    • , Philipp Kukura
    • , Madeline A. Lancaster
    • , Nicholas Loman
    • , Loren Looger
    • , Emma Lundberg
    • , Qingming Luo
    • , Atsushi Miyawaki
    • , Eugene W. Myers Jr.
    • , Garry P. Nolan
    • , Paola Picotti
    • , Wolf Reik
    • , Markus Sauer
    • , Alex K. Shalek
    • , Jay Shendure
    • , Nikolai Slavov
    • , Amos Tanay
    • , Olga Troyanskaya
    • , David van Valen
    • , Hong-Wei Wang
    • , Chengqi Yi
    • , Peng Yin
    • , Magdalena Zernicka-Goetz
    •  & Xiaowei Zhuang

Research Highlights

Technology Feature

  • Technology Feature |

    Labs in different neuropsychiatry subfields don’t always see eye to eye, but convergent approaches help them join forces to study these difficult conditions.

    • Vivien Marx

    Collection:

News & Views

  • News & Views |

    Focused laser light can manipulate the phase of electrons and solve the long-standing phase contrast conundrum in electron microscopy.

    • Radostin Danev

Review Articles

  • Review Article |

    This Review discusses the principles, advantages and limitations of Brillouin microscopy, a non-invasive tool for measuring mechanical properties of biological samples in three dimensions.

    • Robert Prevedel
    • , Alba Diz-Muñoz
    • , Giancarlo Ruocco
    •  & Giuseppe Antonacci

Brief Communications

  • Brief Communication |

    A rapid sample mixing approach enables time-resolved structural studies of enzymatic reactions using serial synchrotron crystallography.

    • Pedram Mehrabi
    • , Eike C. Schulz
    • , Michael Agthe
    • , Sam Horrell
    • , Gleb Bourenkov
    • , David von Stetten
    • , Jan-Philipp Leimkohl
    • , Hendrik Schikora
    • , Thomas R. Schneider
    • , Arwen R. Pearson
    • , Friedjof Tellkamp
    •  & R. J. Dwayne Miller
  • Brief Communication |

    Garnett uses a hierarchical markup language and machine learning to define cell types and their marker genes and identifies these cell types in scRNA-seq datasets from tissues and whole organisms and across species.

    • Hannah A. Pliner
    • , Jay Shendure
    •  & Cole Trapnell
  • Brief Communication |

    A dense, spatially barcoded bead array captures RNA from histological tissue sections for spatially resolved gene expression analysis.

    • Sanja Vickovic
    • , Gökcen Eraslan
    • , Fredrik Salmén
    • , Johanna Klughammer
    • , Linnea Stenbeck
    • , Denis Schapiro
    • , Tarmo Äijö
    • , Richard Bonneau
    • , Ludvig Bergenstråhle
    • , José Fernandéz Navarro
    • , Joshua Gould
    • , Gabriel K. Griffin
    • , Åke Borg
    • , Mostafa Ronaghi
    • , Jonas Frisén
    • , Joakim Lundeberg
    • , Aviv Regev
    •  & Patrik L. Ståhl
  • Brief Communication |

    Methyl-HiC combines the elucidation of chromatin architecture with the reading of DNA methylomes in pools and single cells. Regions that are distant on the linear-genome but close in three-dimensional space show coordinated DNA methylation.

    • Guoqiang Li
    • , Yaping Liu
    • , Yanxiao Zhang
    • , Naoki Kubo
    • , Miao Yu
    • , Rongxin Fang
    • , Manolis Kellis
    •  & Bing Ren
  • Brief Communication |

    Functional ultrasound (fUS) imaging of neural activity has been extended to volumetric imaging across the whole brain. 4D fUS is demonstrated in the rat brain in response to sensory stimuli and during seizure-like activity.

    • Claire Rabut
    • , Mafalda Correia
    • , Victor Finel
    • , Sophie Pezet
    • , Mathieu Pernot
    • , Thomas Deffieux
    •  & Mickael Tanter

Articles

  • Article |

    Single-nucleus methyl-3C sequencing jointly interrogates 3D chromatin organization and DNA methylation in human cells, and these joint measurements more accurately distinguish different cell types than either unimodal method.

    • Dong-Sung Lee
    • , Chongyuan Luo
    • , Jingtian Zhou
    • , Sahaana Chandran
    • , Angeline Rivkin
    • , Anna Bartlett
    • , Joseph R. Nery
    • , Conor Fitzpatrick
    • , Carolyn O’Connor
    • , Jesse R. Dixon
    •  & Joseph R. Ecker
  • Article |

    CellAssign uses a probabilistic model to assign single cells to a given cell type defined by known marker genes, enabling automated annotation of cell types present in a tumor microenvironment.

    • Allen W. Zhang
    • , Ciara O’Flanagan
    • , Elizabeth A. Chavez
    • , Jamie L. P. Lim
    • , Nicholas Ceglia
    • , Andrew McPherson
    • , Matt Wiens
    • , Pascale Walters
    • , Tim Chan
    • , Brittany Hewitson
    • , Daniel Lai
    • , Anja Mottok
    • , Clementine Sarkozy
    • , Lauren Chong
    • , Tomohiro Aoki
    • , Xuehai Wang
    • , Andrew P Weng
    • , Jessica N. McAlpine
    • , Samuel Aparicio
    • , Christian Steidl
    • , Kieran R. Campbell
    •  & Sohrab P. Shah
  • Article |

    Phase plates improve contrast in cryo-electron microscopy, but suffer from electrostatic charging and electron scattering. A laser phase plate overcomes these problems and may improve imaging of biological specimens.

    • Osip Schwartz
    • , Jeremy J. Axelrod
    • , Sara L. Campbell
    • , Carter Turnbaugh
    • , Robert M. Glaeser
    •  & Holger Müller
  • Article |

    Mass spectrometry imaging with fluoromethylpyridinium-based reactive matrices allows mapping of neurotransmitters at high resolution and at a low limit of detection. The approach is applied to rat, macaque and human brain tissue samples for probing Parkinson’s disease-related changes.

    • Mohammadreza Shariatgorji
    • , Anna Nilsson
    • , Elva Fridjonsdottir
    • , Theodosia Vallianatou
    • , Patrik Källback
    • , Luay Katan
    • , Jonas Sävmarker
    • , Ioannis Mantas
    • , Xiaoqun Zhang
    • , Erwan Bezard
    • , Per Svenningsson
    • , Luke R. Odell
    •  & Per E. Andrén
  • Article |

    Fusion to fluorescent proteins enables efficient two-photon activation of blue-light-controlled optical dimerizers via FRET. FRET-assisted photoactivation was used to study extracellular signal-regulated kinase activation in 3D epithelial cysts, organoids and living mice.

    • Tomoaki Kinjo
    • , Kenta Terai
    • , Shoichiro Horita
    • , Norimichi Nomura
    • , Kenta Sumiyama
    • , Kaori Togashi
    • , So Iwata
    •  & Michiyuki Matsuda
  • Article |

    Cell lines in which Nup96 is endogenously tagged with mEGFP, SNAP-tag, HaloTag or mMaple serve as versatile reference samples, enabling 3D resolution calibration, assessment of labeling efficiency and precise molecular counting.

    • Jervis Vermal Thevathasan
    • , Maurice Kahnwald
    • , Konstanty Cieśliński
    • , Philipp Hoess
    • , Sudheer Kumar Peneti
    • , Manuel Reitberger
    • , Daniel Heid
    • , Krishna Chaitanya Kasuba
    • , Sarah Janice Hoerner
    • , Yiming Li
    • , Yu-Le Wu
    • , Markus Mund
    • , Ulf Matti
    • , Pedro Matos Pereira
    • , Ricardo Henriques
    • , Bianca Nijmeijer
    • , Moritz Kueblbeck
    • , Vilma Jimenez Sabinina
    • , Jan Ellenberg
    •  & Jonas Ries
  • Article |

    SCAPE 2.0 is a versatile imaging platform that enables real-time three-dimensional microscopy of cellular function and dynamic motion in living organisms at over 100 volumes per second with minimal photodamage, and high-throughput structural imaging in fixed, cleared and expanded samples.

    • Venkatakaushik Voleti
    • , Kripa B. Patel
    • , Wenze Li
    • , Citlali Perez Campos
    • , Srinidhi Bharadwaj
    • , Hang Yu
    • , Caitlin Ford
    • , Malte J. Casper
    • , Richard Wenwei Yan
    • , Wenxuan Liang
    • , Chentao Wen
    • , Koutarou D. Kimura
    • , Kimara L. Targoff
    •  & Elizabeth M. C. Hillman

Amendments & Corrections