Nature Methods Contents: October 2012 Volume 9 pp 931 - 1031

Advertisement Light sheet microscopy is a powerful alternative to established fluorescence imaging methods, especially when it comes to 3-D imaging deep within tissue or whole living organisms. Recently, a panel of experts introduced this technique in a webinar. If you want to know more about the advantages of light sheet microscopy, register here to receive a free offline copy of the webinar and related documentation. TABLE OF CONTENTS October 2012 Volume 9, Issue 10 In This Issue Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Brief Communications Articles Corrigenda Errata Advertisement Reduce Polymerase Errors...with PrimeSTAR 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. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement TALEN™ NØW™: efficient gene knock-out at a predefined locus TALEN™ NøW™ is off-the -shelf, ready-to-use TALEN™ mRNA designed for efficient gene knock-out at a predefined locus. For optimized ease of use and guaranteed results our TALEN™ NøW™ are validated. Our first TALEN™ NØW™, targeting the eGFP gene is now available! Click here for more information!   Advertisement Worthington's updated 2012 Tissue Dissociation Guide is available to assist researchers with selecting enzymes, developing and optimizing protocols and better understanding the process of enzymatic primary cell isolation and tissue dissociation. Available online at www.worthington-biochem.com/tissuedissociation or call 800.445.9603 to request a copy!   Advertisement In vivo two-photon microscopic imaging services from the first and only commercial provider. You benefit from our expertise in study customization and data analysis, gain access to dedicated infrastructure, and enjoy speed and flexibility. Special offer for Nature Methods readers: 10% discount on PK and Biodistribution of Large Molecules Across BBB. Contact us.   In This Issue Top In This Issue Editorial Top Genes—to have and to hold   p931 doi:10.1038/nmeth.2203 Methodological advances in genomics will benefit research and personalized medicine most if genes are accessible to all. This Month Top The author file: Marco Capitanio   p933 Vivien Marx doi:10.1038/nmeth.2176 Tugging at single molecules shows how they shake hands. Points of view: Power of the plane   p935 Nils Gehlenborg and Bang Wong doi:10.1038/nmeth.2186 Two-dimensional visualizations of multivariate data are most effective when combined. Correspondence Top A coincidence reporter-gene system for high-throughput screening   p937 Ken C-C Cheng and James Inglese doi:10.1038/nmeth.2170 Aptamers as potential tools for super-resolution microscopy   pp938 - 939 Felipe Opazo, Matthew Levy, Michelle Byrom, Christina Schäfer, Claudia Geisler, Teja W Groemer, Andrew D Ellington and Silvio O Rizzoli doi:10.1038/nmeth.2179 Research Highlights Top For every protein its tag New research explores in vivo protein function in the worm—at the genome scale. The root of all evil Two studies of tumor ancestry reveal evidence for discrete populations of cancer stem cells. Uber-accurate sequencing Looking for agreement between Watson and Crick strands weeds out sequencing artifacts. More dyes enter the realm of nanoscopy Widely used dyes for conventional microscopy of subcellular structures can also be used for super-resolution imaging. Peeking below the belt in C. elegans A map of the male worm's posterior nervous system offers some surprises. How vesicles put on their coat Single-molecule imaging helps researchers to begin a biography for clathrin-coated vesicles. Targeting with PRM Parallel reaction monitoring (PRM)-based targeted mass spectrometry is comparable in performance to selected reaction monitoring (SRM) but requires much less investment in assay development for targeted proteomics applications. Methods JOBS of the week Developing IDMS-based Methods for the Analysis of Selected Elements in Environmental Reference Materials Joint Research Centre - Institute for Reference Materials and Measurements Assistant or Associate Professor University of Southern California (USC) Research Scientist Braskem Tenure Track Faculty Position Memorial Sloan-Kettering Cancer Center More Science jobs from Methods EVENT Sterilization Procedures Technology, Equipment & Validation 14th November - 15th November 2012 PA, US More science events from Methods in Brief Top Genome editing in bacteria | Expanding the fly's genetic code | Mass-barcoded cells | Functional variants from chromatin changes Tools in Brief Top Programming transcription | Improved TALE tools | Towards single-molecule mass spectrometry | More optogenetic mouse lines Technology Feature Top Rendering the brain-behavior link visible   pp953 - 958 Vivien Marx doi:10.1038/nmeth.2183 In vivo imaging scientists broadcast from inside the brains of moving animals. News and Views Top Zooming in on genome organization   pp961 - 963 Xianghong Jasmine Zhou and Frank Alber doi:10.1038/nmeth.2181 Two studies plant a signpost on the road toward a robust and detailed chromatin interaction map. See also: Brief Communication by van de Werken et al. | Article by Imakaev et al. Shedding light on G protein-coupled receptor signaling   pp965 - 966 Marc Parmentier doi:10.1038/nmeth.2178 A new high-throughput method for monitoring G protein-coupled receptor activation is highly suited to assaying Gα12/13-coupled receptors and is used to deorphanize a group of receptors activated by lysophosphatidylserine. See also: Article by Inoue et al. Brief Communications Top Robust 4C-seq data analysis to screen for regulatory DNA interactions   pp969 - 972 Harmen J G van de Werken, Gilad Landan, Sjoerd J B Holwerda, Michael Hoichman, Petra Klous, Ran Chachik, Erik Splinter, Christian Valdes-Quezada, Yuva Öz, Britta A M Bouwman, Marjon J A M Verstegen, Elzo de Wit, Amos Tanay and Wouter de Laat doi:10.1038/nmeth.2173 A high-resolution 4C-seq protocol involving two restriction digests and a revised analysis pipeline allows robust detection of physical interactions between regulatory DNA elements. See also: News and Views by Zhou & Alber Coupling endonucleases with DNA end-processing enzymes to drive gene disruption   pp973 - 975 Michael T Certo, Kamila S Gwiazda, Ryan Kuhar, Blythe Sather, Gabrielle Curinga, Tyler Mandt, Michelle Brault, Abigail R Lambert, Sarah K Baxter, Kyle Jacoby, Byoung Y Ryu, Hans-Peter Kiem, Agnes Gouble, Frederic Paques, David J Rawlings and Andrew M Scharenberg doi:10.1038/nmeth.2177 Coexpression of DNA end-processing enzymes with targeted nucleases improves the efficiency of gene disruption in mammalian cells. Autonomous screening of C. elegans identifies genes implicated in synaptogenesis   pp977 - 980 Matthew M Crane, Jeffrey N Stirman, Chan-Yen Ou, Peri T Kurshan, James M Rehg, Kang Shen and Hang Lu doi:10.1038/nmeth.2141 An integrated system composed of a microfluidic device, computer-vision tools and statistical methods for automatically handling, imaging, classifying and sorting C. elegans organisms is presented. The system performs automated screens of subcellular phenotypes and is used here to identify genes involved in synaptogenesis. Reversible labeling of native and fusion-protein motifs   pp981 - 984 Nicolas M Kosa, Robert W Haushalter, Andrew R Smith and Michael D Burkart doi:10.1038/nmeth.2175 Removing phosphopantetheine-tagged labels from acyl carrier proteins (ACPs) and ACP fusion proteins contributes to a versatile labeling method in which tags can be iteratively swapped. Advertisement Serum Replacement Optimized for HFBR (Hollow Fiber Bioreactors) CDMHD from FiberCell Systems, Inc. is a chemically defined, protein-free serum replacement that permits any basal medium such as DMEM or RPMI to be used without serum. CDMHD is optimized for HFBRs and is now cGMP compliant. www.fibercellsystems.com www.fibercellsysetms.com/cdmhd www.fibercellsystems/video   Articles Top A general approach to break the concentration barrier in single-molecule imaging   pp987 - 992 Anna B Loveland, Satoshi Habuchi, Johannes C Walter and Antoine M van Oijen doi:10.1038/nmeth.2174 A method for single-molecule imaging at high protein concentrations is presented and demonstrated in the context of DNA replication in cell extracts. Site-specific genome editing in Plasmodium falciparum using engineered zinc-finger nucleases   pp993 - 998 Judith Straimer, Marcus C S Lee, Andrew H Lee, Bryan Zeitler, April E Williams, Jocelynn R Pearl, Lei Zhang, Edward J Rebar, Philip D Gregory, Manuel Llinas, Fyodor D Urnov and David A Fidock doi:10.1038/nmeth.2143 This paper reports genetic manipulation of the malaria parasite Plasmodium falciparum with zinc-finger nucleases. It demonstrates gene disruption as well as replacement and site-specific editing of both an integrated reporter and an endogenous gene. Iterative correction of Hi-C data reveals hallmarks of chromosome organization   pp999 - 1003 Maxim Imakaev, Geoffrey Fudenberg, Rachel Patton McCord, Natalia Naumova, Anton Goloborodko, Bryan R Lajoie, Job Dekker and Leonid A Mirny doi:10.1038/nmeth.2148 ICE (iterative correction and eigenvector decomposition) provides insight into inter- and intrachromosome interaction patterns. See also: News and Views by Zhou & Alber Improving FRET dynamic range with bright green and red fluorescent proteins   pp1005 - 1012 Amy J Lam, François St-Pierre, Yiyang Gong, Jesse D Marshall, Paula J Cranfill, Michelle A Baird, Michael R McKeown, Jörg Wiedenmann, Michael W Davidson, Mark J Schnitzer, Roger Y Tsien and Michael Z Lin doi:10.1038/nmeth.2171 Development of the bright green and red fluorescent proteins, Clover and mRuby2, creates a fluorescence resonance energy transfer (FRET) pair with the highest Forster radius among existing ratiometric FRET pairs. Substitution of this pair for current FRET pairs in several existing sensors reliably and substantially improves sensor performance. Ultrafast force-clamp spectroscopy of single molecules reveals load dependence of myosin working stroke   pp1013 - 1019 Marco Capitanio, Monica Canepari, Manuela Maffei, Diego Beneventi, Carina Monico, Francesco Vanzi, Roberto Bottinelli and Francesco Saverio Pavone doi:10.1038/nmeth.2152 A dual-trap force-clamp configuration is used to apply a constant load between a binding protein and a single intermittently interacting biological polymer. This allows high-resolution measurements of short-lived molecular complexes and reveals previously undetected complex regulation of the myosin working stroke. TGFα shedding assay: an accurate and versatile method for detecting GPCR activation   pp1021 - 1029 Asuka Inoue, Jun Ishiguro, Hajime Kitamura, Naoaki Arima, Michiyo Okutani, Akira Shuto, Shigeki Higashiyama, Tomohiko Ohwada, Hiroyuki Arai, Kumiko Makide and Junken Aoki doi:10.1038/nmeth.2172 A G protein-coupled receptor (GPCR) signaling assay based on ectodomain shedding of a membrane-bound proform of alkaline phosphatase-tagged TGFα provides a platform for studying poorly characterized Gα12/13-coupled GPCRs. The assay allowed identification of three orphan GPCRs as Gα12/13-coupled lysophosphatidylserine receptors. See also: News and Views by Parmentier Advertisement The New BD FACSJazz™ Cell Sorter Perfectly tuned cell sorting is now available with the new BD FACSJazz. Built on a proven, dependable platform, it may change the way you'll think of cell sorting with ease of operation, affordability, and a benchtop fit. Exceedingly capable performance whether as a soloist or part of your core lab ensemble. bdbiosciences.com/jazz   Corrigenda Top Corrigendum: Biological imaging software tools   p1031 Kevin W Eliceiri, Michael R Berthold, Ilya G Goldberg, Luis Ibáñez, B S Manjunath, Maryann E Martone, Robert F Murphy, Hanchuan Peng, Anne L Plant, Badrinath Roysam, Nico Stuurmann, Jason R Swedlow, Pavel Tomancak and Anne E Carpenter doi:10.1038/nmeth1012-1031a Corrigendum: Biological imaging software tools   p1031 Kevin W Eliceiri, Michael R Berthold, Ilya G Goldberg, Luis Ibáñez, B S Manjunath, Maryann E Martone, Robert F Murphy, Hanchuan Peng, Anne L Plant, Badrinath Roysam, Nico Stuurmann, Jason R Swedlow, Pavel Tomancak and Anne E Carpenter doi:10.1038/nmeth1012-1031b Errata Top Erratum: ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains   p1031 Olaf Ronneberger, Kun Liu, Meta Rath, Dominik Rueß, Thomas Mueller, Henrik Skibbe, Benjamin Drayer, Thorsten Schmidt, Alida Filippi, Roland Nitschke, Thomas Brox, Hans Burkhardt and Wolfgang Driever doi:10.1038/nmeth1012-1031c Erratum: RNA imaging in situ    p1031 Monya Baker doi:10.1038/nmeth1012-1031d Top Advertisement Online-only personal subscriptions now available to Nature Methods For only 49 USD/29 GBP/29 EUR Subscribe now!   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

You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/myaccount (You will need to log in to be recognised as a nature.com registrant) For further technical assistance, please contact our registration department For print subscription enquiries, please contact our subscription department For other enquiries, please contact our customer feedback department Nature Publishing Group | 75 Varick Street, 9th Floor | New York | NY 10013-1917 | USA Nature Publishing Group's worldwide offices: London - Paris - Munich - New Delhi - Tokyo - Melbourne San Diego - San Francisco - Washington - New York - Boston Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.