Nature Methods Contents: January 2012 Volume 9 pp 1 - 110

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Ensure you are abreast of the most significant research by qualifying for your free subscription to Nature Methods.   In This Issue Top PDF Special Feature Top Method of the Year 2011 Contents Editorial News feature Primer Commentary Methods to Watch Video Nature Methods' choice for Method of the Year 2011 is genome editing with engineered nucleases. This collection of articles—and the related video—highlights how the ability to use engineered nucleases to make precise, tailored and specific changes to coding and noncoding sequences of the genome, in cells and in organisms of many species, could revolutionize the study of gene function. The Methods to Watch bring together possible future choices for Method of the Year. Editorial Top Special feature: Method of the Year 2011 Method of the Year 2011 p1 doi:10.1038/nmeth.1852 The ability to introduce targeted, tailored changes into the genomes of several species will make it feasible to ask more precise biological questions. Full Text | PDF This Month Top The author file: Khalid Salaita p3 Monya Baker doi:10.1038/nmeth.1816 Measuring single-molecule forces with light. Full Text | PDF Points of view: Data exploration p5 Noam Shoresh and Bang Wong doi:10.1038/nmeth.1829 Enhancement of pattern discovery through graphical representation of data. Full Text | PDF Correspondence Top GeneProf: analysis of high-throughput sequencing experiments pp7 - 8 Florian Halbritter, Harsh J Vaidya and Simon R Tomlinson doi:10.1038/nmeth.1809 Full Text | PDF Gene expression deconvolution in linear space pp8 - 9 Yi Zhong and Zhandong Liu doi:10.1038/nmeth.1830 Full Text | PDF Gene expression deconvolution in linear space p9 Shai S Shen-Orr, Robert Tibshirani and Atul J Butte doi:10.1038/nmeth.1831 Full Text | PDF Optimal enzymes for amplifying sequencing libraries pp10 - 11 Michael A Quail, Thomas D Otto, Yong Gu, Simon R Harris, Thomas F Skelly, Jacqueline A McQuillan, Harold P Swerdlow and Samuel O Oyola doi:10.1038/nmeth.1814 Full Text | PDF Research Highlights Top Building better bubbles p13 Synthetic clusters of membrane-bound droplets may provide a useful means for simulating tissues or transporting therapeutic payloads. Three-dimensional genetics pp14 - 15 A combination of chromosome conformation capture carbon copy (5C), modeling and automated imaging renders an empirical three-dimensional model of a bacterial genome. Peering deeper into the transcriptome pp14 - 15 Targeting portions of the transcriptome for deep sequencing reveals very rare transcripts. The survival of the fittest p16 An analysis of over 100 human embryonic stem cell lines reveals a genetic change that might confer a growth advantage. Organic chemistry expands imaging options p19 A new fluorination approach enables the synthesis of diverse PET probes. A handle on neurodegenerative disease complexity p21 Combining experiments and calculations makes it possible to measure the prognostic value of toxic protein species in the cell. Methods JOBS of the week Method set up for determination of aromatic amines arising from dyes used in textile industry. ALMA MATER STUDIORUM - UNIVERSITA' DI BOLOGNA - - DIP. CHIMICA ''G.CIAMICIAN'' Cross-border management of operations of the Civil Defense in case of emergency drinking water Università degli Studi di Trieste Head of the Imaging Core Facility Max Planck Institute of Biochemistry Post Doctoral fellow University of Alberta Postdoctoral Research Scientist The Babraham Institute More Science jobs from Methods EVENT The 6th International Conference on Bioinformatics and Biomedical Engineering iCBBE 2012 17th May - 20th May 2012 Shanghai, China More science events from Methods in Brief Top Dark matter translation  | Two-color STED gets easier  | Sub-attoliter volume mixing  | Using bacteria to generate ubiquitylated proteins  Tools in Brief Top Imaging protein interactions in living cells  | Neurophysiology on the move  | Optimizing protein identification  | A fluorescent protein with many faces  News Feature Top Special feature: Method of the Year 2011 Gene-editing nucleases pp23 - 26 Monya Baker doi:10.1038/nmeth.1807 Precise ways to modify the genome arose from unexpected places. Monya Baker reports. Full Text | PDF Primer Top Special feature: Method of the Year 2011 Primer: genome editing with engineered nucleases p27 Natalie de Souza doi:10.1038/nmeth.1848 A brief description of tools for targeted cleavage and tailored modification of genomes is presented. Full Text | PDF Commentaries Top Special feature: Method of the Year 2011 Gene editing: not just for translation anymore pp28 - 31 Moira A McMahon, Meghdad Rahdar and Matthew Porteus doi:10.1038/nmeth.1811 Engineered nucleases have advanced the field of gene therapy with the promise of targeted genome modification as a treatment for human diseases. Here we discuss why engineered nucleases are an exciting research tool for gene editing and consider their applications to a range of biological questions. Full Text | PDF Special feature: Method of the Year 2011 Zinc-finger nucleases: how to play two good hands pp32 - 34 Mark Isalan doi:10.1038/nmeth.1805 Zinc-finger nuclease dimers are more difficult to engineer than single DNA-binding domains, but the development of new methods could help. Full Text | PDF Methods to Watch Top Special feature: Method of the Year 2011 Single-cell methods p35 Natalie de Souza doi:10.1038/nmeth.1819 Improved single-cell methods are helping to unravel biological complexity. Full Text | PDF Special feature: Method of the Year 2011 Functional genomic resources p35 Nicole Rusk doi:10.1038/nmeth.1820 Tools to manipulate murine genes on a genome-wide scale and to phenotype their effects in animals are maturing. Full Text | PDF Special feature: Method of the Year 2011 Glycoproteomics p36 Allison Doerr doi:10.1038/nmeth.1821 Methods for tackling the enormously complex glycoproteome are sorely needed. Full Text | PDF Special feature: Method of the Year 2011 Causal mutations in a haploid landscape p36 Nicole Rusk doi:10.1038/nmeth.1822 Sequencing a haploid genome and understanding the impact of its variants requires technical and computational improvements. Full Text | PDF Special feature: Method of the Year 2011 Imaging life with thin sheets of light p37 Erika Pastrana doi:10.1038/nmeth.1823 The revival of light-sheet microscopy opens new possibilities for the imaging of living processes. Full Text | PDF Special feature: Method of the Year 2011 Non-model organisms p37 Tal Nawy doi:10.1038/nmeth.1824 Next-generation sequencing is broadening the application of genetic and genomic studies to the panoply of life. Full Text | PDF Special feature: Method of the Year 2011 Light-based electrophysiology p38 Erika Pastrana doi:10.1038/nmeth.1825 Genetically encoded voltage sensors are finally measuring up. Full Text | PDF Special feature: Method of the Year 2011 RNA structures p38 Petya V Krasteva doi:10.1038/nmeth.1826 Accurate methods for RNA-structure determination are being developed. Full Text | PDF Technology Feature Top Quantitative data: learning to share pp39 - 41 Monya Baker doi:10.1038/nmeth.1815 Adaptive technologies are helping researchers combine and organize experimental results. Full Text | PDF News and Views Top Running in reverse: rhodopsins sense voltage pp43 - 44 Loren L Looger doi:10.1038/nmeth.1817 Microbial rhodopsins convert light into ion flux; in neurons, this can be used to control activity. New work shows that the opposite is also true: rhodopsins can be used to visualize neural activity. Full Text | PDF See also: Article by Kralj et al. Tracking genomic hydroxymethylation by the base pp45 - 46 Gilles Salbert and Michael Weber doi:10.1038/nmeth.1813 A method uses single-molecule, real-time DNA sequencing to detect the modified base 5-hydroxymethylcytosine, an epigenetic mark recently suspected of having essential roles in genome regulation. Full Text | PDF See also: Brief Communication by Song et al. Review Top Power tools for gene expression and clonal analysis in Drosophila  pp47 - 55 Alberto del Valle Rodriguez, Dominic Didiano and Claude Desplan doi:10.1038/nmeth.1800 This Review covers recent technological developments to label and manipulate genes in selected populations of cells in Drosophila melanogaster. The Review is intended as a user guide to help with the selection of the best expression systems and clonal analysis techniques for developmental studies in the fly. Abstract | Full Text | PDF Perspective Top A guide to analysis of mouse energy metabolism pp57 - 63 Matthias H Tschöp, John R Speakman, Jonathan R S Arch, Johan Auwerx, Jens C Brüning, Lawrence Chan, Robert H Eckel, Robert V Farese Jr, Jose E Galgani, Catherine Hambly, Mark A Herman, Tamas L Horvath, Barbara B Kahn, Sara C Kozma, Eleftheria Maratos-Flier, Timo D Müller, Heike Münzberg, Paul T Pfluger, Leona Plum, Marc L Reitman, Kamal Rahmouni, Gerald I Shulman, George Thomas, C Ronald Kahn and Eric Ravussin doi:10.1038/nmeth.1806 Authors present workflows for the analysis of metabolism phenotypes in mice and recommend analysis of covariance to asses body composition effects. Abstract | Full Text | PDF Brief Communications Top Visualizing mechanical tension across membrane receptors with a fluorescent sensor pp64 - 67 Daniel R Stabley, Carol Jurchenko, Stephen S Marshall and Khalid S Salaita doi:10.1038/nmeth.1747 A fluorescent molecular tension sensor for spatially and temporally mapping the mechanical strain exerted by cell-surface receptors in living cells is described. Abstract | Full Text | PDF Cyanine fluorophore derivatives with enhanced photostability pp68 - 71 Roger B Altman, Daniel S Terry, Zhou Zhou, Qinsi Zheng, Peter Geggier, Rachel A Kolster, Yongfang Zhao, Jonathan A Javitch, J David Warren and Scott C Blanchard doi:10.1038/nmeth.1774 Conjugation of triplet-state quenchers to the small organic cyanine fluorophore, Cy5, increases photostability without affecting its spectral characteristics. This allows longer fluorescence imaging with a concomitant reduction in blinking both in vitro and in living cells. Abstract | Full Text | PDF Counting absolute numbers of molecules using unique molecular identifiers pp72 - 74 Teemu Kivioja, Anna Vähärautio, Kasper Karlsson, Martin Bonke, Martin Enge, Sten Linnarsson and Jussi Taipale doi:10.1038/nmeth.1778 Unique molecular identifiers (UMIs) associate distinct sequences with every DNA or RNA molecule and can be counted after amplification to quantify molecules in the original sample. Using UMIs, the authors obtain a digital karyotype of an individual with Down's syndrome and quantify mRNA in Drosophila melanogaster cells. Abstract | Full Text | PDF Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine pp75 - 77 Chun-Xiao Song, Tyson A Clark, Xing-Yu Lu, Andrey Kislyuk, Qing Dai, Stephen W Turner, Chuan He and Jonas Korlach doi:10.1038/nmeth.1779 The DNA modification 5-hydroxymethylcytosine has recently been implicated in several biological processes. Enrichment by selective chemical labeling in combination with single-molecule, real-time sequencing provides sensitive detection of this epigenetic mark in genomic DNA at base-pair resolution. Abstract | Full Text | PDF Decoding cell lineage from acquired mutations using arbitrary deep sequencing pp78 - 80 Cheryl A Carlson, Arnold Kas, Robert Kirkwood, Laura E Hays, Bradley D Preston, Stephen J Salipante and Marshall S Horwitz doi:10.1038/nmeth.1781 Mutations at arbitrarily sampled genomic positions are identified using next-generation sequencing and are used to infer the lineage of DNA damage-prone 'mutator' mouse cells in culture. Abstract | Full Text | PDF Controlled gene expression in primary Lgr5 organoid cultures pp81 - 83 Bon-Kyoung Koo, Daniel E Stange, Toshiro Sato, Wouter Karthaus, Henner F Farin, Meritxell Huch, Johan H van Es and Hans Clevers doi:10.1038/nmeth.1802 The controlled overexpression or knockdown of gene expression in primary organoid cultures of mouse endodermal epithelia is described. This should enable ex vivo studies of mammalian gene function. Abstract | Full Text | PDF Articles Top Global profiling of dynamic protein palmitoylation pp84 - 89 Brent R Martin, Chu Wang, Alexander Adibekian, Sarah E Tully and Benjamin F Cravatt doi:10.1038/nmeth.1769 A quantitative proteomics approach to characterize protein palmitoylation dynamics on a global scale in cells, as well as to identify enzymes responsible for the regulation of palmitoylation, is described. Abstract | Full Text | PDF Optical recording of action potentials in mammalian neurons using a microbial rhodopsin pp90 - 95 Joel M Kralj, Adam D Douglass, Daniel R Hochbaum, Dougal Maclaurin and Adam E Cohen doi:10.1038/nmeth.1782 The microbial rhodopsin protein, Archaerhodopsin 3, can function as a rapid and highly sensitive genetically encoded voltage indicator in mammalian cells that is capable of detecting single action potentials with a signal-to-noise ratio greater than 10. A mutant lacking proton pumping displays greater sensitivity but a slowed response. Abstract | Full Text | PDF mGRASP enables mapping mammalian synaptic connectivity with light microscopy pp96 - 102 Jinhyun Kim, Ting Zhao, Ronald S Petralia, Yang Yu, Hanchuan Peng, Eugene Myers and Jeffrey C Magee doi:10.1038/nmeth.1784 In this paper, the authors report GFP reconstitution across synaptic partners (GRASP) adapted for synapse visualization in the mammalian brain. Abstract | Full Text | PDF High-efficiency counterselection recombineering for site-directed mutagenesis in bacterial artificial chromosomes pp103 - 109 Alexander W Bird, Axel Erler, Jun Fu, Jean-Karim Hériché, Marcello Maresca, Youming Zhang, Anthony A Hyman and A Francis Stewart doi:10.1038/nmeth.1803 Site-directed seamless modification of bacterial artificial chromosomes is enhanced more than tenfold in efficiency by improving the counterselection step. A set of plasmids and oligonucleotide design software also make this E. coli recombineering approach markedly faster and easier. Abstract | Full Text | PDF Erratum Top Erratum: Reply to “More on color blindness” p110 Bang Wong doi:10.1038/nmeth0112-110 Full Text | PDF Top Advertisement Nature Methods Method of the Year: Genome Editing with Engineered Nucleases www.nature.com/nmeth/focus/moy2011 Nature Methods presents a special feature on engineered nucleases, reporting on development of this technology and its exciting applications in editing the genome.   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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