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Nature Methods Contents: July 2017 Volume 14 pp 637 - 752

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TABLE OF CONTENTS

July 2017 Volume 14, Issue 7

In This Issue
Editorial
This Month
Correspondence
Research Highlights
Commentaries
Technology Feature
News and Views
Analysis
Brief Communications
Articles
Errata
Corrigendum
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In This Issue

Top

In This Issue   

 

Editorial

Top

Seeing red   p637
doi:10.1038/nmeth.4363
The growing advantages of red to near-infrared fluorescent probes should move them beyond being a 'second color' in biological imaging.

 

This Month

Top

The Author File: Alexis Battle   p639
Vivien Marx
doi:10.1038/nmeth.4345
Calculating gene-environment interactions, and the role of a 'why' machine.

 

Points of Significance: Principal component analysis   pp641 - 642
Jake Lever, Martin Krzywinski and Naomi Altman
doi:10.1038/nmeth.4346
PCA helps you interpret your data, but it will not always find the important patterns.

 

Correspondence

Top

Mass spectrometrists should search for all peptides, but assess only the ones they care about   pp643 - 644
Adriaan Sticker, Lennart Martens and Lieven Clement
doi:10.1038/nmeth.4338

See also: Correspondence by Noble & Keich

Response to “Mass spectrometrists should search for all peptides, but assess only the ones they care about”   p644
William Stafford Noble and Uri Keich
doi:10.1038/nmeth.4339

See also: Correspondence by Sticker et al.

ProHits-viz: a suite of web tools for visualizing interaction proteomics data   pp645 - 646
James D R Knight, Hyungwon Choi, Gagan D Gupta, Laurence Pelletier, Brian Raught et al.
doi:10.1038/nmeth.4330

 

PIQED: automated identification and quantification of protein modifications from DIA-MS data   pp646 - 647
Jesse G Meyer, Sushanth Mukkamalla, Hanno Steen, Alexey I Nesvizhskii, Bradford W Gibson et al.
doi:10.1038/nmeth.4334

 

Research Highlights

Top

Better tools for Bacteroides
Two sets of complementary tools extend our capacity to manipulate the gut microbiome.

Charting the subcellular proteome
Human protein subcellular locations light up in the Cell Atlas resource.

CRISPR kinetics
In vitro Cas9-binding assays show the effects of mutations in the target sequence on binding kinetics.

Zooming into the larval zebrafish brain
A serial-section electron microscopy data set of larval zebrafish brain—imaged at several scales—provides a resource for structure-function analyses of the animals' neural circuitry.

Organoid variability examined
Single-cell transcriptomics is used to determine what cell types are present in brain organoids and how much these cell types vary across organoids.

Methods in Brief

Buckets of bacterial genomes | Reconciling small and large scales with FIB-SEM | Ultrafast thermal cycling | Single-protein detection by cryo-EM

Tools in Brief

Self-limiting Cas9 | Functional blood progenitors for mouse and man | The BioPlex network, 2.0 | Supramolecular assemblies for NIR II imaging

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Commentaries

Top

Assessing phototoxicity in live fluorescence imaging   pp657 - 661
P Philippe Laissue, Rana A Alghamdi, Pavel Tomancak, Emmanuel G Reynaud and Hari Shroff
doi:10.1038/nmeth.4344
This Commentary discusses the problem of phototoxicity in live imaging and suggests guidelines to improve its assessment and reporting.

 

Towards a perceptive understanding of size in cellular biology   pp662 - 665
Monica Zoppè
doi:10.1038/nmeth.4300
This piece tackles the question of how to make biological scale more intuitive to human beings, bringing to bear the author's background in scientific visualization.

 

Technology Feature

Top

Metabolism: sweeter paths in glycoscience   pp667 - 670
Vivien Marx
doi:10.1038/nmeth.4333
Carbohydrates are tough molecules to study, but glycoscientists are developing and democratizing the needed tools.

 

News and Views

Top

Illuminating redox biology using NADH- and NADPH-specific sensors   pp671 - 672
Andreas Wiederkehr and Nicolas Demaurex
doi:10.1038/nmeth.4336
Genetically encoded NAD and NADP sensors will revolutionize the study of redox biology.

See also: Article by Tao et al.

Analysis

Top

FISH-ing for captured contacts: towards reconciling FISH and 3C   pp673 - 678
Geoffrey Fudenberg and Maxim Imakaev
doi:10.1038/nmeth.4329
This Analysis explores the relationship between chromosome conformation capture (for example, Hi-C) and FISH datasets, and uses simulations to reconcile measurements from the two technologies.

 

Comparison of computational methods for Hi-C data analysis   pp679 - 685
Mattia Forcato, Chiara Nicoletti, Koustav Pal, Carmen Maria Livi, Francesco Ferrari et al.
doi:10.1038/nmeth.4325
Six tools to call chromatin interactions and seven tools for topologically associating domain calling are systematically compared with real and simulated data. The strengths and weaknesses of each tool are discussed.

 

Brief Communications

Top

Differential analysis of RNA-seq incorporating quantification uncertainty   pp687 - 690
Harold Pimentel, Nicolas L Bray, Suzette Puente, Páll Melsted and Lior Pachter
doi:10.1038/nmeth.4324
By using bootstraps that estimate inferential variance, the sleuth method and software provide fast and highly accurate differential gene expression analysis in an interactive Shiny app.

 

webKnossos: efficient online 3D data annotation for connectomics   pp691 - 694
Kevin M Boergens, Manuel Berning, Tom Bocklisch, Dominic Bräunlein, Florian Drawitsch et al.
doi:10.1038/nmeth.4331
webKnossos is a browser-based tracing and annotation tool for 3D electron microscopy data sets that is optimized for seamless data viewing. The tool/'s flight-mode view facilitates fast neurite tracing because of its egocentric viewpoint.

 

Nm-seq maps 2′-O-methylation sites in human mRNA with base precision   pp695 - 698
Qing Dai, Sharon Moshitch-Moshkovitz, Dali Han, Nitzan Kol, Ninette Amariglio et al.
doi:10.1038/nmeth.4294
Iterative oxidation, elimination and dephosphorylation steps remove nucleotides from the 3′ end of RNA until a 2′-O-methylated ribose that cannot be oxidized is encountered and brings the process to a stop. High-throughput sequencing of these fragments exposes 2′-O-methyl sites at base resolution.

 

Allele-specific expression reveals interactions between genetic variation and environment   pp699 - 702
David A Knowles, Joe R Davis, Hilary Edgington, Anil Raj, Marie-Julie Favé et al.
doi:10.1038/nmeth.4298
The EAGLE algorithm and software identifies replicable gene-by-environment interactions based on associations between environment and allele-specific expression.

 

Quantitative mRNA imaging throughout the entire Drosophila brain   pp703 - 706
Xi Long, Jennifer Colonell, Allan M Wong, Robert H Singer and Timothée Lionnet
doi:10.1038/nmeth.4309
Improved fluorescence in situ hybridization enables smFISH in cleared whole-mount Drosophila brains with confocal microscopy; a custom Bessel beam structured illumination microscope allows single-mRNA detection across the entire brain.

 

Testing for differential abundance in mass cytometry data   pp707 - 709
Aaron T L Lun, Arianne C Richard and John C Marioni
doi:10.1038/nmeth.4295
A statistical approach makes it possible to detect differentially abundant cell populations across biological conditions from high-dimensional mass cytometry data without relying on cell clustering.

 

CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations   pp710 - 712
Cem Kuscu, Mahmut Parlak, Turan Tufan, Jiekun Yang, Karol Szlachta et al.
doi:10.1038/nmeth.4327
Early STOP codons created with CRISPR base editors leads to gene knockout with high efficiency and does not stress cells with double-strand DNA breaks. CRISPR-STOP can target the majority of human genes and is useful for genetic screens.

 
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Articles

Top

Fast high-resolution miniature two-photon microscopy for brain imaging in freely behaving mice   pp713 - 719
Weijian Zong, Runlong Wu, Mingli Li, Yanhui Hu, Yijun Li et al.
doi:10.1038/nmeth.4305
FHIRM-TPM is a miniature two-photon microscope capable of imaging fluorescently labeled neurons in the brains of freely behaving mice. It allows for imaging of spines or recording of neural activity with a frame rate up to 40 Hz.

 

Genetically encoded fluorescent sensors reveal dynamic regulation of NADPH metabolism   pp720 - 728
Rongkun Tao, Yuzheng Zhao, Huanyu Chu, Aoxue Wang, Jiahuan Zhu et al.
doi:10.1038/nmeth.4306
Genetically encoded iNap sensors allow imaging of NADPH with high spatiotemporal resolution in living systems. The iNaps cover physiologically relevant NADPH concentrations and are demonstrated in mammalian cells and live zebrafish.

See also: News and Views by Wiederkehr & Demaurex

Biosynthesis and genetic encoding of phosphothreonine through parallel selection and deep sequencing   pp729 - 736
Michael Shaofei Zhang, Simon F Brunner, Nicolas Huguenin-Dezot, Alexandria Deliz Liang, Wolfgang H Schmied et al.
doi:10.1038/nmeth.4302
A new approach to evolve novel aminoacyl-tRNA synthetase-tRNA pairs with orthogonal substrate specificity is applied to generate a system to site-specifically incorporate phosphothreonine into proteins, enabling functional studies of this post-translational modification.

 

A quantitative and multiplexed approach to uncover the fitness landscape of tumor suppression in vivo   pp737 - 742
Zoë N Rogers, Christopher D McFarland, Ian P Winters, Santiago Naranjo, Chen-Hua Chuang et al.
doi:10.1038/nmeth.4297
The combination of tumor barcoding with CRISPR-mediated targeting of tumor suppressors allows quantitative analysis of tumor-suppressor function during tumor growth in vivo.

 

Fused cerebral organoids model interactions between brain regions   pp743 - 751
Joshua A Bagley, Daniel Reumann, Shan Bian, Julie Lévi-Strauss and Juergen A Knoblich
doi:10.1038/nmeth.4304
The fusion of patterned cerebral organoids into more complex structures enables modeling of inter-regional processes such as neuronal migration.

 
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Errata

Top

Erratum: In vivo imaging of neural activity   p752
Weijian Yang and Rafael Yuste
doi:10.1038/nmeth0717-752a

 

Erratum: Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput   p752
Todd M Gierahn, Marc H Wadsworth II, Travis K Hughes, Bryan D Bryson, Andrew Butler et al.
doi:10.1038/nmeth0717-752c

 

Erratum: Optoacoustic imaging at multiple spatiotemporal scales   p752
Rita Strack
doi:10.1038/nmeth0717-752d

 

Corrigendum

Top

Corrigendum: In vivo imaging of neural activity   p752
Weijian Yang and Rafael Yuste
doi:10.1038/nmeth0717-752b

 
Top
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