Nature Methods Contents: July 2015 Volume 12 pp 587 - 692

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Laser damage thresholds >0.15 J/cm2 using a 355nm laser (10 ns pulse, 10 Hz), and suffer no degradation after 2 hours @ 300ºC. www.chroma.com Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement $99/CRISPR sgRNA Clone  With purchase of IndelCheck™ insertion or deletion detection system - designed to detect CRISPR- or TALEN-mediated insertions/deletions (indels) in your genome edited cells. The IndelCheck™ system let you quickly identify CRISPR sgRNAs with the highest activity before undertaking your screening work to isolate correctly edited cell clones or animals The IndelCheck™ system can also be used to identify clones carrying indel mutations Learn more >>    Advertisement Nature has once again been ranked as the No.1 interdisciplinary science journal with an impact factor score of 41.456*. Stay up to date with the very latest news and research in your field and subscribe for one year at our special offer price of $41, £41 or €41!   Advertisement Nature Collection: Cancer immunotherapy Cancer immunotherapy is a rapidly advancing field with relevance for an expanding list of tumour types. In this collection, Nature presents seven recent articles on cancer immunotherapy.  Access the Collection free online for six months.  Produced with support from:  Genentech, A Member of the Roche Group     In This Issue Top In This Issue    Editorial Top Summer reading: popular science and 'lab lit'   p587 doi:10.1038/nmeth.3474 An idiosyncratic selection of science-themed books for the summer. This Month Top The Author File: Stefan Kappe   p589 Vivien Marx doi:10.1038/nmeth.3445 A way to generate recombinant progeny of Plasmodium falciparum for genetics experiments, and the virtues of scuba diving. Points of View: Unentangling complex plots   p591 Gregor McInerny and Martin Krzywinski doi:10.1038/nmeth.3451 Carefully designed subplots scaled to the data are often superior to a single complex overview plot. Correspondence Top iSMS: single-molecule FRET microscopy software   pp593 - 594 Søren Preus, Sofie L Noer, Lasse L Hildebrandt, Daniel Gudnason and Victoria Birkedal doi:10.1038/nmeth.3435 InferenceMAP: mapping of single-molecule dynamics with Bayesian inference   pp594 - 595 Mohamed El Beheiry, Maxime Dahan and Jean-Baptiste Masson doi:10.1038/nmeth.3441 Chemically defined, albumin-free human cardiomyocyte generation   pp595 - 596 Xiaojun Lian, Xiaoping Bao, Misha Zilberter, Mattias Westman, André Fisahn et al. doi:10.1038/nmeth.3448 Research Highlights Top Catching Pol II in the act Two methods capture the pausing behavior of RNA polymerase II as it generates messages from mammalian genomes. A machine to manage modifications An automated platform mass-produces RNAs incorporating a wide variety of precisely positioned chemical alterations. Cryo-EM goes high-resolution The highest-resolution structure solved by cryo-electron microscopy to date reveals what it takes to reach the resolution realm of X-ray crystallography. Reproducibly generating organ buds in vitro Coculture of three cell types on hydrogel with the appropriate stiffness enables the generation of functional organ buds. Chemogenetic manipulation of neurons The family of designer receptors now includes an orthogonally activated member for multiplexed chemogenetic control of neural activity. Methods in Brief Inhibition with BOLT | Chromatin accessibility in single cells | RNA structure by solid-state NMR | A high-throughput platform for studying chemotaxis Tools in Brief Optogenetic access to opioid signaling | Sub-primed pluripotent stem cells | Efficient transduction of proteins into eukaryotic cells | Neurons on the blink Methods JOBS of the week Postdoctoral researcher: Simulations of the properties and morphology of polymers KU Leuven Scientia Fellows – 2nd Call: Marie Curie Postdoctoral Fellowships in Health Sciences University of Oslo Two PhD positions – Systems Biology / Bioinformatics / Computational Biology University of Regina PhD position Pathways of nanoparticle uptake and trafficking by cells (1.0 fte) Rijksuniversiteit Groningen Postdoctoral Training Fellowship in Cancer Genomics The Francis Crick Institute More Science jobs from Methods EVENT SMODIA "Statistical Methods for Omics Data Integration and Analysis 2015" 14th Sept - 16th Sept 2015 Valencia, Spain More science events from Commentary Top Mass spectrometrists should search only for peptides they care about   pp605 - 608 William Stafford Noble doi:10.1038/nmeth.3450 A Commentary proposes that in order to improve statistical power in mass spectrometry-based proteomics data analysis, irrelevant peptides should be removed from the database prior to searching. Technology Feature Top Metabolism: feeding fruit flies   pp609 - 612 Vivien Marx doi:10.1038/nmeth.3443 Measuring how much a fruit fly eats opens the door to studies of metabolism and aging. But the assays are hotly debated. News and Views Top Co-opting CRISPR to deliver functional RNAs   pp613 - 614 Pei-Chun Lin and Jacob E Corn doi:10.1038/nmeth.3452 Portions of the CRISPR-Cas9 guide RNA can be reworked to carry functional RNA cargos to genomic loci. See also: Article by Shechner et al. Perspective Top Pathway and network analysis of cancer genomes   pp615 - 621 Pau Creixell, Jüri Reimand, Syed Haider, Guanming Wu, Tatsuhiro Shibata, Miguel Vazquez, Ville Mustonen, Abel Gonzalez-Perez, John Pearson, Chris Sander, Benjamin J Raphael, Debora S Marks, B F Francis Ouellette, Alfonso Valencia, Gary D Bader, Paul C Boutros, Joshua M Stuart, Rune Linding, Nuria Lopez-Bigas and Lincoln D Stein for the Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium doi:10.1038/nmeth.3440 International Cancer Genome Consortium members review and recommend approaches to pathway and network analysis to uncover molecular processes that contribute to tumor biology. Analysis Top Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection OPEN   pp623 - 630 Adam D Ewing, Kathleen E Houlahan, Yin Hu, Kyle Ellrott, Cristian Caloian et al. doi:10.1038/nmeth.3407 The first report of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge introduces the BAMSurgeon tool for accurate tumor simulation and reports the performance of 248 submissions in calling single-nucleotide variants from three pairs of synthetic tumor-normal genome benchmarks. Brief Communications Top Plasmodium falciparum genetic crosses in a humanized mouse model   pp631 - 633 Ashley M Vaughan, Richard S Pinapati, Ian H Cheeseman, Nelly Camargo, Matthew Fishbaugher et al. doi:10.1038/nmeth.3432 A human-liver chimeric mouse supports the growth of recombinant Plasmodium falciparum progeny, enabling easy analysis of genetic crosses between parasite strains. Structural analysis of multicellular organisms with cryo-electron tomography   pp634 - 636 Jan Harapin, Mandy Börmel, K Tanuj Sapra, Damian Brunner, Andres Kaech et al. doi:10.1038/nmeth.3401 Tissues from multicellular organisms can be imaged by cryo-electron tomography using an optimized combination of vitrification, milling and application of fiducial markers. Functional differentiation of human pluripotent stem cells on a chip   pp637 - 640 Giovanni G Giobbe, Federica Michielin, Camilla Luni, Stefano Giulitti, Sebastian Martewicz et al. doi:10.1038/nmeth.3411 This paper shows that microfluidic perfusion frequency can be optimized to improve the differentiation of human pluripotent stem cells along different lineages, and uses this principle to achieve functional hPSC differentiation directly on a chip. 3D high- and super-resolution imaging using single-objective SPIM   pp641 - 644 Remi Galland, Gianluca Grenci, Ajay Aravind, Virgile Viasnoff, Vincent Studer et al. doi:10.1038/nmeth.3402 Light-sheet microscopy using a single objective and micromirrors to orient the light sheet enables high- and super-resolution imaging of cells and embryos on a standard microscope. In vivo single-cell labeling by confined primed conversion   pp645 - 648 William P Dempsey, Lada Georgieva, Patrick M Helbling, Ali Y Sonay, Thai V Truong et al. doi:10.1038/nmeth.3405 Primed conversion of proteins such as Dendra2 confines photoconversion to a limited 3Dvolume through a sequential absorption process relying on illumination with two separate low-intensity lasers and enables precise targeting of single cells. Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR   pp649 - 652 Mohammed Kaplan, Abhishek Cukkemane, Gydo C P van Zundert, Siddarth Narasimhan, Mark Daniëls et al. doi:10.1038/nmeth.3406 Dynamic nuclear polarization-based solid-state nuclear magnetic resonance spectroscopyis applied to study the structure of a large bacterial membrane protein complex in its cellular environment. Traction microscopy to identify force modulation in subresolution adhesions   pp653 - 656 Sangyoon J Han, Youbean Oak, Alex Groisman and Gaudenz Danuser doi:10.1038/nmeth.3430 An analytical method, with accompanying software, is described for improved fidelity in traction force microscopy and is used to measure forces at emerging focal adhesions at high resolution. Dexterous robotic manipulation of alert adult Drosophila for high-content experimentation   pp657 - 660 Joan Savall, Eric Tatt Wei Ho, Cheng Huang, Jessica R Maxey and Mark J Schnitzer doi:10.1038/nmeth.3410 A robotic system is described that uses machine vision guidance to pick, manipulate, inspect and dissect individual flies, enabling large-scale and automated approaches to the analysis of morphology, behavior and neural dynamics. Application of BRET to monitor ligand binding to GPCRs   pp661 - 663 Leigh A Stoddart, Elizabeth K M Johnstone, Amanda J Wheal, Joëlle Goulding, Matthew B Robers et al. doi:10.1038/nmeth.3398 Bioluminescence resonance energy transfer, from the substrate of a luciferase fused with a G protein-coupled receptor to a fluorescent dye covalently linked to a receptor ligand, allows the profiling of ligand affinity and binding kinetics. Articles Top Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display   pp664 - 670 David M Shechner, Ezgi Hacisuleyman, Scott T Younger and John L Rinn doi:10.1038/nmeth.3433 CRISPR-Display is a modular and flexible platform that targets natural or synthetic noncoding RNA domains to specific genomic loci for functional studies and synthetic biology. See also: News and Views by Lin & Corn Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture   pp671 - 678 Anca M Paşca, Steven A Sloan, Laura E Clarke, Yuan Tian, Christopher D Makinson et al. doi:10.1038/nmeth.3415 A method for 3D differentiation of human pluripotent stem cells yields brain cortical spheroids with functional neurons and astrocytes. The spheroids can be sliced for imaging and electrophysiological studies. Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement   pp679 - 684 Wojciech Potrzebowski and Ingemar André doi:10.1038/nmeth.3399 A computational approach[mdash]including a cross-validation metric[mdash]for automated model building and refinement using X-ray fiber diffraction data is described and applied to solve structures of protein fibers. A microfluidic device for label-free, physical capture of circulating tumor cell clusters   pp685 - 691 A Fatih Sarioglu, Nicola Aceto, Nikola Kojic, Maria C Donaldson, Mahnaz Zeinali et al. doi:10.1038/nmeth.3404 The Cluster-Chip provides highly efficient and gentle capture of circulating tumor cell clusters from milliliters of unprocessed whole blood, making it possible to study how these clusters contribute to metastasis. Advertisement Automated Cell Sorting - Now Available at a Bench near You Take control of the how, when, and where of cell sorting with the S3e™, a benchtop instrument that makes cell sorting accessible to all. Automated setup and real-time sort monitoring eliminate the need for flow cytometry expertise, while a small footprint ensures that the S3e fits in almost any lab. Learn more.   Corrigenda Top Corrigendum: Fast native-SAD phasing for routine macromolecular structure determination   p692 Tobias Weinert, Vincent Olieric, Sandro Waltersperger, Ezequiel Panepucci, Lirong Chen et al. doi:10.1038/nmeth0715-692a Corrigendum: Simultaneous all-optical manipulation and recording of neural circuit activity with cellular resolution in vivo   p692 Adam M Packer, Lloyd E Russell, Henry W P Dalgleish and Michael Häusser doi:10.1038/nmeth0715-692b Corrigendum: Fixation-resistant photoactivatable fluorescent proteins for CLEM   p692 Maria G Paez-Segala, Mei G Sun, Gleb Shtengel, Sarada Viswanathan, Michelle A Baird et al. doi:10.1038/nmeth0715-692c Corrigendum: Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers   p692 Johan Hattne, Nathaniel Echols, Rosalie Tran, Jan Kern, Richard J Gildea et al. doi:10.1038/nmeth0715-692d Top 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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