Nature Methods Contents: June 2016 Volume 13 pp 459 - 535

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TABLE OF CONTENTS June 2016 Volume 13, Issue 6 In This Issue Editorial This Month Research Highlights Technology Feature News and Views Brief Communications Articles Corrigendum Advertisement   Workflows in today's laboratories are becoming more condensed and the strain of laboratory work is constantly increasing. Thus, the ergonomics of laboratory devices as well as the work environment become more important. The Eppendorf product portfolio offers innovative solutions to lighten the daily work in the lab. Get more information at www.eppendorf.com/physiocare Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Fluorescence-Based Cell Biology Assays  Cell Proliferation & Viability Assays — iClick™ EdU assays, AlamarBlue cell viability assays, LIVE-or-DIE™ cell viability/cytotoxicity assays, cell generation analysis, and more Cell Apoptosis Assays — TUNEL assays, caspase activity assays, annexin V binding assays, mitochondrial membrane potential assays, and more Cell Structure Probes — Cytoskeleton, nucleus, golgi complex, membrane, cytosol, mitochondria, lysosome, endoplasmic Learn more >>   Advertisement Discovery and technology for human health  Now open for submissions Straddling the life sciences, the physical sciences and engineering, Nature Biomedical Engineering will publish — weekly and online-only — biological, medical and engineering advances that can directly inspire or lead to improvements in human health or healthcare.    Advertisement Immune Profiling in Health and Disease Presented by: Adaptive Biotechnologies | Nature Immunology | Nature Medicine | Nature Biotechnology | Nature Genetics October 3-5, 2016 | Bell Harbor International Conference Center, Seattle, WA, USA Register now!   In This Issue Top In This Issue    Editorial Top Mark the methods in human embryo research   p459 doi:10.1038/nmeth.3896 Research on human embryos depends on precious samples that are inherently variable. Rigorous methods reporting should be the goal of published papers in the field. This Month Top The Author File: Richard D. Cummings   p461 Vivien Marx doi:10.1038/nmeth.3874 A bleaching method for glycobiology and some impromptu fund-raising at the piano. Points of View: Binning high-resolution data   p463 Martin Krzywinski doi:10.1038/nmeth.3873 Limitations in print resolution and visual acuity impose limits on data density and detail. Research Highlights Top RNA structure from sequence An approach taken from protein structure prediction makes it possible to computationally identify secondary and tertiary contacts in RNA. PCR for cellular forces A 'mechanically induced catalytic amplification reaction' reads out receptor-mediated forces in cells. Of TRIBE and RNA tagging Genetic approaches profile RNA-protein interactions. Sensing calcium in red Red-shifted calcium sensors are advantageous for deep-tissue imaging, dual-color applications and combining with optogenetic tools. Retraining an editor as a mapmaker A sequence-specific labeling system based on CRISPR/Cas9 enables simultaneous imaging of multiple chromosomal sites in live cells. Tunable light-sheet microscopy Tiling light-sheet microscopy improves live cell imaging of multicellular organisms. Methods in Brief Improved RNA interactomes | Nanopores for multiplexed protein sensing | Variants that change transcription factor binding | Open-source software for structured illumination Tools in Brief Tracking β-galactosidase activity in vivo | Mapping nanopore sequence reads | Optimized tracing of neural circuits | Fast RNA-seq quantification Methods JOBS of the week Postdoctoral positions in stem cell biology and regenerative medicine University of Southern California Post-Doctoral Fellow University of Oklahoma Health Sciences Center Postdoctoral Research Associate Benaroya Research Institute at Virginia Mason (BRI) Postdoctoral Fellow Biomedical Institute for Global Healthcare Research & Technology (BIGHEART) More Science jobs from Methods EVENT Computational Methods in Systems Biology (CMSB 2016) 21st Sept - 23rd Sept 2016 Cambridge, UK More science events from Technology Feature Top PCR: the price of infidelity   pp475 - 479 Vivien Marx doi:10.1038/nmeth.3868 Infidelity is painful in life and in the lab. The former is better left to other publications; the latter is best not ignored, especially in the context of PCR-based DNA amplification. News and Views Top Expansion microscopy passes its first test   pp481 - 482 Hylkje Geertsema and Helge Ewers doi:10.1038/nmeth.3872 Simplification of expansion microscopy makes it broadly accessible and compatible with other approaches. See also: Brief Communication by Chozinski et al. Redesigning CLIP for efficiency, accuracy and speed   pp482 - 483 Georges Martin and Mihaela Zavolan doi:10.1038/nmeth.3870 Two new approaches for target profiling of RNA-binding proteins require less cell material, avoid radioactive reagents and give more accurate data in a shorter time compared to previous methods. See also: Brief Communication by Zarnegar et al. | Article by Van Nostrand et al. Brief Communications Top Expansion microscopy with conventional antibodies and fluorescent proteins   pp485 - 488 Tyler J Chozinski, Aaron R Halpern, Haruhisa Okawa, Hyeon-Jin Kim, Grant J Tremel et al. doi:10.1038/nmeth.3833 Improved sample preparation methods allow super-resolution imaging by expansion microscopy using endogenous fluorescent protein signal and conventional fluorescently labeled antibodies. See also: News and Views by Geertsema & Ewers irCLIP platform for efficient characterization of protein-RNA interactions   pp489 - 492 Brian J Zarnegar, Ryan A Flynn, Ying Shen, Brian T Do, Howard Y Chang et al. doi:10.1038/nmeth.3840 The use of a biotinylated adaptor conjugated to an infrared dye allows rapid, sensitive, and quantitative analysis of protein-RNA interactions. See also: News and Views by Martin & Zavolan Automated mapping of phenotype space with single-cell data   pp493 - 496 Nikolay Samusik, Zinaida Good, Matthew H Spitzer, Kara L Davis and Garry P Nolan doi:10.1038/nmeth.3863 X-shift software allows automated mapping of phenotypic space from large mass cytometry data sets. X-shift and the new representation algorithm Divisive Marker Tree provide a rapid, deterministic approach to navigating complex cellular systems. An unbiased metric of antiproliferative drug effect in vitro   pp497 - 500 Leonard A Harris, Peter L Frick, Shawn P Garbett, Keisha N Hardeman, B Bishal Paudel et al. doi:10.1038/nmeth.3852 Conventional metrics for assessing antiproliferative drug effect have time-dependent biases that may skew results. The drug-induced proliferation rate can be used as an alternative metric for accurate and reproducible assessment of drug performance. siFLIM: single-image frequency-domain FLIM provides fast and photon-efficient lifetime data   pp501 - 504 Marcel Raspe, Katarzyna M Kedziora, Bram van den Broek, Qiaole Zhao, Sander de Jong et al. doi:10.1038/nmeth.3836 Single-image fluorescence lifetime imaging microscopy (siFLIM) uses a modulated-FLIM camera to record lifetimes in a single snapshot, allowing for photon-efficient and quantitative lifetime imaging of rapid cellular processes. Monovar: single-nucleotide variant detection in single cells   pp505 - 507 Hamim Zafar, Yong Wang, Luay Nakhleh, Nicholas Navin and Ken Chen doi:10.1038/nmeth.3835 Monovar efficiently detects single-nucleotide variants in single-cell DNA sequence data with high sensitivity and specificity. Advertisement nature.com webcasts Nature Publishing Group presents a custom webcast on: The promise of integrated cancer genomic analysis to precision cancer care Date: Thursday June 9, 2016 Time: 8AM PDT, 11AM EDT, 4PM BST, 5PM CEST Register for the webcast and live Q&A session Sponsored by: Agilent Technologies     Articles Top Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)   pp508 - 514 Eric L Van Nostrand, Gabriel A Pratt, Alexander A Shishkin, Chelsea Gelboin-Burkhart, Mark Y Fang et al. doi:10.1038/nmeth.3810 Enhanced CLIP yields complex libraries of RNA components of ribonucleoprotein complexes and maintains single-nucleotide resolution of binding sites. eCLIP enables large scale profiling, as demonstrated with the binding profiles of 73 RBPs in two human cancer cell lines. See also: News and Views by Martin & Zavolan Automated structure modeling of large protein assemblies using crosslinks as distance restraints   pp515 - 520 Mathias Ferber, Jan Kosinski, Alessandro Ori, Umar J Rashid, María Moreno-Morcillo et al. doi:10.1038/nmeth.3838 A method and accompanying software tool enables automated modeling of large macromolecular complexes using experimental crosslinking mass spectrometry data as distance restraints, as demonstrated for the 17-subunit yeast RNA polymerase III complex. Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs   pp521 - 527 Marc Hafner, Mario Niepel, Mirra Chung and Peter K Sorger doi:10.1038/nmeth.3853 Growth inhibition metrics allow for robust measurement of drug efficacy independent of variables such as cell growth rate, seeding density, and growth medium; they are a practical alternative to metrics such as IC50 and offer enhanced reproducibility. Oxidative release of natural glycans for functional glycomics   pp528 - 534 Xuezheng Song, Hong Ju, Yi Lasanajak, Matthew R Kudelka, David F Smith et al. doi:10.1038/nmeth.3861 Treating glycoproteins with household bleach releases N- and O-glycans for further structural probing. Bleach treatment of glycosphingolipids releases glycan nitriles. Advertisement Japan is among the top producers of high quality research in the world, but new analysis using the Nature Index reveals this position is being challenged. See the efforts being made to reverse this decline and how international collaborations are playing a role in the strategies of Japan's institutions.     Corrigendum Top Corrigendum: Analyzing outliers: influential or nuisance?   p535 Naomi Altman and Martin Krzywinski doi:10.1038/nmeth0616-535 Top Advertisement MEDTECH DEALMAKERS  A supplement to Nature Biotechnology | Nature Medicine | Nature Reviews Drug Discovery This first-of-its-kind partnering journal is a must read for all medical technology professionals. The latest issue showcases innovative companies seeking partners, and in-depth analysis of dealmaking strategies and trends of the growing med tech industry. Download the issue for FREE   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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