Nature Methods Contents: November 2016 Volume 13 pp 891 - 958

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TABLE OF CONTENTS November 2016 Volume 13, Issue 11 In This Issue Editorial This Month Correspondence Research Highlights Technology Feature News and Views Brief Communications Articles Application Notes Advertisement   Determine the Metabolic Phenotype of Your Cells The Agilent Seahorse XF Cell Energy Phenotype Test uses as few as 15,000 cells, and the Agilent Seahorse XFp Analyzer, to identify your cells' metabolic phenotype, as well as their metabolic potential — the relative utilization of mitochondrial respiration and glycolysis. http://bit.ly/1Caw9Eq Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Pre-made CRISPR-Cas9 Stable Cell Lines  Stably expressing CRISPR Cas9. Ideal for CRISPR sgRNA validation, library screening, and sgRNA mediated knockouts and knockins Human: H1299 - Cas9, HEK293T - Cas9, HeLa - Cas9, A549 - Cas9, MCF-7 - Cas9, MDA-MB-231 - Cas9, HepG2 - Cas9, AGS - Cas9, BXPC-3 - Cas9 Mouse: Neuro2a - Cas9 Learn more»   Advertisement Get +Together. The new Eppendorf Centrifuge 5920 R. The perfect choice for Eppendorf Conical Tubes and Eppendorf DWP/MTP Plates. Get your sample here   Advertisement Nature Collection: Computational Biology Advances in technology across all areas of science have ushered in an era of big data, providing researchers with unprecedented opportunities to understand how biological systems function and interact.  Access this collection free online for six months: Produced with support from: IBM Research & IBM Watson Health     In This Issue Top In This Issue    Editorial Top Whither (reason and science in) America?   p891 doi:10.1038/nmeth.4069 Reasoned, skeptical debate is the lifeblood of science. Its practitioners necessarily sit at the same table with others who disagree with them. This cannot be said of political discourse in America today. This Month Top The Author File: Roger Y Tsien (1952-2016)   p893 Erik A Rodriguez, Nathan C Shaner, Michael Z Lin and Robert E Campbell doi:10.1038/nmeth.4044 A chemist who illuminated biology. Points of View: Intuitive design   p895 Martin Krzywinski doi:10.1038/nmeth.4041 Appeal to intuition when making value judgments Correspondence Top An acquisition and analysis pipeline for scanning angle interference microscopy   pp897 - 898 Catherine B Carbone, Ronald D Vale and Nico Stuurman doi:10.1038/nmeth.4030 Research Highlights Top Capturing metabolic dynamics in mitochondria A rapid method for isolating mitochondria with exquisitely high purity helps researchers profile metabolic dynamics within this organelle. Making human microglia in a dish Researchers have developed a protocol for differentiation of microglia-like cells from human pluripotent stem cells. Unraveling magnetogenetics Recent reports on the magnetogenetic manipulation of neurons are being called into question. Orientation mapping in super-resolution Fluorescence polarization enables super-resolution dipole orientation mapping. RNA detection with C2c2 The discovery of two distinct endonuclease activities in the C2c2 protein explains how template RNAs are processed in type VI CRISPR systems and enables the development of a sensitive RNA detection system. Extreme makeover: protein edition Oxford scientists unleash radical chemistry to explore novel protein activities through synthetic post-translational modifications. Mapmaking with barcoded neurons In the mouse brain, researchers use sequencing to map long-range neuronal projections...a lot of projections. Methods in Brief Unmixing cell lineage states with single-cell RNA sequencing | Specific activation of dopamine neurons in macaques | Apicomplexans submit to CRISPR screening | The proteomes of excitatory and inhibitory synaptic clefts Tools in Brief Making memories with CRISPR–Cas9 | A plant metabolite spectral library | A yeast global genetic interaction map | Monomeric near-infrared fluorescent proteins Methods JOBS of the week Post doc scholarship in Proteomic Hematology Lund University Postdoctoral Associate Baylor College of Medicine (BCM) Dean, College of Sciences University of Nevada, Las Vegas (UNLV) Postdoctoral Research Fellow Children's Hospital Los Angeles Bioinformatician - Core Facility Department of Biomedicine, University of Basel and University Hospital Basel More Science jobs from Technology Feature Top Neurobiology: learning from marmosets   pp911 - 916 Vivien Marx doi:10.1038/nmeth.4036 Many neuroscience labs are intrigued by these social, vocalizing primates. News and Views Top Trail-blAIZin new directions for conditional proteomics   pp917 - 918 Hashim F Motiwala and Brent R Martin doi:10.1038/nmeth.4043 A reagent that labels proteins in close proximity to high concentrations of zinc is used to identify proteins with a role in zinc homeostasis. See also: Article by Miki et al. Brief Communications Top HiChIP: efficient and sensitive analysis of protein-directed genome architecture   pp919 - 922 Maxwell R Mumbach, Adam J Rubin, Ryan A Flynn, Chao Dai, Paul A Khavari et al. doi:10.1038/nmeth.3999 HiChIP combines chromosome conformation capture with immunoprecipitation- and tagmentation-based library preparation to uncover the 3D chromatin architecture focused around a protein of interest. Massively parallel single-nucleotide mutagenesis using reversibly terminated inosine   pp923 - 924 Gabe Haller, David Alvarado, Kevin McCall, Robi D Mitra, Matthew B Dobbs et al. doi:10.1038/nmeth.4015 The incorporation of reversibly terminated deoxyinosine triphosphates during linear amplification allows the incorporation of one mutation per molecule and the generation of a systematic allelic series. Enzyme-catalyzed expressed protein ligation   pp925 - 927 Samuel H Henager, Nam Chu, Zan Chen, David Bolduc, Daniel R Dempsey et al. doi:10.1038/nmeth.4004 The enzyme subtiligase can be used to catalyze expressed protein ligation of proteins of interest with peptides lacking an N-terminal cysteine. This enables the analysis of protein modifications in the context of the native primary sequence. Plasmid-based one-pot saturation mutagenesis   pp928 - 930 Emily E Wrenbeck, Justin R Klesmith, James A Stapleton, Adebola Adeniran, Keith E J Tyo et al. doi:10.1038/nmeth.4029 Nicking mutagenesis is a streamlined protocol for plasmid-based single-pot comprehensive saturation mutagenesis. Advertisement Nature Outlook: Precision Medicine Health care that is tailored on the basis of an individual's genes, lifestyle or environment, is not a modern concept. But advances in genetics and the growing availability of health data for researchers and physicians promise to make this new era of medicine more personalized than ever before. Access the Outlook free online for six months Sponsored by: Illumina, Inc.      Articles Top A conditional proteomics approach to identify proteins involved in zinc homeostasis   pp931 - 937 Takayuki Miki, Masashi Awa, Yuki Nishikawa, Shigeki Kiyonaka, Masaki Wakabayashi et al. doi:10.1038/nmeth.3998 A 'conditional proteomics' approach, as applied here to identify proteins involved in zinc homeostasis, utilizes an activatable labeling reagent to tag proteins affected by a particular biological condition in the cell, enabling them to be isolated and identified using mass spectrometry. See also: News and Views by Motiwala & Martin Directing cellular information flow via CRISPR signal conductors   pp938 - 944 Yuchen Liu, Yonghao Zhan, Zhicong Chen, Anbang He, Jianfa Li et al. doi:10.1038/nmeth.3994 The integration of ligand-responsive riboswitches with single guide RNAs allows Cas9-effector fusions to be targeted in response to ligands and thereby translate a cellular signal into a downstream readout of choice. A bacterial genetic selection system for ubiquitylation cascade discovery   pp945 - 952 Olga Levin-Kravets, Neta Tanner, Noa Shohat, Ilan Attali, Tal Keren-Kaplan et al. doi:10.1038/nmeth.4003 An Escherichia coli-based genetic selection system, constructed from a split antibiotic resistance protein individually tethered to ubiquitin and a target protein, helps discover ubiquitin cascade pathway interactions. Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling   pp953 - 958 Jason A Reuter, Damek V Spacek, Reetesh K Pai and Michael P Snyder doi:10.1038/nmeth.4028 Simul-seq profiles genomes and transcriptomes by uniquely barcoding DNA and RNA reads from the same material. 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