Tuesday, November 29, 2016

Nature Methods Contents: December 2016 Volume 13 pp 959 - 1055

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Nature Methods

ZEISS LSM 880 with Airyscan - Your new standard for fast and gentle confocal imaging Learn how to improve signal-to-noise ratio, resolution and speed of your confocal imaging. Discover how the Fast mode for Airyscan compares to traditional confocal detection and download our free white paper with more information

December 2016 Volume 13, Issue 12

In This Issue
This Month
Research Highlights
Technology Feature
News and Views
Brief Communications
Application Note

Innova® Shakers: Versatile, dependable, and easy to use
For over 60 years, New Brunswick Shakers have been synonymous with quality construction and durability. The dependable operation is due in large part to the Eppendorf triple-eccentric counterbalanced drive; drive shafts are machined to tolerances of 5 micrometers, ensuring stable and vibration-free operation, often over decades of continuous use.

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In This Issue


In This Issue   



Meta-analysis in basic biology   p959
Meta-analysis is common in clinical research, less so in basic biology, but it is also proving useful in some basic research contexts. It should help improve research reproducibility.

This Month


The Author File: Alipasha Vaziri   p961
Vivien Marx
A physicist handy with charcoal and ink uses sculpted light to image the brain.



Temporal accumulation analysis provides simplified artifact-free analysis of membrane-protein nanoclusters   pp963 - 964
Christoph Spahn, Frank Herrmannsdorfer, Thomas Kuner and Mike Heilemann

moFF: a robust and automated approach to extract peptide ion intensities   pp964 - 966
Andrea Argentini, Ludger J E Goeminne, Kenneth Verheggen, Niels Hulstaert, An Staes et al.

OmniPath: guidelines and gateway for literature-curated signaling pathway resources   pp966 - 967
Dénes Türei, Tamás Korcsmáros and Julio Saez-Rodriguez

Research Highlights


A blood less primitive
Cord blood provides important clues for directing human pluripotent stem cells to become pre-hematopoietic stem cells.

Single-molecule force analysis, unplugged
A nanoscopic force clamp enables high-throughput single-molecule analysis of DNA under tension without connection to a macroscopic instrument.

REXER helps design bacterial genomes
A CRISPR-Cas9-based approach identifies synonymous codons that can be reassigned to encode new chemical building blocks.

Proteome quantification compared
Careful benchmarking improves software methods for analyzing data-independent-acquisition mass spectrometry data.

A pluripotent approach
A combination of protein and DNA isolation methods expands our grasp of cellular reprogramming.

Extending super-resolution's FOV
An optimized illumination strategy allows for uniform single-molecule localization microscopy over large regions.

Methods in Brief

Hi-res spatial gene expression in the brain | Man-made mouse eggs | Laser ablation for growing protein crystals | Annotating RNAs by the company they keep

Tools in Brief

CRISPR screens tackle the noncoding genome | Instant tracking of single-molecule position and orientation | Three steps to installing authentic protein modifications | Nanokits for single cells

JOBS of the week
Post-doctoral fellow with a PhD in biological sciences or bioinformatics (m / f)
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Postdoc Position in Bioinformatics
Ludwig Boltzmann Institute Applied Diagnostics
Positions at Center for Precision Medicine, The First Affiliated Hospital of Wenzhou Medical University
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Senior University Lecturer in Geographic Information Science specialising in Geomatics
Lund University
University Lectureship in Multi-Scale, Multi-Dimensional Imaging of Natural and Synthetic Materials
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Technology Feature


Microscopy: OpenSPIM 2.0   pp979 - 982
Vivien Marx
A maturing open hardware and open-source software movement seeks to expand DIY light-sheet microscopy.

News and Views


CRISPR-Cas9-AID base editor is a powerful gain-of-function screening tool   pp983 - 984
Cem Kuscu and Mazhar Adli
Combining CRISPR-Cas9 with an enzyme that induces somatic hypermutations allows the rapid generation of diverse variants for gain-of-function screens.

See also: Article by Ma et al. | Article by Hess et al.

Brief Communications


Bright photoactivatable fluorophores for single-molecule imaging   pp985 - 988
Jonathan B Grimm, Brian P English, Heejun Choi, Anand K Muthusamy, Brian P Mehl et al.
Photoactivatable derivatives of the bright and photostable Janelia Fluor dyes enable improved multicolor single-particle tracking and facile localization microscopy in cells.

Simultaneous dual-color fluorescence lifetime imaging with novel red-shifted fluorescent proteins   pp989 - 992
Tal Laviv, Benjamin B Kim, Jun Chu, Amy J Lam, Michael Z Lin et al.
Two red fluorescent proteins with long Stokes shift enable simultaneous multicolor 2p imaging. CyRFP1 is well-suited for 2p structural imaging, and FRET sensors made with mCyRFP1 and mMaroon1enable multicolor 2pFLIM in brain slices. Also online, a paper by Bajar et al. reports the development of mMaroon1.

See also: Brief Communication by Bajar et al.

Fluorescent indicators for simultaneous reporting of all four cell cycle phases   pp993 - 996
Bryce T Bajar, Amy J Lam, Ryan K Badiee, Young-Hee Oh, Jun Chu et al.
The far-red fluorescent protein mMaroon1 and a reporter based on stem-loop binding protein enables the generation of Fucci4, a 4-color cell cycle reporter system that can be used to distinguish all phases of the cell cycle. Also online, a paper by Laviv et al. uses mMaroon1 as a FRET acceptor for the newly developed CyRFP1.

See also: Brief Communication by Laviv et al.

Genetic code expansion for multiprotein complex engineering   pp997 - 1000
Christine Koehler, Paul F Sauter, Mirella Wawryszyn, Gemma Estrada Girona, Kapil Gupta et al.
A method for producing multiprotein complexes engineered with site-specifically introduced noncanonical amino acids is described, enabling applications in biochemical and biophysical analysis, as well as in biotechnology.

Random-access scanning microscopy for 3D imaging in awake behaving animals   pp1001 - 1004
K M Naga Srinivas Nadella, Hana Roš, Chiara Baragli, Victoria A Griffiths, George Konstantinou et al.
Random-access line scanning enables neural activity to be monitored at high speed in neurons and dendrites that are sparsely distributed in three dimensions. The approach is demonstrated in behaving mice.

Comparison of high-throughput sequencing data compression tools   pp1005 - 1008
Ibrahim Numanagić, James K Bonfield, Faraz Hach, Jan Voges, Jörn Ostermann et al.
A team of international scientists benchmark current compression methods for high-throughput sequencing data.

Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome   pp1009 - 1011
Tsung-Han S Hsieh, Geoffrey Fudenberg, Anton Goloborodko and Oliver J Rando
The combination of short and long crosslinkers during chromosome conformation capture allows the interrogation of structure from the nucleosome to the chromosome-wide level in yeast.

Nature Index 2016 Australia & New Zealand

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ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing   pp1013 - 1020
Xingqi Chen, Ying Shen, Will Draper, Jason D Buenrostro, Ulrike Litzenburger et al.
The covalent insertion of fluorophore-labeled DNA adaptors by Tn5 transposase into open chromatin allows its imaging and subsequent analysis by sequencing from exactly the same samples.

Fast volumetric calcium imaging across multiple cortical layers using sculpted light   pp1021 - 1028
Robert Prevedel, Aart J Verhoef, Alejandro J Pernía-Andrade, Siegfried Weisenburger, Ben S Huang et al.
Two-photon scanning microscopy is inherently slow and thus limits volumetric calcium imaging. Prevedel et al. achieve increased volumetric imaging speed by tailoring the excitation volume via light sculpting.

Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells   pp1029 - 1035
Yunqing Ma, Jiayuan Zhang, Weijie Yin, Zhenchao Zhang, Yan Song et al.
Fusing a cytidine deaminase to dCas9 allows for a forward genetic screen in mammalian cells that identifies mutations conferring drug resistance.

See also: News and Views by Kuscu & Adli

Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells   pp1036 - 1042
Gaelen T Hess, Laure Frésard, Kyuho Han, Cameron H Lee, Amy Li et al.
Recruiting a hyperactive cytidine deaminase via the guide RNA to dCas9 allows for the introduction of diverse point mutations at the CRISPR target locus to create complex libraries of variants for protein engineering or dissection of protein function.

See also: News and Views by Kuscu & Adli

Complex transcriptional modulation with orthogonal and inducible dCas9 regulators   pp1043 - 1049
Yuchen Gao, Xin Xiong, Spencer Wong, Emeric J Charles, Wendell A Lim et al.
The combination of orthogonal dCas9 with two chemical-inducible dimerization systems allows precise induction of gene activation and repression as well as the creation of Boolean logic gates.

Phased diploid genome assembly with single-molecule real-time sequencing   pp1050 - 1054
Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad, Gregory T Concepcion et al.
The open-source FALCON and FALCON-Unzip software utilize long-read sequencing data to generate contiguous, accurate and phased diploid assemblies, even from genomes that are highly heterozygous.

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Erratum: October 2016 cover caption   p1055

Application Note


Robotic Microscopy with the Nikon Ti2 for high-content analysis applications   
John Allen
Robotic Microscopy—a combination of high-content screening methods—enables multivariate experimental approaches with large cell populations and member-level sensitivity. Here we explore how the new Nikon Ti2 line of inverted research microscopes is uniquely suited to Robotic Microscopy applications, focusing on work utilizing induced pluripotent stem cells (iPSCs) as disease models in drug screening.

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