Nature Methods Contents: May 2012 Volume 9 pp 419 - 516

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. TABLE OF CONTENTS May 2012 Volume 9, Issue 5 In This Issue Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Commentary Perspective Brief Communications Articles Advertisement ACCELERATE YOUR RESEARCH Save time & money for your project with our services to: • - DISCOVER novel protein interactions; • - VALIDATE protein functions in cell; • - INHIBIT protein interactions with small molecules. Benefit from our expertise in protein interactions and get high-quality results. Over 200 publications in top-ranking journals and 900 researchers who trusted us. http://www.hybrigenics-services.com +33 (0)1 58 10 38 29 Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement The Eppendorf Mastercycler nexus family of PCR instruments offer excellent reproducibility, low noise emission and the versatility to use all types of consumables. Up to three units may be combined for higher throughput, while software capability enables users to access a booking schedule for the instrument and receive email notification when the PCR cycle is finished.   Advertisement Qualify today for your free subscription! Ensure you are abreast of the most significant research by qualifying for your free subscription to Nature Methods.   In This Issue Top PDF Editorial Top A home for raw proteomics data p419 doi:10.1038/nmeth.2011 A new repository for raw data from proteomics mass spectrometry experiments is available and needs community participation. Full Text | PDF This Month Top The author file: Taekjip Ha p421 Monya Baker doi:10.1038/nmeth.1980 Labeling proteins for single-molecule studies. Full Text | PDF Points of view: Representing the genome p423 Cydney Nielsen and Bang Wong doi:10.1038/nmeth.1992 The choice of visual representation of the linear genome is guided by the question being asked. Full Text | PDF Correspondence Top Fast, accurate error-correction of amplicon pyrosequences using Acacia pp425 - 426 Lauren Bragg, Glenn Stone, Michael Imelfort, Philip Hugenholtz and Gene W Tyson doi:10.1038/nmeth.1990 Full Text | PDF 'Self-healing' dyes: intramolecular stabilization of organic fluorophores pp426 - 427 Philip Tinnefeld and Thorben Cordes doi:10.1038/nmeth.1977 Full Text | PDF See also: Correspondence by Blanchard Reply to "'Self-healing' dyes: intramolecular stabilization of organic fluorophores" pp427 - 428 Scott C Blanchard doi:10.1038/nmeth.1986 Full Text | PDF See also: Correspondence by Tinnefeld & Cordes Enhanced photostability of cyanine fluorophores across the visible spectrum pp428 - 429 Roger B Altman, Qinsi Zheng, Zhou Zhou, Daniel S Terry, J David Warren and Scott C Blanchard doi:10.1038/nmeth.1988 Full Text | PDF Research Highlights Top A technology for memory p431 Two methodological approaches allow researchers to manipulate the formation and reactivation of memories in mice. Together we shine pp432 - 433 A dimerization-dependent red fluorescent protein provides a new strategy for biosensor design. The planarian Prometheus, quantified pp432 - 433 Tools to study stem cell function in planarians continue to accumulate. Researchers now image growing stem cell clones in these animals and make quantitative phenotypic measurements in vivo. Etch-a-cell p434 A milling technique affords researchers a high-resolution glimpse deep into the cell using cryoelectron tomography. AntagoNATs boost gene expression p437 Downregulation of natural antisense transcripts enhances expression of their sense counterparts. The age of yeast p438 A simple microfluidic device allows long-term imaging of single budding yeast cells. Cloning antibodies from serum p440 Proteomics analysis of polyclonal antibodies guides monoclonal production. Methods JOBS of the week Implementation of methods for the analysis of conformational variations in antibodies UNIVERSITA LA SAPIENZA Intervention methods for development and design in urban tissues of small towns of Latium region. DIPARTIMENTO DI ARCHITETTURA E PROGETTO Model-theoretic methods and applications to algebra, analysis, and number theory, focusing on the following topics: model-theoretic study of real and complex exponentiation; 0-minimality Università di Pisa - Dipartimento di Matematica Applicata “Ulisse Dini” Development of novel methods for the analysis of protein sequences, structures and interactions for genome-scale structural and functional annotation MIUR - UNIPD NMR methods for the study of monolayer protected nanoparticles Università degli Studi di Padova More Science jobs from Methods EVENT T2012 AACR/ASCO Workshop: Methods in Clinical Cancer Research 28th July - 3rd August 2012 US More science events from Methods in Brief Top Binders of O-glycosylated proteins  | A better look at the nuclear pore  | In vivo protein targeting with chemical genetics  | Fast two-color structured-illumination microscopy  Tools in Brief Top Tags to disentangle Dicer  | An ideal cyan fluorescent protein?  | Nanocombinatorics for biology  | RNA sensors for small molecules  Technology Feature Top Direct protein control pp443 - 447 Monya Baker doi:10.1038/nmeth.1979 Light and chemicals offer precise ways to manipulate proteins. Full Text | PDF News and Views Top Reprogramming in suspension pp449 - 451 Jiekai Chen and Duanqing Pei doi:10.1038/nmeth.1989 Current practice for the generation and maintenance of induced pluripotent stem cells (iPSCs) involves static culture in dishes. Two groups now report that mouse iPSCs can be generated efficiently in stirred suspension culture. Full Text | PDF See also: Brief Communication by Shafa et al. | Article by Fluri et al. Hitting the sweet spot pp451 - 453 Gauri Kulkarni and William G Wadsworth doi:10.1038/nmeth.1987 A strategy that uses genetically encoded GFP-tagged antibodies allows in vivo imaging of extracellular non-genetically encoded molecules. Full Text | PDF See also: Brief Communication by Attreed et al. Close encounters: integrating nanopores and CMOS amplifiers for single-molecule detection pp453 - 454 John S Oliver and Valentin Dimitrov doi:10.1038/nmeth.1981 Using semiconductor processing to construct integrated circuits that reside close to nanopores, researchers demonstrate high-bandwidth, low-noise measurements of DNA translocation through solid-state nanopores. Full Text | PDF See also: Article by Rosenstein et al. Commentary Top Toward objective evaluation of proteomic algorithms pp455 - 456 John R Yates III, Sung Kyu Robin Park, Claire M Delahunty, Tao Xu, Jeffrey N Savas, Daniel Cociorva and Paulo Costa Carvalho doi:10.1038/nmeth.1983 Informatics has driven mass spectrometry-based protein analysis to create large-scale methods for proteomics. As software algorithms have developed, comparisons between algorithms are inevitable. We outline steps for fair and objective comparisons that will make true innovations apparent. Full Text | PDF Perspective Top The 1000 Genomes Project: data management and community access pp459 - 462 OPEN Laura Clarke, Xiangqun Zheng-Bradley, Richard Smith, Eugene Kulesha, Chunlin Xiao, Iliana Toneva, Brendan Vaughan, Don Preuss, Rasko Leinonen, Martin Shumway, Stephen Sherry, Paul Flicek and The 1000 Genomes Project Consortium:  doi:10.1038/nmeth.1974 Abstract | Full Text | PDF Brief Communications Top Derivation of iPSCs in stirred suspension bioreactors pp465 - 466 Mehdi Shafa, Brad Day, Akihiro Yamashita, Guoliang Meng, Shiying Liu, Roman Krawetz and Derrick E Rancourt doi:10.1038/nmeth.1973 Reprogramming of mouse fibroblasts to induced pluripotency is demonstrated in suspension culture. Also in this issue, Fluri et al. report suspension-culture reprogramming of mouse cells and further differentiation, also in suspension, into cardiac cells. Abstract | Full Text | PDF See also: News and Views by Chen & Pei Tracking protein aggregation and mislocalization in cells with flow cytometry pp467 - 470 Yasmin M Ramdzan, Saskia Polling, Cheryl P Z Chia, Ivan H W Ng, Angelique R Ormsby, Nathan P Croft, Anthony W Purcell, Marie A Bogoyevitch, Dominic C H Ng, Paul A Gleeson and Danny M Hatters doi:10.1038/nmeth.1930 Protein localization changes in cells are monitored at high-throughput applying pulse-shape analysis to flow-cytometry data. The authors use the technique in combination with tetracysteine-based oligomer sensors to monitor toxic protein aggregation in a cellular model of Huntington's disease. Abstract | Full Text | PDF Detecting overlapping protein complexes in protein-protein interaction networks pp471 - 472 Tamás Nepusz, Haiyuan Yu and Alberto Paccanaro doi:10.1038/nmeth.1938 ClusterONE detects overlapping protein complexes from large-scale weighted and unweighted protein-interaction networks. Abstract | Full Text | PDF Unsupervised pattern discovery in human chromatin structure through genomic segmentation pp473 - 476 Michael M Hoffman, Orion J Buske, Jie Wang, Zhiping Weng, Jeff A Bilmes and William Stafford Noble doi:10.1038/nmeth.1937 Segway, a method using dynamic Bayesian network techniques, segments a genome and produces functional labels defined by histone modifications, transcription-factor binding, locations of open chromatin and other genome-wide functional data. Abstract | Full Text | PDF Direct visualization of specifically modified extracellular glycans in living animals pp477 - 479 Matthew Attreed, Muriel Desbois, Toin H van Kuppevelt and Hannes E Bülow doi:10.1038/nmeth.1945 Transgenic expression of secreted antibodies specific for modified heparan sulfates fused to GFP allow the visualization of these modifications in vivo. Abstract | Full Text | PDF See also: News and Views by Kulkarni & Wadsworth Segregation of molecules at cell division reveals native protein localization pp480 - 482 Dirk Landgraf, Burak Okumus, Peter Chien, Tania A Baker and Johan Paulsson doi:10.1038/nmeth.1955 The authors compare segregation of a protein into two daughter cells for the wild-type protein and a fluorescently tagged version, by assessing protein activity in the two cells; differences in segregation between the two protein versions indicate mislocalization artifacts caused by the fluorescent tag. Using this system they identify widespread artifacts in the localization of bacterial proteases. Abstract | Full Text | PDF Integrated genetic and computation methods for in planta cytometry pp483 - 485 Fernán Federici, Lionel Dupuy, Laurent Laplaze, Marcus Heisler and Jim Haseloff doi:10.1038/nmeth.1940 Automated cell segmentation in time-lapse confocal images of growing Arabidopsis combined with ratiometric imaging of fluorescent gene expression reporters permits the correlation of cellular properties with gene expression in the growing plant. Abstract | Full Text | PDF Advertisement RT-PCR that Works...Try a Free Sample Today When doing reverse transcription, you need an enzyme that works. The strong strand displacement of PrimeScript™ RT powers through complex secondary structure, yielding accurate and full-length cDNA up to 12 kb. Protect your precious RNA from degradation by performing RT at 42°C. Put PrimeScript to work for you: try a sample today.   Articles Top Integrated nanopore sensing platform with sub-microsecond temporal resolution pp487 - 492 Jacob K Rosenstein, Meni Wanunu, Christopher A Merchant, Marija Drndic and Kenneth L Shepard doi:10.1038/nmeth.1932 The temporal resolution of current signals from solid-state nanopores is improved by integrating a complementary metal-oxide-semiconductor preamplifier with the nanopores in thin silicon nitride membranes. Abstract | Full Text | PDF See also: News and Views by Oliver & Dimitrov Synchronization of secretory protein traffic in populations of cells pp493 - 498 Gaelle Boncompain, Severine Divoux, Nelly Gareil, Helene de Forges, Aurianne Lescure, Lynda Latreche, Valentina Mercanti, Florence Jollivet, Graca Raposo and Franck Perez doi:10.1038/nmeth.1928 The biotin-reversible interaction between a 'hook' protein localized to a particular cellular compartment and a reporter protein of interest is exploited in a simple system to synchronize protein traffic through the secretory pathway. Abstract | Full Text | PDF Quantitative fluorescence labeling of aldehyde-tagged proteins for single-molecule imaging pp499 - 503 Xinghua Shi, Yonil Jung, Li-Jung Lin, Cheng Liu, Cong Wu, Isaac K O Cann and Taekjip Ha doi:10.1038/nmeth.1954 The combination of a genetically encoded aldehyde tag and optimized labeling method allows high-efficiency, site-specific labeling of tagged proteins after purification or in cell extracts. The authors use the high labeling efficiency for single-molecule measurements of the dynamic interactions between two DNA polymerases and polymerase processivity factor bound to DNA. Abstract | Full Text | PDF FLEXIQinase, a mass spectrometry-based assay, to unveil multikinase mechanisms pp504 - 508 Sasha A Singh, Dominic Winter, Parizad M Bilimoria, Azad Bonni, Hanno Steen and Judith A Steen doi:10.1038/nmeth.1970 An in vitro kinase assay for quantification of site-specific substrate phosphorylation allows identification of kinase-kinase dependencies. Abstract | Full Text | PDF Derivation, expansion and differentiation of induced pluripotent stem cells in continuous suspension cultures pp509 - 516 David A Fluri, Peter D Tonge, Hannah Song, Ricardo P Baptista, Nika Shakiba, Shreya Shukla, Geoffrey Clarke, Andras Nagy and Peter W Zandstra doi:10.1038/nmeth.1939 Mouse cells are reprogrammed to induced pluripotency in suspension culture and can be further differentiated into cardiac cells, also in suspension. Also in this issue, Shafa et al. report suspension-culture reprogramming of mouse cells. Abstract | Full Text | PDF See also: News and Views by Chen & Pei 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   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. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. 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