Nature Methods Contents: January 2016 Volume 13 pp 1 - 101

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Advertisement Like GeneCopoeia on Facebook & win a FREE expression-ready ORF clone  One winner per week Over 86,000 ORF Clones in 150+ vectors  Like us and win now >> TABLE OF CONTENTS January 2016 Volume 13, Issue 1 In This Issue Special Feature Editorial This Month Correspondence Research Highlights News Feature Primer Historical Commentary Commentary Methods to Watch Technology Feature Review Brief Communications Articles Corrigendum Erratum Advertisement   Your Sharpest Results Yet. Optimized for greater imaging depths, Olympus' Multiphoton Laser Scanning Microscopes offer countless possibilities for deep tissue observation. When precision counts and there is no compromise. High-speed millisecond  imaging Perfect for capture of rapid in vivo responses Offers ideal spot excitation with intense energy Take a closer look. Your Science Matters™ Subscribe   Facebook   RSS   Recommend to library   Twitter   In This Issue Top In This Issue    Special Feature Top Method of the Year 2015 Contents Editorial News Feature Primer Historical Commentary Commentary Methods to Watch Our choice for Method of the Year 2015 is single-particle cryo-electron microscopy. A collection of articles discusses how recent technical advances, especially the development of direct-detection cameras, have enabled this structural biology technique to make impressive leaps in achievable resolution and, in turn, provide new insights about protein function. We also highlight methods to watch in the upcoming years. Editorial Top Special feature: Method of the Year 2015 Method of the Year 2015   p1 doi:10.1038/nmeth.3730 The end of 'blob-ology': single-particle cryo-electron microscopy (cryo-EM) is now being used to solve macromolecular structures at high resolution. This Month Top The Author File: Hasan DeMirci   p3 Vivien Marx doi:10.1038/nmeth.3710 The connection between snowboarding and getting more data from protein crystals. Points of View: Pathways   p5 Barbara J Hunnicutt and Martin Krzywinski doi:10.1038/nmeth.3699 Apply visual grouping principles to add clarity to information flow in pathway diagrams. Correspondence Top Polarization modulation adds little additional information to super-resolution fluorescence microscopy   pp7 - 8 Lars Frahm and Jan Keller doi:10.1038/nmeth.3687 See also: Correspondence by Hafi et al. | Article by Hafi et al. Reply to "Polarization modulation adds little additional information to super-resolution fluorescence microscopy"   pp8 - 9 Nour Hafi, Matthias Grunwald, Laura S van den Heuvel, Timo Aspelmeier, Claudia Steinem et al. doi:10.1038/nmeth.3721 See also: Correspondence by Frahm & Keller | Article by Hafi et al. OASIS: web-based platform for exploring cancer multi-omics data   pp9 - 10 Julio Fernandez-Banet, Anthony Esposito, Scott Coffin, Istvan Boerner Horvath, Heather Estrella et al. doi:10.1038/nmeth.3692 Research Highlights Top Localization microscopy goes ultrasonic Ultrafast ultrasound microscopy allows for super-resolution ultrasound imaging of vasculature in whole organs. Jedi cells patrol the mouse Engineered Jedi T cells scour the body to eliminate GFP-expressing cells. A single cell's open chromatin Increasing the sensitivity of DNase-seq allows chromatin accessibility to be profiled from very low numbers of cells. The power of 'weak' interactions A map of mammalian protein interactions highlights the importance of substoichiometric interactions. Sensing some tension Cells are under mechanical tension in their native environment. New genetically encoded tension sensors can make a broader range of these forces visible. Methods in Brief Small-angle X-ray scattering reaches new dimensions | Synthetic data feed machine-learning predictors of splicing | Comprehensive glycoprotein characterization | Cooperative transcription-factor binding Tools in Brief Voltage sensors for in vivo applications | How to prep your metagenomic library | SCRaMbLE put to the test | Wireless optogenetics Methods JOBS of the week Postdoctoral Research Associate University of Liverpool Associate Research Scientist in Bioinformatics Columbia University Postdoctoral Researcher (Fuels Synthesis Division at JBEI) Lawrence Berkeley National Laboratory (LBNL) Research Associate (#79033) California Institute for Biomedical Research Postdoc scholarship in Computational Genomics Bioinformatics Lund University More Science jobs from Methods EVENT 15th Conference on Methods and Applications in Fluorescence (MAF-15) 10th Sept - 13th Sept 2017 KU Leuven, Belgium More science events from News Feature Top Special feature: Method of the Year 2015 The field that came in from the cold   pp19 - 22 Michael Eisenstein doi:10.1038/nmeth.3698 Recent advances in cryo-electron microscopy are enabling researchers to solve protein structures at near-atomic resolutions, expanding the biological applicability of this technique. Michael Eisenstein reports. Primer Top Special feature: Method of the Year 2015 Single-particle cryo-electron microscopy   p23 Allison Doerr doi:10.1038/nmeth.3700 A brief overview of how to solve a macromolecular structure using single-particle cryo-electron microscopy (cryo-EM). Historical Commentary Top Special feature: Method of the Year 2015 The development of cryo-EM into a mainstream structural biology technique   pp24 - 27 Eva Nogales doi:10.1038/nmeth.3694 Single-particle cryo-electron microscopy (cryo-EM) has emerged over the last two decades as a technique capable of studying the structure of challenging systems. The author of this Commentary discusses some of the major historical landmarks in cryo-EM that have led to its present success. Commentary Top Special feature: Method of the Year 2015 How good can cryo-EM become?   pp28 - 32 Robert M Glaeser doi:10.1038/nmeth.3695 Cryo-EM has emerged rapidly as a method for determining high-resolution structures of biological macromolecules. The author of this Commentary discusses just how much better this technology may get and how fast such developments are likely to happen. Methods to Watch Top Special feature: Method of the Year 2015 Protein labeling in cells   p33 Rita Strack doi:10.1038/nmeth.3702 Better protein-labeling strategies will improve imaging. Special feature: Method of the Year 2015 Unraveling nuclear architecture   p33 Nicole Rusk doi:10.1038/nmeth.3703 New approaches are needed to see the dynamics of 3D chromatin structure at high resolution and throughput. Special feature: Method of the Year 2015 Protein structure through time   p34 Allison Doerr doi:10.1038/nmeth.3704 Advances in time-resolved crystallography make it possible to follow ever more rapid protein structural changes. Special feature: Method of the Year 2015 Precision optogenetics   p34 Nina Vogt doi:10.1038/nmeth.3705 Optogenetic manipulation of neurons at cellular resolution holds promise for the dissection of neural microcircuitry. Special feature: Method of the Year 2015 Highly multiplexed imaging   p35 Rita Strack doi:10.1038/nmeth.3706 Methods for imaging multiple targets in a single cell are breaking the color barrier. Special feature: Method of the Year 2015 Deep learning   p35 Nicole Rusk doi:10.1038/nmeth.3707 New computational tools learn complex motifs from large sequence data sets. Special feature: Method of the Year 2015 Subcellular maps   p36 Natalie de Souza doi:10.1038/nmeth.3708 Methods to systematically map the distribution of proteins in cells are evolving. Special feature: Method of the Year 2015 Integrated single-cell profiles   p36 Tal Nawy doi:10.1038/nmeth.3709 Integrated molecular profiles of single cells will provide mechanistic insights into gene regulation and heterogeneity. Technology Feature Top Cell biology: delivering tough cargo into cells   pp37 - 40 Vivien Marx doi:10.1038/nmeth.3693 New approaches expand the range and size of materials that can be inserted into a cell. Review Top Creating and evaluating accurate CRISPR-Cas9 scalpels for genomic surgery   pp41 - 50 Mehmet Fatih Bolukbasi, Ankit Gupta and Scot A Wolfe doi:10.1038/nmeth.3684 This review describes methods for increasing the activity and accuracy of the CRISPR-Cas9 system and discusses approaches for assessing off-target cleavage. Brief Communications Top NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites   pp51 - 54 Tingwei Quan, Hang Zhou, Jing Li, Shiwei Li, Anan Li et al. doi:10.1038/nmeth.3662 NeuroGPS-Tree can reconstruct individual neurons from dense populations of fluorescently labeled neurons using computational strategies inspired by the strategies humans use. Parmbsc1: a refined force field for DNA simulations   pp55 - 58 Ivan Ivani, Pablo D Dans, Agnes Noy, Alberto Perez, Ignacio Faustino et al. doi:10.1038/nmeth.3658 Parmbsc1, a new force field for DNA simulations, was broadly tested on nearly 100 DNA systems and overcame simulation artifacts that affected previous force fields. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II   pp59 - 62 Raymond G Sierra, Cornelius Gati, Hartawan Laksmono, E Han Dao, Sheraz Gul et al. doi:10.1038/nmeth.3667 A concentric-flow microfluidic electrokinetic sample injector enables efficient delivery of microcrystals in their mother liquor for serial femtosecond X-ray crystallography with minimal sample consumption. Efficient genotype compression and analysis of large genetic-variation data sets   pp63 - 65 Ryan M Layer, Neil Kindlon, Konrad J Karczewski, Exome Aggregation Consortium: A list of members and affiliations appears in Supplementary Note 1. Aaron R Quinlan doi:10.1038/nmeth.3654 Genotype Query Tools allows fast individual-centric indexing and mining of large variant data sets. Advertisement The discussion on Alzheimer’s Disease continues Nature Neuroscience presents a community forum on Alzheimer's Disease (AD) research. ACCESS NOW to view videos of our panel event at SfN 2015, read related articles for free, and discuss critical issues facing AD research today. Produced with support from Eli Lilly and Company and vTv Therapeutics   Articles Top Multiscale photoacoustic tomography using reversibly switchable bacterial phytochrome as a near-infrared photochromic probe   pp67 - 73 Junjie Yao, Andrii A Kaberniuk, Lei Li, Daria M Shcherbakova, Ruiying Zhang et al. doi:10.1038/nmeth.3656 Combining a reversibly photoswitchable bacteriophytochrome with photoacoustic imaging allows for exceptionally sensitive tomographic imaging deep in living mice, as well as super-resolution photoacoustic microscopy. Multiplexed analysis of chromosome conformation at vastly improved sensitivity   pp74 - 80 James O J Davies, Jelena M Telenius, Simon J McGowan, Nigel A Roberts, Stephen Taylor et al. doi:10.1038/nmeth.3664 Pooling barcoded 3C libraries and simultaneously capturing interactions at many loci of interest generates reproducible cis- and trans-interaction maps at high resolution from low amounts of input material. This allows for the comparison of interactions in different cell types using common software designed for differential analysis of sequence count data, rather than requiring software specifically designed for 3C experiments. Cellular O-Glycome Reporter/Amplification to explore O-glycans of living cells   pp81 - 86 Matthew R Kudelka, Aristotelis Antonopoulos, Yingchun Wang, Duc M Duong, Xuezheng Song et al. doi:10.1038/nmeth.3675 Addition of a glycan precursor to cells results in the synthesis and secretion of a large variety of O-glycans that can be purified and biochemically analyzed to profile the cellular O-glycome. Fixed single-cell transcriptomic characterization of human radial glial diversity   pp87 - 93 Elliot R Thomsen, John K Mich, Zizhen Yao, Rebecca D Hodge, Adele M Doyle et al. doi:10.1038/nmeth.3629 The Fixed and Recovered Intact Single-cell RNA (FRISCR) method enables robust RNA extraction and sequencing from fixed, stained and sorted single cells and allows unprecedented profiling of rare cell types, including two subpopulations of radial glial cells in the developing human cortex. Quantitative characterization of genetic parts and circuits for plant synthetic biology   pp94 - 100 Katherine A Schaumberg, Mauricio S Antunes, Tessema K Kassaw, Wenlong Xu, Christopher S Zalewski et al. doi:10.1038/nmeth.3659 Quantitative analysis of promoter-repressor pairs in plants will allow the design of predictable gene circuits in multicellular organisms. Corrigendum Top Corrigendum: Fluorescence nanoscopy by polarization modulation and polarization angle narrowing   p101 Nour Hafi, Matthias Grunwald, Laura S van den Heuvel, Timo Aspelmeier, Jian-Hua Chen et al. doi:10.1038/nmeth0116-101a Erratum Top Erratum: MetaPhlAn2 for enhanced metagenomic taxonomic profiling   p101 Duy Tin Truong, Eric A Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart et al. doi:10.1038/nmeth0116-101b Top 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. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com More Nature Events

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