Thursday, April 27, 2017

Nature Methods Contents: May 2017 Volume 14 pp 457 - 540

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Nature Methods

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May 2017 Volume 14, Issue 5

In This Issue
This Month
Research Highlights
Technology Feature
News and Views
Brief Communications
Rapid, real-time T cell activation assay

Tired of waiting for T cell activation results? Accelerate your analysis with Agilent Seahorse XF technology. The XFp analyzer detects real-time T cell activation response within minutes with CD3/CD28 immunogenic beads by measuring discrete changes in cellular glycolysis. 

Learn more

Recommend to library

The 2017 IMB Conference on "Gene Regulation by the Numbers: Quantitative Approaches to Study Transcription" will explore the latest findings and technological developments in the field of gene regulation. The recent surge in omics technologies has generated vast amounts of data, but analysing and interpreting this remains a challenge. The conference will address major open questions that combine quantitative and experimental approaches to understanding gene regulation.
A personal pipetting robot for only $3,000. Affordable automation is here at last. 

Join the hundreds of labs, including Stanford, Harvard, and Mayo Clinic using Opentrons liquid-handling robots for workflow automation. It is as easy as downloading a protocol, loading your deck, and hitting run.


September 17-19, 2017 | Seattle, WA, USA

Presented by: Adaptive Biotechnologies | Nature Immunology | Nature Medicine | Nature Biotechnology


In This Issue


In This Issue   




The politically engaged scientist   p457
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.


This Month


The Author File: Koraljka Husnjak   p459
Vivien Marx
A “simple but a bit crazy idea” to tag ubiquitin and practice multilingual, multidisciplinary proteomics.




Systems biology guided by XCMS Online metabolomics   pp461 - 462
Tao Huan, Erica M Forsberg, Duane Rinehart, Caroline H Johnson, Julijana Ivanisevic et al.

Addressing reproducibility in single-laboratory phenotyping experiments   pp462 - 464
Neri Kafkafi, Ilan Golani, Iman Jaljuli, Hugh Morgan, Tal Sarig et al.


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.

It takes two to make an embryo
In vitro culture of mouse embryonic and extra-embryonic stem cells recapitulates embryogenesis.

A light switch for kinases
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
Proteome thermal stability is probed using limited proteolysis and mass spectrometry.

Dynamic measurement of membrane charges
A FRET sensor enables quantitative characterization of electrostatic potential of membranes in living cells.

Methods in Brief

Raman imaging in 3D cultures | Human lncRNA atlas | Measuring single-molecule charges | A fully designed yeast genome

Tools in Brief

Capturing ubiquitin-binding interactions | Optogenetic protein regulation at near-infrared wavelengths | Brighter and redder fluorescent rhodopsins | Light-dependent inhibition of CaMKII

JOBS of the week
Empire Innovation Scholar Position in Psychiatric Genomics
Upstate Medical University
Scientist, Molecular Interaction and Characterization - Bioanalytical Sciences (BAS)
Genentech, Inc.
Postdoctoral Scholar
The University of Iowa
Staff Scientist in Bioinformatics / Statistical Genetics, Department of Systems Biology and Computational Genomics
Sidra Medical and Research Centre
Project Scientist
University of California - Irvine
More Science jobs from
NETTAB 2017 Methods, tools & platforms for Personalized Medicine in the Big Data Era
Palermo, Italy
More science events from

Technology Feature


How to deduplicate PCR   pp473 - 476
Vivien Marx
PCR duplicates—sequencing reads from the same original genomic fragment—can cause headaches. But there are remedies.


News and Views


Human T cell development notched up a level   pp477 - 478
Anne-Catherine Dolens and Tom Taghon
Two complementary approaches for directing human hematopoietet al.ic 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.


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 et al.
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 et al.
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 et al.
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 et al.
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.


September 27-29, 2017 | Seoul, Korea

Presented by: Institute for Basic Science | Institute of Genetics and Developmental Biology, CAS | Nature | Nature Biotechnology




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 et al.
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 et al.
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 and Alexey I Nesvizhskii
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 et al.
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 et al.
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

April 2017 marks the 25th Anniversary of Nature Genetics! To celebrate, the editors have selected some past papers which are free to read for a limited time. 

Click here to read!



Corrigendum: Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry   p539
Fan Liu, Dirk T S Rijkers, Harm Post and Albert J R Heck

Corrigendum: Control of cerebral ischemia with magnetic nanoparticle   p540
Jie-Min Jia, Praveen D Chowdary, Xiaofei Gao, Bo Ci, Wenjun Li et al.

Corrigendum: Massively parallel single-amino-acid mutagenesis   p540
Jacob O Kitzman, Lea M Starita, Russell S Lo, Stanley Fields and Jay Shendure

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