Nature Methods Contents: April 2012 Volume 9 pp 311 - 418

Advertisement Combine Incubator and Reader: 2-in-1 Tecan's CO2/O2 Gas Control Module for Infinite 200 PRO plate reader! • Consistent physiological conditions • Predictable culture growth • No transport of cell cultures from incubator to reader • Complete data sets overnight Learn more TABLE OF CONTENTS April 2012 Volume 9, Issue 4 In This Issue Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Perspective Analysis Brief Communications Articles Erratum Advertisement Free Sample: New Brilliant Violet™ 421 Reagents Add a brilliant new dimension to your multicolor panels with Brilliant Violet™ 421 from BD Biosciences. Request a free sample of this new violet-excitable dye with significantly improved brightness over other dyes offered for the violet laser and get the high-sensitivity fluorescence needed to better resolve dim populations. bdbiosciences.com/go/brilliant Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement FlowSight: Flow cytometry with vision. The Amnis FlowSight is a compact and affordable 12-channel flow cytometer that images every cell. FlowSight can be upgraded with four lasers, a 96 well AutoSampler, and image analysis package to meet the needs of novice and expert users alike. Starting at only $79,000.   In This Issue Top PDF Editorial Top Mind the technology gap p311 doi:10.1038/nmeth.1968 New technologies are often inherently more complex than the technologies they supplant. Users must be aware of the impact this has on data interpretation. Full Text | PDF This Month Top The author file: Ben Langmead p313 Monya Baker doi:10.1038/nmeth.1933 Building a better sequence alignment program Full Text | PDF Points of view: Integrating data p315 Nils Gehlenborg and Bang Wong doi:10.1038/nmeth.1944 Different analytical tasks require different visual representations. Full Text | PDF Correspondence Top Phosphorylation sites of higher stoichiometry are more conserved p317 Chris Soon Heng Tan and Gary D Bader doi:10.1038/nmeth.1941 Full Text | PDF See also: Correspondence by Gygi et al. Reply to "Phosphorylation sites of higher stoichiometry are more conserved" p318 Steven P Gygi, Edward L Huttlin, Ronghu Wu, Wilhelm Haas, Noah Dephoure, Mathew Sowa and Bo Zhai doi:10.1038/nmeth.1942 Full Text | PDF See also: Correspondence by Tan & Bader Research Highlights Top A 'nano' era for electrophysiology p321 Researchers in three independent laboratories develop nanoscale devices for network-level electrophysiology. A nanopore workhorse pp322 - 323 Voltage-driven and enzyme-regulated control allows precise ratcheting of a DNA strand in and out of a nanopore. In-depth functional dissection of enhancers pp322 - 323 Massively parallel reporter assays enable the functional dissection of enhancer sequences in cells and in vivo. Rare variants and the power of association p324 Statistical methods vary widely in the power to predict which rare genetic sequence variants are functional. siRNA as a sponge p327 New nanostructure delivers potent dose of short interfering RNA A thermometer for cells p328 A small chemical probe allows detailed spatial imaging of the temperature in single cells. Magnetic yeast p330 Manipulating either culture conditions or genes can precipitate iron particles in yeast cells and render them magnetic. Methods JOBS of the week Developing methods for large-scale quantum chemistry simulations University of Southampton Novel computational methods for drug discovery University of Southampton Design Assurance Method Validation Engineer Collins McNicholas Ph.D. position on Methods and algorithms for data processing of the imaging Fourier transform spectrometer GLORIA Karlsruhe Institute of Technology (KIT) - Helmholtz Association Chemist - Pharmaceutical Method Development Kelly Scientific Resources More Science jobs from Methods EVENT T2012 AACR/ASCO Workshop: Methods in Clinical Cancer Research 28th June - 3rd August 2012 US More science events from Methods in Brief Top Bacteria stand in for HIV  | Sequencing broken DNA  | Quantifying RNA localization  | Faster genetic mapping in plants  Tools in Brief Top More photoactivatable fluorescent proteins  | Sensing demethylation in cells  | A dual selection marker for Drosophila   | Yeast pan-genome  Technology Feature Top De novo genome assembly: what every biologist should know pp333 - 337 Monya Baker doi:10.1038/nmeth.1935 As more genomes are assembled from scratch, scientists are struggling to assess and improve their quality. Full Text | PDF News and Views Top Magnetic sequencing pp339 - 341 Sten Linnarsson doi:10.1038/nmeth.1934 Single-molecule DNA sequencing takes an important step in a surprising new direction with a sequence-detection method based on magnetic tweezers. Full Text | PDF See also: Article by Ding et al. Neighboring-gene effect: a genetic uncertainty principle pp341 - 343 Anastasia Baryshnikova and Brenda Andrews doi:10.1038/nmeth.1936 Deletion of a genomic locus may affect the function of neighboring loci, creating genetic uncertainty. Researchers now present a computational algorithm for identifying such neighboring-gene effects and improving the quality of functional annotations. Full Text | PDF See also: Article by Ben-Shitrit et al. Perspective Top Protein interaction data curation: the International Molecular Exchange (IMEx) consortium pp345 - 350 Sandra Orchard, Samuel Kerrien, Sara Abbani, Bruno Aranda, Jignesh Bhate, Shelby Bidwell, Alan Bridge, Leonardo Briganti, Fiona Brinkman, Gianni Cesareni, Andrew Chatr-aryamontri, Emilie Chautard, Carol Chen, Marine Dumousseau, Johannes Goll, Robert Hancock, Linda I Hannick, Igor Jurisica, Jyoti Khadake, David J Lynn, Usha Mahadevan, Livia Perfetto, Arathi Raghunath, Sylvie Ricard-Blum, Bernd Roechert, Lukasz Salwinski, Volker Stumpflen, Mike Tyers, Peter Uetz, Ioannis Xenarios and Henning Hermjakob doi:10.1038/nmeth.1931 Presented is an update on the status and current practices of the International Molecular Exchange (IMEx) consortium and on its efforts to create a single nonredundant set of protein interactions curated from the scientific literature. Abstract | Full Text | PDF Analysis Top Comparative analysis of algorithms for integration of copy number and expression data pp351 - 355 Riku Louhimo, Tatiana Lepikhova, Outi Monni and Sampsa Hautaniemi doi:10.1038/nmeth.1893 Algorithms that integrate genome-wide copy number and gene expression data offer a promising way to uncover genes that drive the progression of cancers. The performance of ten software tools on simulated and real cancer datasets of different sizes is directly compared in this Analysis. Abstract | Full Text | PDF Brief Communications Top Fast gapped-read alignment with Bowtie 2 pp357 - 359 Ben Langmead and Steven L Salzberg doi:10.1038/nmeth.1923 The Bowtie 2 software achieves fast, sensitive, accurate and memory-efficient gapped alignment of sequencing reads using the full-text minute index and hardware-accelerated dynamic programming algorithms. Abstract | Full Text | PDF Combined RNAi and localization for functionally dissecting long noncoding RNAs pp360 - 362 Debojyoti Chakraborty, Dennis Kappei, Mirko Theis, Anja Nitzsche, Li Ding, Maciej Paszkowski-Rogacz, Vineeth Surendranath, Nicolas Berger, Herbert Schulz, Kathrin Saar, Norbert Hubner and Frank Buchholz doi:10.1038/nmeth.1894 The systematic functional dissection of long non-coding RNA (lncRNA) is simplified using a combined knockdown and localization approach based on endoribonuclease-prepared siRNA (esiRNA). A pilot screen reveals lncRNAs involved in the maintenance of pluripotency. Abstract | Full Text | PDF A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens pp363 - 366 Frederic D Sigoillot, Susan Lyman, Jeremy F Huckins, Britt Adamson, Eunah Chung, Brian Quattrochi and Randall W King doi:10.1038/nmeth.1898 Reported is a method, genome-wide enrichment of seed sequence (GESS), to analyze primary data from siRNA screens to identify major off-targeted transcripts. Using GESS the authors identify off-targeted transcripts in several screens. Abstract | Full Text | PDF Advertisement PCR that Works...for High Fidelity When you need high accuracy, you need a PCR polymerase that works regardless of conditions. Use PrimeSTAR GXL on standard templates, GC-rich, AT-rich, even repetitive DNA. It's the most robust high-fidelity enzyme commercially available. Put it to work for you: try a sample today.   Articles Top Single-molecule mechanical identification and sequencing pp367 - 372 Fangyuan Ding, Maria Manosas, Michelle M Spiering, Stephen J Benkovic, David Bensimon, Jean-Francois Allemand and Vincent Croquette doi:10.1038/nmeth.1925 In this proof of principle the authors use magnetic tweezers to unzip a DNA hairpin and then measure the molecule extension during rezipping in the presence of oligomers that transiently block the rezipping process. The extent of these blockages allows them to determine the DNA sequence. Abstract | Full Text | PDF See also: News and Views by Linnarsson Systematic identification of gene annotation errors in the widely used yeast mutation collections pp373 - 378 Taly Ben-Shitrit, Nir Yosef, Keren Shemesh, Roded Sharan, Eytan Ruppin and Martin Kupiec doi:10.1038/nmeth.1890 Comprehensive mutation libraries are an invaluable resource for screens in yeast, but anecdotal cases link phenotypes to the neighbor of a mutated gene rather than the mutant itself. The authors show that the neighboring gene effect is widespread and present software that uses protein-protein interaction networks to predict it. Abstract | Full Text | PDF See also: News and Views by Baryshnikova & Andrews TULIPs: tunable, light-controlled interacting protein tags for cell biology pp379 - 384 Devin Strickland, Yuan Lin, Elizabeth Wagner, C Matthew Hope, Josiah Zayner, Chloe Antoniou, Tobin R Sosnick, Eric L Weiss and Michael Glotzer doi:10.1038/nmeth.1904 Light-inducible dimerization tags are engineered to rapidly recruit proteins to precise points in living yeast and mammalian cells. The affinities and response time of the interactions are tunable, and the authors used the system to activate cell signaling and to direct cell polarization in yeast. Abstract | Full Text | PDF Functionally relevant neutrophilia in CD11c diphtheria toxin receptor transgenic mice pp385 - 390 André P Tittel, Christoph Heuser, Christina Ohliger, Chrystel Llanto, Simon Yona, Gunter J Hämmerling, Daniel R Engel, Natalio Garbi and Christian Kurts doi:10.1038/nmeth.1905 Reported is the unexpected release of polymorphonuclear neutrophilic granulocytes into the blood as a side effect of diphtheria toxin receptor-mediated dendritic cell depletion in two widely used transgenic mouse lines. The authors present a bacterial artificial chromosome transgenic mouse line that circumvents this problem. Abstract | Full Text | PDF Controlling gene expression with the Q repressible binary expression system in Caenorhabditis elegans  pp391 - 395 Xing Wei, Christopher J Potter, Liqun Luo and Kang Shen doi:10.1038/nmeth.1929 The binary 'Q system' for controlling gene expression in Caenorhabditis elegans is reported. The system affords reversible activation of either extrachromosomal or single-copy integrated transgenes; a complementation-based 'split Q' system also permits specific expression in desired cell types. Abstract | Full Text | PDF Rapid optical control of nociception with an ion-channel photoswitch pp396 - 402 Alexandre Mourot, Timm Fehrentz, Yves Le Feuvre, Caleb M Smith, Christian Herold, Deniz Dalkara, Frédéric Nagy, Dirk Trauner and Richard H Kramer doi:10.1038/nmeth.1897 A photoisomerizable molecule, quaternary ammonium-azobenzene-quaternary ammonium (QAQ) enables reversible optical silencing of nociceptive neurons. The selective entry of QAQ into active nociceptive neurons allows spatially and temporally precise regulation of nociceptor activity in vitro and in vivo. Abstract | Full Text | PDF Long-term, efficient inhibition of microRNA function in mice using rAAV vectors pp403 - 409 Jun Xie, Stefan L Ameres, Randall Friedline, Jui-Hung Hung, Yu Zhang, Qing Xie, Li Zhong, Qin Su, Ran He, Mengxin Li, Huapeng Li, Xin Mu, Hongwei Zhang, Jennifer A Broderick, Jason K Kim, Zhiping Weng, Terence R Flotte, Phillip D Zamore and Guangping Gao doi:10.1038/nmeth.1903 Tough decoy microRNA inhibitor, shown to be the most effective of several designs, is packaged in recombinant adeno-associated virus and used for prolonged microRNA inhibition in living mice. A single injection effectively reduces miR-122 in the liver and serum cholesterol for at least 25 weeks. Abstract | Full Text | PDF Computerized video analysis of social interactions in mice pp410 - 417 Fabrice de Chaumont, Renata Dos-Santos Coura, Pierre Serreau, Arnaud Cressant, Jonathan Chabout, Sylvie Granon and Jean-Christophe Olivo-Marin doi:10.1038/nmeth.1924 We describe software, MiceProfiler, for automatic tracking of two interacting mice and analysis of their social interactions without the need of animal tagging. The program allows the identification of key elements that trigger social contact in different mouse strains. Abstract | Full Text | PDF Advertisement Hollow Fiber Bioreactors: Easy Cell Culture Scale Up with Improved Productivity FiberCell® Systems bioreactors are the ideal method for the production of recombinant proteins, monoclonal antibodies and other secreted products from mammalian cells. Request our FREE Hollow Fiber Video Instruction Manual at www.fibercells.com and check out our latest article www.fibercellsystems.com/documents/AL-Cadwell-Reprint.pdf and video www.fibercellsystems.com/video.   Erratum Top Erratum: Gene-editing nucleases p418 Monya Baker doi:10.1038/nmeth0412-418 Full Text | PDF Top Advertisement Subscribe to Nature and receive an exclusive 40% discount this Spring! Your personal subscription includes the following benefits: • 51 weekly issues of Nature in print with instant online access • Supplements: Nature Insights, Nature Collections & Nature Outlooks • Multimedia features: Nature Podcast, Nature Video, blogs • Nature.com apps: for iPhone, iPad & iPod touch. Subscribe today!   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. 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