Volume 14 Issue 5, May 2017

Editorial

The politically engaged scientist

The appetite for political engagement among scientists across the United States has increased since the 2016 election. If well channeled and sustained, this would be a positive development that could last beyond the current administration's tenure.

Editorial 27 Apr 2017

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This Month

Koraljka Husnjak

A “simple but a bit crazy idea” to tag ubiquitin and practice multilingual, multidisciplinary proteomics.

Vivien Marx
This Month 27 Apr 2017

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Correspondence

Systems biology guided by XCMS Online metabolomics

Tao Huan
Erica M Forsberg
Gary Siuzdak
Correspondence 27 Apr 2017
Addressing reproducibility in single-laboratory phenotyping experiments

Neri Kafkafi
Ilan Golani
Yoav Benjamini
Correspondence 27 Apr 2017

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Research Highlights

Defining developmental grammar

An iterative clustering approach finds the few genes that mark discrete cell states and their transitions during early mouse development.

Nicole Rusk
Research Highlights 27 Apr 2017
It takes two to make an embryo

In vitro culture of mouse embryonic and extra-embryonic stem cells recapitulates embryogenesis.

Irene Jarchum
Research Highlights 27 Apr 2017
A light switch for kinases

A photodissociable dimer of the Dronpa fluorescent protein can cage kinases, making these important signal transducers controllable by light.

Nina Vogt
Research Highlights 27 Apr 2017
A proteome-wide view of thermal stability

Proteome thermal stability is probed using limited proteolysis and mass spectrometry.

Allison Doerr
Research Highlights 27 Apr 2017

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Methods in Brief

Raman imaging in 3D cultures

Methods in Brief 27 Apr 2017
Human lncRNA atlas

Collection:

The FANTOM5 Project
Methods in Brief 27 Apr 2017
Measuring single-molecule charges

Methods in Brief 27 Apr 2017
A fully designed yeast genome

Methods in Brief 27 Apr 2017

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Tools in Brief

Capturing ubiquitin-binding interactions

Tools in Brief 27 Apr 2017
Optogenetic protein regulation at near-infrared wavelengths

Tools in Brief 27 Apr 2017
Brighter and redder fluorescent rhodopsins

Tools in Brief 27 Apr 2017
Light-dependent inhibition of CaMKII

Tools in Brief 27 Apr 2017

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Research Highlights

Dynamic measurement of membrane charges

A FRET sensor enables quantitative characterization of electrostatic potential of membranes in living cells.

Rita Strack
Research Highlights 27 Apr 2017

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Technology Feature

How to deduplicate PCR

PCR duplicates—sequencing reads from the same original genomic fragment—can cause headaches. But there are remedies.

Vivien Marx

Collection:

NatureTech
Technology Feature 27 Apr 2017

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News & Views

Human T cell development notched up a level

Two complementary approaches for directing human hematopoietic stem cells along the T cell lineage will have applications in both fundamental and translational research.

Anne-Catherine Dolens
Tom Taghon
News & Views 27 Apr 2017

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Brief Communication

DeActs: genetically encoded tools for perturbing the actin cytoskeleton in single cells

DeActs are genetically encoded tools that perturb the actin cytoskeleton. In contrast to drugs such as latrunculin, they can be targeted to specific cell types, which is demonstrated in the developing mouse brain and in Caenorhabditis elegans.

Martin Harterink
Marta Esteves da Silva
J Bradley Zuchero
Brief Communication 10 Apr 2017
SC3: consensus clustering of single-cell RNA-seq data

Single-cell consensus clustering (SC3) provides user-friendly, robust and accurate cell clustering as well as downstream analysis for single-cell RNA-seq data.

Vladimir Yu Kiselev
Kristina Kirschner
Martin Hemberg
Brief Communication 27 Mar 2017
Structural modeling of protein–RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS

A mass spectrometry–based method to pinpoint UV-induced crosslinks in ribonucleoprotein complexes at protein residue and RNA nucleotide resolution provides key structural information for integrative modeling.

Georg Dorn
Alexander Leitner
Frédéric H-T Allain
Brief Communication 27 Mar 2017
Accurate identification of single-nucleotide variants in whole-genome-amplified single cells

Single-cell multiple displacement amplification (SCMDA) and a tool for single-nucleotide-variant calling (SCcaller) dramatically decrease artifacts in genome-wide variant calling from single cells.

Xiao Dong
Lei Zhang
Jan Vijg
Brief Communication 20 Mar 2017

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Article

Temporally precise labeling and control of neuromodulatory circuits in the mammalian brain

iTango confers access to neuromodulation-sensitive subsets of neurons in a functionally defined and temporally controlled manner. The tool allows for manipulating the subset of neurons that are activated by dopamine during a behavior of interest.

Dongmin Lee
Meaghan Creed
Hyung-Bae Kwon
Article 03 Apr 2017
Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry

A lysine-less, internally affinity-tagged ubiquitin construct is deployed to discover linear polyubiquitinated substrates via a mass-spectrometry-based proteomics approach.

Katarzyna Kliza
Christoph Taumer
Koraljka Husnjak
Article 20 Mar 2017
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

An ultrafast, fragment-ion indexing–based database search tool, MSFragger, makes open searching practical and enables comprehensive identification of modified peptides in mass spectrometry–based proteomics data sets.

Andy T Kong
Felipe V Leprevost
Alexey I Nesvizhskii
Article 10 Apr 2017
Generation of mature T cells from human hematopoietic stem and progenitor cells in artificial thymic organoids

This paper describes an in vitro method to generate human T cells from hematopoietic stem and progenitor cells (HSPCs). It should be useful for both basic and applied studies using T cells.

Christopher S Seet
Chongbin He
Amélie Montel-Hagen

Collections:

Stem cells from development to the clinic

Organoid research
Article 03 Apr 2017
Progenitor T-cell differentiation from hematopoietic stem cells using Delta-like-4 and VCAM-1

This paper describes a fully defined, nonxenogeneic in vitro niche for the differentiation of haematopoietic stem and progenitor cells to progenitor T cells in mouse and human.

Shreya Shukla
Matthew A Langley
Peter W Zandstra

Collection:

Stem cells from development to the clinic
Article 10 Apr 2017

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Corrigendum

Correction: Corrigendum: Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry

Fan Liu
Dirk T S Rijkers
Albert J R Heck
Corrigendum 27 Apr 2017
Correction: Corrigendum: Control of cerebral ischemia with magnetic nanoparticle

Jie-Min Jia
Praveen D Chowdary
Woo-Ping Ge
Corrigendum 27 Apr 2017
Correction: Corrigendum: Massively parallel single-amino-acid mutagenesis

Jacob O Kitzman
Lea M Starita
Jay Shendure
Corrigendum 27 Apr 2017

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Volume 14 Issue 5, May 2017

Editorial

This Month

Correspondence

Research Highlights

Methods in Brief

Tools in Brief

Research Highlights

Technology Feature

News & Views

Brief Communication

Article

Corrigendum

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