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Reading and writing digital data in DNA

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  • Protocol |

    G protein–coupled receptors (GPCRs) play a central role in physiological processes and are common drug targets. This GPCR precrystallization screen uses small culture volumes to determine which conditions result in maximal protein expression and stability.

    • Martin Audet
    • , Kelly Villers
    • , Jeffrey Velasquez
    • , Meihua Chu
    • , Chris Hanson
    •  & Raymond C. Stevens
  • Protocol |

    DNA has the capacity to store large amounts of information for very long durations. This protocol describes encoding of digital files as DNA and the error-free retrieval of the stored data from the sequenced data.

    • Linda C. Meiser
    • , Philipp L. Antkowiak
    • , Julian Koch
    • , Weida D. Chen
    • , A. Xavier Kohll
    • , Wendelin J. Stark
    • , Reinhard Heckel
    •  & Robert N. Grass
  • Protocol |

    Transparent organs are obtained, with retained fluorescent protein signals, upon clearing by immersion in the appropriate CUBIC reagent. The positions of all the cells can be determined using the described software.

    • Katsuhiko Matsumoto
    • , Tomoki T. Mitani
    • , Shuhei A. Horiguchi
    • , Junichi Kaneshiro
    • , Tatsuya C. Murakami
    • , Tomoyuki Mano
    • , Hiroshi Fujishima
    • , Ayumu Konno
    • , Tomonobu M. Watanabe
    • , Hirokazu Hirai
    •  & Hiroki R. Ueda
  • Protocol |

    PheCAP takes structured data and narrative notes from electronic medical records and enables patients with a particular clinical phenotype to be identified.

    • Yichi Zhang
    • , Tianrun Cai
    • , Sheng Yu
    • , Kelly Cho
    • , Chuan Hong
    • , Jiehuan Sun
    • , Jie Huang
    • , Yuk-Lam Ho
    • , Ashwin N. Ananthakrishnan
    • , Zongqi Xia
    • , Stanley Y. Shaw
    • , Vivian Gainer
    • , Victor Castro
    • , Nicholas Link
    • , Jacqueline Honerlaw
    • , Sicong Huang
    • , David Gagnon
    • , Elizabeth W. Karlson
    • , Robert M. Plenge
    • , Peter Szolovits
    • , Guergana Savova
    • , Susanne Churchill
    • , Christopher O’Donnell
    • , Shawn N. Murphy
    • , J. Michael Gaziano
    • , Isaac Kohane
    • , Tianxi Cai
    •  & Katherine P. Liao
  • Protocol |

    hPSCs are differentiated into anterior foregut endoderm and then undergo lineage specification into NKX2-1+ lung progenitor cells. Next, the progenitors undergo distal/alveolar differentiation to produce self-renewing alveolar epithelial type II cells.

    • Anjali Jacob
    • , Marall Vedaie
    • , David A. Roberts
    • , Dylan C. Thomas
    • , Carlos Villacorta-Martin
    • , Konstantinos-Dionysios Alysandratos
    • , Finn Hawkins
    •  & Darrell N. Kotton
  • Protocol |

    This protocol describes how to redesign, characterize, validate and apply genetically encoded dopamine sensors, such as those of the dLight1 family, to measure dopamine transients in cultured cells, neurons, acute brain slices and freely behaving, awake mice.

    • Tommaso Patriarchi
    • , Jounhong Ryan Cho
    • , Katharina Merten
    • , Aaron Marley
    • , Gerard Joey Broussard
    • , Ruqiang Liang
    • , John Williams
    • , Axel Nimmerjahn
    • , Mark von Zastrow
    • , Viviana Gradinaru
    •  & Lin Tian
  • Protocol |

    ICeChIP (internally calibrated ChIP) uses spiked-in, defined nucleosomal standards to overcome the pitfalls of traditional ChIP experiments, enabling the measurement of antibody specificity and the absolute measurement of histone modification density at genomic loci.

    • Adrian T. Grzybowski
    • , Rohan N. Shah
    • , William F. Richter
    •  & Alexander J. Ruthenburg

Collection

Super-resolution microscopy

Bertocchi et al., Nature Cell Biology volume 19, pages 28–37 (2017).

Super-resolution microscopy

Popularization of super-resolution imaging techniques has allowed cell biologists to probe cell structure and function in previously unattainable detail. These methodologies continue to evolve, with new improvements that allow tailoring the available techniques to a particular need and application. This collection showcases primary research articles, reviews and protocols and highlights these recent developments by exemplifying the new, interesting applications of super-resolution microscopy as well as related tool development.

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