Nature Methods Contents: October 2015 Volume 12 pp 895 - 994

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Advertisement ZEISS LSM 8 family with Airyscan - Revolutionize your confocal imaging Learn how to improve signal-to-noise ratio and resolution of your confocal imaging. Discover how Airyscan, the novel detector for the ZEISS LSM 8 family compares to traditional confocal detectors and download our free white paper with more information: www.zeiss.com/airyscan TABLE OF CONTENTS October 2015 Volume 12, Issue 10 In This Issue Editorial This Month Correspondence Research Highlights Commentary Technology Feature News and Views Brief Communications Articles Advertisement Determine the Metabolic Phenotype of Your Cells in One Hour The XFp Cell Energy Phenotype Test Kit from Seahorse Bioscience. Using as few as 15,000 cell and the XFp Analyzer, the XF Cell Energy Phenotype Test identifies your cells' metabolic phenotype as well as their metabolic potential — the relative utilization of mitochondrial respiration and glycolysis.  http://bit.ly/1Caw9Eq Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Download Technical Note:  How to save time and reduce risk for your genome editing work Introducing the IndelCheck™ insertion or deletion detection system   qValidate CRISPR/TALEN efficiency before starting a 3- to 6-month Knockout/Knockin cell line or mouse line work to avoid experimental failure due to low CRISPR/TALEN efficiency qSpeedup your indel detection using a robust integrated system including cell lysis buffer, optimized gDNA PCR mix and primers, and T7 endonuclease I assay reagent. >> Download now   Advertisement Nature Plants: Call for Papers Nature Plants launched in January and covers all aspects of plants be it their evolution, genetics, development or metabolism, their interactions with the environment, or their societal significance. The journal welcomes high quality submissions and encourages you and your colleagues to consider submitting your next research paper to the journal.  Submit your next research paper to the journal.     In This Issue Top In This Issue    Editorial Top Do we need an ethics of self-organizing tissue?   p895 doi:10.1038/nmeth.3618 Some cells have a remarkable capacity to organize into tissue-like structures in vitro. As methods to enable self-organization improve, ethical aspects of some of these experiments will need to be considered. This Month Top The Author File: Zev Gartner   p897 Vivien Marx doi:10.1038/nmeth.3592 Creative chemical techniques to better understand tissue self-organization. Points of Significance: Association, correlation and causation   pp899 - 900 Naomi Altman and Martin Krzywinski doi:10.1038/nmeth.3587 Correspondence Top Widespread nuclease contamination in commonly used oxygen-scavenging systems   pp901 - 902 Gayan Senavirathne, Jiaquan Liu, Miguel A Lopez Jr, Jeungphill Hanne, Juana Martin-Lopez et al. doi:10.1038/nmeth.3588 MetaPhlAn2 for enhanced metagenomic taxonomic profiling   pp902 - 903 Duy Tin Truong, Eric A Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart et al. doi:10.1038/nmeth.3589 Research Highlights Top A digital piece of brain Developments in automated sample preparation, electron microscopy and data analysis enable in-depth characterization of a chunk of mouse neocortex. Cut and paste for RNA structure Proximity ligation allows for the global resolution of RNA secondary structures. A fix for formaldehyde fixation Researchers use chemistry to solve a nagging problem that has challenged the analysis of RNA from formaldehyde-fixed tissue specimens. Keeping track of gut bacteria Fluorescent labeling of bacteria enables tracking of their location. Finding a face in the crowd An analytical algorithm for transcriptomic data reveals rare cell types that were previously hidden in larger populations. Inseparable ribosomes Fusing ribosomal subunits provides answers to basic questions about their function and opens the door to exciting engineering possibilities. Fast track to neurons New protocols generate neurons directly from fibroblasts using only chemical cocktails. Methods in Brief High-throughput discovery of genome organizers | Variation in human repeat sequences | Zapping cells improves genome-editing efficiency | Isotropic super-resolution imaging Tools in Brief Expanding GFP utility beyond imaging | How good are those RNA-seq data? | Ancestral AAVs put to new use | A suite of oligomeric GFP variants Methods JOBS of the week Associate or Full Professor (Bioinformatics) University of Hawaii, John A. Burns School of Medicine Assistant / Associate Professor University of Miami Postdoctoral Scientist John Innes Centre (JIC) Institute Assoc Scientist II The University of Texas MD Anderson Cancer Center Postdoctoral Research Position Harvard Medical School More Science jobs from Methods EVENT International Conference on Structural Engineering, New Technology and Methods (ICSENM'16) 30th Mar - 31st Mar 2016 Prague More science events from Commentary Top What if stem cells turn into embryos in a dish?   pp917 - 919 Martin F Pera, Guido de Wert, Wybo Dondorp, Robin Lovell-Badge, Christine L Mummery et al. doi:10.1038/nmeth.3586 Technology Feature Top Voltage sensors: challenging, but with potential   pp921 - 924 Nina Vogt doi:10.1038/nmeth.3591 Genetically encoded voltage sensors are coming of age, but their use still poses challenges that must be addressed from multiple angles. News and Views Top Diving deeper to predict noncoding sequence function   pp925 - 926 Barbara E Engelhardt and Christopher D Brown doi:10.1038/nmeth.3604 The deep learning-based method DeepSEA predicts the molecular function of noncoding DNA polymorphisms. Brief Communications Top Functional footprinting of regulatory DNA   pp927 - 930 Jeff Vierstra, Andreas Reik, Kai-Hsin Chang, Sandra Stehling-Sun, Yuanyue Zhou et al. doi:10.1038/nmeth.3554 Tiling of regulatory DNA with mutations introduced by genome editing nucleases and linking the resulting alleles to a phenotypic readout allows the precise determination of functional sequence motifs within these regions. Predicting effects of noncoding variants with deep learning-based sequence model   pp931 - 934 Jian Zhou and Olga G Troyanskaya doi:10.1038/nmeth.3547 DeepSEA, a deep-learning algorithm trained on large-scale chromatin-profiling data, predicts chromatin effects from sequence alone, has single-nucleotide sensitivity and can predict effects of noncoding variants. Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy   pp935 - 938 Zhengyang Zhang, Samuel J Kenny, Margaret Hauser, Wan Li and Ke Xu doi:10.1038/nmeth.3528 Spectrally resolved STORM (stochastic optical reconstruction microscopy) uses wide-field spectral measurements of sparsely activated single-molecule emitters to image cells labeled with fluorophores with highly overlapping emission spectra, opening the door to multiplexed super-resolution imaging. Continuous directed evolution of DNA-binding proteins to improve TALEN specificity   pp939 - 942 Basil P Hubbard, Ahmed H Badran, John A Zuris, John P Guilinger, Kevin M Davis et al. doi:10.1038/nmeth.3515 DNA-binding phage-assisted continuous evolution improves the specificity of DNA-binding proteins, as demonstrated with TALENs. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy   pp943 - 946 Benjamin A Barad, Nathaniel Echols, Ray Yu-Ruei Wang, Yifan Cheng, Frank DiMaio et al. doi:10.1038/nmeth.3541 The fit of atomic models of protein structures to high-resolution cryo-electron microscopy maps can be assessed with a validation tool, EMRinger. Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments   pp947 - 950 Ning Leng, Li-Fang Chu, Chris Barry, Yuan Li, Jeea Choi et al. doi:10.1038/nmeth.3549 Oscope enables the detection of oscillating genes and phasing of cell states from snapshot single-cell RNA-seq data. Trajectories of cell-cycle progression from fixed cell populations   pp951 - 954 Gabriele Gut, Michelle D Tadmor, Dana Pe'er, Lucas Pelkmans and Prisca Liberali doi:10.1038/nmeth.3545 Cycler constructs a trajectory of cell-cycle progression from fixed images of cells enabling the correlation of an individual cell's position in the cell cycle with multiple cellular readouts. Inntags: small self-structured epitopes for innocuous protein tagging   pp955 - 958 Maya V Georgieva, Galal Yahya, Laia Codó, Raúl Ortiz, Laura Teixidó et al. doi:10.1038/nmeth.3556 A set of small, innocuous protein tags, named inntags, show advantages over commonly used epitope tags in a variety of biological applications. A microfluidic device for epigenomic profiling using 100 cells   pp959 - 962 Zhenning Cao, Changya Chen, Bing He, Kai Tan and Chang Lu doi:10.1038/nmeth.3488 ChIP-seq performed in a microfluidic device on chromatin isolated from as few as 100 cells allows the profiling of epigenetic histone marks. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors   pp963 - 965 Christian Schmidl, André F Rendeiro, Nathan C Sheffield and Christoph Bock doi:10.1038/nmeth.3542 ChIPmentation combines chromatin immunoprecipitation with on-bead tagmentation for rapid and highly robust ChIP-seq library preparation. SpeedSeq: ultra-fast personal genome analysis and interpretation   pp966 - 968 Colby Chiang, Ryan M Layer, Gregory G Faust, Michael R Lindberg, David B Rose et al. doi:10.1038/nmeth.3505 SpeedSeq is an open-source software suite offering very fast, accurate and comprehensive analysis of single-nucleotide and structural variants from whole genome sequencing data. Advertisement Next Generation NanoDrop Spectrophotometers Coming Soon! Take a peek at the new Thermo Scientific™ NanoDrop™ Microvolume UV-Vis spectrophotometers launching in October when you visit our web site. Find out how you can ensure success in downstream applications with new instrument features that will illuminate your research and make you smile. Visit www.thermoscientific.com/nanodrop   Articles Top Wirelessly powered, fully internal optogenetics for brain, spinal and peripheral circuits in mice   pp969 - 974 Kate L Montgomery, Alexander J Yeh, John S Ho, Vivien Tsao, Shrivats Mohan Iyer et al. doi:10.1038/nmeth.3536 Small, lightweight LED implants and a radio-frequency transducer as a power source enable wireless optogenetic stimulation in the brain, spinal cord and peripheral nervous system of behaving mice. Programmed synthesis of three-dimensional tissues   pp975 - 981 Michael E Todhunter, Noel Y Jee, Alex J Hughes, Maxwell C Coyle, Alec Cerchiari et al. doi:10.1038/nmeth.3553 DNA-programmed assembly of cells (DPAC) allows the reconstitution of organoid-like structures with controlled size, shape, cell-type composition and spatial heterogeneity. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo   pp982 - 988 Miguel A Moreno-Mateos, Charles E Vejnar, Jean-Denis Beaudoin, Juan P Fernandez, Emily K Mis et al. doi:10.1038/nmeth.3543 An sgRNA-scoring algorithm (CRISPRscan) based on molecular features that enhance activity allows users to predict the most efficient sgRNA for in vivo targets. High-throughput cellular RNA device engineering   pp989 - 994 Brent Townshend, Andrew B Kennedy, Joy S Xiang and Christina D Smolke doi:10.1038/nmeth.3486 Screening for tertiary-interaction responsiveness in large RNA ribozyme-aptamer libraries to ligands identifies RNA devices with improved activation ratios and ligand sensitivities. Advertisement Droplet Digital™ PCR (ddPCR™) is leading the way More than 250 peer-reviewed publications have taken advantage of Droplet Digital PCR's unmatched ability to detect rare nucleic acid species. From tracking cancer biomarkers to quantifying rare mutations, gene editing events, and miniscule viral loads, Droplet Digital PCR has led to more discoveries than any other digital PCR platform. Visit our ddPCR page for application guides, publication lists, and webinars that explore the world of ddPCR. Learn more   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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