Nature Methods Contents: November 2018, Volume 15 No 11

Advertisement Get pipetting help from the experts. With over 55 years of experience in liquid handling, Eppendorf has a massive knowledge base of proper pipetting techniques and other solutions to solve just about any liquid handling challenge you face.  Learn more from the Liquid Handling experts and check out our pipetting solutions today. TABLE OF CONTENTS November 2018 Volume 15, Issue 11 Editorial This Month Correspondence Comment Research Highlights Technology Feature News & Views Review Articles Resources Brief Communications Articles Amendments & Corrections Advertisement   Optimize your antibody applications with CST Guides to assist you with your research: IHC, ChIP, IF, and WB.  Download these guides to improve your results, select better suited antibodies, get easy-to-use protocols and find the best companion products for each. Advertisement New Poster on: Epitranscriptome regulation  Download a new poster from Nature Structural & Molecular Biology on epitranscriptome regulation, a key mechanism affecting gene expression as well as cellular functions, development and disease.  Available free online  Produced with support from Accent Therapeutics, Inc.   Editorial The impact of the NIH BRAIN Initiative    p839 doi:10.1038/s41592-018-0210-0 This Month Anna Moroni    p841 Vivien Marx doi:10.1038/s41592-018-0192-y Predicting with confidence and tolerance    pp843 - 845 Naomi Altman & Martin Krzywinski doi:10.1038/s41592-018-0196-7 Advertisement Advanced Imaging with Proven Optics Olympus is dedicated to your work, vision, and science. Through innovation and service, we seek to aide in your discoveries, advance your research, and inspire you to explore new possibilities. Our wide range of microscopes are built with the optical excellence and proven application expertise you can depend on. Your Science Matters™. > Learn more about Olympus microscopes   Correspondence A community-developed open-source computational ecosystem for big neuro data    pp846 - 847 Joshua T. Vogelstein, Eric Perlman, Benjamin Falk, Alex Baden, William Gray Roncal et al. doi:10.1038/s41592-018-0181-1 Striped UniFrac: enabling microbiome analysis at unprecedented scale    pp847 - 848 Daniel McDonald, Yoshiki Vázquez-Baeza, David Koslicki, Jason McClelland, Nicolai Reeve et al. doi:10.1038/s41592-018-0187-8 Comment A call for public archives for biological image data    pp849 - 854 Jan Ellenberg, Jason R. Swedlow, Mary Barlow, Charles E. Cook, Ugis Sarkans et al. doi:10.1038/s41592-018-0195-8 Research Highlights High-speed protein crystallography    p855 Allison Doerr doi:10.1038/s41592-018-0205-x Fluorescent proteins from scratch    p856 Rita Strack doi:10.1038/s41592-018-0206-9 Keeping CRISPR in check    p857 Nicole Rusk doi:10.1038/s41592-018-0207-8 Diploid genome in 3D    p858 Lei Tang doi:10.1038/s41592-018-0208-7 A winning single-cell combination    p859 Tal Nawy doi:10.1038/s41592-018-0197-6 Smarter cell sorting    p859 Rita Strack doi:10.1038/s41592-018-0198-5 Shaking up clearing cocktails    p859 Nina Vogt doi:10.1038/s41592-018-0199-4 Finding S-sulfinylated proteins    p859 Allison Doerr doi:10.1038/s41592-018-0200-2 Protein circuit engineering    p860 Nicole Rusk doi:10.1038/s41592-018-0201-1 Mechanistic microbiota models    p860 Tal Nawy doi:10.1038/s41592-018-0202-0 Blinking in the cold    p860 Rita Strack doi:10.1038/s41592-018-0203-z Improving long-read accuracy    p860 Lei Tang doi:10.1038/s41592-018-0204-y Variants from the deep    p861 Tal Nawy doi:10.1038/s41592-018-0209-6 Technology Feature Neuroscience models: choose your dimension    pp863 - 866 Vivien Marx doi:10.1038/s41592-018-0191-z News & Views Enhancing the glycosciences toolkit: new GAGs in the lineup    pp867 - 868 Jeremy E. Turnbull doi:10.1038/s41592-018-0190-0 Deep learning to predict microscope images    pp868 - 870 Roger Brent & Laura Boucheron doi:10.1038/s41592-018-0194-9 Review Articles Cellular barcoding: lineage tracing, screening and beyond    pp871 - 879 Justus M. Kebschull & Anthony M. Zador doi:10.1038/s41592-018-0185-x A review of cellular barcoding fundamentals and applications, including powerful approaches for lineage reconstruction, genetic screening, and the recording of cellular activity and neuroanatomy. Resources The GAGOme: a cell-based library of displayed glycosaminoglycans    pp881 - 888 Yen-Hsi Chen, Yoshiki Narimatsu, Thomas M. Clausen, Catarina Gomes, Richard Karlsson et al. doi:10.1038/s41592-018-0086-z A CHO cell library displaying a near-complete repertoire of glycosaminoglycan (GAG) modifications provides a resource for cell-based binding assays, recombinant proteoglycan expression, and assembly of GAG glycan microarrays. A mutant-cell library for systematic analysis of heparan sulfate structure–function relationships    pp889 - 899 Hong Qiu, Songshan Shi, Jingwen Yue, Meng Xin, Alison V. Nairn et al. doi:10.1038/s41592-018-0189-6 A library of mutant mouse lung endothelial cells expressing a comprehensive repertoire of heparin sulfate structure modifications enables studies of the structure–function relationships of this complex polysaccharide. Brief Communications The hit-and-return system enables efficient time-resolved serial synchrotron crystallography    pp901 - 904 Eike C. Schulz, Pedram Mehrabi, Henrike M. Müller-Werkmeister, Friedjof Tellkamp, Ajay Jha et al. doi:10.1038/s41592-018-0180-2 A data-collection strategy using a fixed-target crystallography chip allows time-resolved serial synchrotron crystallography experiments to determine enzyme intermediate structures with time resolutions of milliseconds to seconds. A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps    pp905 - 908 Thomas C. Terwilliger, Paul D. Adams, Pavel V. Afonine & Oleg V. Sobolev doi:10.1038/s41592-018-0173-1 A fully automated method for modeling protein and protein–RNA complex structure from cryo-EM data, requiring minimal user intervention, is described. A high-throughput pipeline for validation of antibodies    pp909 - 912 Krzysztof Sikorski, Adi Mehta, Marit Inngjerdingen, Flourina Thakor, Simon Kling et al. doi:10.1038/s41592-018-0179-8 This paper describes a platform for carrying out antibody-based capture and mass spectrometry in parallel, and tests the feasibility of this platform for high-throughput validation of antibodies. Analyzing complex single-molecule emission patterns with deep learning    pp913 - 916 Peiyi Zhang, Sheng Liu, Abhishek Chaurasia, Donghan Ma, Michael J. Mlodzianoski et al. doi:10.1038/s41592-018-0153-5 The deep neural network smNet extracts multiplexed parameters such as 3D position, orientation and wavefront distortion from emission patterns of single molecules. Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy    pp917 - 920 Chawin Ounkomol, Sharmishtaa Seshamani, Mary M. Maleckar, Forrest Collman & Gregory R. Johnson doi:10.1038/s41592-018-0111-2 Convolutional neural networks enable prediction of fluorescently labeled structures from three-dimensional time-lapse transmitted-light images. Applications include multiplexed long time-lapse imaging and prediction of fluorescence in electron micrographs. FLIRT: fast local infrared thermogenetics for subcellular control of protein function    pp921 - 923 Sophia M. Hirsch, Sriramkumar Sundaramoorthy, Tim Davies, Yelena Zhuravlev, Jennifer C. Waters et al. doi:10.1038/s41592-018-0168-y FLIRT enables spatiotemporally precise control of protein function in C. elegans by harnessing existing temperature-sensitive mutations. Proteins can be inactivated at desired sites by infrared laser light targeted to the region(s) of interest. Engineered anti-CRISPR proteins for optogenetic control of CRISPR–Cas9    pp924 - 927 Felix Bubeck, Mareike D. Hoffmann, Zander Harteveld, Sabine Aschenbrenner, Andreas Bietz et al. doi:10.1038/s41592-018-0178-9 CASANOVA uses LOV and blue light to regulate CRISPR activity. CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging    pp928 - 931 Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Yu-Chieh Chung, David Grunwald et al. doi:10.1038/s41592-018-0174-0 Multiple MS2 loops inserted in the first loop of an sgRNA after the spacer sequence stabilize the sgRNA and allow recruitment of multicolor fluorescent proteins for imaging of low-repeat genomic loci. Spatial organization of the somatosensory cortex revealed by osmFISH    pp932 - 935 Simone Codeluppi, Lars E. Borm, Amit Zeisel, Gioele La Manno, Josina A. van Lunteren et al. doi:10.1038/s41592-018-0175-z osmFISH applies automated cycles of single-molecule fluorescence in situ hybridization without barcoding to provide spatial gene expression in tissue sections at high sensitivity, accuracy and throughput. Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR    pp936 - 939 Jonathan S. Marvin, Benjamin Scholl, Daniel E. Wilson, Kaspar Podgorski, Abbas Kazemipour et al. doi:10.1038/s41592-018-0171-3 Variants of the genetically encoded sensor iGluSnFR extend the range of conditions under which glutamate neurotransmission can be visualized. In addition, chromatic variants of iGluSnFR improve compatibility with various illumination schemes. Articles Guide Swap enables genome-scale pooled CRISPR–Cas9 screening in human primary cells    pp941 - 946 Pamela Y. Ting, Albert E. Parker, J. Scott Lee, Chris Trussell, Orzala Sharif et al. doi:10.1038/s41592-018-0149-1 Guide Swap challenges the hypothesis that Cas9–sgRNA binding is irreversible. The authors find that instead, nontargeting sgRNAs are swapped for targeting sgRNAs in the Cas9 complex. The method allows genome-scale functional screens in primary cells De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes    pp947 - 954 Kalli Kappel, Shiheng Liu, Kevin P. Larsen, Georgios Skiniotis, Elisabetta Viani Puglisi et al. doi:10.1038/s41592-018-0172-2 DRRAFTER, a method for RNA modeling into cryo-EM maps, generates accurate models for diverse RNA–protein complexes. emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging    pp955 - 961 Benjamin A. Himes & Peijun Zhang doi:10.1038/s41592-018-0167-z A software tool, emClarity, implements several improvements in cryo-electron tomography image-processing algorithms to achieve sub-nanometer resolution for diverse macromolecular structures. Species-level functional profiling of metagenomes and metatranscriptomes    pp962 - 968 Eric A. Franzosa, Lauren J. McIver, Gholamali Rahnavard, Luke R. Thompson, Melanie Schirmer et al. doi:10.1038/s41592-018-0176-y HUMAnN2 uses a tiered sequence search to provide rapid and accurate species-level functional profiles of microbial communities from metagenomic and metatranscriptomic data. A light-gated potassium channel for sustained neuronal inhibition    pp969 - 976 Laura Alberio, Andrea Locarno, Andrea Saponaro, Edoardo Romano, Valérie Bercier et al. doi:10.1038/s41592-018-0186-9 BLINK2 is a light-activated potassium channel for optogenetic inhibition of neuronal activity. Alberio et al. apply the tool in systems as diverse as cultured rat neurons, mouse brain slices, behaving zebrafish and a rat model of neuropathic pain. Transparent Danionella translucida as a genetically tractable vertebrate brain model    pp977 - 983 Lisanne Schulze, Jörg Henninger, Mykola Kadobianskyi, Thomas Chaigne, Ana Isabel Faustino et al. doi:10.1038/s41592-018-0144-6 The combination of transparency, small brain size and genetic access positions Danionella translucida as a promising model organism for functional imaging of neuronal circuits, especially during complex behaviors in adults. Amendments & Corrections Publisher Correction: Image Data Resource: a bioimage data integration and publication platform    p984 Eleanor Williams, Josh Moore, Simon W Li, Gabriella Rustici, Aleksandra Tarkowska et al. doi:10.1038/s41592-018-0169-x Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study    p984 Björn Hellenkamp, Sonja Schmid, Olga Doroshenko, Oleg Opanasyuk, Ralf Kühnemuth et al. doi:10.1038/s41592-018-0193-x Advertisement Nature Briefing is an essential round-up of science news, opinion and analysis, free in your inbox every weekday. With Nature Briefing, we'll keep you updated on the latest research, so you can focus on yours. Click here to sign up.   Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. 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