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TABLE OF CONTENTS
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May 2017 Volume 14, Issue 5 |
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| In This Issue Editorial This Month Correspondence Research Highlights Technology Feature News and Views Brief Communications Articles Corrigenda | | Advertisement | | | | 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.
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In This Issue | Top |
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In This Issue |
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Editorial | Top |
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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 | Top |
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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 | Top |
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Systems biology guided by XCMS Online metabolomics pp461 - 462 Tao Huan, Erica M Forsberg, Duane Rinehart, Caroline H Johnson, Julijana Ivanisevic et al. doi:10.1038/nmeth.4260 |
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Addressing reproducibility in single-laboratory phenotyping experiments pp462 - 464 Neri Kafkafi, Ilan Golani, Iman Jaljuli, Hugh Morgan, Tal Sarig et al. doi:10.1038/nmeth.4259 |
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Research Highlights | Top |
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Technology Feature | Top |
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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 | Top |
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Human T cell development notched up a level pp477 - 478 Anne-Catherine Dolens and Tom Taghon doi:10.1038/nmeth.4277 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. |
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Brief Communications | Top |
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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. 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. |
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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. 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. |
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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. 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. |
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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. 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 | Top |
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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. 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. |
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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. 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. |
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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 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. |
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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. 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 |
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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. 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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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! | | | |
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Corrigenda | Top |
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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 doi:10.1038/nmeth0517-539 |
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Corrigendum: Control of cerebral ischemia with magnetic nanoparticle p540 Jie-Min Jia, Praveen D Chowdary, Xiaofei Gao, Bo Ci, Wenjun Li et al. doi:10.1038/nmeth0517-540a |
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Corrigendum: Massively parallel single-amino-acid mutagenesis p540 Jacob O Kitzman, Lea M Starita, Russell S Lo, Stanley Fields and Jay Shendure doi:10.1038/nmeth0517-540b |
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nature.com webcasts Springer Nature presents a custom webcast on: Perturb-seq: High Throughput CRISPR Screening via Single-Cell RNA Sequencing Date: Wednesday May 10, 2017 Time: 11AM PDT | 2PM EDT Register FREE Sponsored by: 10x Genomics | | | |
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