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Editorial

The politically engaged scientist p457

doi:10.1038/nmeth.4289

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.


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This Month

The Author File: Koraljka Husnjak p459

Vivien Marx

doi:10.1038/nmeth.4266

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


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Correspondence

Systems biology guided by XCMS Online metabolomics pp461 - 462

Tao Huan, Erica M Forsberg, Duane Rinehart, Caroline H Johnson, Julijana Ivanisevic, H Paul Benton, Mingliang Fang, Aries Aisporna, Brian Hilmers, Farris L Poole, Michael P Thorgersen, Michael W W Adams, Gregory Krantz, Matthew W Fields, Paul D Robbins, Laura J Niedernhofer, Trey Ideker, Erica L Majumder, Judy D Wall, Nicholas J W Rattray, Royston Goodacre, Luke L Lairson & Gary Siuzdak

doi:10.1038/nmeth.4260


Addressing reproducibility in single-laboratory phenotyping experiments pp462 - 464

Neri Kafkafi, Ilan Golani, Iman Jaljuli, Hugh Morgan, Tal Sarig, Hanno Würbel, Shay Yaacoby & Yoav Benjamini

doi:10.1038/nmeth.4259


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Research Highlights

Defining developmental grammar p465

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

It takes two to make an embryo pp466 - 467

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

A light switch for kinases pp466 - 467

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

A proteome-wide view of thermal stability p468

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

Dynamic measurement of membrane charges p471

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

Methods in Brief

Tools in Brief

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Technology Feature

How to deduplicate PCR pp473 - 476

Vivien Marx

doi:10.1038/nmeth.4268

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


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News and Views

Human T cell development notched up a level pp477 - 478

Anne-Catherine Dolens & Tom Taghon

doi:10.1038/nmeth.4277

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

See also: Article by Seet et al. | Article by Shukla et al.


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Brief Communications

DeActs: genetically encoded tools for perturbing the actin cytoskeleton in single cells pp479 - 482

Martin Harterink, Marta Esteves da Silva, Lena Will, Julia Turan, Adiljan Ibrahim, Alexander E Lang, Eljo Y van Battum, R Jeroen Pasterkamp, Lukas C Kapitein, Dmitri Kudryashov, Ben A Barres, Casper C Hoogenraad & J Bradley Zuchero

doi:10.1038/nmeth.4257

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.


SC3: consensus clustering of single-cell RNA-seq data pp483 - 486

Vladimir Yu Kiselev, Kristina Kirschner, Michael T Schaub, Tallulah Andrews, Andrew Yiu, Tamir Chandra, Kedar N Natarajan, Wolf Reik, Mauricio Barahona, Anthony R Green & Martin Hemberg

doi:10.1038/nmeth.4236

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


Structural modeling of protein–RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS pp487 - 490

Georg Dorn, Alexander Leitner, Julien Boudet, Sébastien Campagne, Christine von Schroetter, Ahmed Moursy, Ruedi Aebersold & Frédéric H-T Allain

doi:10.1038/nmeth.4235

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.


Accurate identification of single-nucleotide variants in whole-genome-amplified single cells pp491 - 493

Xiao Dong, Lei Zhang, Brandon Milholland, Moonsook Lee, Alexander Y Maslov, Tao Wang & Jan Vijg

doi:10.1038/nmeth.4227

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.


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Articles

Temporally precise labeling and control of neuromodulatory circuits in the mammalian brain pp495 - 503

Dongmin Lee, Meaghan Creed, Kanghoon Jung, Thomas Stefanelli, Daniel J Wendler, Won Chan Oh, Neymi Layne Mignocchi, Christian Lüscher & Hyung-Bae Kwon

doi:10.1038/nmeth.4234

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.


Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry pp504 - 512

Katarzyna Kliza, Christoph Taumer, Irene Pinzuti, Mirita Franz-Wachtel, Simone Kunzelmann, Benjamin Stieglitz, Boris Macek & Koraljka Husnjak

doi:10.1038/nmeth.4228

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


MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics pp513 - 520

Andy T Kong, Felipe V Leprevost, Dmitry M Avtonomov, Dattatreya Mellacheruvu & Alexey I Nesvizhskii

doi:10.1038/nmeth.4256

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.


Generation of mature T cells from human hematopoietic stem and progenitor cells in artificial thymic organoids pp521 - 530

Christopher S Seet, Chongbin He, Michael T Bethune, Suwen Li, Brent Chick, Eric H Gschweng, Yuhua Zhu, Kenneth Kim, Donald B Kohn, David Baltimore, Gay M Crooks & Amélie Montel-Hagen

doi:10.1038/nmeth.4237

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.

See also: News and Views by Dolens & Taghon


Progenitor T-cell differentiation from hematopoietic stem cells using Delta-like-4 and VCAM-1 pp531 - 538

Shreya Shukla, Matthew A Langley, Jastaranpreet Singh, John M Edgar, Mahmood Mohtashami, Juan Carlos Zúñiga-Pflücker & Peter W Zandstra

doi:10.1038/nmeth.4258

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.

See also: News and Views by Dolens & Taghon


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Corrigenda

Corrigendum: Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry p539

Fan Liu, Dirk T S Rijkers, Harm Post & Albert J R Heck

doi:10.1038/nmeth0517-539


Corrigendum: Control of cerebral ischemia with magnetic nanoparticle p540

Jie-Min Jia, Praveen D Chowdary, Xiaofei Gao, Bo Ci, Wenjun Li, Aditi Mulgaonkar, Erik J Plautz, Gedaa Hassan, Amit Kumar, Ann M Stowe, Shao-Hua Yang, Wei Zhou, Xiankai Sun, Bianxiao Cui & Woo-Ping Ge

doi:10.1038/nmeth0517-540a


Corrigendum: Massively parallel single-amino-acid mutagenesis p540

Jacob O Kitzman, Lea M Starita, Russell S Lo, Stanley Fields & Jay Shendure

doi:10.1038/nmeth0517-540b


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