Nature Methods Contents: June 2015 Volume 12 pp 473 - 585

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UVP LLC (800) 452-6788 Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Optimize your PCR reactions in a single run  Eppendorf Mastercycler® nexus X2 dual block thermal cyclers provide the flexibility to run two independent protocols at the same time. Small assays fit on the 32-well-block with larger assays on the 64-well-block. The larger block is available with gradient function.  Learn more   Advertisement A new open access, online-only journal dedicated to publishing the highest quality research into ways to help the human body repair, replace, restore and regenerate damaged tissues and organs. Published by Nature Publishing Group in partnership with the Australian Regenerative Medicine Institute (ARMI) at Monash University. Find out more   In This Issue Top In This Issue    Editorial Top Windows into the ivory tower   p473 doi:10.1038/nmeth.3436 This Month Top The Author File: Stefan Florian   p475 Vivien Marx doi:10.1038/nmeth.3413 Tracking cell cycles in vivo, and the temptation of science fiction. Points of Significance: Sampling distributions and the bootstrap   pp477 - 478 Anthony Kulesa, Martin Krzywinski, Paul Blainey and Naomi Altman doi:10.1038/nmeth.3414 Correspondence Top Off-target mutations are rare in Cas9-modified mice   p479 Vivek Iyer, Bin Shen, Wensheng Zhang, Alex Hodgkins, Thomas Keane et al. doi:10.1038/nmeth.3408 ClearVolume: open-source live 3D visualization for light-sheet microscopy   pp480 - 481 Loic A Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug et al. doi:10.1038/nmeth.3372 BigDataViewer: visualization and processing for large image data sets   pp481 - 483 Tobias Pietzsch, Stephan Saalfeld, Stephan Preibisch and Pavel Tomancak doi:10.1038/nmeth.3392 MAGI: visualization and collaborative annotation of genomic aberrations   pp483 - 484 Mark D M Leiserson, Connor C Gramazio, Jason Hu, Hsin-Ta Wu, David H Laidlaw et al. doi:10.1038/nmeth.3412 Research Highlights Top Synapses seen at different scales Synapse morphology and molecular composition can be analyzed in detail with conjugate light-electron array tomography, which combines immunofluorescence imaging with electron microscopy in a precisely aligned fashion. A small molecule improves Cas9 specificity Making Cas9 nuclease activity dependent on the self-cleavage of a ligand-responsive intein decreases Cas9's off-target activity. Highly multiplexed transcriptome imaging A single-molecule imaging approach allows for error-robust transcriptomic analyses in single cells. Splice and sequence A ligation-based sequencing method reveals distant exon connections within long RNA molecules. Tinkering with chromatin Protein trans-splicing is used to study chromatin signaling in the cell nucleus. From form to function DNA building blocks that interact on the basis of shape rather than sequence assemble into highly dynamic and complex structures. Solving XFEL's image problem Improved XFEL crystallography data processing methods enable structure determination from limited samples. Methods in Brief Epigenome editing | Chemical modification of native proteins | Transcripts in space | Engineering the mosquito genome Tools in Brief A red calcium indicator dye for dual-color imaging | Enter the diatom | Bright cyan and orange probes for bioluminescence imaging | Pre- and postsynaptic activity reporters Methods JOBS of the week Research Fellow Mayo Medical School - Mayo Clinic Postdoctoral Research Associate Texas A&M University Research Fellow University of Michigan, Department of Otolaryngology-Head and Neck Surgery Postdoctoral Position: Fluorescence Assays & Physical Chemistry Stanford University Research Assistant Professor, Faculty Position University of Massachusetts 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 Reproducibility: changing the policies and culture of cell line authentication   pp493 - 497 Leonard P Freedman, Mark C Gibson, Stephen P Ethier, Howard R Soule, Richard M Neve et al. doi:10.1038/nmeth.3403 Quality control of cell lines used in biomedical research is essential to ensure reproducibility. Although cell line authentication has been widely recommended for many years, misidentification, including cross-contamination, remains a serious problem. We outline a multi-stakeholder, incremental approach and policy-related recommendations to facilitate change in the culture of cell line authentication. Technology Feature Top Visualizing epigenomic data   pp499 - 502 Vivien Marx doi:10.1038/nmeth.3409 Review Top Correlated light and electron microscopy: ultrastructure lights up!   pp503 - 513 Pascal de Boer, Jacob P Hoogenboom and Ben N G Giepmans doi:10.1038/nmeth.3400 Correlated light and electron microscopy (CLEM) gives context to biomolecules studied with fluorescence microscopy. This Review discusses recent improvements and guides readers on probes, instrumentation and sample preparation to implement CLEM. Brief Communications Top A fast- and positively photoswitchable fluorescent protein for ultralow-laser-power RESOLFT nanoscopy   pp515 - 518 Dhermendra K Tiwari, Yoshiyuki Arai, Masahito Yamanaka, Tomoki Matsuda, Masakazu Agetsuma et al. doi:10.1038/nmeth.3362 Kohinoor is a fast- and positively switching fluorescent protein with high photostability over many photoswitching cycles. Its improved photophysical properties enable nanoscopy with low phototoxicity and allow use of a simplified RESOLFT setup. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes   pp519 - 522 Iain C Macaulay, Wilfried Haerty, Parveen Kumar, Yang I Li, Tim Xiaoming Hu et al. doi:10.1038/nmeth.3370 G&T-seq offers robust full-length transcript and whole-genome sequencing simultaneously from a single cell. MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis   pp523 - 526 Hiroshi Tsugawa, Tomas Cajka, Tobias Kind, Yan Ma, Brendan Higgins et al. doi:10.1038/nmeth.3393 A software tool, MS-DIAL, enables the identification of metabolomes by data independent acquisition-based mass spectrometry. CONSERTING: integrating copy-number analysis with structural-variation detection   pp527 - 530 Xiang Chen, Pankaj Gupta, Jianmin Wang, Joy Nakitandwe, Kathryn Roberts et al. doi:10.1038/nmeth.3394 CONSERTING detects somatic copy-number alterations from whole-genome sequence data with high accuracy and sensitivity and identifies breakpoints even in heterogeneous or impure tumors. MIMP: predicting the impact of mutations on kinase-substrate phosphorylation   pp531 - 533 Omar Wagih, Jüri Reimand and Gary D Bader doi:10.1038/nmeth.3396 This machine learning method predicts whether single-nucleotide variants disrupt or create phosphorylation sites. Advertisement Deciding the best containment technology to keep both you and your research protected can be difficult.  Make it easy by downloading the biological safety cabinet decision map. Results include: Class II (Type A1, A2, B1, B2), Class III, Clean Bench, Fume Hood, and Animal Transfer Stations.   Articles Top Rapid reverse genetic screening using CRISPR in zebrafish   pp535 - 540 Arish N Shah, Crystal F Davey, Alex C Whitebirch, Adam C Miller and Cecilia B Moens doi:10.1038/nmeth.3360 Targeting 48 loci in a pooled CRISPR-Cas9 screen reveals new genes essential for electrical-synapse formation. High-resolution whole-brain staining for electron microscopic circuit reconstruction   pp541 - 546 Shawn Mikula and Winfried Denk doi:10.1038/nmeth.3361 An improved method for preparing mouse brains for electron microscopy allows reliable tracing of neurites and identification of synapses and appears suitable for whole-brain connectomic reconstruction. Multispectral labeling technique to map many neighboring axonal projections in the same tissue   pp547 - 552 Shlomo Tsuriel, Sagi Gudes, Ryan W Draft, Alexander M Binshtok and Jeff W Lichtman doi:10.1038/nmeth.3367 The topography of axonal projections can be deciphered by retrograde labeling with multiple overlapping dye injections, as the dye composition in retrogradely transported vesicles is indicative of axonal projection sites. Rapid, optimized interactomic screening   pp553 - 560 Zhanna Hakhverdyan, Michal Domanski, Loren E Hough, Asha A Oroskar, Anil R Oroskar et al. doi:10.1038/nmeth.3395 Extraction conditions can have a substantial effect on protein complexes isolated from within cells. A platform for rapid, systematic screening of these conditions is described, which should enable the identification of biologically relevant complexes. Isotope-targeted glycoproteomics (IsoTaG): a mass-independent platform for intact N- and O-glycopeptide discovery and analysis   pp561 - 567 Christina M Woo, Anthony T Iavarone, David R Spiciarich, Krishnan K Palaniappan and Carolyn R Bertozzi doi:10.1038/nmeth.3366 Metabolically labeling proteins with glycans that enable attachment of an isotopically encoded tag allows for the identification of N- and O- glycopeptides and their glycan structures. High-performance probes for light and electron microscopy   pp568 - 576 Sarada Viswanathan, Megan E Williams, Erik B Bloss, Timothy J Stasevich, Colenso M Speer et al. doi:10.1038/nmeth.3365 'Spaghetti monster' fluorescent proteins combine the power of conventional fluorescent proteins with the benefits of commonly used epitopes. These probes are demonstrated to be extremely versatile in diverse imaging applications. In vivo cell-cycle profiling in xenograft tumors by quantitative intravital microscopy   pp577 - 585 Deepak R Chittajallu, Stefan Florian, Rainer H Kohler, Yoshiko Iwamoto, James D Orth et al. doi:10.1038/nmeth.3363 Methods for quantitative, automated in vivo cell-cycle profiling are applied to tumor xenografts in the mouse to study the effects of drug treatment. Application Note Top Rapid screening for protein solubility and expression    Mark Maffitt, Michele Auldridge, Saurabh Sen, Sally Floyd, Amanda Krerowicz et al. Top Advertisement Nature Genetics in association with the Wellcome Trust present: The Genomics of Common Diseases 2015 September 2-5, 2015 | Cambridge, UK Register now!   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. 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