Nature Methods Contents: August 2015 Volume 12 pp 693 - 793

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Advertisement All-new Nikon Super-Resolution systems extend the capabilities of nanoscale imaging. N-STORM 4.0 provides 10-times faster acquisition rates compared to previous systems, enabling live-cell imaging with super-resolution. Dual-camera N-SIM provides simultaneous, 2-color super-resolution imaging of live-cells. For more information, go to www.nikoninstruments.com/sr. TABLE OF CONTENTS August 2015 Volume 12, Issue 8 In This Issue Editorial This Month Correspondence Research Highlights Technology Feature News and Views Analysis Brief Communications Articles Advertisement   Struggling to clone your gene of interest? Wasting time on cloning troubleshooting? Download our free Molecular Cloning Handbook -with comprehensive troubleshooting guide.  Download Now Subscribe   Facebook   RSS   Recommend to library   Twitter   In This Issue Top In This Issue    Editorial Top On impact   p693 doi:10.1038/nmeth.3520 The journal impact factor is a much-criticized yet still-used number. As with any metric, it should not be used uncritically and without an understanding of what it measures. This Month Top The Author File: Ronald Walsworth   p695 Vivien Marx doi:10.1038/nmeth.3492 How to use diamonds to image single cells, and how to have a career without ever applying for a job. Correspondence Top miRWalk2.0: a comprehensive atlas of microRNA-target interactions   p697 Harsh Dweep and Norbert Gretz doi:10.1038/nmeth.3485 Comparative visualization of genotype-phenotype relationships   pp698 - 699 Gagarine Yaikhom, Hugh Morgan, Duncan Sneddon, Ahmad Retha, Julian Atienza-Herrero et al. doi:10.1038/nmeth.3477 Clarifying the terminology that describes scientific reproducibility   p699 Ron S Kenett and Galit Shmueli doi:10.1038/nmeth.3489 Research Highlights Top Transdifferentiation from the top Fibroblasts pass through a pluripotent state when undergoing transdifferentiation in the presence of pluripotency factors. Injectable meshes for neural recordings Injection of a flexible mesh containing electronics enables neural recordings in the mouse brain in a minimally invasive fashion. Efficient generation of proteins with site-specific phosphoserines An optimized strategy allows genetic encoding of phosphoserine and its nonhydrolyzable analog. 2D protein lattices by design Researchers design programmable two-dimensional (2D) protein lattices that may find broad applications in diverse fields. Engineering Cas9 Cas9 proteins with altered PAM specificities widen the target range of the CRISPR system. Methods in Brief Thousands of cell droplets | Ultra-mass-tolerant database searching | Mapping accessible chromatin in single cells | Axially swept light-sheet microscopy Tools in Brief Light-induced genome editing | A map of the lipid-binding proteome | A DNA-based sensor for intracellular chloride | Light-controlled cell adhesion and dissociation Methods JOBS of the week Postdoctoral Fellow Bioinformatics The University of Texas Health Science Center at San Antonio Research Associate in Chemical Biology and Biocatalysis The University of Manchester Postdoctoral Associate in Genomics and Bioinformatics, USC University of Southern California Professor in Physical Materials Chemistry Stockholm University More Science jobs from Methods EVENT X-Ray Methods in Structural Biology 12th Oct - 27th Oct 2015 Cold Spring Harbor, USA More science events from Technology Feature Top Human phenotyping on a population scale   pp711 - 714 Vivien Marx doi:10.1038/nmeth.3487 Large-scale phenotyping is generating much data that geneticists can harness. Amid the excitement about the possibilities, there are some points of caution. News and Views Top Single in the (Cell) City: a protein-folding story   pp715 - 716 Anne Plochowietz and Achillefs N Kapanidis doi:10.1038/nmeth.3491 An integrated single-molecule fluorescence approach enables the study of nano-to-millisecond protein conformational dynamics in living mammalian cells. See also: Article by Konig et al. Analysis Top Quantitative evaluation of software packages for single-molecule localization microscopy   pp717 - 724 Daniel Sage, Hagai Kirshner, Thomas Pengo, Nico Stuurman, Junhong Min et al. doi:10.1038/nmeth.3442 This Analysis reports a comparison of current software packages for single-molecule localization in localization-based super-resolution imaging. Performance of the participating software on synthetic, biologically inspired ground-truth data was assessed by multiple criteria. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation   pp725 - 731 Edyta Marcon, Harshika Jain, Anandi Bhattacharya, Hongbo Guo, Sadhna Phanse et al. doi:10.1038/nmeth.3472 A quantitative mass spectrometry-based standard operating procedure to classify antibody performance in immunoprecipitation is assessed in a multilaboratory study. Brief Communications Top A complete bacterial genome assembled de novo using only nanopore sequencing data   pp733 - 735 Nicholas J Loman, Joshua Quick and Jared T Simpson doi:10.1038/nmeth.3444 By error-correcting long nanopore reads and calling a consensus sequence using nanopore signal data, an entire bacterial genome is assembled de novo. Single-cell magnetic imaging using a quantum diamond microscope   pp736 - 738 David R Glenn, Kyungheon Lee, Hongkun Park, Ralph Weissleder, Amir Yacoby et al. doi:10.1038/nmeth.3449 This paper reports magnetic imaging of immunolabeled mammalian cells using nitrogen-vacancy centers in diamond and shows that the method can be used for quantitative profiling of markers. Combining protein and mRNA quantification to decipher transcriptional regulation   pp739 - 742 Heng Xu, Leonardo A Sepulveda, Lauren Figard, Anna Marie Sokac and Ido Golding doi:10.1038/nmeth.3446 The combination of immunofluorescence and single-molecule FISH (smFISH) enables a quantitative description of how transcription factor binding drives the kinetics of mRNA production. Multitarget super-resolution microscopy with high-density labeling by exchangeable probes   pp743 - 746 Tai Kiuchi, Makio Higuchi, Akihiro Takamura, Masahiro Maruoka and Naoki Watanabe doi:10.1038/nmeth.3466 Image reconstruction by integrating exchangeable single-molecule localization (IRIS) allows for super-resolution imaging of multiple targets. IRIS yields continuously labeled structures owing to high labeling density and is demonstrated for multiple cytoskeletal components. Homology modeling of larger proteins guided by chemical shifts   pp747 - 750 Yang Shen and Ad Bax doi:10.1038/nmeth.3437 An NMR chemical shift-guided protein alignment method is combined with a comparative modeling pipeline to readily solve structures of large proteins. Protein structure determination by combining sparse NMR data with evolutionary couplings   pp751 - 754 Yuefeng Tang, Yuanpeng Janet Huang, Thomas A Hopf, Chris Sander, Debora S Marks et al. doi:10.1038/nmeth.3455 A hybrid method that combines sparse NMR spectroscopy data with evolutionary residue-residue coupling information is used to solve accurate structures of large proteins. Efficient set tests for the genetic analysis of correlated traits   pp755 - 758 Francesco Paolo Casale, Barbara Rakitsch, Christoph Lippert and Oliver Stegle doi:10.1038/nmeth.3439 The multi-trait set test (mtSet) is an efficient mixed-model method that enables genome-wide association tests for large cohorts and multiple quantitative traits using sets of variants to improve power and sensitivity, while addressing confounding due to population structure. Continuous volumetric imaging via an optical phase-locked ultrasound lens   pp759 - 762 Lingjie Kong, Jianyong Tang, Justin P Little, Yang Yu, Tim Lammermann et al. doi:10.1038/nmeth.3476 An optical phase-locked ultrasound lens integrated into a two-photon microscope enables continuous volumetric imaging of biological processes in vivo. A naturally monomeric infrared fluorescent protein for protein labeling in vivo   pp763 - 765 Dan Yu, Michelle A Baird, John R Allen, Elizabeth S Howe, Matthew P Klassen et al. doi:10.1038/nmeth.3447 An infrared fluorescent protein based on a new monomeric scaffold is described in this paper and is tested for protein fusion in cells and in vivo. Articles Top Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome   pp767 - 772 Bastian Linder, Anya V Grozhik, Anthony O Olarerin-George, Cem Meydan, Christopher E Mason et al. doi:10.1038/nmeth.3453 Unique mutational signatures induced by cross-linking of m6A-specific antibodies to RNA identify m6A and m6Am residues at single-nucleotide resolution, transcriptome-wide. Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells   pp773 - 779 Iwo Konig, Arash Zarrine-Afsar, Mikayel Aznauryan, Andrea Soranno, Bengt Wunderlich et al. doi:10.1038/nmeth.3475 Individual protein dynamics can be studied in live eukaryotic cells from the millisecond to nanosecond level using an integrated approach to confocal single-molecule FRET spectroscopy. See also: News and Views by Plochowietz & Kapanidis Assembly and diploid architecture of an individual human genome via single-molecule technologies   pp780 - 786 Matthew Pendleton, Robert Sebra, Andy Wing Chun Pang, Ajay Ummat, Oscar Franzen et al. doi:10.1038/nmeth.3454 A combination of single-molecule long-read sequencing, single-molecule genome mapping and short-read sequencing provides reference-quality de novo assemblies and also shows improved phasing and variant detection over short-read assemblies when mapping to a reference genome. Quantifying domain-ligand affinities and specificities by high-throughput holdup assay   pp787 - 793 Renaud Vincentelli, Katja Luck, Juline Poirson, Jolanta Polanowska, Julie Abdat et al. doi:10.1038/nmeth.3438 This paper reports an approach to measure equilibrium binding affinities for interacting proteins in high throughput, allowing the rapid and quantitative profiling of the specificity of interaction motifs. 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