Nature Methods Contents: December 2013 Volume 10 pp 1135 - 1253

Advertisement Eppendorf Tubes® 5.0 mL - Discover a new sample handling system! Easy and safe processing of samples up to 5 mL:  www.eppendorf.com/5mL-system TABLE OF CONTENTS December 2013 Volume 10, Issue 12 In This Issue Editorial This Month Research Highlights Technology Feature News and Views Perspective Analysis Brief Communications Articles Advertisement Refer to SIRION Biotech for viral vectors and cell models or cell-based assays, both custom made or ready to go. Delivered within a matter of weeks from our new core facility. Contact us in New Hampshire, Munich or Tokyo. Sign up for a free online lecture series on viral vectors, power tools of cell based research. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Reichert Surface Plasmon Resonance (SPR) systems for biomolecular interaction analysis Monitor real-time binding, obtain detailed information for protein interactions with other molecules: kinetics, affinity, thermodynamics and concentration. Set up a successful experiment with Reichert support, Read about strategies to immobilize a ligand on a sensor chip in our NEW blog ReichertSPR.com   Advertisement Frontiers are launching a new collaborative peer review forum We are excited to announce that we will be launching a new collaborative peer-review forum where referees and authors work together to improve the paper until consensus is met. Our new peer-review forum will provide online-tools and increased efficiency to ensure a transparent and fast review process. Follow us for more information! We'll be posting updates about the launch on Twitter and Facebook   In This Issue Top InThisIssue    Editorial Top Artifacts of light   p1135 doi:10.1038/nmeth.2760 The dangers of phototoxicity in fluorescence microscopy experiments are too often ignored. This Month Top The author file: Paul Bertone   p1137 Vivien Marx doi:10.1038/nmeth.2747 Software can be like music, but an evaluation of software tools can involve some hard-to-play chords. Points of significance: Power and sample size   pp1139 - 1140 Martin Krzywinski and Naomi Altman doi:10.1038/nmeth.2738 The ability to detect experimental effects is undermined in studies that lack power. Research Highlights Top Seeing heterochromatin in early embryos GFP targeted to satellite repeats via transcription activator-like effectors (TALEs) allows the imaging of nuclear dynamics early in mouse development. Naive human pluripotent stem cells Researchers define conditions in which human stem cells can be maintained in the ground state of pluripotency. End-to-end RNA sequencing Long-read sequencing uncovers transcript features missed by short-read methods. Lighting the cellular fuel gauge A genetically encoded sensor of ATP:ADP ratio reveals the energy status of living mammalian cells. Fluorescence microscopy gets a frequency boost An imaging strategy based on telecommunications technology dramatically accelerates fluorescence microscopy. ChIP goes dynamic Chromatin interaction dynamics are quantified using a modified ChIP method that measures cross-linking kinetics. Here comes the neighborhood Laser-guided assembly of protein microscaffolds lets researchers construct multispecies cellular communities. Teaching bacteria a new language Bacteria's ability to withstand broad genomic editing offers a potential route toward more robust and useful genetically modified organisms. Methods in Brief A proteome in an hour | Cell type—specific ChIP | Hydrogel photopatterning | Cellular hierarchies by single-cell RT-qPCR Tools in Brief A growing toolbox to study the epigenome | Light-guiding hydrogels | Gene expression UPCs | Towards stem cell—derived human blood Methods JOBS of the week Postdoc position in top-down proteomics UVic-Genome BC Proteomics Centre PhD student position Goethe University Frankfurt a.M Postdoctoral Fellow Icahn School of Medicine at Mount Sinai Postdoctoral position in Bioinformatics (Dr. Zoghbi Lab) Baylor College of Medicine (BCM) Biostatistical / Computational Postdoctoral Fellow Brigham & Women's Hospital - Harvard Medical School More Science jobs from Methods EVENT Modern Synthetic Methods in Organofluorine Chemistry 6th March 2014 London, UK More science events from Technology Feature Top Is super-resolution microscopy right for you?   pp1157 - 1163 Vivien Marx doi:10.1038/nmeth.2756 Imaging with better than 200-nanometer resolution brings new subcellular-scale details into focus. Practitioners share how they weigh trade-offs in speed, resolution and phototoxicity. News and Views Top Genomics: the state of the art in RNA-seq analysis   pp1165 - 1166 Ian Korf doi:10.1038/nmeth.2735 RNA-seq is a recent and immensely popular technology for cataloging and comparing gene expression. Two papers from the international RGASP consortium report on large-scale competitions to identify the best algorithms for RNA-seq analysis, with surprising variability in the results. See also: Analysis by Steijger et al. | Analysis by Engstrom et al. Perspective Top Using networks to measure similarity between genes: association index selection   pp1169 - 1176 Juan I Fuxman Bass, Alos Diallo, Justin Nelson, Juan M Soto, Chad L Myers et al. doi:10.1038/nmeth.2728 This Perspective describes statistical measures commonly used to quantify whether nodes in biological networks have similar interaction profiles and discusses which indices are best suited for specific tasks. Analysis Top Assessment of transcript reconstruction methods for RNA-seq OPEN   pp1177 - 1184 Tamara Steijger, Josep F Abril, Pär G Engström, Felix Kokocinski, The RGASP Consortium et al. doi:10.1038/nmeth.2714 The RGASP consortium compared 25 RNA-seq analysis programs in their ability to identify exons, reconstruct transcripts and quantify expression levels. Assembly of isoforms and their expression levels in higher eukaryotes remains a challenge. See also: News and Views by Korf Systematic evaluation of spliced alignment programs for RNA-seq data OPEN   pp1185 - 1191 Pär G Engström, Tamara Steijger, Botond Sipos, Gregory R Grant, André Kahles et al. doi:10.1038/nmeth.2722 Authors compare RNA-seq aligners on mouse and human data sets using benchmarks such as alignment yield, splice junction accuracy and suitability for transcript reconstruction. The work highlights the strength of each program and discusses outstanding needs in RNA-seq analysis. See also: News and Views by Korf Brief Communications Top Accelerated discovery via a whole-cell model   pp1192 - 1195 Jayodita C Sanghvi, Sergi Regot, Silvia Carrasco, Jonathan R Karr, Miriam V Gutschow et al. doi:10.1038/nmeth.2724 Discrepancies between model prediction and experimental measurements enable molecular-level discovery with a whole-cell model of Mycoplasma genitalium. Metagenomic species profiling using universal phylogenetic marker genes   pp1196 - 1199 Shinichi Sunagawa, Daniel R Mende, Georg Zeller, Fernando Izquierdo-Carrasco, Simon A Berger et al. doi:10.1038/nmeth.2693 A method and software for profiling microbial communities from shotgun sequence data uses universal single-copy marker sequences for accurate species-level assignment. The method can classify species lacking a reference genome sequence, making it possible to analyze the large fraction of unknown microbes in the human gut. Differential abundance analysis for microbial marker-gene surveys   pp1200 - 1202 Joseph N Paulson, O Colin Stine, Héctor Corrada Bravo and Mihai Pop doi:10.1038/nmeth.2658 The metagenomeSeq tool robustly detects the differential abundance of microbes in marker-based microbial surveys by tackling the problems of data sparsity and undersampling common to these data sets. Formation of targeted monovalent quantum dots by steric exclusion   pp1203 - 1205 Justin Farlow, Daeha Seo, Kyle E Broaders, Marcus J Taylor, Zev J Gartner et al. doi:10.1038/nmeth.2682 A simple method for preparing entirely monovalent quantum dots is described. These reagents can be targeted to protein and lipid tags and used as imaging probes in live cells. Detergent-free mass spectrometry of membrane protein complexes   pp1206 - 1208 Jonathan T S Hopper, Yvonne Ting-Chun Yu, Dianfan Li, Alison Raymond, Mark Bostock et al. doi:10.1038/nmeth.2691 Amphipols, bicelles and nanodiscs are used to study intact membrane protein complexes by mass spectrometry, with better preservation of oligomeric complexes than traditional detergent micelles. DGIdb: mining the druggable genome   pp1209 - 1210 Malachi Griffith, Obi L Griffith, Adam C Coffman, James V Weible, Josh F McMichael et al. doi:10.1038/nmeth.2689 A database of known drug-gene interactions, with information derived from many public sources, allows the identification of genes that are currently targeted by a drug and the membership of genes in a category, such as kinase genes, that have a high potential for drug development. pLogo: a probabilistic approach to visualizing sequence motifs   pp1211 - 1212 Joseph P O'Shea, Michael F Chou, Saad A Quader, James K Ryan, George M Church et al. doi:10.1038/nmeth.2646 pLogo visualizes sequence motifs according to their statistical significance rather than their frequency. Advertisement Save 30%: Enhanced BD Horizon™ Brilliant Violet™ Reagents Innovative new formulations of BD Horizon™ Brilliant Violet™ polymer conjugates are now available. Brighter than traditional dyes, these reagents can help you to resolve rare and dim cell populations, revealing nature's secrets with unprecedented clarity. Request a free sample or take 30% off purchases.  bdbiosciences.com/go/brilliant   Articles Top Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position   pp1213 - 1218 Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang and William J Greenleaf doi:10.1038/nmeth.2688 ATAC-seq queries the location of open chromatin, the binding of DNA-associated proteins and chromatin compaction at nucleotide resolution. A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA   pp1219 - 1224 Rita L Strack, Matthew D Disney and Samie R Jaffrey doi:10.1038/nmeth.2701 The Spinach2 RNA aptamer provides substantially improved imaging over its predecessor Spinach, enabling live-cell imaging of many tagged RNA species including toxic trinucleotide repeat-containing RNAs. High-throughput fingerprinting of human pluripotent stem cell fate responses and lineage bias   pp1225 - 1231 Emanuel J P Nazareth, Joel E E Ostblom, Petra B Lücker, Shreya Shukla, Manuel M Alvarez et al. doi:10.1038/nmeth.2684 This paper describes a platform for high-throughput image-based profiling of human pluripotent stem cells (hPSCs). It is used to quantify differentiation bias and endogenous signaling levels in hPSC lines. Genetically encoded fluorescent thermosensors visualize subcellular thermoregulation in living cells   pp1232 - 1238 Shigeki Kiyonaka, Taketoshi Kajimoto, Reiko Sakaguchi, Daisuke Shinmi, Mariko Omatsu-Kanbe et al. doi:10.1038/nmeth.2690 Genetically encoded sensors based on GFP enable the visualization of subcellular thermal changes noninvasively in intact cells. Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition   pp1239 - 1245 Jean-Philippe Lambert, Gordana Ivosev, Amber L Couzens, Brett Larsen, Mikko Taipale et al. doi:10.1038/nmeth.2702 Changes to protein interactomes as a result of mutations to the bait protein or addition of a pharmacological inhibitor are robustly monitored with affinity purification coupled with data-independent acquisition-based mass spectrometry and an automated data analysis pipeline. Also in this issue, Collins et al. describe a similar method. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system   pp1246 - 1253 Ben C Collins, Ludovic C Gillet, George Rosenberger, Hannes L Röst, Anton Vichalkovski et al. doi:10.1038/nmeth.2703 Dynamic changes to the 14-3-3 protein interactome are robustly followed over time using affinity-purification data-independent analysis-based mass spectrometry. Also in this issue, Lambert et al. describe a similar method. Advertisement Introducing the S3™ Cell Sorter from Bio-Rad. This state-of-the-art benchtop solution features automated setup and costs up to 50% less than traditional systems. Watch the Video   Top Advertisement nature.com webcasts Macmillan Science Communication presents a custom webcast on: Highly-multiplexed Tissue Biomarker Analysis: A Practical Approach for Developmental Biology, Neuroscience and Oncology Thursday December 12th at 10am PST / 1pm EST / 6pm GMT / 7pm CET  Register for the free webcast followed by our live Q & A session  Sponsored by:     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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