Wednesday, August 1, 2018

Nature Methods Contents: August 2018, Volume 15 No 8

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Nature Methods

Nikon's new high-speed N-SIM S super-resolution microscope system achieves acquisition speeds up to 15 frames per second, enabling the acquisition of fast biological processes at twice the spatial resolution of conventional light microscopes. 

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August 2018 Volume 15, Issue 8

This Month
Research Highlights
Technology Feature
News & Views
Brief Communications
2018 longlist - see the full line up

The nominations for the 2018 Nature Research Awards for Inspiring Science and Innovating Science are in. 

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In partnership with The Estée Lauder Companies.


Hamamatsu's W-View Gemini-2C: Multi-wavelength, multi-camera imaging that's built for super-resolution and ready for anything. Now available with our new Extended Focus Device increasing depth of focus up to 5x by using a simple optical filter.



The wisdom of crowds, for a fee    p555

This Month


Ilaria Testa    p557
Vivien Marx

Optimal experimental design    pp559 - 560
Byran Smucker, Martin Krzywinski & Naomi Altman


Advanced Imaging with Proven Optics

Olympus is dedicated to your work, vision, and science. Through innovation and service, we seek to aide in your discoveries, advance your research, and inspire you to explore new possibilities. Our wide range of microscopes are built with the optical excellence and proven application expertise you can depend on. Your Science Matters™.

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Water content, not stiffness, dominates Brillouin spectroscopy measurements in hydrated materials    pp561 - 562
Pei-Jung Wu, Irina V. Kabakova, Jeffrey W. Ruberti, Joseph M. Sherwood, Iain E. Dunlop et al.

Reply to ‘Water content, not stiffness, dominates Brillouin spectroscopy measurements in hydrated materials’    pp562 - 563
Giuliano Scarcelli & Seok Hyun Yun

BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq    pp563 - 565
Ida Lindeman, Guy Emerton, Lira Mamanova, Omri Snir, Krzysztof Polanski et al.

Research Highlights


Transcript constellations in a tissue’s universe    p567
Tal Nawy

An enzymatic oligonucleotide synthesizer    p568
Lei Tang

Surprising CRISPR roadblocks    p569
Nicole Rusk

Probes for molecular crowding    p570
Rita Strack

Sequence-based prediction of variants’ effects    p571
Nicole Rusk

Self-assembled ‘silicages’    p571
Lei Tang

Tumor genetic analysis from single-cell RNA-seq data    p571
Tal Nawy

Improving retrograde labeling of neurons    p571
Nina Vogt

Monitoring molecular jumps    p572
Rita Strack

SPRITE maps the 3D genome    p572
Nicole Rusk

Contrasting PCA across datasets    p572
Tal Nawy

A model gut microbiome    p572
Natalie de Souza

Delighting in dopamine    p573
Nina Vogt

JOBS of the week
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The University of Iowa

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Technology Feature


Calling cell biologists to try cryo-ET    pp575 - 578
Vivien Marx

News & Views


The crowd storms the ivory tower    pp579 - 580
Martin L. Jones & Helen Spiers

Finally: development of humanized lymph nodes    pp580 - 582
Alexandre P. A. Theocharides & Markus G. Manz

Brief Communications


Active PSF shaping and adaptive optics enable volumetric localization microscopy through brain sections    pp583 - 586
Michael J. Mlodzianoski, Paul J. Cheng-Hathaway, Shane M. Bemiller, Tyler J. McCray, Sheng Liu et al.

Active PSF shaping and adaptive optics are combined to enable 3D localization microscopy throughout thick tissues. The method was used to study the nanoscale architecture of amyloid fibrils in a mouse model of Alzheimer’s disease. a tool for rapid, flexible, crowd-based annotation of images    pp587 - 590
Alex J. Hughes, Joseph D. Mornin, Sujoy K. Biswas, Lauren E. Beck, David P. Bauer et al.

Annotated image data are required for image analysis, to test analytical methods, and to train learning algorithms. This paper describes and characterizes a tool that allows researchers to crowdsource image-annotation tasks.


Strelka2: fast and accurate calling of germline and somatic variants    pp591 - 594
Sangtae Kim, Konrad Scheffler, Aaron L. Halpern, Mitchell A. Bekritsky, Eunho Noh et al.

Strelka2 incorporates improvements for fast and accurate calling of somatic and germline single-nucleotide variants and indels.


A synthetic-diploid benchmark for accurate variant-calling evaluation    pp595 - 597
Heng Li, Jonathan M. Bloom, Yossi Farjoun, Mark Fleharty, Laura Gauthier et al.

The synthetic-diploid (Syndip) benchmark dataset, constructed from two fully homozygous long-read assemblies, provides more accurate assessments of error rates in small-variant-calling algorithms than existing benchmarks.


Genome-wide C-SWAT library for high-throughput yeast genome tagging    pp598 - 600
Matthias Meurer, Yuanqiang Duan, Ehud Sass, Ilia Kats, Konrad Herbst et al.

A C-SWAT acceptor library allows the user to easily insert any tag of choice after yeast ORFs by swapping it for the acceptor module.


Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy    pp601 - 604
Francesca Pennacchietti, Ekaterina O. Serebrovskaya, Aline R. Faro, Irina I. Shemyakina, Nina G. Bozhanova et al.

Bright reversibly switching red fluorescent proteins (rsFusionReds) with fast switching kinetics and low fatigue enable RESOLFT and MoNaLISA nanoscopy of live cells with green-orange illumination, which further reduces the risk of phototoxicity.




High-precision automated reconstruction of neurons with flood-filling networks    pp605 - 610
Michał Januszewski, Jörgen Kornfeld, Peter H. Li, Art Pope, Tim Blakely et al.

Flood-filling networks are a deep-learning-based pipeline for reconstruction of neurons from electron microscopy datasets. The approach results in exceptionally low error rates, thereby reducing the need for extensive human proofreading.


An enhanced CRISPR repressor for targeted mammalian gene regulation    pp611 - 616
Nan Cher Yeo, Alejandro Chavez, Alissa Lance-Byrne, Yingleong Chan, David Menn et al.

The fusion of dead Cas9 with KRAB and the transcriptional repressor domain of the chromatin modifier MeCP2 leads to an efficient transcriptional silencer that can be applied to genome-scale screens and genetic circuits.


Genome-wide SWAp-Tag yeast libraries for proteome exploration    pp617 - 622
Uri Weill, Ido Yofe, Ehud Sass, Bram Stynen, Dan Davidi et al.

A genome-wide collection of N-terminally tagged yeast libraries allows easy swapping of tags and exploration of the yeast proteome.


A human immune system mouse model with robust lymph node development    pp623 - 630
Yan Li, Guillemette Masse-Ranson, Zacarias Garcia, Timothée Bruel, Ayrin Kök et al.

Humanized mouse models are useful for studies of human hematopoiesis and immunity. Li et al. report an improved model that harbors lymph nodes and therefore permits investigation of local human adaptive immune processes in secondary lymphoid tissue.


Genetically engineered cerebral organoids model brain tumor formation    pp631 - 639
Shan Bian, Marko Repic, Zhenming Guo, Anoop Kavirayani, Thomas Burkard et al.

Cerebral organoids are developed into in vitro models of human brain cancer by CRISPR–Cas9- and/or transposon-mediated introduction of oncogenic mutations.


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