Nature Methods Contents: June 2014 Volume 11 pp 593 - 694

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Advertisement Deplete rRNA from microbial samples for RNA-Seq Ribo-Zero™ depletes rRNA from bacterial, yeast, and epidemiologic samples. Ribo-Zero (Yeast) is compatible with S. cereviseae and S. pombe, with in silico homology with other yeast species including C. albicans. Ribo-Zero bacteria and epidemiology kits deplete complex bacterial and environmental samples. Use the Ribo-Zero selection guide to find the best match to your research needs. TABLE OF CONTENTS June 2014 Volume 11, Issue 6 In This Issue Editorial This Month Correspondence Research Highlights Technology Feature News and Views Brief Communications Articles Advertisement   Powerful reasons to choose Reichert Surface Plasmon Resonance (SPR) systems for your lab SPR technology at a fraction of the cost of the leading competitor. Less expensive without compromising on performance. Low maintenance costs and no service contract necessary. Our SPR team delivers outstanding technical support. Compare for yourself.  ReichertSPR.com/advantage Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Are you ready for more reliable and consistent flow cytometry results? Bio-Rad's new VivaFix Cell Viability Assays offer improved live/dead cell discrimination.Click here to learn more!   In This Issue Top InThisIssue    Editorial Top A bittersweet celebration of crystallography   p593 doi:10.1038/nmeth.2995 The Protein Structure Initiative will end next year; the aftershocks of this ending should be minimized for the benefit of the broader biology research community. This Month Top The author file: Dmitriy Chudakov   p595 Vivien Marx doi:10.1038/nmeth.2975 He switched from designing fluorescent proteins to investigating immunology. Points of significance: Designing comparative experiments   pp597 - 598 Martin Krzywinski and Naomi Altman doi:10.1038/nmeth.2974 Good experimental designs limit the impact of variability and reduce sample-size requirements. Correspondence Top TCGA-Assembler: open-source software for retrieving and processing TCGA data   pp599 - 600 Yitan Zhu, Peng Qiu and Yuan Ji doi:10.1038/nmeth.2956 Multicolor two-photon light-sheet microscopy   pp600 - 601 Pierre Mahou, Julien Vermot, Emmanuel Beaurepaire and Willy Supatto doi:10.1038/nmeth.2963 A simple image correction method for high-throughput microscopy   p602 Adam D Coster, Chonlarat Wichaidit, Satwik Rajaram, Steven J Altschuler and Lani F Wu doi:10.1038/nmeth.2971 KinomeXplorer: an integrated platform for kinome biology studies   pp603 - 604 Heiko Horn, Erwin M Schoof, Jinho Kim, Xavier Robin, Martin L Miller et al. doi:10.1038/nmeth.2968 Research Highlights Top Where protein and RNAs meet Researchers co-opt a DNA sequencer to quantify RNA-protein interactions on a massive scale. Magnificent myelin Spectral confocal reflectance microscopy helps visualize myelinated axons in vivo without any labeling. Predicting enhancers by their sequence Dinucleotide repeat motifs and transcription factor-binding sites are sufficient to define enhancers. A better way to turn off neurons Engineering of channelrhodopsin into a Cl- channel creates a powerful tool for light-mediated inhibition of neurons. Stepping toward sequencing single proteins An electronic, molecular fingerprinting method may lead to an approach to single-molecule protein sequencing. An alternative to induced pluripotency? Two groups report the derivation of human pluripotent stem cell lines from embryos derived by somatic cell nuclear transfer using adult cells as donors. Proteome labels à la carte A method enables labeling and detection of newly synthesized proteins in an animal in a tissue- and time-specific manner. Methods in Brief Making yeast | Phasing at any level of relatedness | Cellular imaging of single-splice variants | Profiling tumors with sugar Tools in Brief Gene correction with CRISPR in adult mice | A large-scale approach to correlate neurons and behavior | Machining better cantilevers | Chemical tools for yeast Methods JOBS of the week Senior Research Technician Memorial Sloan Kettering Cancer Center (MSKCC) Fellow in Global Health Australian National University Postdoctoral Position University Basel Universität Basel Post-Doctoral Fellow - Community Health & Sustainability University of Massachusetts More Science jobs from Methods EVENT X-Ray Methods in Structural Biology 13th October 2014 Cold Spring Harbor, USA More science events from Technology Feature Top Models: stretching the skills of cell lines and mice   pp617 - 620 Vivien Marx doi:10.1038/nmeth.2966 Cell lines are better. Mice are better. Beyond disagreement about model systems and even passionate discord at times, new strategies help to explore the middle ground so models might better approximate human biology. News and Views Top Of (stressed) mice and men   pp623 - 624 Melissa Bateson doi:10.1038/nmeth.2965 Experimenter gender affects behavioral assays of pain and stress in laboratory mice. See also: Brief Communication by Sorge et al. Brief Communications Top Rapid adaptive optical recovery of optimal resolution over large volumes   pp625 - 628 Kai Wang, Daniel E Milkie, Ankur Saxena, Peter Engerer, Thomas Misgeld et al. doi:10.1038/nmeth.2925 Adaptive optics microscopy using a de-scanned, laser-induced guide star and direct wavefront sensing allows high numerical aperture diffraction-limited imaging of fine dynamic structures deep in the intact living zebrafish brain. Olfactory exposure to males, including men, causes stress and related analgesia in rodents   pp629 - 632 Robert E Sorge, Loren J Martin, Kelsey A Isbester, Susana G Sotocinal, Sarah Rosen et al. doi:10.1038/nmeth.2935 The presence of male experimenters induces stress and stress-induced analgesia, affecting behavioral assays in mice. See also: News and Views by Bateson Reversible protein inactivation by optogenetic trapping in cells   pp633 - 636 Sangkyu Lee, Hyerim Park, Taeyoon Kyung, Na Yeon Kim, Sungsoo Kim et al. doi:10.1038/nmeth.2940 Light-activated reversible inhibition by assembled trap (LARIAT) is a versatile optogenetic method for inactivating proteins, including GFP fusions, in living cells by conditional clustering at high spatiotemporal resolution. Validation of noise models for single-cell transcriptomics   pp637 - 640 Dominic Grün, Lennart Kester and Alexander van Oudenaarden doi:10.1038/nmeth.2930 Noise models based on the identification of major sources of technical variability in single-cell RNA-seq data allow the inference of true biological variability in cellular expression. An infrared reporter to detect spatiotemporal dynamics of protein-protein interactions   pp641 - 644 Emmanuelle Tchekanda, Durga Sivanesan and Stephen W Michnick doi:10.1038/nmeth.2934 A reversible fluorescent protein complementation assay is reported for the study of protein interaction dynamics within living cells. Efficient Bayesian-based multiview deconvolution   pp645 - 648 Stephan Preibisch, Fernando Amat, Evangelia Stamataki, Mihail Sarov, Robert H Singer et al. doi:10.1038/nmeth.2929 A graphical processing unit implementation of an efficient Bayesian-based multiview deconvolution method brings the resolution and contrast advantages of multiview deconvolution to more users of light-sheet fluorescence microscopy. Controlling protein adsorption on graphene for cryo-EM using low-energy hydrogen plasmas   pp649 - 652 Christopher J Russo and Lori A Passmore doi:10.1038/nmeth.2931 Graphene is in many ways an ideal sample support for cryo-electron microscopy, but its hydrophobicity prevents adsorption of protein from aqueous solution. Low-energy hydrogen-plasma treatment renders graphene hydrophilic and enables controlled adsorption of protein to its surface. Towards error-free profiling of immune repertoires   pp653 - 655 Mikhail Shugay, Olga V Britanova, Ekaterina M Merzlyak, Maria A Turchaninova, Ilgar Z Mamedov et al. doi:10.1038/nmeth.2960 A two-step error correction process for high throughput–sequenced T- and B-cell receptors allows the elimination of most errors while not diminishing the natural complexity of the repertoires. Advertisement Save on best-in-class personal flow cytometry  With a combined value package, you can save 10% on the BD Accuri™ C6 personal flow cytometer and 40% on high quality BD Pharmingen™ reagents for 2 full years. There's never been a better time to buy and get the best-in-class power, flexibility, and insight personal flow cytometry can offer. Flow cytometry within reach. bdbiosciences.com/go/accuri   Articles Top Interactive assembly algorithms for molecular cloning   pp657 - 662 Evan Appleton, Jenhan Tao, Traci Haddock and Douglas Densmore doi:10.1038/nmeth.2939 Raven calculates assembly plans for complex genetic constructs from thousands of parts. It integrates user feedback on failed intermediate assemblies to improve the final outcome. Bone marrow–on–a–chip replicates hematopoietic niche physiology in vitro   pp663 - 669 Yu-suke Torisawa, Catherine S Spina, Tadanori Mammoto, Akiko Mammoto, James C Weaver et al. doi:10.1038/nmeth.2938 Bone marrow formed in a cylindrical PDMS device implanted in a mouse can be surgically removed and cultured for a week in vitro without losing any of the hallmarks of in vivo bone marrow niches. Chronic, wireless recordings of large-scale brain activity in freely moving rhesus monkeys   pp670 - 676 David A Schwarz, Mikhail A Lebedev, Timothy L Hanson, Dragan F Dimitrov, Gary Lehew et al. doi:10.1038/nmeth.2936 Movable volumetric three-dimensional multielectrode implants coupled to a modular headcap with wireless capabilities allow simultaneous recording of nearly 500 cortical neurons in freely behaving rhesus monkeys. Single-molecule analysis of cell surface dynamics in Caenorhabditis elegans embryos   pp677 - 682 François B Robin, William M McFadden, Baixue Yao and Edwin M Munro doi:10.1038/nmeth.2928 Experimental and analytical methods are described for in vivo single-molecule imaging of GFP-tagged proteins at the cell surface and are applied to the developing C. elegans embryo. Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling   pp683 - 688 Jacob M Tome, Abdullah Ozer, John M Pagano, Dan Gheba, Gary P Schroth et al. doi:10.1038/nmeth.2970 The high-throughput sequencing-RNA affinity profiling (HiTS-RAP) assay enables large-scale profiling of protein interactions with RNA libraries using a simple protocol on a high-throughput sequencer. Multiscale representation of genomic signals   pp689 - 694 Theo A Knijnenburg, Stephen A Ramsey, Benjamin P Berman, Kathleen A Kennedy, Arian F A Smit et al. doi:10.1038/nmeth.2924 This framework for multiscale signal representation allows global analysis of genomic data at different length scales from base pairs to entire chromosomes and reveals the interplay of information encoded at different scales, such as the regulation of gene expression by methylation patterns that go beyond the single-gene scale. 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