Volume 17 Issue 8, August 2020

Volume 17 Issue 8

Red-shifted rhodamines for cellular imaging

A photo of quartz cuvettes containing 5 µM solutions of the organic rhodamine dyes Janelia Fluor 479 (JF479), JF559, JF571 and JF593 excited at an angle with a 405-nm laser pointer.

See Grimm et al.

Image: Jonathan Grimm. Cover Design: Marina Spence.

Editorial

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    We’ve made some recent updates to our various content type offerings at Nature Methods. Here is a cheat sheet.

This Month

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    A platform for exploring GPCR secrets, powered by community, music and sports.

    • Vivien Marx

Correspondence

Research Highlights

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    Direct imaging of carbohydrates using electrospray ion beam deposition and scanning tunneling microscopy.

    • Arunima Singh
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    Intravital three-dimensional bioprinting enables the biofabrication of constructs in a pre-existing 3D matrix, such as inside tissues of live animals.

    • Lei Tang
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    barRNAseq allows detailed explorations of signaling pathways that control embryonic differentiation.

    • Madhura Mukhopadhyay
  • Research Highlight |

    RIC-seq enables in situ mapping of intra- and intermolecular RNA–RNA interactions.

    • Lin Tang
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    Tethering fluorescent proteins to ribosomes clears up background signals when imaging neural circuits.

    • Nina Vogt

Technology Feature

Perspectives

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    This Perspective highlights recently developed computational models for studying chromosome organization, with a focus on how mechanistic modeling helps biologists to interpret the biological function behind the genome structures.

    • Chris A. Brackey
    • , Davide Marenduzzo
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Resources

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    GPCRmd is a community-driven online platform to visualize, analyze and share G-protein-coupled receptor (GPCR) molecular dynamics data. It currently contains simulation data representing 100% of GPCR classes, 71% of receptor subtypes and 80% of GPCR families.

    • Ismael Rodríguez-Espigares
    • , Mariona Torrens-Fontanals
    • , Johanna K. S. Tiemann
    • , David Aranda-García
    • , Juan Manuel Ramírez-Anguita
    • , Tomasz Maciej Stepniewski
    • , Nathalie Worp
    • , Alejandro Varela-Rial
    • , Adrián Morales-Pastor
    • , Brian Medel-Lacruz
    • , Gáspár Pándy-Szekeres
    • , Eduardo Mayol
    • , Toni Giorgino
    • , Jens Carlsson
    • , Xavier Deupi
    • , Slawomir Filipek
    • , Marta Filizola
    • , José Carlos Gómez-Tamayo
    • , Angel Gonzalez
    • , Hugo Gutiérrez-de-Terán
    • , Mireia Jiménez-Rosés
    • , Willem Jespers
    • , Jon Kapla
    • , George Khelashvili
    • , Peter Kolb
    • , Dorota Latek
    • , Maria Marti-Solano
    • , Pierre Matricon
    • , Minos-Timotheos Matsoukas
    • , Przemyslaw Miszta
    • , Mireia Olivella
    • , Laura Perez-Benito
    • , Davide Provasi
    • , Santiago Ríos
    • , Iván R. Torrecillas
    • , Jessica Sallander
    • , Agnieszka Sztyler
    • , Silvana Vasile
    • , Harel Weinstein
    • , Ulrich Zachariae
    • , Peter W. Hildebrand
    • , Gianni De Fabritiis
    • , Ferran Sanz
    • , David E. Gloriam
    • , Arnau Cordomi
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Brief Communications

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    Hundred-fold-faster DNA-PAINT imaging is enabled by the introduction of concatenated, periodic DNA sequence motifs in the docking strand. Six orthogonal sequences are described for speed-optimized and highly multiplexed cellular imaging.

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Articles

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    Supervised machine-learning models trained using Drosophila epigenetic and STARR-seq data can be transferred to predict mouse and human enhancers.

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    • , Axel Visel
    • , Diane E. Dickel
    • , Kevin Y. Yip
    • , Richard Sutton
    • , Len A. Pennacchio
    •  & Mark Gerstein

    Special:

  • Article |

    A general tuning strategy is introduced for improving the utility of rhodamines for biological imaging applications. The strategy yielded bright, versatile and bioavailable far-red and near-infrared ‘Janelia Fluor’ dyes.

    • Jonathan B. Grimm
    • , Ariana N. Tkachuk
    • , Liangqi Xie
    • , Heejun Choi
    • , Boaz Mohar
    • , Natalie Falco
    • , Kathy Schaefer
    • , Ronak Patel
    • , Qinsi Zheng
    • , Zhe Liu
    • , Jennifer Lippincott-Schwartz
    • , Timothy A. Brown
    •  & Luke D. Lavis
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    OligoFISSEQ combines Oligopaints with fluorescence in situ sequencing to enable the 3D mapping of many regions across the genome in human cells to interrogate genome organization at improved genomic resolution. OligoFISSEQ is compatible with immunochemistry and OligoSTORM for super-resolution imaging.

    • Huy Q. Nguyen
    • , Shyamtanu Chattoraj
    • , David Castillo
    • , Son C. Nguyen
    • , Guy Nir
    • , Antonios Lioutas
    • , Elliot A. Hershberg
    • , Nuno M. C. Martins
    • , Paul L. Reginato
    • , Mohammed Hannan
    • , Brian J. Beliveau
    • , George M. Church
    • , Evan R. Daugharthy
    • , Marc A. Marti-Renom
    •  & C.-ting Wu
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    ZipSeq uses patterned illumination and photocaged oligonucleotides to serially print barcodes onto live, intact tissues for spatially mapping single cell transcriptomes.

    • Kenneth H. Hu
    • , John P. Eichorst
    • , Chris S. McGinnis
    • , David M. Patterson
    • , Eric D. Chow
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    Small vibrational tags (azide, 13C-edited carbonyl and deuterium-labeled probes) were introduced as metabolic probes for mid-infrared imaging. The tags allow unprecedented in situ visualization of metabolism in cells and animals with high information throughput.

    • Lixue Shi
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    NanoLuc substrates with improved solubility and bioavailability, hydrofurimazine and fluorofurimazine, strongly enhance bioluminescence signals in vivo and enable bright dual-color bioluminescent imaging with AkaLuc and AkaLumine.

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Amendments & Corrections

  • Publisher Correction |

    • Ismael Rodríguez-Espigares
    • , Mariona Torrens-Fontanals
    • , Johanna K. S. Tiemann
    • , David Aranda-García
    • , Juan Manuel Ramírez-Anguita
    • , Tomasz Maciej Stepniewski
    • , Nathalie Worp
    • , Alejandro Varela-Rial
    • , Adrián Morales-Pastor
    • , Brian Medel-Lacruz
    • , Gáspár Pándy-Szekeres
    • , Eduardo Mayol
    • , Toni Giorgino
    • , Jens Carlsson
    • , Xavier Deupi
    • , Slawomir Filipek
    • , Marta Filizola
    • , José Carlos Gómez-Tamayo
    • , Angel Gonzalez
    • , Hugo Gutiérrez-de-Terán
    • , Mireia Jiménez-Rosés
    • , Willem Jespers
    • , Jon Kapla
    • , George Khelashvili
    • , Peter Kolb
    • , Dorota Latek
    • , Maria Marti-Solano
    • , Pierre Matricon
    • , Minos-Timotheos Matsoukas
    • , Przemyslaw Miszta
    • , Mireia Olivella
    • , Laura Perez-Benito
    • , Davide Provasi
    • , Santiago Ríos
    • , Iván R. Torrecillas
    • , Jessica Sallander
    • , Agnieszka Sztyler
    • , Silvana Vasile
    • , Harel Weinstein
    • , Ulrich Zachariae
    • , Peter W. Hildebrand
    • , Gianni De Fabritiis
    • , Ferran Sanz
    • , David E. Gloriam
    • , Arnau Cordomi
    • , Ramon Guixà-González
    •  & Jana Selent