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Nature Methods Contents: December 2017, Volume 14 No 12 pp 1115 - 1222

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Nature Methods

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TABLE OF CONTENTS

December 2017 Volume 14, Issue 12

In This Issue
Editorial
This Month
Correspondence
Research Highlights
Methods in Brief
Tools in Brief
Technology Feature
News and Views
Analysis
Brief Communications
Articles
Erratum
Corrigendum
Application Notes
 
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In This Issue

Top

In This Issue   

 

Editorial

Top

So you're writing a paper   p1115
doi:10.1038/nmeth.4532
Writing a clear, accurate and convincing scientific paper is both an art and a skill. It is one well worth mastering.
 

This Month

Top

The Author File: Ulrich Elling   p1117
Vivien Marx
doi:10.1038/nmeth.4507
Improving single-cell data in CRISPR screens, with inspiration from open-air theater performances.
 

Points of Significance: Machine learning: a primer   pp1119 - 1120
Danilo Bzdok, Martin Krzywinski and Naomi Altman
doi:10.1038/nmeth.4526
Machine learning extracts patterns from data without explicit instructions.
 

Correspondence

Top

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data   pp1121 - 1122
David Sehnal, Mandar Deshpande, Radka Svobodová Vařeková, Saqib Mir, Karel Berka et al.
doi:10.1038/nmeth.4499
 

Accessible virtual reality of biomolecular structural models using the Autodesk Molecule Viewer   pp1122 - 1123
Aidin R Balo, Merry Wang and Oliver P Ernst
doi:10.1038/nmeth.4506
 

MDsrv: viewing and sharing molecular dynamics simulations on the web   pp1123 - 1124
Johanna K S Tiemann, Ramon Guixà-Gonzalez, Peter W Hildebrand and Alexander S Rose
doi:10.1038/nmeth.4497
 

Research Highlights

Top

Evolution of an A-base editor
Protein evolution yields a programmable base editor that can revert the most common pathogenic point mutations in the genome.

Sequencing for carbohydrates
A technique combining mass spectrometry and infrared spectroscopy shows promise for unambiguous sequencing of linear oligosaccharides.

Multiscale 3D view of the genome
Ultradeep sequencing of Hi-C data from mouse cells in different developmental stages can address outstanding questions about 3D chromatin function.

Glow-in-the-dark nanoparticles for deep imaging
A class of semiconductor polymer particles can be used for afterglow imaging to avoid autofluorescence when imaging deep structures in living animals.

Imaging deep in the cortex and beyond
Combining red calcium indicators with an optimized illumination strategy enables neuronal activity to be imaged in deep layers of the mouse cortex and hippocampus.

Methods
JOBS of the week
PhD Positions in Cancer Research at the German Cancer Research Center
German Cancer Research Center (DKFZ).
Scientist (Bioinformatics)
IARC
Postdoctoral Research Scientist / Fellow
Columbia University
Tenure Track Assistant Professor
University of Central Florida
Postdoctoral Fellow
Helmholtz Centre for Environmental Research - UFZ - UFZ - Helmholtz Association
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07.06.18
Bacau, Romania
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Methods in Brief

Top

Genome editing in the brain | Freestyle fluidics | Measuring cellular mass with a picobalance | Improving the efficiency of cryo-EM

Tools in Brief

Top

Stem cells tip toward totipotency | Tracking cell migration in vivo | Haplobank of mutated mouse stem cell clones | A yTRAP for protein aggregates

Technology Feature

Top

Microscopy: hello, adaptive optics   pp1133 - 1136
Vivien Marx
doi:10.1038/nmeth.4508
Aberrations hinder clear imaging, but an array of options help to correct much distortion.
 

News and Views

Top

SPOTs fill a major gap in RNA quantification   pp1137 - 1138
Jinzhou Yuan and Peter A Sims
doi:10.1038/nmeth.4515
Direct RNA quantification using barcoded fluorescence hybridization enables accurate and scalable gene expression profiling.

See also: Brief Communication by Eng et al.

Mass spectrometry imaging goes three dimensional   pp1139 - 1140
Klaus Dreisewerd and Joanne Y Yew
doi:10.1038/nmeth.4513
Two complementary approaches improve 3D mass spectrometry imaging of biomolecules on 3D surfaces and within tissue sections and single cells.

See also: Brief Communication by Kompauer et al. | Article by Passarelli et al.

Analysis

Top

An objective comparison of cell-tracking algorithms   pp1141 - 1152
Vladimír Ulman, Martin Maška, Klas E G Magnusson, Olaf Ronneberger, Carsten Haubold et al.
doi:10.1038/nmeth.4473
This analysis describes the results of three Cell Tracking Challenge editions for examining the performance of cell segmentation and tracking algorithms and provides practical feedback for users and developers.
 

Brief Communications

Top

Profiling the transcriptome with RNA SPOTs   pp1153 - 1155
Chee-Huat Linus Eng, Sheel Shah, Julian Thomassie and Long Cai
doi:10.1038/nmeth.4500
RNA SPOTs adapts sequential fluorescence in situ hybridization (seqFISH) for highly accurate and inexpensive transcriptome-scale or targeted RNA quantification in vitro.

See also: News and Views by Yuan & Sims

Autofocusing MALDI mass spectrometry imaging of tissue sections and 3D chemical topography of nonflat surfaces   pp1156 - 1158
Mario Kompauer, Sven Heiles and Bernhard Spengler
doi:10.1038/nmeth.4433
A mass spectrometry imaging system combined with a laser triangulation system provides simultaneous topographic and molecular information for 3D biological samples and eliminates height-related artifacts in imperfect tissue sections.

See also: News and Views by Dreisewerd & Yew

High-throughput, image-based screening of pooled genetic-variant libraries   pp1159 - 1162
George Emanuel, Jeffrey R Moffitt and Xiaowei Zhuang
doi:10.1038/nmeth.4495
Multiplexed FISH readout of barcoded genotypes in single cells allows pooled screening of large genetic-variant libraries for complex, image-based phenotypes.
 

Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors   pp1163 - 1166
Y Esther Tak, Benjamin P Kleinstiver, James K Nuñez, Jonathan Y Hsu, Joy E Horng et al.
doi:10.1038/nmeth.4483
Inducible dCpf1-based transcriptional activators achieve tunable, multiplexed target gene expression.
 

Antibodies to biotin enable large-scale detection of biotinylation sites on proteins   pp1167 - 1170
Namrata D Udeshi, Kayvon Pedram, Tanya Svinkina, Shaunt Fereshetian, Samuel A Myers et al.
doi:10.1038/nmeth.4465
Enrichment of biotinylated peptides using an anti-biotin antibody results in substantially improved biotinylation site identifications by mass spectrometry compared to traditional streptavidin-based biotinylated protein enrichment.
 

Deciphering lipid structures based on platform-independent decision rules   pp1171 - 1174
Jürgen Hartler, Alexander Triebl, Andreas Ziegl, Martin Trotzmuller, Gerald N Rechberger et al.
doi:10.1038/nmeth.4470
The Lipid Data Analyzer uses sets of decision rules to identify lipid subclasses in high-throughput LC-MS/MS data.
 

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Articles

Top

The 3D OrbiSIMS[mdash]label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power   pp1175 - 1183
Melissa K Passarelli, Alexander Pirkl, Rudolf Moellers, Dmitry Grinfeld, Felix Kollmer et al.
doi:10.1038/nmeth.4504
The high spatial resolution of secondary ion mass spectrometry and the high resolving power of the Orbitrap mass spectrometer are combined in a single imaging platform, the 3D OrbiSIMS. The instrument's capabilities for resolving lipids and neurotransmitters in the brain with subcellular spatial resolution, and a drug in a single cell in three dimensions is demonstrated.

See also: News and Views by Dreisewerd & Yew

Localization-based super-resolution imaging meets high-content screening   pp1184 - 1190
Anne Beghin, Adel Kechkar, Corey Butler, Florian Levet, Marine Cabillic et al.
doi:10.1038/nmeth.4486
An automated system for data acquisition and analysis enables high-content screening localization microscopy and increases the throughput and information content of super-resolution microscopy methods such as dSTORM, DNA-PAINT and (spt)PALM.
 

CRISPR-UMI: single-cell lineage tracing of pooled CRISPR-Cas9 screens   pp1191 - 1197
Georg Michlits, Maria Hubmann, Szu-Hsien Wu, Gintautas Vainorius, Elena Budusan et al.
doi:10.1038/nmeth.4466
Combining each sgRNA with a unique molecular identifier in a genome-wide screen increases sensitivity and robustness in both positive and negative selection.
 

Thiol-linked alkylation of RNA to assess expression dynamics   pp1198 - 1204
Veronika A Herzog, Brian Reichholf, Tobias Neumann, Philipp Rescheneder, Pooja Bhat et al.
doi:10.1038/nmeth.4435
SLAM seq detects s4U incorporation into RNA and, combined with 3′-end RNA-seq, provides insight into RNA turnover.
 

Isolation and 3D expansion of multipotent Sox9+ mouse lung progenitors   pp1205 - 1212
Massimo Nichane, Asif Javed, V Sivakamasundari, Monisha Ganesan, Lay Teng Ang et al.
doi:10.1038/nmeth.4498
This paper describes methods for the 3D culture of mouse lung progenitor cells that can differentiate in vitro and in vivo along all epithelial lineages.
 

Protein interaction perturbation profiling at amino-acid resolution   pp1213 - 1221
Jonathan Woodsmith, Luise Apelt, Victoria Casado-Medrano, Ziya Özkan, Bernd Timmermann et al.
doi:10.1038/nmeth.4464
A reverse two-hybrid approach combined with massively parallel programmed mutagenesis and sequencing allows profiling protein interaction determinants at amino-acid resolution, as demonstrated by identifying interaction-disrupting mutations in a cilia protein complex associated with Bardet-Biedl syndrome.
 

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Application Notes

Top

Hardware triggering: maximizing speed and efficiency for live cell imaging   
Michael A Davis

 

The new 2D Superresolution mode for ZEISS Airyscan   
Joseph Huff, Annette Bergter, Jan Birkenbeil, Ingo Kleppe and Ralf Engelmann

 

Corrigendum

Top

Corrigendum: Accurate identification of single-nucleotide variants in whole-genome-amplified single cells   p1222
Xiao Dong, Lei Zhang, Brandon Milholland, Moonsook Lee, Alexander Y Maslov et al.
doi:10.1038/nmeth1217-1222b
 

Erratum

Top

Erratum: Probes: FRET sensor design and optimization   p1222
Vivien Marx
doi:10.1038/nmeth1217-1222a
 

Top
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