Nature Methods Contents: October 2014 Volume 11 pp 973 - 1075

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These recombinant proteins are low endotoxin, carrier-free, highly pure, biologically active and suitable for cell culture and animal studies. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement   Starting a CRISPR/CAS9 project on genome editing? Come to OriGene for a wide selection of tools: All-in-one pCAS-Guide vectors gRNA and donor vector cloning services  Genome-wide gene knockout kit Learn about CRISPR technology from a Youtube video Go to http://www.origene.com/CRISPR-CAS9/ to learn more.     Advertisement Download white paper:  Genome Editing: Which Should I Choose, TALEN or CRISPR? TALEN and CRISPR are great tools for gene knockout, knock-in, gene tagging, and correction of genetic defects. We compare the two technologies by analyzing Specificity Target site selection Efficiency Ease of design and construction Download now>>   Advertisement Super Resolution? Simply upgrade! Revealing the most subtle mechanisms at work within cells or tissue has never been easier with FV-OSR, the new Confocal Super Resolution software module for the FluoView FV1200. The simple upgrade transforms the system, delivering simultaneous multicolor capture at a resolution of 120 nm. Enjoy the finer things in life www.Olympus-europa.com/microscopy   In This Issue Top InThisIssue    Focus Top Ten Year Anniversary Special Contents Ten Years of Methods Editorial Commentaries Nature Methods is ten years old. In this anniversary issue, we highlight our choice of the ten areas of methods development with the most impact on biological research over the past decade, and feature commentaries on a subset of these methods. Visit Methagora to browse Nature Methods papers in these areas. Editorial Top Ten Year Anniversary Special Ten years of Methods   p973 doi:10.1038/nmeth.3141 The decade since the launch of Nature Methods has been one of intense and dynamic development in biological research methods. We predict this will continue. This Month Top The Author File: Paola Picotti   p975 Vivien Marx doi:10.1038/nmeth.3116 Cells brim with activity that a special set of protein assays can help track. Points of Significance: Nested designs   pp977 - 978 Martin Krzywinski, Naomi Altman and Paul Blainey doi:10.1038/nmeth.3137 For studies with hierarchical noise sources, use a nested analysis of variance approach. Correspondence Top PSFj: know your fluorescence microscope   pp981 - 982 Patrick Theer, Cyril Mongis and Michael Knop doi:10.1038/nmeth.3102 Neuronal morphometry directly from bitmap images   pp982 - 984 Tiago A Ferreira, Arne V Blackman, Julia Oyrer, Sriram Jayabal, Andrew J Chung et al. doi:10.1038/nmeth.3125 Research Highlights Top A systems view of cellular reprogramming The CellNet platform, based on cell- and tissue-specific gene regulatory networks, is used to evaluate cells converted to a particular fate by various methods. A windowless peek into the brain Imaging in a narrow region of near-infrared wavelengths reveals blood vessels at unprecedented depth and resolution without the need for a cranial window. Transcription factors without footprints A tool to find specific footprint signatures on DNA shows that regulatory proteins with short residency time do not leave footprints. Imaging without labels Researchers report an optical method to detect and image single proteins without using any labels. Painting a picture of protein interaction The binding interface of interacting proteins is revealed by a novel 'protein painting' technique. Deep mutational scans with targeted editing CRISPR-based gene editing can be scaled up to study the function of sequence variation in the context of native chromatin. A stir in the cytoplasm A combination of techniques reveals that aggregate forces from all enzymes active in the cytoplasm result in randomly fluctuating forces throughout the cell. Methods in Brief Low-input ChIP for immunogenomics | Whole organs and animals rendered transparent | Sampling local sequence with proximity ligation | Compressed interaction networks assign gene function Tools in Brief A new fluorophore for super-resolution imaging | Automated analysis of fly feeding | The structural basis of Spinach | Colorful voltage sensors Methods JOBS of the week Bioinformatician / Software Engineer in Computational Systems Biology Icahn School of Medicine at Mount Sinai Bioinformatics Analyst Cancer Research UK Cambridge Institute Assistant / Associate Professor Yale University Postdoctoral Research Associate University of Notre Dame Research Associate (x 4) for RCaH Advanced Impact Positions University College London (UCL) More Science jobs from Methods EVENT Hybrid Methods in Structural Biology 4 April 2015 Tahoe City, USA More science events from Commentaries Top Ten Year Anniversary Special Ten years of Methods   pp1000 - 1001 doi:10.1038/nmeth1014-1000 Our choice, among many candidates, of the ten areas of methods development with the most impact on biological research over the last decade. Visit Methagora to browse Nature Methods papers in some of these areas. Ten Year Anniversary Special A defining decade in DNA sequencing   pp1003 - 1005 John D McPherson doi:10.1038/nmeth.3106 A revolution in DNA sequencing technology has enabled new insights from thousands of genomes sequenced across taxa. Ten Year Anniversary Special The fate of cell reprogramming   pp1006 - 1008 Peter Karagiannis and Shinya Yamanaka doi:10.1038/nmeth.3109 The ability to convert somatic cells to induced pluripotent stem cells has immense potential to further our understanding of development and disease mechanisms, and for cellular therapy. Before researchers can achieve these goals, they must expand current methodology to incorporate animal models and quantitative descriptions of the essential phenomena driving reprogramming. Ten Year Anniversary Special Genome engineering: the next genomic revolution   pp1009 - 1011 Charles A Gersbach doi:10.1038/nmeth.3113 A decade of advances in genome engineering technologies has enabled the editing of genome sequences much like one edits computer code; many more applications for precisely manipulating genome structure and function are on the horizon. Ten Year Anniversary Special Optogenetics: the age of light   pp1012 - 1014 Michael Häusser doi:10.1038/nmeth.3111 The optogenetic revolution is transforming neuroscience. The dramatic recent progress in using light to both control and read out neural activity has highlighted the need for better probes, improved light delivery and more careful interpretation of results, which will all be required for optogenetics to fully realize its remarkable potential. Ten Year Anniversary Special Single-molecule methods leap ahead   pp1015 - 1018 Taekjip Ha doi:10.1038/nmeth.3107 Much of our knowledge about biological systems has been obtained by examining ensembles of molecules. However, this has begun to change because of the unprecedented precision and clarity afforded by single-molecule measurements. The last decade has seen amazing advances in the resolution and complexity of these methods, making it possible to ask and answer entirely new types of biological questions. Technology Feature Top Gene editing: how to stay on-target with CRISPR   pp1021 - 1026 Vivien Marx doi:10.1038/nmeth.3108 Efficiently cutting a target sequence to effect a desired change in the genome is one gene-editing task. Knowing where else in the genome a tool might have made its mark is quite another. News and Views Top Gene targeting with nucleases: capped templates, semper fidelis?   pp1029 - 1030 Andrew Scharenberg doi:10.1038/nmeth.3110 Use of adenoviral vectors to deliver donor templates for genome editing facilitates precise genome modifications in human cells. This has implications for both basic and translational applications of rare-cleaving nuclease technologies. See also: Article by Holkers et al. Brief Communications Top Accurate de novo and transmitted indel detection in exome-capture data using microassembly   pp1033 - 1036 Giuseppe Narzisi, Jason A O'Rawe, Ivan Iossifov, Han Fang, Yoon-ha Lee et al. doi:10.1038/nmeth.3069 Scalpel combines mapping and assembly to find insertions and deletions in exome sequence data. Multiplexed aberration measurement for deep tissue imaging in vivo   pp1037 - 1040 Chen Wang, Rui Liu, Daniel E Milkie, Wenzhi Sun, Zhongchao Tan et al. doi:10.1038/nmeth.3068 An adaptive optics method using multiplexed light measurement and modulation in multiple pupil segments improves structural and functional in vivo imaging over large volumes in strongly scattering mouse brain with only a single aberration correction. Systematic evaluation of quantotypic peptides for targeted analysis of the human kinome   pp1041 - 1044 Jonathan D Worboys, John Sinclair, Yinyin Yuan and Claus Jørgensen doi:10.1038/nmeth.3072 A method for generating a resource of quantotypic peptides for targeted proteomic analysis of human kinases is presented A sentinel protein assay for simultaneously quantifying cellular processes   pp1045 - 1048 Martin Soste, Rita Hrabakova, Stefanie Wanka, Andre Melnik, Paul Boersema et al. doi:10.1038/nmeth.3101 A set of targeted mass spectrometry assays for 'sentinel' proteins allows the activation of 188 yeast biological processes to be simultaneously monitored in 1 hour. Advertisement News Alert: Observe the Difference. Empirical Bioscience provides the purest products, assayed for the right concentrations and components and tested for rogue DNA and nuclease. Their TAQ is manufactured using proprietary technology and rigorous lot controls. Researchers say Empirical reagents yield outstanding results they don't see using other reagents. Click for a FREE SAMPLE.    Articles Top Adenoviral vector DNA for accurate genome editing with engineered nucleases   pp1051 - 1057 Maarten Holkers, Ignazio Maggio, Sara F D Henriques, Josephine M Janssen, Toni Cathomen et al. doi:10.1038/nmeth.3075 The specificity of exogenous sequence insertion into the genome of human cells following designer nuclease-mediated cleavage is substantially affected by the nature of the donor template, the paper reports. See also: News and Views by Scharenberg Evaluation and statistical inference for human connectomes   pp1058 - 1063 Franco Pestilli, Jason D Yeatman, Ariel Rokem, Kendrick N Kay and Brian A Wandell doi:10.1038/nmeth.3098 LiFE is an algorithm that evaluates human connectome models derived from magnetic resonance imaging (MRI) and tractography methods. The algorithm achieves this goal by assessing the contribution of all the fiber tracts in a connectome to predict the measured MRI signal. Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins   pp1064 - 1070 Katharina Kramer, Timo Sachsenberg, Benedikt M Beckmann, Saadia Qamar, Kum-Loong Boon et al. doi:10.1038/nmeth.3092 RNA interaction sites on proteins are detected using UV-based cross-linking, mass spectrometry analysis and a dedicated data analysis workflow. SeqControl: process control for DNA sequencing   pp1071 - 1075 Lauren C Chong, Marco A Albuquerque, Nicholas J Harding, Cristian Caloian, Michelle Chan-Seng-Yue et al. doi:10.1038/nmeth.3094 SeqControl uses 15 quality metrics of high-throughput sequencing experiments to predict how much sequencing is needed to reach a desired depth of coverage. Advertisement Fluorescence is at your fingertips with ZOE™, a benchtop cell imager you control by touch screen. Features brightfield illumination and three fluorescent channels. Step out of the darkroom, see the light!   Top Advertisement nature.com webcasts Macmillan Science Communication presents a custom webcast on: An integrated OMICs approach to cancer progression Thursday October 23, 8am PDT, 11am EDT, 4pm BST, 5pm CEST  Register for the webcast and live Q and A session  Sponsored by: Agilent       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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