Nature Methods Contents: October 2013 Volume 10 pp 917 - 1035

Advertisement Visit us at Neuroscience, booth #1813 and learn how ZEISS continues to break barriers in microscopy, enabling neuroscientists to visualize their theories and drive research forward. Sign up here for a free workshop on correlative microscopy, and learn first-hand how to get started with imaging your samples with both light and electron microscopy TABLE OF CONTENTS October 2013 Volume 10, Issue 10 In This Issue Editorial This Month Correspondence Research Highlights Technology Feature News and Views Review Perspective Resource Brief Communications Articles Corrigenda Retraction Application Notes Advertisement Accomplish more in a single workday with exceptionally fast Takara-brand PCR enzymes. Perform colony PCR in 60 min, high fidelity PCR with a 10-second extension step, reverse transcription for qPCR in 15 minutes, or fast qPCR, all with robust enzymes optimized for fast workflows. Reliable PCR with less waiting- That's Good Science!™ Learn More... Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement SNEAK PEEK: 2013's Nature | Nature Methods Reprint Collection www.nature.com/advertising/tfc2013  This November, Nature Methods will publish the 2013 Technology Feature Reprint Collection — a special compilation of popular Technology Features that have appeared in Nature and Nature Methods throughout the year.   In This Issue Top InThisIssue    Editorial Top The way you say it   p917 doi:10.1038/nmeth.2686 Wording criticism constructively is important before and after publication. This Month Top The Author File: Jeff Dangl   p919 Vivien Marx doi:10.1038/nmeth.2653 Better surveys of microbial friends and foes. Points of Significance: Error bars   pp921 - 922 Martin Krzywinski and Naomi Altman doi:10.1038/nmeth.2659 The meaning of error bars is often misinterpreted, as is the statistical significance of their overlap. Correspondence Top ExpressionBlast: mining large, unstructured expression databases   pp925 - 926 Guy E Zinman, Shoshana Naiman, Yariv Kanfi, Haim Cohen and Ziv Bar-Joseph doi:10.1038/nmeth.2630 Building an ENCODE-style data compendium on a shoestring   p926 David Ruau, Felicia S L Ng, Nicola K Wilson, Rebecca Hannah, Evangelia Diamanti et al. doi:10.1038/nmeth.2643 Research Highlights Top The developing human brain—modeled in a dish Stem cells grown in three-dimensional cultures self-organize into tissues that resemble the developing human brain. A tool belt for GFP Nanobodies turn any GFP-expressing cells into targets for in vivo functional manipulation. Antibodies, made to order Informed by existing molecular recognition motifs, researchers design effective scaffolds for directed evolution of post-translational modification-specific antibodies. Constructing complicated carbohydrates A stepwise strategy of targeted synthesis enables researchers to reconstruct cellular glycomes in vitro. Self-destruct sequences High-throughput sequencing of massive mutant libraries helps researchers catalog determinants of protein stability. Studying function at the genome scale Genomic position effects are probed in a highly parallel fashion with a clever combination of existing methods. Engineering off the beaten pathway Interfacing synthetic diverters with a native yeast signaling pathway adds a robust layer of cell fate control. Methods in Brief Nanodiamonds to track cells in vivo | Binding-site affinities tune promoter output | Conditional gene knockouts in worms | Allelic effects on translation Tools in Brief Extracting microbial function from phylogeny | The NCI-60 proteomes | Anterograde rabies neural tracers | Highly multiplexed proteome analysis Methods JOBS of the week Excellence Research Fellowships CEA (French Atomic and Alternative Energies Commission) 18 Postdoctoral Fellowships for Energy and Information Technologies CEA (French Atomic and Alternative Energies Commission) Faculty Positions in Genomic, Bioinformatic, Computational, and Evolutionary Approaches to Understanding Gene Regulation University of Texas Southwestern Medical Center Faculty Positions in Molecular Biology of Female Reproductive Systems University of Texas Southwestern Medical Center More Science jobs from Methods EVENT HPLC Analytical Method Development and Validation 28th Nov 2013 London, UK More science events from Technology Feature Top Genomics in the clouds   pp941 - 945 Vivien Marx doi:10.1038/nmeth.2654 Cloud computing can help busy genomics labs. But researchers will want to be cautious shoppers as they scan the skies for the cloud best suited to their needs. News and Views Top hiFRET: some tailwind for FRET resolves weak protein interactions   pp947 - 948 Kees Jalink doi:10.1038/nmeth.2652 Use of helper interactions to encourage weak heteromeric interactions between fluorescent protein pairs helps ensure optimal fluorescence resonance energy transfer (FRET) signals and minimizes the impact on target protein interactions. See also: Article by Grunberg et al. Review Top Recommendations for the design and analysis of epigenome-wide association studies   pp949 - 955 Karin B Michels, Alexandra M Binder, Sarah Dedeurwaerder, Charles B Epstein, John M Greally et al. doi:10.1038/nmeth.2632 Fourteen scientists who participated in a recent workshop to identify and address challenges of epigenome-wide association studies summarize their recommendations in this Review. Perspective Top Cas9 as a versatile tool for engineering biology   pp957 - 963 Prashant Mali, Kevin M Esvelt and George M Church doi:10.1038/nmeth.2649 This Perspective describes current and prospective advances in genome engineering made possible with the CRISPR-Cas9 system. Resource Top A reversible gene trap collection empowers haploid genetics in human cells   pp965 - 971 Tilmann Bürckstummer, Carina Banning, Philipp Hainzl, Richard Schobesberger, Claudia Kerzendorfer et al. doi:10.1038/nmeth.2609 A collection of single-gene-mutant human cells is described. This growing resource is based on gene-trap mutagenesis of a near-haploid human cell line and covers almost 3,500 human genes. Brief Communications Top RNA-guided gene activation by CRISPR-Cas9-based transcription factors   pp973 - 976 Pablo Perez-Pinera, D Dewran Kocak, Christopher M Vockley, Andrew F Adler, Ami M Kabadi et al. doi:10.1038/nmeth.2600 Synthetic transcription factors based on the RNA-guided CRISPR-Cas9 system are used to activate specific endogenous genes in human cells. Also online, Joung and colleagues report similar developments at two other loci. CRISPR RNA-guided activation of endogenous human genes   pp977 - 979 Morgan L Maeder, Samantha J Linder, Vincent M Cascio, Yanfang Fu, Quan H Ho et al. doi:10.1038/nmeth.2598 Synthetic transcription factors based on the RNA-guided CRISPR-Cas9 system are used to activate endogenous genes in human cells. Also online, Gersbach and colleagues report similar developments at multiple other loci. Site-specific characterization of the Asp- and Glu-ADP-ribosylated proteome   pp981 - 984 Yajie Zhang, Jianqi Wang, Ming Ding and Yonghao Yu doi:10.1038/nmeth.2603 A proteomic method to identify human proteins post-translationally modified by poly(ADP-ribosyl)ation is reported, which will help yield further insights into the biological role of this modification. DeNovoGear: de novo indel and point mutation discovery and phasing   pp985 - 987 Avinash Ramu, Michiel J Noordam, Rachel S Schwartz, Arthur Wuster, Matthew E Hurles et al. doi:10.1038/nmeth.2611 The DeNovoGear software detects de novo point mutations and indels with high specificity in familial and somatic tissue sequence data. DMSO enhances electrospray response, boosting sensitivity of proteomic experiments   pp989 - 991 Hannes Hahne, Fiona Pachl, Benjamin Ruprecht, Stefan K Maier, Susan Klaeger et al. doi:10.1038/nmeth.2610 The addition of a low percentage of DMSO into liquid chromatography solvents strongly enhances peptide electrospray ionization, substantially improving proteome analysis by liquid chromatography-tandem mass spectrometry. Recombinant antibodies to histone post-translational modifications   pp992 - 995 Takamitsu Hattori, Joseph M Taft, Kalina M Swist, Hao Luo, Heather Witt et al. doi:10.1038/nmeth.2605 Renewable affinity reagents with high specificity and affinity for histone modifications perform well in ChIP-seq and other applications in epigenetics research. UPARSE: highly accurate OTU sequences from microbial amplicon reads   pp996 - 998 Robert C Edgar doi:10.1038/nmeth.2604 To determine microbial community structure, the UPARSE software extracts operational taxonomic unit (OTU) representative sequences with high accuracy on the basis of amplified marker-gene sequences. Practical innovations for high-throughput amplicon sequencing   pp999 - 1002 Derek S Lundberg, Scott Yourstone, Piotr Mieczkowski, Corbin D Jones and Jeffery L Dangl doi:10.1038/nmeth.2634 A set of practical improvements and software provide more accurate and less biased metagenomic amplicon sequencing at lower sequencing effort. Absolute quantification by droplet digital PCR versus analog real-time PCR   pp1003 - 1005 Christopher M Hindson, John R Chevillet, Hilary A Briggs, Emily N Gallichotte, Ingrid K Ruf et al. doi:10.1038/nmeth.2633 Droplet digital PCR shows greater precision and reproducibility but no consistent gain in sensitivity when compared to real-time PCR. Advertisement The new face of benchtop cell analysis The new BD LSRFortessa™ X-20 is an affordably priced powerhouse for multicolor cell analysis, with up to five lasers detecting up to twenty parameters simultaneously from the most compact footprint available (30" x 29" x 30"). Learn how cell analysis has been re-imagined for limited space and boundless potential. bdbiosciences.com/go/fortessa    Articles Top Solid-state NMR spectroscopy structure determination of a lipid-embedded heptahelical membrane protein   pp1007 - 1012 Shenlin Wang, Rachel A Munro, Lichi Shi, Izuru Kawamura, Takashi Okitsu et al. doi:10.1038/nmeth.2635 A strategy, based on solid-state NMR spectroscopy, for determining the structure of an oligomeric, seven-helix membrane protein (Anabaena sensory rhodopsin) in a lipid environment is described. Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light   pp1013 - 1020 Tina Schrödel, Robert Prevedel, Karin Aumayr, Manuel Zimmer and Alipasha Vaziri doi:10.1038/nmeth.2637 This work describes wide-field temporal focusing, a two-photon volumetric imaging technique based on light sculpting that enables functional imaging of the majority of neurons in the head ganglia of C. elegans with high temporal and spatial resolution. Engineering of weak helper interactions for high-efficiency FRET probes   pp1021 - 1027 Raik Grünberg, Julia V Burnier, Tony Ferrar, Violeta Beltran-Sastre, François Stricher et al. doi:10.1038/nmeth.2625 Addition of weak helper interactions to fluorescent protein pairs by protein engineering provides a simple method to increase FRET efficiency with little or no background. See also: News and Views by Jalink Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination   pp1028 - 1034 Daniel J Dickinson, Jordan D Ward, David J Reiner and Bob Goldstein doi:10.1038/nmeth.2641 CRISPR-Cas9-mediated cleavage is used to stimulate homologous recombination at specific target sites in the C. elegans genome, permitting flexible tagging and sequence modification of endogenous worm genes. Advertisement The award-winning Gel Doc™ EZ System and Image Lab™ software give you publication-quality images with a push of the green button. Choose from a selection of removable trays that make personalization and imager setup fast and simple. Then sit back and relax while its intuitive image acquisition and analysis give you high quality results in just 10 seconds. Now that's easy! Watch the video at bio-rad.com/ad/ez   Corrigenda Top CLARITY for mapping the nervous system   p1035 Kwanghun Chung and Karl Deisseroth doi:10.1038/nmeth1013-1035a Whole-rat conditional gene knockout via genome editing   p1035 Andrew J Brown, Daniel A Fisher, Evguenia Kouranova, Aaron McCoy, Kevin Forbes et al. doi:10.1038/nmeth1013-1035b Retraction Top Marker-independent identification of glioma-initiating cells   p1035 Virginie Clément, Denis Marino, Cristina Cudalbu, Marie-France Hamou, Vladimir Mlynarik et al. doi:10.1038/nmeth1013-1035c Application Notes Top Optimized method for rapid protein electroblotting    Greg Kilmer, Brian Webb, Boguslawa R Dworecki, Eric Hommema, Steve Shiflett et al. EpiGnome™ Methyl-Seq Kit: a novel post-bisulfite conversion library prep method for methylation analysis    Anupama Khanna, Agata Czyz and Fraz Syed High-content analysis of three-dimensional tumor spheroids: investigating signaling pathways using small hairpin RNA    Shane R Horman, Jeremy To, Anthony P Orth, Nicky Slawny, Meghan J Cuddihy et al. Top Advertisement nature.com webcasts Macmillan Science Communication presents a custom webcast on: Investigation of chromosomal microarray analysis as the successor to prenatal karyotyping Tuesday October 8th 8am PDT / 11am EDT / 4pm BST / 5pm CEST  Register for the free webcast followed by our live Q & A session   Sponsored by:     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. 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