Nature Methods Contents: November 2015 Volume 12 pp 995 - 1098

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Advertisement ORCA-Flash4.0 V2 Discover the Breakthrough  The first sCMOS camera with 82% peak Quantum Efficiency. Available for demonstration and shipping NOW from Hamamatsu. What breakthrough will you make with your extra photons? Tel. 908-231-0960 TABLE OF CONTENTS November 2015 Volume 12, Issue 11 In This Issue Editorial This Month Correspondence Research Highlights Technology Feature News and Views Review Analysis Resource Brief Communications Articles Corrigenda Application Notes Advertisement Determine the Metabolic Phenotype of Your Cells in One Hour The XFp Cell Energy Phenotype Test Kit from Seahorse Bioscience. Using as few as 15,000 cell and the XFp Analyzer, the XF Cell Energy Phenotype Test identifies 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 EZShuttle™ Recombination Cloning System -the same principle as Gateway® technology. -based on phage lambda recombination EZRecombinase™ Mixes for catalyzing attL x attR and attB x attP cloning reactions. pEZ™ expression cloning vectors for creating ready-to-use expression clones EZShuttle™ Gateway® PLUS ORF clones. More than 35,000 human and mouse ORFs in pShuttle™ plasmid backbones Learn more >>   Advertisement Announcing new solutions for SNP Genotyping using PCR and HRM Canon BioMedical recently released its new menu of Novallele™ Genotyping Assays for research use. With assays covering oncology, pharmacogenetics, and other inherited targets, we have solutions for your experiments. Discover more: www.canon-biomedical.com   Advertisement Nature Milestones: Mass Spectrometry is a collaboration from Nature Methods, Nature, Nature Biotechnology, Nature Chemical Biology and Nature Protocols.  Access the Milestone articles free online. The accompanying Collection articles will be made freely available for six months.  Produced with support from:  SCIEX   Thermo Fisher Scientific Inc.   Waters Corporation     In This Issue Top In This Issue    Editorial Top DNA profiling in India   p995 doi:10.1038/nmeth.3653 The Indian parliament will soon discuss a bill regarding forensic DNA profiling, the terms of which will affect a vast population. It should not pass without substantial national debate and a provision for independent oversight. This Month Top The Author File: Uwe Sauer   p997 Vivien Marx doi:10.1038/nmeth.3628 How to make cells spill their metabolic guts in high-throughput, and why work does not feel like work. Points of Significance: Simple linear regression   pp999 - 1000 Naomi Altman and Martin Krzywinski doi:10.1038/nmeth.3627 Correspondence Top BrowserGenome.org: web-based RNA-seq data analysis and visualization   p1001 Jonathan L Schmid-Burgk and Veit Hornung doi:10.1038/nmeth.3615 TransVar: a multilevel variant annotator for precision genomics   pp1002 - 1003 Wanding Zhou, Tenghui Chen, Zechen Chong, Mary A Rohrdanz, James M Melott et al. doi:10.1038/nmeth.3622 Avoiding abundance bias in the functional annotation of posttranslationally modified proteins   pp1003 - 1004 Christian Schölz, David Lyon, Jan C Refsgaard, Lars Juhl Jensen, Chunaram Choudhary et al. doi:10.1038/nmeth.3621 Research Highlights Top The strain in metagenomics Two computational tools extract strain-level information from reams of microbial sequence data. Super-resolution in live cells Two strategies improve structured illumination microscopy for use in live-cell super-resolution imaging. Targeting spines A new probe allows for optical erasure of newly activated dendritic spines. Pressuring neurons into action An alternative to optogenetics, sonogenetics uses ultrasound to mechanically stimulate neurons. Ancient protein complexes revealed A systematic analysis of protein-complex composition across a billion years of evolution reveals a spectrum of conservation. How kinases attack signaling networks Two computational tools find residues that determine the specificity of any kinase and the effects of mutations in these residues on the phenotype of cancer cells. Methods in Brief Single-cell DNA amplification gets even | Improving correlated mutation analysis | Growth signatures in bacterial sequence data | Designing protein-DNA nanowires Tools in Brief The United Kingdom's 10K genome project | Optical clearing with a gentle touch | | Lighting up root architecture Methods JOBS of the week Postdoctoral fellow position in iPSC research Icahn School of Medicine at Mount Sinai Tenure-Track Faculty Positions in Genomic Medicine Institute for Genomic Medicine, Columbia University Bioinformatics Postdoctoral Associate Baylor College of Medicine (BCM) Research Manager Wellcome Trust Sanger Institute Postdoctoral Scientist for Computational Genomics and Epigenomics Helmholtz Association More Science jobs from Methods EVENT International Conference on Structural Engineering, New Technology and Methods (ICSENM'16) 30th Mar - 31st Mar 2016 Prague More science events from Technology Feature Top Nanopores: a sequencer in your backpack   pp1015 - 1018 Vivien Marx doi:10.1038/nmeth.3625 It's been a long wait for nanopore sequencing technology. Over 1,000 labs are testing the first commercial device and publishing results. Researchers tell Nature Methods about their experiences putting these early instruments through their paces. And more technology is in the works. News and Views Top Detecting nano-scale protein clustering   pp1019 - 1020 David Baddeley doi:10.1038/nmeth.3641 Two approaches for robust, objective segmentation of single-molecule localization data promise better quantitative insights into protein clustering from super-resolution imaging methods. See also: Article by Levet et al. | Article by Rubin-Delanchy et al. Review Top Focused ion beams in biology   pp1021 - 1031 Kedar Narayan and Sriram Subramaniam doi:10.1038/nmeth.3623 Applications of focused ion beams for biological ultrastructure and chemical imaging, with a particular emphasis on the coupling of this technology with scanning electron microscopy, are discussed in this Review. Analysis Top Comparing the performance of biomedical clustering methods   pp1033 - 1038 Christian Wiwie, Jan Baumbach and Richard Rottger doi:10.1038/nmeth.3583 This analysis compares 13 clustering methods on 24 data sets using the freely accessible ClustEval platform and presents guidelines for how to choose tools and set parameters for clustering biomedical data Resource Top Whole-brain activity mapping onto a zebrafish brain atlas   pp1039 - 1046 Owen Randlett, Caroline L Wee, Eva A Naumann, Onyeka Nnaemeka, David Schoppik et al. doi:10.1038/nmeth.3581 Z-Brain is an atlas of the larval zebrafish brain. It can be combined with pERK-based neural-activity measurements from freely behaving zebrafish to identify brain regions involved in generating behavior. Brief Communications Top Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale   pp1047 - 1050 Bo Xia, Dali Han, Xingyu Lu, Zhaozhu Sun, Ankun Zhou et al. doi:10.1038/nmeth.3569 Chemical modification of 5fC allows its enrichment and genome-wide profiling at single-nucleotide resolution. Cas9 gRNA engineering for genome editing, activation and repression   pp1051 - 1054 Samira Kiani, Alejandro Chavez, Marcelle Tuttle, Richard N Hall, Raj Chari et al. doi:10.1038/nmeth.3580 The length of a single guide RNA (gRNA) determines the function of Cas9. In this study 20-nt gRNAs allowed nuclease activity and genome editing, whereas 14-nt gRNAs mediated transcriptional activation or repression. Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling   pp1055 - 1057 Kilian V M Huber, Karin M Olek, André C Müller, Chris Soon Heng Tan, Keiryn L Bennett et al. doi:10.1038/nmeth.3590 A method for profiling alterations in protein thermal stability after ligand binding using mass spectrometry identifies the cellular protein targets of drugs and metabolites in living cells. Interactive analysis and assessment of single-cell copy-number variations   pp1058 - 1060 Tyler Garvin, Robert Aboukhalil, Jude Kendall, Timour Baslan, Gurinder S Atwal et al. doi:10.1038/nmeth.3578 Gingko is an open-source, flexible, comprehensive and user-friendly web tool for analysis of single-cell copy-number variations. WASP: allele-specific software for robust molecular quantitative trait locus discovery   pp1061 - 1063 Bryce van de Geijn, Graham McVicker, Yoav Gilad and Jonathan K Pritchard doi:10.1038/nmeth.3582 The WASP suite of open-source tools performs unbiased allele-specific sequence read mapping and provides improved power for molecular QTL discovery. Advertisement Tools for Low-Oxygen Cell Culture: Media Conditioning Systems  Unknown or higher-than-desired dissolved oxygen levels in tissue and cell culture media can negatively impact research reliability and validity.  Learn how HypoxyCOOL™, the media conditioning system from Baker Ruskinn, quickly and precisely deoxygenates media to the level your work requires.   Articles Top SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data   pp1065 - 1071 Florian Levet, Eric Hosy, Adel Kechkar, Corey Butler, Anne Beghin et al. doi:10.1038/nmeth.3579 This paper reports a method, including software, for image segmentation and cluster analysis of localization-based super-resolution data. Bayesian cluster identification in single-molecule localization microscopy data   pp1072 - 1076 Patrick Rubin-Delanchy, Garth L Burn, Juliette Griffié, David J Williamson, Nicholas A Heard et al. doi:10.1038/nmeth.3612 This paper reports a Bayesian approach for the automatic identification of the optimal clustering proposal in the analysis of single-molecule localization-based super-resolution data. Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics   pp1077 - 1084 Mario R Blanco, Joshua S Martin, Matthew L Kahlscheuer, Ramya Krishnan, John Abelson et al. doi:10.1038/nmeth.3602 Single Molecule Cluster Analysis (SiMCAn) is a hierarchical clustering method that enables rapid interpretation of the complex single-molecule dynamic behaviors of cellular machines (such as the spliceosome) from single-molecule fluorescence resonance energy transfer data. DNA sense-and-respond protein modules for mammalian cells   pp1085 - 1090 Shimyn Slomovic and James J Collins doi:10.1038/nmeth.3585 A zinc finger-based modular DNA sequence-recognition system produces a customizable response signal that can induce apoptosis or detect virus-infected cells. Real-time metabolome profiling of the metabolic switch between starvation and growth   pp1091 - 1097 Hannes Link, Tobias Fuhrer, Luca Gerosa, Nicola Zamboni and Uwe Sauer doi:10.1038/nmeth.3584 With a method involving the rapid injection of living cells into a mass spectrometer, researchers demonstrate the ability to monitor metabolite profiles in real time over the course of several hours. Advertisement New NanoDrop One Microvolume Spectrophotometers — Pipette. Measure. Know!   Accurately quantify and qualify DNA, RNA, and protein samples with only 1-2 µL in seconds and avoid costly delays from troubleshooting downstream applications. New Thermo Scientific™ NanoDrop™ One UV-Vis spectrophotometers offer standalone design, identify contaminants, calculate corrected concentrations, and provide guided troubleshooting. Auto-Measure feature streamlines workflows and organizes data.   Watch the new NanoDrop One instrument in action here:  http://www.nanodrop.com/ProductOneOverview.aspx   Corrigenda Top Corrigendum: Reporters for sensitive and quantitative measurement of auxin response   p1098 Che-Yang Liao, Wouter Smet, Geraldine Brunoud, Saiko Yoshida, Teva Vernoux et al. doi:10.1038/nmeth1115-1098a Corrigendum: Bayesian statistics   p1098 Jorge López Puga, Martin Krzywinski and Naomi Altman doi:10.1038/nmeth1115-1098b Corrigendum: Comparative visualization of genotype-phenotype relationships   p1098 Gagarine Yaikhom, Hugh Morgan, Duncan Sneddon, Ahmad Retha, Julian Atienza-Herrero et al. doi:10.1038/nmeth1115-1098c Corrigendum: A holidic medium for Drosophila melanogaster   p1098 Matthew D W Piper, Eric Blanc, Ricardo Leitão-Gonçalves, Mingyao Yang, Xiaoli He et al. doi:10.1038/nmeth1115-1098d Application Notes Top DNA library construction using Gibson Assembly®    Steven Thomas, Nathaniel D Maynard and John Gill Quantitative analysis tools and correlative imaging applications for N-STORM    Lynne Chang NGS library preparation for balanced, comprehensive methylome coverage from low-input quantities    Cassie Schumacher, Laurie Kurihara and Kate Cunningham Automated live cell imaging of cell migration across a microfluidic-controlled chemoattractant gradient    Philip Lee, Cindy S Y Chen, Terry Gaige and Paul J Hung Top Advertisement Nature Protocols is setting the benchmark for publishing high-quality peer-reviewed protocols for biological and biomedical research, containing all the technical info you need to reproduce experiments in your own lab. Visit the Nature Protocols website to access our step-by-step guides to using and adapting research techniques from the world's leading laboratories. www.nature.com/nprot      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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