Nature Methods Contents: August 2013 Volume 10 pp 683 - 803

Advertisement What will you create today?  Plasmid-Safe™ ATP-Dependent DNase T7 R&DNA Polymerase RiboShredder™ RNase FAST-Link™ DNA Ligase Baseline-ZERO™ DNase CircLigase™ ssDNA Ligase APex Heat-Labile Alkaline Phosphatase Tobacco Acid Pyrophosphatase EpiScript™ Reverse Transcriptase T4 Beta-glucosyltransferase and more... Learn more: http://www.epibio.com/enzymes   TABLE OF CONTENTS August 2013 Volume 10, Issue 8 In This Issue Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Commentaries Perspective Resource Brief Communications Articles Advertisement   See what nature is hiding BD Horizon™ Brilliant Violet™ polymer conjugates are brighter than traditional dyes and can help identify cell populations with lower receptor density than previously possible. Learn how to resolve rare and dim cell populations with our expanded set of tools and information and request a free sample at bdbiosciences.com/go/brilliant. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement nature.com webcasts Macmillan Science Communication presents a custom webcast on:  Accelerating the discovery and development of monoclonal antibodies Wednesday July 31st 2013 7am PDT / 10am EDT / 3pm BST / 4pm CEST  Register for the free webcast followed by our live Q & A session  Sponsored by:     In This Issue Top InThisIssue    Editorial Top Heritable genetic changes in the open   p683 doi:10.1038/nmeth.2597 To correctly interpret human genetic variation in hereditary disorders, researchers and clinicians should populate databases that distribute aggregated information on the clinical significance of these variants. This Month Top The author file: Anne-Claude Gingras   p685 Vivien Marx doi:10.1038/nmeth.2569 Proteins are sociable and interact with other proteins. A new web resource helps to score experimental data about these relations. Points of view: Storytelling   p687 Martin Krzywinski and Alberto Cairo doi:10.1038/nmeth.2571 Relate your data to the world around them using the age-old custom of telling a story. Correspondence Top ViSP: representing single-particle localizations in three dimensions   pp689 - 690 Mohamed El Beheiry and Maxime Dahan doi:10.1038/nmeth.2566 mentha: a resource for browsing integrated protein-interaction networks   pp690 - 691 Alberto Calderone, Luisa Castagnoli and Gianni Cesareni doi:10.1038/nmeth.2561 Convergence of chromatin binding estimates in live cells   pp691 - 692 Davide Mazza, Florian Mueller, Timothy J Stasevich and James G McNally doi:10.1038/nmeth.2573 See also: Correspondence by Zhao et al. Reply to "Convergence of chromatin binding estimates in live cells"   p692 Ziqing W Zhao, J Christof M Gebhardt, David M Suter and X Sunney Xie doi:10.1038/nmeth.2574 See also: Correspondence by Mazza et al. Research Highlights Top Fishing for fluorescent proteins The first fluorescent protein cloned from a vertebrate species is a promising tool for clinical diagnostics and research. The pull of a cell Researchers leash cells to molecular tethers as an easy way to measure single-molecular binding forces. Protein GPS Antibody-like probes report the localization and amount of endogenous proteins in living cells. Engineering to find function Protein engineering and small-molecule probe design allows the study of individual members of large protease families. Missing the target? Targeted nucleases based on the CRISPR/Cas9 system can in some cases cleave at imperfectly matched 'off-target' sites. Methods JOBS of the week Principal Investigator Positions in Cancer Biology and Immunology Vaccine & Gene Institute of Florida (VGTI Florida) Postdoctoral position in bioinformatics Chalmers University of Technology Lead Scientist Packaging Safety Nestlé Research Center (NRC) Junior Bioinformatician Harvard School of Public Health Postdoctoral Scientists in Biomolecular Chemistry & Engineering CEA (French Atomic and Alternative Energies Commission) More Science jobs from Methods EVENT X-Ray Methods in Structural Biology 14th - 29th Oct 2013 Cold Spring Harbor, USA More science events from Methods in Brief Top Following cell-type-specific gene expression | Dealing with dipoles | Mining for lateral gene transfer | Rapid reaction inspection Tools in Brief Top Analysis of complex traits in rats | An optogenetic toolbox for yeast | An excision-only transposase | Tools for salamander research Technology Feature Top Finding the right antibody for the job   pp703 - 707 Vivien Marx doi:10.1038/nmeth.2570 As new research applications for antibody-based assays emerge, the quest for quality intensifies in a crowded marketplace. News and Views Top Parallel super-resolution imaging   pp709 - 710 Christopher J Rowlands, Elijah Y S Yew and Peter T C So doi:10.1038/nmeth.2567 Massive parallelization of scanning-based super-resolution imaging allows fast imaging of large fields of view. See also: Brief Communication by Chmyrov et al. Enhanced dissection of the regulatory genome   pp710 - 712 Matthew Slattery and Kevin P White doi:10.1038/nmeth.2577 Methods for high-throughput and high-resolution dissection of enhancers in Drosophila are described by two independent groups. See also: Article by Gisselbrecht et al. | Article by Crocker & Stern Commentaries Top Scientific priorities for the BRAIN Initiative   pp713 - 714 Aravi Samuel, Herbert Levine and Krastan B Blagoev doi:10.1038/nmeth.2565 The transience of transient overexpression   pp715 - 721 Toby J Gibson, Markus Seiler and Reiner A Veitia doi:10.1038/nmeth.2534 Perspective Top Computational approaches to identify functional genetic variants in cancer genomes   pp723 - 729 Abel Gonzalez-Perez, Ville Mustonen, Boris Reva, Graham R S Ritchie, Pau Creixell, Rachel Karchin, Miguel Vazquez, J Lynn Fink, Karin S Kassahn, John V Pearson, Gary D Bader, Paul C Boutros, Lakshmi Muthuswamy, B F Francis Ouellette, Jüri Reimand, Rune Linding, Tatsuhiro Shibata, Alfonso Valencia, Adam Butler, Serge Dronov, Paul Flicek, Nick B Shannon, Hannah Carter, Li Ding, Chris Sander, Josh M Stuart, Lincoln D Stein and Nuria Lopez-Bigas for the International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group: doi:10.1038/nmeth.2562 International Cancer Genome Consortium members review and recommend computational approaches for identifying mutations that drive cancer progression from among the many sequence variants present in tumor genomes. Resource Top The CRAPome: a contaminant repository for affinity purification-mass spectrometry data   pp730 - 736 Dattatreya Mellacheruvu, Zachary Wright, Amber L Couzens, Jean-Philippe Lambert, Nicole A St-Denis et al. doi:10.1038/nmeth.2557 The Contaminant Repository for Affinity Purification (CRAPome) is a database of annotated negative control-data that can be used for filtering out nonspecific interactions in affinity purification-mass spectrometry experiments. Brief Communications Top Nanoscopy with more than 100,000 'doughnuts'   pp737 - 740 Andriy Chmyrov, Jan Keller, Tim Grotjohann, Michael Ratz, Elisa d'Este et al. doi:10.1038/nmeth.2556 Two incoherently superimposed orthogonal standing waves are used to create a pattern of 116,000 'doughnuts' for fast, highly parallelized coordinate-targeted super-resolution microscopy of living cells, with a large field of view. See also: News and Views by Rowlands et al. Heritable genome editing in C. elegans via a CRISPR-Cas9 system   pp741 - 743 Ari E Friedland, Yonatan B Tzur, Kevin M Esvelt, Monica P Colaiácovo, George M Church et al. doi:10.1038/nmeth.2532 RNA polymerase III-driven single guide RNA and a germ line promoter-driven expression of Cas9 enzyme allow heritable, targeted genome modifications in Caenorhabditis elegans. Multiplexed MS/MS for improved data-independent acquisition   pp744 - 746 Jarrett D Egertson, Andreas Kuehn, Gennifer E Merrihew, Nicholas W Bateman, Brendan X MacLean et al. doi:10.1038/nmeth.2528 A multiplexing strategy for data-independent acquisition (DIA)-based mass spectrometry addresses the limitation of low precursor selectivity to make DIA more practical for peptide analysis. Genome-wide profiling of human cap-independent translation-enhancing elements   pp747 - 750 Brian P Wellensiek, Andrew C Larsen, Bret Stephens, Kim Kukurba, Karl Waern et al. doi:10.1038/nmeth.2522 A method to identify genomic elements that promote cap-independent translation is described and is used to identify such elements in the human genome. Near-infrared fluorescent proteins for multicolor in vivo imaging   pp751 - 754 Daria M Shcherbakova and Vladislav V Verkhusha doi:10.1038/nmeth.2521 Four spectrally distinct near-infrared fluorescent proteins based on bacterial phytochromes are described, expanding the possibilities for multicolor in vivo imaging experiments in nontransparent organisms. LipidBlast in silico tandem mass spectrometry database for lipid identification   pp755 - 758 Tobias Kind, Kwang-Hyeon Liu, Do Yup Lee, Brian DeFelice, John K Meissen et al. doi:10.1038/nmeth.2551 Lipid Blast is an in silico-generated tandem mass spectral library covering more than 119,000 lipid compounds from 26 different classes, providing a useful tool for lipid identification in metabolomics studies. Engineered nanostructured β-sheet peptides protect membrane proteins   pp759 - 761 Houchao Tao, Sung Chang Lee, Arne Moeller, Rituparna Sinha Roy, Fai Yiu Siu et al. doi:10.1038/nmeth.2533 Designed β-strand peptides stabilize integral membrane proteins for biochemical and structural studies, enabling electron microscopy analysis of the dynamic conformations of the ABC transporter MsbA. Advertisement Move your research forward with sensitive, robust Takara® brand qPCR reagents. Kits for real-time RT-PCR (one-step and two-step) and premixes for SYBR® Green or TaqMan probe detection provide reproducibility, instrument compatibility, and high sensitivity. Reliable reagents for your research at a great value - That's Good Science!™ Learn More...   Articles Top TALE-mediated modulation of transcriptional enhancers in vivo   pp762 - 767 Justin Crocker and David L Stern doi:10.1038/nmeth.2543 Transcription activator-like effectors are used for in vivo activation and repression of endogenous promoters and enhancers in the fruit fly. See also: News and Views by Slattery & White Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments   pp768 - 773 Nicholas P Gauthier, Boumediene Soufi, William E Walkowicz, Virginia A Pedicord, Konstantinos J Mavrakis et al. doi:10.1038/nmeth.2529 A cellular engineering approach coupled with mass spectrometry allows the cell-of-origin of intra- and extracellular proteins to be determined from co-cultured cells. Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos   pp774 - 780 Stephen S Gisselbrecht, Luis A Barrera, Martin Porsch, Anton Aboukhalil, Preston W Estep III et al. doi:10.1038/nmeth.2558 Identifying tissue-specific expression of a selection marker and putative enhancer-driven expression of GFP with flow cytometry enriches for active enhancers. See also: News and Views by Slattery & White Biowire: a platform for maturation of human pluripotent stem cell-derived cardiomyocytes   pp781 - 787 Sara S Nunes, Jason W Miklas, Jie Liu, Roozbeh Aschar-Sobbi, Yun Xiao et al. doi:10.1038/nmeth.2524 The combination of controlled three-dimensional assembly and electrical stimulation allows the maturation of stem cell-derived cardiomyocytes. Tightly anchored tissue-mimetic matrices as instructive stem cell microenvironments   pp788 - 794 Marina C Prewitz, F Philipp Seib, Malte von Bonin, Jens Friedrichs, Aline Stißel et al. doi:10.1038/nmeth.2523 A method to tightly attach cell-derived extracellular matrix (ECM) to the culture surface is described. It is applied to generate bone marrow mesenchymal stem cell-derived ECM, which supports culture of human hematopoietic stem and progenitor cells. Hematopoietic progenitor cell lines with myeloid and lymphoid potential   pp795 - 803 Vanessa Redecke, Ruiqiong Wu, Jingran Zhou, David Finkelstein, Vandana Chaturvedi et al. doi:10.1038/nmeth.2510 A simple method to immortalize largely unfractionated mouse bone marrow cells to generate hematopoietic progenitor cell lines is described. Top Advertisement Naturejobs presents the: Naturejobs Career Expo September 19, 2013 The Business Design Centre, London, UK  Click here for more information or to register for this conference today!   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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