Nature Methods Contents: November 2012 Volume 9 pp 1033 - 1125

Advertisement Roche's X-tremeGENE Transfection Reagents Transfect efficiently with low cytotoxicity - proven in 275 different cell types...over 130 cancer cells. Free sample and protocols at www.x-tremegene.roche.com For life science research only. Not for use in diagnostic procedures. TABLE OF CONTENTS November 2012 Volume 9, Issue 11 In This Issue Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Perspective Brief Communications Articles Advertisement In 16S Metagenomics, Read Length is Key! Get the complete picture with our Roche 454 GS FLX+ Metagenomics Service.  •  Generate more informa- tion from a single read •  Accurately identify organisms in complex samples •  Improve your taxonomic assignments down to the species level Experience the power of Sanger-like reads today!   Our expertise - Your success! Click here for details The publication of this issue was delayed due to Hurricane Sandy closing our New York offices temporarily. We apologize for any inconvenience caused. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement One-STrEP-tag becomes Twin-Strep-tag Twin-Strep-tag, the tandem version of the Strep-tag II combines high affinity with high specificity, therefore allowing isolation of highly pure and functional proteins with high efficiency. Mild elution conditions preserve protein complexes and protein interactions...   Advertisement Custom TALEN™ Services and exclusive support only available at Cellectis bioresearch! With Cellectis bioresearch Custom TALEN™ Services, all gene editing projects can now be achieved. Our dedicated project support managers will provide you with know-how and expertise to achieve customized cells and organisms harboring your genetic modification of choice. Request more information »   Advertisement Horizon is a UK biotech company combining a 20 year heritage in translational research with a world-leading genome editing platform. The Company is a trusted supplier of genetically-defined cell lines, reporter gene assay kits, genomic reference standards, genome editing & drug discovery services to >400 organisations engaged in genomic, diagnostic and pharmaceutical R&D. http://www.horizondiscovery.com/   In This Issue Top In This Issue Editorial Top A necessary supplement   p1033 doi:10.1038/nmeth.2247 Supplementary information has its place in science publishing, but deploying it effectively requires effort from journals and scientists. This Month Top The author file: Peter Lansdorp   p1035 Vivien Marx doi:10.1038/nmeth.2218 Zeroing in on single DNA strands Points of view: Pencil and paper   p1037 Bang Wong and Rikke Schmidt Kjærgaard doi:10.1038/nmeth.2223 A unique set of tools facilitate thinking and hypothesis generation. Correspondence Top Reply to: Gene patents do not hinder academic research   p1039 doi:10.1038/nmeth.2244 See also: Correspondence by Greenwood Gene patents do not hinder academic research   p1039 Jim Greenwood doi:10.1038/nmeth.2245 See also: Correspondence rapidSTORM: accurate, fast open-source software for localization microscopy   pp1040 - 1041 Steve Wolter, Anna Löschberger, Thorge Holm, Sarah Aufmkolk, Marie-Christine Dabauvalle, Sebastian van de Linde and Markus Sauer doi:10.1038/nmeth.2224 ORCAE: online resource for community annotation of eukaryotes   p1041 Lieven Sterck, Kenny Billiau, Thomas Abeel, Pierre Rouzé and Yves Van de Peer doi:10.1038/nmeth.2242 Research Highlights Top Interactomes by mass spectrometry Two different mass spectrometry-based approaches are applied to analyze protein complexes on a global scale. The genetic essence of our brains A freely accessible transcriptional atlas offers unprecedented possibilities for exploring the human brain. The power of TRICEPS Researchers describe a multifunctional reagent for identifying extracellular interactions. The ENCODE project The second, genome-wide phase of the Encyclopedia of DNA Elements (ENCODE) project is being reported. Attention to detail Computational processing allows sub-diffraction-limit resolution imaging with a standard wide-field microscope. Leaner, meaner siRNAs Single-stranded small interfering RNA offers a potent and simple way to silence gene expression in the body. Let's start talking Synthetic networks in mammalian cells can regulate cellular behavior. Methods JOBS of the week Postdoctoral Research Associate in Computational Biology and Bioinformatics Oak Ridge National Laboratory / ORISE Post-Doctoral Position In Epigenetic Research Texas A&M Health Science Center Postdoc fellow Indiana University School of Medicine (IUSM) Postdoc in Physical Chemistry West Virginia University-department of chemistry Chief Nutritional Chemist Morgan McKinley Science More Science jobs from Methods EVENT International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2013) 11th Feb - 14th Feb 2013 Barcelona, Spain More science events from Methods in Brief Top Watching proteins in motion | Single-cell analysis of reprogramming | Many genes, one starting pistol | Soft bacterial chromosomes Tools in Brief Top Editing the fish genome | Accelerated GWAS | PSmOrange2 | A comprehensive database of poly(Q) mouse models Technology Feature Top Genome-editing tools storm ahead   pp1055 - 1059 Vivien Marx doi:10.1038/nmeth.2220 The menu of maturing, diversifying methods calls for careful selections in experimental design. News and Views Top Modular gene-circuit design takes two steps forward   pp1061 - 1063 Jeffrey J Tabor doi:10.1038/nmeth.2217 Work from two independent groups opens the door to designing gene circuits with advanced regulatory functions. See also: Brief Communication by Litcofsky et al. | Article by Liu et al. Spinning up mass spectrometry for whole protein complexes   pp1065 - 1066 Philip D Compton and Neil L Kelleher doi:10.1038/nmeth.2216 Researchers adapt a popular Orbitrap-based mass spectrometer to detect and analyze large, intact protein complexes, accelerating a new frontier in structural biology. See also: Brief Communication by Rose et al. Perspective Top A travel guide to Cytoscape plugins   pp1069 - 1076 Rintaro Saito, Michael E Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Samad Lotia, Alexander R Pico, Gary D Bader and Trey Ideker doi:10.1038/nmeth.2212 This Perspective discusses the registered and publicly available set of Cytoscape plugins to guide potential users to suitable tools. Brief Communications Top Iterative plug-and-play methodology for constructing and modifying synthetic gene networks   pp1077 - 1080 Kevin D Litcofsky, Raffi B Afeyan, Russell J Krom, Ahmad S Khalil and James J Collins doi:10.1038/nmeth.2205 A unique multiple cloning site (MCS) and defined genetic components without MCS restriction sites allow for the rapid construction and iterative tuning of synthetic genetic circuits. See also: News and Views by Tabor Automated velocity mapping of migrating cell populations (AVeMap)   pp1081 - 1083 Maxime Deforet, Maria Carla Parrini, Laurence Petitjean, Marco Biondini, Axel Buguin, Jacques Camonis and Pascal Silberzan doi:10.1038/nmeth.2209 This paper presents AVeMap, a method and software for automated analysis of cell migration in dense monolayers. High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies   pp1084 - 1086 Rebecca J Rose, Eugen Damoc, Eduard Denisov, Alexander Makarov and Albert J R Heck doi:10.1038/nmeth.2208 Modifications to an Orbitrap-based mass spectrometer enable analysis of large protein complexes in native-like states by mass spectrometry with very high sensitivity and mass resolution. See also: News and Views by Compton & Kelleher Advertisement High quality BD reagents are now more affordable  Lower pricing on BD Biosciences reagents means that you don't have to sacrifice quality. Now the consistency and reliability of BD flow cytometry reagents are more affordable, including thousands of proven products and innovative new brilliant dyes. Find the right product for your needs here. bdbiosciences.com/reagents   Articles Top An adaptor from translational to transcriptional control enables predictable assembly of complex regulation   pp1088 - 1094 Chang C Liu, Lei Qi, Julius B Lucks, Thomas H Segall-Shapiro, Denise Wang, Vivek K Mutalik and Adam P Arkin doi:10.1038/nmeth.2184 A genetic tool that converts bacterial regulators of translational initiation into regulators of transcriptional elongation is described. This adaptor is used to engineer several transcriptional attenuators and activators that can be predictably assembled into higher-order gene regulatory functions. See also: News and Views by Tabor Global identification of peptidase specificity by multiplex substrate profiling   pp1095 - 1100 Anthony J O'Donoghue, A Alegra Eroy-Reveles, Giselle M Knudsen, Jessica Ingram, Min Zhou, Jacob B Statnekov, Alexander L Greninger, Daniel R Hostetter, Gang Qu, David A Maltby, Marc O Anderson, Joseph L DeRisi, James H McKerrow, Alma L Burlingame and Charles S Craik doi:10.1038/nmeth.2182 A synthetic peptide library in conjunction with liquid chromatography-tandem mass spectrometry identifies the specificities of endo- and exopeptidases without requiring enrichment of substrates or products. A microfluidic device and computational platform for high-throughput live imaging of gene expression   pp1101 - 1106 Wolfgang Busch, Brad T Moore, Bradley Martsberger, Daniel L Mace, Richard W Twigg, Jee Jung, Iulian Pruteanu-Malinici, Scott J Kennedy, Gregory K Fricke, Robert L Clark, Uwe Ohler and Philip N Benfey doi:10.1038/nmeth.2185 RootArray and RootArray Controller comprise a robust pipeline for acquisition and analysis of gene expression data in plant roots over time. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution   pp1107 - 1112 Ester Falconer, Mark Hills, Ulrike Naumann, Steven S S Poon, Elizabeth A Chavez, Ashley D Sanders, Yongjun Zhao, Martin Hirst and Peter M Lansdorp doi:10.1038/nmeth.2206 The Strand-seq method independently sequences each parental strand of template DNA from single proliferating cells. It can be used to detect sister chromatid exchange and other chromosomal abnormalities at high resolution and to correct contig misorientations in genome assemblies, with potential for strand-inheritance and haplotyping studies. Magnetic nanoparticle-mediated massively parallel mechanical modulation of single-cell behavior   pp1113 - 1119 Peter Tseng, Jack W Judy and Dino Di Carlo doi:10.1038/nmeth.2210 Cells are dosed with magnetic nanoparticles and patterned onto micromagnetic substrates, enabling the application of controlled and variable mechanical force to tens of thousands of cells. Imputing gene expression from selectively reduced probe sets   pp1120 - 1125 Yoni Donner, Ting Feng, Christophe Benoist and Daphne Koller doi:10.1038/nmeth.2207 The probe selection for imputation (PSI) approach accurately imputes global gene expression profiles from a small subset of probes that it chooses based on a training set of full profiles, allowing many more combinatorial experiments to be performed given the same resources. Top Advertisement Save on best-in-class personal flow cytometry With a combined value package, you can save 10% on the BD Accuri™ C6 personal flow cytometer and 40% on high quality BD Pharmingen™ reagents for 2 full years. There's never been a better time to buy and get the best-in-class power, flexibility, and insight personal flow cytometry can offer. Flow cytometry within reach™. bdbiosciences.com/go/accuri   Advertisement Nature Arabic Edition allows Arabic speakers throughout the world to access top quality science news and comment from Nature, as well as summaries of all the research papers from the leading multidisciplinary journal. Access Nature Arabic Edition online and apply for your free subscription arabicedition.nature.com In partnership with: KACST   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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